@article {6585, title = {Base editing of key residues in the BCL11A-XL-specific zinc finger domains derepresses fetal globin expression.}, journal = {Mol Ther}, volume = {32}, year = {2024}, month = {2024 Mar 06}, pages = {663-677}, abstract = {

BCL11A-XL directly binds and represses the fetal globin (HBG1/2) gene promoters, using 3 zinc-finger domains (ZnF4, ZnF5, and ZnF6), and is a potential target for β-hemoglobinopathy treatments. Disrupting BCL11A-XL results in derepression of fetal globin and high HbF, but also affects hematopoietic stem and progenitor cell (HSPC) engraftment and erythroid maturation. Intriguingly, neurodevelopmental patients with ZnF domain mutations have elevated HbF with normal hematological parameters. Inspired by this natural phenomenon, we used both CRISPR-Cas9 and base editing at specific ZnF domains and assessed the impacts on HbF production and hematopoietic differentiation. Generating indels in the various ZnF domains by CRISPR-Cas9 prevented the binding of BCL11A-XL to its site in the HBG1/2 promoters and elevated the HbF levels but affected normal hematopoiesis. Far fewer side effects were observed with base editing- for instance, erythroid maturation in\ vitro was near normal. However, we observed a modest reduction in HSPC engraftment and a complete loss of B cell development in\ vivo, presumably because current base editing is not capable of precisely recapitulating the mutations found in patients with BCL11A-XL-associated neurodevelopment disorders. Overall, our results reveal that disrupting different ZnF domains has different effects. Disrupting ZnF4 elevated HbF levels significantly while leaving many other erythroid target genes unaffected, and interestingly, disrupting ZnF6 also elevated HbF levels, which was unexpected because this region does not directly interact with the HBG1/2 promoters. This first structure/function analysis of ZnF4-6 provides important insights into the domains of BCL11A-XL that are required to repress fetal globin expression and provide framework for exploring the introduction of natural mutations that may enable the derepression of single gene while leaving other functions unaffected.

}, keywords = {Fetal Hemoglobin, gamma-Globins, Gene Editing, Hematopoietic Stem Cells, Humans, Repressor Proteins, Zinc Fingers}, issn = {1525-0024}, doi = {10.1016/j.ymthe.2024.01.023}, author = {Rajendiran, Vignesh and Devaraju, Nivedhitha and Haddad, Mahdi and Ravi, Nithin Sam and Panigrahi, Lokesh and Paul, Joshua and Gopalakrishnan, Chandrasekar and Wyman, Stacia and Ariudainambi, Keerthiga and Mahalingam, Gokulnath and Periyasami, Yogapriya and Prasad, Kirti and George, Anila and Sukumaran, Dhiyaneshwaran and Gopinathan, Sandhiya and Pai, Aswin Anand and Nakamura, Yukio and Balasubramanian, Poonkuzhali and Ramalingam, Rajasekaran and Thangavel, Saravanabhavan and Velayudhan, Shaji R and Corn, Jacon E and Mackay, Joel P and Marepally, Srujan and Srivastava, Alok and Crossley, Merlin and Mohankumar, Kumarasamypet M} } @article {6684, title = {Immunogenicity of SARS-CoV-2 vaccines BBV152 (COVAXIN{\textregistered}) and ChAdOx1 nCoV-19 (COVISHIELD{\texttrademark}) in seronegative and seropositive individuals in India: a multicentre, nonrandomised observational study.}, journal = {Lancet Reg Health Southeast Asia}, volume = {22}, year = {2024}, month = {2024 Mar}, pages = {100361}, abstract = {

BACKGROUND: There are limited global data on head-to-head comparisons of vaccine platforms assessing both humoral and cellular immune responses, stratified by pre-vaccination serostatus. The COVID-19 vaccination drive for the Indian population in the age group 18-45 years began in April 2021 when seropositivity rates in the general population were rising due to the delta wave of COVID-19 pandemic during April-May\ 2021.

METHODS: Between June 30, 2021, and Jan 28, 2022, we enrolled 691 participants in the age group 18-45 years across four clinical sites in India. In this non-randomised and laboratory blinded study, participants received either two doses of Covaxin{\textregistered} (4 weeks apart) or two doses of Covishield{\texttrademark} (12 weeks apart) as per the national vaccination policy. The primary outcome was the seroconversion rate and the geometric mean titre (GMT) of antibodies against the SARS-CoV-2 spike and nucleocapsid proteins post two doses. The secondary outcome was the frequency of cellular immune responses pre- and post-vaccination.

FINDINGS: When compared to pre-vaccination baseline, both vaccines elicited statistically significant seroconversion and binding antibody levels in both seronegative and seropositive individuals. In the per-protocol cohort, Covishield{\texttrademark} elicited higher antibody responses than Covaxin{\textregistered} as measured by seroconversion rate (98.3\% vs 74.4\%, p\ \<\ 0.0001 in seronegative individuals; 91.7\% vs 66.9\%, p\ \<\ 0.0001 in seropositive individuals) as well as by anti-spike antibody levels against the ancestral strain (GMT 1272.1 vs 75.4 binding antibody units/ml [BAU/ml], p\ \<\ 0.0001 in seronegative individuals; 2089.07 vs 585.7 BAU/ml, p\ \<\ 0.0001 in seropositive individuals). As participants at all clinical sites were not recruited at the same time, site-specific immunogenicity was impacted by the timing of vaccination relative to the delta and omicron waves. Surrogate neutralising antibody responses against variants-of-concern including delta and omicron was higher in Covishield{\texttrademark} recipients than in Covaxin{\textregistered} recipients; and in seropositive than in seronegative individuals after both vaccination and asymptomatic infection (omicron variant). T cell responses are reported from only one of the four site cohorts where the vaccination schedule preceded the omicron wave. In seronegative individuals, Covishield{\texttrademark} elicited both CD4+ and CD8+ spike-specific cytokine-producing T cells whereas Covaxin{\textregistered} elicited mainly CD4+ spike-specific T cells. Neither vaccine showed significant post-vaccination expansion of spike-specific T cells in seropositive individuals.

INTERPRETATION: Covishield{\texttrademark} elicited immune responses of higher magnitude and breadth than Covaxin{\textregistered} in both seronegative individuals and seropositive individuals, across cohorts representing the pre-vaccination immune history of most of the vaccinated Indian population.

FUNDING: Corporate social responsibility (CSR) funding from Hindustan Unilever Limited (HUL) and Unilever India Pvt. Ltd. (UIPL).

}, issn = {2772-3682}, doi = {10.1016/j.lansea.2024.100361}, author = {Asokan, Mangaiarkarasi S and Joan, Roshni Florina and Babji, Sudhir and Dayma, Girish and Nadukkandy, Prajitha and Subrahmanyam, Vinutha and Pandey, Archana and Malagi, Girish and Arya, Pooja and Mahajan, Vibhuti and Bhavikatti, Jayateerth and Pawar, Ketakee and Thorat, Aishwarya and Shah, Priyanki and Goud, Ramakrishna B and Roy, Bishnudeo and Rajukutty, Shon and Immanuel, Sushil and Agarwal, Dhiraj and Saha, Sankhanil and Shivaraj, Akshatha and Panikulam, Patricia and Shome, Rajeshwari and Gulzar, Shah-E-Jahan and Sharma, Anusmrithi U and Naik, Ajinkya and Talashi, Shruti and Belekar, Madhuri and Yadav, Ritu and Khude, Poornima and V, Mamatha and Shivalingaiah, Sudarshan and Deshmukh, Urmila and Bhise, Chinmayee and Joshi, Manjiri and Inbaraj, Leeberk Raja and Chandrasingh, Sindhulina and Ghose, Aurnab and Jamora, Colin and Karumbati, Anandi S and Sundaramurthy, Varadharajan and Johnson, Avita and Ramesh, Naveen and Chetan, Nirutha and Parthiban, Chaitra and Ahmed, Asma and Rakshit, Srabanti and Adiga, Vasista and D{\textquoteright}souza, George and Rale, Vinay and George, Carolin Elizabeth and John, Jacob and Kawade, Anand and Chaturvedi, Akanksha and Raghunathan, Anu and Dias, Mary and Bhosale, Anand and Raghu, Padinjat and Shashidhara, L S and Vyakarnam, Annapurna and Bal, Vineeta and Kang, Gagandeep and Mayor, Satyajit} } @article {6591, title = {The PP2A-like phosphatase Ppg1 mediates assembly of the Far complex to balance gluconeogenic outputs and enables adaptation to glucose depletion.}, journal = {PLoS Genet}, volume = {20}, year = {2024}, month = {2024 Mar}, pages = {e1011202}, abstract = {

To sustain growth in changing nutrient conditions, cells reorganize outputs of metabolic networks and appropriately reallocate resources. Signaling by reversible protein phosphorylation can control such metabolic adaptations. In contrast to kinases, the functions of phosphatases that enable metabolic adaptation as glucose depletes are poorly studied. Using a Saccharomyces cerevisiae deletion screen, we identified the PP2A-like phosphatase Ppg1 as required for appropriate carbon allocations towards gluconeogenic outputs-trehalose, glycogen, UDP-glucose, UDP-GlcNAc-after glucose depletion. This Ppg1 function is mediated via regulation of the assembly of the Far complex-a multi-subunit complex that tethers to the ER and mitochondrial outer membranes forming localized signaling hubs. The Far complex assembly is Ppg1 catalytic activity-dependent. Ppg1 regulates the phosphorylation status of multiple ser/thr residues on Far11 to enable the proper assembly of the Far complex. The assembled Far complex is required to maintain gluconeogenic outputs after glucose depletion. Glucose in turn regulates Far complex amounts. This Ppg1-mediated Far complex assembly, and Ppg1-Far complex dependent control of gluconeogenic outputs enables adaptive growth under glucose depletion. Our study illustrates how protein dephosphorylation is required for the assembly of a multi-protein scaffold present in localized cytosolic pools, to thereby alter gluconeogenic flux and enable cells to metabolically adapt to nutrient fluctuations.

}, keywords = {Glucose, Phosphorylation, Protein Phosphatase 2, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Signal Transduction}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1011202}, author = {Niphadkar, Shreyas and Karinje, Lavanya and Laxman, Sunil} } @article {6680, title = {TANGO1 inhibitors reduce collagen secretion and limit tissue scarring.}, journal = {Nat Commun}, volume = {15}, year = {2024}, month = {2024 Apr 24}, pages = {3302}, abstract = {

Uncontrolled secretion of ECM proteins, such as collagen, can lead to excessive scarring and fibrosis and compromise tissue function. Despite the widespread occurrence of fibrotic diseases and scarring, effective therapies are lacking. A promising approach would be to limit the amount of collagen released from hyperactive fibroblasts. We have designed membrane permeant peptide inhibitors that specifically target the primary interface between TANGO1 and cTAGE5, an interaction that is required for collagen export from endoplasmic reticulum exit sites (ERES). Application of the peptide inhibitors leads to reduced TANGO1 and cTAGE5 protein levels and a corresponding inhibition in the secretion of several ECM components, including collagens. Peptide inhibitor treatment in zebrafish results in altered tissue architecture and reduced granulation tissue formation during cutaneous wound healing. The inhibitors reduce secretion of several ECM proteins, including collagens, fibrillin and fibronectin in human dermal fibroblasts and in cells obtained from patients with a generalized fibrotic disease (scleroderma). Taken together, targeted interference of the TANGO1-cTAGE5 binding interface could enable therapeutic modulation of ERES function in ECM hypersecretion, during wound healing and fibrotic processes.

}, keywords = {Animals, Cicatrix, Collagen, Endoplasmic Reticulum, Extracellular Matrix, Fibroblasts, Fibrosis, Humans, Peptides, Scleroderma, Systemic, Skin, Wound Healing, Zebrafish}, issn = {2041-1723}, doi = {10.1038/s41467-024-47004-1}, author = {Raote, Ishier and Rosendahl, Ann-Helen and H{\"a}kkinen, Hanna-Maria and Vibe, Carina and K{\"u}{\c c}{\"u}kaylak, Ismail and Sawant, Mugdha and Keufgens, Lena and Frommelt, Pia and Halwas, Kai and Broadbent, Katrina and Cunquero, Marina and Castro, Gustavo and Villemeur, Marie and N{\"u}chel, Julian and Bornikoel, Anna and Dam, Binita and Zirmire, Ravindra K and Kiran, Ravi and Carolis, Carlo and Andilla, Jordi and Loza-Alvarez, Pablo and Ruprecht, Verena and Jamora, Colin and Campelo, Felix and Kr{\"u}ger, Marcus and Hammerschmidt, Matthias and Eckes, Beate and Neundorf, Ines and Krieg, Thomas and Malhotra, Vivek} } @article {6590, title = {T-cell Response after COVID-19 Vaccination: A Cross-sectional Study.}, journal = {Journal of Clinical \& Diagnostic Research}, volume = {18}, year = {2024}, author = {SOLOMON, JOHN and KALAISELVI, VS and KALAIVANI, MK and NEHIL, JUWAIN SHEHZAD and JOHNSON, WMS and SAIKUMAR, CHITRALEKA and CHRISTUDASS, CHRISTHUNESA SOUNDARARAJAN and RANI, SANDYA} } @article {3870, title = {High-affinity binding of celastrol to monomeric α-synuclein mitigates in~vitro aggregation.}, journal = {J Biomol Struct Dyn}, year = {2023}, month = {2023 Feb 06}, pages = {1-11}, abstract = {

α-Synuclein (αSyn) aggregation is associated with Parkinson{\textquoteright}s disease (PD). The region αSyn acts as the nucleation {\textquoteright}master controller{\textquoteright} and αSyn as a {\textquoteright}secondary nucleation site{\textquoteright}. They drive monomeric αSyn to aggregation. Small molecules targeting these motifs are promising for disease-modifying therapy. Using computational techniques, we screened thirty phytochemicals for αSyn binding. The top three compounds were experimentally validated for their binding affinity. Amongst them, celastrol showed high binding affinity. NMR analysis confirmed stable αSyn-celastrol interactions involving several residues in the N-terminus and NAC regions but not in the C-terminal tail. Importantly, celastrol interacted extensively with the key motifs that drive αSyn aggregation. Thioflavin-T assay indicated that celastrol reduced αSyn aggregation. Thus, celastrol holds promise as a potent drug candidate for PD.Communicated by Ramaswamy H. Sarma.

}, issn = {1538-0254}, doi = {10.1080/07391102.2023.2175379}, author = {R, Kavya and Aouti, Snehal and Jos, Sneha and Prasad, Thazhe Kootteri and K N, Kumuda and Unni, Sruthi and Padmanabhan, Balasundaram and Kamariah, Neelagandan and Padavattan, Sivaraman and Mythri, Rajeswara Babu} } @article {3715, title = {Efficient and error-free correction of sickle mutation in human erythroid cells using prime editor-2.}, journal = {Front Genome Ed}, volume = {4}, year = {2022}, month = {2022}, pages = {1085111}, abstract = {

Sickle cell anaemia (SCA) is one of the common autosomal recessive monogenic disorders, caused by a transverse point mutation (GAG \> GTG) at the sixth codon of the beta-globin gene, which results in haemolytic anaemia due to the fragile RBCs. Recent progress in genome editing has gained attention for the therapeutic cure for SCA. Direct correction of SCA mutation by homology-directed repair relies on a double-strand break (DSB) at the target site and carries the risk of generating beta-thalassaemic mutations if the editing is not error-free. On the other hand, base editors cannot correct the pathogenic SCA mutation resulting from A \> T base transversion. Prime editor (PE), the recently described CRISPR/Cas 9 based gene editing tool that enables precise gene manipulations without DSB and unintended nucleotide changes, is a viable approach for the treatment of SCA. However, the major limitation with the use of prime editing is the lower efficiency especially in human erythroid cell lines and primary cells. To overcome these limitations, we developed a modular lenti-viral based prime editor system and demonstrated its use for the precise modelling of SCA mutation and its subsequent correction in human erythroid cell lines. We achieved highly efficient installation of SCA mutation (up to 72\%) and its subsequent correction in human erythroid cells. For the first time, we demonstrated the functional restoration of adult haemoglobin without any unintended nucleotide changes or indel formations using the PE2 system. We also validated that the off-target effects mediated by the PE2 system is very minimal even with very efficient on-target conversion, making it a safe therapeutic option. Taken together, the modular lenti-viral prime editor system developed in this study not only expands the range of cell lines targetable by prime editor but also improves the efficiency considerably, enabling the use of prime editor for myriad molecular, genetic, and translational studies.

}, issn = {2673-3439}, doi = {10.3389/fgeed.2022.1085111}, author = {George, Anila and Ravi, Nithin Sam and Prasad, Kirti and Panigrahi, Lokesh and Koikkara, Sanya and Rajendiran, Vignesh and Devaraju, Nivedhitha and Paul, Joshua and Pai, Aswin Anand and Nakamura, Yukio and Kurita, Ryo and Balasubramanian, Poonkuzhali and Thangavel, Saravanabhavan and Marepally, Srujan and Velayudhan, Shaji R and Srivastava, Alok and Mohankumar, Kumarasamypet M} } @article {3341, title = {Erythroid lineage-specific lentiviral RNAi vectors suitable for molecular functional studies and therapeutic applications.}, journal = {Sci Rep}, volume = {12}, year = {2022}, month = {2022 08 18}, pages = {14033}, abstract = {

Numerous genes exert multifaceted roles in hematopoiesis. Therefore, we generated novel\ lineage-specific RNA interference\ (RNAi) lentiviral\ vectors, H23B-Ery-Lin-shRNA\ and H234B-Ery-Lin-shRNA, to probe the functions of these genes in erythroid cells\ without affecting other hematopoietic lineages. The lineage specificity of these vectors was confirmed by\ transducing multiple hematopoietic cells to express a fluorescent protein. Unlike the previously reported erythroid lineage RNAi vector, our vectors were designed for cloning the short hairpin RNAs (shRNAs) for\ any gene, and they also provide superior knockdown of the target gene expression with a\ single shRNA integration per cell. High-level lineage-specific downregulation of BCL11A and ZBTB7A,\ two\ well-characterized transcriptional repressors of HBG in adult erythroid cells, was achieved with substantial induction of fetal hemoglobin with a single-copy lentiviral vector integration. Transduction of primary healthy donor CD34 cells with these vectors resulted in\ \>80\% reduction in the target\ protein levels and up to 40\% elevation in the γ-chain levels in the differentiated erythroid cells. Xenotransplantation of the human CD34 cells transduced with H23B-Ery-Lin-shBCL11A\ LV in immunocompromised mice showed ~ 60\% reduction in BCL11A protein expression with ~\ 40\% elevation of γ-chain levels in the erythroid cells derived from the transduced CD34 cells. Overall, the novel erythroid lineage-specific lentiviral RNAi vectors described in this study provide a\ high-level knockdown of target gene expression in the erythroid cells, making them suitable for their use in gene therapy for hemoglobinopathies. Additionally, the design of these vectors also makes them ideal for high-throughput RNAi screening for studying normal and pathological erythropoiesis.

}, keywords = {Animals, Cell Line, Tumor, Cell Lineage, DNA-Binding Proteins, Genetic Vectors, Humans, Lentivirus, Mice, RNA Interference, RNA, Small Interfering, Transcription Factors, Transduction, Genetic}, issn = {2045-2322}, doi = {10.1038/s41598-022-13783-0}, author = {Bagchi, Abhirup and Devaraju, Nivedhitha and Chambayil, Karthik and Rajendiran, Vignesh and Venkatesan, Vigneshwaran and Sayed, Nilofer and Pai, Aswin Anand and Nath, Aneesha and David, Ernest and Nakamura, Yukio and Balasubramanian, Poonkuzhali and Srivastava, Alok and Thangavel, Saravanabhavan and Mohankumar, Kumarasamypet M and Velayudhan, Shaji R} } @article {3346, title = {Function of FMRP Domains in Regulating Distinct Roles of Neuronal Protein Synthesis.}, journal = {Mol Neurobiol}, volume = {59}, year = {2022}, month = {2022 Dec}, pages = {7370-7392}, abstract = {

The Fragile-X Mental Retardation Protein (FMRP) is an RNA binding protein that regulates translation of mRNAs essential for synaptic development and plasticity. FMRP interacts with a specific set of mRNAs, aids in their microtubule-dependent transport and regulates their translation through its association with ribosomes. However, the biochemical role of FMRP{\textquoteright}s domains in forming neuronal granules and associating with microtubules and ribosomes is currently undefined. We report that the C-terminus domain of FMRP is sufficient to bind to ribosomes akin to the full-length protein. Furthermore, the C-terminus domain alone is essential and responsible for FMRP-mediated neuronal translation repression. However, dendritic distribution of FMRP and its microtubule association is favored by the synergistic combination of FMRP domains rather than individual domains. Interestingly, we show that the phosphorylation of hFMRP at Serine-500 is important in modulating the dynamics of translation by controlling ribosome association. This is a fundamental mechanism governing the size and number of FMRP puncta that contain actively translating ribosomes. Finally through the use of pathogenic mutations, we emphasize the hierarchical contribution of FMRP{\textquoteright}s domains in translation regulation.

}, keywords = {Fragile X Mental Retardation Protein, Fragile X Syndrome, Humans, Microtubules, Neurons, Protein Biosynthesis, Ribosomes, RNA, Messenger}, issn = {1559-1182}, doi = {10.1007/s12035-022-03049-1}, author = {D{\textquoteright}Souza, Michelle Ninochka and Ramakrishna, Sarayu and Radhakrishna, Bindushree K and Jhaveri, Vishwaja and Ravindran, Sreenath and Yeramala, Lahari and Nair, Deepak and Palakodeti, Dasaradhi and Muddashetty, Ravi S} } @article {2465, title = {Identification of novel HPFH-like mutations by CRISPR base editing that elevate the expression of fetal hemoglobin.}, journal = {Elife}, volume = {11}, year = {2022}, month = {2022 02 11}, abstract = {

Naturally occurring point mutations in the promoter switch hemoglobin synthesis from defective adult beta-globin to fetal gamma-globin in sickle cell patients with hereditary persistence of fetal hemoglobin (HPFH) and ameliorate the clinical severity. Inspired by this natural phenomenon, we tiled the highly homologous proximal promoters using adenine and cytosine base editors that avoid the generation of large deletions and identified novel regulatory regions including a cluster at the -123 region. Base editing at -123 and -124 bp of promoter induced fetal hemoglobin (HbF) to a higher level than disruption of well-known BCL11A binding site in erythroblasts derived from human CD34+ hematopoietic stem and progenitor cells (HSPC). We further demonstrated in vitro that the introduction of -123T \> C and -124T \> C HPFH-like mutations drives gamma-globin expression by creating a de novo binding site for KLF1. Overall, our findings shed light on so far unknown regulatory elements within the promoter and identified additional targets for therapeutic upregulation of fetal hemoglobin.

}, keywords = {Adenine, Anemia, Sickle Cell, beta-Globins, beta-Thalassemia, Cell Line, Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-Cas Systems, Cytosine, Fetal Hemoglobin, gamma-Globins, Gene Editing, Hematopoietic Stem Cells, Humans, Point Mutation, Promoter Regions, Genetic}, issn = {2050-084X}, doi = {10.7554/eLife.65421}, author = {Ravi, Nithin Sam and Wienert, Beeke and Wyman, Stacia K and Bell, Henry William and George, Anila and Mahalingam, Gokulnath and Vu, Jonathan T and Prasad, Kirti and Bandlamudi, Bhanu Prasad and Devaraju, Nivedhitha and Rajendiran, Vignesh and Syedbasha, Nazar and Pai, Aswin Anand and Nakamura, Yukio and Kurita, Ryo and Narayanasamy, Muthuraman and Balasubramanian, Poonkuzhali and Thangavel, Saravanabhavan and Marepally, Srujan and Velayudhan, Shaji R and Srivastava, Alok and DeWitt, Mark A and Crossley, Merlin and Corn, Jacob E and Mohankumar, Kumarasamypet M} } @article {3342, title = {Methionine uptake via the SLC43A2 transporter is essential for regulatory T-cell survival.}, journal = {Life Sci Alliance}, volume = {5}, year = {2022}, month = {2022 Sep 09}, abstract = {

Cell death, survival, or growth decisions in T-cell subsets depend on interplay between cytokine-dependent and metabolic processes. The metabolic requirements of T-regulatory cells (Tregs) for their survival and how these are satisfied remain unclear. Herein, we identified a necessary requirement of methionine uptake and usage for Tregs survival upon IL-2 deprivation. Activated Tregs have high methionine uptake and usage to S-adenosyl methionine, and this uptake is essential for Tregs survival in conditions of IL-2 deprivation. We identify a solute carrier protein SLC43A2 transporter, regulated in a Notch1-dependent manner that is necessary for this methionine uptake and Tregs viability. Collectively, we uncover a specifically regulated mechanism of methionine import in Tregs that is required for cells to adapt to cytokine withdrawal. We highlight the need for methionine availability and metabolism in contextually regulating cell death in this immunosuppressive population of T cells.

}, keywords = {Interleukin-2, Methionine, Racemethionine, Solute Carrier Proteins, T-Lymphocytes, Regulatory}, issn = {2575-1077}, doi = {10.26508/lsa.202201663}, author = {Saini, Neetu and Naaz, Afsana and Metur, Shree Padma and Gahlot, Pinki and Walvekar, Adhish and Dutta, Anupam and Davathamizhan, Umamaheswari and Sarin, Apurva and Laxman, Sunil} } @article {2399, title = {Microscale engineering of hollow microneedle tips: design, manufacturing, optimization and validation.}, journal = {Drug Deliv Transl Res}, volume = {12}, year = {2022}, month = {2022 Feb}, pages = {350-367}, abstract = {

Transdermal and intradermal drug delivery utilizing microneedles is an emerging front in painless therapeutics. Drug delivery using hollow microneedles is the most preferred method for delivering generic transdermal drugs in the clinical setup. The needle tip must be extremely short as the drug is administered to sub-millimeter depths. Also, they need to be sharp enough to pierce through the skin with minimal skin flexing. There are multiple challenges in engineering a tip profile that is short and sharp at the same time. Stainless steel (SS) hypodermic needles with the lancet tip profile are ubiquitous in subcutaneous and intramuscular injections. They have long bevel lengths that make them inappropriate as microneedles. Thus, designing a unique tip profile and developing the manufacturing technology for microneedle applications are necessary. This article presents the design and optimization of microneedle tip profiles through analytical models. Further, manufacturing strategies for reliably obtaining designed profiles are discussed. The article concludes with experimental validation of improved piercing performance of the optimized tip profile compared to other tip profiles. The article discusses about tip geometries of stainless steel needles for microneedle applications, where depth of delivery is less than 1 mm. Through series of analyses, the optimum needle tip geometry evolved from single plane bevel (SPB) to hex plane bevel (HPB) progressively improving piercing performance.

}, issn = {2190-3948}, doi = {10.1007/s13346-021-01062-w}, author = {Badnikar, Kedar and Jayadevi, Shreyas Nataraja and Pahal, Suman and Vemula, Praveen Kumar and Nayak, Mangalore Manjunatha and Subramanyam, Dinesh Narasimhaiah} } @article {3338, title = {Modulation of biliverdin dynamics and spectral properties by Sandercyanin.}, journal = {RSC Adv}, volume = {12}, year = {2022}, month = {2022 Jul 06}, pages = {20296-20304}, abstract = {

Biliverdin IX-alpha (BV), a tetrapyrrole, is found ubiquitously in most living organisms. It functions as a metabolite, pigment, and signaling compound. While BV is known to bind to diverse protein families such as heme-metabolizing enzymes and phytochromes, not many BV-bound lipocalins (ubiquitous, small lipid-binding proteins) have been studied. The molecular basis of binding and conformational selectivity of BV in lipocalins remains unexplained. Sandercyanin (SFP)-BV complex is a blue lipocalin protein present in the mucus of the Canadian walleye (). In this study, we present the structures and binding modes of BV to SFP. Using a combination of designed site-directed mutations, X-ray crystallography, UV/VIS, and resonance Raman spectroscopy, we have identified multiple conformations of BV that are stabilized in the binding pocket of SFP. In complex with the protein, these conformers generate varied spectroscopic signatures both in their absorption and fluorescence spectra. We show that despite no covalent anchor, structural heterogeneity of the chromophore is primarily driven by the D-ring pyrrole of BV. Our work shows how conformational promiscuity of BV is correlated to the rearrangement of amino acids in the protein matrix leading to modulation of spectral properties.

}, issn = {2046-2069}, doi = {10.1039/d2ra02880h}, author = {Ghosh, Swagatha and Mondal, Sayan and Yadav, Keerti and Aggarwal, Shantanu and Schaefer, Wayne F and Narayana, Chandrabhas and Subramanian, Ramaswamy} } @article {3339, title = {NMDAR mediated dynamic changes in mA inversely correlates with neuronal translation.}, journal = {Sci Rep}, volume = {12}, year = {2022}, month = {2022 07 05}, pages = {11317}, abstract = {

Epitranscriptome modifications are crucial in translation regulation and essential for maintaining cellular homeostasis. N6 methyladenosine (mA) is one of the most abundant and well-conserved epitranscriptome modifications, which is known to play a pivotal role in diverse aspects of neuronal functions. However, the role of mA modifications with respect to activity-mediated translation regulation and synaptic plasticity has not been studied. Here, we investigated the role of mA modification in response to NMDAR stimulation. We have consistently observed that 5\ min NMDAR stimulation causes an increase in eEF2 phosphorylation. Correspondingly, NMDAR stimulation caused a significant increase in the mA signal at 5\ min time point, correlating with the global translation inhibition. The NMDAR induced increase in the mA signal is accompanied by the redistribution of the mA marked RNAs from translating to the non-translating pool of ribosomes. The increased mA levels are well correlated with the reduced FTO levels observed on NMDAR stimulation. Additionally, we show that inhibition of FTO prevents NMDAR mediated changes in mA levels. Overall, our results establish RNA-based molecular readout which corelates with the NMDAR-dependent translation regulation which helps in understanding changes in protein synthesis.

}, keywords = {Adenosine, Neurons, Phosphorylation, Receptors, N-Methyl-D-Aspartate, RNA}, issn = {2045-2322}, doi = {10.1038/s41598-022-14798-3}, author = {Gowda, Naveen Kumar Chandappa and Nawalpuri, Bharti and Ramakrishna, Sarayu and Jhaveri, Vishwaja and Muddashetty, Ravi S} } @article {2422, title = {Novel Mutations in β- Gene in Indian Patients With Dilated Cardiomyopathy.}, journal = {CJC Open}, volume = {4}, year = {2022}, month = {2022 Jan}, pages = {1-11}, abstract = {

Background: Heart failure is a hallmark of severe hypertrophic cardiomyopathy and dilated cardiomyopathy (DCM). Several mutations in the gene lead to hypertrophic cardiomyopathy. Recently, causative mutations in the gene have also been detected in DCM from different populations.

Methods: Here, we sequenced the gene in 137 Indian DCM patients and 167 ethnically matched healthy controls to detect the frequency of mutations and their association.

Results: Our study revealed 27 variations, of which 7 mutations (8.0\%) were detected exclusively in Indian DCM patients for the first time. These included 4 missense mutations-Arg723His, Phe510Leu, His358Leu, and Ser384Tyr (2.9\%); a frameshift mutation-Asn676_T-del (1.5\%); and 2 splice-site mutations (IVS17+2T) T\>G and (IVS19-1G) G\>A (3.6\%). Remarkably, all 4 missense mutations altered evolutionarily conserved amino acids. All 4 missense mutations were predicted to be pathogenic by 2 bioinformatics tools-polymorphism phenotyping v2 (PolyPhen-2) and sorting intolerant from tolerant (SIFT). In addition, the 4 homology models of β-MYH7-p.Leu358, p.Tyr384, p.Leu510, and p.His723-displayed root-mean-square deviations of \~{}2.55 {\r A}, \~{}1.24 {\r A}, \~{}3.36 {\r A}, and \~{}3.86 {\r A}, respectively.

Conclusions: In the present study, we detected numerous novel, unique, and rare mutations in the gene exclusively in Indian DCM patients (8.0\%). Here, we demonstrated how each mutant (missense) uniquely disrupts a critical network of non-bonding interactions at the mutation site (molecular level) and may contribute to development of dilated cardiomyopathy (DCM). Therefore, our findings may provide insight into the understanding of the molecular bases of disease and into diagnosis along with promoting novel therapeutic strategies (through personalized medicine).

}, issn = {2589-790X}, doi = {10.1016/j.cjco.2021.07.020}, author = {Rani, Deepa Selvi and Vijaya Kumar, Archana and Nallari, Pratibha and Sampathkumar, Katakam and Dhandapany, Perundurai S and Narasimhan, Calambur and Rathinavel, Andiappan and Thangaraj, Kumarasamy} } @article {3645, title = {Single step fabrication of hollow microneedles and an experimental package for controlled drug delivery.}, journal = {Int J Pharm}, volume = {632}, year = {2022}, month = {2022 Dec 24}, pages = {122546}, abstract = {

Hollow microneedle arrays (HMNs) are an excellent choice for managing chronic diseases requiring the administration of multiple drug doses over a prolonged duration. However, HMNs have gained partial success due to limitations in their manufacturing capabilities, and cumbersome processes. In the present study, polymeric HMNs were fabricated using a novel single-step drop-casting process without needing cleanroom facilities, and sophisticated instrumentation. When drop casted on the pyramidal tip stainless steel needles, the optimized polymer solution allowed the reproducible formation of desired height HMMs on a detachable acrylic base. To enable broader applications, the base with HMNs was integrated into an experimental package built to deliver a dose of\ \~{}\ 5\ {\textmu}L per 30{\textdegree} clockwise rotation of the actuator, allowing multiple metered drug dose administrations. The fabricated HMNs were optically imaged, and tested for mechanical integrity and stability. The working and functional utility of the HMNs package in delivering metered drug doses was demonstrated by delivering vitamin B12 (ex vivo) and insulin (in vivo), respectively. The optimized process can be used for the large-scale manufacturing of HMNs and the experimental package shows the potential to be further developed into a wearable device.

}, issn = {1873-3476}, doi = {10.1016/j.ijpharm.2022.122546}, author = {Ghate, Vivek and Renjith, Anu and Badnikar, Kedar and Pahal, Suman and Jayadevi, Shreyas N and Nayak, Manjunatha M and Vemula, Praveen K and Subramanyam, Dinesh N} } @article {2463, title = {Whole genome sequencing delineates regulatory, copy number, and cryptic splice variants in early onset cardiomyopathy.}, journal = {NPJ Genom Med}, volume = {7}, year = {2022}, month = {2022 Mar 14}, pages = {18}, abstract = {

Cardiomyopathy (CMP) is a heritable disorder. Over 50\% of cases are gene-elusive on clinical gene panel testing. The contribution of variants in non-coding DNA elements that result in cryptic splicing and regulate gene expression has not been explored. We analyzed whole-genome sequencing (WGS) data in a discovery cohort of 209 pediatric CMP patients and 1953 independent replication genomes and exomes. We searched for protein-coding variants, and non-coding variants predicted to affect the function or expression of genes. Thirty-nine percent of cases harbored pathogenic coding variants in known CMP genes, and 5\% harbored high-risk loss-of-function (LoF) variants in additional candidate CMP genes. Fifteen percent harbored high-risk regulatory variants in promoters and enhancers of CMP genes (odds ratio 2.25, p = 6.70 {\texttimes} 10 versus controls). Genes involved in α-dystroglycan glycosylation (FKTN, DTNA) and desmosomal signaling (DSC2, DSG2) were most highly enriched for regulatory variants (odds ratio 6.7-58.1). Functional effects were confirmed in patient myocardium and reporter assays in human cardiomyocytes, and in zebrafish CRISPR knockouts. We provide strong evidence for the genomic contribution of functionally active variants in new genes and in regulatory elements of known CMP genes to early onset CMP.

}, issn = {2056-7944}, doi = {10.1038/s41525-022-00288-y}, author = {Lesurf, Robert and Said, Abdelrahman and Akinrinade, Oyediran and Breckpot, Jeroen and Delfosse, Kathleen and Liu, Ting and Yao, Roderick and Persad, Gabrielle and McKenna, Fintan and Noche, Ramil R and Oliveros, Winona and Mattioli, Kaia and Shah, Shreya and Miron, Anastasia and Yang, Qian and Meng, Guoliang and Yue, Michelle Chan Seng and Sung, Wilson W L and Thiruvahindrapuram, Bhooma and Lougheed, Jane and Oechslin, Erwin and Mondal, Tapas and Bergin, Lynn and Smythe, John and Jayappa, Shashank and Rao, Vinay J and Shenthar, Jayaprakash and Dhandapany, Perundurai S and Semsarian, Christopher and Weintraub, Robert G and Bagnall, Richard D and Ingles, Jodie and Mel{\'e}, Marta and Maass, Philipp G and Ellis, James and Scherer, Stephen W and Mital, Seema} } @article {2364, title = {Analysis of whole exome sequencing in severe mental illness hints at selection of brain development and immune related genes.}, journal = {Sci Rep}, volume = {11}, year = {2021}, month = {2021 Oct 26}, pages = {21088}, abstract = {

Evolutionary trends may underlie some aspects of the risk for common, non-communicable disorders, including psychiatric disease. We analyzed whole exome sequencing data from 80 unique individuals from India coming from families with two or more individuals with severe mental illness. We used Population Branch Statistics (PBS) to identify variants and genes under positive selection and identified 74 genes as candidates for positive selection. Of these, 20 were previously associated with Schizophrenia, Alzheimer{\textquoteright}s disease and cognitive abilities in genome wide association studies. We then checked whether any of these 74 genes were involved in common biological pathways or related to specific cellular or molecular functions. We found that immune related pathways and functions related to innate immunity such as antigen binding were over-represented. We also evaluated for the presence of Neanderthal introgressed segments in these genes and found Neanderthal introgression in a single gene out of the 74 candidate genes. However, the introgression pattern indicates the region is unlikely to be the source for selection. Our findings hint at how selection pressures in individuals from families with a history of severe mental illness may diverge from the general population. Further, it also provides insights into the genetic architecture of severe mental illness, such as schizophrenia and its link to immune factors.

}, issn = {2045-2322}, doi = {10.1038/s41598-021-00123-x}, author = {Mahadevan, Jayant and Pathak, Ajai Kumar and Vemula, Alekhya and Nadella, Ravi Kumar and Viswanath, Biju and Jain, Sanjeev and Purushottam, Meera and Mondal, Mayukh} } @article {2328, title = {APOE4 Affects Basal and NMDAR-Mediated Protein Synthesis in Neurons by Perturbing Calcium Homeostasis.}, journal = {J Neurosci}, volume = {41}, year = {2021}, month = {2021 Oct 20}, pages = {8686-8709}, abstract = {

Apolipoprotein E (APOE), one of the primary lipoproteins in the brain has three isoforms in humans, APOE2, APOE3, and APOE4. APOE4 is the most well-established risk factor increasing the predisposition for Alzheimer{\textquoteright}s disease (AD). The presence of the APOE4 allele alone is shown to cause synaptic defects in neurons and recent studies have identified multiple pathways directly influenced by APOE4. However, the mechanisms underlying APOE4-induced synaptic dysfunction remain elusive. Here, we report that the acute exposure of primary cortical neurons or synaptoneurosomes to APOE4 leads to a significant decrease in global protein synthesis. Primary cortical neurons were derived from male and female embryos of Sprague Dawley (SD) rats or C57BL/6J mice. Synaptoneurosomes were prepared from P30 male SD rats. APOE4 treatment also abrogates the NMDA-mediated translation response indicating an alteration of synaptic signaling. Importantly, we demonstrate that both APOE3 and APOE4 generate a distinct translation response which is closely linked to their respective calcium signature. Acute exposure of neurons to APOE3 causes a short burst of calcium through NMDA receptors (NMDARs) leading to an initial decrease in protein synthesis which quickly recovers. Contrarily, APOE4 leads to a sustained increase in calcium levels by activating both NMDARs and L-type voltage-gated calcium channels (L-VGCCs), thereby causing sustained translation inhibition through eukaryotic translation elongation factor 2 (eEF2) phosphorylation, which in turn disrupts the NMDAR response. Thus, we show that APOE4 affects basal and activity-mediated protein synthesis responses in neurons by affecting calcium homeostasis. Defective protein synthesis has been shown as an early defect in familial Alzheimer{\textquoteright}s disease (AD). However, this has not been studied in the context of sporadic AD, which constitutes the majority of cases. In our study, we show that Apolipoprotein E4 (APOE4), the predominant risk factor for AD, inhibits global protein synthesis in neurons. APOE4 also affects NMDA activity-mediated protein synthesis response, thus inhibiting synaptic translation. We also show that the defective protein synthesis mediated by APOE4 is closely linked to the perturbation of calcium homeostasis caused by APOE4 in neurons. Thus, we propose the dysregulation of protein synthesis as one of the possible molecular mechanisms to explain APOE4-mediated synaptic and cognitive defects. Hence, the study not only suggests an explanation for the APOE4-mediated predisposition to AD, it also bridges the gap in understanding APOE4-mediated pathology.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0435-21.2021}, author = {Ramakrishna, Sarayu and Jhaveri, Vishwaja and Konings, Sabine C and Nawalpuri, Bharti and Chakraborty, Sumita and Holst, Bj{\o}rn and Schmid, Benjamin and Gouras, Gunnar K and Freude, Kristine K and Muddashetty, Ravi S} } @article {2362, title = {Astrocytic reactivity triggered by defective autophagy and metabolic failure causes neurotoxicity in frontotemporal dementia type 3.}, journal = {Stem Cell Reports}, volume = {16}, year = {2021}, month = {2021 Nov 09}, pages = {2736-2751}, abstract = {

Frontotemporal dementia type 3 (FTD3), caused by a point mutation in the charged multivesicular body protein 2B (CHMP2B), affects mitochondrial ultrastructure and the endolysosomal pathway in neurons. To dissect the astrocyte-specific impact of mutant CHMP2B expression, we generated astrocytes from human induced pluripotent stem cells (hiPSCs) and confirmed our findings in CHMP2B mutant mice. Our data provide mechanistic insights into how defective autophagy causes perturbed mitochondrial dynamics with impaired glycolysis, increased reactive oxygen species, and elongated mitochondrial morphology, indicating increased mitochondrial fusion in FTD3 astrocytes. This shift in astrocyte homeostasis triggers a reactive astrocyte phenotype and increased release of toxic cytokines, which accumulate in nuclear factor kappa b (NF-κB) pathway activation with increased production of CHF, LCN2, and C3 causing neurodegeneration.

}, issn = {2213-6711}, doi = {10.1016/j.stemcr.2021.09.013}, author = {Chandrasekaran, Abinaya and Dittlau, Katarina Stoklund and Corsi, Giulia I and Haukedal, Henriette and Doncheva, Nadezhda T and Ramakrishna, Sarayu and Ambardar, Sheetal and Salcedo, Claudia and Schmidt, Sissel I and Zhang, Yu and Cirera, Susanna and Pihl, Maria and Schmid, Benjamin and Nielsen, Troels Tolstrup and Nielsen, J{\o}rgen E and Kolko, Miriam and Kobol{\'a}k, Julianna and Dinny{\'e}s, Andr{\'a}s and Hyttel, Poul and Palakodeti, Dasaradhi and Gorodkin, Jan and Muddashetty, Ravi S and Meyer, Morten and Aldana, Blanca I and Freude, Kristine K} } @article {2207, title = {Comprehensive annotation and characterization of planarian tRNA and tRNA-derived fragments (tRFs).}, journal = {RNA}, year = {2021}, month = {2021 Jan 14}, abstract = {

tRNA-derived fragments (tRFs) have recently gained a lot of scientific interest due to their diverse regulatory roles in several cellular processes. However, their function in dynamic biological process such as development and regeneration remains unexplored. Here, we show that tRFs are dynamically expressed during planarian regeneration suggesting a possible role for these small RNAs in the regulation of regeneration. In order to characterise planarian tRFs, we first annotated 457 tRNAs in S.mediterranea combining two tRNA prediction algorithms. Annotation of tRNAs facilitated the identification of three main species of tRFs in planarians - the shorter tRF-5s and itRFs, and the abundantly expressed 5{\textquoteright}-tsRNAs. Spatial profiling of tRFs in sequential transverse sections of planarians revealed diverse expression patterns of these small RNAs, including those that are enriched in the head and pharyngeal regions. Expression analysis of these tRF species revealed dynamic expression of these small RNAs over the course of regeneration suggesting an important role in planarian anterior and posterior regeneration. Finally, we show that 5{\textquoteright}-tsRNA in planaria interact with all three SMEDWI proteins and an involvement of Ago1 in the processing of itRFs. In summary, our findings implicate a novel role for tRFs in planarian regeneration, highlighting their importance in regulating complex systemic processes. Our study adds to the catalogue of post-transcriptional regulatory systems in planarian, providing valuable insights on the biogenesis and the function of tRFs in neoblasts and planarian regeneration.

}, issn = {1469-9001}, doi = {10.1261/rna.077701.120}, author = {Lakshmanan, Vairavan and T N, Sujith and Bansal, Dhiru and Padubidri, Shivaprasad V and Palakodeti, Dasaradhi and Krishna, Srikar} } @article {2326, title = {Correction of amygdalar dysfunction in a rat model of fragile X syndrome.}, journal = {Cell Rep}, volume = {37}, year = {2021}, month = {2021 Oct 12}, pages = {109805}, abstract = {

Fragile X syndrome (FXS), a commonly inherited form of autism and intellectual disability, is associated with emotional symptoms that implicate dysfunction of the amygdala. However, current understanding of the pathogenesis of the disease is based primarily on studies in the hippocampus and neocortex, where FXS defects have been corrected by inhibiting group I metabotropic glutamate receptors (mGluRs). Here, we observe that activation, rather than inhibition, of mGluRs in the basolateral amygdala reverses impairments in a rat model of FXS. FXS rats exhibit deficient recall of auditory conditioned fear, which is accompanied by a range of in\ vitro and in\ vivo deficits in synaptic transmission and plasticity. We find presynaptic mGluR5 in the amygdala, activation of which reverses deficient synaptic transmission and plasticity, thereby restoring normal fear learning in FXS rats. This highlights the importance of modifying the prevailing mGluR-based framework for therapeutic strategies to include circuit-specific differences in FXS pathophysiology.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2021.109805}, author = {Fernandes, Giselle and Mishra, Pradeep K and Nawaz, Mohammad Sarfaraz and Donlin-Asp, Paul G and Rahman, Mohammed Mostafizur and Hazra, Anupam and Kedia, Sonal and Kayenaat, Aiman and Songara, Dheeraj and Wyllie, David J A and Schuman, Erin M and Kind, Peter C and Chattarji, Sumantra} } @article {2292, title = {Cross-diagnostic evaluation of minor physical anomalies in psychiatric disorders.}, journal = {J Psychiatr Res}, volume = {142}, year = {2021}, month = {2021 Jul 20}, pages = {54-62}, abstract = {

BACKGROUND: Minor physical anomalies (MPA) are markers of impaired neurodevelopment during the prenatal stage. Assessing MPA across psychiatric disorders may help understand their shared nature. In addition, MPA in family members would indicate a shared liability and endophenotype potential. We examined familial aggregation of MPA and their role as transdiagnostic and disorder-specific markers of 5 major psychiatric/neuropsychiatric conditions (schizophrenia, bipolar disorder, substance dependence, obsessive-compulsive disorder, and Alzheimer{\textquoteright}s dementia).

METHODS: Modified Waldrop{\textquoteright}s MPA scale was applied on 1321 individuals from 439 transdiagnostic multiplex families and 125 healthy population controls (HC). Stage of fetal development (morphogenetic/phenogenetic)- and anatomical location (craniofacial/peripheral)-based sub-scores were calculated. Familiality and endophenotypic potential of MPA were analyzed with serial negative binomial mixed-effect regression. Cross-diagnostic differences and the effect of family history density (FHD) of each diagnosis on MPA were assessed. Mixed-effects Cox models estimated the influence of MPA on age-at-onset of illness (AAO).

RESULTS: MPA were found to be heritable in families with psychiatric disorders, with a familiality of 0.52. MPA were higher in psychotic disorders after controlling for effects of sex and intrafamilial correlation. Morphogenetic variant MPA was noted to be lower in dementia in comparison to HC. FHD of schizophrenia and bipolar disorder predicted higher, and that of dementia and substance dependence predicted lower MPA. MPA brought forward the AAO [HR:1.07 (1.03-1.11)], and this was more apparent in psychotic disorders.

CONCLUSION: MPA are transmissible in families, are specifically related to the risk of developing psychoses, and predict an earlier age at onset. Neurodevelopmentally informed classification of MPA has the potential to enhance the etiopathogenic and translational understanding of psychiatric disorders.

}, issn = {1879-1379}, doi = {10.1016/j.jpsychires.2021.07.028}, author = {Sreeraj, Vanteemar S and Puzhakkal, Joan C and Holla, Bharath and Nadella, Ravi Kumar and Sheth, Sweta and Balachander, Srinivas and Ithal, Dhruva and Ali, Furkhan and Viswanath, Biju and Muralidharan, Kesavan and Venkatasubramanian, Ganesan and John, John P and Benegal, Vivek and Murthy, Pratima and Varghese, Mathew and Reddy, Yc Janardhan and Jain, Sanjeev} } @article {2329, title = {Distinct temporal expression of the GW182 paralog TNRC6A in neurons regulates dendritic arborization.}, journal = {J Cell Sci}, volume = {134}, year = {2021}, month = {2021 Aug 15}, abstract = {

Precise development of the dendritic architecture is a critical determinant of mature neuronal circuitry. MicroRNA (miRNA)-mediated regulation of protein synthesis plays a crucial role in dendritic morphogenesis, but the role of miRNA-induced silencing complex (miRISC) protein components in this process is less studied. Here, we show an important role of a key miRISC protein, the GW182 paralog TNRC6A, in the regulation of dendritic growth. We identified a distinct brain region-specific spatiotemporal expression pattern of GW182 during rat postnatal development. We found that the window of peak GW182 expression coincides with the period of extensive dendritic growth, both in the hippocampus and cerebellum. Perturbation of GW182 function during a specific temporal window resulted in reduced dendritic growth of cultured hippocampal neurons. Mechanistically, we show that GW182 modulates dendritic growth by regulating global somatodendritic translation and actin cytoskeletal dynamics of developing neurons. Furthermore, we found that GW182 affects dendritic architecture by regulating the expression of actin modulator LIMK1. Taken together, our data reveal a previously undescribed neurodevelopmental expression pattern of GW182 and its role in dendritic morphogenesis, which involves both translational control and actin cytoskeletal rearrangement. This article has an associated First Person interview with the first author of the paper.

}, issn = {1477-9137}, doi = {10.1242/jcs.258465}, author = {Nawalpuri, Bharti and Sharma, Arpita and Chattarji, Sumantra and Muddashetty, Ravi S} } @article {2327, title = {Engineered RNA biosensors enable ultrasensitive SARS-CoV-2 detection in a simple color and luminescence assay.}, journal = {Life Sci Alliance}, volume = {4}, year = {2021}, month = {2021 12}, abstract = {

The continued resurgence of the COVID-19 pandemic with multiple variants underlines the need for diagnostics that are adaptable to the virus. We have developed toehold RNA-based sensors across the SARS-CoV-2 genome for direct and ultrasensitive detection of the virus and its prominent variants. Here, isothermal amplification of a fragment of SARS-CoV-2 RNA coupled with activation of our biosensors leads to a conformational switch in the sensor. This leads to translation of a reporter protein, for example, LacZ or nano-lantern that is easily detected using color/luminescence. By optimizing RNA amplification and biosensor design, we have generated a highly sensitive diagnostic assay that is capable of detecting as low as 100 copies of viral RNA with development of bright color. This is easily visualized by the human eye and quantifiable using spectrophotometry. Finally, this PHAsed NASBA-Translation Optical Method (PHANTOM) using our engineered RNA biosensors efficiently detects viral RNA in patient samples. This work presents a powerful and universally accessible strategy for detecting COVID-19 and variants. This strategy is adaptable to further viral evolution and brings RNA bioengineering center-stage.

}, keywords = {Biosensing Techniques, COVID-19, Humans, Luminescence, Nucleic Acid Amplification Techniques, RNA, RNA, Viral, SARS-CoV-2}, issn = {2575-1077}, doi = {10.26508/lsa.202101213}, author = {Chakravarthy, Anirudh and Nandakumar, Anirudh and George, Geen and Ranganathan, Shyamsundar and Umashankar, Suchitta and Shettigar, Nishan and Palakodeti, Dasaradhi and Gulyani, Akash and Ramesh, Arati} } @article {2323, title = {Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India.}, journal = {Science}, year = {2021}, month = {2021 Oct 14}, pages = {eabj9932}, abstract = {

Delhi, the national capital of India, has experienced multiple SARS-CoV-2 outbreaks in 2020 and reached population seropositivity of over 50\% by 2021. During April 2021, the city became overwhelmed by COVID-19 cases and fatalities, as a new variant B.1.617.2 (Delta) replaced B.1.1.7 (Alpha). A Bayesian model explains the growth advantage of Delta through a combination of increased transmissibility and reduced sensitivity to immune responses generated against earlier variants (median estimates; {\texttimes}1.5-fold, 20\% reduction). Seropositivity of an employee and family cohort increased from 42\% to 87.5\% between March and July 2021, with 27\% reinfections, as judged by increased antibody concentration after a previous decline. The likely high transmissibility and partial evasion of immunity by the Delta variant contributed to an overwhelming surge in Delhi.

}, issn = {1095-9203}, doi = {10.1126/science.abj9932}, author = {Dhar, Mahesh S and Marwal, Robin and Vs, Radhakrishnan and Ponnusamy, Kalaiarasan and Jolly, Bani and Bhoyar, Rahul C and Sardana, Viren and Naushin, Salwa and Rophina, Mercy and Mellan, Thomas A and Mishra, Swapnil and Whittaker, Charles and Fatihi, Saman and Datta, Meena and Singh, Priyanka and Sharma, Uma and Ujjainiya, Rajat and Bhatheja, Nitin and Divakar, Mohit Kumar and Singh, Manoj K and Imran, Mohamed and Senthivel, Vigneshwar and Maurya, Ranjeet and Jha, Neha and Mehta, Priyanka and A, Vivekanand and Sharma, Pooja and Vr, Arvinden and Chaudhary, Urmila and Soni, Namita and Thukral, Lipi and Flaxman, Seth and Bhatt, Samir and Pandey, Rajesh and Dash, Debasis and Faruq, Mohammed and Lall, Hemlata and Gogia, Hema and Madan, Preeti and Kulkarni, Sanket and Chauhan, Himanshu and Sengupta, Shantanu and Kabra, Sandhya and Gupta, Ravindra K and Singh, Sujeet K and Agrawal, Anurag and Rakshit, Partha and Nandicoori, Vinay and Tallapaka, Karthik Bharadwaj and Sowpati, Divya Tej and Thangaraj, K and Bashyam, Murali Dharan and Dalal, Ashwin and Sivasubbu, Sridhar and Scaria, Vinod and Parida, Ajay and Raghav, Sunil K and Prasad, Punit and Sarin, Apurva and Mayor, Satyajit and Ramakrishnan, Uma and Palakodeti, Dasaradhi and Seshasayee, Aswin Sai Narain and Bhat, Manoj and Shouche, Yogesh and Pillai, Ajay and Dikid, Tanzin and Das, Saumitra and Maitra, Arindam and Chinnaswamy, Sreedhar and Biswas, Nidhan Kumar and Desai, Anita Sudhir and Pattabiraman, Chitra and Manjunatha, M V and Mani, Reeta S and Arunachal Udupi, Gautam and Abraham, Priya and Atul, Potdar Varsha and Cherian, Sarah S} } @article {2242, title = {Mechanical instability of adherens junctions overrides intrinsic quiescence of hair follicle stem cells.}, journal = {Dev Cell}, volume = {56}, year = {2021}, month = {2021 Mar 22}, pages = {761-780.e7}, abstract = {

Vinculin, a mechanotransducer associated with both adherens junctions (AJs) and focal adhesions (FAs), plays a central role in force transmission through cell-cell and cell-substratum contacts. We generated the conditional knockout (cKO) of vinculin in murine skin that results in the loss of bulge stem cell (BuSC) quiescence and promotes continual cycling of the hair follicles. Surprisingly, we find that the AJs in vinculin cKO cells are mechanically weak and impaired in force generation despite increased junctional expression of E-cadherin and α-catenin. Mechanistically, we demonstrate that vinculin functions by keeping α-catenin in a stretched/open conformation, which in turn regulates the retention of YAP1, another potent mechanotransducer and regulator of cell proliferation, at the AJs. Altogether, our data provide mechanistic insights into the hitherto-unexplored regulatory link between the mechanical stability of cell junctions and contact-inhibition-mediated maintenance of BuSC quiescence.

}, issn = {1878-1551}, doi = {10.1016/j.devcel.2021.02.020}, author = {Biswas, Ritusree and Banerjee, Avinanda and Lembo, Sergio and Zhao, Zhihai and Lakshmanan, Vairavan and Lim, Ryan and Le, Shimin and Nakasaki, Manando and Kutyavin, Vassily and Wright, Graham and Palakodeti, Dasaradhi and Ross, Robert S and Jamora, Colin and Vasioukhin, Valeri and Jie, Yan and Raghavan, Srikala} } @article {2212, title = {Microneedles for Extended Transdermal Therapeutics: A Route to Advanced Healthcare.}, journal = {Eur J Pharm Biopharm}, volume = {159}, year = {2021}, month = {2021 Feb}, pages = {151-169}, abstract = {

Sustained release of drugs over a pre-determined period is required to maintain an effective therapeutic dose for variety of drug delivery applications. Transdermal devices such as polymeric microneedle patches and other microneedle-based devices have been utilized for sustained release of their payload. Swift clearing of drugs can be prevented either by designing a slow-degrading polymeric matrix or by providing physiochemical triggers to different microneedle-based devices for on-demand release. These long-acting transdermal devices prevent the burst release of drugs. This review highlights the recent advances of microneedle-based devices for sustained release of vaccines, hormones, and antiretrovirals with their prospective safe clinical translation.

}, issn = {1873-3441}, doi = {10.1016/j.ejpb.2020.12.020}, author = {Pahal, Suman and Badnikar, Kedar and Ghate, Vivek and Bhutani, Utkarsh and Nayak, Mangalore Manjunatha and Subramanyam, Dinesh Narasimhaiah and Vemula, Praveen Kumar} } @article {2244, title = {Oxylipin biosynthesis reinforces cellular senescence and allows detection of senolysis.}, journal = {Cell Metab}, year = {2021}, month = {2021 Mar 31}, abstract = {

Cellular senescence is a stress or damage response that causes a permanent proliferative arrest and secretion of numerous factors with potent biological activities. This senescence-associated secretory phenotype (SASP) has been characterized largely for secreted proteins that participate in embryogenesis, wound healing, inflammation, and many age-related pathologies. By contrast, lipid components of the SASP are understudied. We show that senescent cells activate the biosynthesis of several oxylipins that promote segments of the SASP and reinforce the proliferative arrest. Notably, senescent cells synthesize and accumulate an unstudied intracellular prostaglandin, 1a,1b-dihomo-15-deoxy-delta-12,14-prostaglandin J2. Released 15-deoxy-delta-12,14-prostaglandin J2 is a biomarker of senolysis in culture and in\ vivo. This and other prostaglandin D2-related lipids promote the senescence arrest and SASP by activating RAS signaling. These data identify an important aspect of cellular senescence and a method to detect senolysis.

}, issn = {1932-7420}, doi = {10.1016/j.cmet.2021.03.008}, author = {Wiley, Christopher D and Sharma, Rishi and Davis, Sonnet S and Lopez-Dominguez, Jose Alberto and Mitchell, Kylie P and Wiley, Samantha and Alimirah, Fatouma and Kim, Dong Eun and Payne, Therese and Rosko, Andrew and Aimontche, Eliezer and Deshpande, Sharvari M and Neri, Francesco and Kuehnemann, Chisaka and Demaria, Marco and Ramanathan, Arvind and Campisi, Judith} } @article {2202, title = {Psychiatric symptoms and syndromes transcending diagnostic boundaries in Indian multiplex families: The cohort of ADBS study.}, journal = {Psychiatry Res}, volume = {296}, year = {2021}, month = {2021 Feb}, pages = {113647}, abstract = {

Syndromes of schizophrenia, bipolar disorder, obsessive-compulsive disorder, substance use disorders and Alzheimer{\textquoteright}s dementia are highly heritable. About 10-20\% of subjects have another affected first degree relative (FDR), and thus represent a {\textquoteright}greater{\textquoteright} genetic susceptibility. We screened 3583 families to identify 481 families with multiple affected members, assessed 1406 individuals in person, and collected information systematically about other relatives. Within the selected families, a third of all FDRs were affected with serious mental illness. Although similar diagnoses aggregated within families, 62\% of the families also had members with other syndromes. Moreover, 15\% of affected individuals met criteria for co-occurrence of two or more syndromes, across their lifetime. Using dimensional assessments, we detected a range of symptom clusters in both affected and unaffected individuals, and across diagnostic categories. Our findings suggest that in multiplex families, there is considerable heterogeneity of clinical syndromes, as well as sub-threshold symptoms. These families would help provide an opportunity for further research using both genetic analyses and biomarkers.

}, issn = {1872-7123}, doi = {10.1016/j.psychres.2020.113647}, author = {Sreeraj, Vanteemar S and Holla, Bharath and Ithal, Dhruva and Nadella, Ravi Kumar and Mahadevan, Jayant and Balachander, Srinivas and Ali, Furkhan and Sheth, Sweta and Narayanaswamy, Janardhanan C and Venkatasubramanian, Ganesan and John, John P and Varghese, Mathew and Benegal, Vivek and Jain, Sanjeev and Reddy, Yc Janardhan and Viswanath, Biju} } @article {2373, title = {A regulatory network of microRNAs confers lineage commitment during early developmental trajectories of B and T lymphocytes.}, journal = {Proc Natl Acad Sci U S A}, volume = {118}, year = {2021}, month = {2021 11 16}, abstract = {

The commitment of hematopoietic multipotent progenitors (MPPs) toward a particular lineage involves activation of cell type-specific genes and silencing of genes that promote alternate cell fates. Although the gene expression programs of early-B and early-T lymphocyte development are mutually exclusive, we show that these cell types exhibit significantly correlated microRNA (miRNA) profiles. However, their corresponding miRNA targetomes are distinct and predominated by transcripts associated with natural killer, dendritic cell, and myeloid lineages, suggesting that miRNAs function in a cell-autonomous manner. The combinatorial expression of miRNAs miR-186-5p, miR-128-3p, and miR-330-5p in MPPs significantly attenuates their myeloid differentiation potential due to repression of myeloid-associated transcripts. Depletion of these miRNAs caused a pronounced de-repression of myeloid lineage targets in differentiating early-B and early-T cells, resulting in a mixed-lineage gene expression pattern. De novo motif analysis combined with an assay of promoter activities indicates that B as well as T lineage determinants drive the expression of these miRNAs in lymphoid lineages. Collectively, we present a paradigm that miRNAs are conserved between developing B and T lymphocytes, yet they target distinct sets of promiscuously expressed lineage-inappropriate genes to suppress the alternate cell-fate options. Thus, our studies provide a comprehensive compendium of miRNAs with functional implications for B and T lymphocyte development.

}, keywords = {Animals, B-Lymphocytes, Cell Differentiation, Cell Lineage, Gene Expression, Gene Expression Profiling, Gene Regulatory Networks, Hematopoietic Stem Cells, Mice, MicroRNAs, Myeloid Cells, T-Lymphocytes}, issn = {1091-6490}, doi = {10.1073/pnas.2104297118}, author = {Nikhat, Sameena and Yadavalli, Anurupa D and Prusty, Arpita and Narayan, Priyanka K and Palakodeti, Dasaradhi and Murre, Cornelis and Pongubala, Jagan M R} } @article {2206, title = {Role of Hypoxia-Mediated Autophagy in Tumor Cell Death and Survival.}, journal = {Cancers (Basel)}, volume = {13}, year = {2021}, month = {2021 Jan 30}, abstract = {

Programmed cell death or type I apoptosis has been extensively studied and its contribution to the pathogenesis of disease is well established. However, autophagy functions together with apoptosis to determine the overall fate of the cell. The cross talk between this active self-destruction process and apoptosis is quite complex and contradictory as well, but it is unquestionably decisive for cell survival or cell death. Autophagy can promote tumor suppression but also tumor growth by inducing cancer-cell development and proliferation. In this review, we will discuss how autophagy reprograms tumor cells in the context of tumor hypoxic stress. We will illustrate how autophagy acts as both a suppressor and a driver of tumorigenesis through tuning survival in a context dependent manner. We also shed light on the relationship between autophagy and immune response in this complex regulation. A better understanding of the autophagy mechanisms and pathways will undoubtedly ameliorate the design of therapeutics aimed at targeting autophagy for future cancer immunotherapies.

}, issn = {2072-6694}, doi = {10.3390/cancers13030533}, author = {Zaarour, Rania F and Azakir, Bilal and Hajam, Edries Y and Nawafleh, Husam and Zeinelabdin, Nagwa A and Engelsen, Agnete S T and Thiery, J{\'e}rome and Jamora, Colin and Chouaib, Salem} } @article {2290, title = {Strategies to target SARS-CoV-2 entry and infection using dual mechanisms of inhibition by acidification inhibitors.}, journal = {PLoS Pathog}, volume = {17}, year = {2021}, month = {2021 07}, pages = {e1009706}, abstract = {

Many viruses utilize the host endo-lysosomal network for infection. Tracing the endocytic itinerary of SARS-CoV-2 can provide insights into viral trafficking and aid in designing new therapeutic strategies. Here, we demonstrate that the receptor binding domain (RBD) of SARS-CoV-2 spike protein is internalized via the pH-dependent CLIC/GEEC (CG) endocytic pathway in human gastric-adenocarcinoma (AGS) cells expressing undetectable levels of ACE2. Ectopic expression of ACE2 (AGS-ACE2) results in RBD traffic via both CG and clathrin-mediated endocytosis. Endosomal acidification inhibitors like BafilomycinA1 and NH4Cl, which inhibit the CG pathway, reduce the uptake of RBD and impede Spike-pseudoviral infection in both AGS and AGS-ACE2 cells. The inhibition by BafilomycinA1 was found to be distinct from Chloroquine which neither affects RBD uptake nor alters endosomal pH, yet attenuates Spike-pseudovirus entry. By screening a subset of FDA-approved inhibitors for functionality similar to BafilomycinA1, we identified Niclosamide as a SARS-CoV-2 entry inhibitor. Further validation using a clinical isolate of SARS-CoV-2 in AGS-ACE2 and Vero cells confirmed its antiviral effect. We propose that Niclosamide, and other drugs which neutralize endosomal pH as well as inhibit the endocytic uptake, could provide broader applicability in subverting infection of viruses entering host cells via a pH-dependent endocytic pathway.

}, keywords = {Ammonium Chloride, Angiotensin-Converting Enzyme 2, Animals, Antiviral Agents, Cell Line, Chlorocebus aethiops, Chloroquine, Clathrin, COVID-19, Drug Synergism, Endocytosis, Endosomes, Humans, Hydrogen-Ion Concentration, Hydroxychloroquine, Macrolides, Niclosamide, Protein Binding, Protein Domains, SARS-CoV-2, Spike Glycoprotein, Coronavirus, Vero Cells, Virus Internalization}, issn = {1553-7374}, doi = {10.1371/journal.ppat.1009706}, author = {Prabhakara, Chaitra and Godbole, Rashmi and Sil, Parijat and Jahnavi, Sowmya and Gulzar, Shah-E-Jahan and van Zanten, Thomas S and Sheth, Dhruv and Subhash, Neeraja and Chandra, Anchal and Shivaraj, Akshatha and Panikulam, Patricia and U, Ibrahim and Nuthakki, Vijay Kumar and Puthiyapurayil, Theja Parassini and Ahmed, Riyaz and Najar, Ashaq Hussain and Lingamallu, Sai Manoz and Das, Snigdhadev and Mahajan, Bhagyashri and Vemula, Praveen and Bharate, Sandip B and Singh, Parvinder Pal and Vishwakarma, Ram and Guha, Arjun and Sundaramurthy, Varadharajan and Mayor, Satyajit} } @article {2156, title = {Adverse childhood experiences in families with multiple members diagnosed to have psychiatric illnesses.}, journal = {Aust N Z J Psychiatry}, volume = {54}, year = {2020}, month = {2020 Nov}, pages = {1086-1094}, abstract = {

OBJECTIVE: Adverse childhood experiences are linked to the development of a number of psychiatric illnesses in adulthood. Our study examined the pattern of adverse childhood experiences and their relation to the age of onset of major psychiatric conditions in individuals from families that had ⩾2 first-degree relatives with major psychiatric conditions (multiplex families), identified as part of an ongoing longitudinal study.

METHODS: Our sample consisted of 509 individuals from 215 families. Of these, 268 were affected, i.e., diagnosed with bipolar disorder ( = 61), obsessive-compulsive disorder ( = 58), schizophrenia ( = 52), substance dependence ( = 59) or co-occurring diagnoses ( = 38), while 241 were at-risk first-degree relatives who were either unaffected ( = 210) or had other depressive or anxiety disorders ( = 31). All individuals were evaluated using the Adverse Childhood Experiences - International Questionnaire and total adverse childhood experiences exposure and severity scores were calculated.

RESULTS: It was seen that affected males, as a group, had the greatest adverse childhood experiences exposure and severity scores in our sample. A Cox mixed effects model fit by gender revealed that a higher total adverse childhood experiences severity score was associated with significantly increased risk for an earlier age of onset of psychiatric diagnoses in males. A similar model that evaluated the interaction of diagnosis revealed an earlier age of onset in obsessive-compulsive disorder and substance dependence, but not in schizophrenia and bipolar disorder.

CONCLUSION: Our study indicates that adverse childhood experiences were associated with an earlier onset of major psychiatric conditions in men and individuals diagnosed with obsessive-compulsive disorder and substance dependence. Ongoing longitudinal assessments in first-degree relatives from these families are expected to identify mechanisms underlying this relationship.

}, issn = {1440-1614}, doi = {10.1177/0004867420931157}, author = {Someshwar, Amala and Holla, Bharath and Pansari Agarwal, Preeti and Thomas, Anza and Jose, Anand and Joseph, Boban and Raju, Birudu and Karle, Hariprasad and Muthukumaran, M and Kodancha, Prabhath G and Kumar, Pramod and Reddy, Preethi V and Kumar Nadella, Ravi and Naik, Sanjay T and Mitra, Sayantanava and Mallappagiri, Sreenivasulu and Sreeraj, Vanteemar S and Balachander, Srinivas and Ganesh, Suhas and Murthy, Pratima and Benegal, Vivek and Reddy, Janardhan Yc and Jain, Sanjeev and Mahadevan, Jayant and Viswanath, Biju} } @article {2251, title = {Generic Molding Platform for Simple, Low-Cost Fabrication of Polymeric Microneedles}, journal = {Macromolecular Materials and Engineering}, volume = {305}, year = {2020}, abstract = {

Micromolding technology is widely used for the fabrication of polymer microneedles for transdermal and intradermal drug delivery applications. Geometric features of microneedles in molding are solely determined by geometry of the master mold template. Fabrication of master mold template usually involves costly and cumbersome technologies due to small feature sizes typical of microneedles. In this research, a novel molding platform is designed that is fabricated using low-cost and simple techniques with flexibility of producing large number of microneedle geometries. The proposed molding platform eliminates need for developing multiple mold templates for fabrication of various geometries of polymer microneedles. Utility of this molding platform is demonstrated in polylactic acid-based solid thermoplastic microneedles and polyacrylic acid-based dissolvable microneedles with various aspect ratio settings. Various microneedles fabricated at heights differing with resolution of as low as 100 {\textmu}m are successfully achieved using specified settings in the molding platform. The suitability of fabricated microneedles for drug delivery applications is evaluated by in vitro and in vivo testing.

}, author = {7. Badnikar, K. and Jayadevi, S. N. and Pahal, S. and Sripada, S. and Nayak, M. M. and Vemula, P. K. and Subrahmanyam, D. N.} } @article {2155, title = {Genetic, clinical, molecular, and pathogenic aspects of the South Asian-specific polymorphic MYBPC3 variant.}, journal = {Biophys Rev}, volume = {12}, year = {2020}, month = {2020 Aug}, pages = {1065-1084}, abstract = {

Hypertrophic cardiomyopathy (HCM) is a cardiac genetic disease characterized by ventricular enlargement, diastolic dysfunction, and increased risk for sudden cardiac death. Sarcomeric genetic defects are the predominant known cause of HCM. In particular, mutations in the myosin-binding protein C gene (MYBPC3) are associated with ~ 40\% of all HCM cases in which a genetic basis has been established. A decade ago, our group reported a 25-base pair deletion in intron 32 of MYBPC3 (MYBPC3) that is uniquely prevalent in South Asians and is associated with autosomal dominant cardiomyopathy. Although our studies suggest that this deletion results in left ventricular dysfunction, cardiomyopathies, and heart failure, the precise mechanism by which this variant predisposes to heart disease remains unclear. Increasingly appreciated, however, is the contribution of secondary risk factors, additional mutations, and lifestyle choices in augmenting or modifying the HCM phenotype in MYBPC3 carriers. Therefore, the goal of this review article is to summarize the current research dedicated to understanding the molecular pathophysiology of HCM in South Asians with the MYBPC3 variant. An emphasis is to review the latest techniques currently applied to explore the MYBPC3 pathogenesis and to provide a foundation for developing new diagnostic strategies and advances in therapeutics.

}, issn = {1867-2450}, doi = {10.1007/s12551-020-00725-1}, author = {Arif, Mohammed and Nabavizadeh, Pooneh and Song, Taejeong and Desai, Darshini and Singh, Rohit and Bazrafshan, Sholeh and Kumar, Mohit and Wang, Yigang and Gilbert, Richard J and Dhandapany, Perundurai S and Becker, Richard C and Kranias, Evangelia G and Sadayappan, Sakthivel} } @article {2247, title = {Genetic drift and bottleneck do not influence diversity in Toll-like receptor genes at a small spatial scale in a Himalayan passerine.}, journal = {Ecol Evol}, volume = {10}, year = {2020}, month = {2020 Nov}, pages = {12246-12263}, abstract = {

Genetic diversity is important for long-term viability of a population. Low genetic diversity reduces persistence and survival of populations and increases susceptibility to diseases. Comparisons of the neutral markers with functional loci such as immune genes [Toll-like receptors; TLR] can provide useful insights into evolutionary potential of a species and how the diversity of pathogens and selection pressures on their hosts are directly linked to their environment. In this study, we compare genetic diversity in neutral (eleven microsatellite loci) and adaptive (seven TLR loci) loci to determine genetic variation in a nonmigratory western Himalayan passerine, the black-throated tit (), distributed across an elevation gradient with varying degree of pathogen-mediated selection pressure. We further compare the diversity in TLR loci with a high-elevation sister species, the white-throated tit (). Our results indicate a lack of population genetic structure in the black-throated tit and signatures of a past bottleneck. In contrast, we found high diversity in TLR loci and locus-specific (TLR7) signatures of pathogen-mediated selection, which was comparable to diversity in the white-throated tit. Levels of diversity at TLR5 locus corresponded very closely with neutral microsatellite variation. We found evidence of positive selection in TLR1LA, TLR5, and TLR7 loci highlighting the importance in pathogen recognition. Our finding demonstrates that reduction in neutral variation does not necessarily lead to reduction in functional genetic diversity and probably helps in revival of population in a widespread species.

}, issn = {2045-7758}, doi = {10.1002/ece3.6855}, author = {Nandakumar, Mridula and Ishtiaq, Farah} } @article {2068, title = {Lithium response in bipolar disorder correlates with improved cell viability of patient derived cell lines.}, journal = {Sci Rep}, volume = {10}, year = {2020}, month = {2020 May 04}, pages = {7428}, abstract = {

Lithium is an effective, well-established treatment for bipolar disorder (BD). However, the mechanisms of its action, and reasons for variations in clinical response, are unclear. We used neural precursor cells (NPCs) and lymphoblastoid cell lines (LCLs), from BD patients characterized for clinical response to lithium (using the "Alda scale" and "NIMH Retrospective Life chart method"), to interrogate cellular phenotypes related to both disease and clinical lithium response. NPCs from two biologically related BD patients who differed in their clinical response to lithium were compared with healthy controls. RNA-Seq and analysis, mitochondrial membrane potential (MMP), cell viability, and cell proliferation parameters were assessed, with and without in vitro lithium. These parameters were also examined in LCLs from 25 BD patients (16 lithium responders and 9 non-responders), and 12 controls. MMP was lower in both NPCs and LCLs from BD; but it was reversed with in vitro lithium only in LCLs, and this was unrelated to clinical lithium response. The higher cell proliferation observed in BD was unaffected by in vitro lithium. Cell death was greater in BD. However, LCLs from clinical lithium responders could be rescued by addition of in vitro lithium. In vitro lithium also enhanced BCL2 and GSK3B expression in these cells. Our findings indicate cellular phenotypes related to the disease (MMP, cell proliferation) in both NPCs and LCLs; and those related to clinical lithium response (cell viability, BCL2/GSK3B expression) in LCLs.

}, issn = {2045-2322}, doi = {10.1038/s41598-020-64202-1}, author = {Paul, Pradip and Iyer, Shruti and Nadella, Ravi Kumar and Nayak, Rashmitha and Chellappa, Anirudh S and Ambardar, Sheetal and Sud, Reeteka and Sukumaran, Salil K and Purushottam, Meera and Jain, Sanjeev and Viswanath, Biju} } @article {2108, title = {A novel polyubiquitin chain linkage formed by viral Ubiquitin is resistant to host deubiquitinating enzymes.}, journal = {Biochem J}, volume = {477}, year = {2020}, month = {2020 Jun 26}, pages = {2193-2219}, abstract = {

The Baculoviridae family of viruses encode a viral Ubiquitin (vUb) gene. Though the vUb is homologous to the host eukaryotic Ubiquitin (Ub), its preservation in the viral genome indicates unique functions that are not compensated by the host Ub. We report the structural, biophysical, and biochemical properties of the vUb from Autographa californica multiple nucleo-polyhedrosis virus (AcMNPV). The packing of central helix α1 to the beta-sheet β1-β5 is different between vUb and Ub. Consequently, its stability is lower compared with Ub. However, the surface properties, ubiquitination activity, and the interaction with Ubiquitin-binding domains are similar between vUb and Ub. Interestingly, vUb forms atypical polyubiquitin chain linked by lysine at the 54th position (K54), and the deubiquitinating enzymes are ineffective against the K54-linked polyubiquitin chains. We propose that the modification of host/viral proteins with the K54-linked chains is an effective way selected by the virus to protect the vUb signal from host DeUbiquitinases.

}, issn = {1470-8728}, doi = {10.1042/BCJ20200289}, author = {Negi, Hitendra and Reddy, Pothula Purushotham and Vengayil, Vineeth and Patole, Chhaya and Laxman, Sunil and Das, Ranabir} } @article {2059, title = {The Role of Dynamic miRISC During Neuronal Development.}, journal = {Front Mol Biosci}, volume = {7}, year = {2020}, month = {2020}, pages = {8}, abstract = {

Activity-dependent protein synthesis plays an important role during neuronal development by fine-tuning the formation and function of neuronal circuits. Recent studies have shown that miRNAs are integral to this regulation because of their ability to control protein synthesis in a rapid, specific and potentially reversible manner. miRNA mediated regulation is a multistep process that involves inhibition of translation before degradation of targeted mRNA, which provides the possibility to store and reverse the inhibition at multiple stages. This flexibility is primarily thought to be derived from the composition of miRNA induced silencing complex (miRISC). AGO2 is likely the only obligatory component of miRISC, while multiple RBPs are shown to be associated with this core miRISC to form diverse miRISC complexes. The formation of these heterogeneous miRISC complexes is intricately regulated by various extracellular signals and cell-specific contexts. In this review, we discuss the composition of miRISC and its functions during neuronal development. Neurodevelopment is guided by both internal programs and external cues. Neuronal activity and external signals play an important role in the formation and refining of the neuronal network. miRISC composition and diversity have a critical role at distinct stages of neurodevelopment. Even though there is a good amount of literature available on the role of miRNAs mediated regulation of neuronal development, surprisingly the role of miRISC composition and its functional dynamics in neuronal development is not much discussed. In this article, we review the available literature on the heterogeneity of the neuronal miRISC composition and how this may influence translation regulation in the context of neuronal development.

}, issn = {2296-889X}, doi = {10.3389/fmolb.2020.00008}, author = {Nawalpuri, Bharti and Ravindran, Sreenath and Muddashetty, Ravi S} } @article {1645, title = {Altered steady state and activity-dependent de novo protein expression in fragile X syndrome.}, journal = {Nat Commun}, volume = {10}, year = {2019}, month = {2019 Apr 12}, pages = {1710}, abstract = {

Whether fragile X mental retardation protein (FMRP) target mRNAs and neuronal activity contributing to elevated basal neuronal protein synthesis in fragile X syndrome (FXS) is unclear. Our proteomic experiments reveal that the de novo translational profile in FXS model mice is altered at steady state and in response to metabotropic glutamate receptor (mGluR) stimulation, but the proteins expressed differ under these conditions. Several altered proteins, including Hexokinase\ 1 and Ras, also are expressed in the blood of\ FXS model mice and pharmacological treatments previously reported to ameliorate phenotypes modify their abundance in blood. In addition, plasma levels of Hexokinase\ 1 and Ras differ between FXS patients and healthy volunteers. Our data suggest that brain-based de novo proteomics in FXS model mice can be used to find altered expression of proteins in blood that could serve as disease-state biomarkers in individuals with FXS.

}, issn = {2041-1723}, doi = {10.1038/s41467-019-09553-8}, author = {Bowling, Heather and Bhattacharya, Aditi and Zhang, Guoan and Alam, Danyal and Lebowitz, Joseph Z and Bohm-Levine, Nathaniel and Lin, Derek and Singha, Priyangvada and Mamcarz, Maggie and Puckett, Rosemary and Zhou, Lili and Aryal, Sameer and Sharp, Kevin and Kirshenbaum, Kent and Berry-Kravis, Elizabeth and Neubert, Thomas A and Klann, Eric} } @article {1646, title = {BDNF Induced Translation of Limk1 in Developing Neurons Regulates Dendrite Growth by Fine-Tuning Cofilin1 Activity.}, journal = {Front Mol Neurosci}, volume = {12}, year = {2019}, month = {2019}, pages = {64}, abstract = {

Dendritic growth and branching are highly regulated processes and are essential for establishing proper neuronal connectivity. There is a critical phase of early dendrite development when these are heavily regulated by external cues such as trophic factors. Brain-derived neurotrophic factor (BDNF) is a major trophic factor known to enhance dendrite growth in cortical neurons, but the molecular underpinnings of this response are not completely understood. We have identified that BDNF induced translational regulation is an important mechanism governing dendrite development in cultured rat cortical neurons. We show that BDNF treatment for 1 h in young neurons leads to translational up-regulation of an important actin regulatory protein LIM domain kinase 1 (Limk1), increasing its level locally in the dendrites. Limk1 is a member of serine/threonine (Ser/Thr) family kinases downstream of the Rho-GTPase pathway. BDNF induced increase in Limk1 levels leads to increased phosphorylation of its target protein cofilin1. We observed that these changes are maintained for long durations of up to 48 h and are mediating increase in number of primary dendrites and total dendrite length. Thus, we show that BDNF induced protein synthesis leads to fine-tuning of the actin cytoskeletal reassembly and thereby mediate dendrite development.

}, issn = {1662-5099}, doi = {10.3389/fnmol.2019.00064}, author = {Ravindran, Sreenath and Nalavadi, Vijayalaxmi C and Muddashetty, Ravi S} } @article {1604, title = {Derivation of iPSC lines from two patients with familial Alzheimer{\textquoteright}s disease from India.}, journal = {Stem Cell Res}, volume = {34}, year = {2019}, month = {2019 Jan}, pages = {101370}, abstract = {

The current prevalence of diagnosable dementia in India is 1\% of people over 60 years (~3.7 million people), but is estimated to increase significantly, as ~15\% world{\textquoteright}s aged population (\>65 years) would be resident here by 2020 (Shah et al., 2016). While several mutations that pose a familial risk have been identified, the ethnic background may influence disease susceptibility, clinical presentation and treatment response. In this study, we report a detailed characterization of two representative HiPSC lines from a well-characterized dementia cohort from India. Availability of these lines, and associated molecular and clinical information, would be useful in the detailed exploration of the genomic contribution(s) to AD.

}, issn = {1876-7753}, doi = {10.1016/j.scr.2018.101370}, author = {Najar, Ashaq H and Sneha, K M and Ashok, Aparna and Babu, Swathy and Subramaniam, Anand G and Kannan, Ramkrishnan and Viswanath, Biju and Purushottam, Meera and Varghese, Mathew and Parvez, Suhel and Panicker, Mitradas M and Mukherjee, Odity and Jain, Sanjeev} } @article {1839, title = {Differential effects of unipolar versus bipolar depression on episodic memory updating.}, journal = {Neurobiol Learn Mem}, volume = {161}, year = {2019}, month = {2019 05}, pages = {158-168}, abstract = {

Episodic memories, when reactivated, can be modified or updated by new learning. Since such dynamic memory processes remain largely unexplored in psychiatric disorders, we examined the impact of depression on episodic memory updating. Unipolar and bipolar depression patients, and age/education matched controls, first learned a set of objects (List-1). Two days later, participants in all three groups were either reminded of the first learning session or not followed by the learning of a new set of objects (List-2). Forty-eight hours later, List-1 recall was impaired in unipolar and bipolar patients compared to control participants. Further, as expected, control participants who received a reminder spontaneously recalled items from List-2 during recall of List-1, indicative of an updated List-1 memory. Such spontaneous intrusions were also seen in the unipolar and bipolar patients that received the reminder, suggesting that memory updating was unaffected in these two patient groups despite impaired recall of List 1. Unexpectedly, we observed a trend towards higher intrusions, albeit statistically insignificant, not only in the reminder but also in the no-reminder subgroups of bipolar patients. We probed this further in a second cohort by testing recall of List-2, which was also impaired in both depression groups. Again bipolar patients showed intrusions, but this time in the reverse order from List-1 into List-2, independent of a reminder. Taken together, despite impaired recall, updating of episodic memories was intact and unidirectional in unipolar depression. In contrast, indiscriminate updating, as evidenced by bidirectional interference between episodic memories, was seen in bipolar depression. These findings reveal a novel distinction between unipolar versus bipolar depression using a reactivation-dependent memory updating paradigm.

}, issn = {1095-9564}, doi = {10.1016/j.nlm.2019.04.008}, author = {Dongaonkar, Bhaktee and Hupbach, Almut and Nadel, Lynn and Chattarji, Sumantra} } @article {1982, title = {Differential Regulation of Translation by FMRP Modulates eEF2 Mediated Response on NMDAR Activity.}, journal = {Front Mol Neurosci}, volume = {12}, year = {2019}, month = {2019}, pages = {97}, abstract = {

SYNGAP1, a Synaptic Ras-GTPase activating protein, regulates synapse maturation during a critical developmental window. Heterozygous mutation in () has been shown to cause Intellectual Disability (ID) in children. Recent studies have provided evidence for altered neuronal protein synthesis in a mouse model of . However, the molecular mechanism behind the same is unclear. Here, we report the reduced expression of a known translation regulator, FMRP, during a specific developmental period in mice. Our results demonstrate that FMRP interacts with and regulates the translation of mRNA. We further show reduced translation leads to decreased FMRP level during development in which results in an increase in translation. These developmental changes are reflected in the altered response of eEF2 phosphorylation downstream of NMDA Receptor (NMDAR)-mediated signaling. In this study, we propose a cross-talk between FMRP and SYNGAP1 mediated signaling which can also explain the compensatory effect of impaired signaling observed in mice.

}, issn = {1662-5099}, doi = {10.3389/fnmol.2019.00097}, author = {Paul, Abhik and Nawalpuri, Bharti and Shah, Devanshi and Sateesh, Shruthi and Muddashetty, Ravi S and Clement, James P} } @article {1607, title = {Exome sequencing in families with severe mental illness identifies novel and rare variants in genes implicated in Mendelian neuropsychiatric syndromes.}, journal = {Psychiatry Clin Neurosci}, volume = {73}, year = {2019}, month = {2019 Jan}, pages = {11-19}, abstract = {

AIM: Severe mental illnesses (SMI), such as bipolar disorder and schizophrenia, are highly heritable, and have a complex pattern of inheritance. Genome-wide association studies detect a part of the heritability, which can be attributed to common genetic variation. Examination of rare variants with next-generation sequencing may add to the understanding of the genetic architecture of SMI.

METHODS: We analyzed 32 ill subjects from eight multiplex families and 33 healthy individuals using whole-exome sequencing. Prioritized variants were selected by a three-step filtering process, which included: deleteriousness by five in silico algorithms; sharing within families by affected individuals; rarity in South Asian sample estimated using the Exome Aggregation Consortium data; and complete absence of these variants in control individuals from the same gene pool.

RESULTS: We identified 42 rare, non-synonymous deleterious variants (~5 per pedigree) in this study. None of the variants were shared across families, indicating a {\textquoteright}private{\textquoteright} mutational profile. Twenty (47.6\%) of the variant harboring genes were previously reported to contribute to the risk of diverse neuropsychiatric syndromes, nine (21.4\%) of which were of Mendelian inheritance. These included genes carrying novel deleterious variants, such as the GRM1 gene implicated in spinocerebellar ataxia 44 and the NIPBL gene implicated in Cornelia de Lange syndrome.

CONCLUSION: Next-generation sequencing approaches in family-based studies are useful to identify novel and rare variants in genes for complex disorders like SMI. The findings of the study suggest a potential phenotypic burden of rare variants in Mendelian disease genes, indicating pleiotropic effects in the etiology of SMI.

}, keywords = {Bipolar Disorder, Exome, Female, Genetic Predisposition to Disease, Genetic Variation, Genome-Wide Association Study, Humans, Male, Pedigree, Phenotype, Schizophrenia}, issn = {1440-1819}, doi = {10.1111/pcn.12788}, author = {Ganesh, Suhas and Ahmed P, Husayn and Nadella, Ravi K and More, Ravi P and Seshadri, Manasa and Viswanath, Biju and Rao, Mahendra and Jain, Sanjeev and Mukherjee, Odity} } @article {1602, title = {Generation of a set of isogenic, gene-edited iPSC lines homozygous for all main APOE variants and an APOE knock-out line.}, journal = {Stem Cell Res}, volume = {34}, year = {2019}, month = {2019 Jan}, pages = {101349}, abstract = {

Alzheimer{\textquoteright}s disease (AD) is the most frequent neurodegenerative disease amongst the elderly. The SNPs rs429358 and rs7412 in the APOE gene are the most common risk factor for sporadic AD, and there are three different alleles commonly referred to as APOE-ε2, APOE-ε3 and APOE-ε4. Induced pluripotent stem cells (iPSCs) hold great promise to model AD as such cells can be differentiated in vitro to the required cell type. Here we report the use of CRISPR/Cas9 technology employed on iPSCs from a healthy individual with an APOE-ε3/ε4 genotype to obtain isogenic APOE-ε2/ε2, APOE-ε3/ε3, APOE-ε4/ε4 lines as well as an APOE-knock-out line.

}, issn = {1876-7753}, doi = {10.1016/j.scr.2018.11.010}, author = {Schmid, Benjamin and Prehn, Kennie R and Nimsanor, Natakarn and Garcia, Blanca Irene Aldana and Poulsen, Ulla and J{\o}rring, Ida and Rasmussen, Mikkel A and Clausen, Christian and Mau-Holzmann, Ulrike A and Ramakrishna, Sarayu and Muddashetty, Ravi and Steeg, Rachel and Bruce, Kevin and Mackintosh, Peter and Ebneth, Andreas and Holst, Bj{\o}rn and Cabrera-Socorro, Alfredo} } @article {1617, title = {Natural monomers: A mine for functional and sustainable materials {\textendash} Occurrence, chemical modification and polymerization}, journal = {Progress in Polymer Science}, volume = {92}, year = {2019}, abstract = {

Owing to the natural abundance, variety of structural features, and highly specific functions, natural monomers render themselves as potential candidates for production of high performance functional polymers. The emerging concept of the biorefinery and development of new biosynthetic routes to synthesize a versatile and broad spectrum of natural monomers and polymers continues to gain momentum. The production of high quality polymers from renewable feedstocks requires innovative chemical modifications and catalytic transformations to achieve higher yields in an efficient manner. A fresh look into monomers available from natural resources such as terpenes, rosin, glycerol, furans, tannins, suberin, their derivatives and miscellaneous monomers may inspire future applications with impactful biobased materials. There are also many areas that require urgent discussion and review pertaining to recent developments in the field; this includes monomer sources that give molecules having special structural features. In particular, cardanol, a naturally occurring low-molecular-weight compound is unique as it contains a phenolic head group and a hydrocarbon chain with different degrees of unsaturation. This molecule possesses functional groups that are amenable for classical chemical modification, which is instrumental in developing a wide range of functional monomers and polymers. A large number of soft and hard materials have been developed from cardanol-based monomers. During the past, a large number of industrial grade materials have been developed from plant-based monomers, including development from microbial and fermentation processes (i.e. lactic acid). This review provides a comprehensive study and survey on recent developments on monomers and polymers derived from urushiol and cardanol based monomers and polymers, vegetable oil-based monomers and polymers, microbially produced monomers and polymers. These all represent emerging fronts giving a vast scope while highlighting important potential material and reagent opportunities.

}, url = {https://www.sciencedirect.com/science/article/pii/S0079670018300273}, author = {John, G., and Nagarajan, S., and Vemula, P. K., and Silverman, J.R., and Pillai, C. K. S.} } @article {1744, title = {NMDAR mediated translation at the synapse is regulated by MOV10 and FMRP.}, journal = {Mol Brain}, volume = {12}, year = {2019}, month = {2019 Jul 10}, pages = {65}, abstract = {

Protein synthesis is crucial for maintaining synaptic plasticity and synaptic signalling. Here we have attempted to understand the role of RNA binding proteins, Fragile X Mental Retardation Protein (FMRP) and Moloney Leukemia Virus 10 (MOV10) protein in N-Methyl-D-Aspartate Receptor (NMDAR) mediated translation regulation. We show that FMRP is required for translation downstream of NMDAR stimulation and MOV10 is the key specificity factor in this process. In rat cortical synaptoneurosomes, MOV10 in association with FMRP and Argonaute 2 (AGO2) forms the inhibitory complex on a subset of NMDAR responsive mRNAs. On NMDAR stimulation, MOV10 dissociates from AGO2 and promotes the translation of its target mRNAs. FMRP is required to form MOV10-AGO2 inhibitory complex and to promote translation of MOV10 associated mRNAs. Phosphorylation of FMRP appears to be the potential switch for NMDAR mediated translation and in the absence of FMRP, the distinct translation response to NMDAR\ stimulation is lost. Thus, FMRP and MOV10 have an important regulatory role in NMDAR mediated translation at the synapse.

}, issn = {1756-6606}, doi = {10.1186/s13041-019-0473-0}, author = {Kute, Preeti Madhav and Ramakrishna, Sarayu and Neelagandan, Nagammal and Chattarji, Sumantra and Muddashetty, Ravi S} } @article {1984, title = {Novel Series of Methyl 3-(Substituted Benzoyl)-7-Substituted-2-Phenylindolizine-1-Carboxylates as Promising Anti-Inflammatory Agents: Molecular Modeling Studies.}, journal = {Biomolecules}, volume = {9}, year = {2019}, month = {2019 Oct 28}, abstract = {

The cyclooxygenase-2 (COX-2) enzyme is considered to be an important target for developing novel anti-inflammatory agents. Selective COX-2 inhibitors offer the advantage of lower adverse effects that are commonly associated with non-selective COX inhibitors. In this work, a novel series of methyl 3-(substituted benzoyl)-7-substituted-2-phenylindolizine-1-carboxylates was synthesized and evaluated for COX-2 inhibitory activity. Compound was identified as the most active compound of the series with an IC of 6.71 M, which is comparable to the IC of indomethacin, a marketed non-steroidal anti-inflammatory drug (NSAID). Molecular modeling and crystallographic studies were conducted to further characterize the compounds and gain better understanding of the binding interactions between the compounds and the residues at the active site of the COX-2 enzyme. The pharmacokinetic properties and potential toxic effects were predicted for all the synthesized compounds, which indicated good drug-like properties. Thus, these synthesized compounds can be considered as potential lead compounds for developing effective anti-inflammatory therapeutic agents.

}, issn = {2218-273X}, doi = {10.3390/biom9110661}, author = {Venugopala, Katharigatta N and Al-Attraqchi, Omar H A and Tratrat, Christophe and Nayak, Susanta K and Morsy, Mohamed A and Aldhubiab, Bandar E and Attimarad, Mahesh and Nair, Anroop B and Sreeharsha, Nagaraja and Venugopala, Rashmi and Haroun, Michelyne and Girish, Meravanige B and Chandrashekharappa, Sandeep and Alwassil, Osama I and Odhav, Bharti} } @article {1612, title = {Stress Elicits Contrasting Effects on the Structure and Number of Astrocytes in the Amygdala versus Hippocampus.}, journal = {eNeuro}, volume = {6}, year = {2019}, month = {2019 Jan-Feb}, abstract = {

Stress causes divergent patterns of structural and physiological plasticity in the hippocampus versus amygdala. However, a majority of earlier studies focused primarily on neurons. Despite growing evidence for the importance of glia in health and disease, relatively little is known about how stress affects astrocytes. Further, previous work focused on hippocampal astrocytes. Hence, we examined the impact of chronic immobilization stress (2 h/d, 10 d), on the number and structure of astrocytes in the rat hippocampus and amygdala. We observed a reduction in the number of glial fibrillary acidic protein (GFAP)-positive astrocytes in the basal amygdala (BA), 1 d after the end of 10 d of chronic stress. Detailed morphometric analysis of individual dye-filled astrocytes also revealed a decrease in the neuropil volume occupied by these astrocytes in the BA, alongside a reduction in the volume fraction of fine astrocytic protrusions rather than larger dendrite-like processes. By contrast, the same chronic stress had no effect on the number or morphology of astrocytes in hippocampal area CA3. We also confirmed previous reports that chronic stress triggers dendritic hypertrophy in dye-filled BA principal neurons that were located adjacent to astrocytes that had undergone atrophy. Thus, building on earlier evidence for contrasting patterns of stress-induced plasticity in neurons across brain areas, our findings offer new evidence that the same stress can also elicit divergent morphological effects in astrocytes in the hippocampus versus the amygdala.

}, issn = {2373-2822}, doi = {10.1523/ENEURO.0338-18.2019}, author = {Naskar, Saptarnab and Chattarji, Sumantra} } @article {1983, title = {Structural and functional characterization of CMP-N-acetylneuraminate synthetase from Vibrio cholerae.}, journal = {Acta Crystallogr D Struct Biol}, volume = {75}, year = {2019}, month = {2019 Jun 01}, pages = {564-577}, abstract = {

Several pathogenic bacteria utilize sialic acid, including host-derived N-acetylneuraminic acid (Neu5Ac), in at least two ways: they use it as a nutrient source and as a host-evasion strategy by coating themselves with Neu5Ac. Given the significant role of sialic acid in pathogenesis and host-gut colonization by various pathogenic bacteria, including Neisseria meningitidis, Haemophilus influenzae, Pasteurella multocida and Vibrio cholerae, several enzymes of the sialic acid catabolic, biosynthetic and incorporation pathways are considered to be potential drug targets. In this work, findings on the structural and functional characterization of CMP-N-acetylneuraminate synthetase (CMAS), a key enzyme in the incorporation pathway, from Vibrio cholerae are reported. CMAS catalyzes the synthesis of CMP-sialic acid by utilizing CTP and sialic acid. Crystal structures of the apo and the CDP-bound forms of the enzyme were determined, which allowed the identification of the metal cofactor Mg in the active site interacting with CDP and the invariant Asp215 residue. While open and closed structural forms of the enzyme from eukaryotic and other bacterial species have already been characterized, a partially closed structure of V.\ cholerae CMAS (VcCMAS) observed upon CDP binding, representing an intermediate state, is reported here. The kinetic data suggest that VcCMAS is capable of activating the two most common sialic acid derivatives, Neu5Ac and Neu5Gc. Amino-acid sequence and structural comparison of the active site of VcCMAS with those of eukaryotic and other bacterial counterparts reveal a diverse hydrophobic pocket that interacts with the C5 substituents of sialic acid. Analyses of the thermodynamic signatures obtained from the binding of the nucleotide (CTP) and the product (CMP-sialic acid) to VcCMAS provide fundamental information on the energetics of the binding process.

}, keywords = {Amino Acid Sequence, Bacterial Proteins, Binding Sites, Catalytic Domain, Crystallization, Crystallography, X-Ray, Cytidine Diphosphate, Cytidine Monophosphate N-Acetylneuraminic Acid, Cytidine Triphosphate, N-Acylneuraminate Cytidylyltransferase, Protein Interaction Domains and Motifs, Protein Structure, Quaternary, Sialic Acids, Vibrio cholerae}, issn = {2059-7983}, doi = {10.1107/S2059798319006831}, author = {Bose, Sucharita and Purkait, Debayan and Joseph, Deepthi and Nayak, Vinod and Subramanian, Ramaswamy} } @article {1840, title = {Structure-Guided Synthesis and Evaluation of Small-Molecule Inhibitors Targeting Protein-Protein Interactions of BRCA1 tBRCT Domain.}, journal = {ChemMedChem}, volume = {14}, year = {2019}, month = {2019 Sep 18}, pages = {1620-1632}, abstract = {

The tandem BRCT domains (tBRCT) of BRCA1 engage phosphoserine-containing motifs in target proteins to propagate intracellular signals initiated by DNA damage, thereby controlling cell cycle arrest and DNA repair. Recently, we identified Bractoppin, the first small-molecule inhibitor of the BRCA1 tBRCT domain, which selectively interrupts BRCA1-mediated cellular responses evoked by DNA damage. Here, we combine structure-guided chemical elaboration, protein mutagenesis and cellular assays to define the structural features responsible for Bractoppin{\textquoteright}s activity. Bractoppin fails to bind mutant forms of BRCA1 tBRCT bearing K1702A, a key residue mediating phosphopeptide recognition, or F1662R or L1701K that adjoin the pSer-recognition site. However, the M1775R mutation, which engages the Phe residue in the consensus phosphopeptide motif pSer-X-X-Phe, does not affect Bractoppin binding, confirming a binding mode distinct from the substrate phosphopeptide binding. We explored these structural features through structure-guided chemical elaboration and characterized structure-activity relationships (SARs) in biochemical assays. Two analogues, CCBT2088 and CCBT2103 were effective in abrogating BRCA1 foci formation and inhibiting G2 arrest induced by irradiation of cells. Collectively, our findings reveal structural features underlying the activity of a novel inhibitor of phosphopeptide recognition by the BRCA1 tBRCT domain, providing fresh insights to guide the development of inhibitors that target protein-protein interactions.

}, issn = {1860-7187}, doi = {10.1002/cmdc.201900300}, author = {Kurdekar, Vadiraj and Giridharan, Saranya and Subbarao, Jasti and Nijaguna, Mamatha B and Periasamy, Jayaprakash and Boggaram, Sanjana and Shivange, Amol V and Sadasivam, Gayathri and Padigaru, Muralidhara and Potluri, Vijay and Venkitaraman, Ashok R and Bharatham, Kavitha} } @article {1582, title = {Urolithin A, a Novel Natural Compound to Target PI3K/AKT/mTOR Pathway in Pancreatic Cancer.}, journal = {Mol Cancer Ther}, volume = {18}, year = {2019}, month = {2019 Feb}, pages = {301-311}, abstract = {

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy and is highly resistant to standard treatment regimens. Targeted therapies against , a mutation present in an overwhelming majority of PDAC cases, have been largely ineffective. However, inhibition of downstream components in the KRAS signaling cascade provides promising therapeutic targets in the management of PDAC and warrants further exploration. Here, we investigated Urolithin A (Uro A), a novel natural compound derived from pomegranates, which targets numerous kinases downstream of KRAS, in particular the PI3K/AKT/mTOR signaling pathways. We showed that treatment of PDAC cells with Uro A blocked the phosphorylation of AKT and p70S6K successfully inhibited the growth of tumor xenografts, and increased overall survival of Ptf1a;LSL-Kras;Tgfbr2 (PKT) mice compared with vehicle or gemcitabine therapy alone. Histologic evaluation of these Uro A-treated tumor samples confirmed mechanistic actions of Uro A via decreased phosphorylation of AKT and p70S6K, reduced proliferation, and increased cellular apoptosis in both xenograft and PKT mouse models. In addition, Uro A treatment reprogrammed the tumor microenvironment, as evidenced by reduced levels of infiltrating immunosuppressive cell populations such as myeloid-derived suppressor cells, tumor-associated macrophages, and regulatory T cells. Overall, this work provides convincing preclinical evidence for the utility of Uro A as a therapeutic agent in PDAC through suppression of the PI3K/AKT/mTOR pathway.

}, issn = {1538-8514}, doi = {10.1158/1535-7163.MCT-18-0464}, author = {Totiger, Tulasigeri M and Srinivasan, Supriya and Jala, Venkatakrishna R and Lamichhane, Purushottam and Dosch, Austin R and Gaidarski, Alexander A and Joshi, Chandrashekhar and Rangappa, Shobith and Castellanos, Jason and Vemula, Praveen Kumar and Chen, Xi and Kwon, Deukwoo and Kashikar, Nilesh and VanSaun, Michael and Merchant, Nipun B and Nagathihalli, Nagaraj S} } @article {1192, title = {Automation aided optimization of cloning, expression and purification of enzymes of the bacterial sialic acid catabolic and sialylation pathways enzymes for structural studies.}, journal = {Microb Biotechnol}, volume = {11}, year = {2018}, month = {2018 Mar}, pages = {420-428}, abstract = {

The process of obtaining a well-expressing, soluble and correctly folded constructs can be made easier and quicker by automating the optimization of cloning, expression and purification. While there are many semiautomated pipelines available for cloning, expression and purification, there is hardly any pipeline that involves complete automation. Here, we achieve complete automation of all the steps involved in cloning and in\ vivo expression screening. This is demonstrated using 18 genes involved in sialic acid catabolism and the surface sialylation pathway. Our main objective was to clone these genes into a His-tagged Gateway vector, followed by their small-scale expression optimization in\ vivo. The constructs that showed best soluble expression were then selected for purification studies and scaled up for crystallization studies. Our technique allowed us to quickly find conditions for producing significant quantities of soluble proteins in Escherichia coli, their large-scale purification and successful crystallization of a number of these proteins. The method can be implemented in other cases where one needs to screen a large number of constructs, clones and expression vectors for successful recombinant production of functional proteins.

}, issn = {1751-7915}, doi = {10.1111/1751-7915.13041}, author = {Bairy, Sneha and Gopalan, Lakshmi Narayanan and Setty, Thanuja Gangi and Srinivasachari, Sathya and Manjunath, Lavanyaa and Kumar, Jay Prakash and Guntupalli, Sai R and Bose, Sucharita and Nayak, Vinod and Ghosh, Swagatha and Sathyanarayanan, Nitish and Caing-Carlsson, Rhawnie and Wahlgren, Weixiao Yuan and Friemann, Rosmarie and Ramaswamy, S and Neerathilingam, Muniasamy} } @article {1597, title = {Crystal structures and kinetics of N-acetylneuraminate lyase from Fusobacterium nucleatum.}, journal = {Acta Crystallogr F Struct Biol Commun}, volume = {74}, year = {2018}, month = {2018 Nov 01}, pages = {725-732}, abstract = {

N-Acetyl-D-neuraminic acid lyase (NanA) catalyzes the breakdown of sialic acid (Neu5Ac) to N-acetyl-D-mannosamine (ManNAc) and pyruvate. NanA plays a key role in Neu5Ac catabolism in many pathogenic and bacterial commensals where sialic acid is available as a carbon and nitrogen source. Several pathogens or commensals decorate their surfaces with sialic acids as a strategy to escape host innate immunity. Catabolism of sialic acid is key to a range of host-pathogen interactions. In this study, atomic resolution structures of NanA from Fusobacterium nucleatum (FnNanA) in ligand-free and ligand-bound forms are reported at 2.32 and 1.76 {\r A} resolution, respectively. F. nucleatum is a Gram-negative pathogen that causes gingival and periodontal diseases in human hosts. Like other bacterial N-acetylneuraminate lyases, FnNanA also shares the triosephosphate isomerase (TIM)-barrel fold. As observed in other homologous enzymes, FnNanA forms a tetramer. In order to characterize the structure-function relationship, the steady-state kinetic parameters of the enzyme are also reported.

}, keywords = {Bacterial Proteins, Crystallography, X-Ray, Fusobacterium nucleatum, Hydrogen Bonding, Models, Molecular, N-Acetylneuraminic Acid, Oxo-Acid-Lyases, Protein Conformation, Protein Folding, Pyruvic Acid, Schiff Bases, Sequence Alignment, Tyrosine}, issn = {2053-230X}, doi = {10.1107/S2053230X18012992}, author = {Kumar, Jay Prakash and Rao, Harshvardhan and Nayak, Vinod and Ramaswamy, S} } @article {1149, title = {Discovery biology of neuropsychiatric syndromes (DBNS): a center for integrating clinical medicine and basic science.}, journal = {BMC Psychiatry}, volume = {18}, year = {2018}, month = {2018 Apr 18}, pages = {106}, abstract = {

BACKGROUND: There is emerging evidence that there are shared genetic, environmental and developmental risk factors in psychiatry, that cut across traditional diagnostic boundaries. With this background, the Discovery biology of neuropsychiatric syndromes (DBNS) proposes to recruit patients from five different syndromes (schizophrenia, bipolar disorder, obsessive compulsive disorder, Alzheimer{\textquoteright}s dementia and substance use disorders), identify those with multiple affected relatives, and invite these families to participate in this study. The families will be assessed: 1) To compare neuro-endophenotype measures between patients, first degree relatives (FDR) and healthy controls., 2) To identify cellular phenotypes which differentiate the groups., 3) To examine the longitudinal course of neuro-endophenotype measures., 4) To identify measures which correlate with outcome, and 5) To create a unified digital database and biorepository.

METHODS: The identification of the index participants will occur at well-established specialty clinics. The selected individuals will have a strong family history (with at least another affected FDR) of mental illness. We will also recruit healthy controls without family history of such illness. All recruited individuals (N = 4500) will undergo brief clinical assessments and a blood sample will be drawn for isolation of DNA and peripheral blood mononuclear cells (PBMCs). From among this set, a subset of 1500 individuals (300 families and 300 controls) will be assessed on several additional assessments [detailed clinical assessments, endophenotype measures (neuroimaging- structural and functional, neuropsychology, psychophysics-electroencephalography, functional near infrared spectroscopy, eye movement tracking)], with the intention of conducting repeated measurements every alternate year. PBMCs from this set will be used to generate lymphoblastoid cell lines, and a subset of these would be converted to induced pluripotent stem cell lines and also undergo whole exome sequencing.

DISCUSSION: We hope to identify unique and overlapping brain endophenotypes for major psychiatric syndromes. In a proportion of subjects, we expect these neuro-endophenotypes to progress over time and to predict treatment outcome. Similarly, cellular assays could differentiate cell lines derived from such groups. The repository of biomaterials as well as digital datasets of clinical parameters, will serve as a valuable resource for the broader scientific community who wish to address research questions in the area.

}, issn = {1471-244X}, doi = {10.1186/s12888-018-1674-2}, author = {Viswanath, Biju and Rao, Naren P and Narayanaswamy, Janardhanan C and Sivakumar, Palanimuthu T and Kandasamy, Arun and Kesavan, Muralidharan and Mehta, Urvakhsh Meherwan and Venkatasubramanian, Ganesan and John, John P and Mukherjee, Odity and Purushottam, Meera and Kannan, Ramakrishnan and Mehta, Bhupesh and Kandavel, Thennarasu and Binukumar, B and Saini, Jitender and Jayarajan, Deepak and Shyamsundar, A and Moirangthem, Sydney and Vijay Kumar, K G and Thirthalli, Jagadisha and Chandra, Prabha S and Gangadhar, Bangalore N and Murthy, Pratima and Panicker, Mitradas M and Bhalla, Upinder S and Chattarji, Sumantra and Benegal, Vivek and Varghese, Mathew and Reddy, Janardhan Y C and Raghu, Padinjat and Rao, Mahendra and Jain, Sanjeev} } @article {1155, title = {"Just a spoonful of sugar...": import of sialic acid across bacterial cell membranes.}, journal = {Biophys Rev}, volume = {10}, year = {2018}, month = {2018 Apr}, pages = {219-227}, abstract = {

Eukaryotic cell surfaces are decorated with a complex array of glycoconjugates that are usually capped with sialic acids, a large family of over 50 structurally distinct nine-carbon amino sugars, the most common member of which is N-acetylneuraminic acid. Once made available through the action of neuraminidases, bacterial pathogens and commensals utilise host-derived sialic acid by degrading it for energy or repurposing the sialic acid onto their own cell surface to camouflage the bacterium from the immune system. A functional sialic acid transporter has been shown to be essential for the uptake of sialic acid in a range of human bacterial pathogens and important for host colonisation and persistence. Here, we review the state-of-play in the field with respect to the molecular mechanisms by which these bio-nanomachines transport sialic acids across bacterial cell membranes.

}, issn = {1867-2450}, doi = {10.1007/s12551-017-0343-x}, author = {North, Rachel A and Horne, Christopher R and Davies, James S and Remus, Daniela M and Muscroft-Taylor, Andrew C and Goyal, Parveen and Wahlgren, Weixiao Yuan and Ramaswamy, S and Friemann, Rosmarie and Dobson, Renwick C J} } @article {1588, title = {The Sodium Sialic Acid Symporter From Has Altered Substrate Specificity.}, journal = {Front Chem}, volume = {6}, year = {2018}, month = {2018}, pages = {233}, abstract = {

Mammalian cell surfaces are decorated with complex glycoconjugates that terminate with negatively charged sialic acids. Commensal and pathogenic bacteria can use host-derived sialic acids for a competitive advantage, but require a functional sialic acid transporter to import the sugar into the cell. This work investigates the sodium sialic acid symporter (SiaT) from (SiaT). We demonstrate that SiaT rescues an strain lacking its endogenous sialic acid transporter when grown on the sialic acids -acetylneuraminic acid (Neu5Ac) or -glycolylneuraminic acid (Neu5Gc). We then develop an expression, purification and detergent solubilization system for SiaT and demonstrate that the protein is largely monodisperse in solution with a stable monomeric oligomeric state. Binding studies reveal that SiaT has a higher affinity for Neu5Gc over Neu5Ac, which was unexpected and is not seen in another SiaT homolog. We develop a homology model and use comparative sequence analyses to identify substitutions in the substrate-binding site of SiaT that may explain the altered specificity. SiaT is shown to be electrogenic, and transport is dependent upon more than one Na ion for every sialic acid molecule. A functional sialic acid transporter is essential for the uptake and utilization of sialic acid in a range of pathogenic bacteria, and developing new inhibitors that target these transporters is a valid mechanism for inhibiting bacterial growth. By demonstrating a route to functional recombinant SiaT, and developing the and assay systems, our work underpins the design of inhibitors to this transporter.

}, issn = {2296-2646}, doi = {10.3389/fchem.2018.00233}, author = {North, Rachel A and Wahlgren, Weixiao Y and Remus, Daniela M and Scalise, Mariafrancesca and Kessans, Sarah A and Dunevall, Elin and Claesson, Elin and Soares da Costa, Tatiana P and Perugini, Matthew A and Ramaswamy, S and Allison, Jane R and Indiveri, Cesare and Friemann, Rosmarie and Dobson, Renwick C J} } @article {1147, title = {Substrate-bound outward-open structure of a Na-coupled sialic acid symporter reveals a new Na site.}, journal = {Nat Commun}, volume = {9}, year = {2018}, month = {2018 May 01}, pages = {1753}, abstract = {

Many pathogenic bacteria utilise sialic acids as an energy source or use them as an external coating to evade immune detection. As such, bacteria that colonise sialylated environments deploy specific transporters to mediate import of scavenged sialic acids. Here, we report a substrate-bound 1.95 {\r A} resolution structure and subsequent characterisation of SiaT, a sialic acid transporter from Proteus mirabilis. SiaT is a secondary active transporter of the sodium solute symporter (SSS) family, which use Na gradients to drive the uptake of extracellular substrates. SiaT adopts the LeuT-fold and is in an outward-open conformation in complex with the sialic acid N-acetylneuraminic acid and two Na ions. One Na binds to the conserved Na2 site, while the second Na binds to a new position, termed Na3, which is conserved in many SSS family members. Functional and molecular dynamics studies validate the substrate-binding site and demonstrate that both Na sites regulate N-acetylneuraminic acid transport.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-04045-7}, author = {Wahlgren, Weixiao Y and Dunevall, Elin and North, Rachel A and Paz, Aviv and Scalise, Mariafrancesca and Bisignano, Paola and Bengtsson-Palme, Johan and Goyal, Parveen and Claesson, Elin and Caing-Carlsson, Rhawnie and Andersson, Rebecka and Beis, Konstantinos and Nilsson, Ulf J and Farewell, Anne and Pochini, Lorena and Indiveri, Cesare and Grabe, Michael and Dobson, Renwick C J and Abramson, Jeff and Ramaswamy, S and Friemann, Rosmarie} } @article {1580, title = {Targeting Phosphopeptide Recognition by the Human BRCA1 Tandem BRCT Domain to Interrupt BRCA1-Dependent Signaling.}, journal = {Cell Chem Biol}, volume = {25}, year = {2018}, month = {2018 06 21}, pages = {677-690.e12}, abstract = {

Intracellular signals triggered by DNA breakage flow through proteins containing BRCT (BRCA1 C-terminal) domains. This family, comprising 23 conserved phosphopeptide-binding modules in man, is inaccessible to small-molecule chemical inhibitors. Here, we develop Bractoppin, a drug-like inhibitor of phosphopeptide recognition by the human BRCA1 tandem (t)BRCT domain, which selectively inhibits substrate binding with nanomolar potency in\ vitro. Structure-activity exploration suggests that Bractoppin engages BRCA1 tBRCT residues recognizing pSer in the consensus motif, pSer-Pro-Thr-Phe, plus an abutting hydrophobic pocket that is distinct in structurally related BRCT domains, conferring selectivity. In cells, Bractoppin inhibits substrate recognition detected by F{\"o}rster resonance energy transfer, and diminishes BRCA1 recruitment to DNA breaks, in turn suppressing damage-induced G2 arrest and assembly of the recombinase, RAD51. But damage-induced MDC1 recruitment, single-stranded DNA (ssDNA) generation, and TOPBP1 recruitment remain unaffected. Thus, an inhibitor of phosphopeptide recognition selectively interrupts BRCA1 tBRCT-dependent signals evoked by DNA damage.

}, issn = {2451-9448}, doi = {10.1016/j.chembiol.2018.02.012}, author = {Periasamy, Jayaprakash and Kurdekar, Vadiraj and Jasti, Subbarao and Nijaguna, Mamatha B and Boggaram, Sanjana and Hurakadli, Manjunath A and Raina, Dhruv and Kurup, Lokavya Meenakshi and Chintha, Chetan and Manjunath, Kavyashree and Goyal, Aneesh and Sadasivam, Gayathri and Bharatham, Kavitha and Padigaru, Muralidhara and Potluri, Vijay and Venkitaraman, Ashok R} } @article {1191, title = {Tunable Emission from Fluorescent Organic Nanoparticles in Water: Insight into the Nature of Self-Assembly and Photoswitching}, journal = {Chemistry {\textendash} A European Journal}, volume = {24}, year = {2018}, pages = {2643-2652}, abstract = {

Abstract Excitation-dependent tuning of the emission behavior of fluorescent organic nanoparticles (FONs) with two simple luminescent pyrenyl{\textendash}pyridyl conjugates as model systems is demonstrated. In the case of the compound with a flexible bis-picolyl moiety, the simultaneous presence of multiple ground-state species with distinct absorption and emission characteristics can be observed. The relative ratios of these species can easily be modulated, and it is possible to selectively stimulate any one of them individually by choosing an appropriate excitation channel. Moreover, at high concentration, a drastic change in the nature of the self-assembly is observed, which shifts from donor{\textendash}acceptor-type self-assembly to exciplex-type self-agglomeration. On the contrary, the compound containing a rigid terpyridine unit has only a single ground state and shows no such tunable emission. However, it can exhibit multiple emission bands in water, whereby the positions of their emission maxima depend on the extent of aggregation-induced planarization of the probe molecules. Overall, this work demonstrates multimodal modulation of FON emission and a gives insight into how molecular order can translate into complete switching of nanoparticle self-assembly and photophysics.

}, keywords = {aggregation, Fluorescence, nanoparticles, self-assembly}, doi = {10.1002/chem.201704607}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/chem.201704607}, author = {Gulyani Akash and Dey Nilanjan and Bhattacharya Santanu} } @article {1185, title = {Crystal structure of N-acetylmannosamine kinase from Fusobacterium nucleatum.}, journal = {Acta Crystallogr F Struct Biol Commun}, volume = {73}, year = {2017}, month = {2017 Jun 01}, pages = {356-362}, abstract = {

Sialic acids comprise a varied group of nine-carbon amino sugars that are widely distributed among mammals and higher metazoans. Some human commensals and bacterial pathogens can scavenge sialic acids from their environment and degrade them for use as a carbon and nitrogen source. The enzyme N-acetylmannosamine kinase (NanK; EC 2.7.1.60) belongs to the transcriptional repressors, uncharacterized open reading frames and sugar kinases (ROK) superfamily. NanK catalyzes the second step of the sialic acid catabolic pathway, transferring a phosphate group from adenosine 5{\textquoteright}-triphosphate to the C6 position of N-acetylmannosamine to generate N-acetylmannosamine 6-phosphate. The structure of NanK from Fusobacterium nucleatum was determined to 2.23 {\r A} resolution by X-ray crystallography. Unlike other NanK enzymes and ROK family members, F. nucleatum NanK does not have a conserved zinc-binding site. In spite of the absence of the zinc-binding site, all of the major structural features of enzymatic activity are conserved.

}, keywords = {Adenosine Triphosphate, Amino Acid Sequence, Bacterial Proteins, Binding Sites, Cloning, Molecular, Crystallography, X-Ray, Escherichia coli, Fusobacterium nucleatum, Gene Expression, Genetic Vectors, Hexosamines, Models, Molecular, Phosphotransferases (Alcohol Group Acceptor), Protein Binding, Protein Conformation, alpha-Helical, Protein Conformation, beta-Strand, Protein Interaction Domains and Motifs, Protein Multimerization, Recombinant Proteins, Sequence Alignment, Sequence Homology, Amino Acid, Substrate Specificity}, issn = {2053-230X}, doi = {10.1107/S2053230X17007439}, author = {Caing-Carlsson, Rhawnie and Goyal, Parveen and Sharma, Amit and Ghosh, Swagatha and Setty, Thanuja Gangi and North, Rachel A and Friemann, Rosmarie and Ramaswamy, S} } @article {1160, title = {Cytoplasmic poly (A)-binding protein critically regulates epidermal maintenance and turnover in the planarian .}, journal = {Development}, volume = {144}, year = {2017}, month = {2017 09 01}, pages = {3066-3079}, abstract = {

Identifying key cellular events that facilitate stem cell function and tissue organization is crucial for understanding the process of regeneration. Planarians are powerful model system to study regeneration and stem cell (neoblast) function. Here, using planaria, we show that the initial events of regeneration, such as epithelialization and epidermal organization are critically regulated by a novel cytoplasmic poly A-binding protein, SMED-PABPC2. Knockdown leads to defects in epidermal lineage specification, disorganization of epidermis and ECM, and deregulated wound healing, resulting in the selective failure of neoblast proliferation near the wound region. Polysome profiling suggests that epidermal lineage transcripts, including , are translationally regulated by SMED-PABPC2 Together, our results uncover a novel role for SMED-PABPC2 in the maintenance of epidermal and ECM integrity, critical for wound healing and subsequent processes for regeneration.

}, keywords = {Animals, Cell Lineage, Cell Proliferation, Cytoplasm, Epidermis, Epithelium, Extracellular Matrix, Gene Knockdown Techniques, Homeostasis, Models, Biological, Planarians, Poly(A)-Binding Protein I, Regeneration, RNA, Messenger, Wound Healing}, issn = {1477-9129}, doi = {10.1242/dev.152942}, author = {Bansal, Dhiru and Kulkarni, Jahnavi and Nadahalli, Kavana and Lakshmanan, Vairavan and Krishna, Srikar and Sasidharan, Vidyanand and Geo, Jini and Dilipkumar, Shilpa and Pasricha, Renu and Gulyani, Akash and Raghavan, Srikala and Palakodeti, Dasaradhi} } @article {1199, title = {The miR-124 family of microRNAs is crucial for regeneration of the brain and visual system in the planarian Schmidtea mediterranea}, journal = {Development}, volume = {144}, year = {2017}, pages = {3211{\textendash}3223}, abstract = {

Brain regeneration in planarians is mediated by precise spatiotemporal control of gene expression and is crucial for multiple aspects of neurogenesis. However, the mechanisms underpinning the gene regulation essential for brain regeneration are largely unknown. Here, we investigated the role of the miR-124 family of microRNAs in planarian brain regeneration. The miR-124 family (miR-124) is highly conserved in animals and regulates neurogenesis by facilitating neural differentiation, yet its role in neural wiring and brain organization is not known. We developed a novel method for delivering anti-miRs using liposomes for the functional knockdown of microRNAs. Smed-miR-124 knockdown revealed a key role for these microRNAs in neuronal organization during planarian brain regeneration. Our results also demonstrated an essential role for miR-124 in the generation of eye progenitors. Additionally, miR-124 regulates Smed-slit-1, which encodes an axon guidance protein, either by targeting slit-1 mRNA or, potentially, by modulating the canonical Notch pathway. Together, our results reveal a role for miR-124 in regulating the regeneration of a functional brain and visual system.

}, issn = {0950-1991}, doi = {10.1242/dev.144758}, url = {http://dev.biologists.org/content/144/18/3211}, author = {Sasidharan, Vidyanand and Marepally, Srujan and Elliott, Sarah A. and Baid, Srishti and Lakshmanan, Vairavan and Nayyar, Nishtha and Bansal, Dhiru and S{\'a}nchez Alvarado, Alejandro and Vemula, Praveen Kumar and Palakodeti, Dasaradhi} } @article {1165, title = {Morphology transition in helical tubules of a supramolecular gel driven by metal ions.}, journal = {Chem Commun (Camb)}, volume = {53}, year = {2017}, month = {2017 Jan 26}, pages = {1538-1541}, abstract = {

Our aim to access a particular chemical functionality on helical tubules has been achieved by the rational molecular design and synthesis of glucono-appended cardanol derivatives. For the first time, we report a chiral molecular packing with α-helical tubules, and chiral symmetry-breaking upon exposure to Cu that generated the final ordered structure via an in situ morphological transition without undergoing any phase change.

}, issn = {1364-548X}, doi = {10.1039/c6cc09120b}, author = {Lalitha, Krishnamoorthy and Sridharan, Vellaisamy and Maheswari, C Uma and Vemula, Praveen Kumar and Nagarajan, Subbiah} } @article {1201, title = {Scaling the effect of hydrophobic chain length on gene transfer properties of di-alkyl{,} di-hydroxy ethylammonium chloride based cationic amphiphiles}, journal = {RSC Adv.}, volume = {7}, year = {2017}, pages = {25398-25405}, abstract = {

The success of gene therapy critically depends on the availability of efficient transfection vectors. Cationic lipids are the most widely studied non-viral vectors. The molecular architecture of the cationic lipid determines its transfection efficiency. Variations in alkyl chain lengths of lipids influence self-assembly and liposomal fusion with the cell membrane. These factors determine the transfection ability of the lipid. Thus{,} to probe the effect of asymmetry in hydrophobic chains on transfection efficiency{,} we designed and synthesized a series of cationic lipids by systematically varying one of the two alkyl chains linked to the quaternary nitrogen centre from C18 to C10 and keeping the other alkyl C18 chain constant (Lip1818-Lip1810). Transfection studies in multiple cultured mammalian cells (CHO{,} B16F10 and HeLa) revealed that the lipids with C18:C14 and C18:C12 alkyl chains (Lip1814 \& Lip1812) showed 20-30\% higher transfection efficacies than their counterparts at 2 : 1 and 4 : 1 lipid to pDNA charge ratios. Cryo-transmission electron images showed unilamellar vesicle structures for the liposomes of lipids. Mechanistic studies involving Small Angle X-ray Scattering (SAXS) revealed that asymmetry in the hydrophobic region has a significant impact on liposomal fusion with the plasma membrane model. Collectively{,} these findings demonstrate that chain length asymmetry in the hydrophobic region of cationic lipids has an important role in their liposome-DNA interactions at optimal 2 : 1 and 4 : 1 lipid to pDNA charge ratios{,} which in turn modulates their gene transfer properties.

}, doi = {10.1039/C7RA02271A}, url = {http://dx.doi.org/10.1039/C7RA02271A}, author = {Hiwale, Ankita A. and Voshavar, Chandrashekhar and Dharmalingam, Priya and Dhayani, Ashish and Mukthavaram, Rajesh and Nadella, Rasajna and Sunnapu, Omprakash and Gandhi, Sivaraman and Naidu, V. G. M. and Chaudhuri, Arabinda and Marepally, Srujan and Vemula, Praveen Kumar} } @article {1172, title = {Low Oxygen Tension Enhances Expression of Myogenic Genes When Human Myoblasts Are Activated from G0 Arrest.}, journal = {PLoS One}, volume = {11}, year = {2016}, month = {2016}, pages = {e0158860}, abstract = {

OBJECTIVES: Most cell culture studies have been performed at atmospheric oxygen tension of 21\%, however the physiological oxygen tension is much lower and is a factor that may affect skeletal muscle myoblasts. In this study we have compared activation of G0 arrested myoblasts in 21\% O2 and in 1\% O2 in order to see how oxygen tension affects activation and proliferation of human myoblasts.

MATERIALS AND METHODS: Human myoblasts were isolated from skeletal muscle tissue and G0 arrested in vitro followed by reactivation at 21\% O2 and 1\% O2. The effect was assesses by Real-time RT-PCR, immunocytochemistry and western blot.

RESULTS AND CONCLUSIONS: We found an increase in proliferation rate of myoblasts when activated at a low oxygen tension (1\% O2) compared to 21\% O2. In addition, the gene expression studies showed up regulation of the myogenesis related genes PAX3, PAX7, MYOD, MYOG (myogenin), MET, NCAM, DES (desmin), MEF2A, MEF2C and CDH15 (M-cadherin), however, the fraction of DES and MYOD positive cells was not increased by low oxygen tension, indicating that 1\% O2 may not have a functional effect on the myogenic response. Furthermore, the expression of genes involved in the TGFβ, Notch and Wnt signaling pathways were also up regulated in low oxygen tension. The differences in gene expression were most pronounced at day one after activation from G0-arrest, thus the initial activation of myoblasts seemed most sensitive to changes in oxygen tension. Protein expression of HES1 and β-catenin indicated that notch signaling may be induced in 21\% O2, while the canonical Wnt signaling may be induced in 1\% O2 during activation and proliferation of myoblasts.

}, keywords = {Adolescent, Cell Cycle Checkpoints, Cell Hypoxia, Cell Proliferation, Cell Separation, Cells, Cultured, Down-Regulation, Female, Gene Expression Regulation, Humans, Ki-67 Antigen, Male, Muscle Development, Muscle Proteins, Myoblasts, Oxygen, Receptors, Notch, Resting Phase, Cell Cycle, Transforming Growth Factor beta, Wnt Signaling Pathway, Young Adult}, issn = {1932-6203}, doi = {10.1371/journal.pone.0158860}, author = {Sellathurai, Jeeva and Nielsen, Joachim and Hejb{\o}l, Eva Kildall and J{\o}rgensen, Louise Helskov and Dhawan, Jyotsna and Nielsen, Michael Friberg Bruun and Schr{\o}der, Henrik Daa} } @article {399, title = {Mechanistic heterogeneity in contractile properties of α-tropomyosin (TPM1) mutants associated with inherited cardiomyopathies.}, journal = {J Biol Chem}, volume = {290}, year = {2015}, month = {2015 Mar 13}, pages = {7003-15}, abstract = {

The most frequent known causes of primary cardiomyopathies are mutations in the genes encoding sarcomeric proteins. Among those are 30 single-residue mutations in TPM1, the gene encoding α-tropomyosin. We examined seven mutant tropomyosins, E62Q, D84N, I172T, L185R, S215L, D230N, and M281T, that were chosen based on their clinical severity and locations along the molecule. The goal of our study was to determine how the biochemical characteristics of each of these mutant proteins are altered, which in turn could provide a structural rationale for treatment of the cardiomyopathies they produce. Measurements of Ca(2+) sensitivity of human β-cardiac myosin ATPase activity are consistent with the hypothesis that hypertrophic cardiomyopathies are hypersensitive to Ca(2+) activation, and dilated cardiomyopathies are hyposensitive. We also report correlations between ATPase activity at maximum Ca(2+) concentrations and conformational changes in TnC measured using a fluorescent probe, which provide evidence that different substitutions perturb the structure of the regulatory complex in different ways. Moreover, we observed changes in protein stability and protein-protein interactions in these mutants. Our results suggest multiple mechanistic pathways to hypertrophic and dilated cardiomyopathies. Finally, we examined a computationally designed mutant, E181K, that is hypersensitive, confirming predictions derived from in silico structural analysis.

}, keywords = {Actins, Adenosine Triphosphatases, Calcium, Cardiomyopathies, Humans, Models, Molecular, Myosins, Point Mutation, Protein Stability, Tropomyosin}, issn = {1083-351X}, doi = {10.1074/jbc.M114.596676}, author = {Gupte, Tejas M and Haque, Farah and Gangadharan, Binnu and Sunitha, Margaret S and Mukherjee, Souhrid and Anandhan, Swetha and Rani, Deepa Selvi and Mukundan, Namita and Jambekar, Amruta and Thangaraj, Kumarasamy and Sowdhamini, Ramanathan and Sommese, Ruth F and Nag, Suman and Spudich, James A and Mercer, John A} } @article {2271, title = {A quantitative metabolomics peek into planarian regeneration.}, journal = {Analyst}, volume = {140}, year = {2015}, month = {2015 May 21}, pages = {3445-64}, abstract = {

The fresh water planarian species Schmidtea mediterranea is an emerging stem cell model because of its capability to regenerate a whole animal from a small piece of tissue. It is one of the best model systems to address the basic mechanisms essential for regeneration. Here, we are interested in studying the roles of various amines, thiols and nucleotides in planarian regeneration, stem cell function and growth. We developed mass spectrometry based quantitative methods and validated the differential enrichment of 35 amines, 7 thiol metabolites and 4 nucleotides from both intact and regenerating planarians. Among the amines, alanine in sexual and asparagine in asexual are the highest (\>1000 ng/mg) in the intact planarians. The levels of thiols such as cysteine and GSH are 651 and 1107 ng mg(-1) in planarians. Among the nucleotides, the level of cGMP is the lowest (0.03 ng mg(-1)) and the level of AMP is the highest (187 ng mg(-1)) in both of the planarian strains. We also noticed increasing levels of amines in both anterior and posterior regenerating planarians. The blastema from day 3 regenerating planarians also showed higher amounts of many amines. Interestingly, the thiol (cysteine and GSH) levels are well maintained during planarian regeneration. This suggests an inherent and effective mechanism to control induced oxidative stress because of the robust regeneration and stem cell proliferation. Like in intact planarians, the level of cGMP is also very low in regenerating planarians. Surprisingly, the levels of amines and thiols in head regenerating blastemas are \~{}3 times higher compared to those for tail regenerating blastemas. Thus our results strongly indicate the potential roles of amines, thiols and nucleotides in planarian regeneration.

}, keywords = {Animals, Calibration, Chromatography, High Pressure Liquid, Limit of Detection, Metabolomics, Planarians, Reference Standards, Regeneration, Reproduction, Asexual, Species Specificity, Tandem Mass Spectrometry}, issn = {1364-5528}, doi = {10.1039/c4an02037e}, author = {Natarajan, Nivedita and Ramakrishnan, Padma and Lakshmanan, Vairavan and Palakodeti, Dasaradhi and Rangiah, Kannan} }