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COVID-19 the modern pandemic has spread across the world at a rapid pace. SARS-CoV 2 is highly transmissible and the rate of infection is exponential for heavily infected countries. Asymptotic carriers and longer incubation period have been key towards such a large-scale distribution of disease. Data released by official authorities on COVID-19 cases is significantly affected by various factors such as size of sample, incubation period of disease and time taken to test the sample. These factors mask the useful pattern (signal) of disease spread. Thus, an ingenious method to group data into cycles of five and seven days, for studying pattern of disease spread is undertaken. Occurrence of recurrent peaks as indicated by Adjusted Rate of infection per day indicated the spread of disease has been non-uniform. Currently, India is yet to reach the critical point (peak of epidemic) with adjusted daily cases more than 1000. Increasing testing capacity along with random sampling and sample pooling can help in preventing formation of these peaks in future. The proposed method helps in assessing the current state and for predicting future scenarios epidemics.

The ability to tune cellular functions in response to nutrient availability has important consequences for immune homeostasis. The activity of the receptor Notch in regulatory T (Treg) cells, which suppress the functions of effector T cells, is indispensable for Treg cell survival under conditions of diminished nutrient supply. Anti-apoptotic signaling induced by the Notch1 intracellular domain (NIC) originates from the cytoplasm and is spatially decoupled from the nuclear, largely transcriptional functions of NIC. We showed that Sirtuin 1 (Sirt1), which is an NAD+ (nicotinamide adenine dinucleotide)-dependent lysine deacetylase that inhibits NIC-dependent gene transcription, stabilized NIC proximal to the plasma membrane to promote the survival and function of activated Treg cells. Sirt1 was required for NIC-dependent protection from apoptosis in cell lines but not for the activity of the anti-apoptotic protein Bcl-xL. In addition, a variant NIC protein in which four lysines were mutated to arginines (NIC4KR) retained anti-apoptotic activity, but was not regulated by Sirt1, and reconstituted the functions of nonnuclear NIC in Notch1-deficient Treg cells. Loss of Sirt1 compromised Treg cell survival, resulting in antigen-induced T cell proliferation and inflammation in two mouse models. Thus, the Sirt1-Notch interaction may constitute an important checkpoint that tunes noncanonical Notch1 signaling.

Survival of differentiated cells is one of several processes regulated by Notch activity, although the general principles underlying this function remain to be characterized. Here, we probe the mechanism underlying Notch-mediated survival, building on emerging evidence that apoptotic responses coordinated by specialized intermediates converge on mitochondria, identifying a core event in death pathways. The Bcl-2 family protein Bax is one such intermediate, which in a unifying response to diverse apoptotic stimuli nucleates multiprotein assemblies on mitochondria, committing cells to irrevocable damage. Using Bax as the prototype stimulus, we analyze Notch signaling for potential interactions with mitochondria, probe intrinsic properties of the Notch receptor, and describe key intermediates in the Notch-activated signaling cascade. Ligand-dependent processing was necessary to generate the Notch intracellular domain (NIC) although signaling was independent of canonical interactions with nuclear factors. Notably, antiapoptotic activity was recapitulated by NIC recombinants, localized outside the nucleus, and compromised by enforced nuclear sequestration. NIC signaled via the kinase Akt to prevent the loss of mitochondrial function, contiguity, and consequent nuclear damage, outcomes critically depend on mitochondrial remodeling proteins Mitofusins-(Mfn)-1 and 2. Thus, the NIC-Akt-Mfn signaling cascade identifies a pathway regulating cell-survival, independent of canonical functions associated with NIC activity.

With limited regenerative capacity and most complex structural and electrophysiological properties; recapitulating the cardiac tissue is a challenging task for the researchers. The cell injection was found unreliable due to the cell loss and low retention of the transplanted cells. This could be overcome by the technique of cell sheet engineering. Scaffold free, thick, cell dense, three dimensional constructs could be generated for suture free transplantation. For the generation of the cardiac constructs the neonatal cardiomyocytes and myoblasts were mostly used. They were tedious to isolate and culture and the risk of arrhythmogenic foci prevailed. Hence the concept of differentiating a suitable allogeneic cell source to myocardial lineage seemed relevant. Human umbilical cord mesenchymal stem cells (hUCMSCs) are emerging with the assistance of differentiating agents and cell sheet engineering for addressing the cardiac regeneration. The preliminary report on this regard has been published. The cells attained cardiomyocyte-like morphology with the expression of alpha-actinin and myosin heavy chain on culturing with cardiac conditioned medium and the inducer sphingosine-1-phosphate. It presented cardiomyocyte-like action potential and voltage gated currents. Hence the cell sheet engineering approach with cells differentiated to cardiac lineage using specific agents is a recent area to be explored.

Tissue homeostasis is a dynamic process involving proliferation and the removal of redundant or damaged cells. This is exemplified in the coordinated deletion - triggered by limiting trophic factors/cytokines in the extracellular milieu - of differentiated T cells overproduced during the mammalian immune response. However, mechanisms by which extracellular cues are perceived and transduced as apoptotic triggers remain incompletely understood. T-effectors are dependent on cytokines for survival and undergo apoptosis following cytokine withdrawal. Here we report that leptomycin B (LMB), an inhibitor of nuclear export machinery, protected T-effectors from apoptosis implicating a nuclear intermediate in the apoptotic pathway. Evidence is presented that the linker histone H1.2 localizes to the cytoplasm, by a mechanism sensitive to regulation by LMB, to activate apoptotic signaling culminating in nuclear and mitochondrial damage in T-effectors in response to cytokine deprivation. H1.2 is detected in a complex with the proapoptotic mitochondrial resident Bak and its subcellular localization regulated by Jun-N-terminal kinase (JNK), an intermediate in the apoptotic cascade in T-effectors. These data suggest that metabolic stressors may impinge on H1.2 dynamics favoring its activity at the mitochondrion, thereby functioning as a molecular switch for T-effector apoptosis. � 2014 Megha Garg et al.

Seed morphology mutations affecting the major seed components in pea (Pisum sativum L.) and maize (Zea mays L.) opened specialty markets for these crops. Peanut (Arachis hypogaea L.) is an important oil and food crop of the world. Genetic alteration of seed composition may be useful in expanding markets for this crop. Some lines from the University of Florida peanut breeding program showed seed shriveling characteristic even when harvested mature. In the present study, three shriveled lines (529B, 563A, and 647A) were chemically characterized and compared with a normal-seeded cultivar, Sunrunner. They were found to have only one third to two thirds the amount of storage lipid and double the amount of sucrose as normal peanuts. Differences were also observed for seed protein concentration, when expressed on a defatted meal basis. Higher relative proportions of phospholipid to triacylglycerol may indicate a block in the biochemical pathway for the conversion of sucrose into triacylglycerol in the shriveled seed mutants. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) patterns revealed that there were differences in the levels of various proteins between normal seed and shriveled seed phenotypes. Differences were identified in the level of accumulation of storage lipid and also in the various proteins during the development of the shriveled seed.

Different Omani alfalfa cultivars were exposed to NaCl concentration in the range of 4, 6, 8 and 10 dSmO¾1 to measure germination, vegetative growth and amylase activity. The results showed moderate tolerance of alfalfa against salt stress. Alfalfa genotypes A215 and A29 appeared to be more tolerant than all other 8 genotypes. Dry matter stress index (DSMI) were calculated which varied from 0.2 to 1.2 with a high index value for 8 dSmO¾1 than the other NaCl dilutions. The amylase activity was found to be directly proportional to the salt stress. Thus the results showed that alfalfa is moderately tolerant to salinity especially A29 and A215 genotypes, which can be recommended for cultivation in semi arid regions.

Tumor metastasis, the spread of tumor cells to distant tissues from its site of initiation is a multi-step and multi-factorial process. Hyperactivation of RAS pathway is reported in >50% of different cancers and is associated with metastasis and poor prognosis. Since Ras signaling pathway is essential for normal development, its been difficult to develop drugs against it in tumors. This led to the identification of several Ras effectors. Ras association (RalGDS/AF-6) domain family (RASSF) proteins are non-enzymatic effectors of Ras. RASSF7 is a member of the less characterized N-terminal RASSFs. Similar to other RASSFs, RASSF7 also associates with Ras. Several mutations within RASSF7 open reading frame as well as differential expression pattern were observed in various tumors. The role of RASSF7 and its downstream signaling is not yet clearly understood. Microarray analysis for RASSF7 identified several differentially regulated genes with enrichment for pathways including cell adhesion, inflammation, actin cytoskeleton and cell-cell communication suggesting that RASSF7 might regulate cell migration. Ectopic expression of RASSF7 inhibited cell migration of multiple cancer cell lines in vitro. RT-qPCR and western blotting analysis suggest that RASSF7 can transcriptionally upregulate Notch1 expression. Knockdown of Notch1 abrogated RASSF7 mediated inhibition of cell migration. Our experiments suggest that RASSF7 alters the localization of Notch1. Cross-talk Notch signaling is a key signaling pathway regulating tumor progression across several different cancers. Collectively, our data suggests that RASSF7 impinges on Notch1 to regulate cell migration. Citation Format: Lakshmi R. Perumalsamy, Mahalingam S. Ras association (RalGDS/AF-6) domain family member integrates with notch signaling to regulate tumor cell migration. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5076.

Epigenetic modifications represent a promising new approach to modulate cell functions as observed in autoimmune diseases. Emerging evidence suggests the utility of HDAC inhibitors in the treatment of chronic immune and inflammatory disorders. However, class and isoform selective inhibition of HDAC is currently favored as it limits the toxicity that has been observed with pan-HDAC inhibitors. HDAC6, a member of the HDAC family, whose major substrate is α-tubulin, is being increasingly implicated in the pathogenesis of inflammatory disorders. The present study was carried out to study the potential anti-inflammatory and anti-rheumatic effects of HDAC6 selective inhibitor Tubastatin. Tubastatin, a potent human HDAC6 inhibitor with an IC50 of 11 nM showed significant inhibition of TNF-α and IL-6 in LPS stimulated human THP-1 macrophages with an IC50 of 272 nM and 712 nM respectively. Additionally, Tubastatin inhibited nitric oxide (NO) secretion in murine Raw 264.7 macrophages dose dependently with an IC50 of 4.2 μM and induced α-tubulin hyperacetylation corresponding to HDAC6 inhibition in THP-1 cells without affecting the cell viability. Tubastatin showed significant inhibition of paw volume at 30 mg/kg i.p. in a Freund's complete adjuvant (FCA) induced animal model of inflammation. The disease modifying activity of Tubastatin was also evident in collagen induced arthritis DBA1 mouse model at 30 mg/kg i.p. The significant attenuation of clinical scores (~70%) by Tubastatin was confirmed histopathologically and was found comparable to dexamethasone (~90% inhibition of clinical scores). Tubastatin showed significant inhibition of IL-6 in paw tissues of arthritic mice. The present work has demonstrated anti-inflammatory and antirheumatic effects of a selective HDAC6 inhibitor Tubastatin.

In this work, Hemigraphis alternata extract incorporated chitosan scaffold was synthesized and characterized for wound healing. The antibacterial activity of Hemigraphis incorporated chitosan scaffold (HIC) against Escherichia coli and Staphylococcus aureus was evaluated which showed a reduction in total colony forming units by 45-folds toward E. coli and 25-fold against S. aureus respectively. Cell viability studies using Human Dermal Fibroblast cells (HDF) showed 90% viability even at 48 h when compared to the chitosan control. The herbal scaffold made from chitosan was highly haemostatic and antibacterial. The obtained results were in support that the herbal scaffold can be effectively applied for infectious wounds.

Variations in the spatial localization of signaling components and crosstalk among signaling cascades are mechanisms through which diversity in signaling networks is generated. The receptor Notch provides an example of regulation by spatial localization: In the canonical Notch signaling pathway, Notch is cleaved to produce the Notch intracellular domain (NICD, also known as NIC), which translocates to the nucleus to regulate gene expression. We describe a T cell receptor-dependent, non-nuclear distribution and function of the processed receptor Notch, which was associated with the improved survival of regulatory T cells (T(regs)) in vitro and in vivo and was compromised by T cell-specific deletion of Notch1. Unlike a nuclear-restricted mutant of NICD, mutant NICD that underwent nuclear export or was targeted to the plasma membrane protected Notch1(-/-) T(regs) from apoptosis induced by nutrient deprivation and oxidative stress. Notch signaling integrated with phosphatidylinositol 3-kinase signaling and mammalian target of rapamycin complex 2 (mTORC2) for this cell survival function. Biochemical and imaging approaches revealed a membrane-proximal complex containing NICD and the mTORC2 component Rictor, and this complex was stabilized by specific interactions with the Notch ligand Delta-like-1 and mediated the survival of T(regs). Together, our evidence for the spatial control of Notch and the crosstalk of Notch signaling with other pathways reveals coupling between the localization of Notch and diverse intracellular signaling pathways.

Cellular differentiation programs are accompanied by large-scale changes in nuclear organization and gene expression. In this context, accompanying transitions in chromatin assembly that facilitates changes in gene expression and cell behavior in a developmental system are poorly understood. Here, we address this gap and map structural changes in chromatin organization during murine T-cell development, to describe an unusual heterogeneity in chromatin organization and associated functional correlates in T-cell lineage. Confocal imaging of DNA assembly in cells isolated from bone marrow, thymus and spleen reveal the emergence of heterogeneous patterns in DNA organization in mature T-cells following their exit from the thymus. The central DNA pattern dominated in immature precursor cells in the thymus whereas both central and peripheral DNA patterns were observed in naïve and memory cells in circulation. Naïve T-cells with central DNA patterns exhibited higher mechanical pliability in response to compressive loads in vitro and transmigration assays in vivo, and demonstrated accelerated expression of activation-induced marker CD69. T-cell activation was characterized by marked redistribution of DNA assembly to a central DNA pattern and increased nuclear size. Notably, heterogeneity in DNA patterns recovered in cells induced into quiescence in culture, suggesting an internal regulatory mechanism for chromatin reorganization. Taken together, our results uncover an important component of plasticity in nuclear organization, reflected in chromatin assembly, during T-cell development, differentiation and transmigration.

AgBase (http://www.agbase.msstate.edu/) provides resources to facilitate modeling of functional genomics data and structural and functional annotation of agriculturally important animal, plant, microbe and parasite genomes. The website is redesigned to improve accessibility and ease of use, including improved search capabilities. Expanded capabilities include new dedicated pages for horse, cat, dog, cotton, rice and soybean. We currently provide 590 240 Gene Ontology (GO) annotations to 105 454 gene products in 64 different species, including GO annotations linked to transcripts represented on agricultural microarrays. For many of these arrays, this provides the only functional annotation available. GO annotations are available for download and we provide comprehensive, species-specific GO annotation files for 18 different organisms. The tools available at AgBase have been expanded and several existing tools improved based upon user feedback. One of seven new tools available at AgBase, GOModeler, supports hypothesis testing from functional genomics data. We host several associated databases and provide genome browsers for three agricultural pathogens. Moreover, we provide comprehensive training resources (including worked examples and tutorials) via links to Educational Resources at the AgBase website.

The regulation of cellular metabolism and survival by trophic factors is not completely understood. Here, we describe a signaling cascade activated by the developmental regulator Notch, which inhibits apoptosis triggered by neglect in mammalian cells. In this pathway, the Notch intracellular domain (NIC), which is released after interaction with ligand, converges on the kinase mammalian target of rapamycin (mTOR) and the substrate-defining protein rapamycin independent companion of mTOR (Rictor), culminating in the activation of the kinase Akt/PKB. Biochemical and molecular approaches using site-directed mutants identified AktS473 as a key downstream target in the antiapoptotic pathway activated by NIC. Despite the demonstrated requirement for Notch processing and its predominant nuclear localization, NIC function was independent of CBF1/RBP-J, an essential DNA-binding component required for canonical signaling. In experiments that placed spatial constraints on NIC, enforced nuclear retention abrogated antiapoptotic activity and a membrane-anchored form of NIC-blocked apoptosis through mTOR, Rictor and Akt-dependent signaling. We show that the NIC-mTORC2-Akt cascade blocks the apoptotic response triggered by removal of medium or serum deprivation. Consistently, membrane-tethered NIC, and AktS473 inhibited apoptosis triggered by cytokine deprivation in activated T cells. Thus, this study identifies a non-canonical signaling cascade wherein NIC integrates with multiple pathways to regulate cell survival.

Background Bcl-2 family proteins are key regulators of mitochondrial integrity and comprise both pro- and anti-apoptotic proteins. Bax a pro-apoptotic member localizes as monomers in the cytosol of healthy cells and accumulates as oligomers in mitochondria of apoptotic cells. The Bcl-2 homology-3 (BH3) domain regulates interactions within the family, but regions other than BH3 are also critical for Bax function. Thus, the N-terminus has been variously implicated in targeting to mitochondria, interactions with BH3-only proteins as well as conformational changes linked to Bax activation. The transmembrane (TM) domains (α5-α6 helices in the core and α9 helix in the C-terminus) in Bax are implicated in localization to mitochondria and triggering cytotoxicity. Here we have investigated N-terminus modulation of TM function in the context of regulation by the anti-apoptotic protein Bcl-xL. Results Deletion of 29 amino acids in the Bax N-terminus (Bax 30–192) caused constitutive accumulation at mitochondria and triggered high levels of cytotoxicity, not inhibited by Bcl-xL. Removal of the TM domains (Bax 30–105) abrogated mitochondrial localization but resulted in Bcl-xL regulated activation of endogenous Bax and Bax-Bak dependent apoptosis. Inclusion of the α5-α6 helices/TMI domain (Bax 30–146) phenocopied Bax 30–192 as it restored mitochondrial localization, Bcl-xL independent cytotoxicity and was not dependent on endogenous Bax-Bak. Inhibition of function and localization by Bcl-xL was restored in Bax 1–146, which included the TM1 domain. Regardless of regulation by Bcl-xL, all N-terminal deleted constructs immunoprecipitated Bcl-xLand converged on caspase-9 dependent apoptosis consistent with mitochondrial involvement in the apoptotic cascade. Sub-optimal sequence alignments of Bax and Bcl-xL indicated a sequence similarity between the α5–α6 helices of Bax and Bcl-xL. Alanine substitutions of three residues (T14A-S15A-S16A) in the N-terminus (Bax-Ala3) attenuated regulation by the serine-threonine kinase Akt/PKB but not by Bcl-xL indicative of distinct regulatory mechanisms. Conclusion Collectively, the analysis of Bax deletion constructs indicates that the N-terminus drives conformational changes facilitating inhibition of cytotoxicity by Bcl-xL. We speculate that the TM1 helices may serve as 'structural antagonists' for BH3-Bcl-xL interactions, with this function being regulated by the N-terminus in the intact protein.

Publisher Summary Integrin adhesion receptors facilitate the movement of blood borne cells into lymphoid and nonlymphoid tissue during both steady state and inflammatory conditions. In addition, integrins promote the stable interaction of T lymphocytes with antigen presenting cells that are necessary for optimal adaptive immune responses. Signal transduction initiated by antigen and chemokine receptors regulates the functional activity of integrin receptors to promote appropriate periods of strong adhesion during lymphocyte migration and antigen recognition. Recent advances in this area of immunological research have come from the identification of transgenic and knockout mouse models with defects in integrin function and/or T cell migration. These mouse models provide powerful new tools for elucidating the mechanisms by which integrin function and T cell migration are regulated. In addition, these models provide unique opportunities for examining the function of integrin-dependent responses in the context of physiological immune responses that can be initiated, manipulated, and monitored in mice.

The functional activity of integrins is dynamically regulated by T cell receptor stimulation and by protein kinase C (PKC). We report a novel function for the PKC effector protein kinase D1 (PKD1) in integrin activation. Constitutively active and kinase-inactive PKD1 mutants lacking the PKD1 pleckstrin homology (PH) domain block phorbol ester- and TCR-mediated activation and clustering of beta1 integrins. The PH domain of PKD1 mediates the association of PKD1 with the GTPase Rap1 and is central to Rap1 activation and membrane translocation in T cells. Furthermore, PKD1 and Rap1 associate with beta1 integrins in a manner that is dependent on the carboxy-terminal end of the beta1 integrin subunit cytoplasmic domain. beta1 integrin expression is required for Rap1 activation and membrane localization of the PKD1-Rap1 complex. Therefore, PKD1 promotes integrin activation in T cells by regulating Rap1 activation and membrane translocation via interactions with the beta1 integrin subunit cytoplasmic domain.

Background & objectives: Plasma amino acid levels are known to be altered in conditions like sepsis and burns which are situations of metabolic stress. Polycystic ovary syndrome (PCOS), a condition which affects a woman throughout her life, is said to be associated with metabolic stress. This study was undertaken to assess if there were significant alterations in the levels of plasma amino acids in women with PCOS. Methods: Sixty five women with PCOS along with the similar number of age matched normal controls were included in this study. Levels of 14 amino acids were determined using reverse phase high performance liquid chromatography. Results: The levels of methionine, cystine, isoleucine, phenylalanine, valine, tyrosine, proline, glycine, lysine and histidine were found to be significantly (P

Cyanobacterin, a secondary metabolite produced by the cysnobacterium, Scytonema hofmanni, inhibits electron transport at a site in photosystem II. It was previously shown that a DCMU-resistant mutant of A. nidulans R2 was still susceptible to cyanobacterin (Gleason et al., Plant Science, 46 (1986) 5–10). Apparently, cyanobacterin acts at a site different from that of DCMU and similar PS II inhibitors. To confirm this conclusion, a cyanobacterin-resistant strain of A. nidulans R2 was produced by nitrosoguanidine mutagenesis and selected by growth in the presence of 4.7 μM cyanobacterin. Hill activity in mutant thylakoids was compared to that of the wild type membranes in the presence of ferricyanide and silicomolybdate as electron acceptors. Photosynthetic electron transport in the mutant membranes shows a high degree of resistance to cyanobacterin in both reactions. In contrast, the mutant exhibits the same susceptibility to DCMU inhibition as the wild type R2. Cyanobacterin acts at a unique site, inhibiting electron flow from quinone-A to quinone-B.