Possible sources of ambient PM10 inside Jadavpur University Campus, Kolkata.

High concentration of particulates in the university and research institutional campus can affect cognitive performance of students and researchers. However, studies on ambient particulate concentration in the campus of universities or research institutes are scarce. The ambient concentration of PM10 was measured in the campus of Jadavpur University, Kolkata, during two different seasons (S1: Post-monsoon; S2: Winter) to identify major sources of pollutant here. Significant seasonal variation of ambient PM10 was recorded in the campus. The average ambient PM10 concentration was recorded higher in S2 compared to S1 of the study period. Morphological characteristics of PM10 during the study period suggest that the roundness of particles was in the range of 0.66 to 0.68, whilst the mean spherical diameter suggests most of the PM10 particles were < 2.5 µ diameter. Based on factorial analysis, three factors were generated which includes factor 1: soil, building material and coal burning particles (53.76% of the variance); factor 2: particles from coal combustion (29.89% of the variance) and factor 3: particles from transport emission (16.33% of the variance). The study suggests that it is important to stop burning coal, reduce vehicular emission and reduce road dust resuspension around the campus to maintain the ambient PM10 concentration within the university campus during the post-monsoon and winter months.

Combine and conquer: surfactants, solvents, and chaotropes for robust mass spectrometry based analyses of membrane proteins.

Mass spectrometry (MS) based proteomic technologies enable the identification and quantification of membrane proteins as well as their post-translational modifications. A prerequisite for their quantitative and reliable MS-based bottom-up analysis is the efficient digestion into peptides by proteases, though digestion of membrane proteins is typically challenging due to their inherent properties such as hydrophobicity. Here, we investigated the effect of eight commercially available MS-compatible surfactants, two organic solvents, and two chaotropes on the enzymatic digestion efficiency of membrane protein-enriched complex mixtures in a multiphase study using a gelfree approach. Multiple parameters, including the number of peptides and proteins identified, total protein sequence coverage, and digestion specificity were used to evaluate transmembrane protein digestion performance. A new open-source software tool was developed to allow for the specific assessment of transmembrane domain sequence coverage. Results demonstrate that while Progenta anionic surfactants outperform other surfactants when tested alone, combinations of guanidine and acetonitrile improve performance of all surfactants to near similar levels as well as enhance trypsin specificity to >90%, which has critical implications for future quantitative and qualitative proteomic studies.

A cell surfaceome map for immunophenotyping and sorting pluripotent stem cells.

Induction of a pluripotent state in somatic cells through nuclear reprogramming has ushered in a new era of regenerative medicine. Heterogeneity and varied differentiation potentials among induced pluripotent stem cell (iPSC) lines are, however, complicating factors that limit their usefulness for disease modeling, drug discovery, and patient therapies. Thus, there is an urgent need to develop nonmutagenic rapid throughput methods capable of distinguishing among putative iPSC lines of variable quality. To address this issue, we have applied a highly specific chemoproteomic targeting strategy for de novo discovery of cell surface N-glycoproteins to increase the knowledge-base of surface exposed proteins and accessible epitopes of pluripotent stem cells. We report the identification of 500 cell surface proteins on four embryonic stem cell and iPSCs lines and demonstrate the biological significance of this resource on mouse fibroblasts containing an oct4-GFP expression cassette that is active in reprogrammed cells. These results together with immunophenotyping, cell sorting, and functional analyses demonstrate that these newly identified surface marker panels are useful for isolating iPSCs from heterogeneous reprogrammed cultures and for isolating functionally distinct stem cell subpopulations.

Redox active molecules cytochrome c and vitamin C enhance heme-enzyme peroxidations by serving as non-specific agents for redox relay.

We report that incorporation of very low concentrations of redox protein cytochrome c and redox active small molecule vitamin C impacted the outcome of one-electron oxidations mediated by structurally distinct plant/fungal heme peroxidases. Evidence suggests that cytochrome c and vitamin C function as a redox relay for diffusible reduced oxygen species in the reaction system, without invoking specific or affinity-based molecular interactions for electron transfers. The findings provide novel perspectives to understanding - (1) the promiscuous role of cytochrome b(5) in the metabolism mediated by liver microsomal xenobiotic metabolizing systems and (2) the roles of antioxidant molecules in affording relief from oxidative stress.

Assessing the social patterning and magnitude of inequalities in sexual violence among young women in Uganda: Findings from 2016 demographic and health survey.

Sexual violence (SV) is a significant global public health problem. To develop effectively targeted interventions to prevent SV and allocate resources equitably requires identifying the most vulnerable groups and the magnitude of these social inequities. However, these data are currently lacking. Using the Uganda Demographic and Health Survey, we examined SV among all young women and ever-married young women. We conducted univariate and bivariate analyses to characterise the prevalence and social patterning of SV, and then utilised the World Health Organization Health Equity Assessment Toolkit (HEAT) to assess the magnitude of social inequities in SV. At the national level, 5.5% among all young women and 20.5% of ever-married young women had experienced SV. For all young women, the largest inequities in SV were based on sub-national region of residence. Among the ever-married young women, we found profound education, wealth and place-based inequities in SV, which favoured young women with higher education, in wealthier households, and within central regions of Uganda. Our findings suggest a need for regionally targeted multi-sectoral interventions that take into consideration that multiple intersecting social dimensions such as education, poverty and the safe built environment, to address young women's risk for SV.

Differentiating Wild and Apiary Honey by Elemental Profiling: a Case Study from Mangroves of Indian Sundarban.

Honey is a natural substance produced by honeybees from the nectar or secretion of flowering plants. Along with the botanical and geographical origin, several environmental factors also play a major role in determining the characteristics of honey. The aim of this study is to determine and compare the elemental concentration of various macro and trace elements in apiary and wild honeys collected from different parts of Indian Sundarbans. The elemental analysis was performed in inductively coupled plasma optical emission spectroscopy preceded by microwave digestion method. The concentrations of 19 elements (Ag, Al, As, B, Ca, Cd, Co, Cr, Cu, Fe, K, Li, Mg, Mn, Na, Ni, Pb, Se and Zn) were investigated from thirteen locations of Indian Sundarbans. This comparative study shows in wild honey samples, the concentration of K was highest followed by Ca, Mg and Na and Zn was lowest among all. In contrast, in apiary honey samples, Ca had maximum concentration followed by K, Mg and Na and Ag had minimum among all. The elemental concentration in honey from apiary was either equal or higher than their wild counterpart. The results of the factor analysis of PCA algorithm for wild and apiary honey samples were highly variable which implies that the elements are not coming from the same origin. The concentration of element was found to be highly variable across sites and across sources of honey samples.

Inhibition of an NAD⁺ salvage pathway provides efficient and selective toxicity to human pluripotent stem cells.

The tumorigenic potential of human pluripotent stem cells (hPSCs) is a major limitation to the widespread use of hPSC derivatives in the clinic. Here, we demonstrate that the small molecule STF-31 is effective at eliminating undifferentiated hPSCs across a broad range of cell culture conditions with important advantages over previously described methods that target metabolic processes. Although STF-31 was originally described as an inhibitor of glucose transporter 1, these data support the reclassification of STF-31 as a specific NAD⁺ salvage pathway inhibitor through the inhibition of nicotinamide phosphoribosyltransferase (NAMPT). These findings demonstrate the importance of an NAD⁺ salvage pathway in hPSC biology and describe how inhibition of NAMPT can effectively eliminate hPSCs from culture. These results will advance and accelerate the development of safe, clinically relevant hPSC-derived cell-based therapies.

N-glycoprotein surfaceomes of four developmentally distinct mouse cell types.

PURPOSE: Detailed knowledge of cell surface proteins present during early embryonic development remains limited for most cell lineages. Due to the relevance of cell surface proteins in their functional roles controlling cell signaling and their utility as accessible, nongenetic markers for cell identification and sorting, the goal of this study was to provide new information regarding the cell surface proteins present during early mouse embryonic development. EXPERIMENTAL DESIGN: Using the cell surface capture technology, the cell surface N-glycoproteomes of three cell lines and one in vitro differentiated cell type representing distinct cell fates and stages in mouse embryogenesis were assessed. RESULTS: Altogether, more than 600 cell surface N-glycoproteins were identified represented by >5500 N-glycopeptides. CONCLUSIONS AND CLINICAL RELEVANCE: The development of new, informative cell surface markers for the reliable identification and isolation of functionally defined subsets of cells from early developmental stages will advance the use of stem cell technologies for mechanistic developmental studies, including disease modeling and drug discovery.

High efficiency differentiation of human pluripotent stem cells to cardiomyocytes and characterization by flow cytometry.

There is an urgent need to develop approaches for repairing the damaged heart, discovering new therapeutic drugs that do not have toxic effects on the heart, and improving strategies to accurately model heart disease. The potential of exploiting human induced pluripotent stem cell (hiPSC) technology to generate cardiac muscle "in a dish" for these applications continues to generate high enthusiasm. In recent years, the ability to efficiently generate cardiomyogenic cells from human pluripotent stem cells (hPSCs) has greatly improved, offering us new opportunities to model very early stages of human cardiac development not otherwise accessible. In contrast to many previous methods, the cardiomyocyte differentiation protocol described here does not require cell aggregation or the addition of Activin A or BMP4 and robustly generates cultures of cells that are highly positive for cardiac troponin I and T (TNNI3, TNNT2), iroquois-class homeodomain protein IRX-4 (IRX4), myosin regulatory light chain 2, ventricular/cardiac muscle isoform (MLC2v) and myosin regulatory light chain 2, atrial isoform (MLC2a) by day 10 across all human embryonic stem cell (hESC) and hiPSC lines tested to date. Cells can be passaged and maintained for more than 90 days in culture. The strategy is technically simple to implement and cost-effective. Characterization of cardiomyocytes derived from pluripotent cells often includes the analysis of reference markers, both at the mRNA and protein level. For protein analysis, flow cytometry is a powerful analytical tool for assessing quality of cells in culture and determining subpopulation homogeneity. However, technical variation in sample preparation can significantly affect quality of flow cytometry data. Thus, standardization of staining protocols should facilitate comparisons among various differentiation strategies. Accordingly, optimized staining protocols for the analysis of IRX4, MLC2v, MLC2a, TNNI3, and TNNT2 by flow cytometry are described.

A human pluripotent stem cell surface N-glycoproteome resource reveals markers, extracellular epitopes, and drug targets.

Detailed knowledge of cell-surface proteins for isolating well-defined populations of human pluripotent stem cells (hPSCs) would significantly enhance their characterization and translational potential. Through a chemoproteomic approach, we developed a cell-surface proteome inventory containing 496 N-linked glycoproteins on human embryonic (hESCs) and induced PSCs (hiPSCs). Against a backdrop of human fibroblasts and 50 other cell types, >100 surface proteins of interest for hPSCs were revealed. The >30 positive and negative markers verified here by orthogonal approaches provide experimental justification for the rational selection of pluripotency and lineage markers, epitopes for cell isolation, and reagents for the characterization of putative hiPSC lines. Comparative differences between the chemoproteomic-defined surfaceome and the transcriptome-predicted surfaceome directly led to the discovery that STF-31, a reported GLUT-1 inhibitor, is toxic to hPSCs and efficient for selective elimination of hPSCs from mixed cultures.