Biology subjects

Sharma, S.

Publications and source records attributed to Sharma, S..

At least 415 records · Page 23Linked to original sources

bioRxiv2019

Exogenous application of KNO3 elevates the salinity tolerance of Stevia rebaudiana through ion homeostasis mechanism

Though relatively little is understood of adaptation, physiological and metabolic changes of Stevia rebaudiana under exposure to salinity stress, it is hypothesized that exogenous application of potassium (K+) could elevates the salinity tolerance through ions homeostasis. Thus, an experiment was conducted with twenty treatment combinations comprising four salinity levels (irrigation with normal water as control and three level of NaCl at 40, 80 and 120 mM) and five different concentrations of KNO3 (0.0, 2.5, 5.0, 7.5, and 10.0 g L-1). Dry leaf yield was not negatively affected with mild salinity (40 mM). However, the detrimental effects were observed at moderate and higher salinity levels (80 and 120 mM). The uptakes of K+, Ca2+, and N were significantly reduced at higher salinity level, whereas accumulations of Na+ and Cl- ions in plant tissues were substantially increased. Proline content in leaf was also increased significantly (P[≤]0.05) in response to salt stress. Among the foliar application, KNO3 at 5.0 gL-1 registered significantly (P[≤]0.05) higher dry leaf yield compared with control. Exogenous application of K+ under moderate salinity stress maintained ion balance in cytosol, particularly K: Na. Thus, the salinity tolerance of stevia can be elevated to some extent through exogenous application of K+.\n\nHighlightThe detrimental effects of moderate and higher salinity levels on growth and dry leaf yield of stevia were observed. However, tolerance level can be elevated through exogenous application of KNO3.

plant biology↗

bioRxiv2019

Neuron subtype-specific effector gene expression in the Motor Ganglion of Ciona

The central nervous system of the Ciona larva contains only 177 neurons. The precise regulation of neuron subtype-specific morphogenesis and differentiation observed in during the formation of this minimal connectome offers a unique opportunity to dissect gene regulatory networks underlying chordate neurodevelopment. Here we compare the transcriptomes of two very distinct neuron types in the hindbrain/spinal cord homolog of Ciona, the Motor Ganglion (MG): the Descending decussating neuron (ddN, proposed homolog of Mauthner Cells in vertebrates) and the MG Interneuron 2 (MGIN2). Both types are invariantly represented by a single bilaterally symmetric left/right pair of cells in every larva. Supernumerary ddNs and MGIN2s were generated in synchronized embryos and isolated by fluorescence-activated cell sorting for transcriptome profiling. Differential gene expression analysis revealed ddN- and MGIN2-specific enrichment of a wide range of genes, including many encoding potential \"effectors\" of subtype-specific morphological and functional traits. More specifically, we identified the upregulation of centrosome-associated, microtubule-stabilizing/bundling proteins and extracellular matrix proteins and axon guidance cues as part of a single intrinsic regulatory program that might underlie the unique polarization of the ddNs, the only descending MG neurons that cross the midline.

developmental biology↗

bioRxiv2019

Spatial Distribution of Cholesterol in Lipid Bilayers

1.We have performed molecular simulations to study spatial distribution and orientation of cholesterol molecules within three symmetric lipid bilayer systems: two binary lipid mixtures, namely, DOPC/CHOL (1, 2-dioleoyl-sn-glycero-3-phosphocholine/cholesterol) and SM/CHOL (d20:1/20:0 sphingomyelin /Cholesterol), and a tertiary mixture of DOPC/SM/CHOL. We have studied the behavior of these bilayers at temperatures varying from 400 K to 210 K and cholesterol molar concentration from 0% to 60%.We observe that the spatial distribution of cholesterol is strongly correlated with the phase of the bilayer. In the disordered phase, cholesterol molecules are predominantly present near the center of the bilayer. In the ordered phase, cholesterol molecules are mainly present in the leaflets. At the order - disorder transition temperature, the fraction of cholesterol molecules is equal in the two leaflets and the center. In the leaflets, cholesterol molecules are oriented parallel to the bilayer normal, while near the center, cholesterol molecules are randomly oriented. In agreement with previous experimental studies, we find that increasing the cholesterol concentration favors ordered phase of the bilayers. The preference of cholesterol molecules to be present in the leaflets in the ordered phase is attributed to their favorable hydrophobic interactions with the lipid tails.\n\n2. Statement of SignificanceCholesterol has an important role in governing the physical properties of lipid bilayers, including their structural integrity, phase behavior and permeability. The spatial distribution of cholesterol in lipid bilayers is not well-understood because of the challenges associated with performing experiments for such a measurement. We show, via molecular simulations, that the spatial distribution of cholesterol molecules is strongly correlated with the phase behavior of the lipid bilayers. In the ordered phase, cholesterol molecules are predominantly present in the leaflets, whereas in the disordered phase, cholesterol molecules are in the center region of the bilayer. These results are important for understanding the relationship between lipid bilayer composition and their biological function and response.

biophysics↗

bioRxiv2019

Mck1 defines a key S-phase checkpoint effector in response to various degrees of replication threats

The S-phase checkpoint plays an essential role in regulation of the ribonucleotide reductase (RNR) activity to maintain the dNTP pools. How eukaryotic cells respond appropriately to different levels of replication threats remains elusive. Here, we have identified that a conserved GSK-3 kinase Mck1 cooperates with Dun1 in regulating this process. Deleting MCK1 sensitizes dun1{Delta} to hydroxyurea (HU) reminiscent of mec1{Delta} or rad53{Delta}. As a kinase at the downstream of Rad53, Mck1 does not participate in the post-translational regulation of RNR as Dun1 does, but Mck1 can release the Crt1 repressor from the promoters of RNR2/3/4 by phosphorylation. Meanwhile, Hug1, an Rnr2 inhibitor, is induced to fine-tune the dNTP levels. When cells suffer a more severe threat, Mck1 can inhibit the transcription of HUG1. Importantly, only a combined deletion of HUG1 and CRT1, can confer a dramatic boost of dNTP levels and the survival of mck1{Delta}dun1{Delta} or mec1{Delta} cells assaulted by a lethal dose of HU. These findings reveal the division-of-labor between Mck1 and Dun1 at the S-phase checkpoint pathway to fine-tune dNTP homeostasis.\n\nAuthor SummaryThe appropriate amount and balance of four dNTPs are crucial for all cells correctly copying and passing on their genetic material generation by generation. Eukaryotes have developed an alert and response system to deal with the disturbance. Here, we uncovered a second-level effector branch. It is activated by the upstream surveillance kinase cascade, which can induce the expression of dNTP-producing enzymes. It can also reduce the inhibitor of these enzymes to further boost their activity according to the degrees of threats. These findings suggest a multi-level response system to guarantee dNTP supply, which is essential to maintain genetic stability under various environmental challenges.

molecular biology↗

bioRxiv2019

Francisella novicida Cas9 interrogates genomic DNA with very high specificity and can be used for mammalian genome editing

Genome editing using the CRISPR Cas9 system has been used to manipulate eukaryotic DNA and make precise heritable changes. Although the widely used Streptococcus pyogenes Cas9 (SpCas9) and its engineered variants have been efficiently harnessed for numerous gene-editing applications across different platforms, concerns remain, regarding their putative off targeting at multiple loci across the genome. Here we report that Francisella novicida Cas9 (FnCas9) shows a very high specificity of binding to its intended targets and negligible binding to off-target loci. The specificity is determined by its minimal binding affinity with DNA when mismatches to the target sgRNA are present in the sgRNA:DNA heteroduplex. FnCas9 produces staggered cleavage, higher HDR rates and very low non-specific genome editing compared to SpCas9. We demonstrate FnCas9 mediated correction of the sickle cell mutation in patient derived iPSCs and propose that it can be used for precise therapeutic genome editing for a wide variety of genetic disorders.\n\nSIGNIFICANCE STATEMENTTherapeutic genome editing has been significantly accentuated by the advent of CRISPR based gene correction. However, genomic off-targeting has been a major setback for clinical translation. Although high fidelity versions of Cas9 have been rationally designed, they recognize and bind to off-targets. In this study, we characterize a naturally occurring Cas9 from Francisella novicida (FnCas9) that shows negligible binding affinity to off targets differing by one or more mismatches, rendering it highly specific in target recognition and editing. We show that FnCas9 can direct both HDR and NHEJ mediated DNA repair, generates higher rate of HDR and negligible off-target editing. Finally we show its potential in therapeutic genome editing by correcting the sickle cell anemia mutation in patient derived iPSCs.

molecular biology↗

bioRxiv2019

Heparan sulfates are critical regulators of the inhibitory megakaryocyte-platelet receptor G6b-B

The immunoreceptor tyrosine-based inhibition motif (ITIM)-containing receptor G6b-B is critical for platelet production and activation, loss of which results in severe macrothrombocytopenia and aberrant platelet function in mice and humans. Using a combination of immunohistochemistry, affinity chromatography and proteomics, we identified the extracellular matrix heparan sulfate (HS) proteoglycan perlecan as a G6b-B binding partner. Subsequent in vitro biochemical studies and a cell-based genetic screen demonstrated that the interaction is specifically mediated by the HS chains of perlecan. Biophysical analysis revealed that heparin forms a high-affinity complex with G6b-B and mediates dimerization. Using platelets from humans and genetically-modified mice, we demonstrate that binding of G6b-B to HS and multivalent heparin inhibits platelet and megakaryocyte function by inducing downstream signaling via the tyrosine phosphatases Shp1 and Shp2. Our findings provide novel insights into how G6b-B is regulated and contribute to our understanding of the interaction of megakaryocytes and platelets with glycans.

biochemistry↗

bioRxiv2019

Overlapping transcriptional expression response of wheat zinc-induced facilitator-like transporters emphasize important role during Fe and Zn stress

BackgroundHexaploid wheat is an important cereal crop that has been targeted to enhance grain micronutrient content including zinc and iron. In this direction, modulating the expression of plant transporters involved in Fe and Zn homeostasis could be one of the promising approaches. Therefore, the present work was undertaken to identify bread wheat Zinc-Induced Facilitator-Like (ZIFL) family of transporters and study their transcriptional expression response during micronutrient fluctuations and exposure to multiple heavy metals.\n\nResultsThe genome-wide analyses resulted in identification of thirty-five putative TaZIFL genes, which were distributed only on Chromosome 3, 4 and 5. Wheat ZIFL proteins subjected to the phylogenetic analysis showed the uniform distribution along with rice, Arabidopsis and maize. In-silico analysis of the promoters of the wheat ZIFL genes suggested the presence of multiple metal binding sites including those which are involved in Fe homeostasis. QRT-PCR analysis of wheat ZIFL genes suggested the differential regulation of the transcripts in roots and shoots under surplus Zn and also during Fe starvation. Specifically, in roots, TaZIFL2.3, TaZIFL4.1, TaZIFL4.2, TaZIFL5, TaZIFL6.1 and TaZIFL6.2 were significantly up-regulated by both Zn and Fe. This suggested that ZIFL could possibly be regulated by both the nutrient stress in a tissue specific manner. Interestingly, upon exposure to heavy metals, TaZIFL4.2 and TaZIFL7.1 showed significant up-regulation, whereas TaZIFL5 and TaZIFL6.2 remained almost unaffected.\n\nConclusionThis is the first report with detailed analysis of wheat ZIFL genes. Our study also identifies closest ortholog for transporter of mugineic acid, a chelator required for Fe uptake. Comprehensive transcript expression pattern during development of wheat seedlings and against various abiotic/biotic stresses resulted in tissue specific responses. Overall, this work addresses the role of wheat ZIFL during the interplay between micronutrient and heavy metal stress in a tissue specific manner.

plant biology↗

bioRxiv2019

Nanopore sequencing for fast determination of plasmids, phages, virulence markers, and antimicrobial resistance genes in Shiga toxin-producing Escherichia coli

Whole genome sequencing can provide essential public health information. However, it is now known that widely used short-read methods have the potential to miss some randomly-distributed segments of genomes. This can prevent phages, plasmids, and virulence factors from being detected or properly identified. Here, we compared assemblies of three complete STEC O26:H11 genomes from two different sequence types (ST21 and 29), each acquired using the MiSeq-Nextera XT, MinION nanopore-based sequencing, and Pacific Biosciences (PacBio) sequencing. Each closed genome consisted of a single chromosome, approximately 5.7 Mb for CFSAN027343, 5.6 Mb for CFSAN027346, and 5.4 MB for CFSAN027350. However, short-read WGS using MiSeq-Nextera failed to identify some virulence genes in plasmids and on the chromosome, both of which were detected using the long-read platforms. Results from long-read MinION and PacBio allowed us to identify differences in plasmid content: a single 88 kb plasmid in CFSAN027343; a 157kb plasmid in CFSAN027350; and two plasmids in CFSAN027346 (one 95 Kb, one 72 Kb). These data enabled rapid characterization of the virulome, detection of antimicrobial genes, and composition/location of Stx phages. Taken together, positive correlations between the two long-read methods for determining plasmids, virulome, antimicrobial resistance genes, and phage composition support MinION sequencing as one accurate and economical option for closing STEC genomes and identifying specific virulence markers.

genomics↗

bioRxiv2019

A common tag nucleotide variant in MMP7 promoter increases risk for hypertension via enhanced interactions with CREB transcription factor

MMP7 (Matrilysin), a potent extracellular matrix degrading enzyme with wide substrate specificity, is emerging as a new regulator of cardiovascular diseases including coronary artery disease and atherosclerosis. However, potential contributions of MMP7 genetic variations to hypertension remain unknown. In this study, we first probed for the association of a tag single nucleotide polymorphism (SNP) in the MMP7 gene promoter (-181A/G; rs11568818) with hypertension in an urban south Indian population (n=1517). The heterozygous A/G genotype showed a strong association with hypertension as compared to the A/A wild-type genotype (OR=1.641, 95% CI=1.276-2.109; p=1x10-4); AG genotype carriers also displayed significantly higher diastolic blood pressure and mean arterial pressure than AA genotype subjects. The study was replicated in a north Indian population (n=977) as well (OR=1.520, 95% CI =1.106-2.090; p=0.01). Transient transfection experiments using MMP7 promoter-luciferase reporter constructs revealed that the variant -181G allele conferred greater promoter activity than the -181A allele. Computational prediction and structure-based conformational and molecular dynamics simulation studies suggested higher binding affinity for the transcription factor CREB to the -181G promoter. In corroboration, over-expression/down-regulation of CREB and chromatin immunoprecipitation experiments provided convincing evidence for stronger binding of CREB with the -181G promoter. Further, the -181G promoter also displayed an enhanced response to hypoxia and epinephrine-treatment. The higher promoter activity of -181G allele also translated to increased MMP7 protein levels. Indeed, MMP7-181A/G heterozygous individuals displayed elevated plasma MMP7 levels which positively correlated with blood pressure. In conclusion, the MMP7 A-181G promoter SNP increased expression of MMP7 under pathophysiological (such as hypoxic stress and catecholamine excess) conditions via increased interactions with the transcription factor CREB and enhanced the risk for hypertension in its carriers.

genetics↗

bioRxiv2019

Targeting the mTORC2 signaling complex in B cell malignancies.

Hyperactive PI3 kinase-Akt (PI3K-Akt) signaling has an important role in cell growth and resistance to apoptosis in B cell malignancies. Inhibition of this pathway by blocking PI3K activity, and or inhibiting mTORC1/2 signaling complexes is an active area of research in B cell leukemia/lymphoma such as chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL). With a tissue-scan array, the expression of Rictor is a component of the mTORC2 complex was determined by quantitative PCR in a number of B cell malignancies. Rictor was found to be over-expressed in CLL and MCL cells as compared to normal B cells with no over-expression in Hodgkins and non-Hodgkins lymphomas. Inactivation of Rictor was performed by shRNA in two Mantle cell lines and these stable Rictor knockdown cell lines demonstrated a slower growth of cells as compared to scrambled shRNA control. In addition, there was a decrease of mTORC2 signaling and B cell receptor (BCR) cross-linking mediated Akt (Ser473) and NDRG1 (Thr 346) phosphorylation. To specifically disrupt the mTORC2 signaling complex and target Rictor overexpression, previously identified inhibitors that block Rictor and MTOR interaction in a yeast two-hybrid system were analyzed. Treatment of primary CLL specimens with these inhibitors followed by immunoprecipitation experiments confirmed the disruption of the mTORC2 complex. These inhibitors also induced apoptosis in CLL specimens and were more effective than rapamycin, an MTOR inhibitor and pp242, an mTORC1 and 2 inhibitors, at equimolar concentrations. Treatment of CLL specimens with the lead inhibitor, compound#6, resulted in inhibition of p-Akt, p-GSK 3 beta, p-PKC alpha, p-Foxo1, and p-Foxo3, with minimal effect on the phosphorylation of an mTORC1 target gene, S6 kinase. In comparison with Idelalisib (CAL-101), a clinically approved PI3Kinase p110 delta inhibitor in CLL, comp#6 is more effective in inducing apoptosis in primary CLL specimens at equimolar concentrations (mean 51.2, SD 21.7 as compared to mean 26.9, SD 17.2). The data support the effectiveness of these novel inhibitors that specifically disrupt the mTORC2 complex in primary CLL specimens.

cancer biology↗

bioRxiv2019

Modeling microbial communities using biochemical resource allocation analysis

To understand the functioning and dynamics of microbial communities remains a fundamental challenge at the forefront of current biology. To tackle this challenge, the construction of computational models of interacting microbes is an indispensable tool. Currently, however, there is a large chasm between ecologically-motivated descriptions of microbial growth used in ecosystems simulations, and detailed metabolic pathway and genome-based descriptions developed within systems and synthetic biology. Here, we seek to demonstrate how current biochemical resource allocation models of microbial growth offer the potential to advance ecosystem simulations and their parameterization. In particular, recent work on quantitative microbial growth and cellular resource allocation allow us to formulate mechanistic models of microbial growth that are physiologically meaningful while remaining computationally tractable. Biochemical resource allocation models go beyond Michaelis-Menten and Monod-type growth models, and allow to account for emergent properties that underlie the remarkable plasticity of microbial growth. We exemplify our approach using a coarse-grained model of cyanobacterial phototrophic growth, and demonstrate how the model allows us to represent physiological acclimation to different environments, co-limitation of growth by several nutrients, as well as emergent switches between alternative nutrient sources. Our approach has implications for building models of microbial communities to understand their interactions, dynamics and response to environmental changes.

systems biology↗

bioRxiv2019

Cyto-architecture constrains a photoactivation induced tubulin gradient in the syncytial Drosophila embryo

Drosophila embryogenesis begins with nuclear division in a common cytoplasm forming a syncytial cell. Morphogen gradient molecules spread across nucleo-cytoplasmic domains to pattern the body axis of the syncytial embryo. The diffusion of molecules across the syncytial nucleo-cytoplasmic domains is potentially constrained by association with the components of cellular architecture, however the extent of restriction has not been examined so far. Here we use photoactivation (PA) to generate a source of cytoplasmic or cytoskeletal molecules in order to monitor the kinetics of their spread in the syncytial Drosophila embryo. Photoactivated PA-GFP and PA-GFP-Tubulin within a fixed anterior area diffused along the antero-posterior axis. These molecules were enriched in cortical cytoplasm above the yolk-filled center suggesting that the cortical cytoplasm is phase separated from the yolk-filled center. The length scales of diffusion were extracted using exponential fits under steady state assumptions. PA-GFP spread to greater distance as compared to PA-GFP-Tubulin. Both gradients were steeper and more restricted when generated in the center of the embryo probably due to a higher density of nucleo-cytoplasmic domains. The length scale of diffusion for PA-GFP-Tubulin gradient increased in mutant embryos containing short plasma membrane furrows and disrupted tubulin cytoskeleton. The PA-GFP gradient shape was unaffected by cyto-architecture perturbation. Taken together, these data show that PA-GFP-Tubulin gradient is largely restricted by its incorporation in the microtubule network and intact plasma membrane furrows. This photoactivation based analysis of protein spread across allows for interpretation of the dependence of gradient formation on the syncytial cyto-architecture.

developmental biology↗

bioRxiv2019

The genetic basis of cis-regulatory divergence between the subspecies of cultivated rice (Oryza sativa)

Cultivated rice consists of two subspecies, Indica and Japonica, that exhibit well-characterized differences at the morphological and genetic levels. However, the differences between these subspecies at the transcriptome level remains largely unexamined. Here, we provide a comprehensive characterization of transcriptome divergence and cis-regulatory variation within rice using transcriptome data from 91 accessions from a rice diversity panel (RDP1). The transcriptomes of the two subspecies of rice are highly divergent. The expression and genetic diversity was significantly lower within Japonica relative to Indica, which is consistent with the known population bottleneck during Japonica domestication. Moreover, 1,860 and 1,325 genes showed differences in heritability in the broad and narrow sense respectively, between the subspecies, which was driven largely by environmental and genetic effects rather than differences in phenotypic variability. We leveraged high-density genotypic data and transcript levels to identify cis-regulatory variants that may explain the genetic divergence between the subspecies. We identified significantly more eQTL that were specific to the Indica subspecies compared to Japonica, suggesting that the observed differences in expression and genetic variability also extends to cis-regulatory variation. We next explored the potential causes of this cis-regulatory divergence by assessing local genetic diversity for cis-eQTL. Local genetic diversity around subspecies-specific cis-eQTL was significantly lower than genome-wide averages in subspecies lacking the eQTL, suggesting that selective pressures may have shaped regulatory variation in each subspecies. This study provides the first comprehensive characterization of transcriptional and cis-regulatory variation in cultivated rice, and could be an important resource for future studies.

genomics↗

bioRxiv2018

Novel Dual Labeled Fluorescence Probe Based Assay to Measure the Telomere Length

Telomeres are highly repetitive regions capping the chromosomes and composed of multiple units of hexa-nucleotides, TTAGGG, making their quantification difficult. Most of the methods developed to estimate telomeres are extensively cumbersome and expensive. The quantitative polymerase chain reaction (qPCR) based assay is relatively easy and cheaper method that applies SyBr Green dye chemistry to measure telomere length. As SyBr Green dye fluoresces after intercalation into the dsDNA, lack of differentiation between specific PCR target products and unspecific products is a limitation and it affects accuracy in quantitation of telomeres. To overcome the limitations of SyBr Green, we developed a dual labeled fluorescence probe based quantitative polymerase chain reaction (qPCR) to measure the telomere length. This robust, accurate and highly reproducible (R2=0.96) proprietary method (patent pending), yet cost effective and easy, utilizes a probe that targets specifically the telomeric DNA.

genetics↗

bioRxiv2018

Enhancer Reprogramming Confers Dependence on Glycolysis and IGF signaling in KMT2D Mutant Melanoma

Epigenetic modifiers have emerged as important regulators of tumor progression. We identified histone methyltransferase KMT2D as a potent tumor-suppressor through an in vivo epigenome-focused pooled RNAi screen in melanoma. KMT2D harbors frequent somatic point mutations in multiple tumor types. How these events contribute to tumorigenesis and whether they impart therapeutic vulnerability are poorly understood. To address these questions, we generated a genetically engineered mouse model of melanoma based on conditional and melanocyte-specific deletion of KMT2D. We demonstrate KMT2D as a bona fide tumor suppressor which cooperates with activated BRAF. KMT2D-deficient tumors showed substantial reprogramming of key metabolic pathways including glycolysis. Glycolysis enzymes, intermediate metabolites and glucose consumption rate were aberrantly upregulated in KMT2D mutant cells. The pharmacological inhibition of glycolysis reduced proliferation and tumorigenesis preferentially in KMT2D mutant cells. Mechanistically, KMT2D loss caused drastic reduction of H3K4me1-marked active enhancer states. Loss of distal enhancer and subsequent reduction in expression of IGFBP5 activated IGF1R-AKT to increase glycolysis in KMT2D-deficient cells. We conclude that KMT2D loss promotes tumorigenesis by facilitating increased usage of glycolysis pathway for enhanced biomass needs via enhancer reprogramming. Our data imply that inhibition of glycolysis or IGFR pathway could be a potential therapeutic strategy in KMT2D mutant tumors.

cancer biology↗

bioRxiv2018

Economic performance and cost-effectiveness of using a DEC-salt social enterprise for eliminating the major neglected tropical disease, lymphatic filariasis

BackgroundSalt fortified with the drug, diethylcarbamazine (DEC), and introduced into a competitive market has the potential to overcome the obstacles associated with tablet-based Lymphatic Filariasis (LF) elimination programs. Questions remain, however, regarding the economic viability, production capacity, and effectiveness of this strategy as a sustainable means to bring about LF elimination in resource poor settings.\n\nMethodology and Principal FindingsWe evaluated the performance and effectiveness of a novel social enterprise-based approach developed and tested in Leogane, Haiti, as a strategy to sustainably and cost-efficiently distribute DEC-medicated salt into a competitive market at quantities sufficient to bring about the elimination of LF. We undertook a cost-revenue analysis to evaluate the production capability and financial feasibility of the developed DEC salt social enterprise, and a modeling study centered on applying a dynamic mathematical model localized to reflect local LF transmission dynamics to evaluate the cost-effectiveness of using this intervention versus standard annual Mass Drug Administration (MDA) for eliminating LF in Leogane. We show that the salt enterprise because of its mixed product business strategy may have already reached the production capacity for delivering sufficient quantities of edible DEC-medicated salt to bring about LF transmission in the Leogane study setting. Due to increasing revenues obtained from the sale of DEC salt over time, expansion of its delivery in the population, and greater cumulative impact on the survival of worms, this strategy could also represent a significantly more cost-effective option than annual DEC tablet-based MDA for accomplishing LF elimination.\n\nSignificanceA social enterprise approach can offer an innovative market-based strategy by which edible salt fortified with DEC could be distributed to communities both on a financially sustainable basis and at sufficient quantity to eliminate LF. Deployment of similarly fashioned intervention strategies would improve current efforts to successfully accomplish the goal of LF elimination, particularly in difficult-to-control settings.\n\nAuthor summaryWith less than three years remaining for meeting the 2020 target set by WHO for accomplishing the global elimination of Lymphatic Filariasis (LF), concerns are emerging regarding the feasibility of meeting this goal using the current tablet-based Mass Drug Administration strategy. Salt fortified with the antifilarial drug, diethylcarbamazine (DEC), could offer an intervention that avoids many of the barriers connected with tablet-based elimination programs. We analyzed the economic performance and cost-effectiveness of a novel DEC-salt social enterprise developed and tested in Leogane arrondissement, Haiti, as a particularly significant strategy for accomplishing sustainable LF elimination in such complex settings. We show that because of increasing revenue from the sale of the DEC salt over time, expansion of its delivery in the population, and the adverse effect of continuous consumption of the drug on worms, the delivery of DEC through a salt enterprise can represent a significantly more cost-effective option than annual DEC tablet-based MDA for accomplishing LF elimination in settings, like Leogane. We indicate that development of policy and research into how to deploy similarly-fashioned interventions, or work with the salt industry to increase population use of medicated salt, would improve present efforts to successfully accomplish the elimination of LF.

epidemiology↗

bioRxiv2018

Viral characteristics associated with sustenance of elite neutralizing activity in chronically HIV-1C infected monozygotic pediatric twins

Broad and potent neutralizing antibodies (bnAbs) with multiple epitope specificities evolve in HIV-1 infected children. Herein we studied two antiretroviral naive chronically HIV-1C in-fected monozygotic pediatric twins AIIMS_329 and AIIMS_330 with potent plasma bnAbs. Elite plasma neutralizing activity was observed since initial sampling at 78 months in AIIMS_330 and persisted throughout, while in AIIMS_329 it was seen at 90-months of age after which potency decreased overtime. We evaluated potential viral characteristics associated with the varied immune profile by generating single genome amplified pseudoviruses. The AIIMS_329 viruses generated from 90-month time point sampling were neutralization sensitive to second generation bnAbs and contemporaneous autologous plasma antibodies, while viruses from 112-months and 117-month timepoints were resistant to most bnAbs and autologous contemporaneous plasma. AIIMS_329 viruses developed resistance to plasma nAbs plausibly by N160-glycan loss, V1- and V4-loop lengthening. The viruses generated from AIIMS_330 at 90-month and 117-month timepoint showed varied susceptibility to bnAbs and autologous contemporaneous plasma antibodies while the viruses of 112-month timepoint, at which plasma nAb specificities mapped to the V2-glycan, V3-glycan and CD4bs, were resistant to autologous contemporaneous plasma antibodies as well as most bnAbs. We observed evolution of a viral pool in AIIMS_330 donor, comprising of plasma antibody neutralization sensitive or resistant diverse autologous viruses that in turn may have contributed to development and maintenance of elite neutralizing activity. The findings of this study provide information towards understanding factors involved in generation and maintenance of potent plasma nAbs.\n\nImportanceChronically HIV-1 infected children that develop elite neutralizing activity are suitable candidates to understand the mechanisms that lead to the co-evolution of virus and antibody response. Here, we evaluated the alterations in virus and antibody responses over time in chronically HIV-1C infected monozygotic pediatric twins, AIIMS_329 and AIIMS_330, who had acquired the infection by vertical transmission. AIIMS_330 retained the elite plasma neutralizing activity throughout, while in AIIMS_329, the potency decreased post 90 months of age. The corresponding viral pool from post 90-month samples in AIIMS_330 showed varied susceptibility, while that in AIIMS_329, developed resistance to bnAbs and autologous plasma antibodies. The findings of this study, conducted in twin children of same genetic make-up and infected at birth with a single source of HIV-1C, suggest that a viral pool with varied susceptibility to antibodies could have been one of the factors responsible for sustained elite neutralizing activity in AIIMS_330.

immunology↗

bioRxiv2018

Identification of novel circadian transcripts in the zebrafish retina

High fecundity, transparent embryos for monitoring the rapid development of organs and the availability of a well-annotated genome has made zebrafish a model organism of choice for developmental biology and neurobiology. This vertebrate model, a favourite in chronobiology studies, shows striking circadian rhythmicity in behaviour. Here, we identify novel genes in the zebrafish genome, which shows their expression in the zebrafish retina. We further resolve the expression pattern over time and assign specific novel transcripts to the retinal cell type, predominantly in the inner nuclear layer. Using chemical ablation and free run experiments we segregate the transcripts that are rhythmic when entrained by light from those that show sustained oscillations in the absence of external cues. The transcripts reported here with rigorous annotation and specific functions in circadian biology provide the groundwork for functional characterisation of novel players in the zebrafish retinal clock.

neuroscience↗