Biology subjects

Dutta, R.

Publications and source records attributed to Dutta, R..

34 records · Page 2Linked to original sources

bioRxiv2022

Bayesian linear models with unknown design over finite alphabets

Our topic is the reconstruction of the unknown matrices S and{omega} for the multivariate linear model Y = S{omega} +{varepsilon} under the assumption that the entries of S are drawn from the finite alphabet [A] = 0, 1 and{omega} is a weight matrix. While a frequentist method has recently been proposed for this purpose, a Bayesian approach seems also desirable. We therefore provide a new hierarchical Bayesian method for this inferential task. Our approach provides estimates of the posterior that may be used to quantify uncertainty. Since matching permutations in both S and{omega} lead to the same reconstruction S{omega}, we introduce an order-preserving shrinkage prior to establish identifiability with respect to permutations.

genetics↗

bioRxiv2022

Joint likelihood-free inference of the number of selected SNPs and the selection coefficient in an evolving population

Given the often intractable exact likelihood, likelihood-free inference plays an important role in population genetics. Indeed, several methodological developments in approximate Bayesian Computation (ABC) were inspired by applications in population genetics. Here, we explore a novel combination of recently proposed ABC tools that can handle high-dimensional summary statistics and apply them to infer selection strength and the number of selected loci from experimental evolution data. While several methods infer selection strength at the single-nucleotide polymorphism (SNP) level, our approach provides additional information about the selective architecture, including the number of selected positions in a candidate window of interest. This is nontrivial, since the spatial correlation induced by genomic linkage can produce selection signals at neighboring SNPs. A further advantage of our approach is that we can readily quantify uncertainty using the ABC posterior. On both simulated and real data, we demonstrate promising performance. This suggests that our ABC variant could also be interesting in other applications.

evolutionary biology↗

bioRxiv2022

Rad51-mediated interhomolog recombination during budding yeast meiosis is promoted by the meiotic recombination checkpoint and the conserved Pif1 helicase

During meiosis, recombination between homologous chromosomes (homologs) generates crossovers that promote proper segregation at the first meiotic division. Recombination is initiated by Spo11-catalyzed double strand breaks (DSBs). 5 end resection of the DSBs creates 3 single strand tails that two recombinases, Rad51 and Dmc1, bind to form presynaptic filaments that search for homology, mediate strand invasion and generate displacement loops (D-loops). D-loop processing then forms crossover and non-crossover recombinants. Meiotic recombination occurs in two temporally distinct phases. During Phase 1, Rad51 is inhibited and Dmc1 mediates the interhomolog recombination that promotes homolog synapsis. In Phase 2, Rad51 becomes active and functions with Rad54 to repair residual DSBs, making increasing use of sister chromatids. The transition from Phase 1 to Phase 2 is controlled by the meiotic recombination checkpoint through the meiosis-specific effector kinase Mek1. This work shows that constitutive activation of Rad51 in Phase 1 results in a subset of DSBs being repaired by a Rad51-mediated interhomolog recombination pathway that is distinct from that of Dmc1. Strand invasion intermediates generated by Rad51 require more time to be processed into recombinants, resulting in a meiotic recombination checkpoint delay in prophase I. Without the checkpoint, Rad51-generated intermediates are more likely to be repaired using a sister chromatid, thereby increasing Meiosis I chromosome nondisjunction. This Rad51 interhomolog recombination pathway is specifically promoted by the conserved 5-3 helicase PIF1 and its paralog, RRM3 and requires Pif1 helicase activity and its interaction with PCNA. This work demonstrates that (1) inhibition of Rad51 during Phase 1 is important to prevent competition with Dmc1 for DSB repair, (2) Rad51-mediated meiotic recombination intermediates are initially processed differently than those made by Dmc1, (3) the meiotic recombination checkpoint provides time during prophase 1 for processing of Rad51-generated recombination intermediates. AUTHOR SUMMARYTo sexually reproduce, cells containing two copies of each chromosome must undergo the specialized cell division of meiosis to sort the chromosomes into gametes containing a single copy of each chromosome. But how do homologous chromosomes know who is who? The answer is by recombination, a process in which double strand breaks on one chromosome are converted to single stranded ends that can search for the complementary sequence on the homolog. In yeast and mammals, this homology search involves binding of single strand ends by two highly conserved recombinases, Rad51 and the meiosis specific Dmc1. Rad51 is used in mitotic cells to repair breaks, primarily using sister chromatids as templates, while Dmc1 functions in meiosis to generate interhomolog crossovers. In budding yeast, Rad51 strand exchange activity is normally inhibited while Dmc1 is active. We show here that when Rad51 and Dmc1 are active at the same time, Rad51 competes with Dmc1 to mediate interhomolog recombination of a subset of double strand breaks. However, because Rad51- generated recombination intermediates take longer to process, there is a need to keep Rad51 inactive while interhomolog recombination is occurring.

genetics↗

bioRxiv2022

IFN-induced protein with tetratricopeptide repeats 2 (Ifit2) limits autoimmune inflammation by regulating myeloid cell activation and metabolic activity

Besides anti-viral functions, Type I IFN expresses potent anti-inflammatory properties and is being widely used to treat certain autoimmune conditions, such as multiple sclerosis (MS). In murine model of MS, experimental autoimmune encephalomyelitis (EAE), administration of IFN{beta} effectively attenuates the disease development. However, the precise mechanisms underlying the treatment remain elusive. In this study, we report that IFN-induced protein with tetratricopeptide repeats 2 (Ifit2), a type I and type III IFN-stimulated gene, plays a previously unrecognized immune regulatory role during autoimmune neuroinflammation. Mice deficient in Ifit2 display greater susceptibility to EAE and escalated immune cell infiltration in the central nervous system. Ifit2 deficiency is also associated with microglial activation and increased myeloid cell infiltration. Unexpectedly, myelin debris clearance and the subsequent remyelination is impaired in Ifit2-/- CNS tissues. Clearing myelin debris is an important property of reparative M2 type myeloid cells to promote remyelination. Indeed, we observed that bone marrow derived macrophages, CNS infiltrating myeloid cells, and microglia from Ifit2-/- mice express cytokine and metabolic genes associated with proinflammatory M1 type subsets. Taken together, our findings uncover a novel regulatory function of Ifit2 in autoimmune inflammation in part by modulating myeloid cell function and metabolic activity.

immunology↗

bioRxiv2022

Single-nucleus RNA-seq of normal-appearing brain regions in relapsing-remitting vs. secondary progressive multiple sclerosis

Multiple sclerosis (MS) is an immune-mediated demyelinating disease that alters central nervous system (CNS) functions. Relapsing-remitting MS (RRMS) is the most common form, which can transform into secondary-progressive MS (SPMS) that is associated with progressive neurodegeneration. Single-nucleus RNA sequencing (snRNA-seq) of MS lesions identified disease-related transcriptomic alterations; however, their relationship to non-lesioned MS brain regions has not been reported and which could identify prodromal or other disease susceptibility signatures. Here, snRNA-seq was used to generate high-quality RRMS vs. SPMS datasets of 33,197 nuclei from 8 normal-appearing MS brains, which revealed divergent cell type-specific changes. Notably, SPMS brains downregulated astrocytic sphingosine kinases (SPHK1/2) - the enzymes required to phosphorylate and activate the MS drug, fingolimod. This reduction was modeled with astrocyte-specific Sphk1/2 null mice in which fingolimod lost activity, supporting functionality of observed transcriptomic changes. These data provide an initial resource for studies of single cells from non-lesioned RRMS and SPMS brains.

neuroscience↗

bioRxiv2020

Phenotypic and molecular characterization of extended spectrum β-lactamase producing Escherichia coli and Klebsiella pneumoniae isolates from various samples of animal origin from Assam, India

Extended-spectrum beta-lactamase (ESBL) producing Enterobacteriaceae has become a major threat globally. Here we have characterized ESBL producing E. coli and K. pneumoniae from various sources, studied antibiogram and resistance gene profiles. Out of 385 samples, 31 (8.05%) were positive for ESBL producing E. coli. Such isolates could be recovered from 10.05, 8.33, 15.63, 6.67 and 4.35 per cent of cattle milk, curd, chicken, pork and cattle faeces samples, respectively. A total of 59 (15.32%) samples were positive for ESBL producing K. pneumoniae, which were isolated from 14.35, 6.25, 21.43 and 34.78 per cent cattle milk, chicken, beef and cattle faeces, respectively. All the 90 isolates were confirmed as ESBL producers by CDT and ESBL-E strip tests. Antibiogram revealed that 74.19% and 69.49% of the ESBL producing E. coli and K. pneumoniae isolates, respectively showed resistance to ceftizoxime, 25.81% and 23.73% to both co-trimoxazole and tetracycline, 19.35% and 25.42% to ciprofloxacin, 9.68% and 16.95% to chloramphenicol, 3.23% and 5.08% to pipercillin-tazobactam, and 3.23% and 3.39% to gentamicin. Resistance gene profiling showed blaCTX-M gene as most predominant (100%). The blaTEM gene was found in 54.84% and 55.93%, blaSHV gene in 90.32% and 77.97%, Sul 1 gene in 90.32% and 86.44% of ESBL producing E. coli and K. pneumoniae isolates, respectively. The Int1 gene was detected in 70.97% and 62.71% isolates, while qnrB gene was found in 3.23% and 10.17% of E. coli and K. pneumoniae isolates, respectively.

molecular biology↗

bioRxiv2020

Overcoming the inhibitory microenvironment surrounding oligodendrocyte progenitor cells following demyelination

Chronic demyelination in the human CNS is characterized by an inhibitory microenvironment that impairs recruitment and differentiation of oligodendrocyte progenitor cells (OPCs) leading to failed remyelination and axonal atrophy. By network-based transcriptomics, we identified sulfatase 2 (Sulf2) mRNA in activated human primary OPCs. Sulf2, an extracellular endosulfatase, modulates the signaling microenvironment by editing the pattern of sulfation on heparan sulfate proteoglycans. We found that Sulf2 was increased in demyelinating lesions in multiple sclerosis and was actively secreted by human OPCs. In experimental demyelination, elevated OPC Sulf1/2 expression directly impaired progenitor recruitment and subsequent generation of oligodendrocytes thereby limiting remyelination. Sulf1/2 potentiates the inhibitory microenvironment by promoting BMP and WNT signaling in OPCs. Importantly, pharmacological sulfatase inhibition using PI-88 accelerated oligodendrocyte recruitment and remyelination by blocking OPC-expressed sulfatases. Our findings define an important inhibitory role of Sulf1/2 and highlight the potential for modulation of the heparanome in the treatment of chronic demyelinating disease.

neuroscience↗

bioRxiv2019

Mating enhances immune function of Drosophila melanogaster populations against bacterial pathogens

Immunity and reproduction are two important processes that affect fitness of an organisms. Sexual activity has been previously shown to determine the degree to which a population is able to survive various infections. While many studies have demonstrated a trade-off between immune function and reproduction, many studies have found synergistic relation between the two fitness determinants. Besides it is generally hypothesised that sexes may differ in immunity due to relative cost they incur during reproduction with males losing in immunity to rather increase their reproductive success. In this study, we test the effect of immune function on the survival of mated and virgin replicates of a large outbred baseline D. melanogaster population that was infected with four different bacterial infections. We find enhanced survival in mated flies than virgin flies in response to all four bacterial infections across all replicates. While investigating sexual dimorphism in immune function, we find no difference in sexes in their ability to survive the imposed bacterial infections. Synergistic interaction between reproduction and immunity may exist if it improves Darwinian fitness of either sexes of a population under selection, and are not necessarily limited by each other due to trade-off over finite resources.

evolutionary biology↗

bioRxiv2019

Molecular epidemiology of Japanese Encephalitis Virus in pig population of Odisha, Assam and Manipur states of India

Japanese encephalitis virus (JEV) comes under the family Flaviviridae and genus flavivirus. It predominantly infects the children under the age of 10 years and the case fatality rate can stretch out as high as 30%. Pigs act as reservoir and amplifying intermediate host for JEV. Recent report suggested longer persistence of JEV in tonsil than in circulation of experimentally infected pigs. The current investigation was conducted to understand the prevalence and molecular epidemiology of JEV infection in pigs in three different geographical sites in India (Odisha, Assam and Manipur). Serum samples were tested by ELISA and RT-PCR for detection of JEV, while only RT-PCR was done in case of tonsils tissues collected from pigs slaughtered in abattoir. Prevalence of JEV was highest in Manipur (25.45% in serum and 10.08% in tonsil) but lower in Assam (3.75% in serum and 0% in tonsils) and Odisha (1.49% in serum and 3.7% in tonsils). The percentage of sero-positivity was found to be 3.75% of IgM and 9.9% of IgG in Assam and Odisha respectively. Genotype III (GIII) of JEV was the dominant genotype and sporadic mutations of S83G, H76P, E78Q, C55S, and S64W along with two consistent mutations V46S and V51I were observed in all the GIII strains. Analysis of the E gene sequence revealed a single mutation, S118N in the GI strain. Older pigs (above 7 months) were found to be infected relatively more (8.6%) than younger pigs (age group 3-7 months). In conclusion, the high JE virus infection rate of pig in the current locations suggests the need for continuous surveillance of this virus in pigs which will ultimately help to adopt an effective control strategy to prevent the spread of JE infection to human.\n\nAuthor summaryJapanese encephalitis is one of the contributing factors in acute encephalitis syndrome cases reported across India as well as Asia. Primarily young naive human population are affected with JEV. The death rate can be as high as 30% and in about 30%-50% surviving population paralysis, brain damage or other serious permanent sequelae may be observed. The viral load gets amplified in pigs and thus plays a crucial role in transmitting the infection in human communities living in close proximity to pig dwelling. The current study was conducted to demonstrate prevalence of JEV in pig population of three geographical regions of India viz. the States of Odisha, Assam and Manipur that have reported JE outbreaks in human population. The current study demonstrates that the rate of infection is 3.28% among pigs in Manipur followed by Assam and Odisha. GIII was found to be the most predominant JEV genotype, while only one GI genotype strain was detected from Odisha region. These findings suggested the need of continuous surveillance of this virus in pigs and proper implementation of human and animal vaccination programme to control the infection.

microbiology↗

bioRxiv2019

Bile acid metabolism is altered in multiple sclerosis and supplementation ameliorates neuroinflammation

Multiple sclerosis (MS) is an inflammatory demyelinating disorder of the CNS. Bile acids are cholesterol metabolites that can signal through receptors on cells throughout the body, including the CNS and immune system. Whether bile acid metabolism is abnormal in MS is unknown. Using global and targeted metabolomic profiling, we identified lower levels of circulating bile acid metabolites in multiple cohorts of adult and pediatric MS patients compared to controls. In white matter lesions from MS brain tissue, we noted the presence of bile acid receptors on immune and glial cells. To mechanistically examine the implications of lower levels of bile acids in MS, we studied the in vitro effects of an endogenous bile acid - tauroursodeoxycholic acid (TUDCA) on astrocyte and microglial polarization. TUDCA prevented neurotoxic (A1) polarization of astrocytes and pro-inflammatory polarization of microglia in a dose-dependent manner. TUDCA supplementation in experimental autoimmune encephalomyelitis reduced severity of disease, based on behavioral and pathological measures. We demonstrate that bile acid metabolism is altered in MS; bile acid supplementation prevents polarization of astrocytes and microglia to neurotoxic phenotypes and ameliorates neuropathology in an animal model of MS. These findings identify dysregulated bile acid metabolism as a potential therapeutic target in MS.

neuroscience↗

bioRxiv2018

Real-time detection of circulating tumor cells in living animals using functionalized large gold nanorods

Optical coherence tomography (OCT) with significant speckle reduction can be used with highly-scattering contrast agents for noninvasive, contrast-enhanced imaging of living tissue at the cellular scale. The advantages of reduced speckle noise and improved targeted contrast can be harnessed to track objects as small as 2 m in vivo, with the potential for cell tracking and counting in living subjects. Here we demonstrate the use of Large Gold Nanorods (LGNRs) as contrast agents for detecting individual micron-sized polystyrene beads and single myeloma cells in blood circulation using speckle modulating-OCT (SM-OCT). This is the first time that OCT has been used to image at the individual cell scale in vivo. This technical capability presents an exciting opportunity for the dynamic detection and quantification of tumor cells circulating in living subjects.

bioengineering↗

bioRxiv2018

Oligodendrocyte Precursor Cells Are Co-Opted by the Immune System to Cross-Present Antigen and Mediate Cytotoxicity

Oligodendrocyte precursor cells (OPCs) are abundant in the adult CNS and can be recruited to form new oligodendrocytes and myelin in response to injury or disease. However, in multiple sclerosis (MS), oligodendrocyte regeneration and remyelination are often incomplete, suggesting that recruitment and maturation of OPCs is impaired. MS and the rodent model experimental autoimmune encephalomyelitis (EAE) are characterized by infiltration of activated T-cells into the CNS. To investigate the mechanisms by which this neuroinflammatory process influences OPC mobilization, we performed in vivo fate tracing in an inflammatory demyelinating animal model. Results of our studies showed that the OPC differentiation and myelin production are inhibited by either adoptive transfer of CNS infiltrating cytokine producing effector T-cells or CNS production of interferon gamma (IFN{gamma}), using an astrocyte specific IFN{gamma} transgene model. In both systems, IFN{gamma} changes the profile of OPCs by inducing functional expression of the immunoproteasome and upregulation of MHC class I. OPCs exposed to IFN{gamma} are shown to cross present exogenous antigen to cytotoxic CD8 T-cells, which then produce proteases and FasL that results in subsequent caspase 3/7 activation and OPC death, both in vitro and in vivo. Cross presentation by OPCs is dependent on the cytosolic processing pathway and can be inhibited by small molecules targeting MHC class I antigen processing and the immunoproteasome subunits. Finally, the immunoproteasome subunit, PSMB8, is shown to be markedly increased on Sox10+ oligodendrocyte lineage cells only in the demyelinated white matter lesions from patients with MS. These findings support the notion that OPCs have multiple functions beyond differentiation into myelinating cells and adapt to their microenvironment by responding to local cues. In MS, OPCs may be co-opted by the immune system to perpetuate the autoimmune response. Strategies aimed at inhibiting the aberrant immune activation pathways in OPCs may allow more efficient remyelination in MS.

neuroscience↗

bioRxiv2018

The role of sexual conflict, sexual selection and ancestry in the evolution of chemical sexual signals

The ability of interlocus sexual conflict to facilitate reproductive isolation is widely anticipated. However, very few experimental evolutionary studies have convincingly demonstrated the evolution of reproductive isolation due to sexual conflict. Recently a study on replicate populations of Drosophila melanogaster under differential sexual conflict found that divergent mate preference evolved among replicate populations under high sexual conflict regime. The precopulatory isolating mechanism underlying such divergent mate preference could be sexual signals such as cuticular hydrocarbons since they evolve rapidly and are involved in D. melanogaster mate recognition. Using D. melanogaster replicates used in the previous study, we investigate whether cuticular hydrocarbon divergence bears signatures of sexually antagonistic coevolution that led to reproductive isolation among replicates of high sexual conflict regime. We found that D. melanogaster cuticular hydrocarbon profiles are sexually dimorphic. Although replicate populations under high sexual conflict displayed assortative mating, we found no significant differences in the cuticular hydrocarbon profile between the high and low sexual conflict regimes. Instead we find cuticular hydrocarbon divergence patterns to be suggestive of the Buridans Ass regime which is one of the six possible mechanisms to resolve sexual conflict. Sexual selection that co-vary between populations under high and low sexual conflict regimes may also have contributed to the evolution of cuticular hydrocarbons. This study indicates that population differentiation as a result of cuticular hydrocarbon divergence cannot be credited to sexual conflict despite high sexual conflict regime evolving divergent cuticular hydrocarbon profiles.

evolutionary biology↗

bioRxiv2018

Gold Nanoprisms as Optical Coherence Tomography Contrast Agents in the Second Near Infrared Window for Enhanced Angiography in Live Animals

Optical coherence tomography angiography (OCTA) is an important tool for investigating vascular networks and microcirculation in living tissue. Traditional OCTA detects blood vessels via intravascular dynamic scattering signals derived from the movements of red blood cells (RBCs). However, the low hematocrit and long latency between RBCs in capillaries makes these OCTA signals discontinuous, leading to incomplete mapping of the vascular networks. OCTA imaging of microvascular circulation is particularly challenging in tumors due to the abnormally slow blood flow in angiogenic tumor vessels and strong attenuation of light by tumor tissue. Here we demonstrate in vivo that gold nanoprisms (GNPRs) can be used as OCT contrast agents working in the second near infrared window, significantly enhancing the dynamic scattering signals in microvessels and improving the sensitivity of OCTA in skin tissue and melanoma tumors in live mice. This is the first demonstration that nanoparticle-based OCT contrast agent work in vivo in the second near infrared window, which allows deeper imaging depth by OCT. With GNPRs as contrast agents, the post-injection OCT angiograms showed 41% and 59% more microvasculature than pre-injection angiograms in healthy mouse skin and melanoma tumors, respectively. By enabling better characterization of microvascular circulation in vivo, GNPR-enhanced OCTA could lead to better understanding of vascular functions during pathological conditions, more accurate measurements of therapeutic response, and improved patient prognoses.

bioengineering↗

bioRxiv2018

High-resolution wide-field human brain tumor margin detection and in vivo murine neuroimaging

Current in vivo neuroimaging techniques provide limited field of view or spatial resolution and often require exogenous contrast. These limitations prohibit detailed structural imaging across wide fields of view and hinder intraoperative tumor margin detection. Here we present a novel neuroimaging technique, speckle-modulating optical coherence tomography (SM-OCT), which allows us to image the brains of live mice and ex vivo human samples with unprecedented resolution and wide field of view using only endogenous contrast. The increased effective resolution provided by speckle elimination reveals white matter fascicles and cortical layer architecture in the brains of live mice. To our knowledge, the data reported herein represents the highest resolution imaging of murine white matter structure achieved in vivo across a wide field of view of several millimeters. When applied to an orthotopic murine glioblastoma xenograft model, SM-OCT readily identifies brain tumor margins with near single-cell resolution. SM-OCT of ex vivo human temporal lobe tissue reveals fine structures including cortical layers and myelinated axons. Finally, when applied to an ex vivo sample of a low-grade glioma resection margin, SM-OCT is able to resolve the brain tumor margin. Based on these findings, SM-OCT represents a novel approach for intraoperative tumor margin detection and in vivo neuroimaging.

bioengineering↗

bioRxiv2017

Wide-field dynamic monitoring of immune cell trafficking in murine models of glioblastoma

Leukocyte populations, especially tumor-associated macrophages (TAMs), are capable of mediating both anti- and pro-tumor processes and play significant roles in the tumor microenvironment. Moreover, TAMs have been shown to exert substantial influence on the efficacy of various cancer immunotherapy treatment strategies. Laboratory investigation into the behavior of TAMs has been limited by a lack of methods capable of resolving the in vivo distribution and dynamics of this cell population across wide fields of view. Recent studies have employed magnetic resonance imaging and intravital microscopy in conjunction with nanoparticle labeling methods to detect TAMs and observe their responses to therapeutic agents. Here we describe a novel method to enable high-resolution, wide-field, longitudinal imaging of leukocytes based on contrast-enhanced Speckle-Modulating Optical Coherence Tomography (SM-OCT), which substantially reduces imaging noise. We were able to specifically label TAMs and activated microglia in vivo with large gold nanorod contrast agents (LGNRs) in an orthotopic murine glioblastoma model. After labeling, we demonstrated near real-time tracking of leukocyte migration and distribution within the tumors. The intrinsic resolution, imaging depth, and sensitivity of this method may facilitate detailed studies of the fundamental behaviors of TAMs in vivo, including their intratumoral distribution heterogeneity and the roles they play in modulating cancer proliferation. In future studies, the method described herein may also provide the necessary means to characterize TAM responses to immunotherapeutic regimens in a range of solid tumors.

bioengineering↗