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Mukherjee, B.

Publications and source records attributed to Mukherjee, B..

32 records · Page 2Linked to original sources

Asymmetric dysregulation of glutamate dynamics across the synaptic cleft in a mouse model of Alzheimer disease

Most research on glutamate spillover focuses on the deleterious consequences of postsynaptic glutamate receptor overactivation. However, two decades ago, it was noted that the glial coverage of hippocampal synapses is asymmetric: astrocytic coverage of postsynaptic sites exceeds coverage of presynaptic sites by a factor of four. The fundamental relevance of this glial asymmetry remains poorly understood. Here, we used the glutamate biosensor iGluSnFR, and restricted its expression to either CA3 or CA1 neurons to visualize glutamate dynamics at pre- and postsynaptic microenvironments, respectively. We demonstrate that inhibition of the primarily astrocytic glutamate transporter-1 (GLT-1) slows glutamate clearance to a greater extent at presynaptic compared to postsynaptic membranes. GLT-1 expression was reduced early in a mouse model of AD, resulting in slower glutamate clearance rates at presynaptic but not postsynaptic membranes that opposed presynaptic short-term plasticity. Overall, our data demonstrate that the presynapse is particularly vulnerable to GLT-1 dysfunction and may have implications for presynaptic impairments in a variety of brain diseases.

neuroscience↗

Sparse Sonomyography-based Estimation of Isometric Force: A Comparison of Methods and Features

Noninvasive methods for estimation of joint and muscle forces have widespread clinical and research applications. Surface electromyography or sEMG provides a measure of the neural activation of muscles which can be used to estimate the force produced by the muscle. However, sEMG based measures of force suffer from poor signal-to-noise ratio and limited spatiotemporal specificity. In this paper, we propose an ultrasound imaging or sonomyography-based approach for estimating continuous isometric force from a sparse set of ultrasound scanlines. Our approach isolates anatomically relevant features from A-mode ultrasound signals, greatly reducing the dimensionality of the feature space and the computational complexity involved in traditional ultrasound-based methods. We evaluate the performance of four regression methodologies for force prediction using the reduced feature set. We also evaluate the feasibility of a practical wearable sonomyography-based system by simulating the effect of transducer placement and varying the number of transducers used in force prediction. Our results demonstrate that Gaussian process regression models outperform other regression methods in predicting continuous force levels from just four equispaced transducers and are tolerant to speckle noise. These findings will aid in the design of wearable sonomyography-based force prediction systems with robust, computationally efficient operation.

bioengineering↗

Thermodynamics of droplets undergoing liquid-liquid phase separation

We study the thermodynamics of binary mixtures wherein the volume fraction of the minority component is less than the amount required to form a flat interface. Based on an explicit microscopic mean field theory, we show that the surface tension dominated equilibrium phase of a polymer mixture forms a single macroscopic droplet. A combination of elastic interactions that renormalize the surface tension, and arrests phase separation for a gel-polymer mixture, stabilize a micro-droplet phase. We compute the droplet size as a function of the interfacial tension, Flory parameter, and elastic moduli of the gel. Our results illustrate the importance of the rheological properties of the solvent in dictating the thermodynamic phase behavior of biopolymers undergoing liquid-liquid phase separation.

biophysics↗

Regulatory adenylnucleotide-mediated binding of the PII-like protein SbtB to the cyanobacterial bicarbonate transporter SbtA is controlled by the cellular energy state

Cyanobacteria have evolved a remarkably powerful CO2 concentrating mechanism (CCM), enabling high photosynthetic rates in environments with limited inorganic carbon (Ci). Therefore, this CCM is a promising system for integration into higher plant chloroplasts to boost photosynthetic efficiency and yield. The CCM depends on active Ci uptake, facilitated by bicarbonate transporters and CO2 pumps, to elevate CO2 concentration around the active sites of the primary CO2 fixing enzyme, Rubisco, which is encapsulated in cytoplasmic micro-compartments (carboxysomes). The essential CCM proteins have been identified, but the molecular signals and regulators that coordinate function in response to light, Ci availability and other environmental cues are largely unknown. Here, we provide evidence, based on a novel in vitro binding system, for a role of the PII-like SbtB protein in regulating Ci uptake by the bicarbonate transporter, SbtA, in response to the cellular adenylate energy charge (AEC) through dynamic protein-protein interaction. Binding of the SbtA and SbtB proteins from two phylogenetically distant species, Cyanobium sp. PCC7001 and Synechococcus elongatus PCC7942, was inhibited by high ATP, and promoted by low [ATP]:[ADP or AMP] ratios in vitro, consistent with a sensory response to the AEC mediated through adenylnucleotide ligand-specific conformation changes in SbtB. In vivo, cell cultures of S. elongatus showed up to 70% SbtB-dependent down-regulation of SbtA bicarbonate uptake activity specifically in the light activation phase during transitions from dark to low light when low cellular AEC is expected to limit metabolic activity. This suggests SbtB may function as a curfew protein during prolonged low cellular AEC and photosynthetically unfavourable conditions to prevent energetically futile and physiologically disadvantageous activation of SbtA.

plant biology↗

Heterogenous adhesion of follower cells affects tension profile and velocity of leader cells in primary keratocyte collective cell migration

Single cell studies demonstrate membrane tension to be a central regulator of lamellipodia-driven motility bringing in front-coherence. During collective cell migration, however, tension mapping or existence of intracellular tension-gradients and the effect of cell-cell interactions have remained unexplored. In this study of membrane fluctuations and fluctuation-tension of migrating primary keratocyte cell-sheets, we first show that some leader cells are followed by followers which remain de-adhered from the substrate while being attached to other cells and thus appear to be "taking a ride". A subtle yet significant enhanced long-timescale velocity in these leaders indicate increased directionality. Intriguingly, such leaders mostly have front-high tension gradients like single keratocytes, while followers and other leaders usually display front-low membrane tension gradients. The front-high tension gradient and higher membrane tension observed in these leaders, despite the high cell-to-cell variability in membrane tension demonstrate how leader-follower interactions and heterogenous adhesion profiles are key in collective cell migration.

biophysics↗

Efficient mixed model approach for large-scale genome-wide association studies of ordinal categorical phenotypes

In genome-wide association studies (GWAS), ordinal categorical phenotypes are widely used to measure human behaviors, satisfaction, and preferences. However, due to the lack of analysis tools, methods designed for binary and quantitative traits have often been used inappropriately to analyze categorical phenotypes, which produces inflated type I error rates or is less powerful. To accurately model the dependence of an ordinal categorical phenotype on covariates, we propose an efficient mixed model association test, Proportional Odds Logistic Mixed Model (POLMM). POLMM is demonstrated to be computationally efficient to analyze large datasets with hundreds of thousands of genetic related samples, can control type I error rates at a stringent significance level regardless of the phenotypic distribution, and is more powerful than other alternative methods. We applied POLMM to 258 ordinal categorical phenotypes on array-genotypes and imputed samples from 408,961 individuals in UK Biobank. In total, we identified 5,885 genome-wide significant variants, of which 424 variants (7.2%) are rare variants with MAF < 0.01.

genetics↗

Cancer PRSweb - an Online Repository with Polygenic Risk Scores (PRS) for Major Cancer Traits and Their Phenome-wide Exploration in Two Independent Biobanks

To facilitate scientific collaboration on polygenic risk scores (PRS) research, we created an extensive PRS online repository for 49 common cancer traits integrating freely available genome-wide association studies (GWAS) summary statistics from three sources: published GWAS, the NHGRI-EBI GWAS Catalog, and UK Biobank-based GWAS. Our framework condenses these summary statistics into PRS using various approaches such as linkage disequilibrium pruning / p-value thresholding (fixed or data-adaptively optimized thresholds) and penalized, genome-wide effect size weighting. We evaluated the PRS in two biobanks: the Michigan Genomics Initiative (MGI), a longitudinal biorepository effort at Michigan Medicine, and the population-based UK Biobank (UKB). For each PRS construct, we provide measures on predictive performance, calibration, and discrimination. Besides PRS evaluation, the Cancer-PRSweb platform features construct downloads and phenome-wide PRS association study results (PRS-PheWAS) for predictive PRS. We expect this integrated platform to accelerate PRS-related cancer research.

genetics↗

Structural basis for the allosteric regulation of the SbtA bicarbonate transporter by the PII-like protein, SbtB, from Cyanobium sp. PCC7001

Cyanobacteria have evolved a suite of enzymes and inorganic carbon (Ci) transporters that improve photosynthetic performance by increasing the localized concentration of CO2 around the primary CO2-fixating enzyme, Rubisco. This CO2-concentrating mechanism (CCM) is highly regulated, responds to illumination/darkness cycles and allows cyanobacteria to thrive under limiting Ci conditions. While the transcriptional control of CCM activity is well understood, less is known about how regulatory proteins might allosterically regulate Ci transporters in response to changing conditions. Cyanobacterial sodium-dependent bicarbonate transporters (SbtAs) are inhibited by PII-like regulatory proteins (SbtBs), with the inhibitory effect being modulated by adenylnucleotides. Here, we used isothermal titration calorimetry to show that SbtB from Cyanobium sp. PCC7001 (SbtB7001) binds AMP, ADP, cAMP and ATP with micromolar-range affinities. X-ray crystal structures of apo- and nucleotide-bound SbtB7001 revealed that while AMP, ADP and cAMP have little effect on the SbtB7001 structure, binding of ATP stabilizes the otherwise flexible T-loop and that the flexible C-terminal C-loop adopts several distinct conformations. We also show that ATP binding affinity is increased ten-fold in the presence of Ca2+ and we present an X-ray crystal structure of Ca2+ATP:SbtB7001 that shows how this metal ion facilitates additional stabilizing interactions with the apex of the T-loop. We propose that the Ca2+ATP-induced conformational change observed in SbtB7001 is important for allosteric regulation of SbtA activity by SbtB and is consistent with changing adenylnucleotide levels in illumination/darkness cycles.\n\nGRAPHICAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC=\"FIGDIR/small/762807v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (43K):\norg.highwire.dtl.DTLVardef@99bac2org.highwire.dtl.DTLVardef@b43082org.highwire.dtl.DTLVardef@1dcac4borg.highwire.dtl.DTLVardef@b38ea1_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

A Modeling Framework for Exploring Sampling and Observation Process Biases in Genome and Phenome-wide Association Studies using Electronic Health Records

Large-scale agnostic association analyses based on existing observational health care databases such as electronic health records have been a topic of increasing interest in the scientific community. However, particular challenges of non-probability sampling and phenotype misclassification associated with the use of these data sources are often ignored in standard analyses. In general, the extent of the bias that may be introduced by ignoring these factors is unknown. In this paper, we develop a statistical framework for characterizing the degree of bias expected in association studies based on electronic health records when disease status misclassification and the sampling mechanism are ignored. Through a sensitivity analysis type approach, this framework can be used to obtain plausible values for parameters of interest given results obtained from standard naive analysis methods under varying degree of misclassification and sampling biases. We develop an online tool for performing this sensitivity analysis in some special cases that occur frequently. Simulations demonstrate promising properties of the proposed way of characterizing biases. We apply our approach to study bias in genetic association studies using data from the Michigan Genomics Initiative, a longitudinal biorepository effort within Michigan Medicine.

epidemiology↗

Bayesian Shrinkage Estimation of High Dimensional Causal Mediation Effects in Omics Studies

Causal mediation analysis aims to examine the role of a mediator or a group of mediators that lie in the pathway between an exposure and an outcome. Recent biomedical studies often involve a large number of potential mediators based on high-throughput technologies. Most of the current analytic methods focus on settings with one or a moderate number of potential mediators. With the expanding growth of omics data, joint analysis of molecular-level genomics data with epidemiological data through mediation analysis is becoming more common. However, such joint analysis requires methods that can simultaneously accommodate high-dimensional mediators and that are currently lacking. To address this problem, we develop a Bayesian inference method using continuous shrinkage priors to extend previous causal mediation analysis techniques to a high-dimensional setting. Simulations demonstrate that our method improves the power of global mediation analysis compared to simpler alternatives and has decent performance to identify true non-null mediators. We also construct tests for natural indirect effects using a permutation procedure. The Bayesian method helps us to understand the structure of the composite null hypotheses. We applied our method to Multi-Ethnic Study of Atherosclerosis (MESA) and identified DNA methylation regions that may actively mediate the effect of socioeconomic status (SES) on cardiometabolic outcome.

epidemiology↗

Proprioceptive Sonomyographic Control: A novel method of intuitive proportional control of multiple degrees of freedom for upper-extremity amputees

Technological advances in multi-articulated prosthetic hands have outpaced the methods available to amputees to intuitively control these devices. Amputees often cite difficulty of use as a key contributing factor for abandoning their prosthesis, creating a pressing need for improved control technology. A major challenge of traditional myoelectric control strategies using surface electromyography electrodes has been the difficulty in achieving intuitive and robust proportional control of multiple degrees of freedom. In this paper, we describe a new control method, proprioceptive sonomyographic control that overcomes several limitations of myoelectric control. In sonomyography, muscle mechanical deformation is sensed using ultrasound, as compared to electrical activation, and therefore the resulting control signals can directly control the position of the end effector. Compared to myoelectric control which controls the velocity of the end-effector device, sonomyographic control is more congruent with residual proprioception in the residual limb. We tested our approach with 5 upper-extremity amputees and able-bodied subjects using a virtual target achievement and holding task. Amputees and able-bodied participants demonstrated the ability to achieve positional control for 5 degrees of freedom with an hour of training. Our results demonstrate the potential of proprioceptive sonomyographic control for intuitive dexterous control of multiarticulated prostheses.

bioengineering↗

Exploring Various Polygenic Risk Scores for Basal Cell Carcinoma, Cutaneous Squamous Cell Carcinoma and Melanoma in the Phenomes of the Michigan Genomics Initiative and the UK Biobank

Polygenic risk scores (PRS) are designed to serve as a single summary measure, condensing information from a large number of genetic variants associated with a disease. They have been used for stratification and prediction of disease risk. The construction of a PRS often depends on the purpose of the study, the available data/summary estimates, and the underlying genetic architecture of a disease. In this paper, we consider several choices for constructing a PRS using summary data obtained from various publicly-available sources including the UK Biobank and evaluate their abilities to predict outcomes derived from electronic health records (EHR). Weexamine the three most common skin cancer subtypes in the USA: basal cellcarcinoma, cutaneous squamous cell carcinoma, and melanoma. The genetic risk profiles of subtypes may consist of both shared and unique elements and we construct PRS to understand the common versus distinct etiology. This study is conducted using data from 30,702 unrelated, genotyped patients of recent European descent from the Michigan Genomics Initiative (MGI), a longitudinal biorepository effort within Michigan Medicine. Using these PRS for various skin cancer subtypes, we conduct a phenome-wide association study (PheWAS) within the MGI data to evaluate their association with secondary traits. PheWAS results are then replicated using population-based UK Biobank data. We develop an accompanying visual catalog called PRSweb that provides detailed PheWAS results and allows users to directly compare different PRS construction methods. The results of this study can provide guidance regarding PRS construction in future PRS-PheWAS studies using EHR data involving disease subtypes.\n\nAuthor summaryIn the study of genetically complex diseases, polygenic risk scores synthesize information from multiple genetic risk factors to provide insight into a patients risk of developing a disease based on his/her genetic profile. These risk scores can be explored in conjunction with health and disease information available in the electronic medical records. They may be associated with diseases that may be related to or precursors of the underlying disease of interest. Limited work is available guiding risk score construction when the goal is to identify associations across the medical phenome. In this paper, we compare different polygenic risk score construction methods in terms of their relationships with the medical phenome. We further propose methods for using these risk scores to decouple the shared and unique genetic profiles of related diseases and to explore related diseases shared and unique secondary associations. Leveraging and harnessing the rich data resources of the Michigan Genomics Initiative, a biorepository effort at Michigan Medicine, and the larger population-based UK Biobank study, we investigated the performance of genetic risk profiling methods for the three most common types of skin cancer: melanoma, basal cell carcinoma and squamous cell carcinoma.

genetics↗

Subset-Based Analysis using Gene-Environment Interactions for Discovery of Genetic Associations across Multiple Studies or Phenotypes

ObjectivesClassical methods for combining summary data from genome-wide association studies (GWAS) only use marginal genetic effects and power can be compromised in the presence of heterogeneity. We aim to enhance the discovery of novel associated loci in the presence of heterogeneity of genetic effects in sub-groups defined by an environmental factor.\n\nMethodsWe present a p-value Assisted Subset Testing for Associations (pASTA) framework that generalizes the previously proposed association analysis based on subsets (ASSET) method by incorporating gene-environment (G-E) interactions into the testing procedure. We conduct simulation studies and provide two data examples.\n\nResultsSimulation studies show that our proposal is more powerful than methods based on marginal associations in the presence of G-E interactions and maintains comparable power even in their absence. Both data examples demonstrate that our method can increase power to detect overall genetic associations and identify novel studies/phenotypes that contribute to the association.\n\nConclusionsOur proposed method can be a useful screening tool to identify candidate single nucleotide polymorphisms (SNPs) that are potentially associated with the trait(s) of interest for further validation. It also allows researchers to determine the most probable subset of traits that exhibit genetic associations in addition to the enhancement of power.

genetics↗

Association of Polygenic Risk Scores for Multiple Cancers in a Phenome-wide Study: Results from The Michigan Genomics Initiative

Health systems are stewards of patient electronic health record (EHR) data with extraordinarily rich depth and breadth, reflecting thousands of diagnoses and exposures. Measures of genomic variation integrated with EHRs offer a potential strategy to accurately stratify patients for risk profiling and discover new relationships between diagnoses and genomes. The objective of this study was to evaluate whether Polygenic Risk Scores (PRS) for common cancers are associated with multiple phenotypes in a Phenome-wide Association Study (PheWAS) conducted in 28,260 unrelated, genotyped patients of recent European ancestry who consented to participate in the Michigan Genomics Initiative, a longitudinal biorepository effort within Michigan Medicine. PRS for 12 cancer traits were calculated using summary statistics from the NHGRI-EBI catalog. A total of 1,711 synthetic case-control studies was used for PheWAS analyses. There were 13,490 (47.7%) patients with at least one cancer diagnosis in this study sample. PRSs exhibited strong association for several cancer traits they were designed for including female breast cancer, prostate cancer, melanoma, basal cell carcinoma, squamous cell carcinoma and thyroid cancer. Phenome-wide significant associations were observed between PRS and many non-cancer diagnoses. To differentiate PRS associations driven by the primary trait from associations arising through shared genetic risk profiles, the idea of \"exclusion PRS PheWAS\" was introduced. This approach led to phenome-wide significant associations between a lower risk for hypothyroidism in patients with high thyroid cancer PRS and a higher risk for actinic keratosis in patients with high squamous cell carcinoma PRS after removing all cases of the primary cancer trait. Further analysis of temporal order of the diagnoses improved our understanding of these secondary associations. This is the first comprehensive PheWAS study using PRS instead of a single variant.

genetics↗