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Biology subjects

Basu, A.

Publications and source records attributed to Basu, A..

At least 55 records · Page 3Linked to original sources

Frontal cortex norepinephrine, serotonin, and dopamine dynamics in an innate fear-reward behavioral model

Animals must survive by foraging for food in an uncertain and dangerous world. Neural circuits for naturalistic decision-making under these conditions must balance competing motivational demands for approaching reward and avoiding danger. To enable flexible switching between motivational states, neuromodulators are released and alter neural excitability and plasticity. The question of how neuromodulators encode motivational state is thus fundamental to systems neuroscience, yet the dynamics of neuromodulators during naturalistic decision making are not fully understood. Here, we developed a naturalistic approach/avoidance task in mice involving a tradeoff between seeking reward versus safety in the presence of looming predation risk. We utilized fiber photometry, computational behavior tracking, and local pharmacology in this task. Silencing medial prefrontal cortex (mPFC) reduced looming defensive behaviors. Moreover, by using fiber photometry combined with GPCR-based sensors, we found that cortical norepinephrine (NE) plays a more prominent role in encoding looming threats while dopamine (DA) represents reward and threat. In contrast, serotonin (5HT) dynamic negatively correlates to both emotional valences. To begin to understand neuromodulatory interactions, we used ex vivo slice physiology to understand 5HT impact on spontaneous firing of locus coeruleus NE neurons. In conclusion, monoamines such as NE, DA, 5HT can converge in their encoding of naturalistic motivated behaviors as well as dissociate from one another. By utilizing this novel innate reward-threat task, we can better understand neurochemical signaling events during natural behavior, and may contribute to the understanding of neural mechanisms underlying emotional decision-making and its implications for psychiatric disorders.

neuroscience↗

Untangling the Role of Pathobionts from Bacteroides Species in Inflammatory Bowel Diseases

Inflammatory bowel diseases (IBD) arise from a convergence of underlying genetic susceptibility, environmental factors, and shifts in gut microbiota function and membership. Although the latter may trigger and contribute to IBD, there is little consensus on a specific causative pathogen. In this study, we demonstrate that commensal Bacteroides fragilis strains from ulcerative colitis (UC) patients before and during the development of ileal pouchitis engraft and promote colitis in specific pathogen free (SPF) IL-10 deficient (IL-10-/-) mice, but not in wild type SPF mice or when mono-associated in germ free mice. The colitis in IL-10-/- mice was also associated with significant alterations in commensal microbiota potentially important for maintaining intestinal and immune homeostasis. UC pouchitis B. fragilis also engrafts in DSS-induced colitis in WT SPF mice, indicating a fitness advantage under conditions of mucosal inflammation over other commensals in the gut microbiota. These findings show that gut inflammation promotes the expansion and fitness of UC-derived Bacteroides species that is associated with changes in the SPF gut microbiota and may be promote colitis in genetically susceptible hosts. ImportanceThis study supports the notion that human inflammatory bowel diseases arise from the emergence of indigenous pathobionts in genetically-prone subjects. Colitis-promoting pathobionts are well-suited to establish themselves in the host inflammatory environment and outcompete endogenous microbiota. Once engrafted, the pathobiont can further aggravate inflammation in a genetically-susceptible host. Such complex interplay among several factors creates a vicious pro-inflammatory cycle and promotes disease development. These findings are consistent with our previous clinical observation that B. fragilis, an otherwise low-abundance commensal species, expands prior to the development of UC pouchitis. We believe these findings are relevant to the pathogenesis of UC pouchitis and possibly human inflammatory bowel diseases in general, underscoring the role of commensal to pathobiont transitions, rather than classical pathogens, in promoting and exacerbating the onset of human IBD.

microbiology↗

Exploring the tumor micro-environment in ovarian cancer histotypes and tumor sites

Ovarian cancer is a highly heterogeneous disease consisting of at least five different histological subtypes with varying clinical features, cells of origin, molecular composition, risk factors, and treatments. While most single-cell studies have focused on High grade serous ovarian cancer, a comprehensive landscape of the constituent cell types and their interactions within the tumor microenvironment are yet to be established in the different ovarian cancer histotypes. Further characterization of tumor progression, metastasis, and various histotypes are also needed to connect molecular signatures to pathological grading for personalized diagnosis and tailored treatment. In this study, we leveraged high-resolution single-cell RNA sequencing technology to elucidate the cellular compositions on 21 solid tumor samples collected from 12 patients with six ovarian cancer histotypes and both primary (ovaries) and metastatic (omentum, rectum) sites. The diverse collection allowed us to deconstruct the histotypes and tumor site-specific expression patterns of cells in the tumor and identify key marker genes and ligand-receptor pairs that are active in the ovarian tumor microenvironment. Our findings can be used in improving precision disease stratification and optimizing treatment options.

cancer biology↗

Taking time to compose thoughts with prefrontal schemata

Under what conditions can prefrontal cortex direct the composition of brain states, to generate coherent streams of thoughts? Using a simplified Potts model of cortical dynamics, crudely differentiated into two halves, we show that once activity levels are regulated, so as to disambiguate a single temporal sequence, whether the contents of the sequence are mainly determined by the frontal or by the posterior half, or by neither, depends on statistical parameters that describe its microcircuits. The frontal cortex tends to lead if it has more local attractors, longer-lasting and stronger ones, in order of increasing importance. Its guidance is particularly effective to the extent that posterior cortices do not tend to transition from state to state on their own. The result may be related to prefrontal cortex enforcing its temporally-oriented schemata driving coherent sequences of brain states, unlike the atemporal "context" contributed by the hippocampus. Modelling a mild prefrontal (vs. posterior) lesion offers an account of mind-wandering and event construction deficits observed in prefrontal patients.

neuroscience↗

A Deep Learning Approach for Modelling the Complex Relationship between Environmental Factors and Biological Features

Environmental factors play a pivotal role in shaping the genetic and phenotypic diversity among organisms. Understanding the influence of the environment on a biological phenomenon is essential for deciphering the mechanisms resulting in trait differences among organisms. In this study, we present a novel approach utilizing an Artificial Neural Network (ANN) model to investigate the impact of environmental factors on a wide range of biological phenomena. Our proposed workflow includes hyperparameter optimization using model-based methods such as Bayesian and direct-search methods such as Random Search, and a new approach combining random search and linear models (RandomSearch+lm) to ensure a robust ANN architecture. Moreover, we employed a generalized version of the variable importance method to generate the feature importance metric using estimated weights from ANN. By applying this comprehensive ANN-based approach to functional genomics, we can gain valuable insights into the mechanisms underlying trait differentiation in organisms, while simultaneously enabling prediction and feature selection tasks. This methodology provides a robust and efficient framework for studying the complex relationships between environmental factors and biological features in biological systems.

genomics↗

Multi-omics analysis of a Bacteroides fragilis isolate from an ulcerative colitis patient defines genetic determinants of fitness in bile

Bacteroides fragilis comprises 1-5% of the gut microbiota in healthy humans but can expand to >50% of the population in ulcerative colitis (UC) patients experiencing inflammation. The mechanisms underlying such microbial blooms are poorly understood, but the gut of UC patients has physicochemical features that differ from healthy patients and likely impact microbial physiology. For example, levels of the secondary bile acid deoxycholate (DC) are highly reduced in the ileoanal J-pouch of UC colectomy patients. We isolated a B. fragilis strain from a UC patient with pouch inflammation (i.e. pouchitis) and developed it as a genetic model system to identify genes and pathways that are regulated by DC and that impact B. fragilis fitness in DC and crude bile. Treatment of B. fragilis with a physiologically relevant concentration of DC reduced cell growth and remodeled transcription of one-quarter of the genome. DC strongly induced expression of chaperones and select transcriptional regulators and efflux systems and downregulated protein synthesis genes. Using a barcoded collection of {approx}50,000 unique insertional mutants, we further defined B. fragilis genes that contribute to fitness in media containing DC or crude bile. Genes impacting cell envelope functions including cardiolipin synthesis, cell surface glycosylation, and systems implicated in sodium-dependent bioenergetics were major bile acid fitness factors. As expected, there was limited overlap between transcriptionally regulated genes and genes that impacted fitness in bile when disrupted. Our study provides a genome-scale view of a B. fragilis bile response and genetic determinants of its fitness in DC and crude bile. ImportanceThe Gram-negative bacterium, Bacteroides fragilis, is a common member of the human gut microbiota that colonizes multiple host niches and can influence human physiology through a variety of mechanisms. Identification of genes that enable B. fragilis to grow across a range of host environments has been impeded in part by the relatively limited genetic tractability of this species. We have developed a high-throughput genetic resource for a B. fragilis strain isolated from a UC pouchitis patient. Bile acids limit microbial growth and are altered in abundance in UC pouches, where B. fragilis often blooms. Using this resource, we uncovered pathways and processes that impact B. fragilis fitness in bile and that may contribute to population expansions during bouts of gut inflammation.

microbiology↗

Computational drug repositioning for the identification of new agents to sensitize drug-resistant breast tumors across treatments and receptor subtypes

Drug resistance is a major obstacle in cancer treatment and can involve a variety of different factors. Identifying effective therapies for drug resistant tumors is integral for improving patient outcomes. In this study, we applied a computational drug repositioning approach to identify potential agents to sensitize primary drug resistant breast cancers. We extracted drug resistance profiles from the I-SPY 2 TRIAL, a neoadjuvant trial for early stage breast cancer, by comparing gene expression profiles of responder and non-responder patients stratified into treatments within HR/HER2 receptor subtypes, yielding 17 treatment-subtype pairs. We then used a rank-based pattern-matching strategy to identify compounds in the Connectivity Map, a database of cell line derived drug perturbation profiles, that can reverse these signatures in a breast cancer cell line. We hypothesize that reversing these drug resistance signatures will sensitize tumors to treatment and prolong survival. We found that few individual genes are shared among the drug resistance profiles of different agents. At the pathway level, however, we found enrichment of immune pathways in the responders in 8 treatments within the HR+HER2+, HR+HER2-, and HR-HER2-receptor subtypes. We also found enrichment of estrogen response pathways in the non-responders in 10 treatments primarily within the hormone receptor positive subtypes. Although most of our drug predictions are unique to treatment arms and receptor subtypes, our drug repositioning pipeline identified the estrogen receptor antagonist fulvestrant as a compound that can potentially reverse resistance across 13/17 of the treatments and receptor subtypes including HR+ and triple negative. While fulvestrant showed limited efficacy when tested in a panel of 5 paclitaxel-resistant breast cancer cell lines, it did increase drug response in combination with paclitaxel in HCC-1937, a triple negative breast cancer cell line.

cell biology↗

Dependence of Nucleosome Mechanical Stability on DNA Mismatches and Histone Variants

The organization of nucleosomes into chromatin and their accessibility are shaped by local DNA mechanics. Conversely, nucleosome positions shape genetic variations, which may originate from mismatches during replication and chemical modification of DNA. To investigate how DNA mismatches affect the mechanical stability and the exposure of nucleosomal DNA, we used an optical trap combined with single-molecule FRET and a single-molecule FRET cyclization assay. We found that a single base-pair C-C mismatch enhances DNA bendability and nucleosome mechanical stability for the 601-nucleosome positioning sequence. An increase in force required for DNA unwrapping from the histone core is observed for single base-pair C-C mismatches placed at three tested positions: at the inner turn, at the outer turn, or at the junction of the inner and outer turn of the nucleosome. The results support a model where nucleosomal DNA accessibility is reduced by mismatches, potentially explaining the preferred accumulation of single nucleotide substitutions in the nucleosome core and serving as the source of genetic variation during evolution and cancer progression. Mechanical stability of an intact nucleosome, i.e., mismatch-free, is also dependent on the species as we find that yeast nucleosomes are mechanically less stable and more symmetrical in the outer turn unwrapping compared to Xenopus nucleosomes.

biophysics↗

Prefrontal norepinephrine represents a threat prediction error under uncertainty

Animals must learn to predict varying threats in the environment to survive by enacting defensive behaviors. Dopamine is involved in the prediction of rewards, encoding a reward prediction error in a similar manner to temporal difference learning algorithm. However, the corresponding molecular and computational form of threat prediction errors is not as well-characterized, although norepinephrine and other neuromodulators and neuropeptides participate in fear learning. Here, we utilized fluorescent norepinephrine recordings over the course of fear learning in concert with reinforcement learning modeling to identify its role in the prediction of threat. By varying timing and sensory uncertainty in the formation of threat associations, we were able to define a precise computational role for norepinephrine in this process. Norepinephrine release approximates the strength of fear associations, and its temporal dynamics are compatible with a prediction error signal. Intriguingly, the release of norepinephrine is influenced by time and sensory feedback, serving as an antithesis of the classical reward prediction error role of dopamine. Thus, these results directly demonstrate a combined cognitive and affective role of norepinephrine in the prediction of threat, with implications for neuropsychiatric disorders such as anxiety and PTSD.

neuroscience↗

Integration of silicon chip microstructures for in-line microbial cell lysis in soft microfluidics

The paper presents fabrication methodologies that integrate silicon components into soft microfluidic devices to perform microbial cell lysis for biological applications. The integration methodology consists of a silicon chip that is fabricated with microstructure arrays and embedded in a microfluidic device, which is driven by piezoelectric actuation to perform cell lysis by physically breaking microbial cell walls via micromechanical impaction. We present different silicon microarray geometries, their fabrication techniques, integration of said microarrays into microfluidic devices, device operation and testing on synthetic microbeads and microbial cells to evaluate their efficacy. The generalized strategy developed for silicon chip integration into soft polymeric devices can serve as an important process step for a new class of hybrid silicon-polymeric devices for future cellular processing applications. The proposed integration methodology can be scalable and integrated as an in-line cell lysis tool with existing microfluidics assays.

bioengineering↗

Mammalian N1-adenosine PARylation is a reversible DNA modification

Poly-ADP-ribosylation (PARylation) is regarded as a protein-specific modification. However, some PARPs were recently shown to modify DNA termini in vitro. Here we use ultrasensitive mass spectrometry (LC-MS/MS), anti-PAR antibodies, and anti-PAR reagents to show that mammalian DNA is physiologically PARylated and to different levels in primary tissues. Inhibition of PAR glycohydrolase (PARG) increases DNA PARylation, supporting that the modification is reversible. DNA PARylation requires PARP1 and in vitro PARP1 PARylates single-stranded DNA, while PARG reverts the modification. DNA PARylation occurs at the N1-position of adenosine residues to form N1-Poly(ADP-ribosyl)-deoxyadenosine. Through partial hydrolysis of mammalian gDNA we identify PAR-DNA via the diagnostic deamination product N1-ribosyl-deoxyinosine to occur in vivo. We conclude that N1-adenosine PARylation is a novel, reversible DNA modification.

molecular biology↗

A molecular atlas of the human postmenopausal fallopian tube and ovary from single-cell RNA and ATAC sequencing

As part of the Human Cell Atlas initiative, we generated transcriptomic (scRNA-seq; 86,708 cells) and regulatory (scATAC-seq; 59,118 cells) profiles of the normal postmenopausal ovary and fallopian tube (FT) at single-cell resolution. In the FT, 22 cell clusters integrated into 11 cell types, including ciliated and secretory epithelial cells, while the ovary had 17 distinct cell clusters defining 6 major cell types. The dominant cell type in both the postmenopausal ovary and FT was stromal cells, which expressed several genes associated with aging. The fimbrial end of the FT had a significant number and variety of immune cells and active communication with the ovary; the ovary contained mostly stromal cells but few immune cells. The epithelial cells of the normal FT expressed multiple ovarian cancer risk-associated genes (CCDC170, RND3, TACC2, STK33, and ADGB). By integrating paired single-cell transcriptomics and chromatin accessibility data we found that the regulatory landscape of the fimbriae was markedly different from the isthmus and ampulla. Intriguingly, several cell types in the FT had comparable gene expression but different transcriptional regulations. Our single-cell transcriptional and regulatory maps allowed us to disentangle the complex cellular makeup of the postmenopausal FT and ovary and will contribute to a better understanding of gynecologic diseases in menopause.

genomics↗

Selection for increased post-infection survival ameliorates mating induced immune suppression in Drosophila melanogaster females

Sexual activity (mating) negatively affects immune function in various insect species, in both sexes. In the experiments reported in this manuscript, we tested if hosts adapted to regular pathogen challenges are less susceptible to mating induced immune suppression, using experimentally evolved Drosophila melanogaster populations selected for increased post-infection survival when infected with a Gram-positive bacterium, Enterococcus faecalis. Mating increased susceptibility of females to bacterial pathogens, but in a pathogen specific manner. Mating-induced increase in susceptibility was also affected by host evolutionary history, with females from selected populations exhibiting similar post-infection survival irrespective of mating status, while females from control populations became more susceptible to bacterial infections after mating. Post-infection survival of males, irrespective of their evolutionary history, was not affected by their mating status. We therefore conclude that hosts evolved to better survive bacterial infections are also better at resisting mating-induced increase in susceptibility to infections in Drosophila melanogaster.

evolutionary biology↗

Correlated responses to experimental evolution of increased post-infection survival in Drosophila melanogaster: Life-history trade-offs and reaction to novel stressors

Evolution of increased immune defence is often limited by costs: correlated changes in other traits (viz. life-history traits) that otherwise reduce the fitness of the host organisms. Experimental evolution studies are useful for understanding the evolution of immune function, and correlated changes in other traits. We experimentally evolved replicate Drosophila melanogaster populations to better survive infection challenge with an entomopathogenic bacteria, Enterococcus faecalis. Within 35 generations of forward selection, selected populations showed marked increase in post-infection survival compared to ancestrally paired controls. We next measured various life-history traits of these populations. Our results show that the selected populations do not differ from control populations for larval development time and body weight at eclosion. No difference is also observed in case of fecundity and longevity (following the acute phase of infection), either when the flies are subjected to infection or when the flies were uninfected; although infected flies from all populations die much earlier compared to uninfected flies. Selected flies and control flies are also equally good at surviving abiotic stressors (starvation and desiccation), although infected flies from all populations are more susceptible to stress than uninfected flies. Therefore, we conclude that (a) D. melanogaster populations can rapidly evolve to be more immune to infection with E. faecalis; (b) evolution of increased defence against E. faecalis entails no life-history cost for the hosts; and (c) evolving defence against a biotic threat (pathogen) does not make flies more resistant to abiotic stressors.

evolutionary biology↗

Pathogen dependence and inter-individual variability of post-infection reproductive fitness in Drosophila melanogaster

In the experiments reported in this manuscript, we explore the effect of bacterial infections on the reproductive output of Drosophila melanogaster females. Canonical view of host-pathogen interactions supposes two possible outcomes. Because of immune defence being an energy/resource intensive function, an infected female reallocates resources away from reproductive processes and towards immune defence, therefore compromising its reproductive output. Alternatively, faced with impending mortality, an infected female increases its reproductive output to compensate for lost opportunities of future reproduction. We tested if pathogen identity, infection outcome (survival vs. death), and/or time of death determines the reproductive output of females infected with three bacterial pathogens. Our results show that pathogen identity is a reliable predictor of population level response of infected females but does not reliably predict the behaviour of individual females. Additionally, females succumbing to infection exhibit greater variability in reproductive output, compared to both survivors and controls, but this variability is not explained by either the time of death or the identity of the infecting pathogen. Furthermore, survivors of infection have reproductive output similar to control females.

evolutionary biology↗

Discordant effects of resource limitation on host survival and systemic pathogen growth in Drosophila-bacteria infection models: resistance vs. tolerance

In the experiments presented here, we explore the effect of resource limitation, in form of starvation (which leads to decrease in accessible resources and depletion of reserves) and sexual activity (which leads to reallocation of resources from somatic defence towards reproduction), on immune function of female Drosophila melanogaster flies. We infected females with five bacterial pathogens and measured their post-infection survival when subjected to either starvation or sexual activity (mating). Additionally, we measured within host pathogen levels in case of three of these pathogens. Based on previous literature, we predicted that both modes of resource limitation will increase post-infection mortality, but only sexual activity will lead to increase of pathogen load (because of compromised immune function), while starvation will either not affect or reduce pathogen loads (because of reduced availability of resources for the pathogen to proliferate within the host). Our results indicate that both starvation and sexual activity can lead to increased within-host pathogen levels, in addition to increased post-infection mortality, but in a pathogen-specific manner.

ecology↗

Recurrent evolution of cross-resistance in response to selection for improved post-infection survival in Drosophila melanogaster

The host susceptibility to one pathogen can decrease, increase, or remain unaffected by virtue of the host evolving resistance towards a second pathogen. Negative correlations between a host susceptibility to different pathogens is an often-cited explanation for maintenance of genetic variation in immune function determining traits in a host population. In this study, we investigated the change in susceptibility of Drosophila melanogaster flies to various novel bacterial pathogens after being experimentally selected for increased resistance to one particular bacterial pathogen. We independently selected flies to become more resistant towards Enterococcus faecalis and Pseudomonas entomophila, and baring a few exceptions the evolved populations exhibited cross-resistance against the range of pathogens tested in the study. Neither the identity of the native pathogen nor the host sex was major determining factors in predicting the pattern of cross-resistance exhibited by the selected populations. We therefore report that a generalized cross-resistance to novel pathogens can repeatedly evolve in response to selection for resistance against a single pathogen.

evolutionary biology↗

Ribonucleotide Reductase Regulatory Subunit M2 as a Driver of Glioblastoma TMZ-Resistance through Modulation of dNTP Production

Glioblastoma (GBM) remains one of the most resistant and fatal forms of cancer. Previous studies have examined primary and recurrent GBM tumors, but it is difficult to study tumor evolution during therapy where resistance develops. To investigate this, we performed an in vivo single-cell RNA sequencing screen in a patient-derived xenograft (PDX) model. Primary GBM was modeled by mice treated with DMSO control, recurrent GBM was modeled by mice treated with temozolomide (TMZ), and during therapy GBM was modeled by mice euthanized after two of five TMZ treatments. Our analysis revealed the cellular population present during therapy to be distinct from primary and recurrent GBM. We found the Ribonucleotide Reductase gene family to exhibit a unique signature in our data due to an observed subunit switch to favor RRM2 during therapy. GBM cells were shown to rely on RRM2 during therapy causing RRM2-knockdown (KD) cells to be TMZ-sensitive. Using targeted metabolomics, we found RRM2-KDs to produce less dGTP and dCTP than control cells in response to TMZ (p<0.0001). Supplementing RRM2-KDs with deoxycytidine and deoxyguanosine rescued TMZ-sensitivity, suggesting an RRM2-driven mechanism of chemoresistance, established by regulating the production of these nucleotides. In vivo, tumor-bearing mice treated with the RRM2-inhibitor, Triapine, in combination with TMZ, survived longer than mice treated with TMZ alone (p<0.01), indicating promising clinical opportunities in targeting RRM2. Our data present a novel understanding of RRM2 activity, and its alteration during therapeutic stress as response to TMZ-induced DNA damage.

cancer biology↗