Biology subjects

Das, A.

Publications and source records attributed to Das, A..

At least 235 records · Page 13Linked to original sources

bioRxiv2019

The draft nuclear genome assembly of Eucalyptus pauciflora: new approaches to comparing de novo assemblies

BackgroundSelecting the best genome assembly from a collection of draft assemblies for the same species remains a difficult task. Here, we combine new and existing approaches to help to address this, using the non-model plant Eucalyptus pauciflora (snow gum) as a test case. Eucalyptus pauciflora is a long-lived tree with high economic and ecological importance. Currently, little genomic information for Eucalyptus pauciflora is available.\n\nFindingsWe generated high coverage of long-(Nanopore, 174x) and short-(Illumina, 228x) read data from a single Eucalyptus pauciflora individual and compared assemblies from four assemblers with a variety of settings: Canu, Flye, Marvel, and MaSuRCA. A key component of our approach is to keep a randomly selected collection of ~10% of both long- and short-reads separate from the assemblies to use as a validation set with which to assess the assemblies. Using this validation set along with a range of existing tools, we compared the assemblies in eight ways: contig N50, BUSCO scores, LAI scores, assembly ploidy, base-level error rate, computing genome assembly likelihoods, structural variation and genome sequence similarity. Our result showed that MaSuRCA generated the best assembly, which is 594.87 Mb in size, with a contig N50 of 3.23 Mb, and an estimated error rate of ~0.006 errors per base.\n\nConclusionsWe report a draft genome of Eucalyptus pauciflora, which will be a valuable resource for further genomic studies of eucalypts. These approaches for assessing and comparing genomes should help in assessing and choosing among many potential genome assemblies for a single species.

genomics↗

bioRxiv2019

The unjamming transition is distinct from the epithelial-to-mesenchymal transition.

Every organ surface and body cavity is lined by a confluent collective of epithelial cells. In homeostatic circumstances the epithelial collective remains effectively solid-like and sedentary. But during morphogenesis, remodeling or repair, as well as during malignant invasion or metastasis, the epithelial collective becomes fluid-like and migratory1-4. This conversion from sedentary to migratory behavior has traditionally been understood as a manifestation of the epithelial-to-mesenchymal transition (EMT) or the partial EMT (pEMT)5-8. However, in certain contexts this conversion has been attributed to the recently discovered unjamming transition (UJT), in which epithelial cells move collectively and cooperatively9-11. UJT and pEMT share certain aspects of collective cellular migration, but the extent to which these processes are distinct, overlapping or perhaps even identical has remained undefined. Using the confluent layer of well-differentiated primary human bronchial epithelial (HBE) cells, here we triggered UJT by exposing the sedentary layer to mechanical compression9-12. Cells thereafter migrated cooperatively, aligned into packs locally, and elongated systematically. Nevertheless, cell-cell junctions, apico-basal polarity, and barrier function remained intact in response, and mesenchymal markers remained unapparent. As such, pEMT was not evident. When we triggered pEMT and associated cellular migration by exposing the sedentary layer to TGF-{beta}1, metrics of UJT versus pEMT diverged. To account for these striking physical observations a new mathematical model attributes the effects of pEMT mainly to diminished junctional tension but attributes those of UJT mainly to augmented cellular propulsion. Together, these findings establish that UJT is sufficient to account for vigorous epithelial layer migration even in the absence of pEMT. Distinct gateways to cellular migration therefore become apparent - UJT as it might apply to migration of epithelial sheets, and EMT/pEMT as it might apply to migration of mesenchymal cells on a solitary or collective basis, activated during development, remodeling, repair or tumor invasion. Through the actions of UJT and pEMT working independently, sequentially, or interactively, living tissue is therefore seen to comprise an active engineering material whose modules for plasticity, self-repair and regeneration, are far richer than had been previously appreciated.

biophysics↗

bioRxiv2019

Homogenization of Rhizosphere Bacterial Communities by Pea (Pisum sativum L.) Cultivated under Different Conservation Agricultural Practices in the Eastern Himalayas

Conservation agriculture offers a suitable system to harmonize agriculture with the environment, especially in fragile ecosystems of North-East India. Soil microbes play pivotal roles in ecosystem functioning and act as indispensable indicators of overall fitness of crop plant and soil health. Here we demonstrated that altercations in residue management and tillage practices lead to the development of differential bacterial communities forcing the pea plants to recruit special groups of bacteria leading to highly homogenous rhizosphere communities. Pea rhizosphere and bulk soil samples were collected, and bacterial community structure was estimated by 16S rRNA gene amplicon sequencing and predictive functional analysis was performed using Tax4Fun. The effect on pea plants was evident in the bacterial communities as the overall diversity of rhizosphere samples was significantly higher to that of bulk soil samples. Bacillus, Staphylococcus, Planomicrobium, Enterobacter, Arthrobacter, Nitrobacter, Geobacter, and Sphingomonas were noticed as the most abundant genera in the rhizosphere and bulk soil samples. The abundance of Firmicutes and Proteobacteria altered significantly in the rhizosphere and bulk samples, which was further validated by qPCR. Selection of specific taxa by pea plant was indicated by the higher values of mean proportion of Rhizobium, Pseudomonas, Pantoea, Nitrobacter, Enterobacter and Sphingomonas in rhizosphere samples, and Massilia, Paenibacillus and Planomicrobium in bulk soil samples. Tillage and residue management treatments did not significantly alter the bacterial diversity, while their influence was observed on the abundance of few genera. Recorded results revealed that pea plant selects specific taxa into its rhizosphere plausibly to meet its requirements for nutrient uptake and stress amelioration under the different tillage and residue management practices.

microbiology↗

bioRxiv2019

Assemblies of F-actin and myosin-II minifilaments: steric hindrance and stratification at the membrane cortex

Recent in-vivo studies have revealed that several membrane proteins are driven to form nanoclusters by active contractile flows arising from F-actin and myosin at the cortex. The mechanism of clustering was shown to be arising from the dynamic patterning of transient contractile platforms (asters) generated by actin and myosin. Myosin-II, which assemble as minifilaments consisting of tens of myosin heads, are rather bulky structures and hence a concern could be that steric considerations might obstruct the emergence of nanoclustering. Here, using coarse-grained, agent-based simulations that respect the size of constituents, we find that in the presence of steric hindrance, the patterns exhibited by actomyosin in two dimensions, do not resemble the steady state patterns observed in our in-vitro reconstitution of actomyosin on a supported bilayer. We then perform simulations in a thin rectangular slab, allowing the separation of a layer of actin filaments from those of myosin-II minifilaments. This recapitulates the observed features of in-vitro patterning. Using super resolution microscopy, we find direct evidence for stratification in our in-vitro system. Our study suggests the possibility that molecular stratification may be an important organising feature of the cortical cytoskeleton in-vivo.

cell biology↗

bioRxiv2019

Programmed Switch in The Mitochondrial Degradation Pathways During Human Retinal Ganglion Cell Differentiation from Stem Cells is Critical for RGC Survival

Retinal ganglion cell (RGC) degeneration is the root cause for vision loss in glaucoma as well as in other forms of optic neuropathies. Genetic analysis indicated abnormal mitochondrial quality control (MQC) as a major risk factor for optic neuropathies. However, nothing is known on how MQC regulates human retinal ganglion cell (hRGC) health and survival. Human pluripotent stem cells (hPSCs) provide opportunity to differentiate hRGCs and understand the abnormal MQC associated hRGC degeneration in great detail. Degradation of damaged mitochondria is a very critical step of MQC, here we have used stem cell derived hRGCs to understand the damaged mitochondrial degradation pathways for hRGC survival. Using pharmacological methods, we have investigated the role of the proteasomal and endo-lysosomal pathways in degrading damaged mitochondria in hRGCs and their precursor stem cells. We find that upon mitochondrial damage with the proton uncoupler carbonyl cyanide m-chlorophenyl hydrazone (CCCP), hRGCs more efficiently degraded mitochondria than their precursor stem cells. We further identified that for degrading damaged mitochondria, stem cells predominantly use the ubiquitine-proteasome system (UPS) while hRGCs use the endo-lysosomal pathway. UPS inhibition causes apoptosis in stem cells, while hRGC viability is dependent on the endo-lysosomal pathway but not on the UPS pathway. This suggests manipulation of the endo-lysosomal pathway could be therapeutically relevant for RGC protection in treating glaucoma. Endo-lysosome dependent cell survival is also conserved for other human neurons as differentiated human cerebral cortical neurons also degenerated upon endo-lysosomal inhibition but not for the proteasome inhibition.\n\nSIGNIFICANCE STATEMENTUsing human stem cells we have shown a switch in the mitochondrial degradation pathway during hRGC differentiation where endo-lysosomal pathway becomes the predominant pathway for cellular homeostasis and hRGC survival which is also true for human cortical neurons. These findings suggest manipulation of the endo-lysosomal pathway could be therapeutically relevant for RGC protection in treating glaucoma as well as for other neurodegenerative diseases.

neuroscience↗

bioRxiv2019

Red blood cell-derived extracellular vesicles mediate intercellular communication in ischemic heart failure

Extracellular vesicles (EV) mediate intercellular signaling by transferring their cargo to recipient cells. Red blood cell (RBC)-derived EVs constitute a significant proportion of circulating EVs and have been implicated in regulating immune responses. Here, we describe a transgenic mouse model for fluorescent-based mapping of RBC-EV target cells based on the functional transfer of EV-contained Cre-recombinase to target cells. In a murine model of ischemic heart failure, we detect an increase in RBC-EV-targeted cardiomyocytes in the hearts and microglial cells in the brains. Cells targeted by RBC-EVs present an enrichment of genes implicated in cell proliferation and metabolism pathways compared to non-recombined (non-targeted) cells. Cardiomyocytes targeted by RBC-EVs are more likely to demonstrate cellular markers of DNA synthesis and proliferation, suggesting functional significance of EV-mediated signaling. In conclusion, we leverage our mouse model for mapping of RBC-EV targets in murine ischemic heart failure to demonstrate quantitative and qualitative changes in RBC-EV recipients.

cell biology↗

bioRxiv2019

High angular resolution diffusion MRI reveals conserved and deviant programs in the paths that guide human cortical circuitry

Diffusion MR tractography represents a novel opportunity to investigate conserved and deviant developmental programs between humans and other species such as mice. To that end, we acquired high angular resolution diffusion MR scans of mice (embryonic day [E] 10.5 to post-natal week [PW] 4) and human brains (gestational week [GW] 17 to 30) at successive stages of fetal development to investigate potential evolutionary changes in radial organization and emerging pathways between humans and mice. We compare radial glial development as well as commissural development (e.g., corpus callosum), primarily because our findings can be integrated with previous work. We also compare corpus callosal growth trajectories across primates (i.e., humans, rhesus macaques) and rodents (i.e., mice). One major finding is that the developing cortex of humans is predominated by pathways likely associated with a radial glial organization at GW 17-20, which is not as evident in age-matched mice (E 16.5, 17.5). Another finding is that, early in development, the corpus callosum follows a similar developmental timetable in primates (i.e., macaques, humans) as in mice. However, the corpus callosum grows for an extended period of time in primates compared with rodents. Taken together, these findings highlight deviant developmental programs underlying the emergence of cortical pathways in the human brain.

neuroscience↗

bioRxiv2019

Cohesin and microtubule dependent mechanisms regulate sister centromere fusion during meiosis I

Sister centromere fusion is a process unique to meiosis that promotes co-orientation of the sister kinetochores, ensuring they attach to microtubules from the same pole. We have found that the kinetochore protein SPC105R/KNL1 and Protein Phosphatase 1 (PP1-87B) are required for this process. The analysis of these two proteins, however, has shown that two independent mechanisms maintain sister centromere fusion during meiosis I in Drosophila oocytes. Double depletion experiments demonstrated that the precocious separation of centromeres in Spc105R RNAi oocytes is Separase-dependent, suggesting cohesin proteins must be maintained at the core centromeres. In contrast, precocious sister centromere separation in Pp1-87B RNAi oocytes does not depend on Separase or Wapl. Further analysis with microtubule destabilizing drugs showed that PP1-87B maintains sister centromeres fusion by regulating microtubule dynamics. Additional double depletion experiments demonstrated that PP1-87B has this function by antagonizing Polo kinase and BubR1, two proteins known to promote kinetochore-microtubule (KT-MT) attachments. These results suggest that PP1-87B maintains sister centromere fusion by inhibiting stable KT-MT attachments. Surprisingly, we found that loss of C(3)G, the transverse element of the synaptonemal complex (SC), suppresses centromere separation in Pp1-87B RNAi oocytes. This is evidence for a functional role of centromeric SC in the meiotic divisions. We propose two mechanisms maintain co-orientation in Drosophila oocytes: one involves SPC105R to protect cohesins at sister centromeres and another involves PP1-87B to regulate spindle forces at end-on attachments.\n\nAuthor SummaryMeiosis involves two cell divisions. In the first division, pairs of homologous chromosomes segregate, in the second division, the sister chromatids segregate. These patterns of division are mediated by regulating microtubule attachments to the kinetochores and stepwise release of cohesion between the sister chromatids. During meiosis I, cohesion fusing sister centromeres must be intact so they attach to microtubules from the same pole. At the same time, arm cohesion must be released for anaphase I. Upon entry into meiosis II, the sister centromeres must separate to allow attachment to opposite poles, while cohesion surrounding the centromeres must remain intact until anaphase II. How these different populations of cohesion are regulated is not understood. We identified two genes required for maintaining sister centromere cohesion, and surprisingly found they define two distinct mechanisms. The first is a kinetochore protein that maintains sister centromere fusion by recruiting proteins that protect cohesion. The second is a phosphatase that antagonizes proteins that stabilize microtubule attachments. We propose that entry into meiosis II coincides with stabilization of microtubule attachments, resulting in the separation of sister centromeres without disrupting cohesion in other regions, facilitating attachment of sister chromatids to opposite poles.

genetics↗

bioRxiv2019

Fast and robust method for drug response biomarker identification and sample stratification.

With unprecedented progress of cancer research, the world is now prepared with versatile arsenal of drugs to combat cancer. However, individuals response to any drug or combination treatment stands as a major challenge and hence there exists the sheer need for personalized medication. Identification of drug response biomarkers from a wholistic tumor microenvironment analysis would guide researchers to develop custom-tailored treatment regimen.\n\nIn this study, a fast and robust method has been developed to identify drug response biomarkers from entire transcriptomics data analysis in a data-driven manner. The biomarkers which were identified by the method, were able to stratify patients between responders vs non-responders population. Furthermore, bayesian network (BN) analysis, done on the data, brought forth a mechanistic insight into the role of identified biomarkers in regulating drugs efficacy.\n\nThe importance of this work lies with the protocol that is time saving and requires less computation power, yet analyzes a whole system data and helps the researchers to take a step forward towards the development of personalized care in effective cancer treatment.\n\nHighlightsO_LISupervised machine learning approach to analyze gene expression data.\nC_LIO_LIDrug response biomarker identification.\nC_LIO_LICategorization of samples for their drug response with the help of identified biomarkers.\nC_LIO_LIFunctional enrichment to understand the biomarkers association with biological processes.\nC_LIO_LIBayesian network analysis to develop causal structure among identified biomarkers and drug targets.\nC_LIO_LITime and cost-effective pipeline for fast and robust prediction of drug response biomarkers.\nC_LI

bioinformatics↗

bioRxiv2019

Systematic errors in connectivity inferred from activity in strongly coupled recurrent circuits

Understanding the mechanisms of neural computation and learning will require knowledge of the underlying circuitry. Because it is slow, expensive, or often infeasible to directly measure the wiring diagrams of neural microcircuits, there has long been an interest in estimating them from neural recordings. We show that even sophisticated inference algorithms, applied to large volumes of data from every node in the circuit, are biased toward inferring connections between unconnected but strongly correlated neurons, a situation that is common in strongly recurrent circuits. This e ect, representing a failure to fully \"explain away\" non-existent connections when correlations are strong, occurs when there is a mismatch between the true network dynamics and the generative model assumed for inference, an inevitable situation when we model the real world. Thus, effective connectivity estimates should be treated with especial caution in strongly connected networks when attempting to infer the mechanistic basis of circuit activity. Finally, we show that activity states of networks injected with strong noise or grossly perturbed away from equilibrium may be a promising way to alleviate the problems of bias error.

neuroscience↗

bioRxiv2018

Task-Related Hemodynamic Responses Are Modulated by Reward and Task-engagement

Hemodynamic recordings from visual cortex contain powerful endogenous task-related responses that may reflect task-engagement distinct from attention. We tested this hypothesis with hemodynamic measurements (intrinsic-signal optical imaging) from monkey V1, while the animals engagement in a periodic fixation task over several hours was varied though reward size, and as animals took breaks. With higher rewards, animals appeared more task-engaged; task-related responses were more temporally precise at the task period (~ 10-20 seconds), and modestly stronger. Surprisingly, 2-5-minute blocks of high-reward trials led to ramp-like decreases in mean local blood volume; these reversed with ramp-like increases during low reward. The blood volume increased even more sharply when the animal shut his eyes and disengaged completely from the task (5-10 minutes). We propose a mechanism that controls vascular tone, likely along with local neural responses, with phasic and tonic components tied to task-engagement.

neuroscience↗

bioRxiv2018

A negative role for the interleukin-2-inducible T-cell kinase (ITK) in human Foxp3+ Treg differentiation

The Tec kinases ITK (interleukin-2-inducible T-cell kinase) and RLK (resting lymphocyte kinase) are critical components of the proximal TCR/CD3 signal transduction machinery, and data in mice suggest that ITK negatively regulates TREG differentiation. However, whether Tec kinases modulate TREG development and/or function in human T cells remains unknown. Using a novel self-delivery siRNA platform (sdRNA), we found that ITK knockdown in primary human naive peripheral blood CD4 T cells increased Foxp3+ TREG differentiation under both TREG and T effector (Teff) cell priming conditions. ITK knockdown also enhanced the expression of the co-inhibitory receptor PD-1 on FoxP3+ T cells. TREGS differentiated in vitro (iTREG) after ITK knockdown displayed suppressive capacity against effector CD4+ T cell proliferation. ITK knockdown decreased IL-17A production in T cells primed under Th17 conditions and increased Th1 differentiation. Finally, a dual ITK/RLK Tec kinase inhibitor blocked TREG differentiation and T cell activation in general. Our data suggest that targeting ITK in human T cells may be an effective approach to boost TREG in the context of autoimmune diseases, but non-specific inhibition of other Tec family kinases may broadly inhibit T cell activation.

immunology↗

bioRxiv2018

Migration rather than proliferation transcriptomic signatures are strongly associated with breast cancer patient survival

The efficacy of prospective cancer treatments is routinely estimated by in vitro cell-line proliferation screens. However, it is unclear whether tumor aggressiveness and patient survival are influenced more by the proliferative or the migratory properties of cancer cells. To address this question, we experimentally measured proliferation and migration phenotypes across more than 40 breast cancer cell-lines. Based on the latter, we built and validated individual predictors of breast cancer proliferation and migration levels from the cells transcriptomics. We then apply these predictors to estimate the proliferation and migration levels of more than 1000 TCGA breast cancer tumors. Reassuringly, both estimates increase with tumors aggressiveness, as qualified by its stage, grade, and subtype. However, predicted tumor migration levels are significantly more strongly associated with patient survival than the proliferation levels. We confirm these finding by conducting siRNA knock-down experiments on the highly migratory MDA-MB-231 cell lines and deriving gene knock-down based proliferation and migration signatures. We show that cytoskeletal drugs might be more beneficial in patients with high predicted migration levels. Taken together, these results testify to the importance of migration levels in determining patient survival.

bioinformatics↗

bioRxiv2018

Engineered cell-to-cell signalling within growing bacterial cellulose pellicles

Bacterial cellulose is a strong and flexible biomaterial produced at high yields by Acetobacter species and has applications in healthcare, biotechnology and electronics. Naturally, bacterial cellulose grows as a large unstructured polymer network around the bacteria that produce it, and tools to enable these bacteria to respond to different locations are required to grow more complex structured materials. Here, we introduce engineered cell-to-cell communication into a bacterial cellulose-producing strain of Komagataeibacter rhaeticus to enable different cells to detect their proximity within growing material and trigger differential gene expression in response. Using synthetic biology tools, we engineer Sender and Receiver strains of K. rhaeticus to produce and respond to the diffusible signalling molecule, acyl-homoserine lactone (AHL). We demonstrate that communication can occur both within and between growing pellicles and use this in a boundary detection experiment, where spliced and joined pellicles sense and reveal their original boundary. This work sets the basis for synthetic cell-to-cell communication within bacterial cellulose and is an important step forward for pattern formation within engineered living materials.

synthetic biology↗

bioRxiv2018

An Assessment of Skin Lesion Measurement Techniques for Use in Clinical Trials of Acute Bacterial Skin and Skin Structure Infections

BackgroundLimited data are available to support a reproducible measurement technique that could be used to assess the response of a skin lesion associated with a bacterial infection to antibacterial therapy.\n\nMethodsThis multicenter, observational study enrolled patients with a major cutaneous abscess, a traumatic wound or surgical site infection, or a cellulitis. The primary objective was to characterize the intra- and inter-observer variability inherent in measuring the size of the erythema associated with the presenting skin infection. At least two observers made ruler measurements of the infection site with the length of the infection measured as the longest dimension of the erythematous area and width measured as the largest dimension perpendicular to the longest length. Intra- and inter-observer variability was determined by the intraclass correlation coefficient (ICC). Photographs, tracings, and thermal imaging were also performed.\n\nResultsThe intra-observer ICC (95% CI) for lesion area as measured by ruler was 0.999 (0.998, 0.999), suggesting only a very small amount of the variability was due to measurement error. The difference in mean lesion area measurements by the same observer was <1%. The inter-observer ICC (95% CI) for lesion area as measured by ruler was 0.990 (0.981, 0.995) suggesting that the results between observers were also highly reliable.\n\nConclusionsMeasurement of infection area as defined by erythema and measured by ruler shows excellent intra- and inter-observer reliability and can be used in future clinical trials of acute bacterial skin infections.

pathology↗

bioRxiv2018

Vitexin alters Staphylococcus aureus surface hydrophobicity to interfere with biofilm formation.

Bacterial surface hydrophobicity is one of the determinant biophysical parameters of bacterial aggregation for being networked to form biofilm. Phytoconstituents like vitexin have long been in use for their antibacterial effect. The present work is aimed to characterise the effect of vitexin on S. aureus surface hydrophobicity and corresponding aggregation to form biofilm. We have found that vitexin shows minimum inhibitory concentration at 252 g/ml against S. aureus. Vitexin reduces cell surface hydrophobicity and membrane permeability at sub-MIC dose of 126 g/ml. The in silico binding analysis showed higher binding affinity of vitexin with surface proteins of S. aureus. Down regulation of dltA, icaAB and reduction in membrane potential under sub-MIC dose of vitexin, explains reduced S. aureus surface hydrophobicity. Vitexin has substantially reduced the intracellular adhesion of planktonic cells to form biofilm through interference of EPS formation, motility and subsequent execution of virulence. This was supported by the observation that vitexin down regulates the expression of icaAB and agrAC genes of S. aureus. In addition, vitexin also found to potentiate antibiofilm activity of sub-MIC dose of gentamicin and azithromycin. Furthermore, CFU count, histological examination of mouse tissue and immunomodulatory study justifies the in vivo protective effect of vitexin from S. aureus biofilm associated infection. Finally it can be inferred that, vitexin has the ability to modulate S. aureus cell surface hydrophobicity which can further interfere biofilm formation of the bacteria.\n\nImportanceThere has been substantial information known about role of bacterial surface hydrophobicity during attachment of single planktonic bacterial cells to any surface and the subsequent development of mature biofilm. This study presents the effect of flavone phytoconstituent vitexin on modulation of cell surface hydrophobicity in reducing formation of biofilm. Our findings also highlight the ability of vitexin in reducing in vivo S. aureus biofilm which will eventually outcompete the corresponding in vitro antibiofilm effect. Synergistic effect of vitexin on azithromycin and gentamicin point to a regime where development of drug tolerance may be addressed. Our findings explore one probable way of overcoming drug tolerance through application of vitexin in addressing the issue of S. aureus biofilm through modulation of cell surface hydrophobicity.

microbiology↗

bioRxiv2018

Inflammatory bowel disease microbiotas alter gut CD4 T-cell homeostasis and drive colitis in mice

To examine the functional contribution of Inflammatory Bowel Disease (IBD) microbes to immune homeostasis and colitis, we colonized unchallenged and colitis-susceptible germ-free mice with over twenty human intestinal microbiotas from healthy and IBD donors. Compared to healthy microbiotas, IBD microbiotas led to expanded ROR{gamma}t+Th17 cells and reduced ROR{gamma}t+Treg in the gut of unchallenged gnotobiotic mice and increased disease severity in colitis-susceptible mice. The proportions of ROR{gamma}t+Th17 and ROR{gamma}t+Treg induced by each microbiota were highly predictive of the human disease status and strongly correlated with disease severity in colitis-susceptible mice colonized with the same human microbiotas. The transmittable functional potential of IBD microbes suggests a mechanism for a microbial contribution to IBD pathogenesis and a potential route for its treatment and prevention.

immunology↗

bioRxiv2018

Beyond synthetic lethality: multiple gene interaction types play a key functional role in cancer

The phenotypic effect of perturbing a genes activity depends on the activity level of other genes, reflecting the notion that phenotypes are emergent properties of a network of functionally interacting genes. In the context of cancer, contemporary investigations have primarily focused on just one type of functional genetic interaction (GI) - synthetic lethality (SL). However, there may be additional types of GIs whose systematic identification would enrich the molecular and functional characterization of cancer. Here, we describe a novel data-driven approach called EnGIne, that applied to TCGA data identifies 71,946 GIs spanning 12 distinct types, only a small minority of which are SLs. The detected GIs explain cancer driver genes tissue-specificity and differences in patients response to drugs, and stratify breast cancer tumors into refined subtypes. These results expand the scope of cancer GIs and lay a conceptual and computational basis for future studies of additional types of GIs and their translational applications. The GI network is accessible online via a web portal [https://amagen.shinyapps.io/cancerapp/].

cancer biology↗