Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene prioritization based on random walks with restarts and absorbing states, to define gene sets regulating drug pharmacodynamics from single-cell analyses

Prioritizing genes for their role in drug sensitivity, is an important step in understanding drugs mechanisms of action and discovering new molecular targets for co-treatment. To formalize this problem, we consider two sets of genes X and P respectively composing the predictive gene signature of sensitivity to a drug and the genes involved in its mechanism of action, as well as a protein interaction network (PPIN) containing the products of X and P as nodes. We introduce Genetrank, a method to prioritize the genes in X for their likelihood to regulate the genes in P. Genetrank uses asymmetric random walks with restarts, absorbing states, and a suitable renormalization scheme. Using novel so-called saturation indices, we show that the conjunction of absorbing states and renormalization yields an exploration of the PPIN which is much more progressive than that afforded by random walks with restarts only. Using MINT as underlying network, we apply Genetrank to a predictive gene signature of cancer cells sensitivity to tumor-necrosis-factor-related apoptosis-inducing ligand (TRAIL), performed in single-cells. Our ranking provides biological insights on drug sensitivity and a gene set considerably enriched in genes regulating TRAIL pharmacodynamics when compared to the most significant differentially expressed genes obtained from a statistical analysis framework alone. We also introduce gene expression radars, a visualization tool to assess all pairwise interactions at a glance. Genetrank is made available in the Structural Bioinformatics Library (https://sbl.inria.fr/doc/Genetrank-user-manual.html). It should prove useful for mining gene sets in conjunction with a signaling pathway, whenever other approaches yield relatively large sets of genes.
High-order interactions maintain or enhance structural robustness of a coffee agroecosystem network

The capacity of highly diverse systems to prevail has proven difficult to explain. In addition to methodological issues, the inherent complexity of ecosystems and issues like multicausality, non-linearity and context-specificity make it hard to establish general and unidirectional explanations. Nevertheless, in recent years, high order interactions have been increasingly discussed as a mechanism that benefits the functioning of highly diverse ecosystems and may add to the mechanisms that explain their persistence. Until now, this idea has been explored by means of hypothetical simulated networks. Here, we test this idea using an updated and empirically documented network for a coffee agroecosystem. We identify potentially key nodes and measure network robustness in the face of node removal with and without incorporation of high order interactions. We find that the system’s robustness is either increased or unaffected by the addition of high order interactions, in contrast with randomized counterparts with similar structural characteristics. We also propose a method for representing networks with high order interactions as ordinary graphs and a method for measuring their robustness. Highlights The robustness of a coffee-associated ecological network is either increased or unaffected by the incorporation of high order interactions. A method is proposed for representing high order interactions in ordinary networks. A method is proposed to measure the robustness of networks with high order interactions. High order interactions may promote the persistence of diverse ecosystems.
Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath

Current pooled CRISPR screens for cis-regulatory elements (CREs) can only accommodate one gene based on its expression level. Here, we describe CRISPRpath, a scalable screening strategy for parallelly characterizing CREs of genes linked to the same biological pathway and converging phenotypes. We demonstrate the ability of CRISPRpath for simultaneously identifying functional enhancers of six genes in the 6-thioguanine-induced DNA mismatch repair pathway using both CRISPR interference (CRISPRi) and CRISPR nuclease (CRISPRn) approaches. 60% of the identified enhancers are known promoters with distinct epigenomic features compared to other active promoters, including increased chromatin accessibility and interactivity. Furthermore, by imposing different levels of selection pressure, CRISPRpath can distinguish enhancers exerting strong impact on gene expression from those exerting weak impact. Our results offer a nuanced view of cis-regulation and demonstrate that CRISPRpath can be leveraged for understanding the complex gene regulatory program beyond transcriptional output at scale.
DpaA Detaches Braun’s Lipoprotein from Peptidoglycan

Gram-negative bacteria have a complex cell envelope with two membranes and a periplasm containing the peptidoglycan layer. The outer membrane is firmly connected to the peptidoglycan by highly abundant proteins. ABSTRACT Gram-negative bacteria have a unique cell envelope with a lipopolysaccharide-containing outer membrane that is tightly connected to a thin layer of peptidoglycan. The tight connection between the outer membrane and peptidoglycan is needed to maintain the outer membrane as an impermeable barrier for many toxic molecules and antibiotics. Enterobacteriaceae such as Escherichia coli covalently attach the abundant outer membrane-anchored lipoprotein Lpp (Braun’s lipoprotein) to tripeptides in peptidoglycan, mediated by the transpeptidases LdtA, LdtB, and LdtC. LdtD and LdtE are members of the same family of ld-transpeptidases but they catalyze a different reaction, the formation of 3-3 cross-links in the peptidoglycan. The function of the sixth homologue in E. coli, LdtF, remains unclear, although it has been shown to become essential in cells with inhibited lipopolysaccharide export to the outer membrane. We now show that LdtF hydrolyzes the Lpp-peptidoglycan linkage, detaching Lpp from peptidoglycan, and have renamed LdtF to peptidoglycan meso-diaminopimelic acid protein amidase A (DpaA). We show that the detachment of Lpp from peptidoglycan is beneficial for the cell under certain stress conditions and that the deletion of dpaA allows frequent transposon inactivation in the lapB (yciM) gene, whose product downregulates lipopolysaccharide biosynthesis. DpaA-like proteins have characteristic sequence motifs and are present in many Gram-negative bacteria, of which some have no Lpp, raising the possibility that DpaA has other substrates in these species. Overall, our data show that the Lpp-peptidoglycan linkage in E. coli is more dynamic than previously appreciated. IMPORTANCE Gram-negative bacteria have a complex cell envelope with two membranes and a periplasm containing the peptidoglycan layer. The outer membrane is firmly connected to the peptidoglycan by highly abundant proteins. The outer membrane-anchored Braun’s lipoprotein (Lpp) is the most abundant protein in E. coli, and about one-third of the Lpp molecules become covalently attached to tripeptides in peptidoglycan. The attachment of Lpp to peptidoglycan stabilizes the cell envelope and is crucial for the outer membrane to function as a permeability barrier for a range of toxic molecules and antibiotics. So far, the attachment of Lpp to peptidoglycan has been considered to be irreversible. We have now identified an amidase, DpaA, which is capable of detaching Lpp from peptidoglycan, and we show that the detachment of Lpp is important under certain stress conditions. DpaA-like proteins are present in many Gram-negative bacteria and may have different substrates in these species.
Formation of Lipofuscin-Like Autofluorescent Granules in the Retinal Pigment Epithelium Requires Lysosome Dysfunction

Purpose We aim to characterize the pathways required for autofluorescent granule (AFG) formation by retinal pigment epithelium (RPE) cells using cultured monolayers. Methods We fed RPE monolayers in culture with a single pulse of photoreceptor outer segments (POS). After 24h the cells started accumulating AFGs similar to lipofuscin in vivo. Using this model, we used a variety of light and electron microscopical techniques, flow cytometry and western blot to analyze the formation of AFGs. We also generated a mutant RPE line lacking Cathepsin D by gene editing. Results AFGs appear to derive from incompletely digested POS-containing phagosomes and are surrounded after 72h by a single membrane containing lysosome markers. We show by various methods that lysosome-phagosome fusion is required for AFG formation but that impairment of lysosomal pH or catalytic activity, particularly Cathepsin D activity, enhances AF accumulation. Conclusions We conclude that lysosomal dysfunction results in incomplete POS degradation and AFG accumulation.
A cytogenetic study of individuals consuming drinking water with high vanadium content

Subjects which had been consuming drinking water with a high vanadium content, namely, 0.34 mg/l (0.34 ppm), for at least 10 years were investigated. Research was aimed at correlating the frequency of sister chromatid exchange (SCE) and chromosomal aberrations (CA) in human lymphocytes with vanadium values in water and urine. A questionnaire was administered to each subject to find any other vanadium‐related symptom. Data collected on both SCE and CA suggest that vanadium at concentrations affecting population under study (i.e. 0.34 mg/l) does not induce a significantly higher response.
Protocol for mapping the spatial variability in cell wall mechanical bending behavior in living leaf pavement cells

An integrated, experimental-computational approach is presented to analyze the variation of elastic bending behavior in the primary cell wall of living Arabidopsis thaliana pavement cells and to measure turgor pressure in the cells quantitatively under different osmotic conditions. Mechanical properties, size and geometry of cells and internal turgor pressure greatly influence their morphogenesis. Computational models of plant morphogenesis require values for wall elastic modulus and turgor pressure but very few experiments were designed to validate the results using measurements that deform the entire thickness of the cell wall. Because new wall material is deposited from inside the cell, full-thickness deformations are needed to quantify relevant changes associated with cell development. The approach here uses laser scanning confocal microscopy to measure the three-dimensional geometry of a single pavement cell, and indentation experiments equipped with high magnification objective lens to probe the local mechanical responses across the same cell wall. These experimental results are matched iteratively using a finite element model of the experiment to determine the local mechanical properties, turgor pressure, and cell height. The resulting modulus distribution along the periclinal wall is shown to be nonuniform. These results are consistent with the characteristics of plant cell walls which have a heterogeneous organization. This research and the resulting model will provide a reference for future work associated with the heterogeneity and anisotropy of mechanical properties of plant cell walls in order to understand morphogenesis of the primary cell walls during growth and to predict quantitatively the magnitudes/directions of cell wall forces. One sentence summary The distribution of elastic modulus of the periclinal cell walls of living Arabidopsis epidermis is nonuniform as measured by bending the entire thickness of the wall. Highlights Experimental characterization of the spatial distribution of elastic bending behavior across the periclinal wall Quantification of the turgor pressure of the living plant epidermal cells validated with osmotic treatments Quantification of the effect of cell geometry on the measured mechanical response Graphical abstract
A neural circuit basis for binasal input-enhanced chemosensory avoidance

Our understanding of how bilaterian animals utilize parallel input channels from paired sensory organs to optimize chemosensory behavior and the underlying neural circuit mechanisms are limited. Here we developed microfluidics-based behavioral and brainwide imaging platforms to study the neural integration of binasal inputs and chemosensory avoidance in larval zebrafish. We show that larval zebrafish efficiently escape from cadaverine-carrying streams by making more frequent swim bouts and larger undirected turns. Binasal inputs are strictly required for the nasal input-dependent component of klinokinesis, while each nasal input additively enhances angular orthokinesis. Throughout brain regions, including those along the olfactory processing pathways, a distributed neural representation with a wide spectrum of ipsilateral-contralateral nasal stimulus selectivity is maintained. Nonlinear sensory information gain with bilateral signal convergence is especially prominent in neurons weakly encoding unilateral cadaverine stimulus, and associated with stronger activation of sensorimotor neurons in the downstream brain regions. Collectively, these results provide insights into how the vertebrate model sums parallel input signals to guide chemosensory avoidance behavior.
A large-scale transcriptome-wide association study (TWAS) of ten blood cell phenotypes reveals complexities of TWAS fine-mapping

Hematological measures are important intermediate clinical phenotypes for many acute and chronic diseases. Hematological measures are highly heritable, and although genome-wide association studies (GWAS) have identified thousands of loci containing trait-associated variants, the causal genes underlying these associations are often uncertain. To better understand the underlying genetic regulatory mechanisms, we performed a transcriptome-wide association study (TWAS) using PrediXcan to systematically investigate the association between genetically-predicted gene expression and hematological measures in 54,542 individuals of European ancestry from the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort. We found 239 significant gene-trait associations with hematological measures. Among this set of 239 associations, we replicated 71 at p < 0.05 with same direction of effect for the blood cell trait in a meta-analysis of TWAS results consisting of up to 35,900 European ancestry individuals from the Women’s Health Initiative (WHI), the Atherosclerosis Risk in Communities Study (ARIC), and BioMe Biobank. We further attempted to refine this list of candidate genes by performing conditional analyses, adjusting for individual variants previously associated with these hematological measures, and performed further fine-mapping of TWAS loci. To assist with the interpretation of TWAS findings, we designed an R Shiny application to interactively visualize TWAS results, one genomic locus at a time, by integrating our TWAS results with additional genetic data sources (GWAS, TWAS from other gene expression reference panels, conditional analyses, known GWAS variants, etc.). Our results and R Shiny application highlight frequently overlooked challenges with TWAS and illustrate the complexity of TWAS fine-mapping efforts. Author Summary Transcriptome-wide association studies (TWAS) have shown great promise in furthering our understanding of the genetic regulatory mechanisms underlying complex trait variation. However, interpreting TWAS results can be incredibly complex, especially in large-scale analyses where hundreds of signals appear throughout the genome, with multiple genes often identified in a single chromosomal region. Our research demonstrates this complexity through real data examples from our analysis of hematological traits, and we provide a useful web application to visualize TWAS results in a broadly approachable format. Together, our results and web application illustrate the importance of interpreting TWAS studies in context and highlight the need to carefully examine results in a region-wide context to draw reasonable conclusions and formulate mechanistic hypotheses.
B/tMSI-CAST: a systematic approach for microsatellite instability detection in both tumor tissue and plasma specimens from next-generation sequencing data

Microsatellite instability (MSI) is a phenotypic manifestation of mismatch repair (MMR) deficiency and has been used as a biomarker through NGS-based assays to aid clinical cancer diagnosis and prognosis, as being advantageous over traditional electrophoresis-based tests and immunohistochemistry. Critical to detection accuracy but seldomly systematically discussed and poorly resolved by currently available methods are topics such as influences of changing experimental conditions, MSI-specific duplication removal and tradeoffs associated with loci selection strategies. In seeking solution to these questions, we have developed b/tMSI-CAST (blood/tissue MSI Caller Adjusted with Sequence duplicaTes), an integrated method consisting of a set of loci selection principles, an MSI-specific duplication removal strategy and a two-mode calling algorithm targeting both blood and tissue samples, equipped with a baseline construction method based on duplication distributions. We benchmarked b/tMSI-CAST against two established tools, mSINGS and MSIsensor-pro and found b/tMSI-CAST showed matched performance as MSIsensor-pro and outperformed mSINGS. We further applied it to a retrospective cohort of 18084 clinical samples to present a comprehensive landscape view on MSI prevalence across 26 cancer types, the largest of its kind in Chinese population so far, and demonstrated it on presurgical cfDNA samples of patients with early stage cancers.
A genome-wide circular RNA transcriptome in rat

Background Circular RNAs are a novel class of non-coding RNAs that backsplice from 5’ donor site and 3’ acceptor site to form a circular structure. A number of circRNAs have been discovered in model organisms including human, mouse, Drosophila, among other organisms. There are a few candidate-based studies on circular RNAs in rat, a well studied model organism. The availability of a recent dataset of transcriptomes encompassing 11 tissues, 4 developmental stages and 2 genders motivated us to explore the landscape of circular RNAs in the organism. Methodology In order to understand the difference among different pipelines, we have used the same bodymap RNA sequencing dataset. A number of pipelines have been published to identify the backsplice junctions for the discovery of circRNAs but studies comparing these tools have suggested that a combination of tools would be a better approach to identify high-confidence circular RNAs. We employed 5 different combinations of tools including tophat_CIRCexplorer2, segemehl_CIRCexplorer2, star_CIRCexplorer, Bowtie2_findcirc and Bowtie2_findcirc (noHisat2) to identify circular RNAs from the dataset. Results Our analysis identified a number of tissue-specific, developmental stage specific and gender specific circular RNAs. We further independently validated 16 circRNA junctions out of 24 selected candidates in 5 tissue samples. We additionally estimated the quantitative expression of 5 circRNA candidates using real-time PCR and our analysis suggests 3 candidates as tissue-enriched Conclusion This study is one of the most comprehensive studies that provides a circular RNA transcriptome as well as to understand the difference among different computational pipelines in Rat.
Loss of FAS1 function reveals rescue of an aberrant intra-S-phase checkpoint by the G2/M checkpoint regulator SOG11[OPEN]

The WEE1 and ATR kinases represent important regulators of the plant intra-S-phase checkpoint, as evidenced by the hypersensitivity of WEE1KO and ATRKO roots to replication inhibitory drugs. Here, we report on the identification of a defective allele of the FASCIATA1 (FAS1) subunit of the chromatin assembly factor 1 (CAF-1) complex as a suppressor of WEE1- or ATR-deficient plants. We demonstrate that lack of FAS1 activity results in the activation of an ATM- and SOG1-mediated G2/M-arrest that makes the ATR and WEE1 checkpoint regulators redundant. This ATM activation accounts for telomere erosion and loss of ribosomal DNA described for the fas1 plants. Knocking out SOG1 in the fas1 wee1 background restores replication stress sensitivity, demonstrating that SOG1 plays a prominent role as secondary checkpoint regulator in plants that fail to activate the intra-S-phase checkpoint. One-Sentence Summary Lack of the chromatin assembly factor-1 subunit FAS1 results in a DNA damage response that overrules the need for replication checkpoint activators.
Suppression of alpha‐band power underlies exogenous attention to emotional distractors

Alpha-band oscillations (8-14 Hz) are essential for attention and perception processes by facilitating the selection of relevant information. Directing visuospatial endogenous (voluntary) attention to a given location consistently results in a power suppression of alpha activity over occipito-parietal areas contralateral to the attended visual field. In contrast, the neural oscillatory dynamics underlying the involuntary capture of attention, or exogenous attention, are currently under debate. By exploiting the inherent capacity of emotionally salient visual stimuli to capture attention, we aimed to investigate whether exogenous attention is characterized by either a reduction or an increase in alpha-band activity. Electroencephalographic activity was recorded while participants completed a Posner visuospatial cueing task, in which a lateralized image with either positive, negative, or neutral emotional content competed with a target stimulus presented in the opposite hemifield. Compared with trials with no distractors, alpha power was reduced over occipital regions contralateral to distracting images. This reduction of alpha activity turned out to be functionally relevant, as it correlated with impaired behavioural performance on the ongoing task and was enhanced for distractors with negative valence. Taken together, our results demonstrate that visuospatial exogenous attention is characterized by a suppression of alpha-band activity contralateral to distractor location, similar to the oscillatory underpinnings of endogenous attention. Further, these results highlight the key role of exogenous attention as an adaptive mechanism for the efficient detection of biologically salient stimuli. Highlights Exogenous attention is indexed by alpha suppression contralateral to distractors. Alpha power decrease is enhanced by distractors with negative emotional valence. Lower levels of alpha power correlate with poorer task performance accuracy. The negativity bias in exogenous attention might reflect an adaptive mechanism.