Transcription proteins are concentrated at nuclear transcriptional condensates. These condensates contain cis-regulatory elements (CREs), including enhancers and promoters, that are thought to regulate genes in the same condensate. The roles of condensates are of great current interest, but research into their function is limited by an inability to comprehensively identify their associated CREs. Here, we present a conceptual framework and algorithm, BOUQUET, for integrating genome topology, chromatin occupancy, and graph theory to associate CREs and transcription protein machinery with target genes and identify exceptionally protein-rich communities that interact with condensates. BOUQUET uncovers surprising quantitative correlations between community protein accumulation and gene expression phenotypes by combining accurate CRE-gene assignment with co-activator binding profiles. A small subset of communities, which we call "3D-super-enhancers (3D-SEs)," is exceptionally protein-rich. BOUQUET-predicted 3D-SEs are comparable in number to co-activator nuclear puncta, and all genes known to interact with co-activator condensates in embryonic stem cells are within 3D-SEs. 3D-SEs are enriched for association with cell identity genes across mammalian tissues. Microscopy analyses show frequent co-localization and co-expression of genes from the same 3D-SE within a single co-activator punctum, suggesting 3D-SE components interact with co-activator condensates. Thus, 3D-SEs correspond to co-activator puncta, and our approaches nominate the CREs and genes within them as being condensate-associated.

Cis-regulatory elements (CREs) contact target genes to regulate their transcription, but CRE interactions are complex and predicting their function is challenging. Contemporary approaches to predict CRE targets generally assume one-to-one associations and linear genomic proximity. These methods fail to account for long-range CRE contacts caused by folding of the genome, for circumstances in which a single CRE regulates multiple genes, or, conversely, when a single gene is regulated by multiple CREs. To address these challenges and investigate three-dimensional (3D) CRE communities, we developed BOUQUET, an integrative, graph-theory-based approach that uses multiple aspects of genome topology to probe communities of CREs, their bound apparatus, and their target genes. Using this approach, we uncover communities of CREs that are undetectable by existing unbiased methods, such as those with interactions that span insulating loop boundaries, and regulatory communities that comprise clustered promoter elements. A subset of these communities, which we term “3D super-enhancer CRE communities” (3DSE CRE communities), accrues exceptional amounts of regulatory apparatus at cell identity-defining genes and evolves the super-enhancer concept. In imaging assays, we observe co-localization and co-expression of in-community genes within puncta of transcriptional co-factors, consistent with microcompartment biology. Genome-wide, pairs of genes within the same 3D CRE community are co-expressed in single cells, and pairs of CREs are co-accessible, suggesting both chromatin activity and transcription within a topologically defined community is coordinated. Our model more accurately reflects the complexity of CRE interaction networks, underscores the need for approaches that incorporate spatial organization in the study of enhancer biology, and provides a framework for the reinterpretation of SEs, their condensates, and their target genes through the lens of 3D chromatin structure.### Competing Interest StatementThe authors have declared no competing interest.

Background: Metallo-(3-lactamases (MBLs) type carbapenemases are produced by pathogenic Pseudomonas spp. and exhibit carbapenemase activity. The study will look into drug resistance and the molecular mechanisms of drug-resistant Pseudomonas aeruginosa variants. Methods: A total of 74 P. aeruginosa strains were isolated from urine, pus, sputum, blood, throat swab, Foley's catheter, and nasal swab. The isolates were screened for antibiotic susceptibility and the identified MDR strains were further tested for (3-lactamase production. Multiplex PCR was used to identify the presence of mcr-1 and blaNDM-1 genes in MDR organisms. The minimum inhibitory concentration for ceftazidime and colistin was also determined, in addition to the biofilm inhibitor activity. Confocal microscopy was used to determine the production of biofilms. Results: The isolated P. aeruginosa strains exhibited antibiotic resistance to aminoglycosides (amikacin and gentamicin). Fifty three percent of the isolated P. aeruginosa strains produced metallo-(3-lactamase and the remaining isolates were non-metallo-(3-lactamase type (46.8 %) (p < 0.0001). The MIC value of (3-lactamase producers against colistin ranges from 0.5 g/mL to 6 mu g/mL. The MDR bacteria exhibited mcr-1 and blaNDM-1 genes. The MDR P. aeruginosa strain treated with colistin and ceftazidime inhibited initial biofilm formation. These combination of antibiotics effectively prevented initial biofilm development than individual antibiotics (p < 0.001). Conclusions: The current analysis detected MDR among P. aeruginosa isolates that carried drug-resistant genes.

Motivation Large scale studies involving exploratory data analysis and important key discoveries require platform that provides comprehensive visualization. Density distribution analysis across multiple datasets is intuitive and summarization, visualization could reveal several biological information. Integration and visualization of sequence and annotation features in the context of composition of genomic mutation, microbiota, population are significantly challenging. Results We propose a simple, novel strategy of visualization of multidimensional datasets involving multiple layers of data distribution which are interconnected. Also, we have implemented this phase diagram in an easy-to-use tool QuartPlotR, a resource for plotting charts from different genomic datasets. A generic data access and plotting framework has been designed and this is implemented as an R package. Availability . Contact alaguraj.veluchamy{at}stjude.org Supplementary information Supplementary data are available at Bioinformatics online. ### Competing Interest Statement The authors have declared no competing interest.

Background: The carbapenem-resistant Klebsiella pneumoniae poses a serious threat to public health because carbapenems are used as a final resort to treat K. pneumoniae -mediated infections in humans. Methods: Samples were collected from various clinical specimens including skin swabs, anal swabs, wound swabs, oral swabs, and sputum by the standard method and K. pneumoniae strains were isolated. Biofilm-forming characters were determined. The antibiotic resistance pattern was analyzed by the Kirby -Bauer disk diffusion method. Carbapenem resistance properties were tested using the imipenem and meropenem antibiotics. The carbapenemase genes (bla KPC and bla NDM ) were determined. Results: A total of 11 cephalosporin-resistant K. pneumoniae (CRKP) strains were isolated from the samples. The screened CRKP strains exhibited multi -drug resistance and non -susceptible to imipenem, ceftazidime, piperacillin, ceftriaxone, cefazolin, ampicillin, aztreonam, and cefotetan antibiotics. A total of 79.4 % K. pneumoniae isolates showed positive results on String -forming test. About 82.1 % of isolates showed mucoid colonies and 59 % of K. pneumoniae strains formed biofilm (p < 0.01). Out of 11 isolates, four strains exhibited Klebsiella pneumoniae carbapenemase type, three strains produced metallo- beta-lactamases (MBL), and four strains exhibited as carbapenemase types. A total of 63.5 % Klebsiella pneumoniae carbapenemase-producing strains showed very low MIC value ( <0.05 mg/L). Conclusions: Drug -resistance K. pneumoniae was isolated from clinical specimens that were screened. The continuous monitoring of drug -resistance genes are required to make policy decisions.

High-light stress strongly limits agricultural production in subtropical and tropical regions owing to photooxidative damage, decreased growth, and decreased yield. Here, we investigated whether beneficial microbes can protect plants under high-light stress. We found that Enterobacter sp. SA187 (SA187) supports the growth of Arabidopsis thaliana under high-light stress by reducing the accumulation of reactive oxygen species and maintaining photosynthesis. Under high-light stress, SA187 triggers dynamic changes in the expression of Arabidopsis genes related to fortified iron metabolism and redox regulation, thereby enhancing the antioxidative glutathione/glutaredoxin redox system of the plant. Genetic analysis showed that the enhancement of iron and sulfur metabolism by SA187 is coordinated by ethylene signaling. In summary, beneficial microbes could be an effective and inexpensive means of enhancing high-light-stress tolerance in plants.

Arabidopsis LIM proteins are named after the initials of three proteins Lin-11, Isl-1, and MEC-3, which belong to a class of transcription factors that play an important role in the developmental regulation of eukaryotes and are also involved in a variety of life processes, including gene transcription, the construction of the cytoskeleton, signal transduction, and metabolic regulation. Plant LIM proteins have been shown to regulate actin bundling in different cells, but their role in immunity remains elusive. Mitogen-activated protein kinases (MAPKs) are a family of conserved serine/threonine protein kinases that link upstream receptors to their downstream targets. Pathogens produce pathogen-associated molecular patterns (PAMPs) that trigger the activation of MAPK cascades in plants. Recently, we conducted a large-scale phosphoproteomic analysis of PAMP-induced Arabidopsis plants to identify putative MAPK targets. One of the identified phospho-proteins was WLIM2A, an Arabidopsis LIM protein. In this study, we investigated the role of WLIM2A in plant immunity. We employed a reverse-genetics approach and generated wlim2a knockout lines using CRISPR-Cas9 technology. We also generated complementation and phosphosite-mutated WLIM2A expression lines in the wlim2a background. The wlim2a lines were compromised in their response to Pseudomonas syringae Pst DC3000 but showed enhanced resistance to the necrotrophic fungus Botrytis cinereae. Transcriptome analyses of wlim2a mutants revealed the deregulation of immune hormone biosynthesis and signaling of salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) pathways. The wlim2a mutants also exhibited altered stomatal phenotypes. Analysis of plants expressing WLIM2A variants of the phospho-dead or phospho-mimicking MAPK phosphorylation site showed opposing stomatal behavior and resistance phenotypes in response to Pst DC3000 infection, proving that phosphorylation of WLIM2A plays a crucial role in plant immunity. Overall, these data demonstrate that phosphorylation of WLIM2A by MAPKs regulates Arabidopsis responses to plant pathogens.

The use of beneficial microbes to mitigate drought stress tolerance of plants is of great potential albeit little understood. We show here that a root endophytic desert bacterium, Pseudomonas argentinensis sp. SA190, enhances drought stress tolerance in Arabidopsis. Transcriptome and genetic analysis demonstrate that SA190-induced root morphogenesis and gene expression is mediated via the plant abscisic acid (ABA) pathway. Moreover, we demonstrate that SA190 primes the promoters of target genes in an epigenetic manner which is ABA-dependent. Application of the SA190 priming technology on crops is demonstrated for alfalfa in field trials, showing enhanced performance under desert agriculture conditions. In summary, a single beneficial root bacterial strain can help to perform agriculture under drought and water limiting conditions. Synopsis Beneficial root endophyte Pseudomonas argentinensis sp. SA190 confers drought tolerance in plants SA190 modulates the expression of genes under drought stress in an ABA-dependent manner SA190 primes genes via H3K4me3 histone mark enrichment SA190 alters host plant physiology by improving the plant water status SA190 enhances crop performance in open field conditions with limited irrigation

The use of beneficial microbes to mitigate drought stress tolerance of plants is of great potential albeit little understood. We show here that a root endophytic desert bacterium, Pseudomonas argentinensis strain SA190, enhances drought stress tolerance in Arabidopsis. Transcriptome and genetic analysis demonstrate that SA190-induced root morphogenesis and gene expression is mediated via the plant abscisic acid (ABA) pathway. Moreover, we demonstrate that SA190 primes the promoters of target genes in an epigenetic ABA-dependent manner. Application of SA190 priming on crops is demonstrated for alfalfa, showing enhanced performance under drought conditions. In summary, a single beneficial root bacterial strain can help plants to resist drought conditions.

In CRISPR-Cas and related nuclease-mediated genome editing, target recognition is based on guide RNAs (gRNAs) that are complementary to selected DNA regions. While single site targeting is fundamental for localized genome editing, targeting to expanded and multiple chromosome elements is desirable for various biological applications such as genome mapping and epigenome editing that make use of different fusion proteins with enzymatically dead Cas9. The current gRNA design tools are not suitable for this task, as these are optimized for defining single gRNAs for unique loci. Here, we introduce CRISPR-broad, a standalone, open-source application that defines gRNAs with multiple but specific targets in large continuous or spread regions of the genome, as defined by the user. This ability to identify multi-targeting gRNAs and corresponding multiple targetable regions in genomes is based on a novel aggregate gRNA scoring derived from on-target windows and off-target sites. Applying the new tool to the genomes of two model species, C. elegans and H. sapiens, we verified its efficiency in determining multi-targeting gRNAs and ranking potential target regions optimized for broad targeting. Further, we demonstrated the general usability of CRISPR-broad by cellular mapping of a large human genome element using dCas9 fused to green fluorescent protein.

MAPKs are a family of highly conserved serine/threonine protein kinases that link upstream receptors to their downstream targets which can be localized in the cytoplasm or the nucleus. Pathogens produce pathogen-associated molecular patterns (PAMPs) that trigger the activation of MAPK cascades in plants. Phosphoproteomic analysis of PAMP-induced Arabidopsis plants led to the identification of several putative MAPK targets, WLIM2A. Here, we investigated the role of WLIM2A in plant immunity via a reverse-genetics approach generating wlim2a knockout lines using CRISPR-Cas9, as well as complementation and phosphosite mutated WLIM2A expression lines in the wlim2a background. The wlim2a lines were compromised in their response to Pst DC3000 but showed enhanced resistance to fungal infection by Botrytis cinereae . Transcriptome analyses revealed that immune hormone signaling and biosynthesis genes of salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) are differentially regulated in the wlim2a knockout lines. Pathogen assays with Pst DC3000 showed altered stomatal phenotypes in wlim2a mutants. Importantly, WLIM2A phosphomutants had opposing stomatal behaviour and resistance phenotypes in response to Pst DC3000 infection. Overall, these data show that phosphorylation of WLIM2A by MAPKs regulates Arabidopsis stomatal immunity.

Early prediction and detection enable reduced transmission of human diseases and provide healthcare professionals ample time to make subsequent diagnoses and treatment strategies. This, in turn, aids in saving more lives and results in lower medical costs. Designing small chemical molecules to treat fatal disorders is also urgently needed to address the high death rate of these diseases worldwide. A recent analysis of published literature suggested that deep learning (DL) based models apply more potential algorithms to hybrid databases of chemical data. Considering the above, we first discussed the concept of DL architectures and their applications in drug development and diagnostics in this review. Although DL-based approaches have applications in several fields, in the following sections of the article, we focus on recent developments of DL-based techniques in biology, notably in structure prediction, cancer drug development, COVID infection diagnostics, and drug repurposing strategies. Each review section summarizes several cutting-edge, recently developed DL-based techniques. Additionally, we introduced the approaches presented in our group, whose prediction accuracy is relatively comparable with current computational models. We concluded the review by discussing the benefits and drawbacks of DL techniques and outlining the future paths for data collecting and developing efficient computational models.

Background: Stroke is one of the leading causes of mortality and disability throughout the world. Recently, antioxidant therapies were attempted to reduce apoptotic cell death in cerebral ischemia ani-mal model.Purpose: To study the neuroprotective properties of polyphenol derived from fungal endophyte analyzed on experimental Albino rat. Methods: Polyphenols producing endophytic fungi was initially isolated from the seeds of Moringa olei-fera Lam. The endophytes were cultured in potato dextrose broth and the potent strain Simplicillium sp. ED7 produced maximum phenolic content (86.42 & PLUSMN; 5.3 mg GAE/g) than other fungi. Polyphenols were extracted with solvent and used for the determination of neuroprotective properties.Results: Isoflurane was used to induce stroke in Albino rat and treated polyphenols showed reduced neu-rological deficits and improved neuroprotective properties. The ischemic Albino rats treated with polyphenols restored memory loss. The increased dosage of polyphenol improved the biosynthesis of more antioxidant enzymes than lower dosages. Central artery occlusion evoked about 2.28-fold increase in reactive oxygen species in brain tissue and the generation of reactive oxygen species was decreased in polyphenol treated animal.Conclusion: Albino rats treated with different doses of polyphenol had decrease ROS amount than sham group. The elevated level of cytochrome revealed mitochondrial damage in stroke induced control Albino rat. After 24 h of reperfusion on Albino rat, upregulation of total p65 and phospho-p65 were determined. The present finding revealed that polyphenl has a neuroprotective property in ischemia and regulate metabolic enzymes and restore brain injury.& COPY; 2022 The Author(s). Published by Elsevier B.V. on behalf of King Saud University. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Recent advances in DNA sequencing technologies particularly long-read sequencing, greatly improved genomes assembly. However, this has created discrepancies between published annotations and epigenome tracks, which have not been updated to keep pace with the new assemblies. Here, we used the latest improved telomere-to-telomere assembly of the model pennate diatom Phaeodactylum tricornutum to lift over the gene models from Phatr3, a previously annotated reference genome. We used the lifted genes annotation and newly published transposable elements to map the epigenome landscape, namely DNA methylation and post-translational modifications of histones. This provides the community with PhaeoEpiView, a browser that allows the visualization of epigenome data and transcripts on an updated and contiguous reference genome, to better understand the biological significance of the mapped data. We updated previously published histone marks with a more accurate peak calling using mono instead of poly(clonal) antibodies and deeper sequencing. PhaeoEpiView ( https://PhaeoEpiView.univ-nantes.fr ) will be continuously updated with the newly published epigenomic data, making it the largest and richest epigenome browser of any stramenopile. In the upcoming era of molecular environmental studies, where epigenetics plays a significant role, we anticipate that PhaeoEpiView will become a widely used tool.

BACKGROUND:An ischemic stroke can be caused by thrombosis and ischemia, which is a major public health problem around the world, resulting in severe disability and a high death rate. The goal of this work is to examine and target various heat shock proteins (HSPs) via their interacting partners, which may have an anti-ischemic stroke impact.METHODS:Various heat shock proteins are identified and used for construction of PPI network through STRING webserver. Networks are analysed and visualized using the cytoscape for checking the protein-protein interactions. Along with this, multiple cytoscape based modules are integrated for the analysis of results, and Gene Ontology results are analysed using GOView.RESULTS:The core PPI network was revealed with 129 nodes and 1174 edges. Through Gene ontology (GO) and KEGG enrichment analysis the promising function of HSPs in two important signaling pathways were mainly recorded, representing the HSPs are necessary for repair and activations of brain cells during ischemic stroke. In addition, the study is revelation for targeting multiple HSPs via their interacting partners, which can provide anti-ischemic stroke effect.CONCLUSION:Overall, this finding provides a network-based framework for future research on HSP as therapeutic molecules for anti-ischemic stroke related applications.

Impaired blood supply to part of the brain results in an ischemic stroke leading to dysfunction of brain tissue. Several genetic and environmental factors can contribute to stroke. Age is one of the most important risk factors for ischemic stroke. An increased incidence of stroke related mortalities is associated with aging. The pathophysiological processes triggered by stroke, such as inflammation, apoptosis, angiogenesis, and post-stroke recovery, are well described. However, the molecular mechanisms underlying disease development remain to be studied in detail. The damage and recovery process triggered by stroke is coordinately regulated by genes involved in inflammation, immune response, and angiogenesis. The transcriptional dynamics of these key pathways determine the recovery of brain tissue from damage.The long intergenic non-coding RNAs are the key regulators of gene expression regulation. In the present study, we sought to uncover the potential lncRNAs associated with stroke and aging. In the comparison of young and old Middle cerebral artery occlusion models (MCAo) mouse models with the age-matched controls, we found an up-regulation of 27 and 89 lncRNAs in the young and old mice, respectively, after stroke induction. Similarly, we found down-regulation of 24 lncRNAs in the old mice. In our study, we also found an up-regulation of the host genes for the microRNAs miR142 and mir-675.The potential cis-targets of the up-regulated lncRNAs are related to blood vessel morphogenesis, vascular development, and the immune system. Among the cis-targets of down-regulated lncRNAs, we find enrichment of genes involved in membrane action potential and regulation of blood circulation. Importantly, the magnitude of the cellular and molecular response to stroke correlates with differential expression of lncRNAs and the target genes. In conclusion, we demonstrate the association of lncRNAs with pathophysiological processes during stroke, such as apoptosis, angiogenesis, inflammation, blood-brain barrier breakdown, and neurogenesis.

The attribution of seizure freedom is yet to be achieved for patients suffering from refractory epilepsy, e.g. Dravet Syndrome (DS). The confined ability of mono-chemical entity-based antiseizure drugs (ASDs) to act directly at genomic level is one of the factors, combined with undetermined seizure triggers lead to recurrent seizure (RS) in DS, abominably affecting the sub-genomic architecture of neural cells. Thus, the RS and ASD appear to be responsible for the spectrum of exorbitant clinical pathology. The RS distresses the 5-HT-serotonin pathway, hypomethylates genes of CNS, and modulates the microRNA (miRNA)/long non-coding RNA (lncRNA), eventually leading to frozen molecular alterations. These changes shall be reverted by compatible epigenetic regulators (EGR) like, miRNA and lncRNA from Breast milk (BML) and Bacopa monnieri (BMI). The absence of studious seizure in SCN1A mutation-positive babies for the first 6 months raises the possibility that the consequences of mutation in SCN1A are subsidized by EGRs from BML. EGR-dependent-modifier gene effect is likely imposed by the other members of the SCN family. Therefore, we advocate that miRNA/lncRNA from BML and bacosides/miRNA from BMI buffer the effect of SCN1A mutation by sustainably maintaining modifier gene effect in the aberrant neurons. The presence of miRNA-155-5p, -30b-5p, and -30c-5p family in BML and miR857, miR168, miR156, and miR158 in BMI target at regulating SCN family and CLCN5 as visualized by Cystoscope. Thus, we envisage that the possible effects of EGR might include (a) upregulating the haploinsufficient SCN1A strand, (b) down-regulating seizure-elevated miRNA, (c) suppressing the seizure-induced methyltransferases, and (d) enhancing the GluN2A subunit of NMDA receptor to improve cognition. The potential of these EGRs from BML and BML is to further experimentally strengthen, long-haul step forward in molecular therapeutics.

The function of Immune control, haematopoiesis, and inflammation all depend on the cytokine Interleukin 6 (IL-6), and higher expression of IL-6 is seen in COVID-19 and other diseases. The immune protein IL-6 activation is dependent on binding interactions with IL-6Rα, mIL-6R, and sIL-6R for its cellular function. Termination of these reaction could benefit for controlling the over-expression in COVID-19 patients and that may arise as inhibitors for controlling COVID-19. Traditionally, the goat milk has been prescribed as medicine in ayurvedic practice and through this work, we have explored the benefits of peptides from goat milk as IL-6 inhibitors, and it have the potential of inhibiting the over expression of IL-6 and control the COVID-19 disease. Computational experiments have shown that goat peptides had strong interactions with IL-6, with higher scoring profiles and energy efficiency ranging from −6.00 kcal/mol to −9.00 kcal/mol in docking score and −39.00 kcal/mol in binding energy. Especially the YLGYLEQLLR, VLVLDTDYK and AMKPWIQPK peptides from goat milk holds better scoring and shows strong interactions were identified as the most potential IL-6 inhibitor candidates in this study. Peptides from Goat proteins, which are capable of binding to the IL-6 receptor with strong binding conformations, have no negative effects on other immune system proteins.

Stroke is a genetic condition comprising multiple subtypes and arising from both genic and other multi factors. Genetic basis of stroke is well established through several studies. Advances in integrating sequencing methods and Genome-wide association studies have shown that genetics of stroke is manifested in several genic disorders. Many of the neurodegenerative disorders show aggravated protein aggregation through amyloid formation. Through the protein aggregation prediction, we observed a higher protein disorder in 46 stroke-associated proteins. Also, we observed a large number of aggregation residues distributed as a pattern in multiple regions of these candidate proteins. Overall, we present a study showing that there is a possible interrelationship between protein aggregation and stroke.

Stroke is a neurological syndrome, and it leads to 5.8 million mortalities worldwide annually. In the Kingdom of Saudi Arabia (KSA), stroke was predicted to have 57%-67% incidence rate against a population growth rate of 12.8%. Current state of the art in stroke research in KSA is limited to epidemiological, prevalence data and there is a lack of genetic basis of stroke among Saudi individuals and their risk for disease traits. Despite the better health care services in KSA, a genetic approach is needed for stroke, as it is a manifestation of both monogenic Mendelian and polygenic disorder. Here, we propose to analyze and annotate Saudi specific genome variations associated with stroke. In this study, we explored the non-coding and genic regions using 28 whole genomes of individuals from Saudi population. We explored stroke susceptible genes for additional variation. Analysis of 49 genes which are stroke-associated for single nucleotide polymorphism (SNPs), obtained from whole genomes, reveals variations in atleast 13 candidate genes. In conclusion, whole genome sequencing and annotation of SNPs in the population of Saudi Arabia provide an insight into genetics of stroke. This analysis furnish a list of probable novel Saudi specific mutations that could be associated with stroke, once a cohort of disease data can beobtained. In addition, we conjecture that, by identifying these mutational signatures, stroke subtype and susceptibility to stroke can be uncovered in the future.