Miracle-dz/UniFAR-FTUs huggingface dataset:
Toward predictive R-loop computational biology: genome-scale prediction of R-loops reveals their association with complex promoter structures, G-quadruplexes and transcriptionally active enhancers

R-loops are three-stranded RNA:DNA hybrid structures essential for many normal and pathobiological processes. Previously, we generated a quantitative R-loop forming sequence (RLFS) model, quantitative model of R-loop-forming sequences (QmRLFS) and predicted ∼660 000 RLFSs; most of them located in genes and gene-flanking regions, G-rich regions and disease-associated genomic loci in the human genome. Here, we conducted a comprehensive comparative analysis of these RLFSs using experimental data and demonstrated the high performance of QmRLFS predictions on the nucleotide and genome scales. The preferential co-localization of RLFS with promoters, U1 splice sites, gene ends, enhancers and non-B DNA structures, such as G-quadruplexes, provides evidence for the mechanical linkage between DNA tertiary structures, transcription initiation and R-loops in critical regulatory genome regions. We introduced and characterized an abundant class of reverse-forward RLFS clusters highly enriched in non-B DNA structures, which localized to promoters, gene ends and enhancers. The RLFS colocalization with promoters and transcriptionally active enhancers suggested new models for in cis and in trans regulation by RNA:DNA hybrids of transcription initiation and formation of 3D-chromatin loops. Overall, this study provides a rationale for the discovery and characterization of the non-B DNA regulatory structures involved in the formation of the RNA:DNA interactome as the basis for an emerging quantitative R-loop biology and pathobiology.
Connexin 43 K63-polyubiquitylation on lysines 264 and 303 regulates gap junction internalization

ABSTRACT Gap junctions (GJs) assembled from connexin (Cx) proteins allow direct cell–cell communication. While phosphorylation is known to regulate multiple GJ functions, much less is known about the role of ubiquitin in these processes. Using ubiquitylation-type-specific antibodies and Cx43 lysine-to-arginine mutants we show that ∼8% of a GJ, localized in central plaque domains, is K63-polyubiquitylated on K264 and K303. Levels and localization of ubiquitylation correlated well with: (1) the short turnover rate of Cxs and GJs; (2) removal of older channels from the plaque center; and (3) the fact that not all Cxs in an internalizing GJ channel need to be ubiquitylated. Connexins mutated at these two sites assembled significantly larger GJs, exhibited much longer protein half-lives and were internalization impaired. Interestingly, these ubiquitin-deficient Cx43 mutants accumulated as hyper-phosphorylated polypeptides in the plasma membrane, suggesting that K63-polyubiquitylation is triggered by phosphorylation. Phospho-specific anti-Cx43 antibodies revealed that upregulated phosphorylation affected serines 368, 279/282 and 255, which are well-known regulatory PKC and MAPK sites. Together, these novel findings suggest that the internalizing portion of channels in a GJ is K63-polyubiquitylated, ubiquitylation is critical for GJ internalization and that phosphorylation induces Cx K63-polyubiquitylation. This article has an associated First Person interview with the first author of the paper. Summary: Connexin 43 in gap junctions becomes K63-polyubiquitylated on lysines 264 and 303, which is required for gap junction endocytosis.
A functional type II-A CRISPR–Cas system from Listeria enables efficient genome editing of large non-integrating bacteriophage

Abstract CRISPR–Cas systems provide bacteria with adaptive immunity against invading DNA elements including bacteriophages and plasmids. While CRISPR technology has revolutionized eukaryotic genome engineering, its application to prokaryotes and their viruses remains less well established. Here we report the first functional CRISPR–Cas system from the genus Listeria and demonstrate its native role in phage defense. LivCRISPR-1 is a type II-A system from the genome of L. ivanovii subspecies londoniensis that uses a small, 1078 amino acid Cas9 variant and a unique NNACAC protospacer adjacent motif. We transferred LivCRISPR-1 cas9 and trans-activating crRNA into Listeria monocytogenes. Along with crRNA encoding plasmids, this programmable interference system enables efficient cleavage of bacterial DNA and incoming phage genomes. We used LivCRISPR-1 to develop an effective engineering platform for large, non-integrating Listeria phages based on allelic replacement and CRISPR-Cas-mediated counterselection. The broad host-range Listeria phage A511 was engineered to encode and express lysostaphin, a cell wall hydrolase that specifically targets Staphylococcus peptidoglycan. In bacterial co-culture, the armed phages not only killed Listeria hosts but also lysed Staphylococcus cells by enzymatic collateral damage. Simultaneous killing of unrelated bacteria by a single phage demonstrates the potential of CRISPR–Cas-assisted phage engineering, beyond single pathogen control.
Selenium positively affects the proteome of 3 × Tg‐AD mice cortex by altering the expression of various key proteins: unveiling the mechanistic role of selenium in AD prevention

Selenium (Se) deficiency is believed to be involved in pathogenesis of Alzheimer's disease (AD) due to failure of antioxidant system. Its supplementation may restore the antioxidant system and compensate the impairments caused by AD. Present study reveals the effect of Se on the proteomic changes in cortex within triple transgenic male AD mice (3 × Tg‐AD) after 4 months sodium selenate supplementation. Using iTRAQ comparative proteomics approach, 142 proteins found significant alterations with 96 down‐regulated and 46 up‐regulated proteins in the cortices of AD mice in comparison with the wild non‐transgenic type mice. On treatment with sodium selenate, 41 proteins showed reverse expression, that is, thirty three proteins were down‐regulated in AD mice but up‐regulated in selenate treated AD mice while eight up‐regulated proteins in AD mice showed lower expression in selenate treated mice. OmicsBean bioinformatics analysis revealed that Se positively affected the proteins vital in biological process, structural cores, and molecular functions, which include metabolic proteins, structural proteins, signaling molecules, oxidative stress balancers, and proteosomal degradation proteins. Results of mass spectrometry (MS) were further confirmed by Western blot analysis of five important proteins, prompting the authenticity of the MS results. This paper fills the protein‐based molecular gap between AD and Se‐treatment, and it provides a full view of Se in reversing the change of cortical protein levels during AD formation.
Characterisation and pure culture of putative health-associated oral bacterium BU063 (Tannerella sp. HOT-286) reveals presence of a potentially novel glycosylated S-layer

Tannerella HOT-286 (phylotype BU063) is a recently identified novel filamentous Gram-negative anaerobic oral bacterium cultured for the first time recently in co-culture with Propionibacterium acnes. In contrast to the related periodontal disease-associated pathobiont Tannerella forsythia, it is considered a putative health-associated bacterium. In this paper, we identified that this organism could be grown in pure culture if N-acetyl muramic acid (NAM) was provided in the media, although surprisingly the genetic basis of this phenomenon is not likely to be due to a lack of NAM synthesis genes. During further microbiological investigations, we showed for the first time that T. HOT-286 possesses a prominent extracellular S-layer with a novel morphology putatively made up of two proteins modified with an unknown glycan. These data further our knowledge of this poorly understood organism and genus that is an important part of the oral and human microbiome.
The epiGenomic Efficient Correlator (epiGeEC) tool allows fast comparison of user datasets with thousands of public epigenomic datasets

Summary: In recent years, major initiatives such as the International Human Epigenome Consortium have generated thousands of high‐quality genome‐wide datasets for a large variety of assays and cell types. This data can be used as a reference to assess whether the signal from a user‐provided dataset corresponds to its expected experiment, as well as to help reveal unexpected biological associations. We have developed the epiGenomic Efficient Correlator (epiGeEC) tool to enable genome‐wide comparisons of very large numbers of datasets. A public Galaxy implementation of epiGeEC allows comparison of user datasets with thousands of public datasets in a few minutes. Availability and implementation: The source code is available at https://bitbucket.org/labjacquespe/epigeec and the Galaxy implementation at http://epigeec.genap. ca. Supplementary information: Supplementary data are available at Bioinformatics online.
Comprehensive analysis of the predictors of neurobehavioral symptom reporting in veterans

Objective This study assessed the strength of military-related concussion-, psychological-, and behavioral-related measures to predict neurobehavioral symptom (NBS) reporting in order to help clarify the extent to which persistent NBS reflect lingering effects of concussion vs other psychological/behavioral factors among veterans. Methods Baseline analysis included 351 consecutively enrolled veterans in the Translational Research Center for Traumatic Brain Injury and Stress Disorders longitudinal cohort study. One hundred eighty-six returned for a follow-up evaluation averaging 24 months post baseline. The Neurobehavioral Symptom Inventory (NSI) was used to measure NBS reporting. Predictor variables included diagnosis of military-related mild traumatic brain injury (M-mTBI), psychological measures, including posttraumatic stress disorder, mood, anxiety, and substance abuse disorders, and behavioral measures, including self-reported current pain and sleep impairment. Hierarchical and multivariable regression analyses examined the relationships between the predictor variables and NSI scores. The k-fold cross-validation assessed generalizability and validity of the regressions. Results Baseline analysis revealed that psychological and behavioral conditions independently accounted for 42.5% of variance in the NSI total score compared to 1.5% for M-mTBI after controlling for psychological and behavioral conditions. Prospective analysis revealed that M-mTBI at baseline did not significantly predict NSI score at follow-up, while psychological and behavioral measures at baseline independently accounted for 24.5% of NSI variance. Posttraumatic stress disorder was the most consistent predictor. Cross-validation analyses supported generalizability of the results. Conclusions Psychological and behavioral-related measures are strong predictors of persistent NBS reporting in veterans, while M-mTBI is negligible. NBS more likely reflect influential comorbidities as opposed to brain injury, per se.
Trade‐offs between temporal stability and level of forest ecosystem services provisioning under climate change

Abstract The ability of forests to continuously provide ecosystem services (ES) is threatened by rapid changes in climate and disturbance regimes. Consequently, these changes present a considerable challenge for forest managers. Management of forests often focuses on maximizing the level of ES provisioning over extended time frames (i.e., rotation periods of more than 100 yr). However, temporal stability is also crucial for many ES, for example, in the context of a steady provisioning of resources to the industry, or the protection of human infrastructure against natural hazards. How temporal stability and the level of ES provisioning are related is of increasing interest, particularly since changing climate and disturbance regimes amplify temporal variability in forest ecosystems. In this simulation study, we investigated whether forest management can simultaneously achieve high levels and temporal stability of ES provisioning. Specifically, we quantified (1) trade‐offs between ES stability and level of ES provisioning, and (2) the effect of tree species diversity on ES stability. Simulating a wide range of future climate scenarios and management strategies, we found a negative relationship between temporal stability and level of ES provisioning for timber production, carbon cycling, and site protection in a landscape in the Austrian Alps. Tree species diversity had a predominantly positive effect on ES stability. We conclude that attempts to maximize the level of ES provisioning may increase its temporal variability, and thus threaten the continuity of ES supply. Consequently, considerations of stability need to be more explicitly included in forest management planning under increasingly variable future conditions.
Gloriosa superba Mediated Synthesis of Platinum and Palladium Nanoparticles for Induction of Apoptosis in Breast Cancer

Green chemistry approaches for designing therapeutically significant nanomedicine have gained considerable attention in the past decade. Herein, we report for the first time on anticancer potential of phytogenic platinum nanoparticles (PtNPs) and palladium nanoparticles (PdNPs) using a medicinal plant Gloriosa superba tuber extract (GSTE). The synthesis of the nanoparticles was completed within 5 hours at 100°C which was confirmed by development of dark brown and black colour for PtNPs and PdNPs, respectively, along with enhancement of the peak intensity in the UV-visible spectra. High-resolution transmission electron microscopy (HRTEM) showed that the monodispersed spherical nanoparticles were within a size range below 10 nm. Energy dispersive spectra (EDS) confirmed the elemental composition, while dynamic light scattering (DLS) helped to evaluate the hydrodynamic size of the particles. Anticancer activity against MCF-7 (human breast adenocarcinoma) cell lines was evaluated using MTT assay, flow cytometry, and confocal microscopy. PtNPs and PdNPs showed 49.65 ± 1.99% and 36.26 ± 0.91% of anticancer activity. Induction of apoptosis was most predominant in the underlying mechanism which was rationalized by externalization of phosphatidyl serine and membrane blebbing. These findings support the efficiency of phytogenic fabrication of nanoscale platinum and palladium drugs for management and therapy against breast cancer.
Comparative Effectiveness of Ultrasound-Guided Intratendinous Prolotherapy Injection with Conventional Treatment to Treat Focal Supraspinatus Tendinosis

Objective To evaluate the efficacy of dextrose prolotherapy injection for focal supraspinatus rotator cuff tendinosis via outcomes such as functional score, range of movement, and real-time ultrasound parameters. Materials and Methods 12 adult patients with focal supraspinatus tendinosis recruited after they had less than 30% improvement in functional (DASH) scores after one month of physiotherapy following initial presentation. Seven patients had 0.5–1.0 ml of prolotherapy injection (12.5% dextrose, 0.5% lignocaine) injected into the area of focal tendinosis under ultrasound guidance. Meanwhile, five patients continued standard physiotherapy with no intervention performed. Regional area of echogenicity in decibels, DASH, range of movements of the shoulder, pain, and sleep scores were measured at baseline and at 12 weeks. Results The prolotherapy group showed significant improvement in shoulder abduction (p=0.030) and an improvement in sleep score (p=0.027). The echogenicity of area of tendinosis significantly increases at the end of treatment (p=0.009). However, there was a nonsignificant reduction in pain score in the injection group (43.5%) and in the control group (25%) at 12 weeks (p > 0.005). Conclusion Ultrasound-guided intratendinous prolotherapy injection significantly improves patient's range of abduction and improves sleep within 12 weeks of treatment compared to conventional physiotherapy management. Trial Registration This study was registered under Current Controlled Trials (UK) and given International Standard Randomised Controlled Trial Number (ISRCTN) of 43520960.
Interspecies Anticancer and Antimicrobial Activities of Genus Solanum and Estimation of Rutin by Validated UPLC-PDA Method

Solanaceae is one of the highly diverse plant families of which Solanum is the largest genera (1700 species) containing several pharmacological properties like anticancer and antimicrobial. This motivated us to explore the anticancer (against HepG2, HEK-293, and MCF-7 cells) and antimicrobial (against S. aureus, E. coli, P. aeruginosa, and C. albicans) properties of S. schimperianum, S. villosum, S. coagulans, S. glabratum, S. incanum, and S. nigrum along with rutin estimation by UPLC-PDA method. Of the studied Solanum extracts, S. nigrum exhibited significant cytotoxic property against HepG2 (IC50: 20.4 μg/mL) and MCF-7 (IC50: 30.1 μg/mL); S. coagulans showed toxicity against HepG2 (IC50: 28.4 μg/mL) and HEK-293 cells (IC50: 25.7 μg/mL) compared to 5-Fluorouracil (standard). Compared to these, extracts of S. coagulans and S. glabratum exhibited relatively high antimicrobial potency (MIC: 0.4-1.6 mg/mL). Nonetheless, all Solanum extracts significantly reduced the biofilm against PAO1-strain. Rutin was detected in all extracts with the highest content (53.79 μg/mg) in S. coagulans that supported its strong antimicrobial and anticancer properties. Molecular docking analysis showing strong binding of rutin with human DNA and proteins (DNA Topoisomerase IIα and E. coli DNA gyrase B) supported the anticancer and antimicrobial activities of Solanum species.
Expanding the miRNA Transcriptome of Human Kidney and Renal Cell Carcinoma

Despite advancements in therapeutic strategies, diagnostic and prognostic molecular markers of kidney cancer remain scarce, particularly in patients who do not harbour well-defined driver mutations. Recent evidence suggests that a large proportion of the human noncoding transcriptome has escaped detection in early genomic explorations. Here, we undertake a large-scale analysis of small RNA-sequencing data from both clear cell renal cell carcinoma (ccRCC) and nonmalignant samples to generate a robust set of miRNAs that remain unannotated in kidney tissues. We find that these novel kidney miRNAs are also expressed in renal cancer cell lines. Moreover, these sequences are differentially expressed between ccRCC and matched nonmalignant tissues, implicating their involvement in ccRCC biology and potential utility as tumour-specific markers of disease. Indeed, we find some of these miRNAs to be significantly associated with patient survival. Finally, target prediction and subsequent pathway analysis reveals that miRNAs previously unannotated in kidney tissues may target genes involved in ccRCC tumourigenesis and disease biology. Taken together, our results represent a new resource for the study of kidney cancer and underscore the need to characterize the unexplored areas of the transcriptome.
MIF mRNA Expression and Soluble Levels in Acute Coronary Syndrome

Acute coronary syndrome (ACS) describes any condition characterized by myocardial ischaemia and reduction in blood flow. The physiopathological process of ACS is the atherosclerosis where MIF operates as a major regulator of inflammation. The aim of this study was to assess the mRNA expression of MIF gene and its serum levels in the clinical manifestations of ACS and unrelated individuals age- and sex-matched with patients as the control group (CG). All samples were run using the conditions indicated in TaqMan Gene Expression Assay protocol. Determination of MIF serum levels were performed by enzyme-linked immunosorbent assay and MIF ELISA Kit. ST-segment elevation myocardial infraction (STEMI) and non-ST-segment elevation myocardial infarction (NSTEMI) showed 0.8 and 0.88, respectively, less expression of MIF mRNA with regard to CG. UA and STEMI presented more expression than NSTEMI 5.23 and 0.68, respectively. Otherwise, ACS patients showed significant higher MIF serum levels (p=0.02) compared with CG. Furthermore, the highest soluble levels of MIF were presented by STEMI (11.21 ng/dL), followed by UA (10.34 ng/dL) and finally NSTEMI patients (8.75 ng/dL); however, the differences were not significant. These novel observations further establish the process of MIF release after cardiovascular events and could support the idea of MIF as a new cardiac biomarker in ACS.
Diagnosis of Encephalopathy Based on Energies of EEG Subbands Using Discrete Wavelet Transform and Support Vector Machine

EEG analysis in the field of neurology is customarily done using frequency domain methods like fast Fourier transform. A complex biomedical signal such as EEG is best analysed using a time-frequency algorithm. Wavelet decomposition based analysis is a relatively novel area in EEG analysis and for extracting its subbands. This work aims at exploring the use of discrete wavelet transform for extracting EEG subbands in encephalopathy. The subband energies were then calculated and given as feature sets to SVM classifier for identifying cases of encephalopathy from normal healthy subjects. Out of various combinations of subband energies, energy of delta subband yielded highest performance parameters for SVM classifier with an accuracy of 90.4% in identifying encephalopathy cases.
Antistaphylococcal and Antibiotic Resistance Modulatory Activities of Thirteen Cameroonian Edible Plants against Resistant Phenotypes

Background In this study, 18 methanol extracts from Cameroonian edible plants were tested for their antibacterial activities against 26 strains of S. aureus; the role of efflux pumps in the resistance of tested bacteria and the antibiotic resistance-modulating activities against selected multidrug-resistant (MDR) phenotypes were also investigated. Methods Broth microdilution assay was used to evaluate the antibacterial activity, the role of efflux pumps, and the antibiotic resistance-modulating effects of plant extracts. Results Extracts from Dacryodes edulis seeds (DES) and Dacryodes edulis bark (DEB) were active against all 26 tested bacterial strains, within the minimal inhibitory concentration (MIC) range of 256–1024 µg/mL. MIC values varied from 64 to 1024 µg/mL against 96.2% of the 26 tested bacteria for Phaseolus vulgaris leaves (PVL), 92.3% for Azadirachta indica bark (AIB), Dacryodes edulis leaves (DEL), and Ricinodendron heudelotii leaves (RHL). The lowest MIC value of 64 µg/mL was obtained with the extract from Cucurbita maxima beans (CMB) against MRSA4 strain and from Uapaca guineensis bark (UGB) against MRSA9 strain. Bacterial efflux pump inhibitor (EPI), carbonyl cyanide m-chlorophenyl hydrazone (CCCP), improved the activity of DES and UGB as well as that of extracts from Hibiscus esculentus leaves (HEL) and Uapaca guineensis leaves (UGL) against resistant S. aureus strains. Antibiotic-modulating effects against more than 70% of the S. aureus strains tested were obtained when RHL (at MIC/2) was combined with CIP, ERY, and KAN (88.89%), CHL (88.89%), TET (77.78%), and STR (88.89%). Conclusion The present study demonstrated that the 13 tested plants had antistaphylococcal effects and that DES, HEL, UGL, and UGB could be used in combination with EPI to combat resistance to Staphylococcus aureus. Also, it demonstrated that some studied extracts and mostly RHL could be used as antibiotic resistance modulators to fight against resistant strains of S. aureus.