Miracle-dz/UniFAR-FTUs huggingface dataset:
Antisense-mediated repression of SAGA-dependent genes involves the HIR histone chaperone

Eukaryotic genomes are pervasively transcribed by RNA polymerase II (RNAPII), and transcription of long non-coding RNAs often overlaps with coding gene promoters. This might lead to coding gene repression in a process named Transcription Interference (TI). In Saccharomyces cerevisiae (S. cerevisiae), TI is mainly driven by antisense non-coding transcription and occurs through re-shaping of promoter Nucleosome-Depleted Regions (NDRs). In this study, we developed a genetic screen to identify new players involved in Antisense-Mediated Transcription Interference (AMTI). Among the candidates, we found the HIR histone chaperone complex known to be involved in de novo histone deposition. Using genome-wide approaches, we reveal that HIR-dependent histone deposition represses the promoters of SAGA-dependent genes via antisense non-coding transcription. However, while antisense transcription is enriched at promoters of SAGA-dependent genes, this feature is not sufficient to define the mode of gene regulation. We further show that the balance between HIR-dependent nucleosome incorporation and transcription factor binding at promoters directs transcription into a SAGA- or TFIID-dependent regulation. This study sheds light on a new connection between antisense non-coding transcription and the nature of coding transcription initiation.
Identification of potential carboxylic acid-containing drug candidate to design novel competitive NDM inhibitors: An in-silico approach comprising combined virtual screening and molecular dynamics simulation

Metallo-β-lactamases (MBLs) producing bacteria especially the ones with New Delhi metallo-beta-lactamase-1 (NDM-1) and its variants can potentially hydrolyse all the major β-lactam antibiotics, ultimately escalating anti-microbial resistance world-wide. There is a dearth of approved inhibitors to combat NDM and other MBLs producing bacteria. Hence we focussed to find novel inhibitor(s) in-silico which can potentially suppress the activity of NDM/ MBLs. 2400 compounds were virtually screened to identify a promising carboxylic acid-containing compound (CID-53986787) analogous to NDM antagonist Captopril. Our lead compound can bind adjacent to the active site zinc ions (Zn1 and Zn2) in all highly resistant NDM variants. CID-53986787 possesses ~5-8% higher binding affinity than Captopril, exhibiting molecular interactions with crucial residues that can destabilize the hydrolytic activity of NDM. CID-53986787 was virtually evaluated to ascertain its safe pharmacological/ toxicity profile. Molecular dynamics simulation studies elucidated its stable interaction with the target protein (NDM-1).
Global evolutionary dynamics and resistome analysis of Clostridioides difficile ribotype 017

Clostridioides difficile PCR ribotype (RT) 017 ranks among the most successful strains of C. difficile in the world. In the past three decades, it has caused outbreaks on four continents, more than other “epidemic” strains, however, our understanding of the genomic epidemiology underpinning the spread of C. difficile RT 017 is limited. Here, we performed high-resolution phylogenomic and Bayesian evolutionary analyses on an updated and more representative dataset of 282 non-clonal C. difficile RT 017 isolates collected worldwide between 1981 and 2019. These analyses place an estimated time of global dissemination between 1953 and 1983 and identified the acquisition of the ermB-positive transposon Tn6194 as a key factor behind global emergence. This coincided with the introduction of clindamycin, a key inciter of C. difficile infection, into clinical practice in the 1960s. Based on the genomic data alone, the origin of C. difficile RT 017 could not be determined, however, geographical data and records of population movement suggest that C. difficile RT 017 had been moving between Asia and Europe since the Middle Ages and was later transported to North America around 1860 (95% CI: 1622 – 1954). A focused epidemiological study of 45 clinical C. difficile RT 017 genomes from a cluster in a tertiary hospital in Thailand revealed that the population consisted of two groups of multidrug-resistant (MDR) C. difficile RT 017 and a group of early, non-MDR C. difficile RT 017. The significant genomic diversity within each MDR group suggests that although they were all isolated from hospitalised patients, there was likely a reservoir of C. difficile RT 017 in the community that contributed to the spread of this pathogen. Impact statement This study utilises genomic sequence data from 282 non-clonal C. difficile ribotype (RT) 017 isolates collected from around the world to delineate the origin and spread of this epidemic lineage, as well as explore possible factors that have driven its success. It also reports a focused epidemiological investigation of a cluster of C. difficile RT 017 in a tertiary hospital in Thailand to identify possible sources of transmission in this specific setting. Data summary All new WGS data generated in this study has been submitted to the European Nucleotide Archive under the BioProject PRJEB44406 (sample accession ERS6268756 – ERS6268798). The complete genome of C. difficile MAR286 was submitted to GenBank under BioProject PRJNA679085 (accession CP072118). Details of all genomes included in the final analyses are available in the Supplementary Document, available at 10.6084/m9.figshare. 14544792.
Transcriptomic response of Cinachyrella cf. cavernosa sponges to spatial competition

Spatial competition in the intertidal zones drives the community structure in marine benthic habitats. Organisms inhabiting these areas not only need to withstand fluctuations of temperature, water level, pH, and salinity, but also need to compete for the best available space. Sponges are key members of the intertidal zones, and their life history processes (e.g. growth, reproduction, and regeneration) are affected by competition. Here we used transcriptomics to investigate the effects of interspecific competition between the tetillid sponge Cinachyrella cf. cavernosa, the zoantharid Zoanthus sansibaricus, and the macroalgae Dictyota ciliolata. The analysis of differentially expressed genes showed that Z. sansibaricus was the most stressful competitor to C. cf. cavernosa, which showed an increased rate of cellular respiration under stress of competition. Similarly, an up-regulation of energy metabolism, lipid metabolism, and the heat-shock protein (HSP) 70 was also observed along with an indication of a viral infection and decreased ability to synthesise protein. A down-regulation of purine and pyrimidine metabolism indicated reduction in physiological activities of the competing sponges. Moreover, a putative case of possible kleptocnidism, not previously reported in Cinachyrella cf. cavernosa was also observed. This study opens the door for more detailed investigations of marine organisms competing for spatial resources using transcriptome data.
A local insulin reservoir ensures developmental progression in condition of nutrient shortage in Drosophila

Insulin/IGF signalling (IIS) controls many aspects of development and physiology. In Drosophila, a conserved family of insulin-like peptides (Ilp) is produced by brain neurosecretory cells and exerts systemic functions. Here, we describe the local uptake and storage of Ilps in the Corpora Cardiaca (CC), a group of alpha cell homolog that produces the glucagon-like hormone AKH. Dilp uptake relies on the expression of Impl2, an IGF-BP that accumulates in the CCs. During nutrient shortage, this specific reserve of Ilps is released and activates IIS in a paracrine manner in the prothoracic gland, securing accelerated entry into pupal development through the production of the steroid hormone ecdysone. We therefore uncover a sparing mechanism whereby local Ilp storage and release activates the production of steroids and ensures early developmental progression in adverse food conditions. Highlights - Dilps are uptaken by CC cells through the IGF-BP Imp-L2 - the CC-Dilp store is released upon nutrient shortage and activates IIS through CC projections on the PG - upon nutrient shortage, IIS activation in the PG ensures an accelerated transition from larval feeding stage to metamorphosis.
A chromatin phase transition protects mitotic chromosomes against microtubule perforation

Dividing eukaryotic cells package extremely long chromosomal DNA molecules into discrete bodies to enable microtubule-mediated transport of one genome copy to each of the newly forming daughter cells1–3. Assembly of mitotic chromosomes involves DNA looping by condensin4–8 and chromatin compaction by global histone deacetylation9–13. While condensin confers mechanical resistance towards spindle pulling forces14–16, it is not known how histone deacetylation affects material properties and segregation mechanics of mitotic chromosomes. Here, we show how global histone deacetylation at the onset of mitosis induces a chromatin-intrinsic phase transition that endows chromosomes with specific characteristics necessary for their precise movement during cellular division. Deacetylation-mediated compaction of chromatin forms a structure dense in negative charge and allows mitotic chromosomes to resist perforation by microtubules as they are pushed to the metaphase plate. Hyperacetylated mitotic chromosomes lack a defined surface boundary, are frequently perforated by microtubules, and are prone to missegregation. Our study highlights the different contributions of DNA loop formation and chromatin-intrinsic phase separation to genome segregation in dividing cells.
CcnA, a novel non-coding RNA regulating the bacterial cell cycle

Bacterial cells are powerful models for understanding how cells divide and accomplish global regulatory programs. In Caulobacter crescentus a cascade of essential master regulators regulate the correct and sequential activation of DNA replication, cell division and development of different cell types. Among them CtrA plays a crucial role coordinating all those functions. Despite decades of investigation, no control by non-coding RNAs (ncRNAs) has been linked to Caulobacter cell cycle. Here, for the first time we describe the role of a novel essential factor named CcnA, a ncRNA located at the origin of replication, activated by CtrA and responsible for the rapid and strong accumulation of CtrA itself. In addition CcnA is also responsible for the inhibition of GcrA translation by direct interaction with its UTR region. By a combination of probing experiments and mutagenesis, we propose a new mechanism by liberation (CtrA) or sequestration (GcrA) of the Ribosome Binding Site (RBS). CcnA role is conserved in other alphaproteobacterial species, such as Sinorhizobium meliloti, representing indeed a conserved and fundamental process regulating cell cycle in Rhizobiales and Caulobacterales.
Of Beavers and Tables: The Role of Animacy in the Processing of Grammatical Gender Within a Picture-Word Interference Task

Grammatical gender processing during language production has classically been studied using the so-called picture-word interference (PWI) task. In this procedure, participants are presented with pictures they must name using target nouns while ignoring superimposed written distractor nouns. Variations in response times are expected depending on the congruency between the gender values of targets and distractors. However, there have been disparate results in terms of the mandatory character of an agreement context to observe competitive gender effects and the interpretation of the direction of these effects in Romance languages, this probably due to uncontrolled variables such as animacy. In the present study, we conducted two PWI experiments with European Portuguese speakers who were asked to produce bare nouns. The percentage of animate targets within the list was manipulated: 0, 25, 50, and 100%. A gender congruency effect was found restricted to the 0% list (all targets were inanimate). Results support the selection of gender in transparent languages in the absence of an agreement context, as predicted by the Gender Acquisition and Processing (GAP) hypothesis (Sá-Leite et al., 2019), and are interpreted through the attentional mechanisms involved in the PWI paradigm, in which the processing of animate targets would be favored to the detriment of distractors due to biological relevance and semantic prioritization.
Facile synthesis of stereoregular carbon fiber precursor polymers by template assisted solid phase polymerization

Predominantly isotactic stereoregular polyacrylonitrile copolymers (PAC) were prepared by solid phase polymerization techniques using hexagonal crystalline metal salts as template compounds. Stereoregular distributions of the prepared polymer were studied using high resolution 13C nuclear magnetic resonance spectroscopy (13C NMR) spectra. The extent of isotacticity was directly determined from the peak intensity of the methine carbon (CH). The triad tacticity from the intensities of methine carbon peaks were examined by statistical methods. It was found that the PAC was predominantly isotactic in stereoregularity, and its sequence distribution obeys Bernoulli statistics. The optimum polymerization conditions ensuring isotactic content over 50% were disclosed experimentally. The chemical composition of PAC was confirmed with 1H NMR data. The obtained polyacrylonitrile copolymers were also characterized for molecular parameters such as viscosity average molecular weight (Mv), number average molecular weight (Mn), weight average molecular weight (Mw) and polydispersity index.
Protein Kinase R in Bacterial Infections: Friend or Foe?

The global antimicrobial resistance crisis poses a significant threat to humankind in the coming decades. Challenges associated with the development of novel antibiotics underscore the urgent need to develop alternative treatment strategies to combat bacterial infections. Host-directed therapy is a promising new therapeutic strategy that aims to boost the host immune response to bacteria rather than target the pathogen itself, thereby circumventing the development of antibiotic resistance. However, host-directed therapy depends on the identification of druggable host targets or proteins with key functions in antibacterial defense. Protein Kinase R (PKR) is a well-characterized human kinase with established roles in cancer, metabolic disorders, neurodegeneration, and antiviral defense. However, its role in antibacterial defense has been surprisingly underappreciated. Although the canonical role of PKR is to inhibit protein translation during viral infection, this kinase senses and responds to multiple types of cellular stress by regulating cell-signaling pathways involved in inflammation, cell death, and autophagy – mechanisms that are all critical for a protective host response against bacterial pathogens. Indeed, there is accumulating evidence to demonstrate that PKR contributes significantly to the immune response to a variety of bacterial pathogens. Importantly, there are existing pharmacological modulators of PKR that are well-tolerated in animals, indicating that PKR is a feasible target for host-directed therapy. In this review, we provide an overview of immune cell functions regulated by PKR and summarize the current knowledge on the role and functions of PKR in bacterial infections. We also review the non-canonical activators of PKR and speculate on the potential mechanisms that trigger activation of PKR during bacterial infection. Finally, we provide an overview of existing pharmacological modulators of PKR that could be explored as novel treatment strategies for bacterial infections.
Mirror Visual Feedback Prior to Robot-Assisted Training Facilitates Rehabilitation After Stroke: A Randomized Controlled Study

Purpose: Robot-assisted training has been widely used in neurorehabilitation, but its effect on facilitating recovery after stroke remains controversial. One possible reason might be lacking consideration of the role of embodiment in robotic systems. Mirror visual feedback is an ideal method to approach embodiment. Thus, we hypothesized that mirror visual feedback priming with subsequent robot-assisted training might provide additional treatment benefits in rehabilitation. Method: This is a prospective, assessor-blinded, randomized, controlled study. Forty subacute stroke patients were randomly assigned into an experimental group (N = 20) or a control group (N = 20). They received either mirror visual feedback or sham-mirror visual feedback prior to robot-assisted training for 1.5 h/day, 5 days/week for 4 weeks. Before and after intervention, the Fugl-Meyer Assessment Upper Limb subscale, the Functional Independence Measure, the modified Barthel Index, and grip strength were measured. Scores of four specified games were recorded pre and post one-time mirror visual feedback priming before intervention in the experimental group. Results: All measurements improved significantly in both groups following interventions. Moreover, the Fugl-Meyer Assessment Upper Limb subscale, self-care subscale of the Functional Independence Measure, and the grip strength were improved significantly in the experimental group after a 4-week intervention, compared with the control group. Significantly higher scores of two games were revealed after one-time priming. Conclusions: Mirror visual feedback prior to robot-assisted training could prompt motor recovery, increase ability of self-care, and potentially enhance grip strength in stroke patients, compared to control treatment. Moreover, mirror visual feedback priming might have the capability to improve the patient's performance and engagement during robot-assisted training, which could prompt the design and development of robotic systems. Clinical Trial Registration: www.ClinicalTrials. gov, identifier: ChiCTR1900023356.
The Sensitivity of the Marine Carbonate System to Regional Ocean Alkalinity Enhancement

Ocean Alkalinity Enhancement (OAE) simultaneously mitigates atmospheric concentrations of CO2 and ocean acidification; however, no previous studies have investigated the response of the non-linear marine carbonate system sensitivity to alkalinity enhancement on regional scales. We hypothesise that regional implementations of OAE can sequester more atmospheric CO2 than a global implementation. To address this, we investigate physical regimes and alkalinity sensitivity as drivers of the carbon-uptake potential response to global and different regional simulations of OAE. In this idealised ocean-only set-up, total alkalinity is enhanced at a rate of 0.25 Pmol a-1 in 75-year simulations using the Max Planck Institute Ocean Model coupled to the HAMburg Ocean Carbon Cycle model with pre-industrial atmospheric forcing. Alkalinity is enhanced globally and in eight regions: the Subpolar and Subtropical Atlantic and Pacific gyres, the Indian Ocean and the Southern Ocean. This study reveals that regional alkalinity enhancement has the capacity to exceed carbon uptake by global OAE. We find that 82–175 Pg more carbon is sequestered into the ocean when alkalinity is enhanced regionally and 156 PgC when enhanced globally, compared with the background-state. The Southern Ocean application is most efficient, sequestering 12% more carbon than the Global experiment despite OAE being applied across a surface area 40 times smaller. For the first time, we find that different carbon-uptake potentials are driven by the surface pattern of total alkalinity redistributed by physical regimes across areas of different carbon-uptake efficiencies. We also show that, while the marine carbonate system becomes less sensitive to alkalinity enhancement in all experiments globally, regional responses to enhanced alkalinity vary depending upon the background concentrations of dissolved inorganic carbon and total alkalinity. Furthermore, the Subpolar North Atlantic displays a previously unexpected alkalinity sensitivity increase in response to high total alkalinity concentrations.
Knockdown of CNN3 Impairs Myoblast Proliferation, Differentiation, and Protein Synthesis via the mTOR Pathway

Background Myogenesis is a complex process that requires optimal outside–in substrate–cell signaling. Calponin 3 (CNN3) plays an important role in regulating myogenic differentiation and muscle regeneration; however, the precise function of CNN3 in myogenesis regulation remains poorly understood. Here, we investigated the role of CNN3 in a knockdown model in the mouse muscle cell line C2C12. Methods Myoblast proliferation, migration, differentiation, fusion, and protein synthesis were examined in CNN3 knockdown C2C12 mouse muscle cells. Involvement of the mTOR pathway in CNN3 signaling was explored by treating cells with the mTOR activator MHY1485. The regulatory mechanisms of CNN3 in myogenesis were further examined by RNA sequencing and subsequent gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene set enrichment analysis (GSEA). Results During proliferation, CNN3 knockdown caused a decrease in cell proliferation and migration. During differentiation, CNN3 knockdown inhibited myogenic differentiation, fusion, and protein synthesis in C2C12 cells via the AKT/mTOR and AMPK/mTOR pathways; this effect was reversed by MHY1485 treatment. Finally, KEGG and GSEA indicated that the NOD-like receptor signaling pathway is affected in CNN3 knockdown cell lines. Conclusion CNN3 may promote C2C12 cell growth by regulating AKT/mTOR and AMPK/mTOR signaling. The KEGG and GSEA indicated that inhibiting CNN3 may activate several pathways, including the NOD-like receptor pathway and pathways involved in necroptosis, apoptosis, and inflammation.
Atrial Natriuretic Peptide31–67: A Novel Therapeutic Factor for Cardiovascular Diseases

The characterization of the cardiac hormone atrial natriuretic peptide (ANP99–126), synthesized and secreted predominantly by atrial myocytes under stimulation by mechanical stretch, has established the heart as an endocrine organ with potent natriuretic, diuretic, and vasodilating actions. Three additional distinct polypeptides resulting from proteolytic cleavage of proANP have been identified in the circulation in humans. The mid-sequence proANP fragment 31–67 (also known as proANP31–67) has unique potent and prolonged diuretic and natriuretic properties. In this review, we report the main effects of this circulating hormone in different tissues and organs, and its mechanisms of actions. We further highlight recent evidence on the cardiorenal protective actions of chronic supplementation of synthetic proANP31–67 in preclinical models of cardiorenal disease. Finally, we evaluate the use of proANP31–67 as a new therapeutic strategy to repair end-organ damage secondary to hypertension, diabetes mellitus, renal diseases, obesity, heart failure, and other morbidities that can lead to impaired cardiac function and structure.