Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacitracin sensing in Bacillus subtilis

The extracellular presence of antibiotics is a common threat in microbial life. Their sensitive detection and subsequent induction of appropriate resistance mechanisms is therefore a prerequisite for survival. The bacitracin stress response network of Bacillus subtilis consists of four signal‐transducing systems, the two‐component systems (TCS) BceRS, YvcPQ and LiaRS, and the extracytoplasmic function (ECF) σ factor σM. Here, we investigated the mechanism of bacitracin perception and the response hierarchy within this network. The BceRS–BceAB TCS/ABC transporter module is the most sensitive and efficient bacitracin resistance determinant. The ABC transporter BceAB not only acts as a bacitracin detoxification pump, but is also crucial for bacitracin sensing, indicative of a novel mechanism of stimulus perception, conserved in Firmicutes bacteria. The Bce system seems to respond to bacitracin directly (drug sensing), whereas the LiaRS TCS and σM respond only at higher concentrations and indirectly to bacitracin action (damage sensing). The YvcPQ–YvcRS system is subject to cross‐activation via the paralogous Bce system, and is therefore only indirectly induced by bacitracin. The bacitracin stress response network is optimized to respond to antibiotic gradients in a way that maximizes the gain and minimizes the costs of this stress response.
A Csr‐type regulatory system, including small non‐coding RNAs, regulates the global virulence regulator RovA of Yersinia pseudotuberculosis through RovM

The MarR‐type regulator RovA controls expression of virulence genes of Yersinia pseudotuberculosis in response to environmental signals. Using a genetic strategy to discover components that influence rovA expression, we identified new regulatory factors with homology to components of the carbon storage regulator system (Csr). We showed that overexpression of a CsrB‐ or a CsrC‐type RNA activates rovA, whereas a CsrA‐like protein represses RovA synthesis. We further demonstrate that influence of the Csr system on rovA is indirect and occurs through control of the LysR regulator RovM, which inhibits rovA transcription. The CsrA protein had also a major influence on the motility of Yersinia, which was independent of RovM. The CsrB and CsrC RNAs are differentially expressed in Yersinia. CsrC is highly induced in complex but not in minimal media, indicating that medium‐dependent rovM expression is mediated through CsrC. CsrB synthesis is generally very low. However, overexpression of the response regulator UvrY was found to activate CsrB production, which in turn represses CsrC synthesis independent of the growth medium. In summary, the post‐transcriptional Csr‐type components were shown to be key regulators in the co‐ordinated environmental control of physiological processes and virulence factors, which are crucial for the initiation of Yersinia infections.
Scavenger receptor gp340 aggregates group A streptococci by binding pili

Group A streptococci (GAS) are the most frequent cause of bacterial pharyngitis. The first obstacle to GAS colonization of the pharynx is saliva. As well as forming a physical barrier, saliva contains components of innate and acquired immunity. Previous work has shown that saliva induces bacterial aggregation, which may serve as a clearance mechanism. As the aggregation of some oral streptococci in saliva is mediated by long proteinaceous appendages, we hypothesized that pili of GAS might behave similarly. Wild‐type GAS M1 strain SF370 aggregated in saliva, while pilus‐defective mutants did not. Similarly, heterologous expression of diverse GAS pili on the surface of Lactococcus lactis induced aggregation in saliva, while control strains were unaffected. Further studies revealed that aggregating bacteria bound salivary component gp340. Purified gp340 aggregated wild‐type GAS and L. lactis expressing GAS pili, but not control strains. GAS pilus‐defective mutants were abrogated in gp340 binding and aggregation. Furthermore, gp340‐mediated aggregation reduced bacterial adhesion to human epithelial cells, suggesting a role in host defence.
The global, ppGpp‐mediated stringent response to amino acid starvation in Escherichia coli

The stringent response to amino acid starvation, whereby stable RNA synthesis is curtailed in favour of transcription of amino acid biosynthetic genes, is controlled by the alarmone ppGpp. To elucidate the extent of gene expression effected by ppGpp, we designed an experimental system based on starvation for isoleucine, which could be applied to both wild‐type Escherichia coli and the multiauxotrophic relA spoT mutant (ppGpp0). We used microarrays to profile the response to amino acid starvation in both strains. The wild‐type response included induction of the general stress response, downregulation of genes involved in production of macromolecular structures and comprehensive restructuring of metabolic gene expression, but not induction of amino acid biosynthesis genes en masse. This restructuring of metabolism was confirmed using kinetic Biolog assays. These responses were profoundly altered in the ppGpp0 strain. Furthermore, upon isoleucine starvation, the ppGpp0 strain exhibited a larger cell size and continued growth, ultimately producing 50% more biomass than the wild‐type, despite producing a similar amount of protein. This mutant phenotype correlated with aberrant gene expression in diverse processes, including DNA replication, cell division, and fatty acid and membrane biosynthesis. We present a model that expands and functionally integrates the ppGpp‐mediated stringent response to include control of virtually all macromolecular synthesis and intermediary metabolism.
The essentiality and involvement of Streptococcus intermedius histone‐like DNA‐binding protein in bacterial viability and normal growth

Streptococcus intermedius histone‐like DNA‐binding protein (Si‐HLP) is a homodimeric protein and, conserved with Escherichia coli HU, a well‐documented nucleoid‐associated protein (NAP). In E. coli, HU plays important roles as both structural and regulatory factors, but it is not essential for E. coli viability. Streptococcal HLP has been found to bind host cells and induce cytokine production, but its physiological role remains poorly defined. In the present study, using gene insertion knockout and tetracycline‐regulated antisense RNA expression techniques, we determined whether Si‐HLP is essential for bacterial viability and normal growth in S. intermedius. The Si‐HLP‐downregulated S. intermedius strain showed alterations in its morphology and surface properties. Downregulation of Si‐HLP led to an expanded nucleoid to fill the intracellular space. Transcription levels of several genes, including virulence‐associated factors, were found to be activated or repressed in the antisense Si‐hlp RNA‐expressing strain by real‐time PCR and reverse‐transcription PCR. Collectively, these data suggest that Si‐HLP serves as an essential NAP governing the nucleoid architecture and controlling the gene transcription profile in S. intermedius.
Fibroblast growth factor 2 (FGF2) regulates cytoglobin expression and activation of human hepatic stellate cells via JNK signaling

Cytoglobin (CYGB) belongs to the mammalian globin family and is exclusively expressed in hepatic stellate cells (HSCs) in the liver. In addition to its gas-binding ability, CYGB is relevant to hepatic inflammation, fibrosis, and cancer because of its anti-oxidative properties; however, the regulation of CYGB gene expression remains unknown. Here, we sought to identify factors that induce CYGB expression in HSCs and to clarify the molecular mechanism involved. We used the human HSC cell line HHSteC and primary human HSCs isolated from intact human liver tissues. In HHSteC cells, treatment with a culture supplement solution that included fibroblast growth factor 2 (FGF2) increased CYGB expression with concomitant and time-dependent α-smooth muscle actin (αSMA) down-regulation. We found that FGF2 is a key factor in inducing the alteration in both CYGB and αSMA expression in HHSteCs and primary HSCs and that FGF2 triggered the rapid phosphorylation of both c-Jun N-terminal kinase (JNK) and c-JUN. Both the JNK inhibitor PS600125 and transfection of c-JUN–targeting siRNA abrogated FGF2-mediated CYGB induction, and conversely, c-JUN overexpression induced CYGB and reduced αSMA expression. Chromatin immunoprecipitation analyses revealed that upon FGF2 stimulation, phospho-c-JUN bound to its consensus motif (5′-TGA(C/G)TCA), located −218 to −222 bases from the transcription initiation site in the CYGB promoter. Of note, in bile duct–ligated mice, FGF2 administration ameliorated liver fibrosis and significantly reduced HSC activation. In conclusion, FGF2 triggers CYGB gene expression and deactivation of myofibroblastic human HSCs, indicating that FGF2 has therapeutic potential for managing liver fibrosis.
Deciphering the role of the signal- and Sty1 kinase-dependent phosphorylation of the stress-responsive transcription factor Atf1 on gene activation

Adaptation to stress triggers the most dramatic shift in gene expression in fission yeast (Schizosaccharomyces pombe), and this response is driven by signaling via the MAPK Sty1. Upon activation, Sty1 accumulates in the nucleus and stimulates expression of hundreds of genes via the nuclear transcription factor Atf1, including expression of atf1 itself. However, the role of stress-induced, Sty1-mediated Atf1 phosphorylation in transcriptional activation is unclear. To this end, we expressed Atf1 phosphorylation mutants from a constitutive promoter to uncouple Atf1 activity from endogenous, stress-activated Atf1 expression. We found that cells expressing a nonphosphorylatable Atf1 variant are sensitive to oxidative stress because of impaired transcription of a subset of stress genes whose expression is also controlled by another transcription factor, Pap1. Furthermore, cells expressing a phospho-mimicking Atf1 mutant display enhanced stress resistance, and although expression of the Pap1-dependent genes still relied on stress induction, another subset of stress-responsive genes was constitutively expressed in these cells. We also observed that, in cells expressing the phospho-mimicking Atf1 mutant, the presence of Sty1 was completely dispensable, with all stress defects of Sty1-deficient cells being suppressed by expression of the Atf1 mutant. We further demonstrated that Sty1-mediated Atf1 phosphorylation does not stimulate binding of Atf1 to DNA but, rather, establishes a platform of interactions with the basal transcriptional machinery to facilitate transcription initiation. In summary, our results provide evidence that Atf1 phosphorylation by the MAPK Sty1 is required for oxidative stress responses in fission yeast cells by promoting transcription initiation.
Levels of immunity parameters underpin bleaching and disease susceptibility of reef corals

Immunity is a key life history trait that may explain hierarchies in the susceptibility of corals to disease and thermal bleaching, two of the greatest current threats to coral health and the persistence of tropical reefs. Despite their ongoing and rapid global decline, there have been few investigations into the immunity mechanisms of reef‐building corals. Variables commonly associated with invertebrate immunity, including the presence of melanin, size of melanin‐containing granular cells, and phenoloxidase (PO) activity, as well as concentrations of fluorescent proteins (FPs), were investigated in hard (Scleractinia) and soft (Alcyonacea) corals spanning 10 families from the Great Barrier Reef. Detectable levels of these indicators were present in all corals investigated, although relative investment differed among coral taxa. Overall levels of investment were inversely correlated to thermal bleaching and disease susceptibility. In addition, PO activity, melanin‐containing granular cell size, and FP concentration were each found to be significant predictors of susceptibility and thus may play key roles in coral immunity. Correlative evidence that taxonomic (family‐level) variation in the levels of these constituent immunity parameters underpins susceptibility to both thermal bleaching and disease indicates that baseline immunity underlies the vulnerability of corals to these two threats. This reinforces the necessity of a holistic approach to understanding bleaching and disease in order to accurately determine the resilience of coral reefs. —Palmer, C. V. , Bythell, J. C, Willis. B. L. Levels of immunity parameters underpin bleaching and disease susceptibility of reef corals. FASEB J. 24, 1935–1946 (2010). www.fasebj. org
aglF, aglG and aglI, novel members of a gene island involved in the N‐glycosylation of the Haloferax volcanii S‐layer glycoprotein

Proteins in all three domains of life can experience N‐glycosylation. The steps involved in the archaeal version of this post‐translational modification remain largely unknown. Hence, as the next step in ongoing efforts to identify components of the N‐glycosylation pathway of the halophilic archaeon Haloferax volcanii, the involvement of three additional gene products in the biosynthesis of the pentasaccharide decorating the S‐layer glycoprotein was demonstrated. The genes encoding AglF, AglI and AglG are found immediately upstream of the gene encoding the archaeal oligosaccharide transferase, AglB. Evidence showing that AglF and AglI are involved in the addition of the hexuronic acid found at position three of the pentasaccharide is provided, while AglG is shown to contribute to the addition of the hexuronic acid found at position two. Given their proximities in the H. volcanii genome, the transcription profiles of aglF, aglI, aglG and aglB were considered. While only aglF and aglI share a common promoter, transcription of the four genes is co‐ordinated, as revealed by determining transcript levels in H. volcanii cells raised in different growth conditions. Such changes in N‐glycosylation gene transcription levels offer additional support for the adaptive role of this post‐translational modification in H. volcanii.
SR-LSTM: State Refinement for LSTM Towards Pedestrian Trajectory Prediction

In crowd scenarios, reliable trajectory prediction of pedestrians requires insightful understanding of their social behaviors. These behaviors have been well investigated by plenty of studies, while it is hard to be fully expressed by hand-craft rules. Recent studies based on LSTM networks have shown great ability to learn social behaviors. However, many of these methods rely on previous neighboring hidden states but ignore the important current intention of the neighbors. In order to address this issue, we propose a data-driven state refinement module for LSTM network (SR-LSTM), which activates the utilization of the current intention of neighbors, and jointly and iteratively refines the current states of all participants in the crowd through a message passing mechanism. To effectively extract the social effect of neighbors, we further introduce a social-aware information selection mechanism consisting of an element-wise motion gate and a pedestrian-wise attention to select useful message from neighboring pedestrians. Experimental results on two public datasets, i.e. ETH and UCY, demonstrate the effectiveness of our proposed SR-LSTM and we achieve state-of-the-art results.
Limiting Network Size within Finite Bounds for Optimization

Largest theoretical contribution to Neural Networks comes from VC Dimension which characterizes the sample complexity of classification model in a probabilistic view and are widely used to study the generalization error. So far in the literature the VC Dimension has only been used to approximate the generalization error bounds on different Neural Network architectures. VC Dimension has not yet been implicitly or explicitly stated to fix the network size which is important as the wrong configuration could lead to high computation effort in training and leads to over fitting. So there is a need to bound these units so that task can be computed with only sufficient number of parameters. For binary classification tasks shallow networks are used as they have universal approximation property and it is enough to size the hidden layer width for such networks. The paper brings out a theoretical justification on required attribute size and its corresponding hidden layer dimension for a given sample set that gives an optimal binary classification results with minimum training complexity in a single layered feed forward network framework. The paper also establishes proof on the existence of bounds on the width of the hidden layer and its range subjected to certain conditions. Findings in this paper are experimentally analyzed on three different dataset using Mathlab 2018 (b) software.
Enhanced water solubility, antioxidant activity, and oral absorption of hesperetin by D-α-tocopheryl polyethylene glycol 1000 succinate and phosphatidylcholine

Hesperetin, an abundant bioactive component of citrus fruits, is poorly water-soluble, resulting in low oral bioavailability. We developed new formulations to improve the water solubility, antioxidant activity, and oral absorption of hesperetin. Two nano-based formulations were developed, namely hesperetin-TPGS (D-α-tocopheryl polyethylene glycol 1000 succinate) micelles and hesperetin-phosphatidylcholine (PC) complexes. These two formulations were prepared by a simple technique called solvent dispersion, using US Food and Drug Administration (FDA)-approved excipients for drugs. Differential scanning calorimetry (DSC) and dynamic light scattering (DLS) were used to characterize the formulations’ physical properties. Cytotoxicity analysis, cellular antioxidant activity assay, and a pharmacokinetic study were performed to evaluate the biological properties of these two formulations. The final weight ratios of both hesperetin to TPGS and hesperetin to PC were 1:12 based on their water solubility, which increased to 21.5- and 20.7-fold, respectively. The hesperetin-TPGS micelles had a small particle size of 26.19 nm, whereas the hesperetin-PC complexes exhibited a larger particle size of 219.15 nm. In addition, the cellular antioxidant activity assay indicated that both hesperetin-TPGS micelles and hesperetin-PC complexes increased the antioxidant activity of hesperetin to 4.2- and 3.9-fold, respectively. Importantly, the in vivo oral absorption study on rats indicated that the micelles and complexes significantly increased the peak plasma concentration (Cmax) from 2.64 μg/mL to 20.67 and 33.09 μg/mL and also increased the area under the concentration–time curve of hesperetin after oral administration to 16.2- and 18.0-fold, respectively. The micelles and complexes increased the solubility and remarkably improved the in vitro antioxidant activity and in vivo oral absorption of hesperetin, indicating these formulations’ potential applications in drugs and healthcare products.
The RGS protein Crg2 regulates both pheromone and cAMP signalling in Cryptococcus neoformans

G proteins orchestrate critical cellular functions by transducing extracellular signals into internal signals and controlling cellular responses to environmental cues. G proteins typically function as switches that are activated by G protein‐coupled receptors (GPCRs) and negatively controlled by regulator of G protein signalling (RGS) proteins. In the human fungal pathogen Cryptococcus neoformans, three G protein α subunits (Gpa1, Gpa2 and Gpa3) have been identified. In a previous study, we identified the RGS protein Crg2 involved in regulating the pheromone response pathway through Gpa2 and Gpa3. In this study, a role for Crg2 was established in the Gpa1‐cAMP signalling pathway that governs mating and virulence. We show that Crg2 physically interacts with Gpa1 and crg2 mutations increase cAMP production. crg2 mutations also enhance mating filament hyphae production, but reduce cell–cell fusion and sporulation efficiency during mating. Although crg2 mutations and the Gpa1 dominant active allele GPA1Q284L enhanced melanin production under normally repressive conditions, virulence was attenuated in a murine model. We conclude that Crg2 participates in controlling both Gpa1‐cAMP‐virulence and pheromone‐mating signalling cascades and hypothesize it may serve as a molecular interface between these two central signalling conduits.
Disease-Associated SNPs in Inflammation-Related lncRNAs

Immune-mediated diseases, such as celiac disease, type 1 diabetes or multiple sclerosis, are a clinically heterogeneous group of diseases that share many key genetic triggers. Although the pathogenic mechanisms responsible for the development of immune mediated disorders is not totally understood, high-throughput genomic studies, such as GWAS and Immunochip, performed in the past few years have provided intriguing hints about underlying mechanisms and pathways that lead to disease. More than a hundred gene variants associated with disease susceptibility have been identified through such studies, but the progress toward understanding the underlying mechanisms has been slow. The majority of the identified risk variants are located in non-coding regions of the genome making it difficult to assign a molecular function to the SNPs. However, recent studies have revealed that many of the non-coding regions bearing disease-associated SNPs generate long non-coding RNAs (lncRNAs). LncRNAs have been implicated in several inflammatory diseases, and many of them have been shown to function as regulators of gene expression. Many of the disease associated SNPs located in lncRNAs modify their secondary structure, or influence expression levels, thereby affecting their regulatory function, hence contributing to the development of disease.
Molecular Mechanisms Underlying Obesity-Induced Hypothalamic Inflammation and Insulin Resistance: Pivotal Role of Resistin/TLR4 Pathways

Low-grade inflammation and insulin resistance are among the clinical features of obesity that are thought to promote the progressive onset of type 2 diabetes. However, the underlying mechanisms linking these disorders remain not fully understood. Recent reports pointed out hypothalamic inflammation as a major step in the onset of obesity-induced insulin resistance. In light of the increasing prevalence of obesity and T2D, two worldwide public health concerns, deciphering mechanisms implicated in hypothalamic inflammation constitutes a major challenge in the field of insulin-resistance/obesity. Several clinical and experimental studies have identified resistin as a key hormone linking insulin-resistance to obesity, notably through the activation of Toll Like Receptor (TLR) 4 signaling pathways. In this review, we present an overview of the molecular mechanisms underlying obesity-induced hypothalamic inflammation and insulin resistance with peculiar focus on the role of resistin/TLR4 signaling pathway.