Miracle-dz/UniFAR-FTUs huggingface dataset:
MsaB and CodY Interact To Regulate Staphylococcus aureus Capsule in a Nutrient-Dependent Manner

Findings from this study define the mechanism of regulation of capsule production in Staphylococcus aureus. Specifically, we show that two key regulators, MsaB and CodY, coordinate their functions to control the expression of capsule in response to nutrients. S. aureus fine-tunes the production of capsule by coordinating the activity of several regulators and by sensing nutrient levels. This study demonstrates the importance of incorporating multiple inputs prior to the expression of costly virulence factors, such as capsule. ABSTRACT Staphylococcus aureus has a complex regulatory network for controlling the production of capsule polysaccharide. In S. aureus, capsule production is controlled by several regulators in response to various environmental stimuli. Previously, we described MsaB as a new regulator that specifically binds to the cap promoter in a growth phase- or nutrient-dependent manner. In addition to MsaB, several other regulators have also been shown to bind the same region. In this study, we examined the interactions between MsaB and other nutrient-sensing regulators (CodY and CcpE) with respect to binding to the cap promoter in a nutrient-dependent manner. We observed that msaABCR and ccpE interact in a complex fashion to regulate capsule production. However, we confirmed that ccpE does not bind cap directly. We also defined the regulatory relationship between msaABCR and CodY. When nutrients (branched-chain amino acids) are abundant, CodY binds to the promoter region of the cap operon and represses its transcription. However, when nutrient concentrations decrease, MsaB, rather than CodY, binds to the cap promoter. Binding of MsaB to the cap promoter activates transcription of the cap operon. We hypothesize that this same mechanism may be used by S. aureus to regulate other virulence factors. IMPORTANCE Findings from this study define the mechanism of regulation of capsule production in Staphylococcus aureus. Specifically, we show that two key regulators, MsaB and CodY, coordinate their functions to control the expression of capsule in response to nutrients. S. aureus fine-tunes the production of capsule by coordinating the activity of several regulators and by sensing nutrient levels. This study demonstrates the importance of incorporating multiple inputs prior to the expression of costly virulence factors, such as capsule.
Review: Minimally Invasive Versus Conventional Dynamic Hip Screw Fixation in Elderly Patients With Intertrochanteric Fractures: A Systematic Review and Meta-Analysis

The classic dynamic hip screw fixation of intertrochanteric fractures may be associated with significant blood loss and soft tissue damage, which may worsen existing comorbidities of frail elderly patients. Recently, minimally invasive dynamic hip screw (MIDHS) technique was developed for osteosynthesis of intertrochanteric fractures. A highly sensitive search strategy was used to identify all published randomized or quasi-randomized controlled trials (RCTs/ qRCTs) and comparative observational studies comparing the MIDHS technique with the conventional dynamic hip screw (CDHS) technique in patients with intertrochanteric fractures. A pooled estimate of effect size was produced using both random and fixed effects models. Four RCTs/qRCTs and 2 retrospective comparative studies were identified. The MIDHS technique resulted in less blood loss, shorter hospitalization, lower pain level, faster fracture healing, and better hip function when compared with the CDHS technique. There was no significance difference between the 2 groups with regard to postoperative complications and implant position. The MIDHS technique may achieve perioperative benefits when compared with the CDHS technique.
Moraxella catarrhalis Expresses a Cardiolipin Synthase That Impacts Adherence to Human Epithelial Cells

ABSTRACT The major phospholipid constituents of Moraxella catarrhalis membranes are phosphatidylglycerol, phosphatidylethanolamine, and cardiolipin (CL). However, very little is known regarding the synthesis and function of these phospholipids in M. catarrhalis. In this study, we discovered that M. catarrhalis expresses a cardiolipin synthase (CLS), termed MclS, that is responsible for the synthesis of CL within the bacterium. The nucleotide sequence of mclS is highly conserved among M. catarrhalis isolates and is predicted to encode a protein with significant amino acid similarity to the recently characterized YmdC/ClsC protein of Escherichia coli. Isogenic mclS mutant strains were generated in M. catarrhalis isolates O35E, O12E, and McGHS1 and contained no observable levels of CL. Site-directed mutagenesis of a highly conserved HKD motif of MclS also resulted in a CL-deficient strain. Moraxella catarrhalis, which depends on adherence to epithelial cells for colonization of the human host, displays significantly reduced levels of adherence to HEp-2 and A549 cell lines in the mclS mutant strains compared to wild-type bacteria. The reduction in adherence appears to be attributed to the absence of CL. These findings mark the first instance in which a CLS has been related to a virulence-associated trait.
AraR, an l-Arabinose-Responsive Transcriptional Regulator in Corynebacterium glutamicum ATCC 31831, Exerts Different Degrees of Repression Depending on the Location of Its Binding Sites within the Three Target Promoter Regions

ABSTRACT In Corynebacterium glutamicum ATCC 31831, a LacI-type transcriptional regulator AraR, represses the expression of l-arabinose catabolism (araBDA), uptake (araE), and the regulator (araR) genes clustered on the chromosome. AraR binds to three sites: one (BSB) between the divergent operons (araBDA and galM-araR) and two (BSE1 and BSE2) upstream of araE. l-Arabinose acts as an inducer of the AraR-mediated regulation. Here, we examined the roles of these AraR-binding sites in the expression of the AraR regulon. BSB mutation resulted in derepression of both araBDA and galM-araR operons. The effects of BSE1 and/or BSE2 mutation on araE expression revealed that the two sites independently function as the cis elements, but BSE1 plays the primary role. However, AraR was shown to bind to these sites with almost the same affinity in vitro. Taken together, the expression of araBDA and araE is strongly repressed by binding of AraR to a single site immediately downstream of the respective transcriptional start sites, whereas the binding site overlapping the −10 or −35 region of the galM-araR and araE promoters is less effective in repression. Furthermore, downregulation of araBDA and araE dependent on l-arabinose catabolism observed in the BSB mutant and the AraR-independent araR promoter identified within galM-araR add complexity to regulation of the AraR regulon derepressed by l-arabinose. IMPORTANCE Corynebacterium glutamicum has a long history as an industrial workhorse for large-scale production of amino acids. An important aspect of industrial microorganisms is the utilization of the broad range of sugars for cell growth and production process. Most C. glutamicum strains are unable to use a pentose sugar l-arabinose as a carbon source. However, genes for l-arabinose utilization and its regulation have been recently identified in C. glutamicum ATCC 31831. This study elucidates the roles of the multiple binding sites of the transcriptional repressor AraR in the derepression by l-arabinose and thereby highlights the complex regulatory feedback loops in combination with l-arabinose catabolism-dependent repression of the AraR regulon in an AraR-independent manner.
Three-Dimensional Topology Preserving Reduction on the 4-Subfields

This paper discusses thinning on 3D binary images with the 4-subfield approach. Although a thinning algorithm concerns binary images, the algorithm itself can be represented as a set of three-color reduction templates. A thinning algorithm is topology preserving if the set of all three-color templates is topology preserving. Sufficient and necessary conditions of time complexity O(n) were proposed for verifying the topological soundness of a 3D 4-subfield thinning algorithm of n three-color templates. Theories and techniques for computerizing such conditions were discussed. Two 4-subfield thinning algorithms on 3D images, one for generating medial curves, and the other one for generating medial surfaces, are proposed and proved to preserve topology by our sufficient and necessary conditions.
An Experimental Study to Evaluate the Fluobeam 800 Imaging System for Fluorescence-Guided Lymphatic Imaging and Sentinel Node Biopsy

Background. Visualization of the lymphatic system is challenging. Lymphatic imaging is a crucial diagnostic tool for benign and malignant lymphatic pathologies. Fluorescence-guided imaging allows selective lymphatic mapping and sentinel lymph node (SLN) identification. There are a few fluorescence systems, but some drawbacks remain due to technical and ergonomic aspects. The aim of this study was to evaluate the feasibility of the new Fluobeam 800 imaging system. Methods. After approval by the ethics committee, the system was evaluated for lymphography and SLN biopsy in an animal model. Five pigs each with 4 lymph node (LN) stations (n = 20 LN stations) were subjected to lymphatic imaging using indocyanine green (ICG). Additionally, the use of ICG was compared with ICG adsorbed to human serum albumin (ICG–HSA). Lymphatic vessels and SLN identification rates were measured. Results. After injection, a clear fluorescence signal of the lymphatic vessels was visualized leading to the LN station. Overall, ICG fluorescence imaging identified a mean of 2.0 lymphatic vessels and 1.1 (range = 1-2) SLN in 20 of 20 LN stations. Reverse lymphography was feasible. A clinical difference in resolution was not detected between use of ICG–HSA and ICG. Conclusion. This is the first study analyzing the feasibility of the Fluobeam 800 imaging system allowing transcutaneous real-time imaging. It enables detection of the SLN by fluorescence retention with increased detection depth and resolution. After fixation to the ceiling, the ergonomics advanced for simultaneous field navigation and dissection. The new system can be applied for lymphatic imaging for lympatico-reconstructive surgery and SLN biopsy.
Genome Sequence of the Phototrophic Betaproteobacterium Rubrivivax benzoatilyticus Strain JA2T

ABSTRACT Herein we report the draft genome sequence of a phototrophic bacterium, Rubrivivax benzoatilyticus strain JA2T, which apparently is the first genome sequence report of a phototrophic member belonging to the class Betaproteobacteria. The unique feature of this strain is its capability to synthesize carotenoids through both spirilloxanthin and spheroidenone pathways. Strain JA2T produces several novel secondary metabolites, and the genome insights help in understanding the unique machinery that the strain adapted.
Genome Sequence of Helicobacter pylori hpEurope Strain N6

ABSTRACT Helicobacter pylori colonizes about half of the world's population. It is a causative agent of stomach diseases, including malignant tumors. We report the genome sequence of strain N6, which is widely used in H. pylori research and appreciated for its large cell size and high transformation efficiency.
The c-Type Cytochrome OmcA Localizes to the Outer Membrane upon Heterologous Expression in Escherichia coli

ABSTRACT We have functionally produced the outer membrane cytochrome OmcA from Shewanella oneidensis in Escherichia coli. Substrate accessibility experiments indicate that OmcA is surface exposed in an E. coli B strain but not in a K-12 strain. We show that a functional type II secretion system is required for surface localization.
Mental Disorder in People Living with HIV/Aids in South Africa

We investigate the prevalence of mental disorder in people living with HIV/AIDS in a developing country context and examine the relationship between the presence of mental disorder and various independent variables. Nine-hundred HIV positive people were interviewed in 18 recruitment sites across five provinces in South Africa, using a cross-culturally validated diagnostic instrument and a structured socio-demographic and health information questionnaire. Prevalence of mental disorder was established using the Composite International Diagnostic Interview (CIDI). Chi-square, Fischer exact test, and binary logistic regression examined the relationship between mental health disorders and demographic characteristics, disease stage, CD4 count, and whether the person was on anti-retroviral treatment. A number of respondents (43.7%) were found to have a diagnosable mental disorder. Depression was the most common disorder (11.1% major and 29.9% mild depression), followed by alcohol abuse disorder (12.4%). The presence of mental disorder was significantly associated with gender, employment status, having children, and the clinical stage of the disease. Gender and the stage of disease were the best predictors of mental disorder. Rates of mental disorder were substantially higher in people living with HIV/AIDS than generally found in populations in developing countries and similar to HIV positive groupings in developed countries. Viral impacts on the brain, psychological reactions, and social conditions all contributed to the higher prevalence rates. Mental health interventions need to become a central part of comprehensive HIV/AIDS support, care, and treatment programmes.
DesT Coordinates the Expression of Anaerobic and Aerobic Pathways for Unsaturated Fatty Acid Biosynthesis in Pseudomonas aeruginosa

ABSTRACT The fabA and fabB genes are responsible for anaerobic unsaturated fatty acid formation in Pseudomonas aeruginosa. Expression of the fabAB operon was repressed by exogenous unsaturated fatty acids, and DNA sequences upstream of the translational start site were used to affinity purify DesT. The single protein interaction with the fabAB promoter detected in wild-type cell extracts was absent in the desT deletion strain, as was the repression of fabAB expression by unsaturated fatty acids. Thus, DesT senses the overall composition of the acyl-coenzyme A pool to coordinate the expression of the operons for the anaerobic (fabAB) and aerobic (desCB) pathways for unsaturated fatty acid synthesis.
Phenotypes of dnaXE145A Mutant Cells Indicate that the Escherichia coli Clamp Loader Has a Role in the Restart of Stalled Replication Forks

ABSTRACT The Escherichia colidnaXE145A mutation was discovered in connection with a screen for multicopy suppressors of the temperature-sensitive topoisomerase IV mutation parE10. The gene for the clamp loader subunits τ and γ, dnaX, but not the mutant dnaXE145A, was found to suppress parE10(Ts) when overexpressed. Purified mutant protein was found to be functional in vitro, and few phenotypes were found in vivo apart from problems with partitioning of DNA in rich medium. We show here that a large number of the replication forks that initiate at oriC never reach the terminus in dnaXE145A mutant cells. The SOS response was found to be induced, and a combination of the dnaXE145A mutation with recBC and recA mutations led to reduced viability. The mutant cells exhibited extensive chromosome fragmentation and degradation upon inactivation of recBC and recA, respectively. The results indicate that the dnaXE145A mutant cells suffer from broken replication forks and that these need to be repaired by homologous recombination. We suggest that the dnaX-encoded τ and γ subunits of the clamp loader, or the clamp loader complex itself, has a role in the restart of stalled replication forks without extensive homologous recombination. IMPORTANCE The E. coli clamp loader complex has a role in coordinating the activity of the replisome at the replication fork and loading β-clamps for lagging-strand synthesis. Replication forks frequently encounter obstacles, such as template lesions, secondary structures, and tightly bound protein complexes, which will lead to fork stalling. Some pathways of fork restart have been characterized, but much is still unknown about the actors and mechanisms involved. We have in this work characterized the dnaXE145A clamp loader mutant. We find that the naturally occurring obstacles encountered by a replication fork are not tackled in a proper way by the mutant clamp loader and suggest a role for the clamp loader in the restart of stalled replication forks.
Complete Genome Sequence of the Probiotic Strain Lactobacillus casei BD-II

ABSTRACT Lactobacillus casei BD-II, a patented probiotic strain (U.S. patent 7,270,994 B2), was isolated from homemade koumiss in China and has been implemented in the industrial production as starter cultures. Here we report the complete genome sequence of BD-II, which shows high similarity with the well-studied probiotic BL23.
Genome Sequence of Diplorickettsia massiliensis, an Emerging Ixodes ricinus-Associated Human Pathogen

ABSTRACT Diplorickettsia massiliensis is a gammaproteobacterium in the order Legionellales and an agent of tick-borne infection. We sequenced the genome from strain 20B, isolated from an Ixodes ricinus tick. The genome consists of a 1,727,973-bp chromosome but no plasmid and includes 2,269 protein-coding genes and 42 RNA genes, including 3 rRNA genes.
An intelligent I-cache prefetch mechanism

Modern, high-performance processors employ techniques such as superscalar execution and super-pipelining to increase their instruction issue rate. As the instruction issue rate of processors increases, however, the negative impact of branches on performance also increases. This paper describes an instruction cache (I-cache) prefetch mechanism to improve processor performance on the taken branches. Under perfect conditions, the mechanism allows the target of a taken branch to be prefetched early enough to completely hide the memory latency of an I-cache miss. <<ETX>>
Genome-Wide Abolishment of Mobile Genetic Elements Using Genome Shuffling and CRISPR/Cas-Assisted MAGE Allows the Efficient Stabilization of a Bacterial Chassis.

The ideal bacterial chassis provides a simplified, stable and predictable host environment for synthetic biological circuits. Mutability and evolution can, however, compromise stability, leading to deterioration of artificial genetic constructs. By eliminating certain sources of instability, these undesired genetic changes can be mitigated. Specifically, deletion of prophages and insertion sequences, nonessential constituents of bacterial genomes, has been shown to be beneficial in cellular and genetic stabilization. Here, we sought to establish a rapid methodology to improve the stability of microbial hosts. The novel workflow involves genome shuffling between a mobile genetic element-free strain and the target cell, and subsequent rounds of CRISPR/Cas-assisted MAGE on multiplex targets. The power and speed of the procedure was demonstrated on E. coli BL21(DE3), a host routinely used for plasmid-based heterologous protein expression. All 9 prophages and 50 insertion elements were efficiently deleted or inactivated. Together with additional targeted manipulations (e.g., inactivation of error-prone DNA-polymerases), the changes resulted in an improved bacterial host with a hybrid (harboring segments of K-12 DNA), 9%-downsized and clean genome. The combined capacity of phage-mediated generalized transduction and CRISPR/Cas-selected MAGE offers a way for rapid, large scale editing of bacterial genomes.
Efficacy of the Novel Medical Adhesive, MAR-VIVO-107, in an Acute Porcine Liver Resection Model

Background. Despite modern surgical techniques, insufficient hemostasis after liver trauma is still a major cause of morbidity and mortality after injury. Therefore, efficient hemostatic agents are indicated. In this study, we evaluated the hemostatic efficacy of a novel synthetic wound adhesive (MAR-VIVO-107) based on polyurethane/polyurea, compared with a widely used fibrin adhesive (Tisseel). Materials and Methods. Twelve German Landrace pigs were randomly assigned to 2 groups. The animals were operated under sterile conditions. A midline laparotomy was performed and the left liver lobe was isolated and resected, using a surgical scissor, in order to induce hepatic trauma. MAR-VIVO-107 or Tisseel was applied to the resected area. The animals were monitored for 60 minutes; thereafter, they were sacrificed under anesthesia. Blood and tissue samples were collected pre- and postresection for biochemical and hematological analyses. Results. MAR-VIVO-107 versus Tisseel (mean ± SD, P value)—postsurgical survival rate was 100% in both groups. Bleeding time was significantly higher in Tisseel compared with MAR-VIVO-107 (10.3 ± 5.0 vs 3.7 ± 1.5 minutes, P = .0124). In trend, blood loss was less in the MAR-VIVO-107 group (54.3 ± 34.9 vs 105.5 ± 65.8 g, P = .222). Aspartate transaminase levels were significantly lower in the MAR-VIVO-107 group when compared with the Tisseel group (39.0 ± 10.0 vs 72.4 ± 23.4 U/L, P = .0459). Conclusion. The efficacy of MAR-VIVO-107 and comparable performance to the gold standard fibrin have been shown under pre-clinical conditions. MAR-VIVO-107 permits hemorrhage control within seconds, even in wet environment.
Engineered control of genetic variability reveals interplay between quorum sensing, feedback regulation and biochemical noise

Stochastic fluctuations in gene expression trigger both beneficial and harmful consequences for cell behavior. Therefore, achieving a desired mean protein expression level while minimizing noise is of interest in many applications, including robust protein production systems in industrial biotechnology. Here we consider a synthetic gene circuit combining intracellular negative feedback and cell-to-cell communication based on quorum sensing. Accounting for both intrinsic and extrinsic noise, stochastic simulations allow us to analyze the capability of the circuit to reduce noise strength as a function of its parameters. We obtain mean expression level and noise strength for all species under different scenarios showing good agreement with system-wide available experimental data of protein abundance and noise in E. coli. Our in silico experiments, validated by preliminary in vivo results, reveal significant noise attenuation in gene
Compression of embedded system programs

Embedded systems are often sensitive to space, weight, and cost considerations. Reducing the size of stored programs can significantly improve these factors. This paper discusses a program compression methodology based on existing processor architectures. The authors examine practical and theoretical measures for the maximum compression rate of a suite of programs across six modern architectures. The theoretical compression rate is reported in terms of the zeroth and first-order entropies, while the practical compression rate is reported in terms of the Huffman-encoded format of the proposed compression methodology and the GNU file compression utility, gzip. These experiments indicate that a practical increase of 15%-30% and a theoretical increase of over 100% in code density can be expected using the techniques examined. In addition, a novel, greedy, variable-length-to variable-length encoding algorithm is presented with preliminary results. <<ETX>>
Complete Genome Sequence of Bifidobacterium longum JDM301

ABSTRACT Bifidobacteria, known as probiotic bacteria, are high-G+C Gram-positive bacteria which naturally inhabit the human gastrointestinal tract and vagina. Recently, we completely sequenced Bifidobacterium longum JDM301, which is a widely used Chinese commercial strain with several probiotic properties.
Fault location based on circuit partitioning

We propose a method of fault diagnosis that reduces the number of simulations required to locate defect site(s) by logically partitioning the circuit into subcircuits. Candidate subcircuits that potentially contain the defect site(s) are identified and further partitioned, until the defect site is located with the required resolution. Experimental results are presented to demonstrate the effectiveness of circuit partitioning in reducing the number of fault simulations.