Miracle-dz/UniFAR-FTUs huggingface dataset:
AmrZ Beta-Sheet Residues Are Essential for DNA Binding and Transcriptional Control of Pseudomonas aeruginosa Virulence Genes

ABSTRACT AmrZ is a putative ribbon-helix-helix (RHH) transcriptional regulator. RHH proteins utilize residues within the β-sheet for DNA binding, while the α-helices promote oligomerization. AmrZ is of interest due to its dual roles as a transcriptional activator and as a repressor, regulating genes encoding virulence factors associated with both chronic and acute Pseudomonas aeruginosa infection. In this study, cross-linking revealed that AmrZ forms oligomers in solution but that the amino terminus, containing an unordered region and a β-sheet, were not required for oligomerization. The first 12 unordered residues (extended amino terminus) contributed minimally to DNA binding. Mutagenesis of the AmrZ β-sheet demonstrated that residues 18, 20, and 22 were essential for DNA binding at both activation and repressor sites, suggesting that AmrZ utilizes a similar mechanism for binding to these sites. Mice infected with amrZ mutants exhibited reduced bacterial burden, morbidity, and mortality. Direct in vivo competition assays showed a 5-fold competitive advantage for the wild type over an isogenic amrZ mutant. Finally, the reduced infection phenotype of the amrZ-null strain was similar to that of a strain expressing a DNA-binding-deficient AmrZ variant, indicating that DNA binding and transcriptional regulation by AmrZ is responsible for the in vivo virulence defect. These recent infection data, along with previously identified AmrZ-regulated virulence factors, suggest the necessity of AmrZ transcriptional regulation for optimal virulence during acute infection.
Handling the young cerebral palsied child at home

What do you do to start reading handling the young cerebral palsied child at home? Searching the book that you love to read first or find an interesting book that will make you want to read? Everybody has difference with their reason of reading a book. Actuary, reading habit must be from earlier. Many people may be love to read, but not a book. It's not fault. Someone will be bored to open the thick book with small words to read. In more, this is the real condition. So do happen probably with this handling the young cerebral palsied child at home.
Saliency-Aware Video Object Segmentation

Video saliency, aiming for estimation of a single dominant object in a sequence, offers strong object-level cues for unsupervised video object segmentation. In this paper, we present a geodesic distance based technique that provides reliable and temporally consistent saliency measurement of superpixels as a prior for pixel-wise labeling. Using undirected intra-frame and inter-frame graphs constructed from spatiotemporal edges or appearance and motion, and a skeleton abstraction step to further enhance saliency estimates, our method formulates the pixel-wise segmentation task as an energy minimization problem on a function that consists of unary terms of global foreground and background models, dynamic location models, and pairwise terms of label smoothness potentials. We perform extensive quantitative and qualitative experiments on benchmark datasets. Our method achieves superior performance in comparison to the current state-of-the-art in terms of accuracy and speed.
Comparative Sequence Analysis of Mycobacterium leprae and the New Leprosy-Causing Mycobacterium lepromatosis

ABSTRACT Mycobacterium lepromatosis is a newly discovered leprosy-causing organism. Preliminary phylogenetic analysis of its 16S rRNA gene and a few other gene segments revealed significant divergence from Mycobacterium leprae, a well-known cause of leprosy, that justifies the status of M. lepromatosis as a new species. In this study we analyzed the sequences of 20 genes and pseudogenes (22,814 nucleotides). Overall, the level of matching of these sequences with M. leprae sequences was 90.9%, which substantiated the species-level difference; the levels of matching for the 16S rRNA genes and 14 protein-encoding genes were 98.0% and 93.1%, respectively, but the level of matching for five pseudogenes was only 79.1%. Five conserved protein-encoding genes were selected to construct phylogenetic trees and to calculate the numbers of synonymous substitutions (dS values) and nonsynonymous substitutions (dN values) in the two species. Robust phylogenetic trees constructed using concatenated alignment of these genes placed M. lepromatosis and M. leprae in a tight cluster with long terminal branches, implying that the divergence occurred long ago. The dS and dN values were also much higher than those for other closest pairs of mycobacteria. The dS values were 14 to 28% of the dS values for M. leprae and Mycobacterium tuberculosis, a more divergent pair of species. These results thus indicate that M. lepromatosis and M. leprae diverged ∼10 million years ago. The M. lepromatosis pseudogenes analyzed that were also pseudogenes in M. leprae showed nearly neutral evolution, and their relative ages were similar to those of M. leprae pseudogenes, suggesting that they were pseudogenes before divergence. Taken together, the results described above indicate that M. lepromatosis and M. leprae diverged from a common ancestor after the massive gene inactivation event described previously for M. leprae.
Genome Sequences of Two Thermophilic Bacillus licheniformis Strains, Efficient Producers of Platform Chemical 2,3-Butanediol

ABSTRACT Both Bacillus licheniformis strains 10-1-A and 5-2-D are efficient producers of 2,3-butanediol. Here we present 4.3-Mb and 4.2-Mb assemblies of their genomes. The key genes for the regulation and metabolism of 2,3-butanediol production were annotated, which may provide further insights into the molecular mechanism for the production of 2,3-butanediol with high yield and productivity.
Polynucleotide Phosphorylase, RNase E/G, and YbeY Are Involved in the Maturation of 4.5S RNA in Corynebacterium glutamicum

ABSTRACT Corynebacterium glutamicum has been applied for the industrial production of various metabolites, such as amino acids. To understand the biosynthesis of the membrane protein in this bacterium, we investigated the process of signal recognition particle (SRP) assembly. SRP is found in all three domains of life and plays an important role in the membrane insertion of proteins. SRP RNA is initially transcribed as precursor molecules; however, relatively little is known about its maturation. In C. glutamicum, SRP consists of the Ffh protein and 4.5S RNA lacking an Alu domain. In this study, we found that 3′-to-5′ exoribonuclease, polynucleotide phosphorylase (PNPase), and two endo-type RNases, RNase E/G and YbeY, are involved in the 3′ maturation of 4.5S RNA in C. glutamicum. The mature form of 4.5S RNA was inefficiently formed in ΔrneG Δpnp mutant cells, suggesting the existence of an alternative pathway for the 3′ maturation of 4.5S RNA. Primer extension analysis also revealed that the 5′ mature end of 4.5S RNA corresponds to that of the transcriptional start site. Immunoprecipitated Ffh protein contained immature 4.5S RNA in Δpnp, ΔrneG, and ΔybeY mutants, suggesting that 4.5S RNA precursors can interact with Ffh. These results imply that the maturation of 4.5S RNA can be performed in the 4.5S RNA-Ffh complex. IMPORTANCE Overproduction of a membrane protein, such as a transporter, is useful for engineering of strains of Corynebacterium glutamicum, which is a workhorse of amino acid production. To understand membrane protein biogenesis in this bacterium, we investigated the process of signal recognition particle (SRP) assembly. SRP contains the Ffh protein and SRP RNA and plays an important role in the membrane insertion of proteins. Although SRP RNA is highly conserved among the three domains of life, relatively little is known about its maturation. We show that PNPase, RNase E/G, and YbeY are involved in the 3′ maturation of the SRP RNA (4.5S RNA) in this bacterium. This indicates that 3′ end processing in this organism is different from that in other bacteria, such as Escherichia coli.
Genome of Helicobacter pylori Strain XZ274, an Isolate from a Tibetan Patient with Gastric Cancer in China

ABSTRACT The infection rate of Helicobacter pylori is high all over the world, especially in the Chinese Tibetan Plateau. Here, we report the genome sequence of Helicobacter pylori strain XZ274 isolated from a Tibetan patient with gastric cancer. The strain contains 1,634,138 bp with 1,654 coding sequences and a pXZ274 plasmid of 22,406 bp with 26 coding sequences. This is the first complete genome sequence of Helicobacter pylori from the Tibetan Plateau in China.
The FtsZ-Like Protein FtsZm of Magnetospirillum gryphiswaldense Likely Interacts with Its Generic Homolog and Is Required for Biomineralization under Nitrate Deprivation

ABSTRACT Midcell selection, septum formation, and cytokinesis in most bacteria are orchestrated by the eukaryotic tubulin homolog FtsZ. The alphaproteobacterium Magnetospirillum gryphiswaldense (MSR-1) septates asymmetrically, and cytokinesis is linked to splitting and segregation of an intracellular chain of membrane-enveloped magnetite crystals (magnetosomes). In addition to a generic, full-length ftsZ gene, MSR-1 contains a truncated ftsZ homolog (ftsZm) which is located adjacent to genes controlling biomineralization and magnetosome chain formation. We analyzed the role of FtsZm in cell division and biomineralization together with the full-length MSR-1 FtsZ protein. Our results indicate that loss of FtsZm has a strong effect on microoxic magnetite biomineralization which, however, could be rescued by the presence of nitrate in the medium. Fluorescence microscopy revealed that FtsZm-mCherry does not colocalize with the magnetosome-related proteins MamC and MamK but is confined to asymmetric spots at midcell and at the cell pole, coinciding with the FtsZ protein position. In Escherichia coli, both FtsZ homologs form distinct structures but colocalize when coexpressed, suggesting an FtsZ-dependent recruitment of FtsZm. In vitro analyses indicate that FtsZm is able to interact with the FtsZ protein. Together, our data suggest that FtsZm shares key features with its full-length homolog but is involved in redox control for magnetite crystallization.
Effect of CCR5-Δ32 heterozygosity on the risk of perinatal HIV-1 infection: A meta-analysis

Several studies have investigated whether heterozygosity for a 32-basepair deletion in the CC chemokine receptor 5 gene (CCR5-Delta32 ) affects susceptibility to perinatal HIV-1 infection, but results have been inconclusive. We performed a meta-analysis of published data from 11 studies of HIV-1 perinatally exposed children who were genotyped for the CCR5-Delta32 polymorphism. The crude overall HIV-1 infection rates, by simple data pooling, were 20% (one of five) amongCCR5-Delta32 homozygote children, 39% (131 of 335) among CCR5-Delta32 heterozygote children, and 40% (1408 of 3526) among wild-type CCR5 homozygote children. Compared with wild-type homozygotes, the random effects risk ratio for heterozygotes was 1.04 (95% confidence interval [CI], 0.92-1.17) among all children (N = 3861) and 1.03 (95% CI, 0.90-1.17) among those of European descent (n = 2890). Results were similar when adjusted for the available data on the CCR2-641 polymorphism (n = 1542). The meta-analysis clarifies that perinatal infection is not significantly altered by heterozygosity for CCR5-Delta32 in the child.
Regulation of Type IV Pili Contributes to Surface Behaviors of Historical and Epidemic Strains of Clostridium difficile

ABSTRACT The intestinal pathogen Clostridium difficile is an urgent public health threat that causes antibiotic-associated diarrhea and is a leading cause of fatal nosocomial infections in the United States. C. difficile rates of recurrence and mortality have increased in recent years due to the emergence of so-called “hypervirulent” epidemic strains. A great deal of the basic biology of C. difficile has not been characterized. Recent findings that flagellar motility, toxin synthesis, and type IV pilus (TFP) formation are regulated by cyclic diguanylate (c-di-GMP) reveal the importance of this second messenger for C. difficile gene regulation. However, the function(s) of TFP in C. difficile remains largely unknown. Here, we examine TFP-dependent phenotypes and the role of c-di-GMP in controlling TFP production in the historical 630 and epidemic R20291 strains of C. difficile. We demonstrate that TFP contribute to C. difficile biofilm formation in both strains, but with a more prominent role in R20291. Moreover, we report that R20291 is capable of TFP-dependent surface motility, which has not previously been described in C. difficile. The expression and regulation of the pilA1 pilin gene differs between R20291 and 630, which may underlie the observed differences in TFP-mediated phenotypes. The differences in pilA1 expression are attributable to greater promoter-driven transcription in R20291. In addition, R20291, but not 630, upregulates c-di-GMP levels during surface-associated growth, suggesting that the bacterium senses its substratum. The differential regulation of surface behaviors in historical and epidemic C. difficile strains may contribute to the different infection outcomes presented by these strains. IMPORTANCE How Clostridium difficile establishes and maintains colonization of the host bowel is poorly understood. Surface behaviors of C. difficile are likely relevant during infection, representing possible interactions between the bacterium and the intestinal environment. Pili mediate bacterial interactions with various surfaces and contribute to the virulence of many pathogens. We report that type IV pili (TFP) contribute to biofilm formation by C. difficile. TFP are also required for surface motility, which has not previously been demonstrated for C. difficile. Furthermore, an epidemic-associated C. difficile strain showed higher pilin gene expression and greater dependence on TFP for biofilm production and surface motility. Differences in TFP regulation and their effects on surface behaviors may contribute to increased virulence in recent epidemic strains.
The Anti-Anti-Sigma Factor BldG Is Involved in Activation of the Stress Response Sigma Factor σH in Streptomyces coelicolor A3(2)

ABSTRACT The alternative stress response sigma factor σH has a role in regulation of the osmotic stress response and in morphological differentiation in Streptomyces coelicolor A3(2). Its gene, sigH, is located in an operon with the gene that encodes its anti-sigma factor UshX (PrsH). However, no gene with similarity to an anti-anti-sigma factor which may have a role in σH activation by a “partner-switching” mechanism is located in the operon. By using a combination of several approaches, including pull-down and bacterial two-hybrid assays and visualization of the complex by native polyacrylamide electrophoresis, we demonstrated a direct interaction between UshX and the pleiotropic sporulation-specific anti-anti-sigma factor BldG. Osmotic induction of transcription of the sigHp2 promoter that is specifically recognized by RNA polymerase containing σH was absent in an S. coelicolor bldG mutant, indicating a role of BldG in σH activation by a partner-switching-like mechanism.
Association of Socio-Economic Factors with the Nutritional Status of the Children Aged 2-8 Years from Slums of Kolkata, West Bengal, India

Background : Undernutrition appears to be a plaguing factor for physical and cognitive development of a large proportion of Indian children living in impoverished conditions. The city of Kolkata, located in the eastern part of India has demonstrated a conspicuous rise in its slum growth profile in the past few decades. Hitherto, studies on physical growth and nutritional status of slum children are lacking. Objectives : To Investigate the nutritional status (stunting, wasting, and underweight) among 2- 8 year old children and to observe the association of socio-economic factors with undernutrition of the studied children. Materials and Methods : This cross sectional study was conducted on 185 children aged 2 to 8 years residing at slums of Tangra, Behala, and Dum Dum regions of Kolkata. Anthropometric measurements (height and weight) were take following standard protocol (Lohman et al ., 1988), Socio-economic information were collected using a semi-structured questionnaire. Stunting, Underweight and Wasting were derived to evaluate the nutritional status of the studied population. Pearson correlation (r) coefficient test was undertaken to measure the association of some socio-economic variables on undernutrition. Results : The prevalence of stunting, underweight, and wasting were 38.91% (boys 32.14% and girls 45.45%), 50.27% (boys 51.16%, girls 49.49%), 31.35% (boys 30.23%, girls 32.32%) respectively. The present study showed the positive correlation (r) between educational levels of the parents and stunting, underweight and wasting independently. But household size has a negative correlation with all the three measures of nutritional status. Conclusion : We conclude that the slum children were facing a nutritional health risk and parental education and household size appeared to be the primary reasons.
Effects of Discrimination on HIV-Related Symptoms in Heterosexual Men of Color

HIV-related symptoms have a deleterious effect on quality of life. One determinant of HIV symptom burden among individuals of color may be discrimination. The aim of this study was to explore whether multiple lifetime discrimination events are associated with a greater number of HIV-related symptoms among heterosexual HIV-positive men of color and to examine the influence of anxiety and social support on this relationship. Data for this study were drawn from a cross-sectional survey of 307 heterosexual HIV-positive men recruited from health and social service agencies in New York City (NYC). This study indicated that the number of discrimination events experienced in one’s lifetime was positively associated with the number of HIV-related symptoms experienced in the past month. Moreover, the direct effect of discrimination on HIV symptoms remained significant after anxiety was included as a mediator in the model, and there was a significant indirect effect of discrimination on HIV symptoms through anxiety. Evidence supported a potential moderated mediation effect involving social support: As social support increased, the indirect effect of discrimination on HIV symptoms through anxiety decreased. The results of this study suggest an association between discrimination and HIV-related symptom burden. Furthermore, the relationship between number of major discrimination experiences and HIV symptom burden was partially mediated by anxiety. Future research should consider how lifetime discrimination might be associated with negative health outcomes among HIV-positive individuals of color.
Predictive Factors of Neurovascular and Tendon Injuries Following Dog Bites to the Upper Extremity

Background: Dog bite injuries to the upper extremity can result in traumatic neurovascular and musculotendinous damage. Currently, there are no clear guidelines dictating which patients may benefit from early operative exploration. The purpose of this study was to identify clinical variables that were predictive of abnormal intraoperative findings in patients who sustained an upper extremity dog bite injury. Methods: All patients who presented to a level I trauma center between 2007 and 2015 with an upper extremity dog bite injury who underwent subsequent surgical exploration were retrospectively screened for inclusion in our study. Patients with inadequate documentation or preexisting neurovascular or motor deficits were excluded. Abnormalities on physical exam and injuries encountered during surgical exploration were recorded for each patient. Contingency tables were constructed comparing normal and abnormal nerve, tendon, and vascular physical exam findings with intact or disrupted neurovascular and musculotendinous structures identified during surgical exploration. Results: Between 2007 and 2014, 117 patients sustained a dog bite injury to the upper extremity, of which 39 underwent subsequent surgical exploration and were included in our analysis. Sixty-nine percent of patients with neuropraxia on exam had intraoperative nerve damage. Seventy-seven percent of patients with an abnormal tendon exam had intraoperative musculotendinous damage. One hundred percent of patients with an abnormal vascular physical exam had intraoperative arterial injury. Conclusions: To date, there are no clear guidelines on what clinical criteria indicate the need for operative exploration and possible repair of neurovascular structures in upper extremity dog bite injuries. In our study, nerve, tendon, and vascular abnormalities noted on physical exam were strongly predictive of discovering neurovascular and musculotendinous damage during surgical exploration.
Complete Genome Sequence of Methanomassiliicoccus luminyensis, the Largest Genome of a Human-Associated Archaea Species

ABSTRACT The present study describes the complete and annotated genome sequence of Methanomassiliicoccus luminyensis strain B10 (DSM 24529T, CSUR P135), which was isolated from human feces. The 2.6-Mb genome represents the largest genome of a methanogenic euryarchaeon isolated from humans. The genome data of M. luminyensis reveal unique features and horizontal gene transfer events, which might have occurred during its adaptation and/or evolution in the human ecosystem.
SMU.746-SMU.747, a Putative Membrane Permease Complex, Is Involved in Aciduricity, Acidogenesis, and Biofilm Formation in Streptococcus mutans

ABSTRACT Dental caries induced by Streptococcus mutans is one of the most prevalent chronic infectious diseases worldwide. The pathogenicity of S. mutans relies on the bacterium's ability to colonize tooth surfaces and survive a strongly acidic environment. We performed an ISS1 transposon mutagenesis to screen for acid-sensitive mutants of S. mutans and identified an SMU.746-SMU.747 gene cluster that is needed for aciduricity. SMU.746 and SMU.747 appear to be organized in an operon and encode a putative membrane-associated permease. SMU.746- and SMU.747-deficient mutants showed a reduced ability to grow in acidified medium. However, the short-term or long-term acid survival capacity and F1F0 ATPase activity remained unaffected in the mutants. Furthermore, deletion of both genes did not change cell membrane permeability and the oxidative and heat stress responses. Growth was severely affected even with slight acidification of the defined medium (pH 6.5). The ability of the mutant strain to acidify the defined medium during growth in the presence of glucose and sucrose was significantly reduced, although the glycolysis rate was only slightly affected. Surprisingly, deletion of the SMU.746-SMU.747 genes triggered increased biofilm formation in low-pH medium. The observed effects were more striking in a chemically defined medium. We speculate that the SMU.746-SMU.747 complex is responsible for amino acid transport, and we discuss its possible role in colonization and survival in the oral environment.