Involvement of the YneS/YgiH and PlsX proteins in phospholipid biosynthesis in both Bacillus subtilis and Escherichia coli

<p>Abstract</p> <p>Background</p> <p>Phospholipid biosynthesis commences with the acylation of glycerol-3-phosphate (G3P) to form 1-acyl-G3P. This step is catalyzed by the PlsB protein in <it>Escherichia coli</it>. The gene encoding this protein has not been identified, however, in the majority of bacterial genome sequences, including that of <it>Bacillus subtilis</it>. Recently, a new two-step pathway catalyzed by PlsX and PlsY proteins for the initiation of phospholipid formation in <it>Streptococcus pneumoniae </it>has been reported.</p> <p>Results</p> <p>In <it>B. subtilis</it>, 271 genes have been reported to be indispensable, when inactivated singly, for growth in LB medium. Among these, 11 genes encode proteins with unknown functions. As part of a genetic study to identify the functions of these genes, we show here that the <it>B. subtilis </it>ortholog of <it>S. pneumoniae </it>PlsY, YneS, is required for G3P acyltransferase activity, together with PlsX. The <it>B. subtilis </it>genome lacks <it>plsB</it>, and we show in vivo that the PlsX/Y pathway is indeed essential for the growth of bacteria lacking <it>plsB</it>. Interestingly, in addition to <it>plsB</it>, <it>E. coli </it>possesses <it>plsX </it>and the <it>plsY </it>ortholog, <it>ygiH</it>. We therefore explored the functional relationship between PlsB, PlsX and YgiH in <it>E. coli</it>, and found that <it>plsB </it>is essential for <it>E. coli </it>growth, indicating that PlsB plays an important role in 1-acyl-G3P synthesis in <it>E. coli</it>. We also found, however, that the simultaneous inactivation of <it>plsX </it>and <it>ygiH </it>was impossible, revealing important roles for PlsX and YgiH in <it>E. coli </it>growth.</p> <p>Conclusion</p> <p>Both <it>plsX </it>and <it>yneS </it>are essential for 1-acyl-G3P synthesis in <it>B. subtilis</it>, in agreement with recent reports on their biochemical functions. In <it>E. coli</it>, PlsB plays a principal role in 1-acyl-G3P synthesis and is also essential for bacterial growth. PlsX and YgiH also, however, play important roles in <it>E. coli </it>growth, possibly by regulating the intracellular concentration of acyl-ACP. These proteins are therefore important targets for development of new antibacterial agents.</p

Regulation of chromosomal replication initiation by oriC-proximal DnaA-box clusters in Bacillus subtilis

Bacterial chromosome replication is initiated by binding of DnaA to a DnaA-box cluster (DBC) within the replication origin (oriC). In Bacillus subtilis, six additional DBCs are found outside of oriC and some are known to be involved in transcriptional regulation of neighboring genes. A deletion mutant lacking the six DBCs (Δ6) initiated replication early. Further, inactivation of spo0J in Δ6 cells yielded a pleiotropic phenotype, accompanied by severe growth inhibition. However, a spontaneous suppressor in soj or a deletion of soj, which stimulates DnaA activity in the absence of Spo0J, counteracted these effects. Such abnormal phenotypic features were not observed in a mutant background in which replication initiation was driven by a plasmid-derived replication origin. Moreover, introduction of a single DBC at various ectopic positions within the Δ6 chromosome partly suppressed the early-initiation phenotype, but this was dependent on insertion location. We propose that DBCs negatively regulate replication initiation by interacting with DnaA molecules and play a major role, together with Spo0J/Soj, in regulating the activity of DnaA

Distribution of Stable DnaA-Binding Sites on the Bacillus Subtilis Genome Detected using a Modified ChIP-chip Method

We developed a modified ChIP-chip method, designated ChAP-chip (Chromatin Affinity Precipitation coupled with tiling chip). The binding sites of Bacillus subtilis Spo0J determined using this technique were consistent with previous findings. A DNA replication initiator protein, DnaA, formed stable complexes at eight intergenic regions on the B. subtilis genome. Characterization of the binding sequences suggested that two factors—the local density of DnaA boxes and their affinities for DnaA—are critical for stable binding. We further showed that in addition to autoregulation, DnaA directly modulate the expression of sda in a positive, and ywlC and yydA in a negative manner. Examination of possible stable DnaA-binding sequences in other Bacillus species suggested that DnaA-dependent regulation of those genes is maintained in most bacteria examined, supporting their biological significance. In addition, a possible stable DnaA-binding site downstream of gcp is also suggested to be conserved. Furthermore, potential DnaA-binding sequences specific for each bacterium have been identified, generally in close proximity to oriC. These findings suggest that DnaA plays several additional roles, such as control of the level of effective initiator, ATP-DnaA, and/or stabilization of the domain structure of the genome around oriC for the proper initiation of chromosome replication

Comprehensive Analysis of Inflammatory Immune Mediators in Vitreoretinal Diseases

Inflammation affects the formation and the progression of various vitreoretinal diseases. We performed a comprehensive analysis of inflammatory immune mediators in the vitreous fluids from total of 345 patients with diabetic macular edema (DME, n = 92), proliferative diabetic retinopathy (PDR, n = 147), branch retinal vein occlusion (BRVO, n = 30), central retinal vein occlusion (CRVO, n = 13) and rhegmatogenous retinal detachment (RRD, n = 63). As a control, we selected a total of 83 patients with either idiopathic macular hole (MH) or idiopathic epiretinal membrane (ERM) that were free of major pathogenic intraocular changes, such as ischemic retina and proliferative membranes. The concentrations of 20 soluble factors (nine cytokines, six chemokines, and five growth factors) were measured simultaneously by multiplex bead analysis system. Out of 20 soluble factors, three factors: interleukin-6 (IL-6), interleukin-8 (IL-8), and monocyte chemoattractant protein-1 (MCP-1) were significantly elevated in all groups of vitreoretinal diseases (DME, PDR, BRVO, CRVO, and RRD) compared with control group. According to the correlation analysis in the individual patient's level, these three factors that were simultaneously increased, did not show any independent upregulation in all the examined diseases. Vascular endothelial growth factor (VEGF) was significantly elevated in patients with PDR and CRVO. In PDR patients, the elevation of VEGF was significantly correlated with the three factors: IL-6, IL-8, and MCP-1, while no significant correlation was observed in CRVO patients. In conclusion, multiplex bead system enabled a comprehensive soluble factor analysis in vitreous fluid derived from variety of patients. Major three factors: IL-6, IL-8, and MCP-1 were strongly correlated with each other indicating a common pathway involved in inflammation process in vitreoretinal diseases

Reliability and Validity of the Nursing Student Competency Assessment Instrument and Related Factors

The purpose of this study was to confirm the reliability and validity of the competency assessment index of nursing students and to identify the factors associated with competency. An anonymous self-administered questionnaire survey was conducted on nursing students enrolled from April 2021 to March 2022. Principal component analysis and Cronbach’s alpha coefficient were used to examine the reliability and validity of the competency factor structure. Multiple regression analysis was used to analyze related factors. As a result, the reliability and validity of the factor structure of competency were statistically clarified. As related factors of competency, “grade level” and “thinking that learning in university education gives students confidence” and “cognitive regulation strategies” were identified. In the analysis by competency sub-factors, other than grade level,［ relationship building］ was affected by “being immersed in university education,” ［ethical care］ and ［cooperation and collaboration］ by “thinking that learning in university education gives students confidence”, and［ health problem-solving］ and［ professional development］ by “cognitive regulation strategies”. The importance of recommending experiential education in clinical practice, strengthening self-regulated learning strategies, and education to increase students’ self-confidence were suggested. The results of this study contribute to the reconstruction of education in which competencies are shared with students

Large scale international replication and meta-analysis study confirms association of the 15q14 locus with myopia. The CREAM consortium

Myopia is a complex genetic disorder and a common cause of visual impairment among working age adults. Genome-wide association studies have identified susceptibility loci on chromosomes 15q14 and 15q25 in Caucasian populations of European ancestry. Here, we present a confirmation and meta-analysis study in which we assessed whether these two loci are also associated with myopia in other populations. The study population comprised 31 cohorts from the Consortium of Refractive Error and Myopia (CREAM) representing 4 different continents with 55,177 individuals; 42,845 Caucasians and 12,332 Asians. We performed a meta-analysis of 14 single nucleotide polymorphisms (SNPs) on 15q14 and 5 SNPs on 15q25 using linear regression analysis with spherical equivalent as a quantitative outcome, adjusted for age and sex. We calculated the odds ratio (OR) of myopia versus hyperopia for carriers of the top-SNP alleles using a fixed effects meta-analysis. At locus 15q14, all SNPs were significantly replicated, with the lowest P value 3.87 × 10 -12 for SNP rs634990 in Caucasians, and 9.65 × 10 -4 for rs8032019 in Asians. The overall meta-analysis provided P value 9.20 × 10 -23 for the top SNP rs634990. The risk of myopia versus hyperopia was OR 1.88 (95 % CI 1.64, 2.16, P < 0.001) for homozygous carriers of the risk allele at the top SNP rs634990, and OR 1.33 (95 % CI 1.19, 1.49, P < 0.001) for heterozygous carriers. SNPs at locus 15q25 did not replicate significantly (P value 5.81 × 10 -2 for top SNP rs939661). We conclude that common variants at chromosome 15q14 influence susceptibility for myopia in Caucasian and Asian populations world-wide. © The Author(s) 2012

Childhood gene-environment interactions and age-dependent effects of genetic variants associated with refractive error and myopia : The CREAM Consortium

Myopia, currently at epidemic levels in East Asia, is a leading cause of untreatable visual impairment. Genome-wide association studies (GWAS) in adults have identified 39 loci associated with refractive error and myopia. Here, the age-of-onset of association between genetic variants at these 39 loci and refractive error was investigated in 5200 children assessed longitudinally across ages 7-15 years, along with gene-environment interactions involving the major environmental risk-factors, nearwork and time outdoors. Specific variants could be categorized as showing evidence of: (a) early-onset effects remaining stable through childhood, (b) early-onset effects that progressed further with increasing age, or (c) onset later in childhood (N = 10, 5 and 11 variants, respectively). A genetic risk score (GRS) for all 39 variants explained 0.6% (P = 6.6E-08) and 2.3% (P = 6.9E-21) of the variance in refractive error at ages 7 and 15, respectively, supporting increased effects from these genetic variants at older ages. Replication in multi-ancestry samples (combined N = 5599) yielded evidence of childhood onset for 6 of 12 variants present in both Asians and Europeans. There was no indication that variant or GRS effects altered depending on time outdoors, however 5 variants showed nominal evidence of interactions with nearwork (top variant, rs7829127 in ZMAT4; P = 6.3E-04).Peer reviewe

SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion

Abstract: The B.1.617.2 (Delta) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in the state of Maharashtra in late 2020 and spread throughout India, outcompeting pre-existing lineages including B.1.617.1 (Kappa) and B.1.1.7 (Alpha)1. In vitro, B.1.617.2 is sixfold less sensitive to serum neutralizing antibodies from recovered individuals, and eightfold less sensitive to vaccine-elicited antibodies, compared with wild-type Wuhan-1 bearing D614G. Serum neutralizing titres against B.1.617.2 were lower in ChAdOx1 vaccinees than in BNT162b2 vaccinees. B.1.617.2 spike pseudotyped viruses exhibited compromised sensitivity to monoclonal antibodies to the receptor-binding domain and the amino-terminal domain. B.1.617.2 demonstrated higher replication efficiency than B.1.1.7 in both airway organoid and human airway epithelial systems, associated with B.1.617.2 spike being in a predominantly cleaved state compared with B.1.1.7 spike. The B.1.617.2 spike protein was able to mediate highly efficient syncytium formation that was less sensitive to inhibition by neutralizing antibody, compared with that of wild-type spike. We also observed that B.1.617.2 had higher replication and spike-mediated entry than B.1.617.1, potentially explaining the B.1.617.2 dominance. In an analysis of more than 130 SARS-CoV-2-infected health care workers across three centres in India during a period of mixed lineage circulation, we observed reduced ChAdOx1 vaccine effectiveness against B.1.617.2 relative to non-B.1.617.2, with the caveat of possible residual confounding. Compromised vaccine efficacy against the highly fit and immune-evasive B.1.617.2 Delta variant warrants continued infection control measures in the post-vaccination era

Characteristics of operations at fish-landing sites managed by private owners in Thailand

This study presents the results of a survey on the operation characteristics of landing sites managed by private owners in Thailand. The survey was conducted by interviewing private landing site owners, managers of fishery cooperatives, middlemen, and fishers. The results of interviews were summarized with respect to scale of business, fisheries, transaction, types of people associated with landing sites, location, and daily schedule. Landing sites were located along canals in coastal provinces. The scale of businesses was variable, depending on the type of middlemen ; local retailers, processing factories, export companies, etc. We visited landing sites for commercial fishing boats. The main fishing boat tipes were trawlers and purse seiners. The most common characteristic in the operation of private landing sites was the reliance of almost all transactions on individual relationships between fishers, landing site owwners, and middlemen. Private landing sites were essential for fishers to land fish near fishing grounds and played the role of wholesaler for middlemen to acquire fishery products as per amounts and species needed. The management system of landing sites and fishery wholesale markets is now in the transition period in Thailand

Trailing the Effectiveness of a Modified Trawl Net in the Northern Java Sea, Indonesia

Overfishing has occurred in several regions around Indonesia, including the Northern Java Sea, primarily due to the large number of artisanal fishers and fishing boats, and the use of "un-environmentally friendly fishing gear", such as trawl nets. Consequently, Presidential Decree No.39 was enacted on July 1, 1980, which prohibited trawl operations in Indonesia to reduce fishing and social conflicts, and to protect resources. Fishers have responded to this government regulation by modifying their gear to elude its enforcement. However, these modifications are oriented more economic than conservation benefits. To rectify this issue, an environmentally-frendly trawl net that enables resource conservation needs to be developed and authorized. Therefore, in this study, a modified trawl net that included a flapper, selector, and square mesh was trialed and compared with a conventional trawl net following the experimental design. It was found that the modified trawl net has the potential to contribute to fishery resource preservation with no associated economic loss to fishers