Screening of Polyvalent Phage-Resistant Escherichia coli Strains Based on Phage Receptor Analysis

Bacteria-based biotechnology processes are constantly under threat from bacteriophage infection, with phage contamination being a non-neglectable problem for microbial fermentation. The essence of this problem is the complex co-evolutionary relationship between phages and bacteria. The development of phage control strategies requires further knowledge about phage-host interactions, while the widespread use of Escherichia coli strain BL21 (DE3) in biotechnological processes makes the study of phage receptors in this strain particularly important. Here, eight phages infecting E. coli BL21 (DE3) via different receptors were isolated and subsequently identified as members of the genera T4virus, Js98virus, Felix01virus, T1virus, and Rtpvirus. Phage receptors were identified by whole-genome sequencing of phage-resistant E. coli strains and sequence comparison with wild-type BL21 (DE3). Results showed that the receptors for the isolated phages, designated vB_EcoS_IME18, vB_EcoS_IME253, vB_EcoM_IME281, vB_EcoM_IME338, vB_EcoM_IME339, vB_EcoM_IME340, vB_EcoM_IME341, and vB_EcoS_IME347 were FhuA, FepA, OmpF, lipopolysaccharide, Tsx, OmpA, FadL, and YncD, respectively. A polyvalent phage-resistant BL21 (DE3)-derived strain, designated PR8, was then identified by screening with a phage cocktail consisting of the eight phages. Strain PR8 is resistant to 23 of 32 tested phages including Myoviridae and Siphoviridae phages. Strains BL21 (DE3) and PR8 showed similar expression levels of enhanced green fluorescent protein. Thus, PR8 may be used as a phage resistant strain for fermentation processes. The findings of this study contribute significantly to our knowledge of phage-host interactions and may help prevent phage contamination in fermentation

Application of indocyanine green-mediated fluorescence molecular imaging technology in liver tumors resection: a systematic review and meta-analysis

BackgroundThis meta-analysis was dedicated to evaluating the safety and effectiveness of indocyanine green (ICG) -mediated fluorescence molecular imaging (FMI) technology in liver tumors resection.MethodsA literature search of PubMed, Embase databases, Cochrane Library, and Web of Science was performed to identify all clinical controlled studies exploring the effects of fluorescence imaging on liver tumors resection. Quality assessment and data extraction of studies were conducted independently by 3 reviewers. Mean difference (MD) and odds ratio (OR) with 95% confidence interval (CI) were calculated using a fixed-effects or random-effects model. The meta-analysis was performed with RevMan 5.3 software.Results14 retrospective cohort studies (RCSs) involving a total of 1227 patients were finally included. The results showed that Fluorescence-assisted liver tumors resection could improve the R0 resection rate (OR = 2.63; 95% CI: 1.46~4.73, p = 0.001), reduce overall complications (OR = 0.66; 95% CI: 0.44~0.97, p = 0.04), biliary fistula (OR = 0.20; 95% CI: 0.05~0.77, p = 0.02), intraoperative blood loss (MD = −70.76, 95% CI: −106.11 to −35.41; p < 0.0001), and shortens hospital stay (MD = −1.41, 95% CI: −1.90 to −0.92; p < 0.00001). There were no significant differences in the incidences of operative time (MD = −8.68, 95% CI: −18.59 to −1.22; p = 0.09), complications of grade III or above (OR = 0.73; 95% CI: 0.43~1.25, p = 0.26), liver failure (OR = 0.86; 95% CI: 0.39~1.89, p = 0.71), and blood transfusion (OR = 0.66; 95% CI: 0.42~1.03, p = 0.07).ConclusionCurrent evidence suggests that ICG-mediated FMI technology could enhance the clinical effectiveness of patients with liver tumors resection and is clinically worthy of promotion.Systematic review registrationPROSPERO, identifier CRD42022368387

Mutations in TUBB8 and Human Oocyte Meiotic Arrest

BACKGROUND Human reproduction depends on the fusion of a mature oocyte with a sperm cell to form a fertilized egg. The genetic events that lead to the arrest of human oocyte maturation are unknown. METHODS We sequenced the exomes of five members of a four-generation family, three of whom had infertility due to oocyte meiosis I arrest. We performed Sanger sequencing of a candidate gene, TUBB8, in DNA samples from these members, additional family members, and members of 23 other affected families. The expression of TUBB8 and all other β-tubulin isotypes was assessed in human oocytes, early embryos, sperm cells, and several somatic tissues by means of a quantitative reverse- transcriptase–polymerase-chain-reaction assay. We evaluated the effect of the TUBB8 mutations on the assembly of the heterodimer consisting of one α-tubulin polypeptide and one β-tubulin polypeptide (α/β-tubulin heterodimer) in vitro, on microtubule architecture in HeLa cells, on microtubule dynamics in yeast cells, and on spindle assembly in mouse and human oocytes. RESULTS We identified seven mutations in the primate-specific gene TUBB8 that were responsible for oocyte meiosis I arrest in 7 of the 24 families. TUBB8 expression is unique to oocytes and the early embryo, in which this gene accounts for almost all the expressed β-tubulin. The mutations affect chaperone-dependent folding and assembly of the α/β-tubulin heterodimer, disrupt microtubule behavior on expression in cultured cells, alter microtubule dynamics in vivo, and cause catastrophic spindle-assembly defects and maturation arrest on expression in mouse and human oocytes. CONCLUSIONS TUBB8 mutations have dominant-negative effects that disrupt microtubule behavior and oocyte meiotic spindle assembly and maturation, causing female infertility. (Funded by the National Basic Research Program of China and others.

Additional file 2 of Identification of novel cell-free RNAs in maternal plasma as preterm biomarkers in combination with placental RNA profiles

Additional file 2: Functional annotation of hub genes in plasma and placental group

Additional file 1 of Identification of novel cell-free RNAs in maternal plasma as preterm biomarkers in combination with placental RNA profiles

Additional file 1: Table S1. Maternal characteristics of participants in this study involved in RT-qPCR. Table S2. Gene primer sequences used in RT-qPCR. Figure S1. Principal component analysis (PCA) for sample clustering using RNA-seq data. Figure S2. Comparison of plasma and placental transcriptome analysis. Figure S3. Complexity of RNA regulatory molecules biotype. Figure S4. Construction of the PPI network. Figure S5. The key genes in plasma and placental PPI network. Figure S6. Comparison of the relative expression levels of ARHGEF28. Figure S7. Predictive models for preterm birth combined with clinical factors. Figure S8. The exploration of relatedness between clinical factors for preterm birth and the expression level of ARHGEF28. Figure S9. The exploration of relatedness between clinical factors for preterm birth and gestational age

Quantitative Methylation Level of the <i>EPHX1</i> Promoter in Peripheral Blood DNA Is Associated with Polycystic Ovary Syndrome

<div><p>Steroid synthesis and metabolic pathways play important roles in the pathophysiology of PCOS, but until now there have been no studies on the methylation profiles of specific genes in steroid synthesis pathways that are known to be associated with PCOS. Here we used MassARRAY quantitative methylation analysis to determine the methylation levels of each CpG site or cluster in the promoters of <i>EPHX1</i>, <i>SRD5A1</i>, and <i>CYP11A1</i> in 64 peripheral blood samples. We further examined the methylation level of <i>EPHX1</i> in an independent cohort consisting of 116 people. Finally, we investigated the role of <i>EPHX1</i> in steroidogenesis in the KGN cell line. For <i>SRD5A1</i> and <i>CYP11A1</i>, there was no significant difference in methylation level between patients and controls. For <i>EPHX1</i>, however, the methylation levels of a few consecutive CpG sites and clusters were found to be significantly associated with PCOS. The methylation levels of a number of CpG clusters or sites were significantly lower in patients than in controls in the first cohort consisting of 64 people, such as clusters 13–14 (<i>P</i><0.05), 15–16 (<i>P</i><0.001), and 19–24 (<i>P</i><0.001) and sites CpG_53 (<i>P</i><0.01) and CpG_54 (<i>P</i><0.05). Among differentiated methylation sites and clusters, the methylation levels of the CpG cluster 13–14 and CpG cluster 19–24 in PCOS patients were significantly lower than in controls in the second cohort of 116 people (<i>P</i><0.05 for both). In addition, knockdown and overexpression experiments in KGN cells showed that <i>EPHX1</i> can regulate estradiol concentrations, and this indicates a role for <i>EPHX1</i> in steroidogenesis. Our study has demonstrated that methylation of the <i>EPHX1</i> promoter might be associated with PCOS. This study provides direct evidence that methylation plays an important role in PCOS and demonstrates a novel role for <i>EPHX1</i> in female reproduction.</p></div

The mean methylation levels for each CpG site of the <i>EPHX1</i> promoter in PCOS patients and healthy women in the first cohort consisting of 64 peripheral blood samples (A) and in the second cohort consisting of 116 peripheral blood samples (B).

<p>Values are mean ± SEM. *** represents <i>p</i><0.001, ** represents <i>p</i><0.01, * represents <i>p</i><0.05.</p

The methylation status (methylation %) of the CpG sites in the promoter region of <i>EPHX1</i> between healthy women and PCOS patients in peripheral blood samples from the first cohort (Control n = 32, PCOS n = 32).

<p>Data represent the mean ± SEM, <i>p</i> values are determined by two-way ANOVA with Bonferroni post-tests.</p

<i>EPHX1</i> affects E₂ synthesis in the KGN cell line.

<p>The E₂ level is increased when cells are transfected with <i>EPHX1</i> siRNA (A). The E₂ level is decreased when cells are transfected with the <i>EPHX1</i> cDNA plasmid (B). *** represents <i>p</i><0.001 and * represents <i>p</i><0.05.</p