Detection of Burkholderia pseudomallei with CRISPR-Cas12a based on specific sequence tags.

Melioidosis is a bacterial infection caused by Burkholderia pseudomallei (B. pseudomallei), posing a significant threat to public health. Rapid and accurate detection of B. pseudomallei is crucial for preventing and controlling melioidosis. However, identifying B. pseudomallei is challenging due to its high similarity to other species in the same genus. To address this issue, this study proposed a dual-target method that can specifically identify B. pseudomallei in less than 40 min. We analyzed 1722 B. pseudomallei genomes to construct large-scale pan-genomes and selected specific sequence tags in their core genomes that effectively distinguish B. pseudomallei from its closely related species. Specifically, we selected two specific tags, LC1 and LC2, which we combined with the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR associated proteins (Cas12a) system and recombinase polymerase amplification (RPA) pre-amplification. Our analysis showed that the dual-target RPA-CRISPR/Cas12a assay has a sensitivity of approximately 0.2 copies/reaction and 10 fg genomic DNA for LC1, and 2 copies/reaction and 20 fg genomic DNA for LC2. Additionally, our method can accurately and rapidly detect B. pseudomallei in human blood and moist soil samples using the specific sequence tags mentioned above. In conclusion, the dual-target RPA-CRISPR/Cas12a method is a valuable tool for the rapid and accurate identification of B. pseudomallei in clinical and environmental samples, aiding in the prevention and control of melioidosis.

A comparison of computed tomography imaging with histopathology in the sensitivity and correlation of evaluating coronary arterial calcification.

Background: The sensitivity and correlation of coronary computed tomography angiography (CTA) as compared with histopathology are unknown in evaluating coronary arterial calcification. In this study, we retrospectively evaluated qualitatively and quantitatively the sensitivity and correlation of coronary CTA compared with histopathology in assessing coronary arterial calcification. Methods: This study was conducted on 12 randomly selected cadavers aged over 40 years at the time of death, and 53 segments of coronary arteries from these 12 cadavers were obtained from the Human Anatomy Laboratory of Tianjin Medical University. The artery segments were scanned using contrasted-enhanced dual-source computed tomography (DSCT) with an axial slice thickness of 0.6 mm. Coronary artery calcification in a coronary segment was defined as the presence of 1 or more voxels with a CT density >130 Hounsfield units. According to the arc of calcification in the cross section of the coronary artery wall, calcified plaques were divided into three categories: mild, moderate, and severe calcification. The coronary artery stenosis caused by calcified plaque was observed and calculated with multiplanar reconstruction (MPR), maximum density projection, volume rendering (VR), and cross-sectional reconstruction. After CT enhancement scanning, the coronary artery specimens were cut into 4-mm long segments and embedded in paraffin for pathological staining. Pathological classification and coronary artery stenosis measured with pathological analysis were used as comparison criteria. Results: Histopathology detected 69 Vb-type plaques, while DSCT detected 57 calcified plaques. The sensitivity of CT for detecting mild, moderate, and severe calcified plaques were 88.3% [95% confidence interval (CI): 74.1-95.6%], 100% (95% CI: 69.8-100%), and 100% (95% CI: 73.2-100%), respectively. DSCT had a significant (P<0.001) correlation with histopathology in quantifying coronary artery stenosis caused by mild, moderate, and severe calcified plaques (R2=0.9278, R2=0.9158, R2=0.7923, respectively). Compared with histopathology, DSCT overestimated coronary artery stenosis caused by mild, moderate, and severe calcified plaques (3.2%±2.0%, 4.9%±4.7%, and 14.7%±8.2%, respectively; P<0.05). Conclusions: DSCT contrast enhancement scanning can detect and characterize coronary artery calcification with a good correlation with histopathologic quantification of coronary artery stenosis caused by different types of calcified plaques, even though coronary CTA may overestimate the stenosis.

Research progress on influencing factors of depressive symptoms in adolescents / 中国学校卫生

Abstract@#In recent years, mental health problems such as anxiety and depression among adolescents in China have attracted attention from all walks of life. Given that adolescence is a transitional and critical period for individual development, mental health affect the developmental opportunities. Therefore, in the review, the effects of environment, psychosocial factors and behavioral patterns on depressive symptoms are analyzed by combining with the characteristics of physical and mental development among adolescents. It is found that early adolescence and even childhood should be the key period for the prevention and intervention of depression. In order to formulate effective interventions and prevention strategies, it is proposed that future research should combine real situation in China with active exploration of protective factors and early predictors of depression.

Correlation between physical fitness condition and depressive symptoms in adolescents / 中国学校卫生

Objective@#To explore the relationship between adolescents physical fitness and depressive symptoms, and to provide reference for the early prevention and intervention of depressive symptoms and improvement of physical fitness in Chinese adolescents.@*Methods@#From September to December 2021, a total of 8 102 adolescents were selected by random cluster sampling method in Shanghai, Urumqi, Changsha and Kunming. The Center for Epidemiologic Studies Depression Scale(CES-D) was used to investigate the depressive symptoms, and completed grip strength, standing long jump, 50 m running, modified sitting forward flexion, 20 s repeated traverse, 30 s sit ups, 20 m round trip running (20 m SRT) test. χ 2 test, Goodman Kruskal Gamma and Logistic regression analysis were used to analyze the relationship between physical fitness index(PFI) and depressive symptoms.@*Results@#The overall detection rate of depressive symptoms in adolescents with high level PFI was 23.4%, and the detection rate of low level adolescents was 26.3%, with a statistically significant difference ( χ 2=6.73, P =0.01). There was a significant positive correlation between PFI and depressive symptoms in the high school group ( G=0.09, P <0.05) and the boy group ( G=0.12, P < 0.05 ), and there was no significant association between PFI and depressive symptoms in the junior high school group and the girl group ( P >0.05). After adjusting for gender and age in the Logistic regression model, compared with those with high PFI, the risk of depressive symptoms in those with low PFI was 1.18 times (95% CI =1.05-1.33).@*Conclusion@#There is a correlation between physical fitness and depressive symptoms in adolescents. Adolescents with low PFI are at higher risk of developing depressive symptoms than those with high PFI.

Correlation between children and adolescents physical activity and socioeconomic status in China / 中国学校卫生

Objective@#To understand the correlation between physical activity (PA) and socioeconomic status (SES) among Chinese children and adolescents, and to provide theoretical basis for physical activity promotion for Chinese children and adolescents.@*Methods@#By using stratified random cluster sampling, a total of 4 269 children and adolescents aged 7 to 18 were selected from six cities in China from September to December 2018. Physical Activity Level Evaluation Questionnaire of Chinese Children and Adolescents Aged 7 to 18 was used to investigate PA and SES, and the height and weight were measured.@*Methods@#In terms of different intensity of PA, the time spent on light intensity physical activity(LPA), moderate intensity physical activity(MPA), moderate to vigorous physical activity(MVPA)and total physical activity(TPA) in low SES group was 28.5(6.9,57.1) min/d, 46.2 (25.7,79.2) min/d, 61.4(34.3,101.9) min/d and 102.9(65.0,145.8)min/d respectively, which was higher than that in middle SES groups [ 21.4 (4.3,50.7), 37.1(18.6,65.7), 50.3(27.1,86.8), 85.7(49.3,127.1) min/d] and high SES groups [24.3( 5.0 ,54.3), 40.0(21.4,69.1), 54.3(32.9,91.4), 89.6(55.7,132.9) min/d]( P <0.01). In terms of different types of PA, the traffic PA [40.0(15.0,68.6) min/d] and entertainment PA[4.3(0,17.1)min/d] accounted the highest proportion in low SES group,while sports PA [36.4(20.7,60.7) min/d] accounted the highest proportion in high SES group( P <0.01).The compliance rates of MVPA in low, middle and high SES groups were 51.1%, 42.5% and 45.2%, respectively, and the differences were statistically significant ( χ 2= 22.02 , P <0.05). After controlling for confounding factors, the detection rate of MVPA in the low SES group was 1.24 times higher than that in the high SES group ( P <0.01).@*Conclusion@#The MVPA and TPA time of children and adolescents with middle SES group were the lowest. Physical activities spent on traffic and entertainment account highest in low SES group, while physical activities spent on sports account highest in high SES group.

Defending the homeland: microbiome molecules provide protection to their vertebrate hosts.

Aim: The resident bacterial microbiome may shape and protect the health of vertebrate host. An array of molecules secreted by microbiome may contribute to the ecological stability of the microbiome itself. Material & methods: ELISA, radioactivity, immunofluorescence and cytokines measurements were used to observe the bioactivity and stability of colicin Ia level in oviparous and viviparous animal circulation. Results: Colicin Ia, a protein antimicrobial produced by Escherichia coli, is not present in animals at birth, but increases in concentration with the establishment of a stable gut microbiome and drops when the microbiome is experimentally disrupted. Colicin introduced in vivo is transported to tissues at concentrations able to prevent or eliminate bacterial infection. Conclusion: Our findings suggest an unexpected benefit provided by the presence of a resident microbiome in the form of active, circulating, bacterially-synthesized antimicrobial molecules.

Liver injury in septic mice were suppressed by a camptothecin-bile acid conjugate via inhibiting NF-κB signaling pathway.

BACKGROUND AND OBJECTIVES: Sepsis is a life-threatening organ dysfunction syndrome arising from uncontrolled inflammatory responses. Liver injury is a crucial factor for the prognosis of sepsis. Camptothecins (CPTs) have been reported to suppress the inflammatory response induced by sepsis. G2, a CPT-bile acid conjugate, has been demonstrated the property of liver targeting in our previous research. This study aimed to research the effects of G2 on liver injury induced by cecal ligation and puncture (CLP). METHODS: C57BL/6 mice were subjected to CLP surgery, and effects of G2 on liver damage and survival rates of CLP-induced mice were evaluated. To detect the related markers of hepatic injury or neutrophil infiltration, inflammatory cytokines and protein levels, hematoxylin-eosin staining assay, corresponding Detection Kits assay, ELISA and Western blot analysis were performed. RESULTS: Intraperitoneal administration of G2 reduced liver injury and enhanced the survival rates in mice with sepsis. Treatment with G2 decreased the levels of hepatic injury markers aspartate aminotransferase (AST) and alanine aminotransferase (ALT) in the serum of mice induced by CLP. The hepatic level of neutrophil infiltration marker myeloperoxidase (MPO) was reduced in G2 administration group. And the levels of serum inflammatory cytokines, including Tumor Necrosis Factor-α (TNFα), Interleukin-6 (IL-6) and IL-1ß, were decreased by G2. Furthermore, the results of Western blot analysis indicated that G2 suppressed the up-regulation of NF-κB p-P65 and p-IκBα. It suggested that G2 suppressed the activation of NF-κB signaling pathway. CONCLUSION: G2 alleviated sepsis-induced liver injury via inhibiting the NF-κB signaling pathway.

High-Quality Draft Genome Sequence of the Green Alga Tetraselmis striata (Chlorophyta) Generated from PacBio Sequencing.

A high-quality draft genome sequence of the microalgal species Tetraselmis striata was generated using PacBio sequencing. The assembled genome is 228 Mb, derived from 3,613 polished contigs at 84× coverage depth. This genome contains an average GC content of 57.9% and 48,906 predicted genes.

Genomic comparison of facultatively anaerobic and obligatory aerobic Caldibacillus debilis strains GB1 and Tf helps explain physiological differences.

Caldibacillus debilis strains GB1 and Tf display distinct phenotypes. Caldibacillus debilis GB1 is capable of anaerobic growth and can synthesize ethanol while C. debilis Tf cannot. Comparison of the GB1 and Tf genome sequences revealed that the genomes were highly similar in gene content and showed a high level of synteny. At the genome scale, there were several large sections of DNA that appeared to be from lateral gene transfer into the GB1 genome. Tf did have unique genetic content but at a much smaller scale: 300 genes in Tf verses 857 genes in GB1 that matched at ≤90% sequence similarity. Gene complement and copy number of genes for the glycolysis, tricarboxylic acid cycle, and electron transport chain pathways were identical in both strains. While Tf is an obligate aerobe, it possesses the gene complement for an anaerobic lifestyle (ldh, ak, pta, adhE, pfl). As a species, other strains of C. debilis should be expected to have the potential for anaerobic growth. Assaying the whole cell lysate for alcohol dehydrogenase activity revealed an approximately 2-fold increase in the enzymatic activity in GB1 when compared with Tf.

A metabolic and genomic assessment of sugar fermentation profiles of the thermophilic Thermotogales, Fervidobacterium pennivorans.

A metabolic, genomic and proteomic assessment of Fervidobacterium pennivorans strains was undertaken to clarify the metabolic and genetic capabilities of this Thermotogales species. The type strain Ven5 originally isolated from a hot mud spa in Italy, and a newly isolated strain (DYC) from a hot spring at Ngatamariki, New Zealand, were compared for metabolic and genomic differences. The fermentation profiles of both strains on cellobiose generated similar major end products (acetate, alanine, glutamate, H2, and CO2). The vast majority of end products produced were redox neutral, and carbon balances were in the range of 95-115%. Each strain showed distinct fermentation profiles on sugar substrates. The genome of strain DYC was sequenced and shown to have high sequence similarity and synteny with F. pennivorans Ven5 genome, suggesting they are the same species. The unique genome regions in Ven5, corresponded to genes involved in the Entner-Doudoroff pathway confirming our observation of DYC's inability to utilize gluconate. Genome analysis was able to elucidate pathways involved in production of the observed end-products with the exception of alanine and glutamate synthesis which were resolved with less clarity due to poor sequence identity and missing critical enzymes within the pathway, respectively.

Contrast dose reduction with shortened injection durations in coronary CT angiography on 16-cm Wide-detector CT scanner.

OBJECTIVES:: To investigate the use of shortened contrast injection with late triggering in coronary CT angiography (CCTA) for decreasing contrast dose and maintaining image quality. METHODS:: 106 patients for CCTA on a 16-cm wide-detector CT were prospectively enrolled into groups A (n = 50) and B (n = 56) randomly. Patient weight-dependent contrast medium (Iopamiro, 370 mgI ml-1) at dose rate of 25 mgI/kg/s was used with 8 s and the standard 10 s injection time in groups A and B, respectively. CT values of the aortic sinus (AS), right coronary artery, left anterior descending and left circumflex at the proximal, middle and distal segments were measured and compared. Subjective image quality was evaluated and analyzed with Fisher exact test. Contrast dose, injection rate and enhancement duration (between the start of enhancement in AS and scan finish) were also compared. RESULTS:: There was no difference in the injection rate and enhancement duration between the two groups (p > 0.05), while the total contrast dose in group A (36.2 ± 5.7 ml) was significantly lower than in group B (46.4 ± 6.3 ml) (p < 0.001). There was no difference for CT values in all major coronary vessels between the two groups and no difference in subjective image quality scores (all p > 0.05). CONCLUSION:: It is feasible to shorten contrast injection to 8 s in CCTA on wide-detector CT systems to significantly reduce contrast dosage, maintain adequate enhancement and reduce contrast-related artifacts. ADVANCES IN KNOWLEDGE:: (1) Coronary CT angiography (CCTA) scans with shortened contrast medium injection duration and late triggering are feasible with a 16-cm wide-detector CT system (2) Compared with the conventional CCTA with 10 s contrast injection duration, the new contrast injection protocol of using shortened injection duration (to 8 s) and late triggering reduces contrast dose to 36.2 ml, while maintaining adequate enhancement in vessels and reducing contrast-related artifacts.

Fatal swine acute diarrhoea syndrome caused by an HKU2-related coronavirus of bat origin.

Cross-species transmission of viruses from wildlife animal reservoirs poses a marked threat to human and animal health 1 . Bats have been recognized as one of the most important reservoirs for emerging viruses and the transmission of a coronavirus that originated in bats to humans via intermediate hosts was responsible for the high-impact emerging zoonosis, severe acute respiratory syndrome (SARS) 2-10 . Here we provide virological, epidemiological, evolutionary and experimental evidence that a novel HKU2-related bat coronavirus, swine acute diarrhoea syndrome coronavirus (SADS-CoV), is the aetiological agent that was responsible for a large-scale outbreak of fatal disease in pigs in China that has caused the death of 24,693 piglets across four farms. Notably, the outbreak began in Guangdong province in the vicinity of the origin of the SARS pandemic. Furthermore, we identified SADS-related CoVs with 96-98% sequence identity in 9.8% (58 out of 591) of anal swabs collected from bats in Guangdong province during 2013-2016, predominantly in horseshoe bats (Rhinolophus spp.) that are known reservoirs of SARS-related CoVs. We found that there were striking similarities between the SADS and SARS outbreaks in geographical, temporal, ecological and aetiological settings. This study highlights the importance of identifying coronavirus diversity and distribution in bats to mitigate future outbreaks that could threaten livestock, public health and economic growth.

Description of a cryptic thermophilic (pro)phage, CBP1 from Caldibacillus debilis strain GB1.

This study characterizes a cryptic (pro)phage-related sequence within the Caldibacillus debilis GB1 genome, designated CBP1.CBP1 is a Siphoviridae-like genome highly related to GBVS1 from Geobacillus sp. 6k51. The CBP1genome is a 37,315 bp region containing 69 putative ORFs with a GC content of 42% flanked on both sides by host DNA integrated into the main bacterial chromosome (contig 16). Bioinformatic analyses identified cassettes of genes within the CBP1 genome that were similar in function, yet distinct in sequence, from genes previously identified in GBVS1. All of CBP1 genes had less than 60% amino acid sequence identity with GBVS1by tBLASTx, with the exception of the TMP repeat gene. CBP1 possessed all the necessary genes to undergo a temperate/lytic phage life cycle, including excision, replication, structural genes, DNA packaging, and cell lyses. Proteomic analysis of CBP1 revealed the expression of 5 proteins. One of the expressed proteins was a transcriptional regulator protein homologous to the bacteriophage λ repressor protein (cI) expressed in high amounts from the CBP1 region, consistent with a lysogenic phage in a repressed state. The CBP1 protein expression profile during host growth provides unique insight into thermophilic Siphoviridae-like phages in the repressed state within their host cells.

Understanding aerobic/anaerobic metabolism in Caldibacillus debilis through a comparison with model organisms.

Caldibacillus debilis GB1 is a facultative anaerobe isolated from a thermophilic aero-tolerant cellulolytic enrichment culture. There is a lack of representative proteomes of facultative anaerobic thermophilic Bacillaceae, exploring aerobic/anaerobic expression. The C. debilis GB1 genome was sequenced and annotated, and the proteome characterized under aerobic and anaerobic conditions while grown on cellobiose. The draft sequence of C. debilis GB1 contains a 3,340,752 bp chromosome and a 5,386 bp plasmid distributed over 49 contigs. Two-dimensional liquid chromatography mass spectrometry/mass spectrometry was used with Isobaric Tags for Relative and Absolute Quantification (iTRAQ) to compare protein expression profiles, focusing on energy production and conversion pathways. Under aerobic conditions, proteins in glycolysis and pyruvate fermentation pathways were down-regulated. Simultaneously, proteins within the tricarboxylic acid cycle, pyruvate dehydrogenase, the electron transport chain, and oxygen scavenging pathways showed increased amounts. Under anaerobic conditions, protein levels in fermentation pathways were consistent with the generated end-products: formate, acetate, ethanol, lactate, and CO2. Under aerobic conditions CO2 and acetate production was consistent with incomplete respiration. Through a direct comparison with gene expression profiles from Escherichia coli, we show that global regulation of core metabolism pathways is similar in thermophilic and mesophilic facultative anaerobes of the Phylum Proteobacteria and Firmicutes.

Draft Genome Sequence of the Bacteriocin-Producing Bradyrhizobium japonicum Strain FN1.

Bradyrhizobium japonicum strain FN1 was found to produce bacteriocin-like zones of clearing when tested against other strains of bradyrhizbia. The genome was sequenced, and several putative bacteriocin-producing genes, in addition to the expected genes involved in nodulation and nitrogen fixation, were identified.

Genetic diversity and evolutionary dynamics of Ebola virus in Sierra Leone.

A novel Ebola virus (EBOV) first identified in March 2014 has infected more than 25,000 people in West Africa, resulting in more than 10,000 deaths. Preliminary analyses of genome sequences of 81 EBOV collected from March to June 2014 from Guinea and Sierra Leone suggest that the 2014 EBOV originated from an independent transmission event from its natural reservoir followed by sustained human-to-human infections. It has been reported that the EBOV genome variation might have an effect on the efficacy of sequence-based virus detection and candidate therapeutics. However, only limited viral information has been available since July 2014, when the outbreak entered a rapid growth phase. Here we describe 175 full-length EBOV genome sequences from five severely stricken districts in Sierra Leone from 28 September to 11 November 2014. We found that the 2014 EBOV has become more phylogenetically and genetically diverse from July to November 2014, characterized by the emergence of multiple novel lineages. The substitution rate for the 2014 EBOV was estimated to be 1.23 × 10(-3) substitutions per site per year (95% highest posterior density interval, 1.04 × 10(-3) to 1.41 × 10(-3) substitutions per site per year), approximating to that observed between previous EBOV outbreaks. The sharp increase in genetic diversity of the 2014 EBOV warrants extensive EBOV surveillance in Sierra Leone, Guinea and Liberia to better understand the viral evolution and transmission dynamics of the ongoing outbreak. These data will facilitate the international efforts to develop vaccines and therapeutics.

An engineered multidomain fungicidal peptide against plant fungal pathogens.

Fungal pathogens represent major problems for human health and agriculture. As eukaryotic organisms, fungi share some important features with mammalian cells. Therefore, current anti-fungal antibiotics often can not distinguish between fungi and mammalian cells, resulting in serious side effects in mammalian cells. Accordingly, there is strong impetus to develop antifungal alternatives that are both safe and effective. The E1 family of colicin are channel-forming bacteriocins produced by Escherichia coli, which are bactericidal only to E. coli and related species. To target the channel-forming domain of colicin to fungal cell membrane, we engineered a sexual mating pheromone of Candida albicans, α-factor pheromone to colicin Ia. A peptide was constructed consisting of an α mating pheromone of C. albicans fused to the channel-forming domain of colicin Ia to create a new fusion protein, pheromonicin-CA (PMC-CA). Indirect immunolabeling showed that the PMC-CA bound to fungal cells and inhibited growth in the laboratory and field. In the field, the protective activity of pheromonicin against rice blast disease was significantly greater, on a molar basis, than that of triazoles, tricyclazole or isoprothiolane. These results suggest that fusion peptides may be of value as fungicidal agents under agricultural conditions.

Peroxisome proliferator-activated receptor alpha expression changes in human pregnant myometrium.

Peroxisome proliferator-activated receptor alpha (PPARα) has been demonstrated to exhibit anti-inflammatory activities that are hypothesized to play a key role in labor suppression and maintenance of uterine quiescence. The aim of this study was to identify pregnancy- and labor-associated changes in PPARα in human myometrium. For this investigation, human myometrium was obtained from premenopausal women, and the study participants were categorized into the following 4 groups: nonpregnant (NP; n = 10), preterm not in labor (PNL; n = 10, gestation range 20-35 weeks), term not in labor (TNL; n = 20, gestation range 37-41 weeks), and term in labor (TL; n = 20, gestation range 37-41 weeks). Immunohistochemistry was used to locate and confirm the expression of PPARα. Relative quantitative real-time polymerase chain reaction (PCR) and Western blotting were employed to study the expression of anti-inflammatory PPARα and proinflammatory interleukin 1ß (IL-1ß). Immunohistochemistry indicated that PPARα was located in the nucleus of uterine smooth muscle cells. Compared to other groups, in PNL group, the PPARα messenger RNA (mRNA) and protein increased significantly. Decreased PPARα mRNA and protein expressions in myometrium were associated with labor while IL-1ß increased remarkably. There were negative correlations between PPARα and IL-1ß on mRNA (r = -.765, P < .01) and protein (r = -.624, P < .01) levels analyzed using Pearson test. In conclusion, human pregnancy is associated with changes in expression of PPARα and IL-1ß in myometrium. The changes observed suggest that PPARα may play a role in maintaining pregnancy or initiating labor through inhibiting the expression of IL-1ß in human myometrium.