Whole-Genome Sequencing Of Mesorhizobium huakuii 7653R Provides Molecular Insights into Host Specificity and Symbiosis Island Dynamics

Background Evidence based on genomic sequences is urgently needed to confirm the phylogenetic relationship between Mesorhizobium strain MAFF303099 and M. huakuii. To define underlying causes for the rather striking difference in host specificity between M. huakuii strain 7653R and MAFF303099, several probable determinants also require comparison at the genomic level. An improved understanding of mobile genetic elements that can be integrated into the main chromosomes of Mesorhizobium to form genomic islands would enrich our knowledge of how genome dynamics may contribute to Mesorhizobium evolution in general. Results In this study, we sequenced the complete genome of 7653R and compared it with five other Mesorhizobium genomes. Genomes of 7653R and MAFF303099 were found to share a large set of orthologs and, most importantly, a conserved chromosomal backbone and even larger perfectly conserved synteny blocks. We also identified candidate molecular differences responsible for the different host specificities of these two strains. Finally, we reconstructed an ancestral Mesorhizobium genomic island that has evolved into diverse forms in different Mesorhizobium species. Conclusions Our ortholog and synteny analyses firmly establish MAFF303099 as a strain of M. huakuii. Differences in nodulation factors and secretion systems T3SS, T4SS, and T6SS may be responsible for the unique host specificities of 7653R and MAFF303099 strains. The plasmids of 7653R may have arisen by excision of the original genomic island from the 7653R chromosome

A Systematic Review of Diet Quality Index and Obesity among Chinese Adults

Diet quality scores are designed mainly based on Western-style dietary patterns. They were demonstrated to be good indicators of obesity in developed but not developing countries. Several diet quality scores were developed based on the Chinese dietary guidelines, yet no systematic review exists regarding how they were related to obesity. We searched research articles published between 2000 and 2021 in PubMed, CINAHL, and Scopus databases. Both cross-sectional and prospective studies that examined the relationship between a diet quality score and weight, body mass index, obesity, or waist circumference conducted in a Chinese population were selected. From the 602 articles searched, 20 articles were selected (12 are cross-sectional studies and 8 are prospective cohort studies). The relationship between internationally used scores and obesity was inconsistent among studies. Scores tailored to the Chinese diet demonstrated a strong relationship with both being underweight and obesity. The heterogeneity of the populations and the major nutrition transition in China may partially explain the discrepancies among studies. In conclusion, diet quality scores tailored to the Chinese diet may be associated with both undernutrition and overnutrition, as well as being underweight and obesity outcomes

Comparative Analysis of ABC Transporter Genes in Pathogenic and Non-pathogenic Nematodes

The ATP-binding cassette (ABC) transporter gene superfamily is a large protein family with diverse physiological functions in different organisms. Recent genome sequencing projects have reported expansion of ABC transporter gene family in parasitic nematodes and hypothesized that such expansion may enable the parasites to become pathogenic or have increased virulence. Some of these reported expansions may reflect the completeness of sequenced genomes, use of bioinformatics programs, and parameters and criteria used in these projects. The goal of this thesis research is to develop a robust bioinformatics pipeline for annotating high-quality ABC transporter genes so that we can reduce the contribution of technical errors. Our comparative analysis of 29 nematode genomes suggests that pathogenic nematodes generally contain fewer ABC transporter genes than non-pathogenic nematodes, suggesting that expansion in ABC superfamily may not be a mechanism for pathogenic nematodes to survive in their host environment. However, many pathogenic nematodes have genome-specific ABC transporter genes

Activation of AMPK ameliorates acute severe pancreatitis by suppressing pancreatic acinar cell necroptosis in obese mice models

Abstract Obese people with acute pancreatitis (AP) have an increased risk of developing severe acute pancreatitis (SAP), which prolongs the length of hospital stay and increases mortality. Thus, elucidation of the mechanisms through which SAP occurs in obese individuals will provide clues for possible treatment targets. Differences in early events in obese or lean patients with AP have not been conclusively reported. We selected C57BL/6 mice as lean mice models, ob/ob mice or diet induced obese (DIO) mice as obese mice models and then induced experimental AP in mice via injections of caerulein. There were suppressed p-AMPK expressions in the pancreas of obese mice, compared with same-age lean C57BL/6 mice, which were further reduced in AP mice models. Obese AP mice were treated using AICAR, a direct AMPK agonist, which prevented pancreatic damage and cell death, suppressed pancreatic enzyme levels in serum, reduced the areas of fat saponification in the peritoneal cavity, prevented injury in other organs and decreased mice mortality rate. Further assays showed that AICAR activates p-AMPK to stabilize pro-caspase-8. Pro-caspase-8 enhances RIPK3 degradation, inhibits pancreatic acinar cell necroptosis, and downregulates the release of pancreatic enzymes. Thus, activation of AMPK by AICAR alleviates pancreatic acinar cell necroptosis and converts SAP to mild acute pancreatitis in obese mice

How Big Data and High-performance Computing Drive Brain Science

Brain science accelerates the study of intelligence and behavior, contributes fundamental insights into human cognition, and offers prospective treatments for brain disease. Faced with the challenges posed by imaging technologies and deep learning computational models, big data and high-performance computing (HPC) play essential roles in studying brain function, brain diseases, and large-scale brain models or connectomes. We review the driving forces behind big data and HPC methods applied to brain science, including deep learning, powerful data analysis capabilities, and computational performance solutions, each of which can be used to improve diagnostic accuracy and research output. This work reinforces predictions that big data and HPC will continue to improve brain science by making ultrahigh-performance analysis possible, by improving data standardization and sharing, and by providing new neuromorphic insights. Keywords: Brain science, Big data, High-performance computing, Brain connectomes, Deep learnin

Dietary Patterns and Obesity in Chinese Adults: A Systematic Review and Meta-Analysis

Certain dietary patterns are associated with an increased risk of obesity and its comorbidities. However, these associations vary across populations. The prevalence of obesity has been rising amid a drastic nutrition transition in China during the country’s rapid economic growth. This systematic review and meta-analysis were conducted to summarize how dietary patterns are associated with obesity in the Chinese population. We searched for articles from 1 January 2000 to 1 February 2022 in PubMed, Cumulative Index to Nursing and Allied Health Literature (CINAHL), and Scopus that assessed the relationship between dietary patterns and obesity outcomes. Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated using a random effects model. From the 2556 articles identified from the search, 23 articles were included in the analysis. We found that the traditional Chinese dietary pattern was associated with a lower risk of overweight/obesity (OR = 0.69, 95% CI: 0.57, 0.84, p < 0.001), whereas the Western dietary pattern was associated with a higher OR of overweight/obesity, but not reaching statistical significance (OR = 1.34, 95% CI: 0.98, 1.84, p = 0.07). There were inconsistent results for other dietary patterns, such as meat/animal protein and plant/vegetarian patterns. In conclusion, the traditional Chinese diet characterized by vegetables, rice, and meat was associated with a lower risk of obesity. The heterogeneity in characterizing dietary patterns contributes to the inconsistency of how dietary patterns are associated with obesity in the Chinese population

Gclust: A Parallel Clustering Tool for Microbial Genomic Data

The accelerating growth of the public microbial genomic data imposes substantial burden on the research community that uses such resources. Building databases for non-redundant reference sequences from massive microbial genomic data based on clustering analysis is essential. However, existing clustering algorithms perform poorly on long genomic sequences. In this article, we present Gclust, a parallel program for clustering complete or draft genomic sequences, where clustering is accelerated with a novel parallelization strategy and a fast sequence comparison algorithm using sparse suffix arrays (SSAs). Moreover, genome identity measures between two sequences are calculated based on their maximal exact matches (MEMs). In this paper, we demonstrate the high speed and clustering quality of Gclust by examining four genome sequence datasets. Gclust is freely available for non-commercial use at https://github.com/niu-lab/gclust. We also introduce a web server for clustering user-uploaded genomes at http://niulab.scgrid.cn/gclust. Keywords: Microbial genome clustering, Parallelization, Sparse suffix array, Maximal exact match, Segment extensio