A metagenomic approach to dissect the genetic composition of enterotypes in Han Chinese and two Muslim groups

Distinct enterotypes have been observed in the human gut but little is known about the genetic basis of the microbiome. Moreover, it is not clear how many genetic differences exist between enterotypes within or between populations. In this study, both the 16S rRNA gene and the metagenomes of the gut microbiota were sequenced from 48 Han Chinese, 48 Kazaks, and 96 Uyghurs, and taxonomies were assigned after de novo assembly. Single nucleotide polymorphisms were also identified by referring to data from the Human Microbiome Project. Systematic analysis of the gut communities in terms of their abundance and genetic composition was also performed, together with a genome-wide association study of the host genomes. The gut microbiota of 192 subjects was clearly classified into two enterotypes (Bacteroides and Prevotella). Interestingly, both enterotypes showed a clear genetic differentiation in terms of their functional catalogue of genes, especially for genes involved in amino acid and carbohydrate metabolism. In addition, several differentiated genera and genes were found among the three populations. Notably, one human variant (rs878394) was identified that showed significant association with the abundance of Prevotella, which is linked to LYPLAL1, a gene associated with body fat distribution, the waist-hip ratio and insulin sensitivity. Taken together, considerable differentiation was observed in gut microbes between enterotypes and among populations that was reflected in both the taxonomic composition and the genetic makeup of their functional genes, which could have been influenced by a variety of factors, such as diet and host genetic variation.     

Isolation of YAC insert sequences by representational difference analysis.

We present a method for the isolation of YAC insert sequences by representational difference analysis (RDA). To achieve maximal representation of the sequences, the amplicons were generated from a Mbol digestion product. RDA was performed using a 970 kb insert YAC clone. After two rounds of re-association and selective amplification 92% of the difference product represented sequences derived from the YAC insert. Twenty insert-specific sequence-tagged sites were readily defined. The difference product was also successfully used to isolate microsatellite markers, to identify clones from a human PAC library and as a chromosome painting probe in fluorescence in situ hybridization.     

FACTORS AFFECTING CORPORA ALLATA ACTIVITY IN THE ADULT LADY BEETLE COCCINELLA SEPTEMPUNCTATA L.

Abstract Corpora allata are the defined site of juvenile hormone (JH) biosynthesis in reproductive adult insects and their activity is regulated by intrinsic and extrinsic factors. In the adult lady beetle Coccinella septempunctata , it has been well established that the development of ovaries is controlled by JH (Guan 1987). The present study aims at the elucidation of the influence of some factors regulating reproduction of the lady beetle. They include topical application of JH analogues, presence of neuropeptides in the extract from the brain, as well as the development of ovary and type of food on CA activity. JH synthesis in CA is monitored with radiochemical assay and immunoelectrophoresis.     

Linkage between vitamin D-binding protein and α-fetoprotein in the mouse

The albumin gene family consists of four evolutionarily related genes that code for serum transport proteins. In rodents, the genes for albumin, |ga-fetoprotein, and |gaALB are physically linked within 100 kilobases of DNA. The fourth gene, Gc, encoding vitamin D-binding protein or group-specific component, maps to the same chromosome as the other family members, but linkage has not been established. This report describes the genetic and physical mapping of Gc in mouse and establishes that, although Gc is genetically linked to the other genes, its physical distance from them extends beyond the resolution range of yeast artificial chromosome cloning and pulsed-field gel electrophoresis. Received: 18 July 1995 / Accepted: 9 September 1995     

Effects of toxins from two strains of Verticillium lecanii (Hyphomycetes) on bioattributes of a predatory ladybeetle, Delphastus catalinae (Col., Coccinellidae)

Abstract:  The aim of this study was to test the hypothesis that the whitefly ( Bemisia tabaci ; Hom., Aleyrodidae) predator ladybird beetles, Delphastus catalinae (Col., Coccinellidae), are not adversely affected in the field by the crude insecticidal toxins extracted from two strains of the fungus Verticillium lecanii , V3450 and Vp28. We developed a method to evaluate sublethal toxicity and its effects on consumption and functional response of D. catalinae . The crude toxins have low toxicity against beetle larva with LC₅₀ values of 1942 (1393–2710) and 2471 (1291–4731) p.p.m., respectively (approximately 10- and 12-fold of field rate of application 200 p.p.m.). The adult beetles had less sensitivity to crude toxins with LC₅₀ values of 4260 (3376–5375) and 4426 (1734–11298) p.p.m., respectively (approximately 20- and 22-fold of field rate 200 p.p.m.). The consumption and foraging capacity were significantly impaired especially in the second-instar larval beetles which took longer time (more than twice of the control beetles) to consume whitefly eggs after exposure to toxins, although D. catalinae suffered no significant effect on fecundity and longevity, when exposed to a toxin dilution of field rate. The data suggest that spraying of V. lecanii or its toxins should be avoided in the field having immature stages of D. catalinae .     

Elevated p62/SQSTM1 determines the fate of autophagy-deficient neural stem cells by increasing superoxide

Autophagy plays important roles in many biological processes, but our understanding of the mechanisms regulating stem cells by autophagy is limited. Interpretations of earlier studies of autophagy using knockouts of single genes are confounded by accumulating evidence for other functions of many autophagy genes. Here, we show that, in contrast to Fip200 deletion, inhibition of autophagy by deletion of Atg5, Atg16L1, or Atg7 does not impair the maintenance and differentiation of postnatal neural stem cells (NSCs). Only Fip200 deletion, but not Atg5, Atg16L1, or Atg7 deletion, caused p62/sequestome1 aggregates to accumulate in NSCs. Fip200 and p62 double conditional knockout mice demonstrated that p62 aggregate formation triggers aberrant superoxide increases by impairing superoxide dismutase functions. By comparing the inhibition of autophagy by deletion of Atg5, Atg16L1, or Atg7 with Fip200 deletion, we revealed a critical role of increased p62 in determining the fate of autophagy-deficient NSCs through intracellular superoxide control.     

Exploiting aberrant mRNA expression in autism for gene discovery and diagnosis

Autism spectrum disorder (ASD) is characterized by substantial phenotypic and genetic heterogeneity, which greatly complicates the identification of genetic factors that contribute to the disease. Study designs have mainly focused on group differences between cases and controls. The problem is that, by their nature, group difference-based methods (e.g., differential expression analysis) blur or collapse the heterogeneity within groups. By ignoring genes with variable within-group expression, an important axis of genetic heterogeneity contributing to expression variability among affected individuals has been overlooked. To this end, we develop a new gene expression analysis method—aberrant gene expression analysis, based on the multivariate distance commonly used for outlier detection. Our method detects the discrepancies in gene expression dispersion between groups and identifies genes with significantly different expression variability. Using this new method, we re-visited RNA sequencing data generated from post-mortem brain tissues of 47 ASD and 57 control samples. We identified 54 functional gene sets whose expression dispersion in ASD samples is more pronounced than that in controls, as well as 76 co-expression modules present in controls but absent in ASD samples due to ASD-specific aberrant gene expression. We also exploited aberrantly expressed genes as biomarkers for ASD diagnosis. With a whole blood expression data set, we identified three aberrantly expressed gene sets whose expression levels serve as discriminating variables achieving >70 % classification accuracy. In summary, our method represents a novel discovery and diagnostic strategy for ASD. Our findings may help open an expression variability-centered research avenue for other genetically heterogeneous disorders.