A missense mutation in PPARD causes a major QTL effect on ear size in pigs

Chinese Erhualian is the most prolific pig breed in the world. The breed exhibits exceptionally large and floppy ears. To identify genes underlying this typical feature, we previously performed a genome scan in a large scale White Duroc × Erhualian cross and mapped a major QTL for ear size to a 2-cM region on chromosome 7. We herein performed an identical-by-descent analysis that defined the QTL within a 750-kb region. Historically, the large-ear feature has been selected for the ancient sacrificial culture in Erhualian pigs. By using a selective sweep analysis, we then refined the critical region to a 630-kb interval containing 9 annotated genes. Four of the 9 genes are expressed in ear tissues of piglets. Of the 4 genes, PPARD stood out as the strongest candidate gene for its established role in skin homeostasis, cartilage development, and fat metabolism. No differential expression of PPARD was found in ear tissues at different growth stages between large-eared Erhualian and small-eared Duroc pigs. We further screened coding sequence variants in the PPARD gene and identified only one missense mutation (G32E) in a conserved functionally important domain. The protein-altering mutation showed perfect concordance (100%) with the QTL genotypes of all 19 founder animals segregating in the White Duroc × Erhualian cross and occurred at high frequencies exclusively in Chinese large-eared breeds. Moreover, the mutation is of functional significance; it mediates down-regulation of β-catenin and its target gene expression that is crucial for fat deposition in skin. Furthermore, the mutation was significantly associated with ear size across the experimental cross and diverse outbred populations. A worldwide survey of haplotype diversity revealed that the mutation event is of Chinese origin, likely after domestication. Taken together, we provide evidence that PPARD G32E is the variation underlying this major QTL.     

Systematic detection of polygenic cis-regulatory evolution

The idea that most morphological adaptations can be attributed to changes in the cis-regulation of gene expression levels has been gaining increasing acceptance, despite the fact that only a handful of such cases have so far been demonstrated. Moreover, because each of these cases involves only one gene, we lack any understanding of how natural selection may act on cis-regulation across entire pathways or networks. Here we apply a genome-wide test for selection on cis-regulation to two subspecies of the mouse Mus musculus. We find evidence for lineage-specific selection at over 100 genes involved in diverse processes such as growth, locomotion, and memory. These gene sets implicate candidate genes that are supported by both quantitative trait loci and a validated causality-testing framework, and they predict a number of phenotypic differences, which we confirm in all four cases tested. Our results suggest that gene expression adaptation is widespread and that these adaptations can be highly polygenic, involving cis-regulatory changes at numerous functionally related genes. These coordinated adaptations may contribute to divergence in a wide range of morphological, physiological, and behavioral phenotypes.     

IFN-α/β and autophagy: tug-of-war between HCV and the host

Hepatitis C virus (HCV) infects approximately 130 million people worldwide. The clinical sequelae of this chronic disease include cirrhosis, functional failure and carcinoma of the liver. HCV induces autophagy, a fundamental cellular process for maintaining homeostasis and mediating innate immune response, and also inhibits autophagic protein degradation and suppresses antiviral immunity. In addition to this ploy, the HCV serine protease composed of the viral non-structural proteins 3/4A (NS3/4A) can enzymatically digest two cellular proteins, mitochondria-associated anti-viral signaling protein (MAVS) and Toll/interleukin-1 receptor domain containing adaptor inducing IFN-β (TRIF). Since these two proteins are the adaptor molecules in the retinoic acid-inducible gene I (RIG-I) and TLR3 pathways, respectively, their cleavage has been suggested as a pivotal mechanism by which HCV blunts the IFN-α/β signaling and antiviral responses. Thus far, how HCV perturbs autophagy and copes with IFN-α/β in the liver remains unclear.     

Phenolic compounds from Selaginella moellendorfii

Chemical investigation of the leaves and roots of Selaginella moellendorfii Hieron has resulted in the isolation and characterization of two new flavone glucosides, 7‐O‐(β‐glucopyranosyl(1→2)‐[β‐glucopyranosyl(1→6)]‐β‐glucopyranosyl)flavone‐3′,4′,5,7‐tetraol ( 1 ) and 7‐O‐(β‐glucopyranosyl(1→2)‐[β‐glucopyranosyl(1→6)]‐β‐glucopyranosyl)flavone‐4′,5,7‐triol ( 2 ), two new biflavonoids, 2,3‐dihydroflavone‐5,7,4′‐triol‐(3′→8″)‐flavone‐5″,6″,7″,4′′′‐tetraol ( 3 ) and 6‐methylflavone‐5,7,4′‐triol‐(3′→O→4′′′)‐6″‐methylflavone‐5″,7″‐diol ( 4 ), two new lignans, (7′E)‐3,5,3′,5′‐tetramethoxy‐8 : 4′‐oxyneolign‐7′‐ene‐4,9,9′‐triol ( 5 ) and 3,3′‐dimethoxylign‐8′‐ene‐4,4′,9‐triol ( 6 ), together with two known monolignans, four known lignans, and four known biflavonoids. Their structures were established by spectroscopic means and by comparison with literature values.     

IL-1 polymorphisms in children with peptic symptoms in South China

Background: Polymorphisms of IL‐1 gene cluster are reported to be associated with histological changes and IL‐1β expression in the gastric mucosa in adults, especially in Helicobacter pylori–infected subjects. As H. pylori infecting adults and children own different virulence genotypes, the aim of this study was to investigate whether IL‐1 polymorphisms are risk factors in young children in South China. Materials and Methods: A total of 128 children with peptic symptoms were enrolled in this study. Polymorphisms of IL‐1B‐511 and IL‐1B‐31 were identified by dual fluorescence PCR. Variable number of tandem repeat region in IL‐1RN was detected by conventional PCR and IL‐1β mRNA expression by real‐time PCR ddCT assay. Results: IL‐1B‐31T and IL‐1B‐511C were completely linked in this study. Significant differences of IL‐1B‐511/‐31 genotypes were observed among different clinical outcomes (p = .001). The IL‐1B‐511TT/‐31CC was mostly found in the moderate gastritis and the above (severe gastritis or gastric ulcer) groups, with percentage of 60.7%. While no association was observed between IL‐1RN genotypes and the gastric mucosal histological changes (p = .128). Also no relationships were found between IL‐1 polymorphisms and H. pylori infection or gastric mucosal IL‐1β mRNA expression level. Conclusion: Children with IL‐1B‐511TT/‐31CC may have a risk to develop relatively severe gastric mucosal histological changes in South China.     

Diversity analysis of Burkholderia cepacia complex in the water bodies of West Lake, Hangzhou, China

A survey of Burkholderia cepacia complex (Bcc) species was conducted in water bodies of West Lake in China. A total of 670 bacterial isolates were recovered on selective media. Out of them, 39.6% (265 isolates) were assigned to the following species: Burkholderia multivorans, Burkholderia cenocepacia recA lineage IIIA, IIIB, Burkholderia stabilis, Burkholderia vietnamiensis, and Burkholderia seminalis while B. cenocepacia is documented as a dominant Bcc species in water of West Lake. In addition, all Bcc isolates tested were PCR negative for the cblA and esmR transmissibility marker genes except B. cenocepacia IIIB A8 which was positive for esmR genelater. The present study raises great concerns on the role of West Lake as a “reservoir” for potential Bcc pathogenic strains.     

Continuous preparation of (S)-3-hydroxy-3-phenylpropionate by asymmetric reduction of 3-oxo-3-phenylpropionic acid ethyl ester with <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> CGMCC No.2266 in a membrane reactor

In this study, (S)-3-hydroxy-3-phenylpropionate was prepared continuously by coupling microbial transformation and membrane separation. The effect of several factors on membrane flux, reactor capacity, and reaction conversion were investigated. A kinetic model of the continuous reduction process was also developed. The appropriate molecular weight cut-off of the ultrafiltration membrane was 30 kDa. The reactor capacity reached a maximum of 0.136/h at a biomass concentration and membrane flux of 86 g/L (dry weight/reaction volume) and 20 mL/h, respectively. The (S)-3-hydroxy-3-phenylpropionate yield was 3.68 mmol/L/day after continuous reduction over seven days. The enantiometric excess of (S)-3-hydroxy-3-phenylpropionate reached above 99.5%. The kinetic constants of continuous reduction were as follows: r _m = 3.00 × 10⁻³ mol/L/h, k _cat = 3.49 × 10⁻⁴ mol/L/h, k ₁ = 3.09 × 10⁻² mol/L, and k ₂ = 5.00 × 10⁻⁷ mol/L. The kinetic model was in good agreement with the experimental data obtained during continuous reduction. Compared with batch reduction, continuous reduction can significantly improve the catalytic efficiency of microbial cells and increase the reactor capacity.     

Applicability of the fluorescein diacetate assay for metabolic activity measurement of Microcystis aeruginosa (Chroococcales,Cyanobacteria)

The fluorescein diacetate (FDA) assay has been widely used to measure metabolic activity in phytoplankton. It was found that FDA fluorescence values did not decrease in some stressed cells, demonstrating that the applicability of the method needs to be assessed further in the context of growth‐influencing conditions. In the present study, changes of FDA fluorescence values were studied in bloom‐forming cyanobacterial Microcystis aeruginosa Kütz cells under stress conditions such as nitrogen (N) or phosphorus (P) deficiency, or darkness and low temperature (10°C), respectively. The results demonstrated that esterase activity decreased immediately in dark‐stressed cells, which correlated with the decline of biomass and photosynthetic activity. Under the other three stress conditions, however, especially at low temperature, the cells lost photosynthetic activity but had the highest esterase activity, which was five times higher than the control group. These findings contrast with the assay criteria that the expression of a stain should reflect the change of photosynthetic activity and that stressed cells should have a lower staining intensity than the control cells. According to these results, the esterase activity response was dependent on environmental factors. Furthermore, higher fluorescence intensity did not mean higher metabolic activity, but a discrepant value indicated a severe stress.