A Genome-Wide Association Study Reveals That Genes with Functions for Bone Development Are Associated with Body Conformation in Catfish

Body conformation is of great scientific and commercial interest for aquaculture fish species because it affects biological adaptation of the organism to environments, and is of economic importance to the aquaculture industry considering its direct effect on fillet yield. Catfish is the primary aquaculture species in the USA. Two major species used in the aquaculture industry, channel catfish and blue catfish, differ in body shape and therefore the backcross progenies serve as a good model for quantitative trait locus (QTL) analysis. Here, a genome-wide association study (GWAS) with hybrid catfish was conducted to identify the QTL for body conformation, including deheaded body length (DBL), body length (BL), body depth (BD), and body breadth (BB), which were all standardized by cubic root of body weight. Overall, the results indicate that the traits are polygenic. For DBL, linkage group (LG) 2 and LG 24 contain significant QTL, and LG 13 and LG 26 contain suggestively associated QTL (?log₁₀(P value) > 4.5). Compared with DBL, additional SNPs were identified to be associated with body length on LG 2, LG 7, and LG 18. Although no significant QTL for body depth was found, three suggestively associated QTLs were identified on LG 5, LG 13, and LG 14. No SNP for body breadth reached the threshold for suggestive association. Genes close to the associated SNPs were determined, many of which are known to be involved in bone development. This work therefore provides the basis for future identification of causal genes for the control of body conformation.     

Genome-Wide Association Study Reveals Multiple Novel QTL Associated with Low Oxygen Tolerance in Hybrid Catfish

Hypoxic condition is common in aquaculture, leading to major economic losses. Genetic analysis of hypoxia tolerance, therefore, is not only scientifically significant, but also economically important. Catfish is generally regarded as being highly tolerant to low dissolved oxygen, but variations exist among various populations, strains, and species. In this study, we conducted a genome-wide association study (GWAS) using the catfish 250 K SNP array to identify quantitative trait locus (QTL) associated with tolerance to low dissolved oxygen in the channel catfish × blue catfish interspecific system. Four linkage groups (LG2, LG4, LG23, and LG29) were found to be associated with low oxygen tolerance in hybrid catfish. Multiple significant SNPs were found to be physically linked in genomic regions containing significant QTL for low oxygen tolerance on LG2 and LG23, and in those regions containing suggestively significant QTL on LG2, LG4, LG23, and LG29, suggesting that the physically linked SNPs were genuinely segregating and related with low oxygen tolerance. Analysis of genes within the associated genomic regions suggested that many of these genes were involved in VEGF, MAPK, mTOR, PI3K-Akt, P53-mediated apoptosis, and DNA damage checkpoint pathways. Comparative analysis indicated that most of the QTL at the species level, as analyzed by using the interspecific system, did not overlap with those identified from six strains of channel catfish, confirming the complexity of the genetic architecture of hypoxia tolerance in catfish.     

Microbial Degradation and Preliminary Chemical Characterization of Microcystis Exopolysaccharides from a Cyanobacterial Water Bloom of Lake Taihu

A bloom biomass composed mainly of Microcystis spp. was harvested from Lake Taihu, China. Exopolysaccharides (FEPS, exopolysaccharides from field‐grown Microcystis spp.) were extracted from the bloom mass with 3% glutaraldehyde. FEPS contained 5.4% protein and 6.9% uronic acid (glucuronic acid and galacturonic acid). The neutral sugar composition of FEPS consisted of rhamnose, arabinose, mannose, glucose and galactose in a relative molar ratio of 4.8: 4.2: 2.1: 3.7: 1.0, respectively. The dialyzed FEPS exhibited strong interaction with metal ions. Besides macromineral elements Ca, Mg, Na and K, micromineral elements Zn, Mn, Sr, Fe, Cu and Al were also detected in FEPS. The composition of FEPS is discussed with respect to its possible effects on colony formation, and bioavailability and cycling of metals in the lake. FEPS was able to be degraded rapidly at a rate of 50% in 18 d in the beginning at 25 °C after inoculation of the natural bacterial community from the bloom zone, indicating that FEPS could be recycled in nature. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Breeding bird species richness in Taiwan: distribution on gradients of elevation, primary productivity and urbanization

Aim To examine the richness of breeding bird species in relation to elevation, primary productivity and urbanization. Location The island of Taiwan (120°–122° E, 22°–25° N). Methods We arranged bird species richness (BSR) data from 288 bird censuses undertaken in Taiwan into a 2 × 2 km quadrat system and calculated average values of elevation, primary productivity [surrogated by normalized difference vegetation index (NDVI)], and urbanization (surrogated by road density and percentage of built area) for each 2 × 2 km quadrat. Results Bird species richness showed a hump‐shaped relationship with elevation. It increased with elevation from sea level (10–64 species per 2 × 2 km quadrat), peaked around 2000 m (43–76 species), and then decreased with elevation towards its minimum at the highest elevation. Road density and percentage of built area decreased with elevation, and NDVI showed a hump‐shaped relationship with elevation and inverse relationships with road density and percentage of built area. BSR increased with NDVI and decreased with road density and percentage of built area. Linear and cubic terms of elevation together explained 31.3% of the variance in BSR, and road density explained additional 3.4%. The explanatory power of NDVI on BSR was insignificant after the effects of elevation and road density had been justified. Main conclusions We argue that urbanization plays an important role in the BSR of Taiwan. Urbanization might indirectly decrease BSR through decreasing primary productivity and therefore change the hypothetical inverse relationship between BSR and elevation into a hump‐shaped relationship. We also propose a time hypothesis that the biotic communities in the mid‐elevation zone of Taiwan had relatively longer periods of existence during the Pleistocene glacial cycles, which might be one underlying process of the observed hump‐shaped relationship between species diversity and elevation.     

The heterogeneity of cell subtypes from a primary culture of human amniotic fluid

Heterogeneous human amniotic fluid contains various cell types. Herein, we report on the possibility of simultaneously isolating three subtypes of cells from one primary culture. Using a stainless steel instrument named a colony poculum, two of the three cell subtypes could be efficiently cultured, and these were further characterized. The results indicated that these two cell subtypes had different morphologies and were characterized by different cell marker expression profiles, including the differential expression of CD105, CD117 and EBAF. Furthermore, their gene expression array data revealed their different gene expression profiles. Although both cell types expressed several embryonic stem cell-specific markers, they were non-tumorigenic in vivo. This paper not only provides new insight into the heterogeneity of human amniotic fluid, it also presents a simple yet efficient cell isolation method. These results will contribute to the thorough investigation of the properties and potential future applications of human amniotic fluid-derived cells.     

Autophagy decreases alveolar epithelial cell injury by regulating the release of inflammatory mediators

To research the impact of autophagy on alveolar epithelial cell inflammation and its possible mechanism in the early stages of hypoxia, we established a cell hypoxia–reoxygenation model and orthotopic left lung ischemia–reperfusion model. Rat alveolar epithelial cells stably expressing GFP-LC3 were treated with an autophagy inhibitor (3-MA) or an autophagy promoter (rapamycin), followed by hypoxia–reoxygenation treatment for 2, 4, and 6 hr in vitro. In vivo, 20 male Sprague Dawley rats were randomly divided into four groups (model group: No blocking of the hilum in the left lung; control group: Blocking of the hilum in the left lung for 1 hr with dimethyl sulfoxide lavage; 3-MA group: Blocking of the hilum in the left lung for 1 hr with 100 ml/kg of 3-MA (5 μmol/L) solution lavage; and rapamycin group: Blocking of the hilum in the left lung for 1 hr with 100 ml/kg of rapamycin (250 nmol/L) solution lavage) to establish an orthotopic left lung ischemia model. This study demonstrated that rapamycin significantly suppressed the nuclear factor kappa B signaling pathway and limited the expression of proinflammatory factors. A contrary result was found after the 3-MA pretreatment. These findings indicate that autophagy reduces ischemia–reperfusion injury by repressing inflammatory signaling pathways in the early stages of hypoxia in vitro and in vivo. Autophagy could be a new protective method for application in lung ischemia–reperfusion injury.     

A modified multiplex ligation-dependent probe amplification method for the detection of 22q11.2 copy number variations in patients with congenital heart disease

Background

Copy number variations (CNVs) of chromosomal region 22q11.2 are associated with a subset of patients with congenital heart disease (CHD). Accurate and efficient detection of CNV is important for genetic analysis of CHD. The aim of the study was to introduce a novel approach named CNVplex®, a high-throughput analysis technique designed for efficient detection of chromosomal CNVs, and to explore the prevalence of sub-chromosomal imbalances in 22q11.2 loci in patients with CHD from a single institute.

Results

We developed a novel technique, CNVplex®, for high-throughput detection of sub-chromosomal copy number aberrations. Modified from the multiplex ligation-dependent probe amplification (MLPA) method, it introduced a lengthening ligation system and four universal primer sets, which simplified the synthesis of probes and significantly improved the flexibility of the experiment. We used 110 samples, which were extensively characterized with chromosomal microarray analysis and MLPA, to validate the performance of the newly developed method. Furthermore, CNVplex® was used to screen for sub-chromosomal imbalances in 22q11.2 loci in 818 CHD patients consecutively enrolled from Shanghai Children’s Medical Center. In the methodology development phase, CNVplex® detected all copy number aberrations that were previously identified with both chromosomal microarray analysis and MLPA, demonstrating 100% sensitivity and specificity. In the validation phase, 22q11.2 deletion and 22q11.2 duplication were detected in 39 and 1 of 818 patients with CHD by CNVplex®, respectively. Our data demonstrated that the frequency of 22q11.2 deletion varied among sub-groups of CHD patients. Notably, 22q11.2 deletion was more commonly observed in cases with conotruncal defect (CTD) than in cases with non-CTD (P < 0.001). With higher resolution and more probes against selected chromosomal loci, CNVplex® also identified several individuals with small CNVs and alterations in other chromosomes.

Conclusions

CNVplex® is sensitive and specific in its detection of CNVs, and it is an alternative to MLPA for batch screening of pathogenetic CNVs in known genomic loci.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1590-5) contains supplementary material, which is available to authorized users.     

Active Site Loop Conformation Regulates Promiscuous Activity in a Lactonase from Geobacillus kaustophilus HTA426

Enzyme promiscuity is a prerequisite for fast divergent evolution of biocatalysts. A phosphotriesterase-like lactonase (PLL) from Geobacillus kaustophilus HTA426 (GkaP) exhibits main lactonase and promiscuous phosphotriesterase activities. To understand its catalytic and evolutionary mechanisms, we investigated a “hot spot” in the active site by saturation mutagenesis as well as X-ray crystallographic analyses. We found that position 99 in the active site was involved in substrate discrimination. One mutant, Y99L, exhibited 11-fold improvement over wild-type in reactivity (k_cat/K_m) toward the phosphotriesterase substrate ethyl-paraoxon, but showed 15-fold decrease toward the lactonase substrate δ-decanolactone, resulting in a 157-fold inversion of the substrate specificity. Structural analysis of Y99L revealed that the mutation causes a ∼6.6 Å outward shift of adjacent loop 7, which may cause increased flexibility of the active site and facilitate accommodation and/or catalysis of organophosphate substrate. This study provides for the PLL family an example of how the evolutionary route from promiscuity to specificity can derive from very few mutations, which promotes alteration in the conformational adjustment of the active site loops, in turn draws the capacity of substrate binding and activity.     

牛疱疹病毒Ⅰ型前早期基因BICPO的表达对牛免疫缺陷病毒LTR的反式激活作用

由含有ＢＨＢＶ－１（ＢｏｖｉｎｅＨｅｒｐｅｓＶｉｒｕｓ－１）前早期基因的基因组片段亚克隆ＢＩＣＰＯ（ＢＨＶ－１ＩｎｆｅｃｔｅｄＣｅｌｌＰｒｏｔｅｉｎＯ）的ＤＮＡ序列至表达载体ｐＳＶＫ３,构建质粒ｐＳＶ２．９。将该质粒与ｐＢＬＴＲ－Ｌｕｃ共转染小牛肺细胞,检测转染细胞裂解物的荧光素酶活性,ＢＩＣＰＯ的表达产物可以显著地激活ＢＩＶＬＴＲ启动子控制下的荧光素酶基因的表达。根据ｐＳＶ２．９与含有ＢＩＶＬＴＲ不同区段缺失的质粒ｐＤ－３１９－Ｌｕｃ、ｐＤ－１１５－Ｌｕｃ、ｐＤ－５２－Ｌｕｃ共转染小牛肺细胞的实验结果,推测ＢＩＶＬＴＲ－３１９位上游区的ＤＮＡ序列影响ＢＩＣＰＯ基因产物对ＢＩＶＬＴＲ表达的激活作用。