The gekkonid genus Cyrtodactylus is the third most speciose vertebrate genus in the world, containing well over 300 species that collectively range from South Asia to Melanesia across some of the most diverse landscapes and imperiled habitats on the planet. A genus-wide phylogeny of the group has never been presented because researchers working on different groups were using different genetic markers to construct phylogenies that could not be integrated. We present here Maximum likelihood and Bayesian inference mitochondrial and mito-nuclear phylogenies incorporating of 310 species that include dozens of species that had never been included in a genus-wide analysis. Based on the mitochondrial phylogeny, we partition Cyrtodactylus into 31 well-supported monophyletic species groups which, if used as recommended herein, will increase the information content of future integrative taxonomic analyses that continue to add new species to this genus at an ever-increasing annual rate. Data presented here reiterate the outcome of several previous studies indicating that Cyrtodactylus comprises an unprecedented number of narrow-range endemics restricted to single mountain tops, small islands, or karst formations that still remain unprotected. This phylogeny can provide a platform for various comparative ecological studies that can be integrated with conservation management programs across the broad diversity of landscapes and habitats occupied by this genus. Additionally, these data indicate that the true number of Cyrtodactylus remains substantially underrepresented.

South China and Indochina host striking species diversity and endemism. Complex tectonic and climatic evolutions appear to be the main drivers of the biogeographic patterns. In this study, based on the geologic history of this region, we test 2 hypotheses using the evolutionary history of Microhyla fissipes species complex. Using DNA sequence data from both mitochondrial and nuclear genes, we first test the hypothesis that the Red River is a barrier to gene flow and dispersal. Second, we test the hypothesis that Pleistocene climatic cycling affected the genetic structure and population history of these frogs. We detect 2 major genetic splits that associate with the Red River. Time estimation suggests that late Miocene tectonic movement associated with the Red River drove their diversification. Species distribution modeling (SDM) resolves significant ecological differences between sides of the Red River. Thus, ecological divergence also probably promoted and maintained the diversification. Genogeography, historical demography, and SDM associate patterns in southern China with climate changes of the last glacial maximum (LGM), but not Indochina. Differences in geography and climate between the 2 areas best explain the discovery. Responses to the Pleistocene glacial–interglacial cycling vary among species and regions.

Karstic landscapes are immense reservoirs of biodiversity and range-restricted endemism. Nowhere is this more evident than in the world’s third-largest vertebrate genus Cyrtodactylus (Gekkonidae) which contains well over 300 species. A stochastic character mapping analysis of 10 different habitat preferences across a phylogeny containing 345 described and undescribed species recovered a karst habitat preference occurring in 25.0% of the species, whereas that of the other eight specific habitat preferences occurred in only 0.2–11.0% of the species. The tenth category—general habitat preference—occurred in 38.7% of the species and was the ancestral habitat preference for Cyrtodactylus and the ultimate origin of all other habitat preferences. This study echoes the results of a previous study illustrating that karstic landscapes are generators of species diversity within Cyrtodactylus and not simply “imperiled arks of biodiversity” serving as refugia for relics. Unfortunately, the immense financial returns of mineral extraction to developing nations largely outweighs concerns for biodiversity conservation, leaving approximately 99% of karstic landscapes with no legal protection. This study continues to underscore the urgent need for their appropriate management and conservation. Additionally, this analysis supports the monophyly of the recently proposed 31 species groups and adds one additional species group.

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A 3204-bp full-length cDNA of bovine NALP9 was cloned and its genomic organization was analyzed. The 2988-bp open reading frame covers 9 exons and encodes a deduced protein of 996 amino acids containing Pyrin, Nacht and leucine-rich repeat domains like the human NALP gene family members. Mapping with the WGRH5000 panel and fluorescence in situ hybridization assigned NALP9 in close vicinity to BM2078 (LOD score 25.71; distance 0.0 cR5000) on bovine chromosome 18, BTA18q25-q26, within a previously identified QTL region for reproductive traits flanked by the bovine marker BM2078 and TGLA227. BAC contig analysis revealed that NALP9, NALP8, and NALP5 map in this QTL region. Temporospatial expression of these members of the NALP gene family was monitored. Among the adult tissues examined, transcripts of NALP8 and NALP9 were detected exclusively in testis and ovary, whereas transcripts of the NALP5 gene are limited to the ovary. The transcripts of NALP9, NALP8, and NALP5 were detected in oocytes before and after in vitro maturation and with a gradual decline from 2-cell to 8-cell stage, suggesting no reactivation at the time of bovine maternal to embryonic transition. Assignment to a QTL region for reproductive traits and preferential expression of NALP9, NALP8, and NALP5 in oocyte, germinal lineage, and gonad cells may suggest their functional relevance to reproduction and possible contribution to phenotypic variation.

Expression microarrays including the Affymetrix GeneChip Porcine Genome Arrays are valuable tools for studying genes and functional networks relevant for the expression of complex traits and the responsiveness of the organism to various treatments. An updated annotation and, for the first time, localization on the porcine physical genome map of »Affymetrix GeneChip Porcine Genome Array probe sets« was made through a workflow of 3 pipelines of comparisions addressing various NCBI (National Center for Biotechnology Information) and EnsEMBL (Ensembl project) databases. »BLAST« (Basic Local Alignment Search Tool) comparisons of Affymetrix probe set consensus sequences with the EnsEMBL Sscrofa 9 cDNA database provided 23 799 probe sets with hits. After annotation 19 730 gene symbols were obtained using the data management system BioMart. Comparison of the Affymetrix probe set consensus sequences with the porcine genome sequence (EnsEMBL Sscrofa 9 LatestGP database) revealed 23 298 probe sets with BLAST hits. In the third pipeline in addition to EnsEMBL Sscrofa 9 cDNA and genomic sequence databases also human, mouse and pig NCBI reference sequence RNA databases were interrogated in an integrated approach where also a threshold of bit score >50 or >90 % identity over >100 bp was applied in order to filter questionable annotations and localizations. Gene symbols and gene names were queried from HGNC (human genome organization (HUGO) gene nomenclature committee), EASE (EASE: the Expression Analysis Systematic Explorer) and Entrez Gene revealing 20 269 annotated probe sets. 20 467 probe sets were in silico mapped addressing various sources: EnsEMBL Sscrofa 9 LatestGP, pre-EnsEMBL Sscrofa 8.52 LatestGP, NCBI pig reference sequence RNA and genomic databases and PigQTLdb (Pig Quantitative Trait Locus [QTL] database). Using the new annotation and localization data in functional genomics studies will facilitate improving the understanding of the control of quantitative traits in pigs.

BackgroundRed yeast rice (RYR) is a fermented product used as a food supplement to promote blood circulation and lower blood cholesterol levels in eastern Asia. Interestingly, monacolin K is the most active compound in RYR that proved to inhibit HMG-CoA reductase in the cholesterol biosynthesis pathway.MethodsThe hypocholesterolemic effects of oral administration of Thai RYR, produced by fermentation of Thai glutinous rice (Oryza sativa L. var. Niaw San-pah-tawng) with Monascus purpureus CMU 002U, were determined in normal and hypercholesterolemic rats. The rats were divided into six groups, and fed two different kinds of diet. Groups I-II, normal rats fed with a normal diet (SP-diet), were treated with distilled water (SP-control) and 2.0 g/kg/day of RYR extract (SP-2 g). In Groups III-VI, the rats were rendered hypercholesterolemic by feeding them a high fat and cholesterol diet (HFC-diet), and were treated with distilled water (HFC-control), 1.0 g/kg/day (HFC-1 g), 2.0 g/kg/day (HFC-2 g) of RYR extract, and 5.0 mg/kg/day of rosuvastatin (HFC-rosuvastatin) for 30 days, respectively.ResultsThe RYR extract significantly decreased the concentrations of serum total cholesterol and low density lipoprotein cholesterol (LDL-C), atherosclerotic index, LDL-C/HDL-C ratio and hepatic cholesterol levels in both HFC-1 g and HFC-2 g groups (p < 0.05) as compared with the HFC-control group, and with no significant change in high density lipoprotein cholesterol (HDL-C) concentrations among all six groups. The reduction of serum TC and LDL-C also paralleled the observed changes in mRNA expressions of the genes involved in cholesterol biosynthesis and homeostasis in the liver. The hypercholesterolemic rats treated with RYR extract were significantly higher in LDLR and HMGR expression, but lower in CYP7A1 expression when compared to the untreated hypercholesterolemic rats (HFC-control) (p < 0.05). The hepatic injuries in hypercholesterolemic rats were also obviously alleviated by RYR extract.ConclusionsThe extract of Thai RYR possessed potent hypocholesterolemic and anti-atherogenic activities in diet-induced hypercholesterolemic rats. The possible mechanism involving cholesterol-lowering potential of the extract might contribute to its ability to increase LDL-C endocytosis in hepatocyte and to competitively inhibit HMG-CoA reductase, a key enzyme for cholesterol biosynthesis in liver.

The sequence data of mtCOI can be used to investigate the phylogenetic relationships of trematodes at the genus level. Each clade of different genera of heterophyid trematodes can be separated into sister groups that correlated with the morphological characteristic, kind of secondary intermediate host and geographic distribution.