BackgroundAn emerging cavefish model, the cyprinid genus Sinocyclocheilus, is endemic to the massive southwestern karst area adjacent to the Qinghai-Tibetan Plateau of China. In order to understand whether orogeny influenced the evolution of these species, and how genomes change under isolation, especially in subterranean habitats, we performed whole-genome sequencing and comparative analyses of three species in this genus, S. grahami, S. rhinocerous and S. anshuiensis. These species are surface-dwelling, semi-cave-dwelling and cave-restricted, respectively.ResultsThe assembled genome sizes of S. grahami, S. rhinocerous and S. anshuiensis are 1.75 Gb, 1.73 Gb and 1.68 Gb, respectively. Divergence time and population history analyses of these species reveal that their speciation and population dynamics are correlated with the different stages of uplifting of the Qinghai-Tibetan Plateau. We carried out comparative analyses of these genomes and found that many genetic changes, such as gene loss (e.g. opsin genes), pseudogenes (e.g. crystallin genes), mutations (e.g. melanogenesis-related genes), deletions (e.g. scale-related genes) and down-regulation (e.g. circadian rhythm pathway genes), are possibly associated with the regressive features (such as eye degeneration, albinism, rudimentary scales and lack of circadian rhythms), and that some gene expansion (e.g. taste-related transcription factor gene) may point to the constructive features (such as enhanced taste buds) which evolved in these cave fishes.ConclusionAs the first report on cavefish genomes among distinct species in Sinocyclocheilus, our work provides not only insights into genetic mechanisms of cave adaptation, but also represents a fundamental resource for a better understanding of cavefish biology.Electronic supplementary materialThe online version of this article (doi:10.1186/s12915-015-0223-4) contains supplementary material, which is available to authorized users.

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Previous studies suggested that the topological properties of brain anatomical networks may be aberrant in schizophrenia (SCZ), and most of them focused on the chronic and antipsychotic-medicated SCZ patients which may introduce various confounding factors due to antipsychotic medication and duration of illness. To avoid those potential confounders, a desirable approach is to select medication-naïve, first-episode schizophrenia (FE-SCZ) patients. In this study, we acquired diffusion tensor imaging datasets from 30 FE-SCZ patients and 34 age- and gender-matched healthy controls. Taking a distinct gray matter region as a node, inter-regional connectivity as edge and the corresponding streamline counts as edge weight, we constructed whole-brain anatomical networks for both groups, calculated their topological parameters using graph theory, and compared their between-group differences using nonparametric permutation tests. In addition, network-based statistic method was utilized to identify inter-regional connections which were impaired in the FE-SCZ patients. We detected only significantly decreased inter-regional connections in the FE-SCZ patients compared to the controls. These connections were primarily located in the frontal, parietal, occipital, and subcortical regions. Although small-worldness was conserved in the FE-SCZ patients, we found that the network strength and global efficiency as well as the degree were significantly decreased, and shortest path length was significantly increased in the FE-SCZ patients compared to the controls. Most of the regions that showed significantly decreased nodal parameters belonged to the top-down control, sensorimotor, basal ganglia, and limbic-visual system systems. Correlation analysis indicated that the nodal efficiency in the sensorimotor system was negatively correlated with the severity of psychosis symptoms in the FE-SCZ patients. Our results suggest that the network organization is changed in the early stages of the SCZ disease process. Our findings provide useful information for further understanding the brain white matter dysconnectivity of schizophrenia.

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Esophageal cancer is the eighth most common cancer and sixth leading cause of cancer associated death worldwide. Besides environmental risk factors, genetic factors might play an important role in the esophageal cancer carcinogenesis. We conducted a hospital based case–control study to evaluate the genetic susceptibility of functional single nucleotide polymorphisms (SNPs) in the microRNAs on the development of esophageal cancer. A total of 629 esophageal squamous cell carcinoma (ESCC) cases and 686 controls were recruited for this study. The hsa-miR-34b/c rs4938723 T>C, pri-miR-124-1 rs531564 C>G, pre-miR-125a rs12975333 G>T and hsa-miR-423 rs6505162 C>A genotypes were determined using Ligation Detection Reaction (LDR) method. Our results demonstrated that hsa-miR-34b/c rs4938723 CC genotype had a decreased risk of ESCC. The association was evident among patients who never drinking. Hsa-miR-423 rs6505162 C>A might associated with a significantly increased risk of ESCC in patients who smoking. These findings indicated that functional polymorphisms hsa-miR-34b/c rs4938723 T>C and hsa-miR-423 rs6505162 C>A might alter individual susceptibility to ESCC. However, our results were obtained with a limited sample size. Future larger studies with other ethnic populations are required to confirm current findings.

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2010) Phylogenetic relationships of the Chinese Labeoninae (Teleostei, Cypriniformes) derived from two nuclear and three mitochondrial genes. -Zoologica Scripta, 39, 559-571. The majority of genera within the Labeoninae occur in the South of China and the phylogeny of the subfamily Labeoninae has been a controversial topic over the years. The early and more recent phylogenetic results based on morphology are not in agreement, and some of the molecular analyses contradict those based on morphology. However, none of the previous studies has included an extensive sampling of Labeoninae genera. In this study, partial sequences of two nuclear (exon 3 of recombination activating protein 1 and rhodopsin) and three mitochondrial genes (cytochrome b, cytochrome oxidase subunit I and 16S ribosomal RNA) from 39 ingroup taxa and 11 outgroup taxa were used analysed to provide a hypothesis of phylogenetic relationships within the Chinese Labeoninae. The results supported the monophyly of Labeoninae and refuted the subdivision within Labeoninae based on the oromandibular morphology. It also further confirmed that the presence of a disc on lower lip arose through convergent evolution. Labeo was the basal clade and Osteochilus was closely related to Cirrhinus, forming the second basal clade. The monophyly of Garra and Bangana was refuted in this study, and they were both subdivided into two lineages. One lineage of Garra had closer relationships with Crossocheilus and Akrokolioplax, and the other lineage had closer relationships with Placocheilus. One lineage of Bangana represented the species with broadly interrupted postlabial groove; these species represented the true Bangana. The other lineage of Bangana included the species with continuous postlabial groove, and these species should be assigned to a new genus. Discogobio, as currently conceived, was paraphyletic, but it rendered monophyletic with the inclusion of Discocheilus. These results indicated that Discocheilus should be synonymised with Discogobio. Hongshuia and Sinocrossocheilus, respectively, formed independent lineages related to a lineage consisting of Pseudocrossocheilus plus seven other nominal genera. The relationships received weak support, but the repeatability of the clades could form the basis of recognising only the three genera mentioned above.

PTENP1 has been demonstrated to function as a tumor suppressor in several cancer cells. However, its expression and biological roles in gastric cancer (GC) have not yet been investigated. In this study, we demonstrated that PTENP1 was frequently decreased in GC tissues and cell lines, which might be partly associated with DNA hypermethylation, and lower PTENP1 expression was associated with larger tumor size, more advanced stage, deeper invasion depth and lymphatic metastasis. In addition, our data suggested that PTENP1 could regulate GC cell proliferation, apoptosis, migration and invasion in vitro. Furthermore, we demonstrated that PTENP1 could modulate the PTEN protein expression. Taken together, these results suggest that PTENP1 functions as a novel tumor suppressor in GC and its suppressive ability may be involved in the modulation of PTEN.