Comparative mitochondrial genome analysis of Neodontobutis hainanensis and Perccottus glenii reveals conserved genome organization and phylogeny.

To investigate the molecular evolution of mitochondrial genomes among the family Odontobutidae, the complete mitochondrial genomes of Neodontobutis hainanensis and Perccottus glenii were sequenced and compared with seven odontobutids species. The genome organization, base composition, codon usage, and gene arrangement of N. hainanensis exhibited high similarity to P. glenii compared to those of other Odontobutidae species. Reconstructed phylogenetic analyses of Odontobutidae strongly supported that Neodontobutis and Perccottus formed a unifying group sister to Odontobutis. Our molecular dating time revealed that the two species diverged approximately 21.7 Ma during Miocene, later than that of Odontobutis. Selection analyses showed stronger selective constraints in mitochondrial genes for P. glenii. However, two positively selected sites in NADH4 and NADH6 genes were respectively detected in N. hainanensis and P. glenii, indicating that they might evolve different metabolic performance in response to the contrasting environments.

FishDB: an integrated functional genomics database for fishes.

BACKGROUND: Hundreds of genomes and transcriptomes of fish species have been sequenced in recent years. However, fish scholarship currently lacks a comprehensive, integrated, and up-to-date collection of fish genomic data. RESULTS: Here we present FishDB, the first database for fish multi-level omics data, available online at http://fishdb.ihb.ac.cn . The database contains 233 fish genomes, 201 fish transcriptomes, 5841 fish mitochondrial genomes, 88 fish gene sets, 16,239 miRNAs of 65 fishes, 1,330,692 piRNAs and 4852 lncRNAs of Danio rerio, 59,040 Mb untranslated regions (UTR) of 230 fishes, and 31,918 Mb coding sequences (CDS) of 230 fishes. Among these, we newly generated a total of 11 fish genomes and 53 fish transcriptomes. CONCLUSIONS: This release contains over 410,721.67 Mb sequences and provides search functionality, a BLAST server, JBrowse, and PrimerServer modules.

Chromosome-level genome assembly of hadal snailfish reveals mechanisms of deep-sea adaptation in vertebrates.

As the deepest vertebrate in the ocean, the hadal snailfish (Pseudoliparis swirei), which lives at a depth of 6,000-8,000 m, is a representative case for studying adaptation to extreme environments. Despite some preliminary studies on this species in recent years, including their loss of pigmentation, visual and skeletal calcification genes, and the role of trimethylamine N-oxide in adaptation to high-hydrostatic pressure, it is still unknown how they evolved and why they are among the few vertebrate species that have successfully adapted to the deep-sea environment. Using genomic data from different trenches, we found that the hadal snailfish may have entered and fully adapted to such extreme environments only in the last few million years. Meanwhile, phylogenetic relationships show that they spread into different trenches in the Pacific Ocean within a million years. Comparative genomic analysis has also revealed that the genes associated with perception, circadian rhythms, and metabolism have been extensively modified in the hadal snailfish to adapt to its unique environment. More importantly, the tandem duplication of a gene encoding ferritin significantly increased their tolerance to reactive oxygen species, which may be one of the important factors in their adaptation to high-hydrostatic pressure.

[Correlation between genotypes and biochemical phenotypes of phenylalanine hydroxylase in patients with phenylketonuria].

OBJECTIVE: To investigate the correlation between genotypes and biochemical phenotypes of phenylalanine hydroxylase (PAH) in patients with phenylketonuria (PKU). METHODS: Thirteen exons and flanking introns of PAH gene in 102 patients with high blood phenylalanine levels (Phe > 120 umol/L) at initial diagnosis were amplified with polymerase chain reaction and analyzed with single strand conformation polymorphism (SSCP), denaturing high performance liquid chromatography (DHPLC) and DNA sequencing. Correlation between genotypes and biochemical phenotypes was analyzed. RESULTS: Biochemical assaying has indicated that 69 patients had classical PKU (Phe> 1200 umol/L), 31 were moderate (Phe 600-1200 umol/L), and 2 were mild (Phe 400-600 umol/L). More than 41 mutations and 75 genotypes have been identified. There were 9 (8.8%) homozygous mutations, which included 3 cases with R111X/R111X, 1 case with IVS4-1G>A/IVS4-1G>A, 3 cases with R243Q/R243Q and 2 cases with V399V/V399V. Among these 8 belonged to classic PKU phenotypes, except for a R243Q/R243Q genotype which has led to a moderate phenotype. In 91 patients carrying compound PAH mutations, 61 were classic, 29 were moderate, and 1 was mild. Patients who were heterozygous for R111X/R243Q and EX6-96A>G(Y204C)/R243Q were found with both classic and moderate PKU phenotypes. Certain individuals who have carried 2 null mutant alleles such as R111X/V399V, EX6-96A>G/Y356X and EX6-96A>G/V399V only showed a moderate phenotype. Individuals with R111X/A165D and R176X/A165D genotypes, on the other hand, respectively presented moderate and classic PKU phenotypes. CONCLUSION: Ninety percent of our patients are compound heterozygotes. Independent assortment of mutant alleles has resulted in a complex genotype-phenotype correlation. Although in most cases a correlation may be found, caution should still be taken upon genetic counseling. The phenomena where similar or even identical genotype may give rise to different biochemical phenotypes have implied that other factors may also influence the phenylalanine metabolism.

Molecular Mechanisms of the Convergent Adaptation of Bathypelagic and Abyssopelagic Fishes.

Harsh environments provide opportunities to study how different species adapt, at the molecular level, to similar environmental stressors. High hydrostatic pressure, low temperature, and absence of sunlight in the deep-sea environment are challenging conditions for gene expression, cell morphology and vision. Adaptation of fish to this environment appears independently in at least 22 orders of fish, but it remains uncertain whether these adaptations represent convergent evolution. In this study, we performed comparative genomic analysis of 80 fish species to determine genetic evidences for adaptations to the deep-sea environment. The 80 fishes were divided into six groups according to their order. Positive selection and convergent evolutionary analysis were performed and functional enrichment analysis of candidate genes was performed. Positively selected genes (pik3ca, pik3cg, vcl and sphk2) were identified to be associated with the cytoskeletal response to mechanical forces and gene expression. Consistent signs of molecular convergence genes (grk1, ednrb, and nox1) in dark vision, skin color, and bone rarefaction were revealed. Functional assays of Grk1 showed that the convergent sites improved dark vision in deep-sea fish. By identifying candidate genes and functional profiles potentially involved in cold, dark, and high-pressure responses, the results of this study further enrich the understanding of fish adaptations to deep-sea environments.

Sympatric or micro-allopatric speciation in a glacial lake? Genomic islands support neither.

Apparent cases of sympatric speciation may actually be due to micro-allopatric or micro-parapatric speciation. One way to distinguish between these models is to examine the existence and nature of genomic islands of divergence, wherein divergent DNA segments are interspersed with low-divergence segments. Such islands should be rare or absent under micro-allopatric speciation but common in cases of speciation with gene flow. Sympatric divergence of endemic fishes is known from isolated saline, crater, postglacial, and ancient lakes. Two morphologically distinct cyprinid fishes, Gymnocypris eckloni scoliostomus (GS) and G. eckloni eckloni (GE), in a small glacial lake on the Qinghai-Tibet Plateau, Lake Sunmcuo, match the biogeographic criteria of sympatric speciation. In this study, we examined genome-wide variation in 46 individuals from these two groups. The divergence time between the GS and GE lineages was estimated to be 20-60 Kya. We identified 54 large genomic islands (≥100 kb) of speciation, which accounted for 89.4% of the total length of all genomic islands. These islands harboured divergent genes related to olfactory receptors and olfaction signals that may play important roles in food selection and assortative mating in fishes. Although the genomic islands clearly indicated speciation with gene flow and rejected micro-allopatric speciation, they were too large to support the hypothesis of sympatric speciation. Theoretical and recent empirical studies suggested that continual gene flow in sympatry should give rise to many small genomic islands (as small as a few kilobases in size). Thus, the observed pattern is consistent with the extensive evidence on parapatric speciation, in which adjacent habitats facilitate divergent selection but also permit gene flow during speciation. We suggest that many, if not most, of the reported cases of sympatric speciation are likely to be micro-parapatric speciation.

Two new species of the family Megalyridae (Hymenoptera) from China.

Two new species of the small and rarely collected family Megalyridae are described from China: Carminator daliensis Chen & Liuhe, sp. nov. from Yunnan and Ettchellsia hainanensis Chen & Liuhe, sp. nov. from Hainan. A key to megalyrid species of China is provided. The biogeographical implication of the new taxa is discussed.

Genome of the butterfly hillstream loach provides insights into adaptations to torrential mountain stream life.

Butterfly hillstream loach (Beaufortia kweichowensis), a benthic fish in the torrential mountain streams, possesses a totally flat ventrum, flattened craniofacial and body skeletons, and enlarged paired fins covered by substantially small keratinous structures. However, little is known about the genetic basis of these specialized morphological adaptations. Here we present a 448.52-Mb genome assembly with contig N50 length of 5.53 Mb by integrating Illumina short-read sequencing, Nanopore long-read sequencing and HiC-based chromatin map. Demographic history reconstruction of the butterfly hillstream loach reveals that the population dynamics is correlated with the different stages of uplifting of the Tibetan Plateau. Comparative genomic analysis finds evidence of six keratin genes in butterfly hillstream loach evolving under positive selection. Within these genes, two keratin genes exhibit species-specific and divergent amino acid changes, suggesting a role in the formation of the unculi. Additionally, a series of positively selected genes, rapid evolving genes, specific variant genes and expanded gene families are found, including genes related to Hedgehog, Notch and BMP pathways, which may be involved in craniofacial development. These findings may have important implications for understanding the genetic basis of phenotypic adaptation to torrential mountain stream life.

The design and the performance of an ultrahigh vacuum 3He fridge-based scanning tunneling microscope with a double deck sample stage for in-situ tip treatment.

Scanning tunneling microscope (STM) is a powerful tool for studying the structural and electronic properties of materials at the atomic scale. The combination of low temperature and high magnetic field for STM and related spectroscopy techniques allows us to investigate the novel physical properties of materials at these extreme conditions with high energy resolution. Here, we present the construction and the performance of an ultrahigh vacuum 3He fridge-based STM system with a 7 Tesla superconducting magnet. It features a double deck sample stage on the STM head so we can clean the tip by field emission or prepare a spin-polarized tip in situ without removing the sample from the STM. It is also capable of in situ sample and tip exchange and preparation. The energy resolution of scanning tunneling spectroscopy at T = 310 mK is determined to be 400 mK by measuring the superconducting gap with a niobium tip on a gold surface. We demonstrate the performance of this STM system by imaging the bicollinear magnetic order of Fe1+xTe at T = 5 K.

Common occurrence of Theileria annulata and the first report of T. ovis in dairy cattle from Southern Xinjiang, China.

Bovine theileriosis is a common tick-born disease infected by Theileria spp. causing loss of beef and dairy cattle worldwide, therefore, the aim of this study was to determine the prevalence and genetic diversity of Theileria spp. in Southern Xinjiang Uyghur Autonomous Region, China. We screened 493 dairy cattle blood samples from Southern Xinjiang to detect Theileria spp. by PCR. The overall prevalence of Theileria spp. was 23.5% (116/493). The most frequent Theileria sp. was Theileria annulata 22.5% (111/493), followed by T. orientalis (0.6%, 3/493) and T. ovis (0.2%, 1/493). Additionally, one sample was co-infected with T. annulata and T. orientalis. Phylogenetic analysis showed that the 11 T. annulata Tams1 sequences grouped into three sequence clusters that belonged to group 2 (Asia group) and shared 96.4% to 99.9% identity with to each other. Furthermore, our results revealed the presence of several T. orientalis MPSP genotypes (types 1, 2, and 5) in this region. In this study, T. annulata was found to be the most prevalent Theileria species in dairy cattle from Southern Xinjiang. Theileria ovis was detected in one DNA sample of a free-grazing dairy cow from China for the first time.

[Relationship between HLA Gene Polymorphism and Aplastic Anemia in Northern Chinese Han Patients].

OBJECTIVE: To explore the relationship between HLA-A, -B, -C, -DRB1, -DQB1 gene polymorphism and aplastic anemia （AA）of 65 cases in Northern China. METHODS: The high resolution genotyping of HLA-A, -B, -C, -DRB1, -DQB1 alleles in 65 AA patients and 772 healthy controls was performed with polymerase chain reaction-sequence specific oligonucleotide (PCR-SSO), the relationship between HLA-A, -B, -C, -DRB1, -DQB1 gene polymorphism and aplastic anemia was analyzed by Pearson Chi-square，Continuity Correction， Two-sided Fisher's Exact Test and Odds Ratio. RESULTS: The HLA-B*1302（10% vs 4.21%）, B*3501（7.69% vs 3.89%）, DRB1* 0701（10% vs 4.73%）, DRB1*0901（19.23% vs 7.58%）, DQB1*0202（9.23% vs 3.76%） gene frequency in AA patients was higher than those in health controls, the difference was statistically significant (P<0.05), the χ2 were 9.049, 4.336, 6.838, 20.974 and 8.968, OR ratio was 2.528, 2.061, 2.239, 2.904 and 2.605. However, the HLA-A*3303（1.54% vs 6.93%）, DQB1*0302（1.54% vs 6.02%） gene frequency in AA patients was lower than those in healthy controls, the difference was statistically significant (P<0.05), the χ2 was 5.726 and 4.505, the OR ratio were 0.210 and 0.244. CONCLUSION: The polymorphism of HLA-A, -B, -DRB1, -DQB1 alleles is associate with AA in these patient cases, the HLA-B*1302, HLA-B*3501, HLA-DRB1*0701, HLA-DRB1*0901 and HLA-DQB1*0202 may be sensitive genes to AA, while the HLA-A*3303 and HLA-DQB1*0302 may be protective genes on AA.

Changes of porcine growth hormone and pituitary nitrogen monoxide production as a response to cadmium toxicity.

The present study was designed to investigate the effects of various cadmium concentrations on porcine growth hormone (GH) secretion in serum and cultured pituitary cells and to explore the possible mechanisms of cadmium toxicity. In feeding trial, 192 barrows (Duroc x Landrace x Yorkshire), with similar initial body weights, were randomly divided into four different treatment groups with three replicates for each treatment. The diets were supplemented for 83 days with 0, 0.5, 5.0, and 10.0 mg/kg cadmium (as CdCl2). For the cell culture trial, dispersed pituitary cells were incubated with graded doses of cadmium (0, 5, 10, 15, or 20 microM) for 24 h. Pigs treated with 10 mg/kg cadmium had significantly decreased serum GH content. 3-(4,5-dimethyl-2-yl)-2,5-diphenyl tetrazolium bromide assay showed that Cd toxicity was dose-dependent. Cell viability was reduced to 50% at 15 microM concentration. Administration of cadmium significantly reduced GH secretion, whereas cellular NO content and inducible nitric oxide synthase activity increased to a certain extent. These findings suggest that the decrease of GH might be related to NO production and to a change of NO signal pathway caused by cadmium.

Calcifying fibrous tumor of stomach: A case report.

RATIONALE: Calcifying fibrous tumor (CFT) is a rare benign soft tissue mesenchymal neoplasm. Although the gastrointestinal (GI) tract is the most common predilection site of CFT, the clinicians, even including pathologist, generally consider it as GI stromal tumor (GIST) or other submucosal tumors such as schwannoma and leiomyoma. PATIENT CONCERNS: A 55-year-old man presented with complaints of epigastric discomfort and abdominal distention for more than 1 year. DIAGNOSES: On the basis of endoscopic and computed tomography examination, preliminary diagnosis was GIST. INTERVENTIONS: Endoscopic submucosal dissection (ESD) surgery was performed to remove the gastric mass. OUTCOMES: The histopathological examination revealed a gastric CFT. LESSONS: We present a case of gastric CFT, which was misdiagnosed as GIST based on endoscopic and radiologic findings.

Construction of a plasmid for human brain-derived neurotrophic factor and its effect on retinal pigment epithelial cell viability.

Several studies have investigated the protective functions of brain-derived neurotrophic factor (BDNF) in retinitis pigmentosa. However, a BDNF-based therapy for retinitis pigmentosa is not yet available. To develop an efficient treatment for fundus disease, an eukaryotic expression plasmid was generated and used to transfect human 293T cells to assess the expression and bioactivity of BDNF on acute retinal pigment epithelial-19 (ARPE-19) cells, a human retinal epithelial cell line. After 96 hours of co-culture in a Transwell chamber, ARPE-19 cells exposed to BDNF secreted by 293T cells were more viable than ARPE-19 cells not exposed to secreted BDNF. Western blot assay showed that Bax levels were downregulated and that Bcl-2 levels were upregulated in human ARPE-19 cells exposed to BDNF. Furthermore, 293T cells transfected with the BDNF gene steadily secreted the protein. The powerful anti-apoptotic function of this BDNF may be useful for the treatment of retinitis pigmentosa and other retinal degenerative diseases.

[Using compost of agricultural solid waste to produce organic-inorganic compound fertilizer].

Techniques of compound fertilizer production from solid waste compost were studied. Different ratio of water moisture, proportion between organic and inorganic and infection of different granularity to the effect of granulation is separately determined through experiments at the pilot scale in the field. The optimal parameters of the techniques are determined. The moisture content is 35%-40%; the rate of organic matter is 80%-90%; granularity is 20 mu. According the data of the organism's concentration, height and weight in crop, the crop was fertilized compound fertilizer is batter than chemical fertilizer. And the ability of increasing the production of the compound fertilizer was testified.

[Studies on the antithrombotic effects of anti-platelet mAb SZ-21 F(ab')(2) fragment].

AIM: To research the biological effect of the F(ab')(2) of anti-platelet GPIIIa mAb SZ-21. METHODS: The F(ab')(2) fragment was obtained with papain digestion for 20 hours at 4 degrees Celsius, under acid condition(pH 5.5). The products were purified through DEAE-52 ion exchange column and the first eluted peak components were verified as F(ab')(2) by SDS-PAGE. The immunoactivity and its antithrombotic effects of fragment were detected by ELISA and platelet aggregation inhibition test, respectively. RESULTS: The recovery rate of the fragment was 60.32%, its immunoactivity was 0.8 x10(-9) mol/L by ELISA. The 50% effective dose (ED(50)) in the platelet aggregate inhibition test was 3.395 mg/L. CONCLUSION: The F(ab')(2) fragment was superior to intact IgG in binding to platelets and inhibiting platelet aggregation. Thus the F(ab')(2) fragment of mAb SZ-21 opens up broad prospects for its application to the clinical antithrombotic therapy.