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1.
Plant Foods Hum Nutr ; 77(2): 206-211, 2022 Jun.
Article in English | MEDLINE | ID: mdl-35441311

ABSTRACT

Recently, there has been renewed interest in biorefining of agricultural onion into functional products. In this study, onion vinegar (OV) are prepared by a two-stage semi-continuous fermentation method, and its content of total flavonoids (3.01 mg/mL) and polyphenols (976.76 µg/mL) is superior to other commercial vinegars. OV possesses a high radical scavenging activity and enhances the antioxidant enzyme activities in vivo, alleviating intracellular oxidative stress in Caenorhabditis elegans. Treated by OV, the 1,1-diphenyl-2-picryl-hydrazyl radical (DPPH·), diammonium 2,2'-azino-bis (3-ethylbenzo thiazoline-6-sulfonic acid) (ABTS+·) and 2-phenyl-4,4,5,5- tetramethylimidazoline-1-oxyl 3-Oxide (PTIO·) free radicals clearance rates are 88.76, 98.76 and 90.54%, respectively in vitro. Whereas the glutathione peroxidase (GSH-Px), superoxide dismutase (SOD) and catalase (CAT) enzyme activities in C. elegans reach 271.57, 129.26, and 314.68%, respectively. Using RNAi and RT-PCR, it has been further confirmed that OV modulates transcription factor SKN-1, the nuclear factor erythroid 2-related factor 2 (Nrf2) homologous, in C. elegans, enhancing the resistance of C. elegans against sodium arsenite stress. Lifespan analysis reveals that 1 mL OV extends the maximum lifespan of the nematode to 26 days. Evidence is presented which shows that OV increases the lifespan of C. elegans by activating the SKN-1 signaling pathway. Overall, the OV is a well functional condiment, enhancing the value-added of onion.


Subject(s)
Caenorhabditis elegans Proteins , Caenorhabditis elegans , Acetic Acid/analysis , Acetic Acid/metabolism , Animals , Antioxidants/analysis , Caenorhabditis elegans/metabolism , Caenorhabditis elegans Proteins/genetics , Caenorhabditis elegans Proteins/metabolism , DNA-Binding Proteins/metabolism , Longevity , Onions/metabolism , Oxidative Stress , Transcription Factors/metabolism
2.
Fish Shellfish Immunol ; 121: 305-315, 2022 Feb.
Article in English | MEDLINE | ID: mdl-35031476

ABSTRACT

Ichthyophthirius multifiliis is a protozoan ciliate that causes white spot disease (also known as ichthyophthiriasis) in freshwater fish. Holland's spinibarbel (Spinibarbus hollandi) was less susceptible to white spot disease than grass carp (Ctenopharyngodon Idella). In this study, grass carp and Holland's spinibarbel are infected by I. multifiliis and the amount of infection is 10,000 theronts per fish. All grass carp died within 12 days after infection, and the survival rate of Holland's spinibarbel was more than 80%. In order to study the difference in sensitivity of these two fish species to I. multifiliis, transcriptome analysis was conducted using gill, skin, liver, spleen and head kidney of Holland's spinibarbel and grass carp at 48 h post-infection with I. multifiliis. A total of 489,296,696 clean reads were obtained by sequencing. A total of 105 significantly up-regulated immune-related genes were obtained by Gene Ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis in grass carp. Cluster of differentiation 40 (CD40), cluster of differentiation 80 (CD 80), tumor necrosis factor-alpha (TNF-α), toll-like receptor 4 (TLR-4), interleukin 1 beta (IL-1ß) and other inflammatory-related genes in grass carp were enriched in the cytokine-cytokine receptor interaction pathway and toll-like receptor pathway. In Holland's spinibarbel, a total of 46 significantly up-regulated immune-related genes were obtained by GO classification and KEGG pathway enrichment analysis. Immune-related genes, such as Immunoglobin heavy chain (IgH), cathepsin S (CTSS), complement C1q A chain (C1qA), complement component 3 (C3) and complement component (C9) were enriched in phagosome pathway, lysosome pathway and complement and coagulation concatenation pathway. C3 was significantly up-regulated in gill and head kidney. Fluorescence in situ hybridization (FISH) showed that the C3 gene was highly expressed in gill tissue of Holland's spinibarbel infected with I. multifiliis. A small amount of C3 gene was expressed in the gill arch of grass carp after infected with I. multifiliis. In conclusion, the severe inflammatory response in vivo after infecting grass carp with I. multifiliis might be the main cause of the death of grass carp. The extrahepatic expression of the gene of Holland's spinibarbel might play an important role in the immune defense against I. multifiliis.


Subject(s)
Carps , Ciliophora Infections , Cyprinidae , Fish Diseases , Hymenostomatida , Animals , Carps/genetics , Carps/parasitology , Ciliophora Infections/genetics , Ciliophora Infections/veterinary , Cyprinidae/genetics , Cyprinidae/parasitology , Fish Diseases/parasitology , Fish Proteins/genetics , Gene Expression Profiling , Hymenostomatida/pathogenicity , Netherlands
3.
Mar Genomics ; 61: 100902, 2022 Feb.
Article in English | MEDLINE | ID: mdl-35058035

ABSTRACT

Sturgeon is one of the ancient fish species with the fossil records over 200 million years ago. However, the sturgeon genomes are rather complicated, owing to several rounds of genome polyploidizations, which makes it difficult to assemble a high quality genome so that only a few studies analyze their whole genome evolutions (WGDs). This study applied the PacBio sequencing technology to sequence the full-length transcriptomes of blood samples of octoploid Huso dauricus, octoploid Acipenser schrenckii and tetraploid Acipenser stellatus. A total of non-redundant 33,407 transcript assemblies of the three sturgeons were finally generated and fully annotated with different gene function databases, as well as the predictions of simple sequence repeats, transcription factors and long non-coding RNAs. Data valuation exhibited that annotations of the three transcriptomes had the higher quality than those of the previously sequenced sturgeon genomes. A phylogeny of eight typical sturgeons was constructed using the low copy genes, which illustrated that Acipenser and Huso might share a single origin. The sturgeon WGDs were parallelly timed by calculating the divergence times of 2-member gene clusters and heterozygous-SNP-carried genes, which both suggested the occurrence of the WGDs later than 150 mya. The full-length transcriptome sequences were supposed to be the reliable reference data for the study of sturgeon.


Subject(s)
Gene Duplication , Transcriptome , Animals , Fishes/genetics , Genome/genetics , Sequence Analysis, DNA
4.
BMC Zool ; 7(1): 24, 2022 May 19.
Article in English | MEDLINE | ID: mdl-37170336

ABSTRACT

BACKGROUND: Hoplobatrachus rugulosus (Anura: Dicroglossidae) is distributed in China and Thailand and the former can survive substantially lower temperatures than the latter. The mitochondrial genomes of the two subspecies also differ: Chinese tiger frogs (CT frogs) display two identical ND5 genes whereas Thai tiger frogs (TT frogs) have two different ND5 genes. Metabolism of ectotherms is very sensitive to temperature change and different organs have different demands on energy metabolism at low temperatures. Therefore, we conducted studies to understand: (1) the differences in mitochondrial gene expression of tiger frogs from China (CT frogs) versus Thailand (TT frogs); (2) the differences in mitochondrial gene expression of tiger frogs (CT and TT frogs) under short term 24 h hypothermia exposure at 25 °C and 8 °C; (3) the differences in mitochondrial gene expression in three organs (brain, liver and kidney) of CT and TT frogs. RESULTS: Utilizing RT-qPCR and comparing control groups at 25 °C with low temperature groups at 8 °C, we came to the following results. (1) At the same temperature, mitochondrial gene expression was significantly different in two subspecies. The transcript levels of two identical ND5 of CT frogs were observed to decrease significantly at low temperatures (P < 0.05) whereas the two different copies of ND5 in TT frogs were not. (2) Under low temperature stress, most of the genes in the brain, liver and kidney were down-regulated (except for COI and ATP6 measured in brain and COI measured in liver of CT frogs). (3) For both CT and TT frogs, the changes in overall pattern of mitochondrial gene expression in different organs under low temperature and normal temperature was brain > liver > kidney. CONCLUSIONS: We mainly drew the following conclusions: (1) The differences in the structure and expression of the ND5 gene between CT and TT frogs could result in the different tolerances to low temperature stress. (2) At low temperatures, the transcript levels of most of mitochondrial protein-encoding genes were down-regulated, which could have a significant effect in reducing metabolic rate and supporting long term survival at low temperatures. (3) The expression pattern of mitochondrial genes in different organs was related to mitochondrial activity and mtDNA replication in different organs.

5.
Mol Ecol Resour ; 22(4): 1545-1558, 2022 May.
Article in English | MEDLINE | ID: mdl-34837460

ABSTRACT

Quasipaa spinosa is an Asian commercial Dicroglossidae species noted for its spiny chest found in adult males. Here, we report the first chromosomal level Q. spinosa genome employing PacBio long read sequencing and high-resolution chromosome conformation capture (Hi-C) technology. The total length of the final assembled genome was 2,839,292,578 bp, with contig N50 of 3.79 Mb and scaffold N50 of 327.44 Mb. Approximately 99.30% of the length of the assembled genome sequences were anchored to 13 chromosomes with the assistance of Hi-C reads. A total of 26,173 protein-coding genes were predicted, and 95.98% of the genes were functionally annotated. The annotated genes covered a total of 92.10% of the complete vertebrate core gene set according to the BUSCO pipeline evaluation. Approximately 41 million years ago, Q. spinosa began to diverge from its dicroglossid sister taxon Nanorana parkeri. The Q. spinosa genome revealed obvious chromosomal fissions compared with Xenopus tropicalis, which probably represented a specific chromosome evolutionary history within frogs. Population analysis showed that Chinese Q. spinosa could be divided into eastern and western genetic clusters, with the western population showing higher diversity than the eastern population. The effective population size of Q. spinosa showed a continuously decreasing trend from one million years ago to 10,000 years ago. In summary, this study sheds light on Q. spinosa evolution and population differentiation, providing a valuable genomic resource for further biological and genetic studies on this species, and other closely related frog taxa.


Subject(s)
Chromosomes , Genome , Animals , Anura/genetics , Chromosomes/genetics , Male , Phylogeny , Sequence Analysis, DNA
6.
BMC Evol Biol ; 18(1): 26, 2018 02 27.
Article in English | MEDLINE | ID: mdl-29486721

ABSTRACT

BACKGROUND: Complete mitochondrial (mt) genomes have been used extensively to test hypotheses about microevolution and to study population structure, phylogeography, and phylogenetic relationships of Anura at various taxonomic levels. Large-scale mt genomic reorganizations have been observed among many fork-tongued frogs (family Dicroglossidae). The relationships among Dicroglossidae and validation of the genus Feirana are still problematic. Hence, we sequenced the complete mt genomes of Nanorana taihangnica (=F. taihangnica) and N. yunnanensis as well as partial mt genomes of six Quasipaa species (dicroglossid taxa), two Odorrana and two Amolops species (Ranidae), and one Rhacophorus species (Rhacophoridae) in order to identify unknown mt gene rearrangements, to investigate the validity of the genus Feirana, and to test the phylogenetic relationship of Dicroglossidae. RESULTS: In the mt genome of N. taihangnica two trnM genes, two trnP genes and two control regions were found. In addition, the trnA, trnN, trnC, and trnQ genes were translocated from their typical positions. In the mt genome of N. yunnanensis, three control regions were found and eight genes (ND6, trnP, trnQ, trnA, trnN, trnC, trnY and trnS genes) in the L-stand were translocated from their typical position and grouped together. We also found intraspecific rearrangement of the mitochondrial genomes in N. taihangnica and Quasipaa boulengeri. In phylogenetic trees, the genus Feirana nested deeply within the clade of genus Nanorana, indicating that the genus Feirana may be a synonym to Nanorana. Ranidae as a sister clade to Dicroglossidae and the clade of (Ranidae + Dicroglossidae) as a sister clade to (Mantellidae + Rhacophoridae) were well supported in BI analysis but low bootstrap in ML analysis. CONCLUSIONS: We found that the gene arrangements of N. taihangnica and N. yunnanensis differed from other published dicroglossid mt genomes. The gene arrangements in N. taihangnica and N. yunnanensis could be explained by the Tandem Duplication and Random Loss (TDRL) and the Dimer-Mitogenome and Non-Random Loss (DMNR) models, respectively. The invalidation of the genus Feirana is supported in this study.


Subject(s)
Anura/genetics , Gene Rearrangement , Genome, Mitochondrial , Phylogeny , Animals , Base Sequence , DNA, Mitochondrial/genetics , Gene Order , Genes, Mitochondrial , Nucleic Acid Conformation , Phylogeography , RNA, Transfer/genetics
7.
Sheng Wu Gong Cheng Xue Bao ; 34(1): 132-139, 2018 Jan 25.
Article in Chinese | MEDLINE | ID: mdl-29380578

ABSTRACT

Antibacterial peptide can be easily degraded by protease and has the lethal effect on the host Escherichia coli. In order to solve these problems and further improve the expression ability of the Escherichia coli system, the antimicrobial peptide Spinosan-C of Paa spinosa was studied. First, the codon of Spinosan-C was optimized according to E. coli codon usage frequency. Then, the 8 multimeric Spinosan-C gene (8×Spinosan-C) was synthesized and cloned into prokaryotic expression vector pET-28a. The fusion antimicrobial peptide 8×Spinosan-C was further highly expressed in Escherichia coli strain Rosetta. The recombinant 8×Spinosan-C protein was then purified and cleaved specially by formic acid to generate the Spinosan-C monomer. Antibacterial test in vitro suggested that the cleaved Spinosan-C monomer had antibacterial bioactivity against the test bacteria. This study provides a technical reference for the largescale preparation of frog antimicrobial peptides.


Subject(s)
Antimicrobial Cationic Peptides/pharmacology , Benzofurans/pharmacology , Escherichia coli/drug effects , Ranidae , Animals , Anti-Infective Agents , Recombinant Fusion Proteins
8.
Ecol Evol ; 8(2): 1260-1270, 2018 01.
Article in English | MEDLINE | ID: mdl-29375796

ABSTRACT

Introgression may lead to discordant patterns of variation among loci and traits. For example, previous phylogeographic studies on the genus Quasipaa detected signs of genetic introgression from genetically and morphologically divergent Quasipaa shini or Quasipaa spinosa. In this study, we used mitochondrial and nuclear DNA sequence data to verify the widespread introgressive hybridization in the closely related species of the genus Quasipaa, evaluate the level of genetic diversity, and reveal the formation mechanism of introgressive hybridization. In Longsheng, Guangxi Province, signs of asymmetrical nuclear introgression were detected between Quasipaa boulengeri and Q. shini. Unidirectional mitochondrial introgression was revealed from Q. spinosa to Q. shini. By contrast, bidirectional mitochondrial gene introgression was detected between Q. spinosa and Q. shini in Lushan, Jiangxi Province. Our study also detected ancient hybridizations between a female Q. spinosa and a male Q. jiulongensis in Zhejiang Province. Analyses on mitochondrial and nuclear genes verified three candidate cryptic species in Q. spinosa, and a cryptic species may also exist in Q. boulengeri. However, no evidence of introgressive hybridization was found between Q. spinosa and Q. boulengeri. Quasipaa exilispinosa from all the sampling localities appeared to be deeply divergent from other communities. Our results suggest widespread introgressive hybridization in closely related species of Quasipaa and provide a fundamental basis for illumination of the forming mechanism of introgressive hybridization, classification of species, and biodiversity assessment in Quasipaa.

9.
Mitochondrial DNA A DNA Mapp Seq Anal ; 27(4): 2460-1, 2016 07.
Article in English | MEDLINE | ID: mdl-26016875

ABSTRACT

The complete mitochondrial genome of Lithobates sylvaticus (Anura: Ranidae) was sequenced. The genome is a circular molecule of 17,343 bp in length and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a large non-coding region. The gene order and mitochondrial genome information of L. sylvaticus is similar to most other frogs. The overall AT content of L. sylvaticus mitochondrial DNA is 59.3%. In BI and MLtrees, we found L. sylvaticus is a sister clade to L. catesbeianus. The monophyly of Lithobates, Rana, Odorrana, Glandirana, Pelophylax, and Amolops is well supported, but the paraphyly of Babina is supported.


Subject(s)
Genome, Mitochondrial , Genomics , Ranidae/classification , Ranidae/genetics , Animals , Base Composition , Genes, Mitochondrial , Genome Size , Open Reading Frames , Phylogeny , Sequence Analysis, DNA , Whole Genome Sequencing
10.
PLoS One ; 10(4): e0124825, 2015.
Article in English | MEDLINE | ID: mdl-25875761

ABSTRACT

he Chinese tiger frog Hoplobatrachus rugulosus is widely distributed in southern China, Malaysia, Myanmar, Thailand, and Vietnam. It is listed in Appendix II of CITES as the only Class II nationally-protected frog in China. The bred tiger frog known as the Thailand tiger frog, is also identified as H. rugulosus. Our analysis of the Cyt b gene showed high genetic divergence (13.8%) between wild and bred samples of tiger frog. Unexpected genetic divergence of the complete mt genome (14.0%) was also observed between wild and bred samples of tiger frog. Yet, the nuclear genes (NCX1, Rag1, Rhod, Tyr) showed little divergence between them. Despite this and their very similar morphology, the features of the mitochondrial genome including genetic divergence of other genes, different three-dimensional structures of ND5 proteins, and gene rearrangements indicate that H. rugulosus may be a cryptic species complex. Using Bayesian inference, maximum likelihood, and maximum parsimony analyses, Hoplobatrachus was resolved as a sister clade to Euphlyctis, and H. rugulosus (BT) as a sister clade to H. rugulosus (WT). We suggest that we should prevent Thailand tiger frogs (bred type) from escaping into wild environments lest they produce hybrids with Chinese tiger frogs (wild type).


Subject(s)
Cytochromes b/genetics , DNA, Mitochondrial/genetics , Genome, Mitochondrial/genetics , Nuclear Proteins/genetics , Ranidae/classification , Ranidae/genetics , Animals , Bayes Theorem , Evolution, Molecular , Gene Rearrangement , Genetic Drift , Phylogeny , Sequence Analysis, DNA/methods
11.
Dongwuxue Yanjiu ; 36(1): 34-40, 2015 Jan 18.
Article in English | MEDLINE | ID: mdl-25730459

ABSTRACT

Lamprotula leai is one of the most commercially important freshwater pearl mussels in China, but there is limited data on its genetic diversity and population structure. In the present study, 119 individuals from four major geographical populations were investigated using 15 microsatellite loci identified via cross-species amplification. A total of 114 alleles were detected, with an average of 7.6 alleles per locus (range: 2 to 21). Among the four stocks, those from Hung-tse Lake and Poyang Lake had the lowest (0.412) and highest (0.455) observed heterozygosity respectively. The polymorphism information content (PIC) ranged from 0.374 to 0.927 (mean: 0.907). AMOVA showed that 12.56% and 44.68% genetic variances were among populations and within individuals, respectively. Pairwise Fst ranged from 0.073 to 0.146, indicating medium genetic differentiation among the populations. In aggregate, our results suggest that inbreeding is a crucial factor accounting for deviations from Hardy-Weinberg equilibrium at 12 loci. Moreover, the genetic distance among four stocks ranged from 0.192 to 0.890. Poyang Lake and Hung-tse Lake were clustered together, joined with Dongting Lake and Anqing Lake. Given that specimens from Hung-tse Lake showed the highest average allele richness, expected heterozygosity and PIC, this location may be the source of the highest quality germplasm resources and the stock from this area may be the best for future breeding efforts.


Subject(s)
Animal Distribution , Bivalvia/genetics , Genetic Variation , Microsatellite Repeats , Animals , China
12.
Infect Genet Evol ; 28: 175-82, 2014 Dec.
Article in English | MEDLINE | ID: mdl-25269786

ABSTRACT

Major histocompatibility complex (MHC) genes are candidates for determining disease susceptibility due to their pivotal role in both innate and adaptive immune responses. Accordingly, the association between the genetic variation of MHC genes and the pathogen resistance has been investigated in numerous vertebrates. To date, however, little is reported in amphibians. In this study, we investigate the genetic variation at the MHC class IIB gene in the giant spiny frog Quasipaa spinosa, which has high commercial value in China. The full length of MHC class IIB cDNA was cloned from Q. spinosa by homology cloning and rapid amplification of cDNA end-polymerase chain reaction (RACE-PCR). Two MHC class IIB loci were identified in Q. spinosa. We also developed PCR primers for a portion of the second exon of the MHC class IIB gene. A total of 26 MHC class IIB alleles were identified. The dN rate was significantly higher than the dS rate in the putative peptide-binding region, thereby proving the positive selection hypothesis. In addition, individuals intraperitoneally injected with Aeromonas hydrophila were used to study the association between MHC class IIB alleles and pathogen resistance/susceptibility, to explore the specific alleles in balancing selection. Eighty frogs were used after exposure to A. hydrophila infection. Nine alleles were used to study the association between the alleles and disease resistance. Two alleles, namely, Pasa-DAB(∗)1301 and Pasa-DAB(∗)0901, were significantly associated with resistance against A. hydrophila. This study provides valuable information on the structure of the MHC class IIB gene and confirms the association between MHC class IIB gene alleles and disease resistance to bacterial infection in Q. spinosa. Moreover, pathogen resistance-related MHC markers can be used for the selective breeding of the giant spiny frog.


Subject(s)
Aeromonas hydrophila/physiology , Genes, MHC Class II , Ranidae/genetics , Ranidae/immunology , Animals , China , Cloning, Molecular , Disease Resistance , Exons , Gram-Negative Bacterial Infections/genetics , Gram-Negative Bacterial Infections/microbiology , Polymorphism, Genetic , Ranidae/microbiology , Selection, Genetic , Sequence Analysis
13.
PLoS One ; 8(7): e70403, 2013.
Article in English | MEDLINE | ID: mdl-23936199

ABSTRACT

Species identification is one of the most basic yet crucial issues in biology with potentially far-reaching implications for fields such as conservation, population ecology, and epidemiology. The widely distributed but threatened frog Paa spinosa has been speculated to represent a complex of multiple species. In this study, 254 individuals representing species of the genus Paa were investigated along the entire range of P. spinosa: 196 specimens of P. spinosa, 8 specimens of P. jiulongensis, 5 specimens of P. boulengeri, 20 specimens of P. exilispinosa, and 25 specimens of P. shini. Approximately 1333 bp of mtDNA sequence data (genes 12S rRNA and 16S rRNA) were used. Phylogenetic analyses were conducted using maximum parsimony, maximum likelihood and Bayesian inference. BEAST was used to estimate divergence dates of major clades. Results suggest that P. spinosa can be divided into three distinct major lineages. Each major lineage totally corresponds to geographical regions, revealing the presence of three candidate cryptic species. Isolation and differentiation among lineages are further supported by the great genetic distances between the lineages. The bifurcating phylogenetic pattern also suggests an east-west dispersal trend during historic cryptic speciation. Dating analysis estimates that P. spinosa from Western China split from the remaining P. spinosa populations in the Miocene and that P. spinosa from Eastern China diverged from Central China in the Pliocene. We also found that P. exilispinosa from Mainland China and Hong Kong might have a complex of multiple species. After identifying cryptic lineages, we then determine the discrepancy between the mtDNA and the morphotypes in several individuals. This discrepancy may have been caused by introgressive hybridization between P. spinosa and P. shini.


Subject(s)
Anura/genetics , Evolution, Molecular , Genetic Speciation , Hybridization, Genetic , Phylogeny , Animals , Anura/classification , Bayes Theorem , DNA, Mitochondrial/chemistry , DNA, Mitochondrial/genetics , Genetic Variation , Geography , Haplotypes , Molecular Sequence Data , Phylogeography , RNA, Ribosomal/genetics , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Species Specificity
14.
Mitochondrial DNA ; 23(6): 423-5, 2012 Dec.
Article in English | MEDLINE | ID: mdl-22943433

ABSTRACT

The mitochondrial (mt) genome of Babina adenopleura (Anura: Ranidae) is a circular molecule of 18,982 bp in length, containing 38 genes as well as other anurans. The complete mtDNA of B. adenopleura is 18,982 bp in length, and the A+T content of the overall base composition of H-strand is 58.9% (T, 29.8%; C, 26.6%; A, 29.1%; G, 14.4%). The control regions are 3159 bp in length, and the A+T content of this region is 70.2% (A, 36.6%; C, 16.8%; G, 12.9%; T, 33.6%). The control region possesses distinct repeat regions at both 5' and 3' sides. A long space region between ND5 and ND6 genes is 461 bp.


Subject(s)
Genome, Mitochondrial , Ranidae/genetics , Animals , Anura/genetics , Gene Rearrangement , Genome, Mitochondrial/genetics , Molecular Sequence Data , Open Reading Frames/genetics , RNA, Transfer/genetics , RNA, Untranslated/genetics , Sequence Analysis, DNA
15.
Mitochondrial DNA ; 23(5): 336-7, 2012 Oct.
Article in English | MEDLINE | ID: mdl-22708866

ABSTRACT

The mitochondrial genome of Hoplobatrachus rugulosus (Anura: Dicroglossidae) is a circular molecule of 20,309 bp in length, containing 39 genes (including the extra copy of ND5 and tRNA(Met) genes). The following four distinctive features are observed: the cluster of rearranged tRNA genes (TPF tRNA gene cluster), the translocation of tRNA(Leu(CUN)) and ND5 genes, the tandem duplication of tRNA(Met) genes (Met1 and Met2), and the duplicated d-loop-ND5 regions.


Subject(s)
Anura/genetics , Genome, Mitochondrial , Animals , DNA, Mitochondrial/chemistry , Gene Rearrangement , Multigene Family , Phylogeny , RNA, Transfer, Leu/genetics
16.
Gene ; 447(2): 86-96, 2009 Nov 15.
Article in English | MEDLINE | ID: mdl-19631263

ABSTRACT

The mt genome of Paa spinosa (Anura: Ranoidae) is a circular molecule of 18,012 bp in length, containing 38 genes (including an extra copy of tRNA-Met gene). This mt genome is characterized by three distinctive features: a cluster of rearranged tRNA genes (LTPF tRNA gene cluster), a tandem duplication of tRNA-Met gene (Met1 and Met2), and distinct repeat regions at both 5' and 3'-sides in the control region. Comparing the locations and the sequences of all tRNA-Met genes among Ranoidae, and constructing NJ tree of the nucleotide of those tRNA-Met genes, we suggested a tandem duplication of tRNA-Met gene can be regarded as a synapomorphy of Dicroglossinae. To further investigate the phylogenetic relationships of anurans, phylogenetic analyses (BI, ML and MP) based on the nucleotide dataset and the corresponding amino acid dataset of 11 protein-coding genes (except ND5 and ATP8) arrived at the similar topology.


Subject(s)
Anura/classification , Anura/genetics , Genome, Mitochondrial , Phylogeny , Animals , Base Composition , Base Sequence , Bayes Theorem , Chromosome Mapping , DNA Primers/genetics , DNA, Mitochondrial/chemistry , DNA, Mitochondrial/genetics , Evolution, Molecular , Gene Duplication , Gene Rearrangement , Likelihood Functions , Models, Genetic , Multigene Family , Nucleic Acid Conformation , RNA, Transfer, Met/chemistry , RNA, Transfer, Met/genetics , Tandem Repeat Sequences
17.
J Environ Sci (China) ; 21(5): 691-5, 2009.
Article in English | MEDLINE | ID: mdl-20108673

ABSTRACT

To provide basic toxicity data for formulating risk characterization benchmarks, the effects of lead on survival, locomotion, and sperm morphology were investigated in the Asian earthworm Pheretima guillelmi. The LC50 of P. guillelmi for 7 and 14 d were 4285 +/- 339 mg/kg and 3207 +/- 248 mg/kg, which shows P. guillelmi can tolerate a higher concentration of lead nitrate. The average weight of the surviving earthworms decreased at concentration of 2800 mg Pb/kg soil, and the locomotor ability of earthworms exposed to a range of soil Pb concentrations showed a general decrease with increasing Pb concentrations. We also presented data depicting the sperm morphology of earthworms, which shows potential as a sensitive biomarker for measuring the effects of heavy metal on reproduction.


Subject(s)
Environmental Pollutants/toxicity , Lead/toxicity , Locomotion/drug effects , Oligochaeta/drug effects , Spermatozoa/drug effects , Animals , Male , Oligochaeta/physiology
18.
Mol Ecol Resour ; 9(1): 336-8, 2009 Jan.
Article in English | MEDLINE | ID: mdl-21564643

ABSTRACT

We characterized 15 polymorphic microsatellite loci for the giant spiny frog, Paa spinosa. These loci were highly polymorphic when screened in 38 individuals from two different populations, with nine to 23 alleles per locus. The range of observed and expected heterozygosities was 0.231-0.916 and 0.296-0.944, respectively. These polymorphic loci will be useful for assessing genetic diversity, population structure, gene flow, population assignment and determining paternity in the giant spiny frog.

19.
Guang Pu Xue Yu Guang Pu Fen Xi ; 24(11): 1342-4, 2004 Nov.
Article in Chinese | MEDLINE | ID: mdl-15762471

ABSTRACT

Tissues of cancerous and normal lungs were analysed directly and fast by Fourier transform infrared spectroscopy with OMNI-sampler. The result indicated that some remarkable spectral differences were among normal and cancerous lung tissues in frequency, intensity and shape of the absorption peaks. These facts indicated significant differences of content, structure and conformation of proteins, nucleic acids and lipids in different types of lung tissues. The present results suggested that Fourier transform infrared spectrometry (FTIR) could show the properties of normal and cancerous lung tissues at the molecular level. It was able to provide rich and reliable information for investigation of normal and cancerous lung tissues and could be used as a convenient and reliable diagnostic tool for some tumors.


Subject(s)
Carcinoma, Bronchogenic/diagnosis , Lipids/chemistry , Lung Neoplasms/diagnosis , Lung/chemistry , Carcinoma, Bronchogenic/pathology , Diagnosis, Differential , Humans , Lung Neoplasms/pathology , Neoplasm Proteins/chemistry , Nucleic Acids/chemistry , Reference Values , Spectroscopy, Fourier Transform Infrared/methods
20.
Ecotoxicol Environ Saf ; 52(1): 57-61, 2002 May.
Article in English | MEDLINE | ID: mdl-12051808

ABSTRACT

Growth-inhibiting tests were carried out for 12 pesticides (including 11 fungicides: fosetyl-aluminum, benomyl, metalaxyl, iprodione, dimetachlone, carbendazim, thiophanate-methyl, bismerthiazol, procymidone, zineb, chlorothalonil, and the acaricide abamectin) in the green algae Chlorella pyrenoidosa and Scenedesmus obliqnus and the differential sensitivities of the two green algae to those pesticides were compared. The results indicate that the acute toxicity of benomyl to C. pyrenoidosa and S. obliqnus is the highest among all of the pesticides tested and is close to that of the photosynthesis-inhibiting herbicides atrazine, simazine, and chlorotoluron. Meanwhile, algal species vary widely in their response to the pesticides. The results demonstrated that there was a differential response to various pesticides by the two species of algae and that the sensitivity of various species of algae exposed to chlorothalonil varied by nearly two orders of magnitude; sensitivity to thiophanate-methyl varied by more than one order. Investigations using different algal species as test organisms have demonstrated that algae vary greatly in their response to chemicals. Differential sensitivity of green species to the compounds could induce species shifts within communities.


Subject(s)
Chlorella/drug effects , Chlorophyta/drug effects , Pesticides/toxicity , Water Pollutants, Chemical/toxicity , Biological Assay/methods , Lethal Dose 50 , Reproducibility of Results , Sensitivity and Specificity
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