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1. Stronger selective constraint on downstream genes in the oxidative phosphorylation pathway of cetaceans | |||
Tian Ran,Xu Shixia,Chai Simin,Yin Daiqing,Harold Zakon,Yang Guang | |||
Biology 21 November 2017 | |||
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Abstract:The oxidative phosphorylation (OXPHOS) signaling pathway is an efficient way to produce energy of adenosine triphosphate (ATP), which is most crucial for sustaining an energy supply for cetaceans in a hypoxic environment. Several studies have shown that natural selection may shape the evolution of the genes involved in OXPHOS. However, how network architecture drives OXPHOS protein sequence evolution remains poorly explored. In this project, we investigated the evolutionary patterns of genes in the OXPHOS signaling pathways across six cetacean genomes within the framework of functional network. Our results show that a negative correlation was inferred between the strength of purifying selection and pathway position. This result indicates the downstream genes were subjected to stronger evolutionary constraints, which may be because of the dual function of ATP synthase required to transduce signals of the OXPHOS pathway. We also found that there was a positive correlation between codon usage bias and ω, and a negative correlation with dS, indicating a stronger selective constraint on genes (with less biased codon usage) along the OXPHOS signaling pathway is attributable to an increase in the rate of synonymous substitution. Surprisingly, there was no significant correlation between the protein-protein interactions (PPIs) and the evolutionary estimates, implying that highly connected enzymes showing greater evolutionary constraint may not be a more general mechanism. Compared with that observed for terrestrial mammals, we found that the signature of positive selection detected in five genes (ATP5J, LHPP, PPA1, UQCRC1, UQCRQ) was cetacean-specific, reflecting the importance of OXPHOS for survival in hypoxic, aquatic environments. | |||
TO cite this article:Tian Ran,Xu Shixia,Chai Simin, et al. Stronger selective constraint on downstream genes in the oxidative phosphorylation pathway of cetaceans[OL].[21 November 2017] http://en.paper.edu.cn/en_releasepaper/content/4742252 |
2. The complete mitogenome and gene organization of the Chinese water dragon (Physignathus cocincinus) | |||
YAN Long,YAN Peng | |||
Biology 29 April 2017 | |||
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Abstract:The complete mitochondrial DNA sequence of the Chinese water dragon (Physignathus cocincinus) was determined using PCR and sequenced with a primer walking method. The complete mitochondrial genome is 16,451 bp in length, which contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one control region (CR). The gene arrangement and composition of P. cocincinus was similar to most other vertebrate, but the order of the tRNA-Ile and tRNA-Gln was switched and lack of the origin of L-strand replication (OL). Meanwhile, there was only one CR in P. cocincinus mitogenome, where it was located between the tRNA-Pro and tRNA-Phe gene. Duplication of the control region was not found in P. cocincinus, which was often observed in the mitogenomes of Agamidae. | |||
TO cite this article:YAN Long,YAN Peng. The complete mitogenome and gene organization of the Chinese water dragon (Physignathus cocincinus)[OL].[29 April 2017] http://en.paper.edu.cn/en_releasepaper/content/4730948 |
3. Mitochondrial genome sequencing of three firefly beetles and phylogenetic analysis of 18 species of beetles | |||
WANG Kai,HONG Wei,JIAO Hengwu,MU Feng-Juan,ZHAO Huabin | |||
Biology 24 April 2017 | |||
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Abstract:To validate the phylogenetic inference based on transcriptome data, we employed the traditional Sanger sequencing to obtain two complete mitogenomes (Aquatica ficta and A. wuhana) and one nearly complete mitogenome (Lamprigera yunnana); we also identified the 13 protein coding genes (PCGs) in mitogenomes from each of the four whole-body transcriptomes; and we additionally retrieved 12 published complete mitogenomes from members of Rhagophthalmidae, Lampyridae, Phengodidae, Elateridae, Lycidae, Cantharidae, and Tenebrionidae. Our mitogenome analysis confirmed the distinctiveness of Rhagophthalmidae from Lampyridae, which is consistent to our earlier transcriptome analysis. | |||
TO cite this article:WANG Kai,HONG Wei,JIAO Hengwu, et al. Mitochondrial genome sequencing of three firefly beetles and phylogenetic analysis of 18 species of beetles[OL].[24 April 2017] http://en.paper.edu.cn/en_releasepaper/content/4727742 |
4. Transcriptome sequencing and phylogenetic analysis of four species of luminescent beetles | |||
WANG Kai,HONG Wei,JIAO Hengwu,ZHAO Huabin | |||
Biology 24 April 2017 | |||
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Abstract:The evolution of bioluminescence has prompted scientific attention to illuminate phylogenetic relationships of luminescent beetles. However, genomic resources are virtually lacking in rhagophthalmids (Rhagophthalmidae) and their related firefly beetles lampyrids (Lampyridae). Here, we employed the Illumina Hiseq 2000 platform and sequenced the whole-body transcriptomes of the four luminescent beetles: one rhagophthalmid (Rhagophthalmus sp.) and three fireflies (Asymmetricata circumdata, Aquatica ficta, and Pyrocoelia pectoralis). We obtained 55.4, 43.4, 38.6, and 36.7 million clean reads for the four species, respectively. All reads were assembled into contigs from which unigenes were derived. All unigenes were annotated by publicly available databases, and a total of 4325 orthologous genes were identified. Using multiple phylogenetic approaches, our transcriptome data confirmed the distinctiveness of Rhagophthalmidae from Lampyridae. Together, this study is the first report of whole transcriptome sequencing data in Rhagophthalmidae and Lampyridae species, representing a valuable genomic resource for studying the origin and evolution of some remarkable traits in these beetles such as bioluminescence. Moreover, our transcriptome data provide useful phylogenetic information that could be of importance in future studies of phylogenetic inference. | |||
TO cite this article:WANG Kai,HONG Wei,JIAO Hengwu, et al. Transcriptome sequencing and phylogenetic analysis of four species of luminescent beetles[OL].[24 April 2017] http://en.paper.edu.cn/en_releasepaper/content/4727609 |
5. Scanning Electron Microscopy Studies of Scale Structures and Skin Sense Organs of Phrynocephalus frontalis (Squamata:Agamidae) | |||
Liu Jianyu,Chang Cheng | |||
Biology 25 December 2015 | |||
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Abstract:Toad-headed lizards of the Phrynocephalus frontalis are the dominant and endemic reptiles in the desert of northern China, the difference in scale structures and density of SSOs of P. frontalis have been described poorly. To overcome this, we studied the scale structure and density of SSOs in the integument of P. frontalis by scanning electron microscopy. We found that the structure of scales varies by location of the scale. Maximal number of SSOs per scale is found on the infralabials. The highest mean density of SSOs is located on the ventral caudals, and the lowest is encountered on the middle dorsals. The function of SSOs of P. frontalis was suggested to be mechanoreceptive and was sensible to vibration on basis of them morphology and distribution. | |||
TO cite this article:Liu Jianyu,Chang Cheng. Scanning Electron Microscopy Studies of Scale Structures and Skin Sense Organs of Phrynocephalus frontalis (Squamata:Agamidae)[OL].[25 December 2015] http://en.paper.edu.cn/en_releasepaper/content/4673665 |
6. Complete nucleotide sequences and gene organization of the Mt. Mang Pit Viper (Zhaoermia mangshanensis) mtDNA | |||
GENG Zhangzhen,YAN Peng | |||
Biology 13 December 2015 | |||
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Abstract:The complete mitochondrial DNA sequence of Mang Mountain Pit Viper (Zhaoermia mangshanensis) was determined by using the polymerase chain reaction (PCR) method in this study. The entire length of the complete mitochondrial genome is 17,628 base pairs (bp). Just like most snakes, besides 2 control regions (CRI and CRII), the nucleotide contains 37 coding genes, exactly, 13 protein-coding genes, 22 tRNA genes and 2 rRNA genes. The gene content, organization and arrangement of the new mtDNA are highly similar to those of other vipers reported so far. It confirms again to the order and rearrangement of two tRNA genes (tRNA-Pro and tRNA-LeuUUR), which differs from the typical organization found for many vertebrates. Duplication of the control region and translocation of the tRNALeu(UUR) gene are two notable features of the snake mt genome (except the scolecophidians: blindsnakes and threadsnakes). | |||
TO cite this article:GENG Zhangzhen,YAN Peng. Complete nucleotide sequences and gene organization of the Mt. Mang Pit Viper (Zhaoermia mangshanensis) mtDNA[OL].[13 December 2015] http://en.paper.edu.cn/en_releasepaper/content/4670835 |
7. iTRAQ-based quantitative proteomic analysis of myofibrillar contents and relevant proteolytic proteins in soleus muscle of hibernating Daurian ground squirrels | |||
Hui Chang,Shan-Feng Jiang,Kai Dang,Hui-Ping Wang,Yun-Fang Gao | |||
Biology 26 November 2015 | |||
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Abstract:Hibernators like Daurian ground squirrels (Spermophilus dauricus) appear to deviate from significant increase of protein catabolism and loss of myofibrillar contents, which provides a useful model to study mechanisms of preventing disuse-induced skeletal muscle atrophy. We explored proteomic assessment of soleus muscle (SOL) in Daurian ground squirrels to test a hypothesis that expression levels of major myofibrillar proteins are retained during hibernation, with inhibition of protein degradation as a key potential mechanism to prevent disuse atrophy. Here we use iTRAQ-based quantitative analysis to examine proteomic changes in myofibrillar contents and proteolytic pathways from the SOL of squirrels in no hibernation (PRE) and hibernation (HB) states. We found the SOL in squirrels showed limited sign of atrophy over 60-day winter dormancy. Levels of most cytoskeletal and contractile proteins examined were maintained through hibernation period, with 2 cytoskeletal proteins (vimentin and calreticulin) and 2 contractile proteins (myosin-2 and troponin C) 1.2- to 2.1-fold upregulated in HB compared to PRE, whereas 2 cytoskeletal proteins (fibrinogen and tropomodulin) and 1 contractile protein (myosin-3) were respectively reduced by 46%, 30%, 41% in HB compared to PRE. Moreover, expression levels of six protease subunits from ubiquitin-proteasome proteolytic pathway were 1.2- to 1.5-fold higher in HB than in PRE, meanwhile, the level of catalase from lysosomal proteolytic pathway was 1.2-fold higher in HB than in PRE. Consistent with our previous study (Yang CX, 2014. COMP BIOCHEM PHYS A. 176:26-31), proteomics showed that calpain proteolytic pathway did not change significantly in hibernation. Thus, suppression of myofibrillar proteolysis was likely responsible for preventing skeletal muscle atrophy during prolonged disuse in hibernation. | |||
TO cite this article:Hui Chang,Shan-Feng Jiang,Kai Dang, et al. iTRAQ-based quantitative proteomic analysis of myofibrillar contents and relevant proteolytic proteins in soleus muscle of hibernating Daurian ground squirrels[OL].[26 November 2015] http://en.paper.edu.cn/en_releasepaper/content/4665590 |
8. Rspo1/Wnt signaling molecules are sufficient to induce ovarian differentiation in the XY Medaka (Oryzias latipes) | |||
Linyan Zhou,Tapas Charkraborty,Yoshitaka Nagahama | |||
Biology 28 November 2014 | |||
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Abstract:In mammals, R-spondin1 (Rspo1), an activator of the Wnt/β-catenin signaling pathway, had been shown to lie upstream of female sex determination pathway. However, in non-mammalian species, the functions of Rspo1 in ovarian differentiation remain to be elusive. To further elucidate the functions of Rspo/Wnt signaling pathway in fish sex determination/differentiation, ectopic expression of Rspo1 gene in XY fish were carried out in a teleost fish, medaka (Oryzias latipes). Our results demonstrated that gain of function of Rspo1 in XY fish induces the sex reversal from male to female and further induce ovarian formation. Excessive Rspo1 expression could completely suppress the expression of male-specific genes and testicular differentiation. On the contrary, Rspo1 in XY individuals could stimulate the expression of female specific genes, activate female follicular/germ cell program, and induce the development female-specific secondary sexual characteristics. Both real-time PCR and in situ hybridization (ISH) analysis revealed that over-expression of Rspo1 could efficiently induce the up-regulation of ovary-dominant genes expression, including foxl2, figlα, cyp19a1a and β-catenin. On the contrary, expressions of testis-dominant genes, such as dmrt1, gsdf, cyp11b2, were completely inhibited in XY gonad with ectopic expression of Rspo1. Moreover, the XY female induced by Rspo1 over-expression are fertile to produce successive generation. Taken together, our results strongly suggested that Rspo1/Wnt signaling was sufficient to activate ovarian development in medaka whatever the genetic background is. | |||
TO cite this article:Linyan Zhou,Tapas Charkraborty,Yoshitaka Nagahama. Rspo1/Wnt signaling molecules are sufficient to induce ovarian differentiation in the XY Medaka (Oryzias latipes)[OL].[28 November 2014] http://en.paper.edu.cn/en_releasepaper/content/4620959 |
9. The evolution and origin of animal Toll-like receptor signaling pathway revealed by network-level molecular evolutionary analyses | |||
Xiaojun Song,Ping Jin,Sheng Qin,Liming Chen,Fei Ma | |||
Biology 24 March 2014 | |||
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Abstract:Genes carry out their biological functions through pathways in complex networks consisting of many interacting molecules. Studies on the effect of network architecture on the evolution of individual proteins will provide valuable information for understanding the origin and evolution as well as functional conservation of signaling pathways. However, the relationship between the network architecture and the individual protein sequence evolution is yet little known. In current study, we carried out network-level molecular evolution analysis on TLR (Toll-like receptor) signaling pathway, which plays an important role in innate immunity in insects and mammals, and we found that: 1) The selection constraint of genes was negatively correlated with its position along TLR signaling pathway; 2) all genes in TLR signaling pathway were highly conserved and underwent strong purifying selection; 3) the distribution of selective pressure along the pathway was driven by differential nonsynonymous substitution levels; 4) The TLR signaling pathway might present in a common ancestor of sponges and eumetazoa, and evolve via the TLR, IKK, I?B and NF-?B genes underwent duplication events as well as adaptor molecular enlargement, and gene structure and conservation motif of NF-?B genes shifted in their evolutionary history. Our results will improve our understanding on the evolutionary history of animal TLR signaling pathway as well as the relationship between the network architecture and the sequences evolution of individual protein. | |||
TO cite this article:Xiaojun Song,Ping Jin,Sheng Qin, et al. The evolution and origin of animal Toll-like receptor signaling pathway revealed by network-level molecular evolutionary analyses[OL].[24 March 2014] http://en.paper.edu.cn/en_releasepaper/content/4591159 |
10. Evolutionary Rate Patterns of Genes Involved in The Drosophila Toll and Imd Signaling Pathway | |||
Han Ming,Qin Sheng,Song Xiaojun,Li Yafang,Jin Ping,Chen Liming,Ma Fei | |||
Biology 24 March 2014 | |||
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Abstract:In this paper, we analyzed the molecular evolutionary patterns of genes in the Toll and Imd innate immune signaling pathways across six Drosophila genomes within the context of a functional network. Based on published literature, we identified 50 genes that are directly involved in the Drosophila Toll and Imd signaling pathways. Of those genes, only two (Sphinx1 and Dnr1) exhibited signals of positive selection. There existed a negative correlation between the strength of purifying selection and gene position within the pathway; the downstream genes were more conserved, indicating that they were subjected to stronger evolutionary constraints. Interestingly, there was also a significantly negative correlation between the rate of protein evolution and the number of regulatory microRNAs, implying that genes regulated by more miRNAs experience stronger functional constraints and therefore evolve more slowly. Taken together, our results suggested that both network architecture and miRNA regulation affect protein sequence evolution. These findings improve our understanding of the evolutionary patterns of genes involved in Drosophila innate immune pathways. | |||
TO cite this article:Han Ming,Qin Sheng,Song Xiaojun, et al. Evolutionary Rate Patterns of Genes Involved in The Drosophila Toll and Imd Signaling Pathway[OL].[24 March 2014] http://en.paper.edu.cn/en_releasepaper/content/4591122 |
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