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Background
Horizontal gene transfer (HGT) has been widely identified in complete prokaryotic genomes. However, the roles of HGT among members of a microbial community and in evolution remain largely unknown. With the emergence of metagenomics, it is nontrivial to investigate such horizontal flow of genetic materials among members in a microbial community from the natural environment. Because of the lack of suitable methods for metagenomics gene transfer detection, microorganisms from a low-complexity community acid mine drainage (AMD) with near-complete genomes were used to detect possible gene transfer events and suggest the biological significance.Results
Using the annotation of coding regions by the current tools, a phylogenetic approach, and an approximately unbiased test, we found that HGTs in AMD organisms are not rare, and we predicted 119 putative transferred genes. Among them, 14 HGT events were determined to be transfer events among the AMD members. Further analysis of the 14 transferred genes revealed that the HGT events affected the functional evolution of archaea or bacteria in AMD, and it probably shaped the community structure, such as the dominance of G-plasma in archaea in AMD through HGT.Conclusions
Our study provides a novel insight into HGT events among microorganisms in natural communities. The interconnectedness between HGT and community evolution is essential to understand microbial community formation and development.Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1720-0) contains supplementary material, which is available to authorized users. 相似文献985.
Xiang Luo Chaozhi Ma Yao Yue Kaining Hu Yaya Li Zhiqiang Duan Ming Wu Jinxing Tu Jinxiong Shen Bin Yi Tingdong Fu 《BMC genomics》2015,16(1)
Background
Harvest index (HI), the ratio of grain yield to total biomass, is considered as a measure of biological success in partitioning assimilated photosynthate to the harvestable product. While crop production can be dramatically improved by increasing HI, the underlying molecular genetic mechanism of HI in rapeseed remains to be shown.Results
In this study, we examined the genetic architecture of HI using 35,791 high-throughput single nucleotide polymorphisms (SNPs) genotyped by the Illumina BrassicaSNP60 Bead Chip in an association panel with 155 accessions. Five traits including plant height (PH), branch number (BN), biomass yield per plant (BY), harvest index (HI) and seed yield per plant (SY), were phenotyped in four environments. HI was found to be strongly positively correlated with SY, but negatively or not strongly correlated with PH. Model comparisons revealed that the A–D test (ADGWAS model) could perfectly balance false positives and statistical power for HI and associated traits. A total of nine SNPs on the C genome were identified to be significantly associated with HI, and five of them were identified to be simultaneously associated with HI and SY. These nine SNPs explained 3.42 % of the phenotypic variance in HI.Conclusions
Our results showed that HI is a complex polygenic phenomenon that is strongly influenced by both environmental and genotype factors. The implications of these results are that HI can be increased by decreasing PH or reducing inefficient transport from pods to seeds in rapeseed. The results from this association mapping study can contribute to a better understanding of natural variations of HI, and facilitate marker-based breeding for HI.Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1607-0) contains supplementary material, which is available to authorized users. 相似文献986.
987.
Yao YW Shi Y Jia ZF Jiang YH Gu Z Wang J Aljofan M Sun ZG 《Histochemistry and cell biology》2011,136(2):205-215
To investigate the biological significance of ubiquitin carboxyl-terminal hydrolase L1 (UCH-L1) involvement in oocyte maturation,
we screened for proteins that bound to UCH-L1 in mouse ovaries, and we found that the prostate tumor overexpressed-1 (PTOV1)
protein was able to bind to UCH-L1. PTOV1 is highly expressed in prostate cancers and considered as a potential marker for
carcinogenesis and the progress of prostate cancer. It was reported that PTOV1 plays an important role in cell cycle regulation,
but its role in mammalian oocyte development and meiosis is still unclear. In this paper, it was found that the expression
levels of PTOV1 in mouse ovaries progressively increased from prepubescence to adulthood. And we found by immunohistochemistry
that PTOV1 spreaded in both the cytoplasm and nuclei of oocytes during prepuberty, but in normal adult mouse oocytes, it concentrated
not only in nuclei but also on the plasma membrane, though in some oocytes with abnormal shapes, PTOV1 did not display the
typical distribution patterns. In granulosa cells, however, it was found to locate in the cytoplasm at all the selected ages.
In postnatal mouse ovaries (28 days), estradiol treatment induced the adult-specific distribution pattern of PTOV1 in oocytes.
In addition, UCH-L1 was shown to be associated with CDK1, which participated in the regulation of cell cycle and oocyte maturation.
Therefore, we propose that the distribution changes of PTOV1 are age-dependent, and significant for mouse oocyte development
and maturation. Moreover, the discovery that PTOV1 is associated with UCH-L1 in mouse oocytes supports the explanations for
that UCH-L1 is involved in oocyte development and maturation, especially under the regulation of estrogen. 相似文献
988.
Ultrasensitive electrochemical aptasensor for thrombin based on the amplification of aptamer-AuNPs-HRP conjugates 总被引:1,自引:0,他引:1
Successful development of an ultrasensitive and highly specific electrochemical aptasensor for thrombin based on amplification of aptamer-gold nanoparticles-horseradish peroxidase (aptamer-AuNPs-HRP) conjugates was reported. In this electrochemical protocol, aptamer1 (Apt1) was immobilized on core/shell Fe(3)O(4)/Au magnetic nanoparticles (AuMNPs) and served as capture probe. Aptamer2 (Apt2) was dual labeled with AuNPs and HRP and used as detection probe. In the presence of thrombin, the sandwich format of AuMNPs-Apt1/thrombin/Apt2-AuNPs-HRP was fabricated. Remarkable signal amplification was realized by taking the advantage of AuNPs and catalytic reactions of HRP. Other proteins, such as human serum albumin, lysozyme, fibrinogen, and IgG did not show significant interference with the assay for thrombin. Linear response to thrombin concentration in the range of 0.1-60 pM and lower detection limit down to 30 fM (S/N=3) was obtained with the proposed method. This electrochemical aptasensor is simple, rapid (the whole detection period for a thrombin sample is less than 35 min), sensitive and highly specific, it shows promising potential in protein detection and disease diagnosis. 相似文献
989.
Xu Yu Chen Yao Dong Qi Jian He Wei Zheng Zhang De Li Wang Jin Dong Feng Bing Chun Gan 《World journal of microbiology & biotechnology》2011,27(3):495-503
Fifty-two endophytic fungi strains with different colony morphologies were isolated from stems, leaves and roots of Huperzia serrata (Thunb. ex Murray) Trevis. collected from Bawangling Reserve of Hainan Province in southern China. They were identified mainly
based on rDNA ITS sequences and phylogenetic analysis. The results showed that all strains belonged to four classes, i.e.
Sordariomycetes (92.31%), Dothideomycetes (3.85%), Pezizomycetes (1.92%) and Agaricomycetes (1.92%). Forty-seven strains were identified at the genus level, including Glomerella (Colletotrichum), Hypocrea (Trichoderma), Pleurostoma, Chaetomium, Coniochaeta (Lecythophora), Daldinia, Xylaria, Hypoxylon,
Nodulisporium, Cazia and Phellinus. As to the other five strains, three were identified at the order level and two at the family level, indicating that a great
diversity of fungi taxa exists in H. serrata. Most isolated strains belonged to the genus of Glomerella (Colletotrichum) and Hypoxylon, twenty-one from Glomerella and its anamorph Colletotrichum (42.3% of total isolated strains) and ten from Hypoxylon (19.2% of total isolated strains). Pleurostoma, Chaetomium, Coniochaeta (Lecythophora), Daldinia, Xylaria, Hypoxylon,
Nodulisporium, Cazia and Phellinus were reported as endophytic fungi isolated from H. serrata for the first time. 相似文献
990.
Meizhen Wang Guiqin Yang Xin Wang Yanlai Yao Hang Min Zhenmei Lu 《World journal of microbiology & biotechnology》2011,27(7):1633-1640
Two novel nicotine-degrading bacterial strains were isolated from tobacco waste and identified as Acinetobacter sp. TW and Sphingomonas sp. TY based on morphology, physiological and biochemical tests, Biolog analysis and 16S rDNA sequencing. The 16S rDNA sequences
have been deposited in GenBank under the accession numbers FJ753401 for TW and FJ754274 for TY. The best culture conditions
for nicotine degradation were 25–37°C and pH 7.0–8.0 for strain TW and 25–30°C and pH 6.0–7.0 for strain TY. Under the best
conditions, the cell growth and nicotine-degradation kinetics of the two isolates were assessed, and 1.0 g/l nicotine was
completely degraded within 12 and 18 h for TW and TY, respectively. Moreover, the presence of four widely-used commercial
neonicotinoid insecticides in the medium had no effects on nicotine degradation by TW; among the four tested neonicotinoids,
only thiamethoxam significantly delayed nicotine degradation by TY. TW and TY were also able to degrade selected neonicotinoids.
This is the first report of nicotine degradation by Acinetobacter sp. and Sphingomonas sp. This study showed that these two newly isolated bacteria may be suitable for the disposal of tobacco waste and the reduction
of nicotine in tobacco leaves. 相似文献