Metagenome, a term first dubbed by Handelsman in 1998 as “the genomes of the total microbiota found in nature”, refers to sequence data directly sampled from the environment (which may be any habitat in which microbes live, such as the guts of humans and animals, milk, soil, lakes, glaciers, and oceans). Metagenomic technologies originated from environmental microbiology studies and their wide application has been greatly facilitated by next-generation high throughput sequencing technologies. Like genomics studies, the bottle neck of metagenomic research is how to effectively and efficiently analyze the gigantic amount of metagenomic sequence data using the bioinformatics pipelines to obtain meaningful biological insights. In this article, we briefly review the state-of-the-art bioinformatics software tools in metagenomic research. Due to the differences between the metagenomic data obtained from whole genome sequencing (i.e., shotgun metagenomics) and amplicon sequencing (i.e., 16S-rRNA and gene-targeted metagenomics) methods, there are significant differences between the corresponding bioinformatics tools for these data; accordingly, we review the computational pipelines separately for these two types of data.
To test the effectiveness of introducing live zooplankton against direct manuring in ornamental fish ponds upon their survival and production, larvae of koi carp, Cyprinus carpio L., were cultured for 11 weeks in earthen ponds maintained according to four management regimes: (1) live zooplankton fed to carp larvae (LF); (2) direct fertilization with poultry manure (PM); (3) direct fertilization with cowdung (CD); and (4) a control treatment (C). There were three replicates for each treatment. The growth of heterotrophic bacteria and pathogenic microorganisms like Aeromonas sp. and Pseudomonas sp. were also examined in response to pond management. Values of dissolved oxygen were significantly higher (P<0.05) in the water of LF ponds, compared to other treatments, while the PM and CD treatments recorded were significantly higher (P<0.05) values of PO4 – P, NH4 – N, NO3 – N, NO2 – N, specific conductivity, alkalinity, and BOD, compared to the LF and C treatments. The percentages of organic carbon and total nitrogen in the bottom sediments were higher in the PM and CD treatments compared to LF (P<0.05). Average counts of heterotrophic bacteria in the water of PM and CD ponds were significantly higher than other treatments (P<0.05). The development of Aeromonas sp. and Pseudomonas sp. were significantly higher (P<0.05) in the PM and CD treatments. Weight gain of koi carp stocked in LF was significantly higher (P<0.05) than that of fish in the other treatments. There was a significant difference in the survival rate of koi carp among the treatments ranging from 67.21% in C to 90.11% in LF. The results suggest that raising koi carp larvae in ponds and feeding them exogenously with zooplankton would support high rates of survival and production through maintenance of better water quality and greater abundance of zooplankton in the system. Significantly lower abundance of Aeromonas sp. and Pseudomonas sp. in the LF treatment considerably lowered any possibility of occurrence of bacterial disease.
Coxsackie virus A16 (CA16) is commonly recognized as one of the main human pathogens of hand-foot-mouth disease (HFMD). The clinical manifestations of HFMD include vesicles of hand, foot and mouth in young children and severe inflammatory CNS lesions. In this study, experimentally CA16 infected tree shrews(Tupaia belangeri) were used to investigate CA16 pathogenesis. The results showed that both the body temperature and the percentages of blood neutrophilic granulocytes / monocytes of CA16 infected tree shrews increased at 4-7 days post infection. Dynamic distributions of CA16 in different tissues and stools were found at different infection stages. Moreover, the pathological changes in CNS and other organs were also observed. These findings indicate that tree shrews can be used as a viable animal model to study CA16 infection.
Bird diversity was surveyed in five urban parks of Guangzhou from January 1999 to April 2000, and from July 2006 to June 2007, using a transect line method. A total of sixty-four bird species were recorded. Japanese White-eye (Zosterops japonica), Chinese Bulbul (Pycnonotus sinensis), and Black-crowned Night Heron (Nycticorax nyctinorax) were dominant species. Residents, winter visitors and summer visitors accounted for 64.1%, 26.6% and 7.8% of recorded bird species, respectively. The greatest number of species was recorded in September (31), the least was recorded in July (20) and November (20). The mean encounter rates of birds was 65±;5 ind./h (±SE), with the highest in March (98±29 ind./h) and lowest in January (35±11 ind./h). There was fluctuation, but it did not differ significantly between months (F 11,48=1.35, P= 0.226). There were a greater number of migratory species in April, September and December. Encounter rates of migratory birds significantly differed between months (F 11，48=3.098，P=0.003). Bird richness differed among the five parks and significantly and positively correlated with the park area (R=0.905, P=0.035), with S=11.02 A0.28 (S：bird species richness, A：park area). This meant that a greater number of bird species occurred in larger parks. Parks with an area of about 65 hm2 were better for avian diversity conservation and land use in Guangzhou.
Nucleotide sequence coding for SgI-52 with amino acid residues of 85-136 form mature human semenogelin I was amplified by PCR technique from the cDNA of a human seminal vesicle. The obtained PCR products were inserted into vector pMAL-p2X. The constructed expression vector of pMAL-p2X/SgI-52 was transformed into Escherichia coli DH5α. Fusion protein was expressed in the periplasma of the E. coli DH5αafter IPTG inducement. Recombinant SgI-52 was purified after factor X cleavage and a ultrafiltering process. MALDI-TOF- MS results indicated that the purified recombinant SgI-52 was the target peptide. Recombinant SgI-52 showed antibacterial activities on E. coli ATCC 25922 and E. coli ML-35P with MIC values of 32.45 and 46.30 μg/mL, respectively. Our results and other relevant works suggested that different human semenogelin I degradation fragments during the liquefaction might have various biological functions and deserve to be investigated further.
The possibility of ghrelin expressed in sheep oocytes and pre-implantation embryos produced in vivo was investigated in this study. The observed ghrelin immunoreactivity of oocytes and embryos at all stages was predominantly in the cytoplasm. Relative real-time reverse-transciptase (RT)-PCR experiments confirmed that the ghrelin mRNA levels varied depending on the developmental stage, with the highest expression in the blastocyst, metaphase II (MII) oocytes, 2- and 8-cell stages had a significantly higher expression in the germinal vesicle (GV) oocytes, 4-stage and morula. Dynamic changes and the persistent presence of the ghrelin signaling system within oocytes and pre-implantation embryos opens up the possibility of a potential regulatory role of this novel molecule during oocyte maturation and embryonic development.
This paper investigated the classification of the genus Perca based on the 32 multivariate morphometrics and the 1 134 bp sequences of mitochondrial cytochrome b (Cyt b) gene. The result of multivariate morphometric analyses showed that the distance between P. fluviatilis and P. schrenki, between P. schrenki and P. flavescens, between P. fluviatilis and P. flavescens was 0.15, 0.14, 0.09, respectively. Perca fluviatilis and P. flavescens were much more similar in morphology, and there was a remarkable difference between P. schrenki and the two other species. In the scatter-plot figure based on principal components 1 to 2, there was an overlapping section between P. fluviatilis and P. flavescens, but there was no overlapping section between P. schrenki and the two others. In the analysis of mitochondrial cytchrome b gene, the percentage nucleotide sequence divergence between P. fluviatilis and P. schrenki, between P. schrenki and P. flavescens, between P. fluviatilis and P. flavescens was 13.08%, 10.68%, 11.47% respectively. The sequence divergences among the three Perca species were within interspecific divergence. Molecular phylogenetic trees were constructed based on the sequences of 20 samples with maximum parsimony (MP), neighbor-joining (NJ) and Maximum likelihood methods. The topological structures of the three trees were consistent, and they all showed that the relationship between the P. schrenki and P. flavescens was much closer than that between P. fluviatilis and P. flavescens. From the genetic divergence of the Cyt b gene and the isolation in geographic distribution, we further concluded that P. fluviatilis and P. flavescens were different species. The genus Perca therefore, includes three species, P. fluviatilis, P.schrenki and P. flavescens.
According to the distribution of Phrynocephalus vlangalii hongyuanensis in Zoige Wetland，three geographic units: Zoige Xiaman (XM)，Hongyuan (HY)，both in Sichuan Province and Maqu (MQ) in Gansu Province were defined. We used molecular methods to reveal these unit’s genetic variation and diversity. A 785bp fragment of the mtDNA ND4-tRNAleu was determined from 72 samp1es in seven populations of P. vlangalii hongyuanensis. Seven variable nucleotide sites and nine haplotypes were identified in the 785bp fragments. As a whole，the haplotype diversity was high (0.806±0.024)，but the nucleotide diversity was low (0.00231±0.00016). In a single population，MQa，MQb and XMb had very low genetic diversities，and XMc had a much higher one. The Kimura 2-parameter distances among all the populations were small (0.001-0.005)，and the distance between MQa and XMa was the greatest. Analysis of molecular variance (AMOVA) showed that the three units were distinctly different (P<0.01)，and 62.61% of the total genetic diversity was attributable to variation among units. There were 3 haplotypes shared among XM and HY，and no geographic clustering was observed except MQ from the TCS network. The results from the mismatch distribution analysis and Fu’s Fs test (Fs=－2.21937) implied that there might be a recent population expansion in the XM unit，and this may be the reason why XM had a high haplotype diversity but a low nucleotide diversity. We estimate that the MQ and XMb have lower diversities because of some very recent geographic events，such as the formation of the Yellow river’s upriver and the Zoige Wetland. Although they are distinctly different，not enough time has passed for them to have diverged a great genetic distance.
Mitochondria are old organelles found in most eukaryotic cells. Due to its rapid mutation ratio, mitochondrial DNA (mtDNA) has been widely used as a DNA marker in molecular studies and has long been suggested to undergo neutral evolution or purifying selection. Mitochondria produces 95% of the adenosine triphosphate (ATP) needed for locomotion, and heat for thermoregulation. Recent studies had found that mitochondria play critical roles in energy metabolism, and proved that functional constraints acting on mitochondria, due to energy metabolism and/or thermoregulation, influence the evolution of mtDNA. This review summarizes mitochondrial genome composition, evolution, and its applications in molecular evolution studies (reconstruction of species phylogenesis, the relationship between biological energy metabolism and mtDNA evolution, and the mtDNA codon reassignment influences the adaptation in different creatures).
The sequences of mitochondrial control region (CR) of Macroclemys temminckii, Chelydra serpentina and Platysternon megacephalum were obtained using PCR and sequencing techniques, with gene-specific primers, based on the CR and its flanking sequences from other species. The CR lengths of the three species were 1089 bp, 1124 bp and 1119 bp respectively, and the base composition of A+T were 68.97%, 69.34% and 69.44% respectively. One fragment of (TA)20 microsatellite was found in M. temminckii; one fragment of (TATAT) 13 direct tandem repeats followed by (TA)15 microsatellites were found in C.serpentina; and one fragment of (AGTATGTTAT)4 direct tandem repeats followed by (GTTGTTATATAACATAT) 13 repeats were found in P. megacephalum. The distribution of mtDNA microsatellites in tortoises was discussed based on the CR sequences of the three species and other six tortoises published in GenBank. The result suggested that all the nine tortoises have microsatellites, and there are obvious differences both at the site and the sequences.
The delimitation between Tylototriton shanjing and T. verrucosus was not clear. Forty individuals of T. verrucosus and T. shanjing were collected from fourteen localities in Southwest China and 753?bp of partial mitochondrial Cyt b gene sequence were sequenced. Molecular phylogenetic trees of T. verrucosus group were reconstructed using neighbor-joining, maximum parsimony and Bayesian inference methods. Pairwise sequence comparisons to determine the amount of variation were performed using MEGA 3.0 software. According to the results of phylogeny analysis and Kimura 2-parameter distance, the species validities were evaluated. The results showed that: (1) the T. shanjing did not form a monophyletic group; (2) the genetic distance was low between T. shanjing and T. verrucosus, it was only 1.2% on average. Therefore, T. shanjing as a valid species is not supported and can be argued to be a synonym of T. verrucosus. According to our phylogenetic tree, the genetic divergences and geographic distribution, T. verrucosus' distribution in the Yunnan Province can be divided into three geographic groups, i.e. the Pianma group, the Middle and West Yunnan group and the Southeast Yunnan group.
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