2012, 33(6): 574-585. doi: 10.3724/SP.J.1141.2012.06574
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.
2012, 33(E5-6): .
2014, 35(1): 20-32. doi: 10.11813/j.issn.0254-5853.2014.1.020
Garra imberba is widely distributed in China. At the moment, both Garra yiliangensis and G. hainanensis are treated as valid species, but they were initially named as a subspecies of G. pingi, a junior synonym of G. imberba. Garra alticorpora and G. nujiangensis also have similar morphological characters to G. imberba, but the taxonomic statuses and phylogenetic relationships of these species with G. imberba remains uncertain. In this study, 128 samples from the Jinshajiang, Red, Nanpanjiang, Lancangjiang, Nujiang Rivers as well as Hainan Island were measured while 1 mitochondrial gene and 1 nuclear intron of 24 samples were sequenced to explore the phylogenetic relationship of these five species. The results showed that G. hainanensis, G. yiliangensis, G. alticorpora and G. imberba are the same species with G. imberba being the valid species name, while G. nujiangensis is a valid species in and of itself.
Fish Production, Water Quality and Bacteriological Parameters of Koi Carp Ponds Under Live-food and Manure Based Management Regimes
2008, 29(2): 165-173. doi: 10.3724/SP.J.1141.2008.02165
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.
2012, 33(6): 566-573. doi: 10.3724/SP.J.1141.2012.06566
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).
2003, 24(4): 311-317.
The primary goal of all semen analyses is to accurately determine the fertilizing potential of semen samples rapidly.Since a spermatozoon must possess many attributes in order to fertilize an oocyte,the only way that we can more precisely predict the fertility is to develop unbiased assays that measure several sperm traits simultaneously.Conventional laboratory assays of spermatozoa,using subjective method,many are time consuming,and are necessarily conducted on samples of relatively small size,fall short of predicting the sperm function.Flow cytometry (FCM) permits us to objectively measure thousands of sperm for multiple characteristics in a short time with minimum preparation.The applications of FCM to evaluation of semen quality including sperm plasma membrane integrity,acrosome status,chromatin structure,mitochondrial activity as well as apoptosis etc,provide us valuable information regarding sperm function.FCM offers powerful tools and exciting opportunities for improving our ability to accurately evaluate semen quality with new fluorescent probes and techniques continuously being developed.
2014, 35(4): 249-352.
2014, 35(6): 485-491. doi: 10.13918/j.issn.2095-8137.2014.6.485
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.
2014, 35(1): 1-80.
2004, 25(4): 356-362.
A limitation in advancing the study of HIV-1 is the lack of a suitable small animal model system that allows for HIV-1 infection to be monitored.A mouse model of AIDS would be very useful because of it practicality and the ready availability of knowledge,reagents and immunogenetics.SCID-hu (Thy/Liv) mouse model,in which human fetal thymus and liver tissue are co-implanted into severe combined immunodeficient mice and resulting in a functional human hematopoietic organ (Thy/Liv),recapitulates the effects of HIV-1 infection in the human thymus.SCID-hu (Thy/Liv) mice are attractive and well-established small animal models for the study of HIV-1 infection in vivo.The humanized SCID mouse model would be served as valuable tools for in vivo studying pathogenesis of HIV,analysis of candidate anti-HIV drugs and vaccines prior to their clinical evaluation in human.
2008, 29(2): 203-211. doi: 10.3724/SP.J.1141.2008.02203
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.
2014, 35(3): 161-248.
Expression of Human Semenogelin I-52 and Antibacterial Activity Investigation of Recombinant Peptide
2008, 29(2): 139-144. doi: 10.3724/SP.J.1141.2008.02139
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.
Systematics of Perca Species Based on Multivariate Morphometrics and Mitochondrial Cytochrome b Gene Variation Analysis
2008, 29(2): 113-120. doi: 10.3724/SP.J.1141.2008.02113
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.
2004, 25(1): 73-80.
In the 1960s,the neutral theory proposed by Kimura caused an unprecedented challenge to the classical Darwin s theory of natural selection.However,recent advances in evolutionary genetics have provided a great deal of evidence on the role played by natural selection at the DNA level.These progresses have been stemmed from the appearance of enormous DNA sequence data of populations and genomes as well as the development of theoretical population genetics.There are mainly two kinds of approaches to detect selection at the DNA level:intraspecific polymorphism tests and interspecific divergence tests.The former one is represented by Tajima s (1989) D test while the latter one is based on the principle that the intraspecific polymorphism should be consistent with the interspecific divergence under neutrality.These methods are usually called "neutrality tests" because the neutrality hypothesis is taken as the null hypothesis in the tests.They are important tools not only in solving the basic theoretical questions in evolutionary biology but also in interpreting data and results obtained in the studies of human genetics and bioinformatics.In this paper,we shall review the progresses in detecting natural selection at the DNA sequence level and introduce the basis and application of several widely used tests.
Sinocyclocheilus xichouensis, a new species of golden-line fish from the Red River drainage in Yunnan, China (Teleostei: Cypriniformes)
2013, 34(4): 368-373. doi: 10.11813/j.issn.0254-5853.2013.4.0368
In the present study, a new species of the genus Sinocyclocheilus Fang 1936, Sinocyclocheilus xichouensis, was described from the Ganhaizi tributary of Chouyang River, Red River drainage, located in southeast Yunnan, China. This species has normal eyes and a strong dorsal spine with serrations on the lower 3/5 part. In general, this species is similar in morphology to S. macrophthalmus, S. guishanensis, S. angustiporus, S. lateristritus, S. qiubeiensis, S. grahami, S. qujingensis, S. maculatus and S. purpureus distributed in the Nanpanjiang River, and S. qiubeiensis distributed in the Red River. It is distinguished from S. macrophthalmus by possessing fewer than 9 gill rakers. However, S. xichouensis can be distinguished from S. guishanensis by its interorbital width/SL of 8.1~9.9%, rostral barbels extended to posterior margin of eye and maxillary barbels extended to posterior preopercular. It is distinct from S. lateristritus by dorsal-fin origin opposite of pelvic fin origin, with no a black stripe along the lateral line. It is distinguished from S. grahami by 74~88 lateral-line scales, 20 scale rows above the lateral line, and 16 scale rows below the lateral line. It is distinguished from S. qujingensis by a curved lateral line, 74-88 lateral-line scales, 48 circumpeduncular scales. It can be distinguished from S. yimenensis by the ratio of predorsal length, dorsal-fin base length, preanal length, anal fin length, prepectoral length, caudal-peduncle length and lower jaw length to SL, 47.1%-53.7%, 12.8%-15.8%, 66.0%-71.0%, 13.7%-17.1%, 26.0%-29.5%, 19.3%-24.7%, 4.7%-7.0%, respectively. It is distinguished from S. maculatus and S. purpureus by possession of lateral line and scaled body and distinguished from S. angustiporus and S. qiubeiensis by 35~39 predorsal scales, 6 gill rakers, and interorbital width/SL of 8.1%-9.9%.