To expand knowledge on microbial communities of various metal-rich levels of mine drainage environments in Anhui province, China, the archaeal and bacterial diversities were examined using a PCR-based cloning approach...To expand knowledge on microbial communities of various metal-rich levels of mine drainage environments in Anhui province, China, the archaeal and bacterial diversities were examined using a PCR-based cloning approach. Eight acid mine water samples were collected from five areas in Tongling. Phylogenetic analyses revealed that bacteria mainly fell into ten divisions, which were Betaproteobacteria, Gammaproteobacteria, Alphaproteobacteria, Deinococcus-Thermus, Nitrospira, Firmicutes, Actinobacteria, Deltaproteobacteria, Bacteroidetes, Chloroflexi. Archaea fell into three phylogenetic divisions, Thermoplasma, Ferroplasma and Thermogymnomonas. The unweighted pair group method with arithmetic mean（UPGMA） cluster analysis based on the microbial communities’ compositions revealed that five samples shared similarity with the dominance of Meiothermus and Thermomonas. Two samples had the preponderant existence of Acidithiobacillus and Leptospirillum. The remaining sample owned higher microbial communities’ diversity with the Shannon-Weaver H up to 2.91. Canonical correlation analysis（CCA） suggested that microbial community structures had great association with p H and the concentration of Hg2＋, Pb2＋, Fe3＋, Cl-, SO2- 4in water.展开更多
Histological development of Japanese flounder Paralichthys olivaceus larval skin and ultrastructural difference of skin between reared normal and malpigmented Japanese flounder were studied with light microscopy (LM) ...Histological development of Japanese flounder Paralichthys olivaceus larval skin and ultrastructural difference of skin between reared normal and malpigmented Japanese flounder were studied with light microscopy (LM) and transmission electron microscopy (TEM). The results show that the skin develops slowly before the metamorphosis, while at the onset of metamorphosis, the skin develops quickly and becomes complete in structure till about 50 d after being hatched. Ultrastructural observation on the normal and malpigmented skins shows that the iridophore and melanophore are adjacent to each other. Profile and structure of the two kinds of pigment cells are more complete in the skin of normal ocular side than in the skin of pigmented blind side. The ultrastructure of typical chloride cell was observed in the skin of Japanese flounder larvae for the first time.展开更多
The structural evolution of the chars from pyrolysis of biomass components （cellulose, hemicellulose and lignin） in a xenon lamp radiation reactor was investigated. The elemental composition analysis showed that the...The structural evolution of the chars from pyrolysis of biomass components （cellulose, hemicellulose and lignin） in a xenon lamp radiation reactor was investigated. The elemental composition analysis showed that the C content increased at the expense of H and O contents during the chars formation. The values of AH/C/ZSO/c for the formation of cellulose and hemicellulose chars were close to 2, indicating that dehydration was the dominant reaction. Meanwhile, the value was more than 3 for lignin char formation, suggesting that the occurrence of demethoxylation was prevalent. FTIR and XRD analyses further disclosed that the cellulose pyrolysis needed to break down the stable crystal structure prior to the severe depolymerization. As for hemicellulose and lignin pyrolysis, the weak branches and linkages decomposed firstly, followed by the major decomposition. After the devolatilization at the main pyrolysis stage, the three components encountered a slow carbonization process to form condensed aromatic chars. The SEM results showed that the three components underwent different devolatilization behaviors, which induced various surface mornhologies of the chars.展开更多
Chilo iridescent virus (CIV) is the type species for genus Iridovirus, and belongs to the family Iridoviridae. Since the discovery of CIV in 1966, many attempts were made to elucidate the viral genome structure. The v...Chilo iridescent virus (CIV) is the type species for genus Iridovirus, and belongs to the family Iridoviridae. Since the discovery of CIV in 1966, many attempts were made to elucidate the viral genome structure. The virions contain a single linear ds DNA molecule that is circularly permuted and terminally redundant. The genome of CIV has been entirely sequenced. The CIV virion consists of an unusual three-layer structure containing an outer proteinaceous capsid, an intermediate lipid membrane, and a core DNA-protein complex containing the genome. CIV has a broad host spectrum and has, in general, a limited mortality effect on its hosts. Up to now there have been several studies about CIV describing its structure, ecology, and molecular biology. In this review study we present all these studies together to describe the CIV.展开更多
With the rapid accumulation of high-throughput metagenomic sequencing data,it is possible to infer microbial species relations in a microbial community systematically.In recent years,some approaches have been proposed...With the rapid accumulation of high-throughput metagenomic sequencing data,it is possible to infer microbial species relations in a microbial community systematically.In recent years,some approaches have been proposed for identifying microbial interaction network.These methods often focus on one dataset without considering the advantage of data integration.In this study,we propose to use a similarity network fusion(SNF)method to infer microbial relations.The SNF efficiently integrates the similarities of species derived from different datasets by a cross-network diffusion process.We also introduce consensus k-nearest neighborhood(Ck-NN)method instead of k-NN in the original SNF(we call the approach CSNF).The final network represents the augmented species relationships with aggregated evidence from various datasets,taking advantage of complementarity in the data.We apply the method on genus profiles derived from three microbiome datasets and we find that CSNF can discover the modular structure of microbial interaction network which cannot be identified by analyzing a single dataset.展开更多
Protein thermostability is an inherent characteristic of proteins from thermophilic microorganisms,and therefore enables these organisms to survive at extreme temperatures.Although it is well-known that thermostable p...Protein thermostability is an inherent characteristic of proteins from thermophilic microorganisms,and therefore enables these organisms to survive at extreme temperatures.Although it is well-known that thermostable proteins are critical for the growth of thermophilic organisms,the structural basis of protein thermostability is not yet fully understood.The histidine-containing phosphocarrier (HPr) protein,a phosphate shuttle protein in the phosphoenolpyruvate-dependent sugar transport system (PTS) of bacterial species,is an ideal model for investigating protein thermostability with respect to its small size and deficiency in disulphide bonds or cofactors.In this study,the HPr protein from Thermoanaerobacter tengcongensis (TtHPr) is cloned and purified.Crystal structure with good quality has been determined at 2.3 resolution,which provides a firm foundation for exploring the thermostable mechanism.However,it shows that the crystal structure is conserved and no clue can be obtained from this single structure.Furthermore,detailed comparison of sequence and structure with the homologs from mesoor thermophilic bacteria shows no obvious rule for thermostability,but the extra salt-bridge existing only in thermophilic bacteria might be a better explanation for thermostability of HPr.Thus,mutations are performed to interrupt the salt-bridge in HPrs in thermophilic bacteria.Using site-directed mutations and the circular dichroism method,thermostability is evaluated,and the mutational variations are shown to have a faster denaturing rate than for wild-type viruses,indicating that mutations cause instability in the HPrs.Understanding the higher-temperature resistance of thermophilic and hyperthermophilic proteins is essential to studies on protein folding and stability,and is critical in engineering efficient enzymes that can work at a high temperature.展开更多
Researchers hope that establishing a notion of proximity using topology will help to clarify the biological processes underlying the evolution of living organisms. The simple model presented here, using RNA shapes, ca...Researchers hope that establishing a notion of proximity using topology will help to clarify the biological processes underlying the evolution of living organisms. The simple model presented here, using RNA shapes, can carry over to more general and complex genotype-phenotype systems. Proximity is an important component of continuity, in both real-world and topological terms. Consequently, phenotype spaces provide an appropriate setting for modeling and investigating continuous and discontinuous evolutionary change.展开更多
In this paper, we present a method for constructing a Dulac function for mathematical models in population biology, in the form of systems of ordinary differential equations in the plane.
基金Project(41171418)supported by the National Natural Science Foundation of China
文摘To expand knowledge on microbial communities of various metal-rich levels of mine drainage environments in Anhui province, China, the archaeal and bacterial diversities were examined using a PCR-based cloning approach. Eight acid mine water samples were collected from five areas in Tongling. Phylogenetic analyses revealed that bacteria mainly fell into ten divisions, which were Betaproteobacteria, Gammaproteobacteria, Alphaproteobacteria, Deinococcus-Thermus, Nitrospira, Firmicutes, Actinobacteria, Deltaproteobacteria, Bacteroidetes, Chloroflexi. Archaea fell into three phylogenetic divisions, Thermoplasma, Ferroplasma and Thermogymnomonas. The unweighted pair group method with arithmetic mean（UPGMA） cluster analysis based on the microbial communities’ compositions revealed that five samples shared similarity with the dominance of Meiothermus and Thermomonas. Two samples had the preponderant existence of Acidithiobacillus and Leptospirillum. The remaining sample owned higher microbial communities’ diversity with the Shannon-Weaver H up to 2.91. Canonical correlation analysis（CCA） suggested that microbial community structures had great association with p H and the concentration of Hg2＋, Pb2＋, Fe3＋, Cl-, SO2- 4in water.
基金funded by the NNSF of China(No.30070593)SNSF(No.Y2002D10).
文摘Histological development of Japanese flounder Paralichthys olivaceus larval skin and ultrastructural difference of skin between reared normal and malpigmented Japanese flounder were studied with light microscopy (LM) and transmission electron microscopy (TEM). The results show that the skin develops slowly before the metamorphosis, while at the onset of metamorphosis, the skin develops quickly and becomes complete in structure till about 50 d after being hatched. Ultrastructural observation on the normal and malpigmented skins shows that the iridophore and melanophore are adjacent to each other. Profile and structure of the two kinds of pigment cells are more complete in the skin of normal ocular side than in the skin of pigmented blind side. The ultrastructure of typical chloride cell was observed in the skin of Japanese flounder larvae for the first time.
基金Supported by the National Natural Science Foundation of China(51276166)the National Basic Research Program of China(2013CB228101)the National Science and Technology Supporting Plan Through Contract(2015BAD15B06)
文摘The structural evolution of the chars from pyrolysis of biomass components （cellulose, hemicellulose and lignin） in a xenon lamp radiation reactor was investigated. The elemental composition analysis showed that the C content increased at the expense of H and O contents during the chars formation. The values of AH/C/ZSO/c for the formation of cellulose and hemicellulose chars were close to 2, indicating that dehydration was the dominant reaction. Meanwhile, the value was more than 3 for lignin char formation, suggesting that the occurrence of demethoxylation was prevalent. FTIR and XRD analyses further disclosed that the cellulose pyrolysis needed to break down the stable crystal structure prior to the severe depolymerization. As for hemicellulose and lignin pyrolysis, the weak branches and linkages decomposed firstly, followed by the major decomposition. After the devolatilization at the main pyrolysis stage, the three components encountered a slow carbonization process to form condensed aromatic chars. The SEM results showed that the three components underwent different devolatilization behaviors, which induced various surface mornhologies of the chars.
文摘Chilo iridescent virus (CIV) is the type species for genus Iridovirus, and belongs to the family Iridoviridae. Since the discovery of CIV in 1966, many attempts were made to elucidate the viral genome structure. The virions contain a single linear ds DNA molecule that is circularly permuted and terminally redundant. The genome of CIV has been entirely sequenced. The CIV virion consists of an unusual three-layer structure containing an outer proteinaceous capsid, an intermediate lipid membrane, and a core DNA-protein complex containing the genome. CIV has a broad host spectrum and has, in general, a limited mortality effect on its hosts. Up to now there have been several studies about CIV describing its structure, ecology, and molecular biology. In this review study we present all these studies together to describe the CIV.
基金supported in part by US National Science Foundation,Division of Industrial Innovation and Partnerships(1160960 and 1332024)Computing and Communication Foundations(0905291)+2 种基金National Natural Science Foundation of China(90920005,61170189)the Twelfth Five-year Plan of China(2012BAK24B01)National Social Science Funds of China(12&2D223,13&ZD183)
文摘With the rapid accumulation of high-throughput metagenomic sequencing data,it is possible to infer microbial species relations in a microbial community systematically.In recent years,some approaches have been proposed for identifying microbial interaction network.These methods often focus on one dataset without considering the advantage of data integration.In this study,we propose to use a similarity network fusion(SNF)method to infer microbial relations.The SNF efficiently integrates the similarities of species derived from different datasets by a cross-network diffusion process.We also introduce consensus k-nearest neighborhood(Ck-NN)method instead of k-NN in the original SNF(we call the approach CSNF).The final network represents the augmented species relationships with aggregated evidence from various datasets,taking advantage of complementarity in the data.We apply the method on genus profiles derived from three microbiome datasets and we find that CSNF can discover the modular structure of microbial interaction network which cannot be identified by analyzing a single dataset.
基金supported by the National High Technology Research and Development Program of China (Grant No. 2006BAD06A04) from Ministry of Science and Technology of ChinaGeorge F. Gao is a leading principal investigator of the Innovative Research Group of the National Natural Science Foundation of China (Grant No. 80121003)
文摘Protein thermostability is an inherent characteristic of proteins from thermophilic microorganisms,and therefore enables these organisms to survive at extreme temperatures.Although it is well-known that thermostable proteins are critical for the growth of thermophilic organisms,the structural basis of protein thermostability is not yet fully understood.The histidine-containing phosphocarrier (HPr) protein,a phosphate shuttle protein in the phosphoenolpyruvate-dependent sugar transport system (PTS) of bacterial species,is an ideal model for investigating protein thermostability with respect to its small size and deficiency in disulphide bonds or cofactors.In this study,the HPr protein from Thermoanaerobacter tengcongensis (TtHPr) is cloned and purified.Crystal structure with good quality has been determined at 2.3 resolution,which provides a firm foundation for exploring the thermostable mechanism.However,it shows that the crystal structure is conserved and no clue can be obtained from this single structure.Furthermore,detailed comparison of sequence and structure with the homologs from mesoor thermophilic bacteria shows no obvious rule for thermostability,but the extra salt-bridge existing only in thermophilic bacteria might be a better explanation for thermostability of HPr.Thus,mutations are performed to interrupt the salt-bridge in HPrs in thermophilic bacteria.Using site-directed mutations and the circular dichroism method,thermostability is evaluated,and the mutational variations are shown to have a faster denaturing rate than for wild-type viruses,indicating that mutations cause instability in the HPrs.Understanding the higher-temperature resistance of thermophilic and hyperthermophilic proteins is essential to studies on protein folding and stability,and is critical in engineering efficient enzymes that can work at a high temperature.
文摘Researchers hope that establishing a notion of proximity using topology will help to clarify the biological processes underlying the evolution of living organisms. The simple model presented here, using RNA shapes, can carry over to more general and complex genotype-phenotype systems. Proximity is an important component of continuity, in both real-world and topological terms. Consequently, phenotype spaces provide an appropriate setting for modeling and investigating continuous and discontinuous evolutionary change.
文摘In this paper, we present a method for constructing a Dulac function for mathematical models in population biology, in the form of systems of ordinary differential equations in the plane.
