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diversity of Gene Expression in Hepatocellular Carcinoma Cells

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Genomics, Proteomics & Bioinformatics 2015年第6期13卷 377-382页

作者： Fan Zhang Li Cui Michael D.Kuo Department of Molecular and Medical Genetics University of North Texas Health Science Center Department of Neurosciences School of Medicine University of California Department of Radiological Sciences University of California Los Angeles David Geffen School of Medicine

Understanding tumor diversity has been a long-lasting and challenging question for researchers in the field of cancer heterogeneity or tumor evolution. Studies have reported that com- pared to normal cells, there is a higher genetic diversity in tumor cells, while higher genetic diversity is associated with higher progression risks of tumor. We thus hypothesized that tumor diversity also holds true at the gene expression level. To test this hypothesis, we used t-test to compare the means of Simpson＇s diversity index for gene expression （SDIG） between tumor and non-tumor samples. We found that the mean SDIG in tumor tissues is significantly higher than that in the non-tumor or normal tissues （P 〈 0.05） for most datasets. We also combined microarrays and next-generation sequencing data for validation. This cross-platform and cross-experimental validation greatly increased the reliability of our results.

关键词： Gene expression Hepatocellular carcinomacell diversity Mieroarray Next-generation sequencing

diversity and Genetic Differentiation of the Whitefly Bemisia tabaci Species Complex in China Based on mtCOI and cDNA-AFLP Analysis

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Journal of Integrative Agriculture 2012年第2期11卷 206-214页

作者： GUO Xiao-jun RAO Qiong ZHANG Fan LUO Chen ZHANG Hong-yu GAO Xi-wu Department of Entomology China Agricultural University Beijing 100193 P.R.China Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences Beijing 100097 P.R. China College of Plant Science and Technology Huazhong Agricultural University Wuhan 430070 PR. China

The whitefly Bemisia tabaci are considered as a taxonomically complex that contained some destructive *** of the most prevalent cryptic species are *** Middle East-Asia Minor 1（MEAM1）and Mediterranean（MED）.In an extensive field survey of the *** complex present throughout part of China from 2004 to 2007,we obtained 93 samples of *** from 22 *** determined that these Chinese haplotypes included 2 invasive species（MEAM1 and MED）,and 4 indigenous cryptic species（Asia II 1,Asia II 3,China 3 and Asia II 7）by sequencing mitochondrial cytochrome oxidose one gene（mtCOI）.The diversity and genetic differentiation of a subset of 19 populations of *** were studied using cDNA amplified fragment length polymorphism（AFLP）.Prior to 2007,MEAM1 was a dominant species in many provinces in *** 2007,MED was dominant in 11 *** invasive and indigenous species were simultaneously found in some *** species of *** were found in six provinces in southern *** and MEAM1 have broad ranges of host plants,and indigenous species appeared to have much narrower host *** Asia II 3 samples were found on cotton except one on *** 3 has more host plants than Asia II *** samples of China 3 were collected from sweet potato,Japanese hop,squash and cotton.A total of 677 reproducible bands amplified with 5 AFLP primer combinations were *** highest proportion of polymorphic bands was 98.7% and the lowest was 91.9%.Unweighted pair-group method analysis indicated that the clustering was independent of the different *** showed the lowest degree of similarity than the other *** data indicate that both MEAM1and MED were rapidly established in China.

关键词： Bemisia tabaci mtCOI cDNA-AFLP diversity whitefly

diversity history of Ordovician graptolites and its relationship with environmental change

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Science China Earth Sciences 2008年第2期51卷 161-171页

作者： Zhang YuanDong Chen Xu LPS Nanjing Institute of Geology and Palaeontology Chinese Academy of Sciences Nanjing 210008 China

Statistical analysis based on global data indicated that the planktonic graptolites presented a distinguished pattern from that of benthic communities during the great Ordovician biodiversification. The graptolites st... 详细信息

关键词： South China Ordovician graptolite diversity deep-water origin sea-level change

diversity and distribution of proteorhodopsin-containing microorganisms in marine environments

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Frontiers of Environmental Science & Engineering 2012年第1期6卷 98-106页

作者： Bo WEI School of Life Sciences Xiamen UniversityXiamen 361005China

Proteorhodopsin （PR） is a recently discovered protein involved in the utilization of light energy. Several studies have shown that PR-containing microorganisms are widespread and compose a large proportion of the biomass in marine ecosystems. A better understanding of the ecological role of PR will help clarify the effect of the global flow of energy and the carbon cycle on marine communities. In this study, a bioinformatical database of PR codon sequences, the Global Distribution Database of Proteorhodopsin （GDDP）, as a tool for analyzing the diversity and distribution of PR-containing microorgan- isms in marine environments throughout the world was designed. The community structure of PR microorganisms were also compared using PCR assays and UniFrac analyses of 12 samples collected from three water layers （0, 75, and 200 m） at four representative sites in the Pacific, Atlantic, and Indian Oceans. The results indicate that PR- containing microorganisms can be grouped into two distribution types： widespread and location-specific. Representative cases of the former include SARll-PR and HOT2C01-PR. Interestingly, PR communities cluster by geographic locale but not by water depth.

关键词： proteorhodopsin (PR) microorganism com- munity diversity marine environments

diversity of oligotrich ciliates(Ciliophora, Spirotrichea) in the northern coast of South China Sea as revealed in LSU rDNA sequences

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Journal of Oceanology and Limnology 2020年第1期38卷 156-167,I0001-I0011页

作者： LU Kaihui LIU Weiwei Alan WARREN XU Yusen ZHU Changyu ZHAO Yan YI Zhenzhen Laboratory of Protozoology Guangzhou Key Laboratory of Subtropical Biodiversity and BiomonitoringSchool of Life ScienceSouth China Normal UniversityGuangzhou 510631China Key Laboratory of Tropical Marine Bio-resources and Ecology South China Sea Institute of OceanologyChinese Academy of SciencesGuangzhou 510301China Department of Life Sciences Natural History MuseumLondon SW75BDUnited K ingdom College of Life Sciences Capital Normal UniversityBeijing 100048China

Although the taxonomy of oligotrich ciliates has been widely investigated,yet the species diversity remains poorly *** newly designed a pair of oligotrich-specific LSU rDNA primers covering the 600-bp D1/D2 region,and it was effective for detecting oligotrich *** the primers,we constructed the cloning libraries to investigate the species diversity of oligotrichs in the northern coastal waters of the South China *** total,165 oligotrich sequences were obtained from five widely separated sampling *** operational taxonomic units(OTUs)were obtained at 99%similarity threshold,and low-abundance OTUs with no more than two sequences contributed most of these(about 78%).Our findings are consistent with previous morphological studies,Strombidium was found the most abundant and widely distributed genus in this *** addition,the BLAST search in the NCBI database resulted in 95%OTUs matching with named oligotrich species in similarity below 99%.Therefore,oligotrich morphospecies diversity has been underestimated as low-abundance species,and the LSU rDNA oligotrich sequence database needs to be better promoted.

关键词： diversity low-abundance species oligotrich ciliates operational taxonomic units (OTUs)

diversity of root-associated fungi of Rhododendron simsii in subtropical forests: fungal communities with high resistance to anthropogenic disturbances

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Journal of Forestry Research 2019年第6期30卷 2321-2330页

作者： Yanhua Zhang Fangping Tang Jian Ni Lijia Dong Lifu Sun College of Life Sciences Shaoxing University

Species of the Ericaceae or heath family are widely distribute in continental ecosystems and their special ericoid mycorrhizas(ERM)are considered benefi cial to their survival and persistence in variable ***,increasing anthropogenic disturbances and improper forest management are aff ecting subtropical forests of China where these native species *** activities not only aff ect plant communities above-ground,but also impose pressures on microbial communities *** this study,rootassociated fungal communities of Rhododendron simsii in four forest types under diff erent anthropogenic disturbances were identifi ed using an Illumina Miseq platform,i.e.,old growth forests,secondary forests with one cutting(SECⅠ),secondary forests with two cuttings(SECⅡ),and Chinesefi r plantations(PLF).Intra-and inter-annual variations were analyzed by comparing samples taken in diff erent seasons and *** results show that:(1)over 1000 OTUs were found in hair roots with most from the division Ascomycota and Basidiomycota belonging to diff erent functional groups;(2)while there were a few indicator OTUs specifi c to diff erent forest types,seasons and years,the proportion of shared taxa was quite large,accounting for 44.9–79.4%of the total OTUs;(3)signifi cantly positive correlations were found between disturbance sensitivity and temporal variations in common fungal orders,and both in major fungal orders were signifi cantly diff erent among fungal functional groups in which putative and possible ERM fungi were highly resistant to disturbances and low temporal *** high disturbance resistance and temporal persistence of putative ERM fungi may be essential for the successful adaptation of *** in disturbed subtropical forests of China.

关键词： Rhododendron simsii Mycorrhiza Fungal community diversity Subtropical forests Human disturbance

diversity of the endophytic filamentous fungal leaf community at different development stages of eucalyptus

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Journal of Forestry Research 2019年第3期30卷 1093-1103页

作者： Paulo Sergio Balbino Miguel Fabio Balbino Miguel Bruno Coutinho Moreira Marcelo Nagem Valerio de Oliveira Julio Cesar Delvaux Fernanda de Souza Freitas Arnaldo Chaer Borges Maurcio Dutra Costa Departamento de Medicina e Enfermagem Universidade Federal de VicosaVicosaMinas Gerais 36570-000Brazil Departamento de Quimica Universidade Federal de Juiz de ForaJuiz de ForaMinas Gerais 36036-300Brazil Colegiado de Engenharia Agronomica Universidade Federal do Vale do Sao FranciscoPetrolinaPernambuco 56300-990 Brazil Departamento de Ciencias Basicas da Vida Campus Governador Valadares Universidade Federal de Juiz de Fora Governador ValadaresMinas Gerais 35012-140Brazil Coordenacao Geral de Ensino Pesquisa e Extensao Instituto Federal do Triangulo MineiroItuiutabaMinas Gerais 38035-200Brazil Departamento de Microbiologia Instituto de Biotecnologia Aplicada aAgropecuariaUniversidade Federal de Vicosa VicosaMinas Gerais 36570-000Brazil

Fungal endophytic species inhabiting the leaves of eucalypts are capable of utilising leaf sugars and can influence both plant growth and health. Endophytic fungal symbionts can use simple soluble sugars in leaves as their main carbon source. This study set out to determine the diversity and distribution of the endophytic filamentous fungal leaf community in the hybrid Eucalyptus urograndis due to its economic importance. The fungal leaf community was characterised using denaturing gradient electrophoresis (DGGE) and correlated with levels of leaf nutrients and sugars throughout plant development. Sequencing of DGGE bands revealed the presence of Basidiomycota and Ascomycota phyla. Fourteen species and three genera of filamentous fungi were identified, and the population structure was affected by the plant developmental stage. Levels of K, Cu, N and Mn influenced communities from the clonal garden, whereas leaves in the field had higher glucose, fructose and sucrose. Many fungi were found to be specific to a certain development stages: Diplomitoporus crustulinus, Podosphaera tridactyla and Aspergillus restrictus to the clonal garden stage;Chaetomella acutiseta and Ascotricha chartarum to the shading stage;Erratomyces patelii and Saxomyces sp. to the shading output stage;Lepidostroma sp. and Saxomyces sp. to the dispatch stage;and Mycosphaerella populicola to the field stage. Teratosphaeria toledana and Teratosphaeria acidotherma were found at more than one developmental stage. Cladosporium sp. and Rhodosporidium fluviale colonized and persisted in plants at the dispatch and field stages. This is the first report of P. tridactyla, A. restrictus, E. patelii, Saxomyces and Lepidostroma sp. as endophytes in eucalipt.

关键词： diversity 18S rRNA Denaturing gradient electrophoresis(DGGE) Sequencing

diversity and Dynamics of Soil Free-Living Nematode Populations in a Mediterranean Agroecosystem

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Pedosphere 2005年第2期15卷 204-215页

作者： LIANGWen-Ju I.LAVIAN S.PEN-MOURATOV Y.STEINBERGER FacultyofLifeSciences Bar-IlanUniversityRamat-Gan52900（Israel）.／／InstituteofAppliedEcologyChineseAcademyofSciencesShenyang110016（China） FacultyofLifeSciences Bar-IlanUniversityRamat-Gan52900（Israel）

To determine the effect of agricultural management on the dynamics and functional diversity of soil nematode communities in a carrot field at Kibbutz Ramat Hakovesh, Israel, soil samples from 0-10 cm and 10-20 cm depths were collected during the growing season of carrot. Indices were used to compare and assess the response of soil free-living nernatode communities to agricultural management. Eighteen nematode families and 20 genera were observed during the growing period, with Cephalobus, Rhabditidae, Aphelenchus, Tylenchus, and Dorylaimus being the dominant genera/families. During the planting, mid-season and post-harvest periods the total number of nematodes at both depths was significantly lower (P < 0.01) in the carrot treatment than in the control plots, while during the harvest period at both depths total nematodes and bacterivores were significantly higher in the treatment plots (P < 0.01). The values of the maturity index (MI) at both depths were found to be significantly lower in the treatment plots than in the control plots during the pre-planting period (P < 0.05). Overall, WI, MI and PPI were found to be more sensitive indicators than other ecological indices for assessing the response of nematode communities to agricultural management in a Mediterranean agroecosystem

关键词： agricultural management carrot-growing season diversity maturity index nematode community

diversity,Distribution and Prioritization of Fodder Species for Conservation in Kullu District,Northwestern Himalaya,India

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Journal of Mountain Science 2007年第3期4卷 259-274页

作者： S. S. Samant Man Singh Manohar Lal Shreekar Pant G.B.Pant Institute of Himalayan Environment & Development Himachal UnitMohal-Kullu175 126Himachal PradeshIndia

In the Indian Himalayan Region predominantly rural in character, livestock is one of the main sources of livelihood and integral part of the economy. Livestock mostly rely on fodder from wild. The diversity, distribution, utilization pattern, nativity, endemism, rarity, seasonality of availability, nutritive values, perceived economic values and pressure use index of livestock have not been studied. The present study attempts to enumerate 150 species of fodder representing trees (51 spp.), shrubs (54 spp.) and herbs (45 spp.). Poaceae (19 spp.) and Fabaceae (13 spp.) amongst families and Salix (6 spp.), Ficus, Clematis, and Desmodium (5 spp., each) amongst genera are rich in species. Maximum species were found in the 1801 ~ 2600 m zone, and the remaining two zones showed relatively low diversity. Out of the 150 species, 109 are used in summer, 5 winter and 36 throughout year. During rainy season, mostly grasses are used as fodder. Only 83 species are native to the Himalayan region, one species, Strobilanthus atropuroureus is endemic and 35 species are near endemic. The nutritive values of the fodder species were reviewed, and economic values and status of the species were also assessed. The pressure use index of the species was calculated on the basis of cumulative values of the utilization pattern, altitudinal distribution, availability, status, nativity and endemism. Amongst the species, Grewia oppositifoilia, Morus serrata, Indigofera heterantha, Quercus leucotrichphora, Ulmus villosa, U. wallichiana and Aesculus indica showed highest PUI indicating high preference and pressure. Season wise prioritization of the species for different altitudinal zones has been done. Appropriate strategy and action plan have been suggested for the conservation and management of fodder species.

关键词： diversity utilization native endemic nutritive and economic value pressure use index prioritization conservation Indian Himalayan Region