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1. chinaXiv:202004.00019 [pdf]

The phylogenetic position of Cladiucha within Tenthredinidae based on comprehensive mitochondrial phylogenomics and the evidence from comparative analyses of rRNA secondary structure

Niu, Gengyun; Jiang Sijia; Do?an, ?zgül ; Korkmaz, Ertan Mahir; Budak, Mahir ; Wu, Duo; Wei, Meicai
Subjects: Biology >> Entomology

Two mitogenomes of Cladiucha were newly reported and shown typical pattern of gene arrangement. The phylogenetic position of Cladiucha was obtained from tree reconstruction using various data treatment methods and substitution models. Significant heterogeneity in the nucleotide composition and mutational biases was found in the mitochondrial protein-coding genes, and the third codon position exhibited high levels of saturation. Therefore, 14 datasets were conducted under both site-homogeneous and site-heterogeneous models. The following conclusions were drawn from the phylogenetic analyses: (i) the monophyly of Tenthredinidae was confirmed, (ii) the monophyly of Allantinae + Tenthredininae + Megabelesinae was approved, and (iii) within the family, ((((Tenthredininae + Fenusinae) + Allantinae) + Megabelesinae) + Nematinae) is probably the most acceptable cladogram for the phylogeny of Tenthredinidae, which is also supported by the morphological analysis and a comparative study on the rRNA secondary structure. Divergence time estimation analyses indicated that diversification of the major superfamilies of the suborder Symphyta occurred around 232.9 Ma, and the splits of Tenthredinidae were dated to 146 Ma, which corresponding to the origin of the earliest lineages of flowering plants and major diversifications of core angiosperms, respectively. The Cladiucha arose in the Mid-Miocene; at that time, magnoliids are rapidly undergoing genus-species differentiation. "

submitted time 2020-04-19 Hits10596Downloads935 Comment 0

2. chinaXiv:202002.00081 [pdf]

SARS-coronavirus-2 nsp13 possesses NTPase and RNA helicase activities

Shu, Ting; Huang, Muhan; Wu, Di; Ren, Yujie; Zhang, Xueyi; Han, Yang; Mu, Jingfang; Wang, Ruibing; Qiu, Yang; Zhang, Ding-Yu; Zhou, Xi
Subjects: Biology >> Virology

The ongoing outbreak of Coronavirus Disease 2019 (COVID-19) has become a global pandemic and crisis. SARS-coronavirus-2 (SARS-CoV-2), the causative pathogen of COVID-19, is a positive-sense single-stranded RNA virus belonging to the family Coronaviridae. For RNA viruses, virus-encoded RNA helicases have long been recognized to play pivotal roles during viral life cycles by facilitating the correct folding and replication of viral RNAs. Here, our studies show that SARS-CoV-2-encoded nonstructural protein 13 (nsp13) possesses the nucleoside triphosphate hydrolase (NTPase) and RNA helicase activities that can hydrolyze all types of NTPs and unwind RNA helices dependently of the presence of NTP, and further characterize the biochemical characteristics of these two enzymatic activities associated with SARS-CoV-2 nsp13. Moreover, we found that some bismuth salts could effectively inhibit both the NTPase and RNA helicase activities of SARS-CoV-2 nsp13 in a dose-dependent manner. Thus, our findings demonstrate the NTPase and helicase activities of SARS-CoV-2 nsp13, which may play an important role in SARS-CoV-2 replication and serve as a target for antivirals.

submitted time 2020-04-19 Hits16008Downloads1736 Comment 0

3. chinaXiv:202003.00008 [pdf]

Germline Polymorphisms and Length of Survival of Nasopharyngeal Carcinoma: An Exome-Wide Association Study in Multiple Cohorts

Yun-Miao Guo; Jie-Rong Chen; Yan-Chun Feng; Chua, Melvin L. K. ; Zeng, Yanni ; Edwin Pun Hui; Allen K. C. Chan; Lin-Quan Tang; Lin Wang; Qian Cui; Hui-Qiong Han; Chun-Ling Luo; Guo-Wang Lin; Yan Liang; Yang Liu; Zhong-Lian He; Yu-Xiang Liu; Pan-Pan Wei; Chu-Jun Liu; Wan Peng
Subjects: Medicine, Pharmacy >> Clinical Medicine

Germline polymorphisms have been linked with differential survival outcomes in cancers but have not been well studied in nasopharyngeal carcinoma (NPC). Here, two-phase association study is conducted to discover germline polymorphisms that are associated with the prognosis of NPC. The discovery phase includes two consecutive hospital cohorts of patients with NPC from Southern China. Exome-wide genotypes at 246,173 single nucleotide polymorphisms (SNPs) are determined, followed by survival analysis for each SNP under Cox proportional hazards regression model. Candidate SNP is replicated in another two independent cohorts from Southern China and Singapore. Meta-analysis of all samples (n = 5,553) confirm that the presence of rs1131636-T, located in the 3′-UTR of RPA1, confers an inferior overall survival (HR = 1.33, 95% CI = 1.20-1.47, P = 6.31 × 10-8). Bioinformatics and biological assays show that rs1131636 has regulatory effects on upstream RPA1. Functional studies further demonstrate that RPA1 promoted the growth, invasion, migration, and radioresistance of NPC cells. Additionally, miR-1253 has been identified as a suppressor for RPA1 expression, likely through regulation of its binding affinity to rs1131636 locus. Collectively, these findings provide a promising biomarker aiding in stratifying patients with poor survival, as well as a potential drug target for NPC.

submitted time 2020-03-06 Hits24511Downloads1461 Comment 0

4. chinaXiv:202002.00074 [pdf]

Molecular karyotypes of loquat (Eriobotrya japonica) aneuploids can be detected by using SSR markers combined with quantitative PCR irrespective of heterozygosity

Wen, Guo; Dang, Jiangbo; Xie, Zhongyi; Wang, Jinying; Jiang, Pengfei; Guo, Qigao; Liang, Guolu
Comment:This article has been published online in Plant Methods (https://plantmethods.biomedcentral.com/articles/10.1186/s13007-020-00568-7)
Subjects: Biology >> Botany
Subjects: Agriculture, Forestry,Livestock & Aquatic Products Science >> Horticulture

Background: Aneuploidy, a condition caused by an imbalance between the relative dosages of chromosomes, generally produces a novel phenotype specific to the molecular karyotype. Few techniques are currently available for detecting the molecular karyotypes of aneuploids in plants. Methods: By PCR amplification of 209 pairs of SSR primers, 17 pairs of SSR primers with no polymorphism and stable amplification in 23 different ploidy loquat were screened out. Seventeen SSR markers combined with qPCR for detection of aneuploid loquat H39 (2n=2x+5=39) karyotype variation. To verify the method for detection of aneuploid karyotype variation, 9 hybrid offspring of Q24 × ‘Huabai No. 1’ and 16 open-pollination progeny of the triploid loquat A313 and A322 were obtained, and we detected their chromosome numbers using conventional cytological methods. The SSR-qPCR method was used to detect the molecular karyotypes of aneuploids in the 9 hybrid offspring of Q24 × ‘Huabai No. 1’ and 16 open-pollination progeny of the triploid loquat A313 and A322. Results: Based on this imbalance in chromosome dosage, a new approach (referred to as ‘SSR-qPCR’) combining simple sequence repeat (SSR) markers and quantitative real-time PCR (qPCR) has been developed and utilized to detect some common aneuploids irrespective of heterozygosity. We screened 17 specific SSR markers covering all loquat linkage groups and redesigned 6 pairs of primers for SSR markers that can detect loquat chromosome aneuploidies. The SSR-qPCR detection results obtained for hybrid progeny and open-pollination progeny of triploid loquat showed diagnostic accuracies of 88.9% and 62.5%, respectively, compared with the chromosome preparation results. Limitations: Loquat genome sequences have not been published, available SSR markers are currently limited. Conclusion: SSR-qPCR can detect loquat aneuploids and be used to construct the entire molecular karyotypes of aneuploid individuals. Therefore, this method offers a novel alternative for the detection of chromosome aneuploidies.

submitted time 2020-03-03 Hits12131Downloads1204 Comment 0

5. chinaXiv:201904.00073 [pdf]

Prevent culture-driven invasive species spread

Xiong Li; Supriyo Basak; Rui Zhou; Wei-zhe Zhang; Yao Fu; Xin-mao Zhou; Chao Shi; Hou-Cheng Xi; Yong-ping Yang
Subjects: Biology >> Ecology

地区文化(如宗教、饮食或旅游文化)有时会驱动入侵生物的扩散,我们必须采取措施来阻止入侵生物融入大众文化。

submitted time 2020-02-24 Hits11211Downloads961 Comment 0

6. chinaXiv:202002.00009 [pdf]

一种新型冠状病毒肺炎(COVID-19)药物与天然产物快速发现的计算药理学方法

全源; 梁峰吉; 熊江辉
Subjects: Biology >> Virology

新发传染病爆发流行期间,亟需提出候选药物功效与机制的科学假说。疫苗或新药研发均需要一定时间,因而药物重定位(老药新用)策略有其独特价值。但是新发疾病其病原体、宿主反应的临床数据不充分,制约了候选药物假设的提出。此阶段常根据病人临床特征进行广谱抗病毒药物的尝试。本文借鉴人工智能领域常见的启发式搜索思路,提出一种新方法(aCODE),基于前期有一定疗效提示的广谱抗病毒药,获得其宿主靶蛋白集合,在全基因组尺度上搜索与之相关性最高的基因模块组合,进而对候选化合物(如已批准上市药物、天然产物)进行模式匹配与统计检验排序。本方法可根据临床实践的进展更新输入药物,迭代输出更精准结果,输出的天然产物或中药、药食同源成分结合其它信息后可实施快速测试,形成敏捷研发测试闭环。本方法的第二版更新及其与文献证据的比对分析请参考:http://chinaxiv.org/abs/202002.00024。

submitted time 2020-02-21 Hits26914Downloads2649 Comment 0

7. chinaXiv:202002.00033 [pdf]

Decoding evolution and transmissions of novel pneumonia coronavirus using the whole genomic data

Yu, Wen-Bin; Tang, Guang-Da; Zhang, Li; Corlett, Richard T.
Subjects: Biology >> Virology
Subjects: Biology >> Genetics

Background. The outbreak of COVID-19 started in mid-December 2019 in Wuhan, Central China. Up to February 18, 2020, SARS-CoV-2 has infected more than 70,000 people in China, and another 25 countries across five continents. In this study, we used 93 complete genomes of SARS-CoV-2 from the GISAID EpiFluTM database to decode the evolution and human-to-human transmissions of SARS-CoV-2 in the recent two months. Methods. Alignment of coding-regions was conducted haplotype analyses using DnaSP. Substitution sites were analyzed in codon. Evolutionary analysis of haplotypes used NETWORK. Population size changes were estimated using both DnaSP and Arlequin. Expansion date of population size was calculated based on the expansion parameter tau (τ) using the formula t=τ/2u. Findings. Eight coding-regions have 120 substitution sites, including 79 non-synonymous and 40 synonymous substitutions. Forty-two non-synonymous substitutions changed the biochemical property of amino acids. No evident combination was found. Fifty-eight haplotypes were classified as five groups, and 31 haplotypes were found in samples from both China and other countries, respectively. The rooted network suggested H13 and H35 to be ancestral haplotypes, and H1 (and its descendent haplotypes including all samples from the Hua Nan market) was derived H3 haplotype. Population size of SARS-CoV-2 were estimated to have a recent expansion on 6 January 2020, and an early expansion on 8 December 2019. Interpretation. Genomic variations of SARS-CoV-2 are still low in comparisons with published genomes of SARS-CoV and MERS-CoV. Phyloepidemiologic analyses indicated the SARS-CoV-2 source at the Hua Nan market should be imported from other places. The crowded market boosted SARS-CoV-2 rapid circulations in the market and spread it to the whole city in early December 2019. Furthermore, phyloepidemiologic approaches have recovered specific direction of human-to-human transmissions, and the import sources of international infectious cases.

submitted time 2020-02-21 Hits293161Downloads74151 Comment 0

8. chinaXiv:202002.00004 [pdf]

武汉2019冠状病毒S蛋白可能存在Furin蛋白酶切位点

李鑫; 段广有; 张伟; 施劲松; 陈嘉源; 陈舜梅; 高山; 阮吉寿
Subjects: Biology >> Virology

摘要:2019年12月,中国武汉报道了2019新型冠状病毒(2019 novel Coronavirus,2019-nCoV)引起的肺炎。基于基因组信息,我们前期研究结果显示2019-nCoV与SARS冠状病毒虽然同属于Beta冠状病毒B亚群(BB冠状病毒),但两种病毒差异很大,这一结果与两者临床症状差异一致。前期研究还发现了BB冠状病毒存在大量的可变翻译,并从分子水平揭示了BB冠状病毒变异快、多样性高的特点。本研究在国际上首次报道BB冠状病毒S蛋白上的一个重要突变,这个突变使2019-nCoV具有了一个可供Furin蛋白酶切的位点,是除鼠肝炎冠状病毒外所有的其它BB冠状病毒(包括SARS和SARS样(SARS-like)冠状病毒)所不具有的。这个突变有可能增强了2019-nCoV侵染细胞的效率,进而使其传播力显著大于SARS冠状病毒。由于这个突变,2019冠状病毒的包装机制也会不同于SARS等其它大部分Beta冠状病毒,而有可能与鼠肝炎冠状病毒、HIV、埃博拉病毒和一些禽流感病毒的包装机制相同。作为一个意外发现,一些禽流感病毒也可以通过突变获得Furin蛋白酶切位点。对这个重要突变的后续研究将为揭示2019-nCoV传播力强的原因,以及为药物、抗体和疫苗的开发等工作奠定基础。

submitted time 2020-02-14 Hits89839Downloads17220 Comment 0

9. chinaXiv:201912.00032 [pdf]

水体环境DNA监测流域生态系统生物多样性的有效度:以环境微生物为例

杨海乐; 杜浩; 祁洪芳; 俞录贤; 侯新东; 张辉; 李君轶; 危起伟
Subjects: Biology >> Ecology

近年来,环境DNA技术在生态学研究中的应用日益广泛。基于自然径流驱动的流域生态系统过程,利用水体环境DNA,可以实现以下游样点监测上游河段生物组成状况,以及以水体样点监测汇水区内生物组成状况,但监测的有效度尚缺乏系统验证,影响了其应用的可信度。为了研究水体环境DNA分析在流域生态系统生物多样性监测中的有效度,我们以流域生物信息流为分析框架来探讨上述水体环境DNA监测应用的两种类型及其有效度。我们以青海湖主要入湖河流——沙柳河为研究区域,用环境DNA技术对河流水体微生物组成和岸带土壤微生物组成进行了对比分析。结果显示,(1)利用下游环境DNA监测上游微生物生物多样性的有效度主要受温度和流量影响,春季的监测有效度较低(上游1公里处的生物只有76%左右可被监测到),夏秋季的监测有效度较高(上游1公里处的生物有大于96%可被监测到);(2)利用水体环境DNA监测水系汇水区内陆地微生物生物多样性的有效度主要受季节和降雨影响,春季的监测有效度较低(相邻岸带土壤中的生物只有17%左右被监测到),夏秋季的监测有效度较高(相邻岸带土壤中的生物被监测到的比例可超过62%)。由此提出,(1)以下游样点监测上游生物多样性,夏秋繁殖季是费效比最好的监测期,春季的监测样点应适当增加密度;(2)以水体样点监测陆地生物多样性,夏秋季生物活动活跃期的降雨天及雨后水浊时是费效比最好的监测期,但检测有效度的问题值得一直关注。

submitted time 2019-12-30 Hits2989Downloads1555 Comment 0

10. chinaXiv:201911.00075 [pdf]

自然径流驱动的以环境微生物为指标的流域生物信息流量化特征

杨海乐; 杜浩; 祁洪芳; 俞录贤; 危起伟
Subjects: Biology >> Ecology

物质流、能量流、信息流是生态系统过程研究中的三大主题。流域是生态系统的一个基本单元,流域信息流理应是流域生态学研究的核心主题之一,然而截至目前尚未对其有系统的研究。为了推动流域信息流研究,本文从生物信息流切入,提出了“流域生物信息流”概念,将其定义为“生物信息依托于流域生态系统过程在不同空间和系统之间进行传递、交流、作用、反馈的路径、过程与控制”,并将其研究内容明确为主要关注于水陆间、干支流间、上下游间、不同生态斑块间的流域生物信息流及其周期性节律和趋势性变迁,以及地貌、水文、人类活动等对这些生物信息流的影响等。本文以青海湖重要入湖河流——沙柳河的河流水体微生物和岸带土壤微生物为研究对象,利用环境DNA技术,对沙柳河流域的自然径流驱动的流域生物信息流进行量化研究。结果表明(1)岸带土壤到水体的流域生物信息流由地表表面流和地下潜流驱动,并受环境过滤效应影响,水体上游到下游的流域生物信息流由河川径流驱动,并受衰减效应影响;(2)由岸带土壤到水体的流域生物信息流输移效率降雨天约为62.76%、晴天约为44.16%,其中输移能力降雨天约为68.49%、晴天约为56.82%,环境过滤效应降雨天约为8.38%、晴天约为22.28%;(3)由河流上游到下游的流域生物信息流的基础综合输移效率约为80.30%,其中径流输移能力约为99.42%每千米,无效流域生物信息流占比约为43.46%,无效流域生物信息流的半衰距离约为14.52千米;(4)降雨通过增加地表表面流和地下潜流的冲蚀和搬运能力并削弱环境过滤效应,促使岸带土壤到水体的流域生物信息流输移能力和输移效率增大;(5)流域生物信息流的输入在一定程度上增加了输入地的可检出生物多样性,但这种增加对于流水水生态来讲是非累积的。

submitted time 2019-12-11 Hits4945Downloads903 Comment 0

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