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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 Hits8806Downloads633 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 Hits13035Downloads1335 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 Hits17779Downloads1034 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 Hits11349Downloads766 Comment 0