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1. 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 Hits284907Downloads72313 Comment 0

2. 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 Hits85217Downloads16120 Comment 0

3. chinaXiv:201606.00145 [pdf]

生物磁受体蛋白MagR/IscA研究进展

汪红霞; 向远彩; 张义国
Subjects: Biology >> Molecular Biology

铁硫簇蛋白是一类重要的线粒体功能蛋白,在细胞能量代谢、电子传递、底物结合与激活、铁/硫存储、酶促反应、基因表达调控等诸多过程中均发挥了关键作用. 一旦铁硫簇组装及转运过程发生障碍,必将严重影响细胞内铁的稳态及铁硫蛋白的功能. 其中,分子量约 11-kDa 的 IscA,是铁硫蛋白亚家族 hesB 之一的高保守性成员,能结合铁离子及[2Fe-2S]簇,从而参与铁硫簇蛋白的合成,因此在铁硫簇组装蛋白系统中具有重要的作用. 更值得关注的是,2015 年谢灿和张生家各自研究组分别发现了 IscA1 具有独特的磁感应(magnetic sensor,MagS)与磁受体(magnetic receptor,MagR)功能. 尤为重要的是,通过外磁场刺激相关磁基因表达,能够调控神经活动及行为定位. 鉴于磁受体的独特功能并结合相关技术,遂将其统称为磁遗传学(磁基因学). 本文简要介绍 IscA 蛋白的始初发现与鉴定历程、进化保守性及其独特的生理生物学功能,并凝练出磁遗传假说机制调控模型.

submitted time 2016-06-16 Hits50794Downloads4198 Comment 0

4. chinaXiv:201712.00001 [pdf]

孤独症脑自发活动动态性及其整合的异常机制

鲁彬; 陈骁; 李乐; 沈杨千; 陈宁轩; 梅婷; 周会霞; 刘靖; 严超赣
Subjects: Psychology >> Medical Psychology

孤独症谱系障碍(autism spectrum disorder, ASD)是一种病因未明,发病率较高的神经发育疾病。目前大多数静息态功能磁共振成像(resting-state fMRI, R-fMRI)研究仅考察了ASD患者脑活动的静态特征,忽视了动态特征。近期研究发现,不同R-fMRI局部指标的动态性之间存在一致性。本研究基于ASD公开数据库,使用滑动时间窗方法系统计算了480名ASD患者和539名健康对照(typical control, TC)被试的主流R-fMRI局部指标的动态性及R-fMRI局部指标之间的一致性动态特征,并考察了这些指标与ASD行为指标之间的关系。我们发现ASD患者在外侧额叶呈现出动态性显著升高,该现象在低频振幅(amplitude of low-frequency fluctuations, ALFF)和度中心性(degree centrality, DC)的动态性中都有体现。我们也发现ALFF、DC和局部一致性(regional homogeneity, ReHo)的动态性在视觉相关脑区,如梭状回、距状沟和舌回呈现下降。在进一步考察了这些指标之间的一致性动态特征后,发现ASD患者的一致性动态特征显著低于TC组被试,表现出显著下降的功能整合能力。我们的结果表明ASD患者存在着脑自发活动动态性及其整合的异常。

submitted time 2018-04-02 Hits24031Downloads3566 Comment 0

5. chinaXiv:201802.00670 [pdf]

负载NGF的可注射壳聚糖透明质酸水凝胶材料理化性能及生物相容性研究

段思腾; 李光然; 马义勇; 邱裕佳; 李宇; 王伟
Subjects: Biology >> Bioengineering

目的:制备负载NGF的可注射壳聚糖透明质酸复合水凝胶,探讨其理化性能以及生物相容性。方法:首先京尼平交联制备壳聚糖透明质酸复合水凝胶材料,采用倒置法检测凝胶时间;扫描电镜观察材料形态结构;NGF释放实验、体外溶胀以及降解实验等检测凝胶材料的物理化学性能;通过MTT实验、NGF活性检测、材料与细胞共培养检测凝胶材料生物学性能。结果:在37℃条件下,可注射凝胶材料凝胶时间在37min左右,凝胶材料为多孔网络状结构,凝胶材料8周最多能够降解76%,缓释21天的NGF具有生物活性,凝胶材料能促进RSC96细胞的粘附、增殖、迁移以及细胞活性物质的释放。结论:京尼平交联的壳聚糖透明质酸水凝胶具有良好的生物相容性,能作为NGF的载体材料,具有成为神经导管内填充材料的潜能。

submitted time 2018-02-11 From cooperative journals:《中国生物工程杂志》 Hits13496Downloads3473 Comment 0

6. chinaXiv:201903.00232 [pdf]

Conversion of cropland into agroforestry land versus naturally-restored grassland alters soil macro-faunal diversity and trophic structure in the semi-arid agro-pasture zone of northern China

LIU Rentao
Subjects: Biology >> Ecology

Restoration of cropland (termed 'Farm') after abandonment including shrubs (termed 'Shrub'), trees (termed 'Tree') and natural grassland (termed 'Grass') has become a routine process aimed to improve land productivity and control desertification. During this restoration process, soil macro-faunal diversity, and trophic structure were investigated at four types of sites (Farm, Shrub, Tree, and Grass) during growing season in the semi-arid agro-pasture zone of northern China. Results indicated that the Staphylinidae family was found to dominate at the Grass, Shrub, and Tree sites, whiles larval Pyralidae individuals were found at the Grass site only. The density of the omnivores (i.e., Formicidae family) was significantly (P<0.05) greater at the Grass site than at the Tree and Farm sites. The total density and richness of predator and phytophages were found to be markedly (P<0.05) greater at the Grass site than at the Farm site. Meanwhile, we found the taxon richness of predators was significantly (P<0.05) higher at the Shrub site than at the Farm and Tree sites. Compared with the Farm and afforested Shrub/Tree sites, the Grass site had greater density, taxon richness, and Shannon index (P<0.05). In conclusion, natural restoration of abandoned croplands toward grassland was an effective strategy relative to artificial afforestation for improvement of soil biological diversity. Moreover, planting shrub is a preferable measure in abandoned croplands for land development in the semi-arid agro-pasture zone of northern China.

submitted time 2019-03-28 From cooperative journals:《Journal of Arid Land》 Hits7573Downloads2765 Comment 0

7. chinaXiv:202002.00018 [pdf]

2019-novel coronavirus (2019-nCoV) infections trigger an exaggerated cytokine response aggravating lung injury

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