盐磷胁迫对木麻黄和台湾相思种子萌发及幼苗生长的影响

恶劣环境下,人工海防林因面临养分胁迫而经营困难。为探讨盐、磷胁迫对主要海防林树种木麻黄和台湾相思种子萌发及生长的影响,该研究分别用不同浓度的NaCl(盐)和KH₂PO₄(磷)溶液处理种子和浇灌幼苗,测定种子萌发和幼苗生长指标。结果表明：(1)高盐胁迫显著抑制种子萌发,对幼苗生长有一定影响,但两种植物影响程度不同;台湾相思种子萌发耐盐性高于木麻黄,前者相对盐害率最大值为23.03%,后者为89.15%;随着盐浓度增加,木麻黄和台湾相思种子的发芽率、发芽势、发芽指数和活力指数均降低,对应最大值分别为38.70%、34.67%、18.70、0.055和76.67%、62.22%、48.46、6.11。(2)两种植物的株高和根长随盐浓度增加而降低,木麻黄和台湾相思株高分别为12.29～6.01 mm和48.27～17.33 mm,根长分别为8.57～1.45 mm和33.41～5.88 mm;台湾相思根、茎、叶生物量及根冠比均随盐浓度的增加逐渐减小,木麻黄各处理差异较小。(3)台湾相思的种子和幼苗较木麻黄更耐低磷环境,二者最适磷浓度存在差异;木麻黄种...     

转铁蛋白分型及其基因频率分布

用固相pH梯度(pH 5.05～5.60)等电聚焦技术对随机抽取的188名北京地区健康汉族人的血清转铁蛋白(Tf)进行分型调查,并统计基因频率,检出了在中国还未见报道的Tf^C3基因.其表型分别是：TfC1, TfC2, TfC1C2, TfC1C3, TfC1Dchi, TfC2Dchi.Tf^C1=0.7420, Tf^C2=0.2420, Tf^C3=0.0027, Tf^Dchi=0.0133, 符合Hardy-Weinberg定律, 并与其他已见报道的汉族 Tf基因频率大致相符.     

DNA barcoding of Oryza: conventional,specific, and super barcodes

Key message

We applied the phylogenomics to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity.

Abstract

Rice (genus Oryza) is one of the most important crops in the world, supporting half of the world’s population. Breeding of high-yielding and quality cultivars relies on genetic resources from both cultivated and wild species, which are collected and maintained in seed banks. Unfortunately, numerous seeds are mislabeled due to taxonomic issues or misidentifications. Here, we applied the phylogenomics of 58 complete chloroplast genomes and two hypervariable nuclear genes to determine species identity in rice seeds. Twenty-one Oryza species were identified. Conspecific relationships were determined between O. glaberrima and O. barthii, O. glumipatula and O. longistaminata, O. grandiglumis and O. alta, O. meyeriana and O. granulata, O. minuta and O. malampuzhaensis, O. nivara and O. sativa subsp. indica, and O. sativa subsp. japonica and O. rufipogon. D and L genome types were not found and the H genome type was extinct. Importantly, we evaluated the performance of four conventional plant DNA barcodes (matK, rbcL, psbA-trnH, and ITS), six rice-specific chloroplast DNA barcodes (psaJ-rpl33, trnC-rpoB, rps16-trnQ, rpl22-rps19, trnK-matK, and ndhC-trnV), two rice-specific nuclear DNA barcodes (NP78 and R22), and a chloroplast genome super DNA barcode. The latter was the most reliable marker. The six rice-specific chloroplast barcodes revealed that 17% of the 53 seed accessions from rice seed banks or field collections were mislabeled. These results are expected to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity.

     

多基因联合揭示海南鲌的遗传结构与遗传多样性

海南鲌(Culter recurviceps)是我国华南地区重要经济鱼类, 由于受到近些年水利开发、过度捕捞、环境污染等诸多因素的影响, 其资源量快速下降, 亟需得到更多的关注和保护。为保护和合理开发海南鲌种质资源, 本研究采集了华南地区23个地理群体207尾海南鲌样本, 测定了2个线粒体基因(Cytb和ND2)并从Barcode of Life Data System数据库获得相对应线粒体COI基因, 结合多种分析方法(系统发育分析、分化时间估算、单倍型网状图、群体遗传分析和Mantel检验)对海南鲌的遗传结构和遗传多样性展开研究。系统发育分析和单倍型网状图表明华南地区海南鲌群体被分成3个谱系(I、II和III), 其中谱系I和III由珠江的群体组成, 谱系II由海南岛的群体组成。分化时间估算发现3个谱系之间的分化时间介于0.028-0.251 Ma之间, 表明华南地区更新世气候变化可能是造成海南鲌谱系分化的重要原因。群体遗传分析发现海南鲌群体之间存在极显著的遗传分化(F_ST = 0.511, P < 0.001), 并且符合距离隔离模式(R = 0.348, P = 0.0010)。群体动态历史分析表明, 海南鲌群体可能在0.010-0.025 Ma经历了群体扩张, 表明更新世的气候波动也影响了海南鲌的群体大小和分布。综上所述, 海南鲌群体由3个谱系组成, 更新世气候变化是导致3个谱系分化和影响海南鲌群体动态历史的重要因素。此外, 海南鲌群体之间的遗传分化也可能受到了空间距离的影响。     

Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients

Bacterial pneumonia is a major cause of morbidity and mortality in elderly. We hypothesize that dysbiosis between regular residents of the upper respiratory tract (URT) microbiome, that is balance between commensals and potential pathogens, is involved in pathogen overgrowth and consequently disease. We compared oropharyngeal microbiota of elderly pneumonia patients (n=100) with healthy elderly (n=91) by 16S-rRNA-based sequencing and verified our findings in young adult pneumonia patients (n=27) and young healthy adults (n=187). Microbiota profiles differed significantly between elderly pneumonia patients and healthy elderly (PERMANOVA, P<0.0005). Highly similar differences were observed between microbiota profiles of young adult pneumonia patients and their healthy controls. Clustering resulted in 11 (sub)clusters including 95% (386/405) of samples. We observed three microbiota profiles strongly associated with pneumonia (P<0.05) and either dominated by lactobacilli (n=11), Rothia (n=51) or Streptococcus (pseudo)pneumoniae (n=42). In contrast, three other microbiota clusters (in total n=183) were correlated with health (P<0.05) and were all characterized by more diverse profiles containing higher abundances of especially Prevotella melaninogenica, Veillonella and Leptotrichia. For the remaining clusters (n=99), the association with health or disease was less clear. A decision tree model based on the relative abundance of five bacterial community members in URT microbiota showed high specificity of 95% and sensitivity of 84% (89% and 73%, respectively, after cross-validation) for differentiating pneumonia patients from healthy individuals. These results suggest that pneumonia in elderly and young adults is associated with dysbiosis of the URT microbiome with bacterial overgrowth of single species and absence of distinct anaerobic bacteria. Whether the observed microbiome changes are a cause or a consequence of the development of pneumonia or merely coincide with disease status remains a question for future research.     

Temporal Patterns of Larval Fish Occurrence in a Large Subtropical River

Knowledge of temporal patterns of larval fish occurrence is limited in south China, despite its ecological importance. This research examines the annual and seasonal patterns of fish larval presence in the large subtropical Pearl River. Data is based on samples collected every two days, from 2006 to 2013. In total, 45 taxa representing 13 families and eight orders were sampled. The dominant larval family was Cyprinidae, accounting for 27 taxa. Squaliobarbus curriculus was the most abundant species, followed by Megalobrama terminalis, Xenocypris davidi, Cirrhinus molitorella, Hemiculter leuscisculus and Squalidus argentatus. Fish larvae abundances varied significantly throughout the seasons (multivariate analyses: Cluster, SIMPROF and ANOSIM). The greatest numbers occurred between May and September, peaking from June through August, which corresponds to the reproductive season. In this study, redundancy analysis was used to describe the relationship between fish larval abundance and associated environmental factors. Mean water temperature, river discharge, atmospheric pressure, maximum temperature and precipitation play important roles in larval occurrence patterns. According to seasonal variations, fish larvae occurrence is mainly affected by water temperature. It was also noted that the occurrence of Salanx reevesii and Cyprinus carpio larvae is associated with higher dissolved oxygen (DO) concentrations, higher atmospheric pressure and lower water temperatures which occur in the spring. On the other hand, M. terminalis, X. davidi, and C. molitorella are associated with high precipitation, high river discharge, low atmospheric pressure and low DO concentrations which featured during the summer months. S. curriculus also peaks in the summer and is associated with peak water temperatures and minimum NH₃–N concentrations. Rhinogobius giurinus occur when higher atmospheric pressure, lower precipitation and lower river discharges occur in the autumn. Dominant fish species stagger their spawning period to avoid intraspecific competition for food resources during early life stages; a coexistence strategy to some extent. This research outlines the environmental requirements for successful spawning for different fish species. Understanding processes such as those outlined in this research paper is the basis of conservation of fish community diversity which is a critical resource to a successful sustainable fishery in the Pearl River.     

Differential Regulation of TLR Signaling on the Induction of Antiviral Interferons in Human Intestinal Epithelial Cells Infected with Enterovirus 71

Enterovirus 71 (EV71) causes hand-foot-and-mouth disease, which can lead to fatal neurological complications in young children and infants. Few gastrointestinal symptoms are observed clinically, suggesting the presence of a unique immunity to EV71 in the gut. We reported a robust induction of interferons (IFNs) in human intestinal epithelial cells (HT-29), which was suppressed in other types such as RD and HeLa cells. The underlying mechanism for the apparent difference remains obscure. In this study we report that in EV71-infected HT-29 cells, TLR/TRIF signaling was essential to IFN induction; viral replication increased and the induction of IFN-α, -β, -ω, -κ, and -ε decreased markedly in TRIF-silenced HT-29 cells. Importantly, TRIF was degraded by viral 3C^pro in RD cells, but resisted cleavage, and IRF3 was activated and translocated into the nucleus in HT-29 cells. Taken together, our data suggest that IFNs were induced differentially in human HT-29 cells through an intact TLR/TRIF signaling, which differs from other cell types and may be implicated in viral pathogenesis in EV71 infection.     

Exploring taxonomic diversity and biogeography of the family Nemacheilinae (Cypriniformes)

Nemacheilidae, in the superfamily Cobitoidea, is comprised of many of morphologically similar fish species that occur in Eurasian water bodies. This large group shows inconsistencies between traditional morphological taxonomy and molecular phylogenetic data. We used mitochondrial genomes, recombinase‐activating gene proteins 1 (RAG1) and the mitochondrial cytochrome c oxidase I gene (COI) to study the phylogenetic relationships among Nemacheilidae species using Bayesian inference and maximum likelihood approaches. Phylogenetic analyses based on mitogenomes provided support for two clades (I and II). The mitogenomes, RAG1, and COI results indicated that several species and genera were not consistent with the traditional morphological subdivisions. The two clades inferred from mitogenomes showed clear geographical patterns. The Tibetan Plateau, Hengduan Mountains, and the Iran Plateau may act as a barrier dividing the clades. The estimated timing of clades separation (36.05 million years ago) coincides with the first uplift of the Tibetan Plateau. We conclude that the geological history of the Tibetan Plateau played a role in the diversification and distribution of the Nemacheilidae taxa. These results provided a phylogenetic framework for future studies of this complex group.     

长期施肥对黄土高原典型草原群落稳定性的影响及机制研究

施肥是当前草地生态系统最常见的人为干扰方式之一,可导致草地生物多样性和生态系统稳定性发生显著变化.该研究以黄土高原典型草原为研究对象,通过连续8年的氮肥(尿素)野外添加试验,分析不同氮肥处理(分别为0、5、10、20、40和80 g·m-2)对草地群落稳定性的影响,并分析检验可能影响群落稳定性的四个潜在机制(物种多样性...     

Impact of nonrandom selection mechanisms on the causal effect estimation for two-sample Mendelian randomization methods

Nonrandom selection in one-sample Mendelian Randomization (MR) results in biased estimates and inflated type I error rates only when the selection effects are sufficiently large. In two-sample MR, the different selection mechanisms in two samples may more seriously affect the causal effect estimation. Firstly, we propose sufficient conditions for causal effect invariance under different selection mechanisms using two-sample MR methods. In the simulation study, we consider 49 possible selection mechanisms in two-sample MR, which depend on genetic variants (G), exposures (X), outcomes (Y) and their combination. We further compare eight pleiotropy-robust methods under different selection mechanisms. Results of simulation reveal that nonrandom selection in sample II has a larger influence on biases and type I error rates than those in sample I. Furthermore, selections depending on X+Y, G+Y, or G+X+Y in sample II lead to larger biases than other selection mechanisms. Notably, when selection depends on Y, bias of causal estimation for non-zero causal effect is larger than that for null causal effect. Especially, the mode based estimate has the largest standard errors among the eight methods. In the absence of pleiotropy, selections depending on Y or G in sample II show nearly unbiased causal effect estimations when the casual effect is null. In the scenarios of balanced pleiotropy, all eight MR methods, especially MR-Egger, demonstrate large biases because the nonrandom selections result in the violation of the Instrument Strength Independent of Direct Effect (InSIDE) assumption. When directional pleiotropy exists, nonrandom selections have a severe impact on the eight MR methods. Application demonstrates that the nonrandom selection in sample II (coronary heart disease patients) can magnify the causal effect estimation of obesity on HbA1c levels. In conclusion, nonrandom selection in two-sample MR exacerbates the bias of causal effect estimation for pleiotropy-robust MR methods.