Temporal dynamics of soil bacterial network regulate soil resistomes

Soil bacteria are diverse and form complicated ecological networks through various microbial interactions, which play important roles in soil multi-functionality. However, the seasonal effects on the bacterial network, especially the relationship between bacterial network topological features and soil resistomes remains underexplored, which impedes our ability to unveil the mechanisms of the temporal-dynamics of antibiotic resistance genes (ARGs). Here, a field investigation was conducted across four seasons at the watershed scale. We observed significant seasonal variation in bacterial networks, with lower complexity and stability in autumn, and a wider bacterial community niche in summer. Similar to bacterial communities, the co-occurrence networks among ARGs also shift with seasonal change, particularly with respect to the topological features of the node degree, which on average was higher in summer than in the other seasons. Furthermore, the nodes with higher betweenness, stress, degree, and closeness centrality in the bacterial network showed strong relationships with the 10 major classes of ARGs. These findings highlighted the changes in the topological properties of bacterial networks that could further alter antibiotic resistance in soil. Together, our results reveal the temporal dynamics of bacterial ecological networks at the watershed scale, and provide new insights into antibiotic resistance management under environmental changes.     

Upgrading the genome of an elite japonica rice variety Kongyu 131 for lodging resistance improvement

Developing a new rice variety requires tremendous efforts and years of input. To improve the defect traits of the excellent varieties becomes more cost and time efficient than breeding a completely new variety. Kongyu 131 is a high-performing japonica variety with early maturity, high yield, wide adaptability and cold resistance, but the poor-lodging resistance hinders the industrial production of Kongyu 131 in the Northeastern China. In this study, we attempted to improve the lodging resistance of Kongyu 131 from perspectives of both gene and trait. On the one hand, by QTL analysis and fine mapping we discovered the candidate gene loci. The following CRISPR/Cas9 and transgenic complementation study confirmed that Sd1 dominated the lodging resistance and favourable allele was mined for precise introduction and improvement. On the other hand, the Sd1 allelic variant was identified in Kongyu 131 by sequence alignment, then introduced another excellent allelic variation by backcrossing. Then, the two new resulting Kongyu 131 went through the field evaluation under different environments, planting densities and nitrogen fertilizer conditions. The results showed that the plant height of upgraded Kongyu 131 was 17%–26% lower than Kongyu 131 without penalty in yield. This study demonstrated a precise and targeted way to update the rice genome and upgrade the elite rice varieties by improving only a few gene defects from the perspective of breeding.     

Effect of density on larval development and female productivity ofTisbe holothuriae (Copepoda,Harpacticoida) under laboratory conditions

The harpacticoid copepodTisbe holothuriae has been cultivated in the Helgoland laboratory for more than 20 years. The effects of density on the larval development and the female productivity were studied by comparing two culture systems: (1) enclosed system, and (2) running-water system. In both systems, a nutritious mixed diet ofDunaliella tertiolecta, Skeletonema costatum, and granulatedMytilus edulis was offered. Larval mortality, larval development and female productivity are found to be significantly dependent on both the population density and specificity of the culture system. Increasing density causes higher larval mortality, longer larval development time, and a reduction in female productivity. In comparison with the enclosed system, the running-water system shows decisive advantages: larval mortality is about 20% lower, the rate of larval development is about two days shorter, and there is a very high rate of nauplii production. The sex ratio exhibits high variations, but in general, there is no clear relationship between sex ratio and population density. Nevertheless, when reared in the running-water system, a relatively high percentage of females (>45%) was found at lower densities.     

Rice ubiquitin-conjugating enzyme OsUbc13 negatively regulates immunity against pathogens by enhancing the activity of OsSnRK1a

Ubc13 is required for Lys63-linked polyubiquitination and innate immune responses in mammals, but its functions in plant immunity still remain largely unknown. Here, we used molecular biological, pathological, biochemical, and genetic approaches to evaluate the roles of rice OsUbc13 in response to pathogens. The OsUbc13-RNA interference (RNAi) lines with lesion mimic phenotypes displayed a significant increase in the accumulation of flg22- and chitin-induced reactive oxygen species, and in defence-related genes expression or hormones as well as resistance to Magnaporthe oryzae and Xanthomonas oryzae pv oryzae. Strikingly, OsUbc13 directly interacts with OsSnRK1a, which is the α catalytic subunit of SnRK1 (sucrose non-fermenting-1-related protein kinase-1) and acts as a positive regulator of broad-spectrum disease resistance in rice. In the OsUbc13-RNAi plants, although the protein level of OsSnRK1a did not change, its activity and ABA sensitivity were obviously enhanced, and the K63-linked polyubiquitination was weaker than that of wild-type Dongjin (DJ). Overexpression of the deubiquitinase-encoding gene OsOTUB1.1 produced similar effects with inhibition of OsUbc13 in affecting immunity responses, M. oryzae resistance, OsSnRK1a ubiquitination, and OsSnRK1a activity. Furthermore, re-interfering with OsSnRK1a in one OsUbc13-RNAi line (Ri-3) partially restored its M. oryzae resistance to a level between those of Ri-3 and DJ. Our data demonstrate OsUbc13 negatively regulates immunity against pathogens by enhancing the activity of OsSnRK1a.     

三江源国家公园草地地上生物量时空动态及其气候影响

三江源区位于青藏高原腹地,作为长江、黄河、澜沧江三大河流的发源地,是我国重要的生态安全屏障。基于三江源区域草地AGB的野外调查数据,本研究采用多种机器学习算法集成分析的方式构建模型,实现了高精度的三江源国家公园草地AGB时空估算。基于AGB时空模拟结果,分析了近19年(2000—2018年)三江源国家公园区域草地AGB的时空动态变化。研究结果显示：(1)通过多种机器学习结合贝叶斯平均模型,草地AGB模拟值与实测值的r为0.88,RMSE为71.60g/m²,表明多模型集成分析的方式对草地AGB估算获得了较好的模拟效果。(2)三江源国家公园区域草地AGB的空间分布具有明显的空间异质性,呈从东南向西北递减的趋势。(3)2000—2018年长江源国家公园、黄河源国家公园和澜沧江国家公园区域草地AGB多年平均值分别为82.96 g/m²、117.54g/m²和168.39 g/m²。(4)近19年间,在黄河和长江源园区受到温度上升的影响草地AGB呈现出非显著性上升趋势;澜沧江区域,由于2015和2016年的...     

1985—2015年中国不同生态系统NDVI时空变化及其对气候因子的响应

植被是陆地生态系统不可或缺的部分,气候是影响其动态变化的重要驱动因素。因此,探究植被的时空变化及其与气候因子的响应关系,有助于理解陆地生态系统的内在演化机制。目前,不同生态系统尺度下的植被动态变化与气候因子的时间响应关系仍未被完整剖析。因此,为了厘清过去30年不同生态系统植被生长对气候因子的响应关系,利用GIMMS NDVI3g数据和气候资料数据,通过Theil-Sen Median趋势分析和Mann-Kendall检验分析了1985—2015年中国陆地NDVI的时空变化特征,结合时间序列相关分析探究了NDVI变化与降水、温度和饱和水汽压差的内部关联,探讨了中国不同生态系统植被与气候因子间的时间响应机制。结果表明：(1) 1985—2015年中国陆地植被呈现改善趋势,年均NDVI先减小后增加,拐点时间在1995年左右,整体变化率为0.5×10^-3/a。农田、森林和草地生态系统的植被显著改善的程度最高,湿地生态系统的植被退化趋势最显著。(2)中国陆地植被NDVI与气候因子的相关性存在明显的空间异质性,且受不同生态系统分区影响。内蒙古高原中部草地生态系统NDVI与降水...     

-cyano-substituted analogoues of decarboxylated S-adenosylmethionine as enzyme activated, irreversible inhibitors of S-adenosylmethionine decarboxylase

A pair of -cyano analogues of decarboxylated S-adenosylmethionine (2a and 2b) were synthesized as potential enzyme activated, irreversible inhibitors of the[pyruvoyl enzyme S-adenosylmethionine decarboxylase (AdoMet-DC). Each of these analogues acts as an irreversible inactivator for ADoMet-DC from Escherichia coli (IC₅₀ values of 9 and 50 μM, respectively). These analogues also inactivate human AdoMet-DC, with K_I values of 246.6 and 7.2 μM, and k_inact values of 0.29 and 0.03 min⁻¹, respectively.     

论Paracarinachitids

研究证明Paracarinachitids的外骨骼都不是由8个骨板组成,骨片具有清楚的微层构造,表明它们是由叠覆的生长层组成,每个生长节上有一个小刺,在顶端下侧面前端都有肾形缺凹。同一标本上存在顶端部的融合和远顶端部的分节彼此递交的现象表明这种表象上的差异是后期次生磷灰石包裹或腐蚀的结果;其下侧缘融合和下侧面无缝隙的现象说明将Paracarinachites spinus的骨片分成头板、中间板和尾板是没有根据的。骨片表面存在的针状体是成岩作用的产物,它是粘土矿物和磷酸盐针状结晶体而不是多板纲的骨针。凡此强有力地说明Yangtzechiton是Paracarinachites的晚出同义名。根据形态功能、组织结构,特别是叠覆状排列的骨片和孤立的生长节等特征,paracarinachitids 可能与zhijinitids有密切关系,但两者是否同源尚缺少进一步的证据、据此,笔者认为将paracarinachitids 暂置于分类位置未定的具骨片后生动物较妥。     

Preparation of the pure diastereomeric forms of S- (5′-deoxy-5′-adenosyl)-1-ammonio-4-methylsulfonio-2- cyclopentene and their evaluation as irreversible inhibitors of S-adenosylmethionine decarboxylase from Escherichia coli

The conformationally restricted S-adenosylmethionine analogue AdoMac (S-(5′-deoxy-5′-adenosyl)-1-ammonio-4-methylsulfonio-2-cyclopentene has been shown to act as an enzyme activated, irreversible inhibitor of theEscherichia coli form of the enzyme S-adenosylmethionine decarboxylase. Inactivation of the enzyme is presumably initiated by formation of an imine linkage between the inhibitor and the terminal pyruvate of the enzyme, followed by base-catalyzed elimination of methylthioadenosine and generation of a latent electrophile. Removal of the driving force for the elimination of methylthioadenosine resulted in a reversibly binding inhibitor. Thus, the thioether analogue corresponding to AdoMac, and the corresponding dihydro derivative (H₂-AdoMac), reversibly inhibit the enzyme. AdoMac was resolved into its four pure diastereomeric forms, and each diastereomer was evaluated as an irreversible inhibitor of the enzyme. The K_I values for the individual diastereomers range between 3.83 and 39.6 μM, with the cis-1S,4R diastereomer being the most potent inhibitor. However, the k_inact values for the four diastereomers are not significantly different, suggesting that the binding of each diastereomer to the enzyme is configuration-dependent, while the subsequent inactivation likely proceeds through a single intermediate which is formed from each of the four diastereomers. Since each pure diastereomer represents a distinct conformational mimic exhibiting restricted sidechain rotation, the data suggests that these and related analogues may be useful as conformational probes for the catalytic site of AdoMet-DC.     

Nonparametric and semiparametric estimation with sequentially truncated survival data

In observational cohort studies with complex sampling schemes, truncation arises when the time to event of interest is observed only when it falls below or exceeds another random time, that is, the truncation time. In more complex settings, observation may require a particular ordering of event times; we refer to this as sequential truncation. Estimators of the event time distribution have been developed for simple left-truncated or right-truncated data. However, these estimators may be inconsistent under sequential truncation. We propose nonparametric and semiparametric maximum likelihood estimators for the distribution of the event time of interest in the presence of sequential truncation, under two truncation models. We show the equivalence of an inverse probability weighted estimator and a product limit estimator under one of these models. We study the large sample properties of the proposed estimators and derive their asymptotic variance estimators. We evaluate the proposed methods through simulation studies and apply the methods to an Alzheimer's disease study. We have developed an R package, seqTrun , for implementation of our method.