Partitioning controls on Amazon forest photosynthesis between environmental and biotic factors at hourly to interannual timescales

Gross ecosystem productivity (GEP) in tropical forests varies both with the environment and with biotic changes in photosynthetic infrastructure, but our understanding of the relative effects of these factors across timescales is limited. Here, we used a statistical model to partition the variability of seven years of eddy covariance‐derived GEP in a central Amazon evergreen forest into two main causes: variation in environmental drivers (solar radiation, diffuse light fraction, and vapor pressure deficit) that interact with model parameters that govern photosynthesis and biotic variation in canopy photosynthetic light‐use efficiency associated with changes in the parameters themselves. Our fitted model was able to explain most of the variability in GEP at hourly (R² = 0.77) to interannual (R² = 0.80) timescales. At hourly timescales, we found that 75% of observed GEP variability could be attributed to environmental variability. When aggregating GEP to the longer timescales (daily, monthly, and yearly), however, environmental variation explained progressively less GEP variability: At monthly timescales, it explained only 3%, much less than biotic variation in canopy photosynthetic light‐use efficiency, which accounted for 63%. These results challenge modeling approaches that assume GEP is primarily controlled by the environment at both short and long timescales. Our approach distinguishing biotic from environmental variability can help to resolve debates about environmental limitations to tropical forest photosynthesis. For example, we found that biotically regulated canopy photosynthetic light‐use efficiency (associated with leaf phenology) increased with sunlight during dry seasons (consistent with light but not water limitation of canopy development) but that realized GEP was nonetheless lower relative to its potential efficiency during dry than wet seasons (consistent with water limitation of photosynthesis in given assemblages of leaves). This work highlights the importance of accounting for differential regulation of GEP at different timescales and of identifying the underlying feedbacks and adaptive mechanisms.     

The stabilizing contribution of thymine in duplexes of (dA)24 with (dU)24, (dT)24, (dU12-dT12), (dU-dT)12, (dU2-dT2)6, or (dU3-dT3)4: nearest neighbor and next-nearest neighbor effects

Ultraviolet melting curves are used to determine the effect of the pyrimidine 5-methyl group on the stability of duplexes of (dA)(24) with (dU)(24), (dT)(24), (dU(12)-dT(12)), (dU-dT)(12), (dU(2)-dT(2))(6), and (dU(3)-dT(3))(4). Substitution of a T for a U results in an increase in stability, which is attributed to an increase in strength of dipole-induced dipole and dispersion (van der Waals) interactions. Significant additional enhancement occurs when two T residues are adjacent. A further increase in the number of adjacent T's has a relatively slight effect on T(m). The sequence effect appears to be largely attributable to an increment in dispersion forces.The CD spectra of the duplexes are all closely similar except in the region between 260 and 290 nm. A band near 272 nm associated with the presence of U in the spectrum of (dA)(24).(dU)(24) decreases in intensity when T's are incorporated in the pyrimidine strand. The band is completely replaced in the spectrum of (dA)(24).(dT)(24) with a new maximum at 282 nm and a minimum at 268 nm, both of lower magnitude. The emergence of the two new bands is correlated with the presence of adjacent T's once more, and only two adjacent T's appear necessary for a major part of the change to occur. The degree of cation release on thermal dissociation of the oligomer dimers ranges from Deltai = 0.14 to 0.16, about the same or slightly less than values reported for polynucleotide duplexes and less than predicted from theoretical calculations.     

RNA干扰下调PTEN表达对体外活化肝星状细胞α-微管蛋白及γ-微管蛋白表达的影响

目的: 探讨RNA干扰下调第10号染色体缺失的磷酸酶张力蛋白同源物基因(PTEN)表达对体外活化肝星状细胞 (HSC) α-微管蛋白(α-tubulin)及γ-微管蛋白(γ-tubulin)表达的影响。方法: 2017年9月至2018年3月,以腺病毒为载体将靶向PTEN的RNA干扰序列—短发夹RNA (shRNA)转染体外培养的活化大鼠肝星状细胞系HSC-T6,实验分为3组:对照组(Control组, 以DMEM代替腺病毒液进行腺病毒转染)、Ad-GFP组(以对照空病毒Ad-GFP转染体外活化HSC)、 Ad-shRNA/PTEN组(以携带靶向PTEN的shRNA的重组腺病毒Ad-shRNA/PTEN转染体外活化HSC),每组设6个复孔。采用Western blot及实时荧光定量PCR技术检测各组HSC的PTEN蛋白及mRNA表达;免疫荧光法检测各组HSC的α-tubulin及γ-tubulin表达。结果: 与对照组及Ad-GFP组比较,Ad-shRNA/PTEN组HSC的PTEN蛋白及mRNA表达明显降低 (P＜0.05)。 HSC的α-tubulin主要表达于细胞浆,对照组和Ad-GFP组HSC的α-tubulin呈丝网状、辐射状均匀分布于细胞核周围,而Ad-shRNA/PTEN 组HSC的α-tubulin向细胞两端末梢逐渐聚集并在细胞两端稍增多;与对照组HSC的α-tubulin荧光积分光密度值(IOD) (40803.00±2006.59)及Ad-GFP组HSC的α-tubulin荧光 IOD (42302.50±2537.93)比较,Ad-shRNA/PTEN组HSC的α-tubulin荧光 IOD (101495.17 ±5005.39)明显升高(P＜0.05),而对照组与Ad-GFP组HSC的α-tubulin 荧光IOD比较差异无统计学意义(P＞0.05)。 HSC的γ-tubulin也主要表达于胞浆,并在胞浆中有散在点状聚集,但Ad-shRNA/PTEN组HSC的γ-tubulin点状聚集更明显;与对照组HSC的γ-tubulin荧光IOD (20410.68±1815.53)及Ad-GFP组HSC的γ-tubulin荧光IOD (20137.50±1469.49)比较,Ad-shRNA/PTEN组HSC的γ-tubulin荧光IOD (41310.83±1544.68) 明显升高(P＜0.05),而对照组与Ad-GFP组HSC的γ-tubulin荧光IOD比较差异无统计学意义(P＞0.05)。结论: 下调体外活化肝星状细胞的PTEN表达可显著增加其α-微管蛋白及γ-微管蛋白表达,并引起上述微管蛋白在胞浆中的分布发生变化。     

Resprouting after disturbance in the short-lived herb Rorippa palustris (Brassicaceae): an experiment with juveniles

The impact of plant age, severity of injury and nutrient levels on the ability to resprout from roots was experimentally assessed in juveniles of the short-lived herb Rorippa palustris (L.) Besser. In a chamber experiment, six cohorts of young plants (1–6 week old) were injured to obtain data on the threshold age for the ability to resprout from roots. We found that plant age was an important factor influencing resprouting ability: injured individuals older than 5 weeks were able to resprout, but not plants younger than 3 weeks. The impact of injury severity (defoliation and removal of axillary buds) and nutrient levels on resprouting ability was assessed on juveniles in a greenhouse experiment. Injury induced growth of new shoots from root buds, while the number of adventitious buds on roots was not influenced by injury. Both injury treatments had a similar effect in this respect, and the amount of regenerated biomass and the extent of regeneration were not different among injury treatments. The number of new shoots produced after injury was higher at the high nutrient level, but the number of formed adventitious buds on roots was not influenced by nutrient level. Nutrient level also influenced the amount of regenerated biomass, but the extent of regeneration (regenerated/removed biomass) was not influenced. The short-lived monocarpic species R. palustris is able to resprout from roots relatively easily. This ability seems to be advantageous in disturbed habitats and this idea is discussed throughout the paper.     

Reproductive niche differentiation in syntopic tropical tree frogs (Agalychnis)

Small differences in syntopic Agalychnis callidryas and A. spurrelli oviposition sites and embryo predation via snakes and invertebrates provide context for a previously unexplainable difference in embryonic behavioral risk responses. Correlations in reproductive and ecological traits suggest directional selection in the syntopic populations of these species. [Correction added on 10 November 2022: The abstract was updated to clarify that there was only one difference. The words character displacement were replaced by directional selection.]     

二次等距抽样

本文提出了一种二次等距抽样方法,并提出了总体平均值的一个估计量：拼配部分的比型估计与轮换部分的样本均值的加权平均。当样本量较大时,求出了估计量的方差及最优轮换比．并对特殊情形进行了讨论和数值比较．     

Design and coverage of high throughput genotyping arrays optimized for individuals of East Asian, African American, and Latino race/ethnicity using imputation and a novel hybrid SNP selection algorithm

Four custom Axiom genotyping arrays were designed for a genome-wide association (GWA) study of 100,000 participants from the Kaiser Permanente Research Program on Genes, Environment and Health. The array optimized for individuals of European race/ethnicity was previously described. Here we detail the development of three additional microarrays optimized for individuals of East Asian, African American, and Latino race/ethnicity. For these arrays, we decreased redundancy of high-performing SNPs to increase SNP capacity. The East Asian array was designed using greedy pairwise SNP selection. However, removing SNPs from the target set based on imputation coverage is more efficient than pairwise tagging. Therefore, we developed a novel hybrid SNP selection method for the African American and Latino arrays utilizing rounds of greedy pairwise SNP selection, followed by removal from the target set of SNPs covered by imputation. The arrays provide excellent genome-wide coverage and are valuable additions for large-scale GWA studies.     

A cytokine super cyclone in COVID-19 patients with risk factors: the therapeutic potential of BCG immunization

The seventh human coronavirus SARS-CoV2 belongs to the cluster of extremely pathogenic coronaviruses including SARS-CoV and MERS-CoV, which can cause fatal lower respiratory tract infection. Likewise, SARS-CoV2 infection can be fatal as the disease advances to pneumonia, followed by acute respiratory distress syndrome (ARDS). The development of lethal clinical symptons is associated with an exaggerated production of inflammatory cytokines, referred to as the cytokine storm, is a consequence of a hyperactivated immune response aginst the infection. In this article, we discuss the pathogenic consequences of the cytokine storm and its relationship with COVID-19 associated risk factors. The increased pro-inflammatory immune status in patients with risk factors (diabetes, hypertension, cardiovascular disease, COPD) exacerbates the Cytokine-storm of COVID-19 into a ‘Cytokine Super Cyclone’. We also evaluate the antiviral immune responses provided by BCG vaccination and the potential role of ‘trained immunity’ in early protection against SARS-CoV2.     

侵占城郊型林地的生态环境损害案例分析及评估方法

城市周边森林生态系统不断被蚕食,导致生态系统功能退化,严重威胁到城市的生态安全。增强"环境有价,损害担责,应赔尽赔"理念和提升城市生态系统质量势在必行。结合某城市一宗非法侵占近郊林地案,首先完整和系统地分析了生态环境损害鉴定评估流程：包括接受委托、初步调查、方案设计、时空范围确定、基线确认、因果关系分析、损害确认等,直至形成评估结果并被法院采纳,以期凝练总结针对城市生态系统的生态环境损害鉴定评估业务化流程。结合本案破坏行为持续时间长（约为13年）,涉案林地面积逐年递增（从最初的6550 m²到最终的24040 m²）等特点,以周边同期未破坏林地为"对照样地",通过实地调查及相关资料分析,确定损害基线种群密度（2066株/hm²）、林分高度（6.4 m）、生物量（104600 kg/hm²）等关键参数,最终计算生态环境损害价值量为2182573元。研究侵占城郊型林地生态环境损害典型案例,对突显城市生态系统损害案件的鉴定评估环节具有重要引领作用。     

Computational identification of human long intergenic non-coding RNAs using a GA–SVM algorithm

Long intergenic non-coding RNAs (lincRNAs) are a new type of non-coding RNAs and are closely related with the occurrence and development of diseases. In previous studies, most lincRNAs have been identified through next-generation sequencing. Because lincRNAs exhibit tissue-specific expression, the reproducibility of lincRNA discovery in different studies is very poor. In this study, not including lincRNA expression, we used the sequence, structural and protein-coding potential features as potential features to construct a classifier that can be used to distinguish lincRNAs from non-lincRNAs. The GA–SVM algorithm was performed to extract the optimized feature subset. Compared with several feature subsets, the five-fold cross validation results showed that this optimized feature subset exhibited the best performance for the identification of human lincRNAs. Moreover, the LincRNA Classifier based on Selected Features (linc-SF) was constructed by support vector machine (SVM) based on the optimized feature subset. The performance of this classifier was further evaluated by predicting lincRNAs from two independent lincRNA sets. Because the recognition rates for the two lincRNA sets were 100% and 99.8%, the linc-SF was found to be effective for the prediction of human lincRNAs.