樟子松人工固沙林衰退的主要特征

针对辽宁省章古台地区樟子松人工固沙林出现的衰退枯死现象,系统地研究了樟子松人工固沙林衰退的主要特征.结果表明,衰退的樟子松人工固沙林外貌景观呈灰绿色,针叶纤细,开花结实率低,平均单株球果数量为10.4～16.5个,成熟种子千粒重为6.96～7.39g,种子空粒、涩粒较多.生长季内2年生针叶营养元素季节变化规律相似,但N、P含量下降,K含量明显增高,表明养分循环失调;衰退林分2年生针叶叶绿素含量较高,健康林分1年生较高且增幅较大.松枯梢病的侵害是樟子松人工固沙林衰退的最明显标志.林分衰退后,树高和胸径生长量下降明显,林分胸径分布结构“左移”(径级小的株数增多),衰弱(亡)木数量增加了15.9%～27.2%;根量分别减少了22.9%～28.9%,其中吸收根减少量最大.     

Ptk2b deletion improves mice folliculogenesis and fecundity via inhibiting follicle loss mediated by Erk pathway

Ptk2b has been found playing critical roles in oocyte maturation and subsequent fertilization in vitro. But what is the exact in vivo function in reproduction still elusive. Here, by constructing Ptk2b mutant mice, we found Ptk2b was not essential for mice fertility, unexpectedly, contrary to previously reported in vitro findings, we found Ptk2b ablation significantly improved female fecundity. Follicle counting indicated that the number of primordial follicles and growing follicles in matured mice was significantly increased in the absence of Ptk2b, whereas the primordial follicle formation showed no defects. We also found this regulation was in an autophosphorylation independent pathway, as autophosphorylation site mutant mice (PTK2B^Y402F) show no phenotype in female fertility. Further biochemistry studies revealed that Ptk2b ablation promotes folliculogenesis via Erk pathway mediate follicle survival. Together, we found a novel biological function of Ptk2b in folliculogenesis, which could be potentially used as a therapeutic target for corresponding infertility.     

Combining biocatalysis and chemoselective chemistries for glycopeptide antibiotics modification

Glycopeptide antibiotics are clinically important medicines to treat serious Gram-positive bacterial infections. The emergence of glycopeptide resistance among pathogens has motivated considerable interest in expanding structural diversity of glycopeptide to counteract resistance. The complex structure of glycopeptide poses substantial barriers to conventional chemical methods for structural modifications. By contrast, biochemical approaches have attracted great attention because ample biosynthetic information and sophisticated toolboxes have been made available to change reaction specificity through protein engineering, domain swapping, pathway engineering, addition of substrate analogs, and mutagenesis.     

吉林珲春自然保护区东北虎和东北豹及其有蹄类猎物的多度与分布

珲春国家级自然保护区是东北虎(Panthera tigris altaica)、东北豹(Panthera pardus orientalis)等濒危物种在中国的核心分布区。为了探究该区域野生动物的多度水平和空间分布, 了解人类干扰情况, 我们运用相对多度指数(relative abundance index, RAI)分析了2013年4-6月设置于此的83个红外相机位点的监测数据。红外相机的总捕获天数6,060 d, 共捕获10科18种野生哺乳动物, 其中鼬科4种, 猫科动物3种, 犬科、鹿科和松鼠科各2种, 猪科、熊科、麝科、猬科和兔科各1种。研究期间共拍摄到东北虎11只个体, 东北豹13只个体。从相对多度指数来看, 东北虎的相对多度(0.84)远高于东北豹(0.48), 它们的有蹄类猎物中梅花鹿(Cervus nippon)的相对多度最高(2.18), 其次为狍(Capreolus pygargus)(1.53)和野猪(Sus scrofa)(0.92)。人类活动和放牧的相对多度水平(分别为40.64和2.76)显著高于野生动物。在空间分布上, 东北虎和梅花鹿主要在保护区的核心区分布, 且与保护区社区共管区的多度水平差异显著, 而东北豹在不同功能区之间的分布差异不显著, 狍在保护区北部的多度水平较高, 但各功能区之间差异不显著, 野猪在社区共管区的多度水平显著高于核心区。可见, 核心区频繁的人类活动和放牧活动对野生动物的保护产生了影响, 未来应加强关于人类干扰对虎、豹种群及其有蹄类猎物的影响评估。     

Structural insights into the T6SS effector protein Tse3 and the Tse3–Tsi3 complex from Pseudomonas aeruginosa reveal a calcium‐dependent membrane‐binding mechanism

The opportunistic pathogen Pseudomonas aeruginosa uses the type VI secretion system (T6SS) to deliver the muramidase Tse3 into the periplasm of rival bacteria to degrade their peptidoglycan (PG). Concomitantly, P. aeruginosa uses the periplasm‐localized immunity protein Tsi3 to prevent potential self‐intoxication caused by Tse3, and thus gains an edge over rival bacteria in fierce niche competition. Here, we report the crystal structures of Tse3 and the Tse3–Tsi3 complex. Tse3 contains an annexin repeat‐like fold at the N‐terminus and a G‐type lysozyme fold at the C‐terminus. One loop in the N‐terminal domain (Loop 12) and one helix (α9) from the C‐terminal domain together anchor Tse3 and the Tse3–Tsi3 complex to membrane in a calcium‐dependent manner in vitro, and this membrane‐binding ability is essential for Tse3's activity. In the C‐terminal domain, a Y‐shaped groove present on the surface likely serves as the PG binding site. Two calcium‐binding motifs are also observed in the groove and these are necessary for Tse3 activity. In the Tse3–Tsi3 structure, three loops of Tsi3 insert into the substrate‐binding groove of Tse3, and three calcium ions present at the interface of the complex are indispensable for the formation of the Tse3–Tsi3 complex.     

Deep learning for DNase I hypersensitive sites identification

Background

The DNase I hypersensitive sites (DHSs) are associated with the cis-regulatory DNA elements. An efficient method of identifying DHSs can enhance the understanding on the accessibility of chromatin. Despite a multitude of resources available on line including experimental datasets and computational tools, the complex language of DHSs remains incompletely understood.

Methods

Here, we address this challenge using an approach based on a state-of-the-art machine learning method. We present a novel convolutional neural network (CNN) which combined Inception like networks with a gating mechanism for the response of multiple patterns and longterm association in DNA sequences to predict multi-scale DHSs in Arabidopsis, rice and Homo sapiens.

Results

Our method obtains 0.961 area under curve (AUC) on Arabidopsis, 0.969 AUC on rice and 0.918 AUC on Homo sapiens.

Conclusions

Our method provides an efficient and accurate way to identify multi-scale DHSs sequences by deep learning.

     

A semi-parametric statistical model for integrating gene expression profiles across different platforms

Determining differentially expressed genes (DEGs) between biological samples is the key to understand how genotype gives rise to phenotype. RNA-seq and microarray are two main technologies for profiling gene expression levels. However, considerable discrepancy has been found between DEGs detected using the two technologies. Integration data across these two platforms has the potential to improve the power and reliability of DEG detection. We propose a rank-based semi-parametric model to determine DEGs using information across different sources and apply it to the integration of RNA-seq and microarray data. By incorporating both the significance of differential expression and the consistency across platforms, our method effectively detects DEGs with moderate but consistent signals. We demonstrate the effectiveness of our method using simulation studies, MAQC/SEQC data and a synthetic microRNA dataset. Our integration method is not only robust to noise and heterogeneity in the data, but also adaptive to the structure of data. In our simulations and real data studies, our approach shows a higher discriminate power and identifies more biologically relevant DEGs than eBayes, DEseq and some commonly used meta-analysis methods.     

The preventive effect of vaccine prophylaxis on severe respiratory syncytial virus infection:A meta-analysis

Respiratory syncytial virus(RSV) is the key underlying cause of acute lower respiratory tract infection in infants; however, no licensed vaccine against RSV infection is currently available. This study was undertaken to assess the preventive effect of vaccine on RSV infection. In this metaanalysis, 1,792 published randomized clinical trials of RSV vaccines from Jan 1973 to Sep 2015 were examined. Among thirteen studies that met the inclusion criteria, eleven studies estimated the impact of RSV vaccines and four studies estimated the effect of adjuvants. The odds ratios(ORs) were 0.31(95% CI, 0.15–0.67) and 0.62(95% CI, 0.29–1.34), respectively. We found that RSV subunit vaccines can significantly reduce the incidence of RSV infection and that whether vaccination with adjuvant therapy was an effective strategy still remained to be studied. This analysis of the preventive effect of vaccines on RSV infection has direct applications for the prevention of RSV infections.     

Leaf meristems: an easily ignored component of the response to human disturbance in alpine grasslands

Grazing and fencing are two important factors that influence productivity and biomass allocation in alpine grasslands. The relationship between root (R) and shoot (S) biomass and the root:shoot ratio (R/S) are critical parameters for estimating the terrestrial carbon stocks and biomass allocation mechanism responses to human activities. Previous studies have often used the belowground:aboveground biomass ratio (M_b/M_a) to replace the R/S in alpine ecosystems. However, these studies may have neglected the leaf meristem biomass, which belongs to the shoot but occurs below the soil surface, leading to a significant overestimation of the R/S ratio. We conducted a comparative study to explore the differences between the R/S and M_b/M_a at both the species (Stipa purpurea, Carex moorcroftii, and Artemisia nanschanica) and community levels on a Tibetan alpine grassland with grazing and fencing management blocks. The results revealed that the use of the M_b/M_a to express the R/S appeared to overestimate the actual value of the R/S, both at species and community levels. For S. purpurea, the M_b/M_a was three times higher than the R/S. The M_b/M_a was approximately two times higher than the R/S for the species of C. moorcroftii and A. nanschanica and at the community level. The relationships between the R‐S and M_b‐M_a exhibited different slopes for the alpine plants across all the management practices. Compared to the fenced grasslands, the plants in the grazing blocks not only allocated more biomass to the roots but also to the leaf meristems. The present study highlights the contribution of leaf meristems to the accurate assessment of shoot and belowground biomasses. The R/S and M_b/M_a should be cautiously used in combination in the future research. The understanding of the distinction between the R‐S and M_b‐M_a may help to improve the biomass allocation mechanism response to human disturbances in an alpine area.     

YphC and YsxC GTPases assist the maturation of the central protuberance,GTPase associated region and functional core of the 50S ribosomal subunit

YphC and YsxC are GTPases in Bacillus subtilis that facilitate the assembly of the 50S ribosomal subunit, however their roles in this process are still uncharacterized. To explore their function, we used strains in which the only copy of the yphC or ysxC genes were under the control of an inducible promoter. Under depletion conditions, they accumulated incomplete ribosomal subunits that we named 45S_YphC and 44.5S_YsxC particles. Quantitative mass spectrometry analysis and the 5–6 Å resolution cryo-EM maps of the 45S_YphC and 44.5S_YsxC particles revealed that the two GTPases participate in the maturation of the central protuberance, GTPase associated region and key RNA helices in the A, P and E functional sites of the 50S subunit. We observed that YphC and YsxC bind specifically to the two immature particles, suggesting that they represent either on-pathway intermediates or that their structure has not significantly diverged from that of the actual substrate. These results describe the nature of these immature particles, a widely used tool to study the assembly process of the ribosome. They also provide the first insights into the function of YphC and YsxC in 50S subunit assembly and are consistent with this process occurring through multiple parallel pathways, as it has been described for the 30S subunit.