模拟喀斯特不同土壤生境下黑麦草对水分胁迫的生长和光合生理响应

以多年生草本黑麦草为对象,模拟喀斯特生境土壤特征设置浅而宽(Shallow and wide, SW:30×30×5 cm~3)和深而窄(Deep and narrow, DN:10×10×45 cm~3)两种土壤容器,以正常降水量为对照供水(W100%),设减水50%(W50%)和减水70%(W30%)共3种水分处理进行盆栽实验,探究了两种不同土壤生境中土壤水分变化对黑麦草生长及光合生理的影响,以进一步理解喀斯特地区植物的适应对策。结果显示:(1)SW生境对水分变化敏感,随供水减少土壤含水量显著下降。轻度减水下植物叶面积增大,光合速率提高,地上部分生长得到促进,但水分严重减少对其生长和光合生理有抑制作用,但地上质量分数和水分利用效率却显著升高;(2)DN生境保水能力较好,随供水减少土壤水分含量下降较为平缓。叶片相对含水量、气孔导度和比叶面积在各水分处理之间差异不显著,但严重减水条件下总生物量、地上质量分数和水分利用效率均有回升。研究表明:浅而宽生境中植物倾向于通过提高地上部分的生长,保持较高的光合速率,并向地上部分分配较多生物量来应对水分胁迫;而深而窄生境中植物会充分利用土壤空间条件,促进根系的生长来提高对水分的吸收,从而维持植物的生长。     

Identification of RNA-binding sites in proteins by integrating various sequence information

RNA–protein interactions play a pivotal role in various biological processes, such as mRNA processing, protein synthesis, assembly, and function of ribosome. In this work, we have introduced a computational method for predicting RNA-binding sites in proteins based on support vector machines by using a variety of features from amino acid sequence information including position-specific scoring matrix (PSSM) profiles, physicochemical properties and predicted solvent accessibility. Considering the influence of the surrounding residues of an amino acid and the dependency effect from the neighboring amino acids, a sliding window and a smoothing window are used to encode the PSSM profiles. The outer fivefold cross-validation method is evaluated on the data set of 77 RNA-binding proteins (RBP77). It achieves an overall accuracy of 88.66% with the Matthew’s correlation coefficient (MCC) of 0.69. Furthermore, an independent data set of 39 RNA-binding proteins (RBP39) is employed to further evaluate the performance and achieves an overall accuracy of 82.36% with the MCC of 0.44. The result shows that our method has good generalization abilities in predicting RNA-binding sites for novel proteins. Compared with other previous methods, our method performs well on the same data set. The prediction results suggest that the used features are effective in predicting RNA-binding sites in proteins. The code and all data sets used in this article are freely available at .     

The formation of the polyploid hybrids from different subfamily fish crossings and its evolutionary significance

This study provides genetic evidences at the chromosome, DNA content, DNA fragment and sequence, and morphological levels to support the successful establishment of the polyploid hybrids of red crucian carp x blunt snout bream, which belonged to a different subfamily of fish (Cyprininae subfamily and Cultrinae subfamily) in the catalog. We successfully obtained the sterile triploid hybrids and bisexual fertile tetraploid hybrids of red crucian carp (RCC) (female symbol) x blunt snout bream (BSB) (male symbol) as well as their pentaploid hybrids. The triploid hybrids possessed 124 chromosomes with two sets from RCC and one set from BSB; the tetraploid hybrids had 148 chromosomes with two sets from RCC and two sets from BSB. The females of tetraploid hybrids produced unreduced tetraploid eggs that were fertilized with the haploid sperm of BSB to generate pentaploid hybrids with 172 chromosomes with three sets from BSB and two sets from RCC. The ploidy levels of triploid, tetraploid, and pentaploid hybrids were confirmed by counting chromosomal number, forming chromosomal karyotype, and measuring DNA content and erythrocyte nuclear volume. The similar and different DNA fragments were PCR amplified and sequenced in triploid, tetraploid hybrids, and their parents, indicating their molecular genetic relationship and genetic markers. In addition, this study also presents results about the phenotypes and feeding habits of polyploid hybrids and discusses the formation mechanism of the polyploid hybrids. It is the first report on the formation of the triploid, tetraploid, and pentaploid hybrids by crossing parents with a different chromosome number in vertebrates. The formation of the polyploid hybrids is potentially interesting in both evolution and fish genetic breeding.     

陕西省生态恢复综合效益评估

开展区域内生态恢复综合效益评估工作,将为地区生态恢复成果梳理及生态系统管理提供决策支持,为未来生态恢复工作的开展提供理论依据。以陕西省为研究区,基于空间遥感数据和生态模型模拟,从生态系统结构、质量和服务3个方面综合评估区域内2000-2015年生态恢复效益。研究结果表明：1）近16年间陕西省土地利用类型呈现林地增加,耕地减少的态势,同时关中地区建设用地大量增加。陕西省87.95%和72.72%的区域分别呈现植被覆盖和生态系统服务总值增加的趋势,尽管区域内人类活动占地增加,但整体生态恢复效果明显。2）陕南地区植被覆盖及生态系统服务总值相对较高,特别是秦岭地区,生态环境较为优越。陕北地区植被覆盖及生态系统服务均值虽相对较低,但均呈现显著增加趋势,未来区域范围内生态环境有着较大的发展潜力。3）尽管不同生态工程基本覆盖了陕西省全境,但受气象因素影响,生态系统服务总值在关中及陕南地区仍呈现出了一定的下降趋势。在未来相关区域的生态恢复资源投入中,应注意干旱环境对生态恢复效果的影响,因地制宜地选取适宜生态工程措施,以保证生态恢复的有效性和持续性,将生态恢复资源的成效最大化。     

嘉宝果不同发育期花果叶的挥发性成分分析

为了解嘉宝果(Myrciaria cauliflora)的挥发性成分,利用顶空-气相色谱/质谱联用技术对其不同发育期的花、果、叶的挥发性成分进行测量。结果表明,萜烯类是花、果、叶的主要挥发性成分,随开花进程呈增加趋势,随果实和叶片成熟进程而下降,单萜类是其中的优势成分,主要有α-蒎烯、β-蒎烯、D-柠檬烯、β-罗勒烯等;花苞期、初花期和嫩叶以β-蒎烯含量最高,盛花期和老叶以α-蒎烯最高,末花期和果实中均以D-柠檬烯含量最高,嫩叶中α-蒎烯和β-蒎烯的总含量高达62.07%。酯类在花期中以初花期含量最高(16.92%),在果实中以完熟期含量最高(14.81%),老叶中酯类含量(4.35%)显著高于嫩叶(0.26%)。因此,α-蒎烯和β-蒎烯是花、果、叶共有主香成分,柳酸甲酯和苯乙醇是花苞期和初花期特征主香成分,毕澄茄烯是完熟果特征风味物质,β-石竹烯是嫩叶特征主香成分,桉叶油醇和β-胡椒烯是老叶特征主香成分。     

Daphnetin attenuates LPS-induced osteolysis and RANKL mediated osteoclastogenesis through suppression of ERK and NFATc1 pathways

Aseptic prosthetic loosening and periprosthetic infection resulting in inflammatory osteolysis is a leading complication of total joint arthroplasty (TJA). Excessive bone destruction around the bone and prosthesis interface plays a key role in the loosening prostheses leading to revision surgery. The bacterial endotoxins or implant-derived wear particles-induced inflammatory response is the major cause of the elevated osteoclast formation and activity. Thus, agents or compounds that can attenuate the inflammatory response and/or inhibit the elevated osteoclastogenesis and excessive bone resorption would provide a promising therapeutic avenue to prevent aseptic prosthetic loosening in TJA. Daphnetin (DAP), a natural coumarin derivative, is clinically used in Traditional Chinese Medicine for the treatment of rheumatoid arthritis due to its anti-inflammatory properties. In this study, we report for the first time that DAP could protect against lipopolysaccharide-induced inflammatory bone destruction in a murine calvarial osteolysis model in vivo. This protective effect of DAP can in part be attributed to its direct inhibitory effect on RANKL-induced osteoclast differentiation, fusion, and bone resorption in vitro. Biochemical analysis found that DAP inhibited the activation of the ERK and NFATc1 signaling cascades. Collectively, our findings suggest that DAP as a natural compound has potential for the treatment of inflammatory osteolysis.     

Explore mediated co-varying dynamics in microbial community using integrated local similarity and liquid association analysis

Background

Discovering the key microbial species and environmental factors of microbial community and characterizing their relationships with other members are critical to ecosystem studies. The microbial co-occurrence patterns across a variety of environmental settings have been extensively characterized. However, previous studies were limited by their restriction toward pairwise relationships, while there was ample evidence of third-party mediated co-occurrence in microbial communities.

Methods

We implemented and applied the triplet-based liquid association analysis in combination with the local similarity analysis procedure to microbial ecology data. We developed an intuitive scheme to visualize those complex triplet associations along with pairwise correlations. Using a time series from the marine microbial ecosystem as example, we identified pairs of operational taxonomic units (OTUs) where the strength of their associations appeared to relate to the values of a third “mediator” variable. These “mediator” variables appear to modulate the associations between pairs of bacteria.

Results

Using this analysis, we were able to assess the OTUs’ ability to regulate its functional partners in the community, typically not manifested in the pairwise correlation patterns. For example, we identified Flavobacteria as a multifaceted player in the marine microbial ecosystem, and its clades were involved in mediating other OTU pairs. By contrast, SAR11 clades were not active mediators of the community, despite being abundant and highly correlated with other OTUs. Our results suggested that Flavobacteria are more likely to respond to situations where particles and unusual sources of dissolved organic material are prevalent, such as after a plankton bloom. On the other hand, SAR11s are oligotrophic chemoheterotrophs with inflexible metabolisms, and their relationships with other organisms may be less governed by environmental or biological factors.

Conclusions

By integrating liquid association with local similarity analysis to explore the mediated co-varying dynamics, we presented a novel perspective and a useful toolkit to analyze and interpret time series data from microbial community. Our augmented association network analysis is thus more representative of the true underlying dynamic structure of the microbial community. The analytic software in this study was implemented as new functionalities of the ELSA (Extended local similarity analysis) tool, which is available for free download (http://bitbucket.org/charade/elsa).

     

Rare variants in novel and known genes associated with primary angle closure glaucoma based on whole exome sequencing of 549 probands

<正>Primary angle closure glaucoma(PACG)is one of the most common causes of irreversible blindness in Asia and about 80%of PACG are present in Asia(Song et al.,2017).Genetics plays an important role in the development of PACG(Gramer et al.,2014).Recently,eight common SNPs were found to be strongly associated with PACG(Vithana et al.,2012;Khor et al.,2016)and mutations in MYRF cause high hyperopia accompanied with PACG(Xiao et al.,2019).However,the genetic defects underlying PACG are still