Assessing the latitudinal gradient in herbivory

Plant–herbivore interactions occur in all ecosystems and provide a major avenue for energy flow to higher trophic levels. A long‐standing hypothesis to explain the latitudinal gradient in species diversity proposes that the relatively stable and frost‐free climate of the tropics should lead to more intense biotic interactions in tropical compared with temperate environments, giving rise to a greater diversity of plants and herbivores. Herbivory rates have been compared across latitudes to test this biotic interactions hypothesis, with herbivory typically being measured from observable leaf damage. However, we argue that a measure of percentage leaf damage alone does not straightforwardly reflect the cost of herbivory to the plant, and on its own does not constitute an appropriate test of the biotic interactions hypothesis. For a given amount of herbivory, the impact of herbivory is dependent upon many factors, such as the construction cost of the leaf, the growth and replacement rates and leaf life span. We investigate the latitudinal gradient in herbivory by analysing a large dataset of herbivory rates for 452 tree species and separating the species into those with short and long leaf life spans. We show that annual herbivory rates tend to be greater at lower latitudes for evergreen species (which have long‐lived leaves), but no trend in herbivory rate with latitude was found for species with short leaf life spans. Phylogenetic least squares regression assuming Ornstein‐Uhlenbeck processes also showed a negative effect of latitude on herbivory rate for evergreen trees, but we caution that viewing herbivory as a species trait is problematic. An integrative approach that incorporates leaf life span, as well as the costs of investment in growth and potential costs of losing leaf tissue, is needed to further our understanding of the ecological and evolutionary dynamics of herbivory.     

大黄鱼主要致病菌拮抗菌株的分离鉴定、抑菌谱及安全性分析

大黄鱼是我国重要的海水养殖鱼类,随着大黄鱼养殖规模的扩大,病害也日益增多,其中细菌性疾病是造成大黄鱼疾病暴发、死亡的重要病原。近年来,哈维弧菌(Vibrio harveyi)、溶藻弧菌(Vibrio alginolyticus)、杀香鱼假单胞菌(Pseudomonas plecoglossicida)、鰤鱼诺卡菌(Nocardia seriolea)等细菌造成了大黄鱼养殖重大经济损失。为寻找大黄鱼主要致病菌的拮抗菌,用于大黄鱼细菌病的生态控制,作者对大黄鱼及周边环境进行了拮抗菌的分离和鉴定。以哈维弧菌、杀香鱼假单胞菌作为拮抗活性筛选指示菌,用纸片法(KB)、菌落接种法从大黄鱼体内、养殖池周边土壤、藻类、芦苇等筛选出具抗菌活性物质菌株10株;分离菌株用16S rDNA通用引物序列分析鉴定为芽孢杆菌(Bacillus sp.)、产碱杆菌(Alcaligenes sp.)、类芽孢杆菌(Paenibacillus sp.)、赖氨酸芽孢杆菌(Lysinibacillus sp.)、弧菌(Vibrio sp.)和异常球菌(Daenococcus sp.)等。对具较强抑菌活性的碱性杆菌NBPa-7(Alcaligenes faecalis)和芽孢杆菌NBlm-36(Bacillus amyloliquefaciens)进行了抑菌活性测定,结果表明NBPa-7对溶藻弧菌、杀香鱼假单胞菌有良好拮抗作用,抑菌直径分别为23.20 mm、12.00 mm;NBlm-36对创伤弧菌(Vibrio vulnificus)、哈维弧菌、嗜水气单胞菌(Aeromonas hydrophila)、大肠杆菌(Escherichia coli)及葡萄球菌(Staphylococcus sp.)有拮抗作用,抑菌直径为6.00 mm-14.00 mm。胞外抑菌产物对热、酸、碱有较好耐受性。将拮抗菌以1×108CFU/ind腹腔注射成年鼠、口喂新生鼠,48 h内未出现毒性和死亡,将拮抗菌以3×108CFU/ind腹腔注射大黄鱼,2周内未出现发病死亡,大黄鱼内脏未发生病变,白细胞未出现明显升高现象,初步表明拮抗菌株不具有致病力。     

Eco‐morphological differentiation in Lake Magadi tilapia,an extremophile cichlid fish living in hot,alkaline and hypersaline lakes in East Africa

Ecological diversification through divergent selection is thought to be a major force during the process of adaptive radiations. However, the large sizes and complexity of most radiations such as those of the cichlids in the African Great Lakes make it impossible to infer the exact evolutionary history of any population divergence event. The genus Alcolapia, a small cichlid lineage endemic to Lakes Magadi and Natron in East Africa, exhibits phenotypes similar to some of those found in cichlids of the radiations of the African Great Lakes. The simplicity within Alcolapia makes it an excellent model system to investigate ecological diversification and speciation. We used an integrated approach including population genomics based on RAD‐seq data, geometric morphometrics and stable isotope analyses to investigate the eco‐morphological diversification of tilapia in Lake Magadi and its satellite lake Little Magadi. Additionally, we reconstructed the demographic history of the species using coalescent simulations based on the joint site frequency spectrum. The population in Little Magadi has a characteristically upturned mouth—possibly an adaptation to feeding on prey from the water surface. Eco‐morphological differences between populations within Lake Magadi are more subtle, but are consistent with known ecological differences between its lagoons such as high concentrations of nitrogen attributable to extensive guano deposits in Rest of Magadi relative to Fish Springs Lagoon. All populations diverged simultaneously only about 1100 generations ago. Differences in levels of gene flow between populations and the effective population sizes have likely resulted in the inferred heterogeneous patterns of genome‐wide differentiation.     

皮肤组织显微共聚焦拉曼光谱成像研究

显微共聚焦拉曼光谱成像技术(Confocal Raman Microspectroscopy Imaging,CRMI)能够对样品微区进行精确无损的拉曼光谱分析和光谱图像扫描,提供生物样品的无损高分辨光学信息。本项研究工作,利用CRMI技术实验获取了正常人体离体皮肤组织的拉曼光谱特征,并结合典型特征峰的扫描图像,探讨了脂类、蛋白质等成分在皮肤真皮层的分布特点。实验发现皮肤组织真皮层内胶原蛋白的拉曼特征峰1 248 cm-1强度及其空间分布尤为突出,这一实验结果与组织学中胶原纤维占真皮结缔组织95%的事实相符。实验结果显示,CRMI技术能够全面诠释生物组织内部生化组成与分布信息,在实验描述皮肤组织病理变化的分子生物学机制方面具有广阔的应用前景。     

Can pollen match shoes to a previously visited indoor location?

This paper is part of an investigation dedicated to indoor pollen from a forensic point of view. Previous studies documented the ‘natural’ pollen content of a flat and how it was ‘artificially’ altered by ornamental plants. The present study investigated if this ‘artificial pollen trace’ can be transferred to shoes. Brand new sneakers were worn in the flat and afterwards examined for pollen on their soles. The results showed that the shoes gathered pollen and that some pollen types correlated to those found in the flat. Afterwards, some of these shoes were worn while walking through the city for approximately 1.8 km. On these shoes, flat pollen was also detectable, but in low abundances. This study shows that, from a palynological point of view, shoes are worth a look at when a crime is investigated. Uncommon pollen grains on shoes can point to an indoor location with the corresponding ornamental plants.     

Investigation on the Interaction of Hydroxyethyl Starch 130/0.4 (Voluven) and Serum Albumin for Pharmacokinetic and Toxicological Implications

The interaction of hydroxyethyl starch 130/0.4 (Voluven) with human serum albumin (HSA) has been investigated by fluorescence (steady state and synchronous), Fourier transforms infrared (FT‐IR), and circular dichroism (CD) spectroscopies. Analysis of the fluorescence quenching data of HSA by Voluven using the Stern–Volmer method revealed the formation of 1:1 ground‐state complex. Evaluation of binding parameters and binding energy indicated that the binding reaction was exothermic. On the basis of fluorescence measurements, it was concluded that electrostatic forces play a crucial role in stabilizing the complex. The binding distance was calculated by using Förster resonance energy transfer (FRET) theory. The conformational changes of HSA were obtained qualitatively as well as quantitatively using synchronous fluorescence, FT‐IR, and CD. The HSA underwent partial unfolding in the presence of Voluven.     

油麻藤凝集素的荧光光谱研究

用化学修饰、内源荧光和荧光淬灭等方法研究了油麻藤凝集素（ＭＳＬ）的溶液构象变化和微环境的构象特征。研究发现ＭＳＬ分子中总共有９个色氨酸（Ｔｒｐ）残基,它们的荧光能被丙烯酰胺淬灭,但不易为ＫＩ接近而淬灭,ＭＳＬ经Ｎ－溴代琥珀酰亚胺（ＮＢＳ）修饰后,其内源性荧光发射谱发生相应变化,结果表明ＭＳＬ分子中部分Ｔｒｐ残基埋藏于分子内部,而位于分子表面的Ｔｒｐ残基可能处于分子的疏水袋中。     

Recombinase-mediated cassette exchange (RMCE) — A rapidly-expanding toolbox for targeted genomic modifications

Starting in 1991, the advance of Tyr-recombinases Flp and Cre enabled superior strategies for the predictable insertion of transgenes into compatible target sites of mammalian cells. Early approaches suffered from the reversibility of integration routes and the fact that co-introduction of prokaryotic vector parts triggered uncontrolled heterochromatization. Shortcomings of this kind were overcome when Flp-Recombinase Mediated Cassette Exchange entered the field in 1994. RMCE enables enhanced tag-and-exchange strategies by precisely replacing a genomic target cassette by a compatible donor construct. After “gene swapping” the donor cassette is safely locked in, but can nevertheless be re-mobilized in case other compatible donor cassettes are provided (“serial RMCE”). These features considerably expand the options for systematic, stepwise genome modifications. The first decade was dominated by the systematic generation of cell lines for biotechnological purposes. Based on the reproducible expression capacity of the resulting strains, a comprehensive toolbox emerged to serve a multitude of purposes, which constitute the first part of this review. The concept per se did not, however, provide access to high-producer strains able to outcompete industrial multiple-copy cell lines. This fact gave rise to systematic improvements, among these certain accumulative site-specific integration pathways. The exceptional value of RMCE emerged after its entry into the stem cell field, where it started to contribute to the generation of induced pluripotent stem (iPS-) cells and their subsequent differentiation yielding a variety of cell types for diagnostic and therapeutic purposes. This topic firmly relies on the strategies developed in the first decade and can be seen as the major ambition of the present article. In this context an unanticipated, potent property of serial Flp-RMCE setups concerns the potential to re-open loci that have served to establish the iPS status before the site underwent the obligatory silencing process. Other relevant options relate to the introduction of composite Flp-recognition target sites (“heterospecific FRT-doublets”), into the LTRs of lentiviral vectors. These “twin sites” enhance the safety of iPS re-programming and -differentiation as they enable the subsequent quantitative excision of a transgene, leaving behind a single “FRT-twin”. Such a strategy combines the established expression potential of the common retro- and lentiviral systems with options to terminate the process at will. The remaining genomic tag serves to identify and characterize the insertion site with the goal to identify genomic “safe harbors” (GOIs) for re-use. This is enabled by the capacity of “FRT-twins” to accommodate any incoming RMCE-donor cassette with a compatible design.     

Rule extraction in gene–disease relationship discovery

Background

Biomedical data available to researchers and clinicians have increased dramatically over the past years because of the exponential growth of knowledge in medical biology. It is difficult for curators to go through all of the unstructured documents so as to curate the information to the database. Associating genes with diseases is important because it is a fundamental challenge in human health with applications to understanding disease properties and developing new techniques for prevention, diagnosis and therapy.

Methods

Our study uses the automatic rule-learning approach to gene–disease relationship extraction. We first prepare the experimental corpus from MEDLINE and OMIM. A parser is applied to produce some grammatical information. We then learn all possible rules that discriminate relevant from irrelevant sentences. After that, we compute the scores of the learned rules in order to select rules of interest. As a result, a set of rules is generated.

Results

We produce the learned rules automatically from the 1000 positive and 1000 negative sentences. The test set includes 400 sentences composed of 200 positives and 200 negatives. Precision, recall and F-score served as our evaluation metrics. The results reveal that the maximal precision rate is 77.8% and the maximal recall rate is 63.5%. The maximal F-score is 66.9% where the precision rate is 70.6% and the recall rate is 63.5%.

Conclusions

We employ the rule-learning approach to extract gene–disease relationships. Our main contributions are to build rules automatically and to support a more complete set of rules than a manually generated one. The experiments show exhilarating results and some improving efforts will be made in the future.