How does farmer connectivity influence livestock genetic structure? A case‐study in a Vietnamese goat population

Assessing how genes flow across populations is a key component of conservation genetics. Gene flow in a natural population depends on ecological traits and the local environment, whereas for a livestock population, gene flow is driven by human activities. Spatial organization, relationships between farmers and their husbandry practices will define the farmer's network and so determine farmer connectivity. It is thus assumed that farmer connectivity will affect the genetic structure of their livestock. To test this hypothesis, goats reared by four different ethnic groups in a Vietnamese province were genotyped using 16 microsatellites. A Bayesian approach and spatial multivariate analysis (spatial principal component analysis, sPCA) were used to identify subpopulations and spatial organization. Ethnic group frequencies, husbandry practices and altitude were used to create cost maps that were implemented in a least-cost path approach. Genetic diversity in the Vietnamese goat population was low (0.508) compared to other local Asian breeds. Using a Bayesian approach, three clusters were identified. sPCA confirmed these three clusters and also that the genetic structure showed a significant spatial pattern. The least-cost path analysis showed that genetic differentiation was significantly correlated (0.131–0.207) to ethnic frequencies and husbandry practices. In brief, the spatial pattern observed in the goat population was the result of complex gene flow governed by the spatial distribution of ethnic groups, ethnicity and husbandry practices. In this study, we clearly linked the livestock genetic pattern to farmer connectivity and showed the importance of taking into account spatial information in genetic studies.     

Anthranilate synthase subunit organization in Chromobacterium violaceum

Tryptophan is an aromatic amino acid used for protein synthesis and cellular growth. Chromobacterium violaceum ATCC 12472 uses two tryptophan molecules to synthesize violacein, a secondary metabolite of pharmacological interest. The genome analysis of this bacterium revealed that the genes trpA-F and pabA-B encode the enzymes of the tryptophan pathway in which the first reaction is the conversion of chorismate to anthranilate by anthranilate synthase (AS), an enzyme complex. In the present study, the organization and structure of AS protein subunits from C. violaceum were analyzed using bioinformatics tools available on the Web. We showed by calculating molecular masses that AS in C. violaceum is composed of alpha (TrpE) and beta (PabA) subunits. This is in agreement with values determined experimentally. Catalytic and regulatory sites of the AS subunits were identified. The TrpE and PabA subunits contribute to the catalytic site while the TrpE subunit is involved in the allosteric site. Protein models for the TrpE and PabA subunits were built by restraint-based homology modeling using AS enzyme, chains A and B, from Salmonella typhimurium (PDB ID 1I1Q).     

武陵山东部蚤类区系及不同样地群落物种多样性比较

于2000～2004年对武陵山东部7个不同样地、3个不同海拔梯度和6个不同生境类型的蚤类,进行了5年调查与研究.结果:1)在获得的7科17属30种4 320只蚤类中,有4种为古北界种类,占13.33%,22种为东洋界种类,占73.34%,4种为广布种,占13.33%;该结果与云南无量山及临沧地区的蚤类有着相同或相似的区系渊源,而与一江之隔的大巴山东部地区区系则明显不同,该地区以古北界成分为优势;2)武陵山东部地区蚤类的垂直分布规律主要表现在,1 100 m以下主要为东洋界成分,1 200 m以上有少量古北界种类分布,并随海拔升高,古北界成分略有增加;3)在7个不同样地中,物种丰富度和个体数量随海拔升高而增加,在优势种上,多数样地以偏远古蚤为优势,但在优势数量上缺乏明显规律性,并不是随海拔升高而增加;4)在6个不同生境类型中,优势种与优势数量都具明显的规律性,其中以偏远古蚤为主分为两组,山脊侧缘林、小溪山边林和坡地林为一组,人工林和农田山侧灌木林为另一组,前者平均优势数量达80.03%,后者优势数量在31.56%～48.92%之间;5)相似性系数(q值):在整个山体多数样地中,由北向南相似性系数(q值)随海拔降低和空间距离增大而逐渐降低,仅绿丛坡与牛庄、绿丛坡与独岭有例外,表明整个山体植被的片断化、或斑块化,一方面加剧或减低了样地与样地之间蚤类群落的相似程度,另一方面还要受海拔及空间距离的双重影响与制约,即海拔高度和空间距离愈大,蚤类群落的相似性及多样性越低,山体的片断、斑块或破碎化就越明显,这显然与人为过多或过频干扰有关.     

Dissecting spindle architecture with a laser

Microtubules in spindles are too dense to resolve by light microscopy, even with super-resolution methods. Using a new method based on laser-ablation techniques, Brugués et?al. present the first quantitative characterization of the vertebrate meiotic spindle and propose an assembly mechanism for building this architecture.     

Response of workers of Atta sexdens rubropilosa (Hymenoptera: Formicidae) to mandibular gland compounds of virgin males and females

Abstract.  The secretion from the mandibular glands of males of the leaf-cutting ant Atta sexdens rubropilosa is responsible for the reaction of workers outside the nest at the time of sexual swarming. Workers respond with excitability and aggression when presented with the natural mixture of 4-methyl-3-heptanol and 4-methyl-3-heptanone, which is contained in the secretion of the male mandibular glands. Workers respond quickly to fractional amounts of one male equivalent. 4-Methyl-3-heptanone, from the virgin female mandibular glands causes much less response in workers, whereas an equimolar mixture of male and female pheromones gives a still less clear response. The male pheromone plays the most important part in the communication of workers outside the nest at this time.     

A diminution in ascorbate oxidase activity affects carbon allocation and improves yield in tomato under water deficit

The regulation of carbon allocation between photosynthetic source leaves and sink tissues in response to stress is an important factor controlling plant yield. Ascorbate oxidase is an apoplastic enzyme, which controls the redox state of the apoplastic ascorbate pool. RNA interference was used to decrease ascorbate oxidase activity in tomato (Solanum lycopersicum L.). Fruit yield was increased in these lines under three conditions where assimilate became limiting for wild‐type plants: when fruit trusses were left unpruned, when leaves were removed or when water supply was limited. Several alterations in the transgenic lines could contribute to the improved yield and favour transport of assimilate from leaves to fruits in the ascorbate oxidase lines. Ascorbate oxidase plants showed increases in stomatal conductance and leaf and fruit sugar content, as well as an altered apoplastic hexose : sucrose ratio. Modifications in gene expression, enzyme activity and the fruit metabolome were coherent with the notion of the ascorbate oxidase RNAi lines showing altered sink strength. Ascorbate oxidase may therefore be a target for strategies aimed at improving water productivity in crop species.     

钟冠报春苣苔(苦苣苔科)的分类鉴定

原唇柱苣苔属(Chirita Buch.-Ham. ex D. Don)为一个人为界定的属, 2011年在分子系统学研究的基础上对该属及其近缘属开展了系统发育重建工作,其中绝大部分的原唇柱苣苔属唇柱苣苔组(Sect. Gibbosaccus C. B. Clark)的物种被并入了广义报春苣苔属(Primulina Hance)。然而,由于历史原因和早期经典分类学在研究方法上的局限性以及对现报春苣苔属部分物种的营养器官与生殖器官的认知不够,该属下一些物种的分类仍存在一些问题,亟待深入研究。比如,在对中国和越南分布的苦苣苔科植物开展研究的过程中,作者发现两个报春苣苔属的物种——广布于中国西南和华南直至中南半岛中部的钟冠报春苣苔[Primulina swinglei(Merr.)Mich. Möller & A. Weber]命名人和原被认为是中国与广西特有种的疏花报春苣苔[P. laxiflora(W. T. Wang)Yin. Z. Wang]之间的鉴定存在分类学问题,需要进一步厘清两者之间的关系。该文对这两个物种进行了形态比较,同时通过对这两种植物的原始描述对比、植物标本检查、栽培观察以及野外实地观察,确定疏花报春苣苔是钟冠报春苣苔的异名。此外,还明确了钟冠报春苣苔的后选指定模式标本。     

A general method for manipulating DNA sequences from any organism with optical tweezers

Mechanical manipulation of single DNA molecules can provide novel information about DNA properties and protein–DNA interactions. Here we describe and characterize a useful method for manipulating desired DNA sequences from any organism with optical tweezers. Molecules are produced from either genomic or cloned DNA by PCR using labeled primers and are tethered between two optically trapped microspheres. We demonstrate that human, insect, plant, bacterial and viral sequences ranging from ~10 to 40 kilobasepairs can be manipulated. Force-extension measurements show that these constructs exhibit uniform elastic properties in accord with the expected contour lengths for the targeted sequences. Detailed protocols for preparing and manipulating these molecules are presented, and tethering efficiency is characterized as a function of DNA concentration, ionic strength and pH. Attachment strength is characterized by measuring the unbinding time as a function of applied force. An alternative stronger attachment method using an amino–carboxyl linkage, which allows for reliable DNA overstretching, is also described.