Patterns of diversity and adaptation in Glomeromycota from three prairie grasslands

Arbuscular mycorrhizal (AM) fungi are widespread root symbionts that often improve the fitness of their plant hosts. We tested whether local adaptation in mycorrhizal symbioses would shape the community structure of these root symbionts in a way that maximizes their symbiotic functioning. We grew a native prairie grass (Andropogon gerardii) with all possible combinations of soils and AM fungal inocula from three different prairies that varied in soil characteristics and disturbance history (two native prairie remnants and one recently restored). We identified the AM fungi colonizing A. gerardii roots using PCR amplification and cloning of the small subunit rRNA gene. We observed 13 operational taxonomic units (OTUs) belonging to six genera in three families. Taxonomic richness was higher in the restored than the native prairies with one member of the Gigaspora dominating the roots of plants grown with inocula from native prairies. Inoculum source and the soil environment influenced the composition of AM fungi that colonized plant roots. Correspondingly, host plants and AM fungi responded significantly to the soil–inoculum combinations such that home fungi often had the highest fitness and provided the greatest benefit to A. gerardii. Similar patterns were observed within the soil–inoculum combinations originating from two native prairies, where five sequence types of a single Gigaspora OTU were virtually the only root colonizers. Our results indicate that indigenous assemblages of AM fungi were adapted to the local soil environment and that this process occurred both at a community scale and at the scale of fungal sequence types within a dominant OTU.     

Personal experience and reputation interact in human decisions to help reciprocally

There is ample evidence that human cooperative behaviour towards other individuals is often conditioned on information about previous interactions. This information derives both from personal experience (direct reciprocity) and from experience of others (i.e. reputation; indirect reciprocity). Direct and indirect reciprocity have been studied separately, but humans often have access to both types of information. Here, we experimentally investigate information use in a repeated helping game. When acting as donor, subjects can condition their decisions to help recipients with both types of information at a small cost to access such information. We find that information from direct interactions weighs more heavily in decisions to help, and participants tend to react less forgivingly to negative personal experience than to negative reputation. Moreover, effects of personal experience and reputation interact in decisions to help. If a recipient''s reputation is positive, the personal experience of the donor has a weak effect on the decision to help, and vice versa. Yet if the two types of information indicate conflicting signatures of helpfulness, most decisions to help follow personal experience. To understand the roles of direct and indirect reciprocity in human cooperation, they should be studied in concert, not in isolation.     

Maladaptation beyond a geographic range limit driven by antagonistic and mutualistic biotic interactions across an abiotic gradient

Species’ geographic range limits often result from maladaptation to the novel environments beyond the range margin. However, we rarely know which aspects of the n‐dimensional environment are driving this maladaptation. Especially of interest is the influence of abiotic versus biotic factors in delimiting species’ distributions. We conducted a 2‐year reciprocal transplant experiment involving manipulations of the biotic environment to explore how spatiotemporal gradients in precipitation, fatal mammalian herbivory, and pollination affected lifetime fitness within and beyond the range of the California annual plant, Clarkia xantiana ssp. xantiana. In the first, drier year of the experiment, fitness outside the range edge was limited mainly by low precipitation, and there was some evidence for local adaptation within the range. In the second, wetter year, we did not observe abiotic limitations to plant fitness outside the range; instead biotic interactions, especially herbivory, limited fitness outside the range. Together, protection from herbivory and supplementation of pollen resulted in three‐ to sevenfold increases in lifetime fitness outside the range margin in the abiotically benign year. Overall, our work demonstrates the importance of biotic interactions, particularly as they interact with the abiotic environment, in determining fitness beyond geographic range boundaries.     

Breakpoint mapping of a novel de novo translocation t(X;20)(q11.1;p13) by positional cloning and long read sequencing

Disease associated chromosomal rearrangements often have break points located within disease causing genes or in their vicinity. The purpose of this study is to characterize a balanced reciprocal translocation in a girl with intellectual disability and seizures by positional cloning and whole genome sequencing. The translocation was identification by G- banding and confirmed by WCP FISH. Fine mapping using BAC clones and whole genome sequencing using Oxford nanopore long read sequencing technology for a 1.46 X coverage of the genome was done. The positional cloning showed split signals with BAC RP11-943 J20. Long read sequencing analysis of chimeric reads carrying parts of chromosomes X and 20 helped to identify the breakpoints to be in intron 2 of ARHGEF9 gene on Xp11.1 and on 20p13 between RASSF2 and SLC23A2 genes. This is the first report of translocation which successfully delineated to single base resolution using Nanopore sequencing. The genotype-phenotype correlation is discussed.     

Putative local adaptations modulate the interactions of the carnivorous plant Drosera uniflora Willd (1809) (Droseraceae) with cushion and shrub nurse plants

Cushion and shrub plants are typical high mountain nurse plants. In Magellanic tundras of the Cordillera del Sarao on the coast of Chile, the carnivorous plant Drosera uniflora grows in association with cushions of Donatia fascicularis and the shrubs Chusquea montana var. nigricans and Lepidothamnus fonkii. The different microhabitats for recruitment, in addition to the limited gene flow of D. uniflora, enable us to hypothesise that this plant manifests putative local adaptations, expressed in seed germination and population abundance. Our aim was to evaluate the local adaptation of D. uniflora to cushion and shrub microhabitats by estimating germination and abundance. Local adaptation of seed germination was determined by means of reciprocal transplant experiments. Abundance was determined in small plots located inside, on the edge and outside the nurse plants. Seed origin and growth substrate play a decisive role in D. uniflora germination. Seeds that originate from cushions plant habitat and germinate in the same substrate do so in greater numbers than when those which originate from shrubby habitats. Conversely, seeds that originate from shrubby habitat and germinate in the same substrate do not exhibit significant differences. Abundance was always greater inside than outside of the nurse plants. We concluded that availability and quality of different microhabitats for seed germination and recruitment, together with a limited gene flow, would trigger putative local adaptations in D. uniflora, modulating a long history of interactions with the plants that act as nurse plants.     

Geometrical comparison of two protein structures using Wigner‐D functions

In this article, we develop a quantitative comparison method for two arbitrary protein structures. This method uses a root‐mean‐square deviation characterization and employs a series expansion of the protein's shape function in terms of the Wigner‐D functions to define a new criterion, which is called a “similarity value.” We further demonstrate that the expansion coefficients for the shape function obtained with the help of the Wigner‐D functions correspond to structure factors. Our method addresses the common problem of comparing two proteins with different numbers of atoms. We illustrate it with a worked example. Proteins 2014; 82:2756–2769. © 2014 Wiley Periodicals, Inc.     

Controlling death--compromising life: chronic disease, prognostication, and the new biotechnologies

Within the modern culture of control, patients and physicians seek to actively shape the uncertainty of prognostications concerning the course of disease and the anticipated effects of therapeutic and surgical interventions. This article discusses the results of a three-year ethnographic study of persons with cystic fibrosis (CF) who undergo double-lung transplant. It draws on interviews with a difficult-to-access patient group, adult CF sufferers, and investigates their dilemmas with regard to having or not having a double-lung transplant. It situates their decisions within a complex framework: the denial of death and disability in technological modernity, the consequent emphasis on cure and saving life at any cost, rather than the management of chronic illness, the extent to which health and illness constitute identity, and the problems of CF patients conceiving their life narrative when life will be short. This framework produces two key questions: Do patient beliefs in the progress narratives of medicine overshadow other considerations, and are biotechnologies such as organ transplant a calculated gamble on a better life or an uncertain reliance on biomedical expertise? I argue that risk interpretation is heavily influenced by the constant introduction of new therapeutics that intersect with social technologies of normalization to strongly influence patient decisions concerning the pursuit of high-risk surgeries such as organ transplant, surgeries that sometimes hasten a patient's decline and death.     

野黄瓜与栽培黄瓜正反交异源四倍体序列消除的初步研究

不同分类群的异源多倍体在二倍化过程中, 正反交序列消除往往表现出不同特征, 暗示了在不同物种中, 核质互作在多倍体进化过程的作用不同。利用13对EcoRI-NN/MseI-NNN选择性引物, 对野黄瓜Cucumis hystrix (2n=24)与栽培黄瓜C. sativus (2n=14)的正反交F1、异源四倍体及二倍体亲本DNA进行AFLP分析。结果表明: 杂交后代基因组的杂合性诱发了F1与异源四倍体广泛的序列消除; 细胞质可能会影响部分亲本序列消除的频率, 但是正反交在序列消除频率上差异不显著, 并且在序列消除时间(均始于F1代)及消除类型上也表现出一致性, 表明核质互作并不是影响序列消除的主要因素; 实验还发现, 正反交不能影响序列的倾向性丢失, 染色体数少的黄瓜条带易发生丢失。