The Mating System of the Wild-to-Domesticated Complex of Gossypium hirsutum L. Is Mixed

The domestication syndrome of many plants includes changes in their mating systems. The evolution of the latter is shaped by ecological and genetic factors that are particular to an area. Thus, the reproductive biology of wild relatives must be studied in their natural distribution to understand the mating system of a crop species as a whole. Gossypium hirsutum (upland cotton) includes both domesticated varieties and wild populations of the same species. Most studies on mating systems describe cultivated cotton as self-pollinated, while studies on pollen dispersal report outcrossing; however, the mating system of upland cotton has not been described as mixed and little is known about its wild relatives. In this study we selected two wild metapopulations for comparison with domesticated plants and one metapopulation with evidence of recent gene flow between wild relatives and the crop to evaluate the mating system of cotton’s wild-to-domesticated complex. Using classic reproductive biology methods, our data demonstrate that upland cotton presents a mixed mating system throughout the complex. Given cotton’s capacity for outcrossing, differences caused by the domestication process in cultivated individuals can have consequences for its wild relatives. This characterization of the diversity of the wild relatives in their natural distribution, as well as their interactions with the crop, will be useful to design and implement adequate strategies for conservation and biosecurity

Close Packing of Atoms, Geometric Frustration and the Formation of Heterogeneous States in Crystals

To describe structural peculiarities in inhomogeneous media caused by the tendency to the close packing of atoms a formalism based on the using of the Riemann geometry methods (which were successfully applied lately to the description of structures of quasicrystals and glasses) is developed. Basing on this formalism we find in particular the criterion of stability of precipitates of the Frank-Kasper phases in metallic systems. The nature of the ''rhenium effect'' in W-Re alloys is discussed.Comment: 14 pages, RevTex, 2 PostScript figure

Влияние кровенаполнения сосудов головного мозга на гемодинамику глаза и течение глаукомного процесса

PURPOSE: To investigate the effect of cerebral blood flow on ocular haemodynamics in control subjects and in patients with primary open-angle glaucoma (POAG), depending on the age and dynamics of glaucoma process. METHODS: Blood filling of cerebral and ocular vessels was investigated with the use of rheoencephalography and rheoophthalmography in 115 patients with POAG and in 31 subjects of the control group with no signs of glaucoma, including 33 patients (66 eyes) with non-progressive glaucoma and 82 patients (164 eyes) with progressive POAG. The age range was 50-89 years. Intraocular pressure in all subjects was between 19-21mm Hg. Cerebral hemodynamics was analyzed by the intensity of blood vessel pulse in the cerebral vessels (rheographic index), by the maximum speed of blood during the periods of rapid and slow blood flow, as well as the dicrotic and diastolic indices. Intraocular perfusion was analyzed by the following parameters: largest pulse volume, time of rapid and slow blood flow in ocular vessels, Kedrov’s pulse volume and Yantchu rheographic coefficient. RESULTS: Control group members aged 70-79 and 80-89 showed a significant decrease of blood filling of cerebral and ocular vessels (p=0.02). In patients’ age groups 50-59 and 60-69, with nonprogressive course of POAG no significant decrease of hemodynamics of cerebral and ocular vessels has been revealed as compared to the control group (p=0.02). In age groups of 70-79, 80-89 there was a decrease in blood flow speed in cerebral and ocular vessels. In patients with progressive glaucoma a significant decrease in cerebral and ocular hemodynamics parameters has been revealed starting at the age of 50-59 with further deterioration in the following age groups: 60-69, 70-79, 80-89 (p=0.02). CONCLUSION: A correlation between ocular blood supply and cerebral hemodynamics has been established. A more prominent correlation is detected in patients with progressive course of POAG (p=0.01, r=0.97).ЦЕЛЬ. Исследовать влияние пульсового кровенаполнения сосудов головного мозга на гемодинамику глаза у лиц контрольной группы и у больных с первичной открытоугольной глаукомой (ПОУГ) в зависимости от возраста и динамики глаукомного процесса. МАТЕРИАЛЫ И МЕТОДЫ. Исследование проводили с помощью реоэнцефалографии и реоофтальмографии. Обследованы 115 больных ПОУГ и 31 человек контрольной группы без признаков глаукомы, в возрасте от 50 до 89 лет. Тонометрическое внутриглазное давление у всех исследуемых находилось в пределах 19-21 мм рт.ст. Со стабилизированным течением ПОУГ было 33 больных (66 глаз), с нестабилизированным течением - 82 больных (164 глаза). Церебральную гемодинамику анализировали по интенсивности пульсового кровенаполнения сосудов головного мозга - реографическому индексу, по максимальной скорости периода быстрого и медленного кровенаполнения, по дикротическому и диастолическому индексам. Внутриглазное кровенаполнение анализировали по величине пульсового кровенаполнения, времени быстрого и медленного кровенаполнения сосудов глаза, пульсовому объему по Кедрову и реографическому коэффициенту по Янтчу. РЕЗУЛЬТАТЫ. У лиц контрольной группы в возрасте 70-79 и 80-89 лет выявлено снижение кровенаполнения сосудов головного мозга и глаза (p=0,02). У больных со стабилизированным течением ПОУГ во всех возрастных группах выявлено незначительное снижение гемодинамики в сосудах головного мозга и глаза и оно недостоверно (p=0,06-0,08). При нестабилизированном течении ПОУГ обнаружено существенное снижение кровенаполнения в церебральных и интраокулярных сосудах у больных в возрасте 50-59 лет, эти показатели продолжали ухудшаться в возрастных группах 60-69, 70-79 и 80-89 лет (p=0,01). ЗАКЛЮЧЕНИЕ. Выявлено существенное влияние кровенаполнения сосудов головного мозга на гемодинамику глаза и тяжесть течения глаукомы, особенно у больных с нестабилизированным течением ПОУГ, у которых имеется достоверное снижение кровоснабжения глаза во всех возрастных группах (p=0,01, r=0,97)

Developing European conservation and mitigation tools for pollination services: approaches of the STEP (Status and Trends of European Pollinators) project

Pollinating insects form a key component of European biodiversity, and provide a vital ecosystem service to crops and wild plants. There is growing evidence of declines in both wild and domesticated pollinators, and parallel declines in plants relying upon them. The STEP project (Status and Trends of European Pollinators, 2010-2015, www.stepproject.net) is documenting critical elements in the nature and extent of these declines, examining key functional traits associated with pollination deficits, and developing a Red List for some European pollinator groups. Together these activities are laying the groundwork for future pollinator monitoring programmes. STEP is also assessing the relative importance of potential drivers of pollinator declines, including climate change, habitat loss and fragmentation, agrochemicals, pathogens, alien species, light pollution, and their interactions. We are measuring the ecological and economic impacts of declining pollinator services and floral resources, including effects on wild plant populations, crop production and human nutrition. STEP is reviewing existing and potential mitigation options, and providing novel tests of their effectiveness across Europe. Our work is building upon existing and newly developed datasets and models, complemented by spatially-replicated campaigns of field research to fill gaps in current knowledge. Findings are being integrated into a policy-relevant framework to create evidence-based decision support tools. STEP is establishing communication links to a wide range of stakeholders across Europe and beyond, including policy makers, beekeepers, farmers, academics and the general public. Taken together, the STEP research programme aims to improve our understanding of the nature, causes, consequences and potential mitigation of declines in pollination services at local, national, continental and global scales

The closest elastic tensor of arbitrary symmetry to an elasticity tensor of lower symmetry

The closest tensors of higher symmetry classes are derived in explicit form for a given elasticity tensor of arbitrary symmetry. The mathematical problem is to minimize the elastic length or distance between the given tensor and the closest elasticity tensor of the specified symmetry. Solutions are presented for three distance functions, with particular attention to the Riemannian and log-Euclidean distances. These yield solutions that are invariant under inversion, i.e., the same whether elastic stiffness or compliance are considered. The Frobenius distance function, which corresponds to common notions of Euclidean length, is not invariant although it is simple to apply using projection operators. A complete description of the Euclidean projection method is presented. The three metrics are considered at a level of detail far greater than heretofore, as we develop the general framework to best fit a given set of moduli onto higher elastic symmetries. The procedures for finding the closest elasticity tensor are illustrated by application to a set of 21 moduli with no underlying symmetry.Comment: 48 pages, 1 figur

Distinctive Gut Microbiota of Honey Bees Assessed Using Deep Sampling from Individual Worker Bees

Surveys of 16S rDNA sequences from the honey bee, Apis mellifera, have revealed the presence of eight distinctive bacterial phylotypes in intestinal tracts of adult worker bees. Because previous studies have been limited to relatively few sequences from samples pooled from multiple hosts, the extent of variation in this microbiota among individuals within and between colonies and locations has been unclear. We surveyed the gut microbiota of 40 individual workers from two sites, Arizona and Maryland USA, sampling four colonies per site. Universal primers were used to amplify regions of 16S ribosomal RNA genes, and amplicons were sequenced using 454 pyrotag methods, enabling analysis of about 330,000 bacterial reads. Over 99% of these sequences belonged to clusters for which the first blastn hits in GenBank were members of the known bee phylotypes. Four phylotypes, one within Gammaproteobacteria (corresponding to “Candidatus Gilliamella apicola”) one within Betaproteobacteria (“Candidatus Snodgrassella alvi”), and two within Lactobacillus, were present in every bee, though their frequencies varied. The same typical bacterial phylotypes were present in all colonies and at both sites. Community profiles differed significantly among colonies and between sites, mostly due to the presence in some Arizona colonies of two species of Enterobacteriaceae not retrieved previously from bees. Analysis of Sanger sequences of rRNA of the Snodgrassella and Gilliamella phylotypes revealed that single bees contain numerous distinct strains of each phylotype. Strains showed some differentiation between localities, especially for the Snodgrassella phylotype

Scaling properties of protein family phylogenies

One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth scaling, as a characterization of balance) of a large set of protein phylogenies with a set of species phylogenies. The comparative analysis shows that both sets of phylogenies share remarkably similar scaling behavior, suggesting the universality of branching rules and of the evolutionary processes that drive biological diversification from gene to species level. In order to explain such generality, we propose a simple model which allows us to estimate the proportion of evolvability/robustness needed to approximate the scaling behavior observed in the phylogenies, highlighting the relevance of the robustness of a biological system (species or protein) in the scaling properties of the phylogenetic trees. Thus, the rules that govern the incapability of a biological system to diversify are equally relevant both at the gene and at the species level.Comment: Replaced with final published versio

ANDES: Statistical tools for the ANalyses of DEep Sequencing

<p>Abstract</p> <p>Background</p> <p>The advancements in DNA sequencing technologies have allowed researchers to progress from the analyses of a single organism towards the deep sequencing of a sample of organisms. With sufficient sequencing depth, it is now possible to detect subtle variations between members of the same species, or between mixed species with shared biomarkers, such as the 16S rRNA gene. However, traditional sequencing analyses of samples from largely homogeneous populations are often still based on multiple sequence alignments (MSA), where each sequence is placed along a separate row and similarities between aligned bases can be followed down each column. While this visual format is intuitive for a small set of aligned sequences, the representation quickly becomes cumbersome as sequencing depths cover loci hundreds or thousands of reads deep.</p> <p>Findings</p> <p>We have developed ANDES, a software library and a suite of applications, written in Perl and R, for the statistical ANalyses of DEep Sequencing. The fundamental data structure underlying ANDES is the position profile, which contains the nucleotide distributions for each genomic position resultant from a multiple sequence alignment (MSA). Tools include the root mean square deviation (RMSD) plot, which allows for the visual comparison of multiple samples on a position-by-position basis, and the computation of base conversion frequencies (transition/transversion rates), variation (Shannon entropy), inter-sample clustering and visualization (dendrogram and multidimensional scaling (MDS) plot), threshold-driven consensus sequence generation and polymorphism detection, and the estimation of empirically determined sequencing quality values.</p> <p>Conclusions</p> <p>As new sequencing technologies evolve, deep sequencing will become increasingly cost-efficient and the inter and intra-sample comparisons of largely homogeneous sequences will become more common. We have provided a software package and demonstrated its application on various empirically-derived datasets. Investigators may download the software from Sourceforge at <url>https://sourceforge.net/projects/andestools</url>.</p

Non-singular screw dislocations as the Coulomb gas with smoothed out coupling and the renormalization of the shear modulus

A field theory is developed for a thermodynamical description of array of parallel non-singular screw dislocations in elastic cylinder. The partition function of the system is considered in the functional integral form. Self-energy of the dislocation cores is chosen in the form suggested by the gauge-translational model of non-singular screw dislocation. It is shown that the system of the dislocations is equivalent to the two-dimensional Coulomb gas. The coupling potential is prevented from a short-distance divergency since the core energies are taken into account. Two-point correlation functions of the stress components are obtained. Renormalization of the shear modulus caused by the presence of the dislocations is studied in the approximation of non-interacting dislocation dipoles. It is demonstrated that the finite size of the dislocation cores results in a modification of the renormalization law.Comment: 20 pages, LaTe