Ondersoek na seleksiemaatstawwe by Afrinoskape. Genetiese parameters van groei- en woleienskappe

Investigation of selection criteria for Afrino sheep. Genetic parameters of growth and wool traits. The data used in this study were obtained from the Carnarvon Afrino stud. The genetic and phenotypic parameters for the various growth and wool traits were estimated by means of Henderson's Method III. The following traits were considered as possible selection criteria for ram selection: weaning weight (h2 = 0,21 ± O,07), yearling weight (h2 = 0,22 ± 0,07), ADG: weaning-year-old (h2 = 0,22 ± 0,07), Kleiber: weaning-year-old (h = 0,23 ± 0,07), and eighteen-month mass (h2 = 0,28 ± 0,08). However, the traits yearling weight, ADG: weaning-year-old and eighteen month mass cannot be considered as possible selection criteria because of their undesirable genetic correlations with birth mass and eighteen-month mass. Kleiber: weaning-year-old had a non-significant negative genetic correlation of -0,12 ± 0,22 with birth mass, a medium positive correlation with yearling weight (0,35 ± 0,21) and it is almost unrelated to eighteen-month mass (rg = 0,10 ± 0,22). At 12 months of age, rams can be selected on the basis of the following selection index: I=3 X weaning mass -- 1 X Kleiber: weaning-year-old- 18 X fibre diameter.Ondersoek is ingestel na geskikte seleksiemaatstawwe vir Afrino-skape. Data vanaf die Camarvonse Afrinokudde is vir hierdie ondersoek gebruik. Genetiese en fenotipiese parameters van die onderskeie groei- en woleienskappe is met behulp van Henderson se Metode III beraam. Die volgende eienskappe is as moontlike seleksiemaatstawwe vir ramseleksie oorweeg: speenmassa (h2 = 0,21 ± 0,07), jaarmassa (h2 = 0,22 ± 0,07), GDT: speen-jaar (h2 = 0,22 ± 0,07), Kleiber: speen-jaar (h2 = 0,23 ± 0,07), en agtienmaandemassa (h2 = 0,28 ± 0,08). Jaarmassa, GDT: speenjaar en agtienmaandemassa is as gevolg van hul ongunstige genetiese korrelasies met geboortemassa en agtienmaandemassa as seleksiemaatstawwe geelimineer. Kleiber: speen-jaar het 'n nie-betekenisvolle negatiewe korrelasie van -0,12 ± 0,22 met geboortemassa, 'n matig-positiewe korrelasie van 0,35 ± 0,21 met jaarmassa en is feitlik onafhanklik van agtienmaandemassa (rg = 0,10 ± 0,22). Ramme kan op 12-maande-ouderdom op grond van die volgende seleksie-indeks geselekteer word: I = 3 X speenmassa + 1 X Kleiber: speen-jaar - 18 X veseldikte.Keywords: Afrino, genetic parameters, growth traits, Kleiber ratio

Giardia duodenalis and Cryptosporidium occurrence in Australian sea lions (Neophoca cinerea) exposed to varied levels of human interaction

AbstractGiardia and Cryptosporidium are amongst the most common protozoan parasites identified as causing enteric disease in pinnipeds. A number of Giardia assemblages and Cryptosporidium species and genotypes are common in humans and terrestrial mammals and have also been identified in marine mammals. To investigate the occurrence of these parasites in an endangered marine mammal, the Australian sea lion (Neophoca cinerea), genomic DNA was extracted from faecal samples collected from wild populations (n = 271) in Southern and Western Australia and three Australian captive populations (n = 19). These were screened using PCR targeting the 18S rRNA of Giardia and Cryptosporidium. Giardia duodenalis was detected in 28 wild sea lions and in seven captive individuals. Successful sequencing of the 18S rRNA gene assigned 27 Giardia isolates to assemblage B and one to assemblage A, both assemblages commonly found in humans. Subsequent screening at the gdh and β-giardin loci resulted in amplification of only one of the 35 18S rRNA positive samples at the β-giardin locus. Sequencing at the β-giardin locus assigned the assemblage B 18S rRNA confirmed isolate to assemblage AI. The geographic distribution of sea lion populations sampled in relation to human settlements indicated that Giardia presence in sea lions was highest in populations less than 25 km from humans. Cryptosporidium was not detected by PCR screening in either wild colonies or captive sea lion populations. These data suggest that the presence of G. duodenalis in the endangered Australian sea lion is likely the result of dispersal from human sources. Multilocus molecular analyses are essential for the determination of G. duodenalis assemblages and subsequent inferences on transmission routes to endangered marine mammal populations

Congenital anomalies in black South African liveborn neonates at an urban academic hospital

Study objective. The aim was to study the spectrum of clinical problems and outcomes in infants born at an urban academic hospital. In consequence, as part of the overall study, the incidence of congenital anomalies and the outcomes of affected infants were recorded.Design. This was a prospective, hospital-based study, undertaken on liveborn infants born over a 3-year period, 1 May 1986 to 30 April 1989.Setting. Kalafong Hospital, Pretoria.Main results. A total of 17 351 liveborn infants was examined and the total congenital anomalies incidence was 11 ,87 per 1 000 Iivebirths. The central nervous system was the system most frequently involved (2,30 per 1 000 livebirths), followed by the musculoskeletal system (2,13 per 1 000 livebirths). The commonest individual congenital anomaly was Down syndrome (1,33 per 1 000 Iivebirths), followed by neural tube defects (0,99 per 1 000 livebirths) and ventricular septal defects (0,69 per 1 000 livebirths). In 11 % (2,25 per 1 000 livebirths) of neonatal deaths, infant loss was attributable to congenital anomalies.Conclusions. The incidence of congenital anomalies in black South African neonates, born in an urban setting, is as high as in other First- and Third-World countries, and the incidence of some individual congenital anomalies is higher. This study indicates the need for further research and the establishment of prenatal, genetics and paediatric facilities to manage these problems

Selective Constraints on Amino Acids Estimated by a Mechanistic Codon Substitution Model with Multiple Nucleotide Changes

Empirical substitution matrices represent the average tendencies of substitutions over various protein families by sacrificing gene-level resolution. We develop a codon-based model, in which mutational tendencies of codon, a genetic code, and the strength of selective constraints against amino acid replacements can be tailored to a given gene. First, selective constraints averaged over proteins are estimated by maximizing the likelihood of each 1-PAM matrix of empirical amino acid (JTT, WAG, and LG) and codon (KHG) substitution matrices. Then, selective constraints specific to given proteins are approximated as a linear function of those estimated from the empirical substitution matrices. Akaike information criterion (AIC) values indicate that a model allowing multiple nucleotide changes fits the empirical substitution matrices significantly better. Also, the ML estimates of transition-transversion bias obtained from these empirical matrices are not so large as previously estimated. The selective constraints are characteristic of proteins rather than species. However, their relative strengths among amino acid pairs can be approximated not to depend very much on protein families but amino acid pairs, because the present model, in which selective constraints are approximated to be a linear function of those estimated from the JTT/WAG/LG/KHG matrices, can provide a good fit to other empirical substitution matrices including cpREV for chloroplast proteins and mtREV for vertebrate mitochondrial proteins. The present codon-based model with the ML estimates of selective constraints and with adjustable mutation rates of nucleotide would be useful as a simple substitution model in ML and Bayesian inferences of molecular phylogenetic trees, and enables us to obtain biologically meaningful information at both nucleotide and amino acid levels from codon and protein sequences.Comment: Table 9 in this article includes corrections for errata in the Table 9 published in 10.1371/journal.pone.0017244. Supporting information is attached at the end of the article, and a computer-readable dataset of the ML estimates of selective constraints is available from 10.1371/journal.pone.001724

The use of dexamethasone in women with preterm premature rupture of membranes - A multicentre, double-blind, placebocontrolled, randomised trial

No Abstract

Evolutionary distances in the twilight zone -- a rational kernel approach

Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential alignment problems. However, in general they are not biologically motivated and ignore our knowledge about the evolution of sequences. Thus, it is still a major open question how to define an evolutionary distance metric between divergent sequences that makes use of indel information and known substitution models without the need for a multiple alignment. Here we propose a new evolutionary distance metric to close this gap. It uses finite-state transducers to create a biologically motivated similarity score which models substitutions and indels, and does not depend on a multiple sequence alignment. The sequence similarity score is defined in analogy to pairwise alignments and additionally has the positive semi-definite property. We describe its derivation and show in simulation studies and real-world examples that it is more accurate in reconstructing phylogenies than competing methods. The result is a new and accurate way of determining evolutionary distances in and beyond the twilight zone of sequence alignments that is suitable for large datasets.Comment: to appear in PLoS ON

Fermi level shift in carbon nanotubes by dye confinement

International audienceDye confinement into carbon nanotube significantly affects the electronic charge density distribution of the final hybrid system. Using the electron-phonon coupling sensitivity of the Raman G-band, we quantify experimentally how charge transfer from thiophene oligomers to single walled carbon nanotube is modulated by the diameter of the nano-container and its metallic or semiconducting character. This charge transfer is shown to restore the electron-phonon coupling into defected metallic nanotubes. For sub-nanometer diameter tube, an electron transfer optically activated is observed when the excitation energy matches the HOMO-LUMO transition of the confined oligothiophene. This electron doping accounts for an important enhancement of the photoluminescence intensity up to a factor of nearly six for optimal confinement configuration. This electron transfer shifts the Fermi level, acting on the photoluminescence efficiency. Therefore, thiophene oligomer encapsulation allows modulating the electronic structure and then the optical properties of the hybrid system

Dietary glycaemic index labelling: A global perspective

The glycaemic index (GI) is a food metric that ranks the acute impact of available (digest-ible) carbohydrates on blood glucose. At present, few countries regulate the inclusion of GI on food labels even though the information may assist consumers to manage blood glucose levels. Australia and New Zealand regulate GI claims as nutrition content claims and also recognize the GI Founda-tion’s certified Low GI trademark as an endorsement. The GI Foundation of South Africa endorses foods with low, medium and high GI symbols. In Asia, Singapore’s Healthier Choice Symbol has specific provisions for low GI claims. Low GI claims are also permitted on food labels in India. In China, there are no national regulations specific to GI; however, voluntary claims are permitted. In the USA, GI claims are not specifically regulated but are permitted, as they are deemed to fall under general food-labelling provisions. In Canada and the European Union, GI claims are not legal under current food law. Inconsistences in food regulation around the world undermine consumer and health professional confidence and call for harmonization. Global provisions for GI claims/endorse-ments in food standard codes would be in the best interests of people with diabetes and those at risk

Advantages of a Mechanistic Codon Substitution Model for Evolutionary Analysis of Protein-Coding Sequences

A mechanistic codon substitution model, in which each codon substitution rate is proportional to the product of a codon mutation rate and the average fixation probability depending on the type of amino acid replacement, has advantages over nucleotide, amino acid, and empirical codon substitution models in evolutionary analysis of protein-coding sequences. It can approximate a wide range of codon substitution processes. If no selection pressure on amino acids is taken into account, it will become equivalent to a nucleotide substitution model. If mutation rates are assumed not to depend on the codon type, then it will become essentially equivalent to an amino acid substitution model. Mutation at the nucleotide level and selection at the amino acid level can be separately evaluated.The present scheme for single nucleotide mutations is equivalent to the general time-reversible model, but multiple nucleotide changes in infinitesimal time are allowed. Selective constraints on the respective types of amino acid replacements are tailored to each gene in a linear function of a given estimate of selective constraints. Their good estimates are those calculated by maximizing the respective likelihoods of empirical amino acid or codon substitution frequency matrices. Akaike and Bayesian information criteria indicate that the present model performs far better than the other substitution models for all five phylogenetic trees of highly-divergent to highly-homologous sequences of chloroplast, mitochondrial, and nuclear genes. It is also shown that multiple nucleotide changes in infinitesimal time are significant in long branches, although they may be caused by compensatory substitutions or other mechanisms. The variation of selective constraint over sites fits the datasets significantly better than variable mutation rates, except for 10 slow-evolving nuclear genes of 10 mammals. An critical finding for phylogenetic analysis is that assuming variable mutation rates over sites lead to the overestimation of branch lengths

Molecular evolution of HoxA13 and the multiple origins of limbless morphologies in amphibians and reptiles

Developmental processes and their results, morphological characters, are inherited through transmission of genes regulating development. While there is ample evidence that cis-regulatory elements tend to be modular, with sequence segments dedicated to different roles, the situation for proteins is less clear, being particularly complex for transcription factors with multiple functions. Some motifs mediating protein-protein interactions may be exclusive to particular developmental roles, but it is also possible that motifs are mostly shared among different processes. Here we focus on HoxA13, a protein essential for limb development. We asked whether the HoxA13 amino acid sequence evolved similarly in three limbless clades: Gymnophiona, Amphisbaenia and Serpentes. We explored variation in ω (dN/dS) using a maximum-likelihood framework and HoxA13sequences from 47 species. Comparisons of evolutionary models provided low ω global values and no evidence that HoxA13 experienced relaxed selection in limbless clades. Branch-site models failed to detect evidence for positive selection acting on any site along branches of Amphisbaena and Gymnophiona, while three sites were identified in Serpentes. Examination of alignments did not reveal consistent sequence differences between limbed and limbless species. We conclude that HoxA13 has no modules exclusive to limb development, which may be explained by its involvement in multiple developmental processes