Novel polymorphisms of SIX4 gene and their association with body measurement traits in Qinchuan cattle

Sine oculis homeobox homolog 4 (SIX4) gene belongs to the sine oculis/SIX gene family, which includes six members in vertebrates. SIX4 gene plays a crucial role in skeletal myogenesis, and its genetic variations or deficiency may cause hypopituitarism, suggesting that SIX4 gene is a potential candidate gene affecting body measurement traits (BMTs) in animals. Herein, the objectives of this study were to identify genetic polymorphisms of bovine SIX4 gene and to analyze potential association between single nucleotide polymorphisms (SNPs) and body measurement traits in Qinchuan cattle. In the present study, we investigated polymorphisms of SIX4 gene in 426 Qinchuan cattle using DNA sequencing and polymerase chain reaction–restriction fragment length polymorphisms. Three novel SNPs were identified within bovine SIX4 gene. Associations between body measurement traits and SIX4 gene polymorphisms were investigated, and significant statistical associations were found between polymorphisms of these three SNPs and body measurement traits (P < 0.05). Hence, based on results obtained from this study, we conjectured that SIX4 gene may have potential effects on body measurement traits in Qinchuan cattle population and could be used for marker-assisted selection.     

An informational diversity framework,illustrated with sexually deceptive orchids in early stages of speciation

Reconstructing evolutionary history for emerging species complexes is notoriously difficult, with newly isolated taxa often morphologically cryptic and the signature of reproductive isolation often restricted to a few genes. Evidence from multiple loci and genomes is highly desirable, but multiple inputs require ‘common currency’ translation. Here we deploy a Shannon information framework, converting into diversity analogue, which provides a common currency analysis for maternally inherited haploid and bi‐parentally inherited diploid nuclear markers, and then extend that analysis to construction of minimum‐spanning networks for both genomes. The new approach is illustrated with a quartet of cryptic congeners from the sexually deceptive Australian orchid genus Chiloglottis, still in the early stages of speciation. Divergence is more rapid for haploid plastids than for nuclear markers, consistent with the effective population size differential (N_ep < N_en), but divergence patterns are broadly correlated for the two genomes. There are nevertheless intriguing discrepancies between the emerging plastid and nuclear signals of early phylogenetic radiation of these taxa, and neither pattern is entirely consistent with the available information on the sexual cues used by the orchids to lure the pollinators enforcing reproductive isolation. We describe possible extensions of this methodology to multiple ploidy levels and other types of markers, which should increase the range of application to any taxonomic assemblage in the very early stages of reproductive isolation and speciation.     

The utility of deformable image registration for small artery visualisation in contrast-enhanced whole body MR angiography

PurposeAn investigation was carried out into the effect of three image registration techniques on the diagnostic image quality of contrast-enhanced magnetic resonance angiography (CE-MRA) images.MethodsWhole-body CE-MRA data from the lower legs of 27 patients recruited onto a study of asymptomatic atherosclerosis were processed using three deformable image registration algorithms. The resultant diagnostic image quality was evaluated qualitatively in a clinical evaluation by four expert observers, and quantitatively by measuring contrast-to-noise ratios and volumes of blood vessels, and assessing the techniques' ability to correct for varying degrees of motion.ResultsThe first registration algorithm (‘AIR’) introduced significant stenosis-mimicking artefacts into the blood vessels' appearance, observed both qualitatively (clinical evaluation) and quantitatively (vessel volume measurements). The two other algorithms (‘Slicer’ and ‘SEMI’), based on the normalised mutual information (NMI) concept and designed specifically to deal with variations in signal intensity as found in contrast-enhanced image data, did not suffer from this serious issue but were rather found to significantly improve the diagnostic image quality both qualitatively and quantitatively, and demonstrated a significantly improved ability to deal with the common problem of patient motion.ConclusionsThis work highlights both the significant benefits to be gained through the use of suitable registration algorithms and the deleterious effects of an inappropriate choice of algorithm for contrast-enhanced MRI data. The maximum benefit was found in the lower legs, where the small arterial vessel diameters and propensity for leg movement during image acquisitions posed considerable problems in making accurate diagnoses from the un-registered images.     

ANCESTRAL CHARACTER ESTIMATION UNDER THE THRESHOLD MODEL FROM QUANTITATIVE GENETICS

Evolutionary biology is a study of life's history on Earth. In researching this history, biologists are often interested in attempting to reconstruct phenotypes for the long extinct ancestors of living species. Various methods have been developed to do this on a phylogeny from the data for extant taxa. In the present article, I introduce a new approach for ancestral character estimation for discretely valued traits. This approach is based on the threshold model from evolutionary quantitative genetics. Under the threshold model, the value exhibited by an individual or species for a discrete character is determined by an underlying, unobserved continuous trait called “liability.” In this new method for ancestral state reconstruction, I use Bayesian Markov chain Monte Carlo (MCMC) to sample the liabilities of ancestral and tip species, and the relative positions of two or more thresholds, from their joint posterior probability distribution. Using data simulated under the model, I find that the method has very good performance in ancestral character estimation. Use of the threshold model for ancestral state reconstruction relies on a priori specification of the order of the discrete character states along the liability axis. I test the use of a Bayesian MCMC information theoretic criterion based approach to choose among different hypothesized orderings for the discrete character. Finally, I apply the method to the evolution of feeding mode in centrarchid fishes.     

The cumulative effects of management on the population dynamics of the Double‐crested Cormorant Phalacrocorax auritus in the Great Lakes

Wildlife species have been subject to control efforts throughout human history due to real or alleged human–wildlife conflicts. The Double‐crested Cormorant Phalacrocorax auritus in the interior of North America is no exception, with recent population growth leading to increased conflicts and consequently the development of many control programmes. These control programmes are usually conducted at local scales, often with little or no effort to assess their cumulative effects at the population level. We attempted the first comprehensive assessment of the cumulative effects of control at various spatio‐temporal scales, focusing on 199 colonies of Double‐crested Cormorant monitored during a 29‐year period. Linear models were used to assess the relationship between colony‐specific growth rates and a set of candidate factors using an information‐theoretic approach. Colony‐level density‐dependent effects and local control efforts had the greatest influences on population growth. We detected a cumulative effect of management, whereby (i) the reduction in population growth rate was generally stronger when different control activities such as culling or egg oiling were combined, and (ii) past control operations tended to have a pervasive impact on growth rates, especially egg oiling and nest destruction, which negatively affected local recruitment. However, our results also suggest that catastrophic events and the culling of breeding adults that occurred at least 2 years previously could fuel subsequent recruitment or natural immigration from nearby colonies, for instance if the breeding success of remaining pairs was increased through a diminution of density‐dependent regulatory processes. Density‐dependence at the metapopulation level constituted a third source of regulation, as local growth rates were reduced with increasing number or proximity of active neighbouring colonies. We also found evidence that the culling of Double‐crested Cormorants wintering in the southeastern USA could negatively impact the population growth of individual breeding colonies in the Great Lakes, although further research integrating models of migratory connectivity is needed to reach more definitive conclusions. Finally, despite previous studies emphasizing its importance, the net effect of management‐induced dispersal appeared small at large spatial scales. We show that this can be explained in part by control strategies (e.g. spatially clustered operations). The continuation of Cormorant management efforts will provide an opportunity to refine the present assessment of the relative importance of density‐dependence, breeding vs. non‐breeding season management and dispersal, particularly if population models are coupled with monitoring programmes within an adaptive management framework.     

Genetic and physical mapping of <Emphasis Type="Italic">Pi36</Emphasis>(t), a novel rice blast resistance gene located on rice chromosome 8

Blast resistance in the indica cultivar (cv.) Q61 was inherited as a single dominant gene in two F₂ populations, F₂-1 and F₂-2, derived from crosses between the donor cv. and two susceptible japonica cvs. Aichi Asahi and Lijiangxintuanheigu (LTH), respectively. To rapidly determine the chromosomal location of the resistance (R) gene detected in Q61, random amplified polymorphic DNA (RAPD) analysis was performed in the F₂-1 population using bulked-segregant analysis (BSA) in combination with recessive-class analysis (RCA). One of the three linked markers identified, BA1126₅₅₀, was cloned and sequenced. The R gene locus was roughly mapped on rice chromosome 8 by comparison of the BA1126₅₅₀ sequence with rice sequences in the databases (chromosome landing). To confirm this finding, seven known markers, including four sequence-tagged-site (STS) markers and three simple-sequence repeat (SSR) markers flanking BA1126₅₅₀ on chromosome 8, were subjected to linkage analysis in the two F₂ populations. The locus was mapped to a 5.8 cM interval bounded by RM5647 and RM8018 on the short arm of chromosome 8. This novel R gene is therefore tentatively designated as Pi36(t). For fine mapping of the Pi36(t) locus, five additional markers including one STS marker and four candidate resistance gene (CRG) markers were developed in the target region, based on the genomic sequence of the corresponding region of the reference japonica cv. Nipponbare. The Pi36(t) locus was finally localized to an interval of about 0.6 cM flanked by the markers RM5647 and CRG2, and co-segregated with the markers CRG3 and CRG4. To physically map this locus, the Pi36(t)-linked markers were mapped by electronic hybridization to bacterial artificial chromosome (BAC) or P1 artificial chromosome (PAC) clones of Nipponbare, and a contig map was constructed in silico through Pairwise BLAST analysis. The Pi36(t) locus was physically delimited to an interval of about 17.0 kb, based on the genomic sequence of Nipponbare.     

Dynamic proteome changes of Shigella flexneri 2a during transition from exponential growth to stationary phase

Shigella flexneri is an infectious pathogen that causes dysentery to human, which remains a serious threat to public health, particularly in developing countries. In this study, the global protein expression patterns of S. flexneri during transition from exponential growth to stationary phase in vitro were analyzed by using 2-D PAGE combined with MALDI-TOF MS. In a time-course experiment with five time points, the relative abundance of 49 protein spots varied significantly. Interestingly, a putative outer membrane protein YciD （OmpW） was almost not detected in the exponential growth phase but became one of the most abundant proteins in the whole stationary-phase proteome. Some proteins regulated by the global regulator FNR were also significantly induced （such as AnsB, AspA, FrdAB, and KatG） or repressed （such as AceEF, OmpX, SodA, and SucAB） during the growth phase transition. These proteins may be the key effectors of the bacterial cell cycle or play important roles in the cellular maintenance and stress responses. Our expression profile data provide valuable information for the study of bacterial physiology and form the basis for future proteomic analyses of this pathogen.