Intense harvesting of eastern wolves facilitated hybridization with coyotes

Despite ethical arguments against lethal control of wildlife populations, culling is routinely used for the management of predators, invasive or pest species, and infectious diseases. Here, we demonstrate that culling of wildlife can have unforeseen impacts that can be detrimental to future conservation efforts. Specifically, we analyzed genetic data from eastern wolves (Canis lycaon) sampled in Algonquin Provincial Park (APP), Ontario, Canada from 1964 to 2007. Research culls in 1964 and 1965 killed the majority of wolves within a study region of APP, accounting for approximately 36% of the park's wolf population at a time when coyotes were colonizing the region. The culls were followed by a significant decrease in an eastern wolf mitochondrial DNA (mtDNA) haplotype (C1) in the Park's wolf population, as well as an increase in coyote mitochondrial and nuclear DNA. The introgression of nuclear DNA from coyotes, however, appears to have been curtailed by legislation that extended wolf protection outside park boundaries in 2001, although eastern wolf mtDNA haplotype C1 continued to decline and is now rare within the park population. We conclude that the wolf culls transformed the genetic composition of this unique eastern wolf population by facilitating coyote introgression. These results demonstrate that intense localized harvest of a seemingly abundant species can lead to unexpected hybridization events that encumber future conservation efforts. Ultimately, researchers need to contemplate not only the ethics of research methods, but also that future implications may be obscured by gaps in our current scientific understanding.     

β-turn tendency in N-methylated peptides with dehydrophenylalanine residue: DFT study

The tendency to adopt β‐turn conformation by model dipeptides with α,β‐dehydrophenylalanine (ΔPhe) residue in the gas phase and in solution is investigated by theoretical methods. We pay special attention to a dependence of conformational properties on the side‐chain configuration of dehydro residue and the influence of N‐methylation on β‐turn stability. An extensive computational study of the conformational preferences of Z and E isomers of dipeptides Ac‐Gly‐(E/Z)‐ΔPhe‐NHMe ( 1a / 1b ) and Ac‐Gly‐(E/Z)‐ΔPhe‐NMe₂ ( 2a / 2b ) by B3LYP/6‐311++G(d,p) and MP2/6‐311++G(d,p) methods is reported. It is shown that, in agreement with experimental data, Ac‐Gly‐(Z)‐ΔPhe‐NHMe has a great tendency to adopt β‐turn conformation. In the gas phase the type II β‐turn is preferred, whereas in the polar environment, the type I. On the other hand, dehydro residue in Ac‐Gly‐(E)‐ΔPhe‐NHMe has a preference to adopt extended conformations in all environments. N‐methylation of C‐terminal amide group, which prevents the formation of 1←4 intramolecular hydrogen bond, change dramatically the conformational properties of studied dehydropeptides. Especially, the tendency to adopt β‐turn conformations is much weaker for the N‐methylated Z isomer (Ac‐Gly‐(Z)‐ΔPhe‐NMe₂), both in vacuo and in the polar environment. On the contrary, N‐methylated E isomer (Ac‐Gly‐(E)‐ΔPhe‐NMe₂) can easier adopt β‐turn conformation, but the backbone torsion angles (?₁, ψ₁, ?₂, ψ₂) are off the limits for common β‐turn types. © 2012 Wiley Periodicals, Inc. Biopolymers 97:518–528, 2012.     

Single-step methods for genomic evaluation in pigs

Genetic evaluation based on information from phenotypes, pedigree and markers can be implemented using a recently developed single-step method. In this paper we compare accuracies of predicted breeding values for daily gain and feed conversion ratio (FCR) in Danish Duroc pigs obtained from different versions of single-step methods, the traditional pedigree-based method and the genomic BLUP (GBLUP) method. In particular, we present a single-step method with an adjustment of the genomic relationship matrix so that it is compatible to the pedigree-based relationship matrix. Comparisons are made for both genotyped and non-genotyped animals and univariate and bivariate models. The results show that the three methods with marker information (two single-step methods and GBLUP) produce more accurate predictions of genotyped animals than the pedigree-based method. In addition, single-step methods provide more accurate predictions for non-genotyped animals. The results also show that the single-step method with adjusted genomic relationship matrix produce more accurate predictions than the original single-step method. Finally, the results for the bivariate analyses show a somewhat improved accuracy and reduced inflation of predictions for FCR for the two single-step methods compared with the univariate analyses. The conclusions are: first, the methods with marker information improve prediction compared with the pedigree-based method; second, a single-step method, contrary to GBLUP, provides improved predictions for all animals compared to the pedigree-based method; and third, a single-step method should be used with an adjustment of the genomic relationship matrix.     

Strategies for membrane interaction proteomics: no mass spectrometry required

Membrane-bound proteins are one of the most important protein types in the cell, and are involved in many major cell processes and signaling pathways. Most proteins, including those at membranes, must interact with other proteins to form complexes, which are essential for their function(s). In this review, we describe some of the major non-mass spectrometry-based methods and technologies used for the investigation of intracellular membrane protein complexes including Tango, fluorescence/bioluminescence resonance energy transfer (F/BRET), luminescence-based mammalian interactome mapping (LUMIER), protein-fragment complementation assay (PCA), and membrane yeast two-hybrid assay (MYTH). We highlight the advantages and drawbacks of these methods, describe recent studies utilizing these methods, and discuss some of the major findings in the study of membrane protein-based cell pathways.     

Chaotic dynamics of a three species prey-predator competition model with bionomic harvesting due to delayed environmental noise as external driving force

We consider a biological economic model based on prey-predator interactions to study the dynamical behaviour of a fishery resource system consisting of one prey and two predators surviving on the same prey. The mathematical model is a set of first order non-linear differential equations in three variables with the population densities of one prey and the two predators. All the possible equilibrium points of the model are identified, where the local and global stabilities are investigated. Biological and bionomical equilibriums of the system are also derived. We have analysed the population intensities of fluctuations i.e., variances around the positive equilibrium due to noise with incorporation of a constant delay leading to chaos, and lastly have investigated the stability and chaotic phenomena with a computer simulation.     

α-螺旋跨膜蛋白拓扑结构预测方法的评价

在基因组数据中,有20%～30%的产物被预测为跨膜蛋白,本文通过对膜蛋白拓扑结构预测方法进行分析,并评价其结果,为选择更合适的拓扑结构预测方法预测膜蛋白结构。通过对目前已有的拓扑结构预测方法的评价分析,可以为我们在实际工作中提供重要的参考。比如对一个未知拓扑结构的跨膜蛋白序列,我们可以先进行是否含有信号肽的预测,参考Polyphobius和SignalP两种方法,若两种方法预测结果不一致,综合上述对两种方法的评价,Polyphobius预测的综合能力较好,可取其预测的结果,一旦确定含有信号肽,则N端必然位于膜外侧。然后结合序列的长度,判断蛋白是单跨膜还是多重跨膜,即可参照上述评价结果,选择合适的拓扑结构预测方法进行预测。     

Developing bioimaging and quantitative methods to study 3D genome

The recent advances in chromosome configuration capture (3C)-based series molecular methods and optical super-resolution (SR) techniques offer powerful tools to investigate three dimensional (3D) genomic structure in prokaryotic and eukaryotic cell nucleus. In this review, we focus on the progress during the last decade in this exciting field. Here we at first introduce briefly genome organization at chromosome, domain and sub-domain level, respectively; then we provide a short introduction to various super-resolution microscopy techniques which can be employed to detect genome 3D structure. We also reviewed the progress of quantitative and visualization tools to evaluate and visualize chromatin interactions in 3D genome derived from Hi-C data. We end up with the discussion that imaging methods and 3C-based molecular methods are not mutually exclusive - - - - actually they are complemental to each other and can be combined together to study 3D genome organization.     

Microbial Source Tracking for Identification of Fecal Pollution

Fecal pollution is a serious environmental problem that affects many coastal and inland waters worldwide. Both human and animal fecal pollution impose risks to human health from exposure to pathogenic bacteria, viruses, and protozoa. To assist authorities with the implementation of the changes suggested by more restricted legislation concering water quality in Europe, methods are needed which can identify the sources of fecal pollution. Management of fecal contamination of water would be improved if the origin of the fecal pollution could be correctly identified since remediation efforts could then be allocated in a more effective manner. The concept that the origin of fecal pollution can be traced has been termed microbial source tracking. In microbial source tracking (MST) endogenous markers of fecal sources are used for identification of the fecal pollution in aquatic environments. Chemical MST-methods can be used to trace mainly sewage pollution, but the used chemical targets have no direct relationship with pathogenic bacteria. This is not the case in microbial MST-methods where source-specific bacteria or viruses are cultured to identify fecal pollution sources. However, sometimes these microbial targets can be present in too low numbers to be detected. This is circumvented by using molecular assays for host-specific marker detection. Phenotypic and genotypic library-based methods can be used to discriminate among different fecal sources. However, the isolation step makes this procedure very labour-intensive, and issues as temporal and geographical variability remain unresolved. The underlying assumptions will be discussed and the methods mostly used in microbial source tracking will be described in more detail.     

The membrane bioreactor: a novel tool to grow anammox bacteria as free cells

In a membrane bioreactor (MBR), fast growth of anammox bacteria was achieved with a sludge residence time (SRT) of 12 days. This relatively short SRT resulted in a--for anammox bacteria--unprecedented purity of the enrichment of 97.6%. The absence of a selective pressure for settling, and dedicated cultivation conditions led to growth in suspension as free cells and the complete absence of flocs or granules. Fast growth, low levels of calcium and magnesium, and possibly the presence of yeast extract and a low shear stress are critical for the obtainment of a completely suspended culture consisting of free anammox cells. During cultivation, a population shift was observed from Candidatus "Brocadia" to Candidatus "Kuenenia stuttgartiensis." It is hypothesized that the reason for this shift is the higher affinity for nitrite of "Kuenenia." The production of anammox bacteria in suspension with high purity and productivity makes the MBR a promising tool for the cultivation and study of anammox bacteria.