Genetic diversity and population structure of food-borne Staphylococcus carnosus strains

The species Staphylococcus carnosus is a non-pathogenic representative of the coagulase negative staphylococci. Specific strains are applied as meat starter cultures. The species consists of two subspecies, S. carnosus ssp. carnosus and S. carnosus ssp. utilis. In order to place S. carnosus strains, characterized in former studies, in a genetic background that allows a typing of candidates for starter cultures, a Multilocus Sequence Typing (MLST) scheme was developed. Internal fragments of the genes tpiA, xprT, dat, gmk, glpK, narG, cstA, encoding triosephosphate isomerase, xanthine phosphoribosyltransferase, d-amino acid aminotransferase, guanylate kinase, glycerol kinase, the α-chain of the respiratory nitrate reductase, and a carbon starvation protein where chosen. Genes were selected based on their equal distribution in the genome, taxonomic value in subspecies differentiation and metabolic function. This MLST was applied to 44 S. carnosus strains, most of them previously analyzed for their suitability as starter cultures.The number of alleles varied between zero (tpiA) and five (cstA) and allowed the definition of nine sequence types (ST). ST1 was most abundant (18 strains), followed by ST2 (8) and ST4 (6). The nine STs confirmed a close relationship of all strains despite their isolation source and year, but lacked correlation with physiological activities relevant for starter cultures. The low amount of STs in the strain set lets us suggest that recombination between strains is rare. Thus, it is hypothesized that evolutionary events seem to be due to single point mutations rather than intrachromosomal recombination, and that the species possesses a clonal population structure.     

世界生态旅游区划

生态旅游区划是揭示全球尺度生态旅游资源与生态旅游业空间布局的重要手段,有助于从整体上把握世界生态旅游的发展。本文在探讨生态旅游区划定义与理论依据的基础上,提出生态旅游区划的理论基础是地域分异规律与生态学原理,并根据全局谋划、综合分析、主导因索、与行政区协调、兼顾自然区划等原则。将世界生态旅游地域系统划分为6个生态旅游洲、29个生态旅游大区、71个生态旅游区以及若干生态旅游地。文章还对各洲的生态旅游特点进行了阐述。     

Nonparametric comparison for panel count data with unequal observation processes

This article considers nonparametric comparison of several treatment groups based on panel count data, which often occur in, among others, medical follow-up studies and reliability experiments concerning recurrent events. For the problem, most of the existing procedures require that observation processes are identical across different treatment groups among other requirements. We propose a new class of nonparametric test procedures that allow different observation processes. The new test statistics are constructed based on the integrated weighted differences between the estimated mean functions of the underlying recurrent event processes. The asymptotic distributions of the proposed test statistics are established and their finite-sample properties are examined through Monte Carlo simulations, which indicate that the proposed approach works well for practical situations. An illustrative example is provided.     

The provision of winter bird food by the English Environmental Stewardship scheme

Environmental Stewardship (ES) is the main mechanism for reversing the decline in farmland birds in England, and includes a range of options designed to provide winter foraging for seed‐eating species. We estimated granivorous songbird densities on ES options designed to provide winter food, on farms within the Entry Level (ELS) or Higher Level (HLS) strata of ES. ES Wild Bird Mixtures (WBMs) hosted higher densities and a wider range of granivores than non‐ES game covers, although in East Anglia the enhanced HLS WBM was used no more than the basic ELS WBM. In the West Midlands there were low densities of granivores on all WBMs and game covers. The widespread ELS WBM appeared to provide little food for buntings but supported finches, partially through greater weed burdens. There was a weak, non‐significant trend for Skylarks Alauda arvensis to make greater use of ELS cereal stubbles than non‐ES stubbles, possibly because of post‐harvest herbicide restrictions allowing overwinter weed growth. At the field scale, this work demonstrates that although some ES options provide winter food resources for birds, there is limited evidence for additional benefits of Higher Level vs. Entry Level Stewardship to wintering farmland songbirds.     

A simple mathematical model for Ebola in Africa

We deal with the following question: Can the consumption of contaminated bush meat, the funeral practices and the environmental contamination explain the recurrence and persistence of Ebola virus disease outbreaks in Africa? We develop an SIR-type model which, incorporates both the direct and indirect transmissions in such a manner that there is a provision of Ebola viruses. We prove that the full model has one (endemic) equilibrium which is locally asymptotically stable whereas, it is globally asymptotically stable in the absence of the Ebola virus shedding in the environment. For the sub-model without the provision of Ebola viruses, the disease dies out or stabilizes globally at an endemic equilibrium. At the endemic level, the number of infectious is larger for the full model than for the sub-model without provision of Ebola viruses. We design a nonstandard finite difference scheme, which preserves the dynamics of the model. Numerical simulations are provided.     

空肠弯曲菌生物学分型的研究

用马尿酸水解,28℃中生长及10种试剂抗性试验,研究了空肠弯曲菌的生物学分型,每株菌按3种方法,4组实验进行计数,我们对86株弯曲菌进行了生物学分型,其中空肠弯曲菌79株,分为17种类型,结肠弯曲菌5株为5种类型,海鸥弯曲菌2株为2种类型。这对菌株在流行病学上分析有一定意义。     

Incongruence in molecular species delimitation schemes: What to do when adding more data is difficult

Using multiple, independent approaches to molecular species delimitation is advocated to accommodate limitations and assumptions of a single approach. Incongruence in delimitation schemes is a potential by‐product of employing multiple methods on the same data, and little attention has been paid to its reconciliation. Instead, a particular scheme is prioritized, and/or molecular delimitations are coupled with additional, independent lines of evidence that mitigate incongruence. We advocate that incongruence within a line of evidence should be accounted for before comparing across lines of evidence that can themselves be incongruent. Additionally, it is not uncommon for empiricists working in nonmodel systems to be data‐limited, generating some concern for the adequacy of available data to address the question of interest. With conservation and management decisions often hinging on the status of species, it seems prudent to understand the capabilities of approaches we use given the data we have. Here, we apply two molecular species delimitation approaches, spedeSTEM and BPP, to the Castilleja ambigua (Orobanchaceae) species complex, a relatively young plant lineage in western North America. Upon finding incongruence in our delimitation, we employed a post hoc simulation study to examine the power of these approaches to delimit species. Given the data we collected, we find that spedeSTEM lacks the power to delimit while BPP is capable, thus allowing us to address incongruence before proceeding in delimitation. We suggest post hoc simulation studies like this compliment empirical delimitation and serve as a means of exploring conflict within a line of evidence and dealing with it appropriately.     

Occurrence of potato virus X strain group 1 in seed stocks of potato cultivars lacking resistance genes

Potato virus X (PVX) isolates were obtained from a simple seed potato production scheme or from ware potatoes produced by seed potatoes obtained from it. In this scheme, PVX infection is widespread in seed stocks and most of the potatoes grown lack PVX resistance genes. Thirteen PVX isolates were typed to strain group by inoculation to potato cultivars containing different combinations of hypersensitivity genes Nx and Nb. Six failed to overcome either gene and therefore belonged to strain group 1, four overcame Nb only and were placed in strain group 3 and three were mixtures of the two. All 13 isolates failed to overcome extreme resistance/immunity gene Rx. Naturally infected cultivars of genotype nx.nb contained strain group 1 alone or strain groups 1 and 3, while those of genotype nx:Nb contained only strain group 3. The widespread occurrence of strain group 1 contrasts with the predominant occurrence of strain group 3 in potatoes in the UK. However, it resembles the UK situation before sophisticated seed potato production schemes were introduced and before PVX hypersensitivity genes Nx and Nb were deliberately exploited in potato breeding. Prior infection with potato leafroll virus (PLRV) did not affect expression of hypersensitivity to PVX in inoculated leaves of an nx:Nb genotype.     

Building anisotropic sampling schemes for the estimation of anisotropic dispersal

Anisotropy, a structural property of dispersal, is observed in dispersal patterns occurring for a wide range of biological systems. While dispersal models more and more often incorporate anisotropy, the sampling schemes required to collect data for validation usually do not account for the anisotropy of dispersal data. Using a parametric model already published to describe the spatial spread of a plant disease, the wheat yellow rust, we carry out a study aimed at recommending an appropriate sampling scheme for anisotropic data. In a first step, we show with a simulation study that prior knowledge of dispersal anisotropy can be used to improve the sampling scheme. One of the main guidelines to be proposed is the orientation of the sampling grid around the main dispersal directions. In a second step, we propose a sequential sampling procedure (SSP) used to automatically build anisotropic sampling schemes adapted to the actual anisotropy of dispersal. The SSP is applied to simulated and real data. The proposed methodology is expected to be adapted easily to any kind of organisms with wind-borne propagule dispersal because it does not require the inclusion of biological features specific of the considered organism.