Amino acids and insulin act additively to regulate components of the ubiquitin-proteasome pathway in C2C12 myotubes

Background  

The ubiquitin-proteasome system is the predominant pathway for myofibrillar proteolysis but a previous study in C2C12 myotubes only observed alterations in lysosome-dependent proteolysis in response to complete starvation of amino acids or leucine from the media. Here, we determined the interaction between insulin and amino acids in the regulation of myotube proteolysis     

Two non-homologous brain diseases-related genes, <Emphasis Type="Italic">SERPINI1</Emphasis> and <Emphasis Type="Italic">PDCD10</Emphasis>, are tightly linked by an asymmetric bidirectional promoter in an evolutionarily conserved manner

Background  

Despite of the fact that mammalian genomes are far more spacious than prokaryotic genomes, recent nucleotide sequencing data have revealed that many mammalian genes are arranged in a head-to-head orientation and separated by a small intergenic sequence. Extensive studies on some of these neighboring genes, in particular homologous gene pairs, have shown that these genes are often co-expressed in a symmetric manner and regulated by a shared promoter region. Here we report the identification of two non-homologous brain disease-related genes, with one coding for a serine protease inhibitor (SERPINI1) and the other for a programmed cell death-related gene (PDCD10), being tightly linked together by an asymmetric bidirectional promoter in an evolutionarily conserved fashion. This asymmetric bidirectional promoter, in cooperation with some cis-acting elements, is responsible for the co-regulation of the gene expression pattern as well as the tissue specificity of SERPINI1 and PDCD10.     

A comprehensive evaluation of SAM,the SAM R-package and a simple modification to improve its performance

Background  

The Significance Analysis of Microarrays (SAM) is a popular method for detecting significantly expressed genes and controlling the false discovery rate (FDR). Recently, it has been reported in the literature that the FDR is not well controlled by SAM. Due to the vast application of SAM in microarray data analysis, it is of great importance to have an extensive evaluation of SAM and its associated R-package (sam2.20).     

High variability and non-neutral evolution of the mammalian <Emphasis Type="Italic">avpr1a</Emphasis> gene

Background  

The arginine-vasopressin 1a receptor has been identified as a key determinant for social behaviour in Microtus voles, humans and other mammals. Nevertheless, the genetic bases of complex phenotypic traits like differences in social and mating behaviour among species and individuals remain largely unknown. Contrary to previous studies focusing on differences in the promotor region of the gene, we investigate here the level of functional variation in the coding region (exon 1) of this locus.     

Sympatric snow leopards and Tibetan wolves: coexistence of large carnivores with human-driven potential competition

The snow leopard Panthera uncia coexists with the wolf Canis lupus throughout most of its distribution range. We analysed the food habits of snow leopards and wolves in their sympatric range in the Karakoram mountains of Pakistan. A total of 131 genotyped scats (N?=?74, snow leopard; N?=?57, Tibetan wolf) were collected during the cold periods (i.e. winter and spring) of 2011 and 2012 in the Hushey valley. Large mammals, i.e. livestock and ibex, accounted for 84.8 and 83.1% of the diet (relative frequency) of the snow leopard and the wolf, respectively. Domestic prey was the staple of the diet of both snow leopards (66.6%) and wolves (75.1%). Ibex Capra ibex, the only wild ungulate in our study area, contributed 18.2 and 16.9% of relative frequencies in the diets of the snow leopard and the wolf, respectively. In winter, the snow leopard heavily relied on domestic sheep (43.3%) for food, whereas the wolf preyed mainly on domestic goats (43.4%). Differently from other study areas, both snow leopards and wolves showed no apparent prey preference (Jacobs index: snow leopard min. ??0.098, max. 0.102; Tibetan wolf min. ??0.120, max. 0.03). In human depauperate areas, with livestock and only a few wild prey, should competitive interactions arise, two main scenarios could be expected, with either predator as a winner. In both cases, the best solution could primarily impinge on habitat restoration, so that a balance could be found between these predators, who have already coexisted for thousands of years.     

Enterocin B3A-B3B produced by LAB collected from infant faeces: potential utilization in the food industry for <Emphasis Type="Italic">Listeria monocytogenes</Emphasis> biofilm management

Enterococcus faecalis B3A-B3B produces the bacteriocin B3A-B3B with activity against Listeria monocytogenes, Staphylococcus aureus, methicillin-resistant Staphylococcus aureus (MRSA) and Clostridium perfringens, but apparently not against fungi or Gram-negative bacteria, except for Salmonella Newport. B3A-B3B enterocin has two different nucleotides but similar amino acid composition to the class IIb MR10A-MR10B enterocin. B3A-B3B consists of two peptides of predicted molecular mass of 5176.31 Da (B3A) and 5182.21 Da (B3B). Importantly, B3A-B3B impeded biofilm formation of the foodborne pathogen L. monocytogenes 162 grown on stainless steel. The antimicrobial treatment of stainless steel with nisin (1 or 16 mg ml^?1) decreased the cell numbers by about 2 log CFU ml^?1, thereby impeding the biofilm formation by L. monocytogenes 162 or its nisin-resistant derivative strain L. monocytogenes 162R. Furthermore, the combination of nisin and B3A-B3B enterocin reduced the MIC required to inhibit this pathogen grown in planktonic or biofilm cultures.     

Inference on diversity from forest inventories: a review

A number of international agreements and commitments emphasize the importance of appropriate monitoring protocols and assessments as prerequisites for sound conservation and management of the world’s forest ecosystems. Mandated periodic surveys, like forest inventories, provide a unique opportunity to identify and properly satisfy natural resource management information needs. Distinctively, there is an increasing need for detecting diversity by means of unambiguous diversity measures. Because all diversity measures are functions of tree species abundances, estimation of tree diversity indices and profiles is inevitably performed by estimating tree species abundances and then estimating indices and profiles as functions of the abundance estimates. This strategy can be readily implemented in the framework of current forest inventory approaches, where tree species abundances are routinely estimated by means of plots placed onto the surveyed area in accordance with probabilistic schemes. The purpose of this paper is to assess the effectiveness of this strategy by reviewing theoretical results from published case studies. Under uniform random sampling (URS), that is when plots are uniformly and independently located on the study region, consistency and asymptotic normality of diversity index estimators follow from standard limit theorems as the sampling effort increases. In addition, variance estimation and bias reduction are achieved using the jackknife method. Despite its theoretical simplicity, URS may lead to uneven coverage of the study region. In order to avoid unbalanced sampling, the use of tessellation stratified sampling (TSS) is suggested. TSS involves covering the study region by a polygonal grid and randomly selecting a plot in each polygon. Under TSS, the diversity index estimators are consistent, asymptotically normal and more precise than those achieved using URS. Variance estimation is possible and there is no need to reduce bias.     

Identifying conservation hotspots in non-breeding areas: a case study of Lake Sturgeon (<Emphasis Type="Italic">Acipenser fulvescens</Emphasis>) in the Great Lakes

Limited conservation resources necessitate the prioritization of management efforts and one of the mechanisms for prioritization is the identification of hotspots. For some species of conservation concern, hotspots have been delineated, often using individual abundance as the metric. However, areas that attract individuals from multiple breeding populations may be a higher priority for conservation. These areas may have more abundant resources or habitat quality, and multiple breeding populations simultaneously benefit from conservation actions in these areas. We identified non-spawning aggregations of Lake Sturgeon Acipenser fulvescens in lakes Huron and Erie of the Great Lakes. The spawning period in Lake Sturgeon only represents a brief portion of their life and conservation goals need to include non-spawning areas. Based on 12 microsatellite loci, we determined the population of origin of individuals in the aggregations and computed a modified population-level Simpson’s diversity index (pD). Using this criterion, two hotspots were identified. The North Channel of Lake Huron had the highest diversity of represented populations (pD = 3.14). The second identified hotspot was Saginaw Bay in Lake Huron (pD = 1.78). Both hotspots had evidence of long-distance movement into the area. Monitoring of aggregations should continue to assess temporal variability in hotspot delineation.