A microarray system for Y chromosomal and mitochondrial single nucleotide polymorphism analysis in chimpanzee populations

Chimpanzee populations are diminishing as a consequence of human activities, and as a result this species is now endangered. In the context of conservation programmes, genetic data can add vital information, for instance on the genetic diversity and structure of threatened populations. Single nucleotide polymorphisms (SNP) are biallelic markers that are widely used in human molecular studies and can be implemented in efficient microarray systems. This technology offers the potential of robust, multiplexed SNP genotyping at low reagent cost in other organisms than humans, but it is not commonly used yet in wild population studies. Here, we describe the characterization of new SNPs in Y-chromosomal intronic regions in chimpanzees and also identify SNPs from mitochondrial genes, with the aim of developing a microarray system that permits the simultaneous study of both paternal and maternal lineages. Our system consists of 42 SNPs for the Y chromosome and 45 SNPs for the mitochondrial genome. We demonstrate the applicability of this microarray in a captive population where genotypes accurately reflected its large pedigree. Two wild-living populations were also analysed and the results show that the microarray will be a useful tool alongside microsatellite markers, since it supplies complementary information about population structure and ecology. SNP genotyping using microarray technology, therefore, is a promising approach and may become an essential tool in conservation genetics to help in the management and study of captive and wild-living populations. Moreover, microarrays that combine SNPs from different genomic regions could replace microsatellite typing in the future.     

Construction of complex receptive fields in cat primary visual cortex.

In primary visual cortex, neurons are classified into simple cells and complex cells based on their response properties. Although the role of these two cell types in vision is still unknown, an attractive hypothesis is that simple cells are necessary to construct complex receptive fields. This hierarchical model puts forward two main predictions. First, simple cells should connect monosynaptically to complex cells. Second, complex cells should become silent when simple cells are inactivated. We have recently provided evidence for the first prediction, and here we do the same for the second. In summary, our results suggest that the receptive fields of most layer 2+3 complex cells are generated by a mechanism that requires simple cell inputs.     

Assessing sub-seafloor microbial activity by combined stable isotope probing with deuterated water and 13C-bicarbonate

Sub‐seafloor sediments are populated by large numbers of microbial cells but not much is known about their metabolic activities, growth rates and carbon assimilation pathways. Here we introduce a new method enabling the sensitive detection of microbial lipid production and the distinction of auto‐ and heterotrophic carbon assimilation. Application of this approach to anoxic sediments from a Swedish fjord allowed to compare the activity of different functional groups, the growth and turnover times of the bacterial and archaeal communities. The assay involves dual stable isotope probing (SIP) with deuterated water (D₂O) and ¹³C_DIC (d issolved i norganic c arbon). Culture experiments confirmed that the D content in newly synthesized lipids is in equilibrium with the D content in labelled water, independent of whether the culture grew hetero‐ or autotrophically. The ratio of ¹³C_DIC to D₂O incorporation enables distinction between these two carbon pathways in studies of microbial cultures and in environmental communities. Furthermore, D₂O‐SIP is sufficiently sensitive to detect the formation of few hundred cells per day in a gram of sediment. In anoxic sediments from a Swedish fjord, we found that > 99% of newly formed lipids were attributed to predominantly heterotrophic bacteria. The production rate of bacterial lipids was highest in the top 5 cm and decreased 60‐fold below this depth while the production rate of archaeal lipids was rather low throughout the top meter of seabed. The contrasting patterns in the rates of archaeal and bacterial lipid formation indicate that the factors controlling the presence of these two lipid groups must differ fundamentally.     

Residence of the leopard seal in the Magellan Strait: a potential sub-Antarctic population inhabiting the waters of Southern Chile?

The leopard seal is widely distributed on the Antarctic pack ice, but a number of individuals are also thought to displace north from the pack ice to the sub-Antarctic Islands or venture even farther north. In Chile, the leopard seal has been reported mainly in the Fueguian Archipelago, with individuals sighted year-round; however, the data to date have been unable to determine whether it is the same individuals who remain year-round. Thus, one of the questions to be resolved is whether there is a northward dispersion of individuals from the Southern Ocean returning to the Antarctic continent, or alternatively if there is a potential sub-Antarctic population that delay or suspend their migration toward the Antarctic region. Opportunistic sightings of a solitary seal at Ballena Sound (53°41′S, 72°37′W), Magellan Region, Chile, were documented in photographs on six occasions from January to May 2012. Based on the review of the photographs, the leopard seal was identified as the same individual. This finding provides the first evidence of a long occupation by a leopard seal in the fjords and channels of Fueguian Region, suggesting the existence of a small population inhabiting the waters of Southern Chile year-round.     

Ribosomal Proteins RPL37, RPS15 and RPS20 Regulate the Mdm2-p53-MdmX Network

Changes to the nucleolus, the site of ribosome production, have long been linked to cancer, and mutations in several ribosomal proteins (RPs) have been associated with an increased risk for cancer in human diseases. Relevantly, a number of RPs have been shown to bind to MDM2 and inhibit MDM2 E3 ligase activity, leading to p53 stabilization and cell cycle arrest, thus revealing a RP-Mdm2-p53 signaling pathway that is critical for ribosome biogenesis surveillance. Here, we have identified RPL37, RPS15, and RPS20 as RPs that can also bind Mdm2 and activate p53. We found that each of the aforementioned RPs, when ectopically expressed, can stabilize both co-expressed Flag-tagged Mdm2 and HA-tagged p53 in p53-null cells as well as endogenous p53 in a p53-containing cell line. For each RP, the mechanism of Mdm2 and p53 stabilization appears to be through inhibiting the E3 ubiquitin ligase activity of Mdm2. Interestingly, although they are each capable of inducing cell death and cell cycle arrest, these RPs differ in the p53 target genes that are regulated upon their respective introduction into cells. Furthermore, each RP can downregulate MdmX levels but in distinct ways. Thus, RPL37, RPS15 and RPS20 regulate the Mdm2-p53-MdmX network but employ different mechanisms to do so.     

Genome-wide association mapping of three important traits using bread wheat elite breeding populations

The exponential development of molecular markers enables a more effective study of the genetic architecture of traits of economic importance, like test weight in wheat (Triticum aestivum L.), for which a high value is desired by most end-users. The association mapping (AM) method now allows more precise exploration of the entire genome. AM requires populations with substantial genetic variability of the traits of interest. The breeding lines at the end of a selection cycle, characterized for numerous traits, represent a potentially useful population for AM studies. Using three elite line populations, selected by several breeders and genotyped with about 2,500 Diversity Arrays Technology markers, several associations were identified between these markers and test weight, grain yield and heading date. To minimize spurious associations, we compared the general linear model and mixed linear model (MLM), which adjust for population structure and kinship differently. The MLM model with the kinship matrix was the most efficient. Finally, elite lines from several breeding programs had sufficient genetic variability to allow for the mapping of several chromosomal regions involved in the variation of three important traits.     

Nitric oxide inhibits prostanoid synthesis in the rat oviduct

We have studied the effect of nitric oxide (NO) on the production of arachidonic acid ([14C]-AA) metabolites in the rat oviduct. The basal synthesis of eicosanoids was measured by the conversion of ([14C]-AA) to the different radiolabeled products of cyclooxygenase (COX). The oviducts incubated for 1 h with the labeled substrate of COX were able to convert 3.3 +/- 0.3% of ([14C]-AA) to 6-ceto-PGF1alpha, 10.7 +/- 1.0% to PGF2alpha, 13.5 +/- 1.2% to PGE2 and 6.3 +/- 0.5% to TXB2. The tissues were incubated with different doses of two NO donors: SIN-1 and Spermine NONOate. The results indicated that SIN-1 produces a significant decrease (50%; P < 0.05) in all prostanoids evaluated in a dose-response fashion. The inhibitory effect was completely reversed by addition of 20 microg/ml of hemoglobin (Hb), a NO scavenger. The addition of Spermine NONOate to the incubation medium diminished significantly (65%) the synthesis of COX metabolites suggesting that NO acts by inhibiting COX activity in the rat oviduct. However, NOS inhibitors, N(G)-L-arginine-methyl-ester (L-NAME) nd N(G)-L-monomethyl-arginine (L-NMMA) had no effect on basal production of the prostanoids. These results indicate that in the rat oviduct the synthesis of COX metabolites is negatively regulated by nitric oxide.     

Extracellular Bacterial Pathogen Induces Host Cell Surface Reorganization to Resist Shear Stress

Bacterial infections targeting the bloodstream lead to a wide array of devastating diseases such as septic shock and meningitis. To study this crucial type of infection, its specific environment needs to be taken into account, in particular the mechanical forces generated by the blood flow. In a previous study using Neisseria meningitidis as a model, we observed that bacterial microcolonies forming on the endothelial cell surface in the vessel lumen are remarkably resistant to mechanical stress. The present study aims to identify the molecular basis of this resistance. N. meningitidis forms aggregates independently of host cells, yet we demonstrate here that cohesive forces involved in these bacterial aggregates are not sufficient to explain the stability of colonies on cell surfaces. Results imply that host cell attributes enhance microcolony cohesion. Microcolonies on the cell surface induce a cellular response consisting of numerous cellular protrusions similar to filopodia that come in close contact with all the bacteria in the microcolony. Consistent with a role of this cellular response, host cell lipid microdomain disruption simultaneously inhibited this response and rendered microcolonies sensitive to blood flow–generated drag forces. We then identified, by a genetic approach, the type IV pili component PilV as a triggering factor of plasma membrane reorganization, and consistently found that microcolonies formed by a pilV mutant are highly sensitive to shear stress. Our study shows that bacteria manipulate host cell functions to reorganize the host cell surface to form filopodia-like structures that enhance the cohesion of the microcolonies and therefore blood vessel colonization under the harsh conditions of the bloodstream.