NMR analyses on the interactions of the yeast Tim50 C-terminal region with the presequence and Tim50 core domain

The mitochondrial targeting signal in the presequence of mitochondrial precursor proteins is recognized by Tom20 and subsequently by Tim50 in mitochondria. Yeast Tim50 contains two presequence binding sites in the conserved core domain and in the fungi-specific C-terminal presequence binding domain (PBD). We report the NMR analyses on interactions of a shorter variant of PBD (sPBD), a shorter variant of PBD, with presequences. The presequence is recognized by sPBD in a similar manner to Tom20. sPBD can also bind to the core domain of Tim50 through the presequence binding region, which could promote transfer of the presequence from sPBD to the core domain in Tim50.     

VDAC electronics: 2. A new,anaerobic mechanism of generation of the membrane potentials in mitochondria

Mitochondrial hexokinase (HK) and creatine kinase (CK) known to form complexes with a voltage dependent anion channel (VDAC) have been reported to increase cell death resistance under hypoxia/anoxia. In this work we propose a new, non-Mitchell mechanism of generation of the inner and outer membrane potentials at anaerobic conditions. The driving force is provided by the Gibbs free energy of the HK and CK reactions associated with the VDAC–HK and the ANT (adenine nucleotide translocator)–CK–VDAC complexes, respectively, both functioning as voltage generators. In the absence of oxygen, the cytosolic creatine phosphate can be directly used by the ANT–CK–VDAC contact sites to produce ATP from ADP in the mitochondrial matrix. After that, ATP released through the fraction of unbound ANTs in exchange for ADP is used in the mitochondrial intermembrane space by the outer membrane VDAC–HK electrogenic complexes to convert cytosolic glucose into glucose-6-phosphate. A simple computational model based on the application of Ohm's law to an equivalent electrical circuit showed a possibility of generation of the inner membrane potential up to − 160 mV, under certain conditions, and of relatively high outer membrane potential without wasting of ATP that normally leads to cell death. The calculated membrane potentials depended on the restriction of ATP/ADP diffusion in narrow cristae and through the cristae junctions. We suggest that high inner membrane potential and calcium extrusion from the mitochondrial intermembrane space by generated positive outer membrane potential prevent mitochondrial permeability transition, thus allowing the maintenance of mitochondrial integrity and cell survival in the absence of oxygen.     

Genomic prediction in CIMMYT maize and wheat breeding programs

Genomic selection (GS) has been implemented in animal and plant species, and is regarded as a useful tool for accelerating genetic gains. Varying levels of genomic prediction accuracy have been obtained in plants, depending on the prediction problem assessed and on several other factors, such as trait heritability, the relationship between the individuals to be predicted and those used to train the models for prediction, number of markers, sample size and genotype × environment interaction (GE). The main objective of this article is to describe the results of genomic prediction in International Maize and Wheat Improvement Center''s (CIMMYT''s) maize and wheat breeding programs, from the initial assessment of the predictive ability of different models using pedigree and marker information to the present, when methods for implementing GS in practical global maize and wheat breeding programs are being studied and investigated. Results show that pedigree (population structure) accounts for a sizeable proportion of the prediction accuracy when a global population is the prediction problem to be assessed. However, when the prediction uses unrelated populations to train the prediction equations, prediction accuracy becomes negligible. When genomic prediction includes modeling GE, an increase in prediction accuracy can be achieved by borrowing information from correlated environments. Several questions on how to incorporate GS into CIMMYT''s maize and wheat programs remain unanswered and subject to further investigation, for example, prediction within and between related bi-parental crosses. Further research on the quantification of breeding value components for GS in plant breeding populations is required.     

BuildBeta—A system for automatically constructing beta sheets

We describe a method that can thoroughly sample a protein conformational space given the protein primary sequence of amino acids and secondary structure predictions. Specifically, we target proteins with β‐sheets because they are particularly challenging for ab initio protein structure prediction because of the complexity of sampling long‐range strand pairings. Using some basic packing principles, inverse kinematics (IK), and β‐pairing scores, this method creates all possible β‐sheet arrangements including those that have the correct packing of β‐strands. It uses the IK algorithms of ProteinShop to move α‐helices and β‐strands as rigid bodies by rotating the dihedral angles in the coil regions. Our results show that our approach produces structures that are within 4–6 Å RMSD of the native one regardless of the protein size and β‐sheet topology although this number may increase if the protein has long loops or complex α‐helical regions. Proteins 2010. © Published 2009 Wiley‐Liss, Inc.     

Assessing the impact of deforestation and climate change on the range size and environmental niche of bird species in the Atlantic forests,Brazil

Aim Habitat loss and climate change are two major drivers of biological diversity. Here we quantify how deforestation has already changed, and how future climate scenarios may change, environmental conditions within the highly disturbed Atlantic forests of Brazil. We also examine how environmental conditions have been altered within the range of selected bird species. Location Atlantic forests of south‐eastern Brazil. Methods The historical distribution of 21 bird species was estimated using Maxent . After superimposing the present‐day forest cover, we examined the environmental niches hypothesized to be occupied by these birds pre‐ and post‐deforestation using environmental niche factor analysis (ENFA). ENFA was also used to compare conditions in the entire Atlantic forest ecosystem pre‐ and post‐deforestation. The relative influence of land use and climate change on environmental conditions was examined using analysis of similarity and principal components analysis. Results Deforestation in the region has resulted in a decrease in suitable habitat of between 78% and 93% for the Atlantic forest birds included here. Further, Atlantic forest birds today experience generally wetter and less seasonal forest environments than they did historically. Models of future environmental conditions within forest remnants suggest generally warmer conditions and lower annual variation in rainfall due to greater precipitation in the driest quarter of the year. We found that deforestation resulted in a greater divergence of environmental conditions within Atlantic forests than that predicted by climate change. Main conclusions The changes in environmental conditions that have occurred with large‐scale deforestation suggest that selective regimes may have shifted and, as a consequence, spatial patterns of intra‐specific variation in morphology, behaviour and genes have probably been altered. Although the observed shifts in available environmental conditions resulting from deforestation are greater than those predicted by climate change, the latter will result in novel environments that exceed temperatures in any present‐day climates and may lead to biotic attrition unless organisms can adapt to these warmer conditions. Conserving intra‐specific diversity over the long term will require considering both how changes in the recent past have influenced contemporary populations and the impact of future environmental change.     

Evidence for an interaction between the SH3 domain and the N-terminal extension of the essential light chain in class II myosins

The function of the src-homology 3 (SH3) domain in class II myosins, a distinct beta-barrel structure, remains unknown. Here, we provide evidence, using electron cryomicroscopy, in conjunction with light-scattering, fluorescence and kinetic analyses, that the SH3 domain facilitates the binding of the N-terminal extension of the essential light chain isoform (ELC-1) to actin. The 41 residue extension contains four conserved lysine residues followed by a repeating sequence of seven Pro/Ala residues. It is widely believed that the highly charged region interacts with actin, while the Pro/Ala-rich sequence forms a rigid tether that bridges the approximately 9 nm distance between the myosin lever arm and the thin filament. In order to localize the N terminus of ELC in the actomyosin complex, an engineered Cys was reacted with undecagold-maleimide, and the labeled ELC was exchanged into myosin subfragment-1 (S1). Electron cryomicroscopy of S1-bound actin filaments, together with computer-based docking of the skeletal S1 crystal structure into 3D reconstructions, showed a well-defined peak for the gold cluster near the SH3 domain. Given that SH3 domains are known to bind proline-rich ligands, we suggest that the N-terminal extension of ELC interacts with actin and modulates myosin kinetics by binding to the SH3 domain during the ATPase cycle.     

Effects of Joint Space Use and Group Membership on Contact Rates Among White-Tailed Deer

Abstract: Establishment and spread of infectious diseases are controlled by the frequency of contacts among hosts. Although managers can estimate transmission coefficients from the relationship between disease prevalence and age or time, they may wish to quantify or compare contact rates before a disease is established or while it is at very low prevalence. Our objectives were to quantify direct and indirect contacts rates among white-tailed deer (Odocoileus virginianus) and to compare these measures of contact rate with simpler measures of joint space use. We deployed Global Positioning System (GPS) collars on 23 deer near Carbondale, Illinois, USA, from 2002 to 2005. We used location data from the GPS collars to measure pairwise rates of direct and indirect contact, based on a range of proximity criteria and time lags, as well as volume of intersection (VI) of kernel utilization distributions. We analyzed contact rates at a given distance criterion and time lag using mixed-model logistic regression. Direct contact rates increased with increasing VI and were higher in autumn—spring than in summer. After accounting for VI, the estimated odds of direct contact during autumn—spring periods were 5.0–22.1-fold greater (depending on the proximity criterion) for pairs of deer in the same social group than for between-group pairs, but for direct contacts during summer the within:between-group odds ratio did not differ significantly from 1. Indirect contact rates also increased with VI, but the effects of both season and pair-type were much smaller than for direct contacts and differed little as the time lag increased from 1–30 days. These results indicate that simple measures of joint space use are insufficient indices of direct contact because group membership can substantially increase contacts at a given level of joint space use. With indirect transmission, however, group membership had a much smaller influence after accounting for VI. Relationships between contact rates and season, VI, and pair-type were generally robust to changes in the proximity criterion defining a contact, and patterns of indirect contacts were affected little by the choice of time lag from 1–30 days. The use of GPS collars provides a framework for testing hypotheses about the form of contact networks among large mammals and comparing potential direct and indirect contact rates across gradients of ecological factors, such as population density or landscape configuration.     

Space Use and Habitat Selection by Female Louisiana Black Bears in the Tensas River Basin of Louisiana

Abstract: Studies of space use and habitat selection of endangered species are useful for identifying factors that influence fitness of individuals and viability of populations. However, there is a lack of published information regarding these behaviors for the federally threatened Louisiana black bear (Ursus americanus luteolus). We documented space use and habitat selection for 28 female black bears in 2 subpopulations of the Tensas River Basin population in northeast Louisiana, USA. The Tensas subpopulation inhabits a relatively large (>300-km²) contiguous area of bottomland hardwood forest, whereas the Deltic subpopulation exists mainly in 2 small (<7-km²) forested patches surrounded by an agricultural matrix. Females on Deltic maintained smaller seasonal and annual home ranges than females on Tensas (all P < 0.04), except for females with cubs during spring. On Tensas, females with cubs maintained smaller home ranges than females without cubs during spring (P = 0.01), but we did not detect this difference on Deltic or in other seasons. Females on Tensas and Deltic exhibited differences in habitat selection when establishing home ranges and within home ranges (P < 0.001). Deltic females selected mature bottomland hardwood forests and avoided agricultural habitats at both spatial scales. Tensas females selected a mixture of swamps, mature and regenerating forests, and exhibited variation in selection across scale, season, and reproductive status. We suggest that differences in space use and habitat selection between Tensas and Deltic are at least partially due to habitat differences at the landscape (i.e., amount of forested habitat) and patch (i.e., food availability) scales. Our results contribute to the understanding of factors that influence space use and habitat selection by black bears and provide specific information on habitat types selected by Louisiana black bears to agencies involved in habitat protection and restoration for this threatened subspecies.     

Evaluation of a rapid microbial detection method via phage lytic amplification assay coupled with Live/Dead fluorochromic stains

AIMS: To develop a method for rapid detection of bacteria via bacteriophage amplification coupled with exogenous fluorochromic stains. METHODS AND RESULTS: A method for the rapid detection of bacteria was developed which consisted of exposing the sample suspected to contain target cells to host-specific phage. After at least one infection cycle, bacteria known to be infected by the phage (helper cells) were added and the number of nascent phage particles was estimated using the Live/Dead BacLight Bacterial Viability kit. Using Pseudomonas aeruginosa, it was shown that the dead helper cell population following phage infection was proportional to the initial number of target cells present in the original sample. Approximately 1 x 10(1) CFU per ml of P. aeruginosa could be detected within 4 h without the need for enrichment. CONCLUSIONS: The phage lytic amplification assay coupled with exogenous fluorochromic stains was able to detect approx. 1 x 10(1) CFU per ml of the target bacterium within 4 h. SIGNIFICANCE AND IMPACT OF THE STUDY: A method to detect low number of bacterial cells in a sample within 4 h without the need for enrichment was developed.