Side chain NMR assignments in the membrane protein OmpX reconstituted in DHPC micelles

Sequence-specific assignments have been obtained for side chain methyl resonances of Val, Leu and Ile in the outer membrane protein X (OmpX) from Escherichia colireconstituted in 60 kDa micelles in aqueous solution. Using previously established techniques, OmpX was uniformly ²H,¹³C,¹⁵N-labeled with selectively protonated Val-^1,2, Leu-^1,2and Ile-¹methyl groups. The thus labeled protein was studied with the novel experiments 3D (H)C(CC)-TOCSY-(CO)-[¹⁵N,¹H]-TROSY and 3D H(C)(CC)-TOCSY-(CO)-[¹⁵N,¹H]-TROSY. Compared to the corresponding conventional experimental schemes, the TROSY-type experiments yielded a sensitivity gain of about 2 at 500 MHz. The overall sensitivity of the experiments was further enhanced more than two-fold by the use of a cryoprobe. Complete assignments of the proton and carbon chemical shifts were obtained for all isopropyl methyl groups of Val and Leu, as well as for the ¹-methyls of Ile. The present approach is applicable for soluble proteins or micelle-reconstituted membrane proteins in structures with overall molecular weights up to about 100 kDa, and adds to the potentialities of solution NMR for de novostructure determination as well as for functional studies, such as ligand screening with proteins in large structures.     

Variable biotherapeutic effects of Lactobacillus acidophilus isolates on orogastric and systemic candidiasis in immunodeficient mice

Two commercially available isolates of Lactobacillus acidophilus (NCFM and LA-1) were compared for their capacities to protect immunodeficient bg/bg-nu/un and bg/bg-nu/+ mice from candidiasis. L. acidophilus NCFM prolonged survival of adult and neonatal bg/bg-nu/nu mice, inhibited disseminated candidiasis in both mouse strains, suppressed weight loss associated with Candida albicans infection in bg/bg-nu/nu females, but did not decrease the severity or the incidente of orogastric candidiasis in gnotobiotic mice. L. acidophilus LA-1 suppressed numbers of C. albicans in the alimentary tracts of bg/bg-nu/+ mice and reduced the severity of mucosal candidiasis in bg/bg-nu/nuand bg/bg-nu/+ mice; however, L. acidophilus LA-1 did not improve the survival of bg/bg-nu/nu mice after oral challenge (colonization) with C. albicansand it was associated with lethality in gnotobiotic adult female bg/bg-nu/nu mice. These results demonstrate that the two isolates of L. acidophilus differed in their capacity to protect immunodeficient mice from candidiasis.     

Disordered Microbial Communities in Asthmatic Airways

Background

A rich microbial environment in infancy protects against asthma [1], [2] and infections precipitate asthma exacerbations [3]. We compared the airway microbiota at three levels in adult patients with asthma, the related condition of COPD, and controls. We also studied bronchial lavage from asthmatic children and controls.

Principal Findings

We identified 5,054 16S rRNA bacterial sequences from 43 subjects, detecting >70% of species present. The bronchial tree was not sterile, and contained a mean of 2,000 bacterial genomes per cm² surface sampled. Pathogenic Proteobacteria, particularly Haemophilus spp., were much more frequent in bronchi of adult asthmatics or patients with COPD than controls. We found similar highly significant increases in Proteobacteria in asthmatic children. Conversely, Bacteroidetes, particularly Prevotella spp., were more frequent in controls than adult or child asthmatics or COPD patients.

Significance

The results show the bronchial tree to contain a characteristic microbiota, and suggest that this microbiota is disturbed in asthmatic airways.     

African 2, a clonal complex of Mycobacterium bovis epidemiologically important in East Africa

We have identified a clonal complex of Mycobacterium bovis isolated at high frequency from cattle in Uganda, Burundi, Tanzania, and Ethiopia. We have named this related group of M. bovis strains the African 2 (Af2) clonal complex of M. bovis. Af2 strains are defined by a specific chromosomal deletion (RDAf2) and can be identified by the absence of spacers 3 to 7 in their spoligotype patterns. Deletion analysis of M. bovis isolates from Algeria, Mali, Chad, Nigeria, Cameroon, South Africa, and Mozambique did not identify any strains of the Af2 clonal complex, suggesting that this clonal complex of M. bovis is localized in East Africa. The specific spoligotype pattern of the Af2 clonal complex was rarely identified among isolates from outside Africa, and the few isolates that were found and tested were intact at the RDAf2 locus. We conclude that the Af2 clonal complex is localized to cattle in East Africa. We found that strains of the Af2 clonal complex of M. bovis have, in general, four or more copies of the insertion sequence IS6110, in contrast to the majority of M. bovis strains isolated from cattle, which are thought to carry only one or a few copies.     

Effects of high-intensity sprint training on skeletal muscle blood flow in rats.

The regional blood flow response (via radioactive microspheres) was determined for female rats after 6 wk of high-intensity sprint training (HIST) or limited cage activity as the animals exercised at work loads that would elicit maximal O2 uptake. Blood flow to the different organs of the abdominal region was greatly reduced during maximal exercise conditions, and the magnitude of the reduction appeared to be similar for both the HIST group of rats and their sedentary (SED) control counterparts. Of the 20 different hindlimb muscles examined in the present study, blood flow to the soleus, plantaris, gastrocnemius, flexor hallicus longus, vastus lateralis, rectus femoris, biceps femoris, and adductor magnus and brevis muscles was significantly greater (P less than 0.05) in the HIST rats during maximal exercise conditions than in the SED control rats. Correspondingly, blood flow to the total hindlimb during maximal exercise was also significantly greater in the HIST rats than in the SED control rats [240 +/- 18 vs. 192 +/- 15 (SE) ml.min-1.100 g-1]. These results support the contention that the increase in maximal cardiac output that is produced by HIST in the rat is primarily directed toward the working skeletal muscle and not toward the organs found in the abdominal region. We conclude from these experiments that HIST will produce significant adaptations in central cardiac function and skeletal muscle blood flow in the rat.     

NMR-derived dynamic aspects of N-type inactivation of a Kv channel suggest a transient interaction with the T1 domain

Some eukaryotic voltage-gated K+ (Kv) channels contain an N-terminal inactivation peptide (IP), which mediates a fast inactivation process that limits channel function during membrane depolarization and thus shapes the action potential. We obtained sequence-specific nuclear magnetic resonance (NMR) assignments for the polypeptide backbone of a tetrameric N-terminal fragment (amino acids 1-181) of the Aplysia Kv1.1 channel. Additional NMR measurements show that the tetramerization domain 1 (T1) has the same globular structure in solution as previously determined by crystallography and that the IP (residues 1-20) and the linker (residues 21-65) are in a flexibly disordered, predominantly extended conformation. A potential contact site between the T1 domain and the flexible tail (residues 1-65) has been identified on the basis of chemical-shift changes of individual T1 domain amino acids, which map to the T1 surface near the interface between adjacent subunits. Paramagnetic perturbation experiments further indicate that, in the ensemble of solution conformers, there is at least a small population of species with the IP localized in close proximity to the proposed interacting residues of the T1 tetramer. Electrophysiological measurements show that all three mutations in this pocket that we tested slow the rate of inactivation and speed up recovery, as predicted from the preinactivation site model. These results suggest that specific, short-lived transient interactions between the T1 domain and the IP or the linker segment may play a role in defining the regulatory kinetics of fast channel inactivation.     

The Direct Energy Demand of Internet Data Flows

The direct energy demand of Internet data flows can be assessed using a variety of methodological approaches (top‐down, bottom‐up, or hybrid/model based) and different definitions of system boundaries. Because of this diversity, results reported in the literature differ by up to two orders of magnitude and are difficult to compare. We present a first assessment that uses a pure bottom‐up approach and a system boundary that includes only transmission equipment. The assessment is based on the case study of a 40 megabit per second videoconferencing transmission between Switzerland and Japan, yielding a consumption of 0.2 kilowatt‐hours per transmitted gigabyte for 2009, a result that supports the lowest of the existing estimates. We discuss the practical implications of our findings.