How release of phosphate from mammalian F1-ATPase generates a rotary substep.

The rotation of the central stalk of F1-ATPase is driven by energy derived from the sequential binding of an ATP molecule to its three catalytic sites and the release of the products of hydrolysis. In human F1-ATPase, each 360° rotation consists of three 120° steps composed of substeps of about 65°, 25°, and 30°, with intervening ATP binding, phosphate release, and catalytic dwells, respectively. The F1-ATPase inhibitor protein, IF1, halts the rotary cycle at the catalytic dwell. The human and bovine enzymes are essentially identical, and the structure of bovine F1-ATPase inhibited by IF1 represents the catalytic dwell state. Another structure, described here, of bovine F1-ATPase inhibited by an ATP analog and the phosphate analog, thiophosphate, represents the phosphate binding dwell. Thiophosphate is bound to a site in the α(E)β(E)-catalytic interface, whereas in F1-ATPase inhibited with IF1, the equivalent site is changed subtly and the enzyme is incapable of binding thiophosphate. These two structures provide a molecular mechanism of how phosphate release generates a rotary substep as follows. In the active enzyme, phosphate release from the β(E)-subunit is accompanied by a rearrangement of the structure of its binding site that prevents released phosphate from rebinding. The associated extrusion of a loop in the β(E)-subunit disrupts interactions in the α(E)β(E-)catalytic interface and opens it to its fullest extent. Other rearrangements disrupt interactions between the γ-subunit and the C-terminal domain of the α(E)-subunit. To restore most of these interactions, and to make compensatory new ones, the γ-subunit rotates through 25°-30°

An instability of higher-dimensional rotating black holes

We present the first example of a linearized gravitational instability of an asymptotically flat vacuum black hole. We study perturbations of a Myers-Perry black hole with equal angular momenta in an odd number of dimensions. We find no evidence of any instability in five or seven dimensions, but in nine dimensions, for sufficiently rapid rotation, we find perturbations that grow exponentially in time. The onset of instability is associated with the appearance of time-independent perturbations which generically break all but one of the rotational symmetries. This is interpreted as evidence for the existence of a new 70-parameter family of black hole solutions with only a single rotational symmetry. We also present results for the Gregory-Laflamme instability of rotating black strings, demonstrating that rotation makes black strings more unstable.Comment: 38 pages, 13 figure

ATP synthase from Trypanosoma brucei has an elaborated canonical F1-domain and conventional catalytic sites.

The structures and functions of the components of ATP synthases, especially those subunits involved directly in the catalytic formation of ATP, are widely conserved in metazoans, fungi, eubacteria, and plant chloroplasts. On the basis of a map at 32.5-Å resolution determined in situ in the mitochondria of Trypanosoma brucei by electron cryotomography, it has been proposed that the ATP synthase in this species has a noncanonical structure and different catalytic sites in which the catalytically essential arginine finger is provided not by the α-subunit adjacent to the catalytic nucleotide-binding site as in all species investigated to date, but rather by a protein, p18, found only in the euglenozoa. A crystal structure at 3.2-Å resolution of the catalytic domain of the same enzyme demonstrates that this proposal is incorrect. In many respects, the structure is similar to the structures of F1-ATPases determined previously. The α3β3-spherical portion of the catalytic domain in which the three catalytic sites are found, plus the central stalk, are highly conserved, and the arginine finger is provided conventionally by the α-subunits adjacent to each of the three catalytic sites found in the β-subunits. Thus, the enzyme has a conventional catalytic mechanism. The structure differs from previous described structures by the presence of a p18 subunit, identified only in the euglenozoa, associated with the external surface of each of the three α-subunits, thereby elaborating the F1-domain. Subunit p18 is a pentatricopeptide repeat (PPR) protein with three PPRs and appears to have no function in the catalytic mechanism of the enzyme

Evaluation of care and treatment clinics using a four-year retrospective cohort of patients receiving anti-retroviral therapy in Mbeya Region, Tanzania

Evaluations of sub-national anti-retroviral therapy (ART) programmes’ performance are important to support regional programme planning and epidemic response. We constructed a four-year retrospective cohort of clients from 10 care and treatment clinics (CTC) in the Mbeya region of Tanzania using routinely collected data from patients initiating ART between January 1, 2008 and March 31, 2012. Our primary outcomes were mortality rate and lost to follow up. We calculated ART coverage based on regional prevalence estimates and used medical cards, drug registers and quarterly reports to assess data quality. We enrolled 17,813 participants into the cohort. More patients initiated ART at WHO stages 3 (58.9%), and at CD4 cell counts between 50-199 cells/µl (56%). The proportion of patients initiating ARTs at a CD4 counts <50 cells/µl decreased from 40.7% in 2008 to 33.8% in 2012 (p-value <0.001). A total of 10,155 (57.0%) patients were lost to follow up (LTFU) during the 4 years of follow up; 59.2% were female. The overall mortality rate was 17.8 per 1000 person years; the six-month mortality was 6.2 per 1000 person years. The risk of mortality for patients at WHO stage III and IV was more than twice as high (hazard ratio [HR] 2.15; 95% confidence interval [CI], 1.05-4.39 and HR 2.29; 95% CI, 1.39-6.37, respectively) as compared to stage I and II. Those patients initiating ART with CD4 cell count between 50 and 199 cells/µl had significantly lower hazard of death compared to those initiating ART with CD4 cells counts <50 cells/µl (HR 0.51, 95% CI 0.34-0.78). In conclusion, during the study, a high proportion of patients were lost to follow up, and the majority of them were female. Most patients initiated ARTs at lower CD4 count (<200 cells/mm3) and at WHO stages III and IV, and they had higher risk of mortality compared to those initiated at higher CD4 counts and WHO stage I and II. Emphasis needs to be placed on strategies of early diagnosis of HIV infection, prompt initiation of ART, and support for ART adherence to minimise lost to follow up

Does prohibitin expression regulate sperm mitochondrial membrane potential, sperm motility, and male fertility?

Prohibitin (PHB) is a highly conserved major sperm mitochondrial membrane protein whose absence in somatic cells is associated with mitochondrial membrane depolarization and increased generation of reactive oxygen species (ROS). Our recent findings suggest that high levels of oxidants in human semen may contribute to male infertility and that sperm motility could be the earliest and most sensitive indicator of oxidative damage. Based on PHB's roles in mitochondrial sub-compartmentalization and respiratory chain assembly, we examine sperm PHB expression and mitochondrial membrane potential (MITO) in infertile men with poor sperm motility (asthenospermia, A) and/or low sperm concentrations (oligoasthenospermia, OA). Here, we demonstrate that MITO is significantly lower in sperm from A and OA subjects than in normospermic (N) subjects; the decrease is more severe for OA than for A subjects. PHB expression is also significantly lower in sperm from A and OA subjects. Significantly positive correlations are found among PHB expression, MITO, and sperm motility in normospermic, asthenospermic, and oligoasthenospermic subjects. Collectively, our observations lead to the hypothesis that PHB expression is an indicator of sperm quality in infertile men, and that it regulates sperm motility via an alteration in MITO and increased ROS levels. © Copyright 2012, Mary Ann Liebert, Inc.published_or_final_versio

Phylogeny of Prokaryotes and Chloroplasts Revealed by a Simple Composition Approach on All Protein Sequences from Complete Genomes Without Sequence Alignment

The complete genomes of living organisms have provided much information on their phylogenetic relationships. Similarly, the complete genomes of chloroplasts have helped to resolve the evolution of this organelle in photosynthetic eukaryotes. In this paper we propose an alternative method of phylogenetic analysis using compositional statistics for all protein sequences from complete genomes. This new method is conceptually simpler than and computationally as fast as the one proposed by Qi et al. (2004b) and Chu et al. (2004). The same data sets used in Qi et al. (2004b) and Chu et al. (2004) are analyzed using the new method. Our distance-based phylogenic tree of the 109 prokaryotes and eukaryotes agrees with the biologists tree of life based on 16S rRNA comparison in a predominant majority of basic branching and most lower taxa. Our phylogenetic analysis also shows that the chloroplast genomes are separated to two major clades corresponding to chlorophytes s.l. and rhodophytes s.l. The interrelationships among the chloroplasts are largely in agreement with the current understanding on chloroplast evolution