bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ubiquitin‐dependent and ‐independent mitochondrial protein quality controls: implications in ageing and neurodegenerative diseases
Authors: Germain Doris 
Published: November 2008

SummaryThe ubiquitin‐independent protein quality control of matrix proteins of the mitochondrion is well characterized and until recently the mitochondrion was considered a ‘ubiquitination‐free’ organelle. However, a number of studies now indicate multiple roles of the ubiquitin–proteasome pathway in the regulation and maintenance of mitochondrial integrity. Of particular interest to this review is the finding of a mitochondrial ubiquitin‐dependent protein quality control and that this pathway may share similarity to the endoplasmic reticulum‐associated degradation (ERAD) pathway that acts to eliminate misfolded proteins from the lumen of the endoplasmic reticulum. The potential cross‐talk between the ubiquitin‐dependent and ‐independent protein quality controls and their implications in ageing and neurodegenerative diseases, notably in Parkinson's disease, are discussed.
Post‐transcriptional control of Crp–cAMP by RNase LS in Escherichia coli
Authors: Iwamoto Akira , Lemire Sébastien , Yonesaki Tetsuro 
Published: November 2008

Summary Escherichia coli ribonuclease LS was first characterized as a potential antagonist of bacteriophage T4; the E. coli rnlA gene is required for this activity. When rnlA mutant cells were grown on Luria–Bertani agar containing a high concentration of NaCl, their growth was substantially impaired, and introduction of a mutation into crp or cyaA alleviated the NaCl sensitivity. A mutation in rnlA caused fivefold overexpression of Crp. At the same time, the expression of σ38 was lower by two‐ to threefold in an rnlA mutant than in the wild type, which probably accounts for the susceptibility to high NaCl concentration. The overproduction of Crp was eliminated by deletion of the Crp‐site II, to which Crp binds to enhance its own transcription in the presence of abnormally high concentration of cAMP. Consistently, introduction of a mutation into cyaA also eliminated the overproduction of Crp. In fact, all of CyaA, cAMP and cyaA transcripts accumulated to high levels and, after induction, cyaA transcripts were markedly stabilized in an rnlA mutant compared with the wild type. We conclude that RNase LS regulates Crp–cAMP concentration by degrading the cyaA transcripts.
Transcription regulation of the Saccharomyces cerevisiae PIS1 gene by inositol and the pleiotropic regulator, Ume6p
Authors: Jani Niketa M. , Lopes John M. 
Published: November 2008

SummaryIn Saccharomyces cerevisiae, transcription of most of the phospholipid biosynthetic genes (e.g. INO1, CHO1, CHO2 and OPI3) is repressed by growth in the presence of inositol and choline and derepressed in their absence. This regulation requires the Ino2p and Ino4p activators and the Opi1p repressor. The PIS1 structural gene is required for the synthesis of the essential lipid phosphatidylinositol. Previous reports show that PIS1 expression is uncoupled from inositol/choline regulation, but is regulated by carbon source, hypoxia and zinc. However, in this study we found that the expression of PIS1 is induced twofold by inositol. This regulation did not require Ino2p and Ino4p, although Ino4p was required for full expression. Ino4p is a basic helix‐loop‐helix protein that requires a binding partner. Curiously, none of the other basic helix‐loop‐helix proteins affected PIS1 expression. Inositol induction did require another general regulator of phospholipid biosynthesis, Ume6p. Ume6p was found to be a positive regulator of PIS1 gene expression. Ume6p, and several associated factors, were required for inositol‐mediated induction and chromatin immunoprecipitation analysis showed that Ume6p directly regulates PIS1 expression. Thus, we demonstrate novel regulation of the PIS1 gene by Ume6p.
Structure and non‐essential function of glycerol kinase in Plasmodium falciparum blood stages
Authors: Schnick Claudia , Polley Spencer D. , Fivelman Quinton L. , Ranford‐Cartwright Lisa C. , Wilkinson Shane R. , Brannigan James A. , Wilkinson Anthony J. , Baker David A. 
Published: November 2008

SummaryMalaria pathology is caused by multiplication of asexual parasites within erythrocytes, whereas mosquito transmission of malaria is mediated by sexual precursor cells (gametocytes). Microarray analysis identified glycerol kinase (GK) as the second most highly upregulated gene in Plasmodium falciparum gametocytes with no expression detectable in asexual blood stage parasites. Phosphorylation of glycerol by GK is the rate‐limiting step in glycerol utilization. Deletion of this gene from P. falciparum had no effect on asexual parasite growth, but surprisingly also had no effect on gametocyte development or exflagellation, suggesting that these life cycle stages do not utilize host‐derived glycerol as a carbon source. Kinetic studies of purified PfGK showed that the enzyme is not regulated by fructose 1,6 bisphosphate. The high‐resolution crystal structure of P. falciparum GK, the first of a eukaryotic GK, reveals two domains embracing a capacious ligand‐binding groove. In the complexes of PfGK with glycerol and ADP, we observed closed and open forms of the active site respectively. The 27° domain opening is larger than in orthologous systems and exposes an extensive surface with potential for exploitation in selective inhibitor design should the enzyme prove to be essential in vivo either in the human or in the mosquito.
Spontaneous mutagenesis is elevated in protease‐defective cells
Authors: Al Mamun Abu Amar M. , Humayun M. Zafri 
Published: November 2008

SummaryAs a first step towards describing the role of proteolysis in maintaining genomic integrity, we have determined the effect of the loss of ClpXP, a major energy‐dependent cytoplasmic protease that degrades truncated proteins as well as a number of regulatory proteins, on spontaneous mutagenesis. In a rifampicin‐sensitive to rifampicin‐resistance assay that detects base substitution mutations in the essential rpoB gene, there is a modest, but appreciable increase in mutagenesis in Δ(clpP‐clpX) cells relative to wild‐type cells. A colony papillation analysis using a set of lacZ strains revealed that genetic −1 frameshift mutations are strongly elevated in Clp‐defective cells. A quantitative analysis using a valine‐sensitive to valine‐resistance assay that detects frameshift mutations showed that mutagenesis is elevated 50‐fold in Clp‐defective cells. Elevated frameshift mutagenesis observed in Clp‐deficient cells is essentially abolished in lexA1[Ind‐] (SOS‐uninducible) cells, and in cells deleted for the SOS gene dinB, which codes for DNA polymerase IV. In contrast, mutagenesis is unaffected or stimulated in cells deleted for umuC or umuD, which code for critical components of DNA polymerase V. Loss of rpoS, which codes for a stress‐response sigma factor known to upregulate dinB expression in stationary phase, does not affect mutagenesis. We propose that elevated DinB expression, as well as stabilization of UmuD/UmuD′ heterodimers in Δ(clpP‐clpX) cells, contributes to elevated mutagenesis. These findings suggest that in normal cells, Clp‐mediated proteolysis plays an important role in preventing gratuitous mutagenesis.
Protein unfolding is an essential requirement for transport across the parasitophorous vacuolar membrane of Plasmodium falciparum
Authors: Gehde Nina , Hinrichs Corinna , Montilla Irine , Charpian Stefan , Lingelbach Klaus , Przyborski Jude M. 
Published: November 2008

Summary Plasmodium falciparum traffics a large number of proteins to its host cell, the mature human erythrocyte. How exactly these proteins gain access to the red blood cell is poorly understood. Here we have investigated the effect of protein folding on the transport of model substrate proteins to the host cell. We find that proteins must pass into the erythrocyte cytoplasm in an unfolded state. Our data strongly support the presence of a protein‐conducing channel in the parasitophorous vacoular membrane, and additionally imply an important role for molecular chaperones in keeping parasite proteins in a ‘translocation competent’ state prior to membrane passage.
The histidine kinase inhibitor Sda binds near the site of autophosphorylation and may sterically hinder autophosphorylation and phosphotransfer to Spo0F
Authors: Cunningham Katherine A. , Burkholder William F. 
Published: November 2008

SummaryHistidine kinases are widely used by bacteria, fungi and plants to sense and respond to changing environmental conditions. Signals in addition to those directly sensed by the kinase are often integrated by proteins that fine‐tune the biological response by modulating the activity of the kinase or its targets. The Bacillus subtilis histidine kinase KinA promotes the initiation of sporulation when nutrients are limiting, but sporulation can be delayed by two inhibitors of KinA, Sda (when DNA replication is perturbed) or KipI (under unknown conditions). We have identified residues in the dimerization/histidine‐phosphotransfer (DHp) domain of KinA that are functionally important for inhibition by Sda and KipI and overlapping surface‐exposed residues that lie close to or comprise the Sda binding site. Sda inhibits the intermolecular transfer of phosphate from the catalytic ATP‐binding (CA) domain of KinA to the autophosphorylation site in the DHp domain when the domains are split into separate polypeptides, either by steric hindrance or by altering the conformation of the DHp domain. Sda also slows the rate of phosphotransfer from KinA∼P to its target, Spo0F, consistent with our finding that a KinA residue important for Sda function overlaps with the predicted Spo0F binding site on KinA.
SpoT governs Legionella pneumophila differentiation in host macrophages
Authors: Dalebroux Zachary D. , Edwards Rachel L. , Swanson Michele S. 
Published: November 2008

SummaryDuring its life cycle, Legionella pneumophila alternates between a replicative and a transmissive state. To determine their contributions to L. pneumophila differentiation, the two ppGpp synthetases, RelA and SpoT, were disrupted. Synthesis of ppGpp was required for transmission, as relA spoT mutants were killed during entry to and exit from macrophages. RelA, which senses amino acid starvation induced by serine hydroxamate, is dispensable in macrophages, as relA mutants spread efficiently. SpoT monitors fatty acid biosynthesis (FAB), since following cerulenin treatment, wild‐type and relA strains expressed the flaA transmissive gene, but relA spoT mutants did not. As in Escherichia coli, the SpoT response to FAB perturbation likely required an interaction with acyl‐carrier protein (ACP), as judged by the failure of the spoT‐A413E allele to rescue transmissive trait expression of relA spoT bacteria. Furthermore, SpoT was essential for transmission between macrophages, since secondary infections by relA spoT mutants were restored by induction of spoT, but not relA. To resume replication, ppGpp must be degraded, as mutants lacking spoT hydrolase activity failed to convert from the transmissive to the replicative phase in either bacteriological medium or macrophages. Thus, L. pneumophila requires SpoT to monitor FAB and to alternate between replication and transmission in macrophages.
Alcohol oxidase (AOX1) from Pichia pastoris is a novel inhibitor of prion propagation and a potential ATPase
Authors: Zhang Hong , Loovers Harriët M. , Xu Li‐Qiong , Wang Mingzhu , Rowling Pamela J. E. , Itzhaki Laura S. , Gong Weimin , Zhou Jun‐Mei , Jones Gary W. , Perrett Sarah 
Published: November 2008

SummaryPrevious results suggest that methylotrophic yeasts may contain factors that modulate prion stability. Alcohol oxidase (AOX), a key enzyme in methanol metabolism, is an abundant protein that is specific to methylotrophic yeasts. We examined the effect of Pichia pastoris AOX1 on prion phenotypes in Saccharomyces cerevisiae. The S. cerevisiae prion states [PSI+] and [URE3] arise from aggregation of the proteins Sup35p and Ure2p respectively, and correlate with the ability of Sup35p and Ure2p to form amyloid‐like fibrils in vitro. We found that expression of P. pastoris AOX1 in S. cerevisiae had no effect on propagation of the [PSI+] prion, but inhibited propagation of [URE3]. Addition of AOX1 early in the time‐course of fibril formation inhibits Ure2p fibril formation in vitro. AOX1 has not previously been identified as an ATPase. However, we discovered that in addition to its flavin adenine dinucleotide‐dependent AOX activity, AOX1 possesses ATPase activity. This study identifies AOX1 as a novel prion inhibitory factor and a potential ATPase.
Impact of Chemokine ReceptorCCR2andCCR5Gene Polymorphism on Allograft Outcome in North Indian Renal Transplant Recipients
Authors: Singh R. , Kapoor R. , Srivastava A. , Mittal R. D. 
Published: November 2008

AbstractThe CC chemokine receptors, CCR2 and CCR5, contribute to the trafficking of leucocytes into the sites of the immune response in transplanted kidney. Therefore, the inter‐individual differences inCCR2andCCR5gene expression, due to single‐nucleotide polymorphism, have the potential to influence various immune responses within the graft, eventually deciding the allograft outcome. In this study, we genotyped 296 North Indian renal transplant recipients and 277 healthy controls forCCR2V64IandCCR5‐Δ32polymorphisms by sequence‐specific primers and restriction fragment length polymorphism and examined their association with allograft outcome. The frequency ofCCR2+/64I (heterozygous) andCCR2‐64I/64I (homozygous mutant) genotype were comparatively higher in non‐rejecters when compared with transplant recipients experiencing one or more than one rejection episode (20.4% versus 8.2%), thereby resulting in a significantly reduced risk of allograft rejection (OR = 0.331,P = 0.026). The Kaplan–Meier curve also suggested higher mean time for the first rejection episode inCCR2‐64I allele carriers (32.83 ± 1.36 months) when compared withCCR2+/+ recipients (28.09 ± 0.93 months, log P = 0.027). TheCCR5‐Δ32variant had no profound effect on allograft outcome. In conclusion, our study confirmedCCR2‐64I allele to be associated with reduced risk for allograft rejection in North Indian transplant recipients influencing allograft outcome.
Silencing a prohibitin alters plant development and senescence
Authors: Chen Jen‐Chih , Jiang Cai‐Zhong , Reid Michael S. 
Published: November 2008

SummaryProhibitins, highly conserved mitochondrial proteins, have been shown to play important roles in cell cycling and senescence in animals and yeast. Sequences with high similarity to prohibitins have been identified in a number of plant species, but their function has not yet been demonstrated. The deduced amino acid sequences of PhPHB1 and PhPHB2, sequences that we identified in a petunia floral expressed sequence tag (EST) database, show high similarity to those of prohibitin‐1 and prohibitin‐2 proteins, respectively, reported from yeast, animals and plants. Southern analysis suggested that these genes were members of small gene families with at least two prohibitin‐1 homologs and four prohibitin‐2 homologs. When we downregulated expression of prohibitin‐1 using a Tobacco rattle virus‐based (TRV), virus‐induced gene silencing system (VIGS), we observed plants with smaller and distorted leaves and flowers. Cells in silenced flowers were larger than in control flowers, indicating a substantial reduction in the number of cell divisions that took place during corolla development. The life of silenced flowers was shorter than that of controls, whether on the plant or detached. The respiration of silenced flowers was higher than that of controls, and we observed a marked increase in the abundance of transcripts of a catalase and a small heat‐shock protein in the silenced flowers. Our data indicate that prohibitins play a key role in plant development and senescence.
National survey of the health and nutrition of schoolchildren in Ethiopia
Authors: Hall Andrew , Kassa Tamiru , Demissie Tsegaye , Degefie Tedbabe , Lee Seung 
Published: November 2008

SummaryObjective  To estimate the prevalence of chronic health and nutritional conditions of schoolchildren in Ethiopia.Methods  Cross‐sectional survey in schools in each region randomly selected in proportion to size, then a random sample of 50–68 children in grades 3 and 4 in each school. Children were examined for signs of micronutrient deficiencies and chronic infections; weighed and measured; provided a faecal sample to diagnose intestinal parasitic infections; and were interviewed about their recent diet and hygiene practices.Results  A total of 7572 children were studied in 142 schools in all 11 regions of Ethiopia. Nearly 17% of children were orphans. The prevalence of stunting was 22.3% and 23.1% of children were thin for age, but these may be underestimates as there was evidence that age may have been estimated based on stature when children enrol in school. Just under 10% of children were anaemic when altitude was accounted for. The overall prevalence of trachoma was 13% and children who washed their face before school were at lower risk of trachoma than children who had not. Children who reported that they had eaten fruits or vegetables the day before also had a lower risk of xerophthalmia than children who had not. Only 30% of children were infected with intestinal worms.Conclusions  Trachoma is a problem but anaemia and intestinal worms are relatively uncommon in Ethiopian schoolchildren. These data provide a basis for developing a school health policy and programmes.
Antiretroviral treatment and the health workforce in South Africa: how have ART workers been affected by scaling up?
Authors: Tobi Patrick , George Gavin , Schmidt Elena , Renton Adrian 
Published: November 2008

SummaryObjective  To investigate the effect of scaling up antiretroviral treatment (ART) on the working environment and motivation of health workers in South Africa; and to suggest strategies to minimize negative effects and maximise positive effects.Methods  Exploratory interviews with health managers and senior clinical staff were used to identify locally relevant work environment indicators. A self ‐reported Likert scale questionnaire was administered to a randomly selected cohort of 269 health professionals at health facilities in KwaZulu Natal and Western Cape provinces of South Africa that included ART delivery sites. The cohort was disaggregated into ART and non‐ART groups and differences between the two compared with Fisher’s exact test and the non‐parametric Mann–Whitney U‐test.Results  The ART sub‐cohort reported: (i) a lighter workload (P = 0.013), (ii) higher level of staffing (P = 0.010), (iii) lower sickness absence (P = 0.032), (iv) higher overall job satisfaction (P = 0.010), (v) poorer physical state of their work premises (P = 0.003), and (vi) higher staff turnover (P = 0.036).Conclusion  Scale‐up affects the work environment in ways that influence workers’ motivation both positively and negatively. A net negative balance is likely to drive staff out‐migration, undermine the quality of care and compromise the capacity of the programme to achieve significant scale. As health workers are the most important element of the health system, a comprehensive and systematic understanding of scale‐up impacts on their working conditions and motivation needs to be an integral part of any delivery strategy.
User fee exemptions are not enough: out‐of‐pocket payments for ‘free’ delivery services in rural Tanzania
Authors: Kruk Margaret E. , Mbaruku Godfrey , Rockers Peter C. , Galea Sandro 
Published: November 2008

SummaryObjective  To identify the main drivers of costs of facility delivery and the financial consequences for households among rural women in Tanzania, a country with a policy of delivery fee exemptions.Methods  We selected a representative sample of households in a rural district in western Tanzania. Women who given birth within 5 years were asked about payments for doctor’s/nurse’s fees, drugs, non‐medical supplies, medical tests, maternity waiting home, transport and other expenses. Wealth was assessed using a household asset index. We estimated the proportion of women who cut down on spending or borrowed money/sold household items to pay for delivery in each wealth group.Results  In all, 73.3% of women with facility delivery reported having made out‐of‐pocket payments for delivery‐related costs. The average cost was 6272 Tanzanian shillings (TZS), [95% Confidence Interval (CI): 4916, 7628] or 5.0 United States dollars. Transport costs (53.6%) and provider fees (26.6%) were the largest cost components in government facilities. Deliveries in mission facilities were twice as expensive as those in government facilities. Nearly half (48.3%) of women reported cutting down on spending or borrowing money/selling household assets to pay for delivery, with the poor reporting this most frequently.Conclusion  Out‐of‐pocket payments for facility delivery were substantial and were driven by high transport costs, unofficial provider payments, and preference for mission facilities, which levy user charges. Novel approaches to financing maternal health services, such as subsidies for transport and care from private providers, are required to reduce the cost barriers to attended delivery.
Egg size, embryonic development time and ovoviviparity in Drosophila species
Authors: MARKOW T. A. , BEALL S. , MATZKIN L. M. 
Published: November 2008

AbstractLengths, widths and volumes of eggs from 11 species of Drosophila whose genomes have been fully sequenced exhibit significant variation that is not explained by their phylogenetic relationships. Furthermore, egg size differences are unrelated to embryonic development time in these species. In addition, two of the species, Drosophila sechellia and, to a lesser degree, D. yakuba, both ecological specialists, exhibit ovoviviparity, suggesting that female control over oviposition in these species differs from what is observed in D. melanogaster. The interspecific differences in these reproductive characters, coupled with the availability of whole genome sequences for each, provide an unprecedented opportunity to examine their evolution.