bluuebunny/crossref_metadata_2025_split huggingface dataset:
Utility, economic rationalism and the circumscription of agency
Authors: DiRita P. A. , Parmenter T. R. , Stancliffe R. J. 
Published: May 2008

AbstractBackground  Great strides have been achieved over the past few decades in service provision for people with intellectual disability (ID). However, there has also been a growth in the use of economic rationalism and a related rise in managerialism in forming service provision outcomes.Method  An account of the focus on process and means of provision directed within the managerialist agenda to determine how individual authority has become subsumed within patterns of dependence.Results  An underlying influence of utilitarianism has led to a focus on servicing the average through service provision trajectories which in turn have weakened the pace for social change and perpetuated a vulnerable conception of people with ID.Conclusions  There has been a qualification of the idealised intent of providing individualised support, choice and recognition of the moral worth of people with ID into relative features of equality. There remains an overriding static conception of the person with ID within funding frameworks and service provision which relies on economic and rationalist depictions of the individual.
The mRNA interferases, MazF‐mt3 and MazF‐mt7 from Mycobacterium tuberculosis target unique pentad sequences in single‐stranded RNA
Authors: Zhu Ling , Phadtare Sangita , Nariya Hirofumi , Ouyang Ming , Husson Robert N. , Inouye Masayori 
Published: May 2008

SummarymRNA interferases are sequence‐specific endoribonucleases encoded by toxin‐antitoxin (TA) systems in bacterial genomes. Previously, we demonstrated that Mycobacterium tuberculosis contains at least seven genes encoding MazF homologues (MazF‐mt1 to ‐mt7) and determined cleavage specificities for MazF‐mt1 and MazF‐mt6. Here we have developed a new general method for the determination of recognition sequences longer than three bases for mRNA interferases with the use of phage MS2 RNA as a substrate and CspA, an RNA chaperone, which prevents the formation of secondary structures in the RNA substrate. Using this method, we determined that MazF‐mt3 cleaves RNA at UU˘CCU or CU˘CCU and MazF‐mt7 at U˘CGCU (˘indicates the cleavage site). As pentad sequence recognition is more specific than those of previously characterized mRNA interferases, bioinformatics analysis was carried out to identify M. tuberculosis mRNAs that may be resistant to MazF‐mt3 and MazF‐mt7 cleavage. The pentad sequence was found to be significantly underrepresented in several genes, including members of the PE and PPE families, large families of proteins that play a role in tuberculosis immunity and pathogenesis. These data suggest that MazF‐mt3 and MazF‐mt7 or other mRNA interferases that target longer RNA sequences may alter protein expression through differential mRNA degradation, a regulatory mechanism that may allow adaptation to environmental conditions, including those encountered by pathogens such as M. tuberculosis during infection.
A novel pathway of intercellular signalling in Bacillus subtilis involves a protein with similarity to a component of type III secretion channels
Authors: Camp Amy H. , Losick Richard 
Published: May 2008

SummaryDuring spore formation in Bacillus subtilis, σE‐directed gene expression in the mother‐cell compartment of the sporangium triggers the activation of σG in the forespore by a pathway of intercellular signalling that is composed of multiple proteins of unknown function. Here, we confirm that the vegetative protein SpoIIIJ, the forespore protein SpoIIQ and eight membrane proteins (SpoIIIAA through SpoIIIAH) produced in the mother cell under the control of σE are ordinarily required for intercellular signalling. In contrast, an anti‐σG factor previously implicated in the pathway is shown to be dispensable. We also present evidence suggesting that SpoIIIJ is a membrane protein translocase that facilitates the insertion of SpoIIIAE into the membrane. In addition, we report the isolation of a mutation that partially bypasses the requirement for SpoIIIJ and for SpoIIIAA through SpoIIIAG, but not for SpoIIIAH or SpoIIQ, in the activation of σG. We therefore propose that under certain genetic conditions, SpoIIIAH and SpoIIQ can constitute a minimal pathway for the activation of σG. Finally, based on the similarity of SpoIIIAH to a component of type III secretion systems, we speculate that signalling is mediated by a channel that links the mother cell to the forespore.
Molecular characterization of group A Streptococcus maltodextrin catabolism and its role in pharyngitis
Authors: Shelburne Samuel A. , Keith David B. , Davenport Michael T. , Horstmann Nicola , Brennan Richard G. , Musser James M. 
Published: May 2008

SummaryWe previously demonstrated that the cell‐surface lipoprotein MalE contributes to GAS maltose/maltodextrin utilization, but MalE inactivation does not completely abrogate GAS catabolism of maltose or maltotriose. Using a genome‐wide approach, we identified the GAS phosphotransferase system (PTS) responsible for non‐MalE maltose/maltotriose transport. This PTS is encoded by an open reading frame (M5005_spy1692) previously annotated as ptsG based on homology with the glucose PTS in Bacillus subtilis. Genetic inactivation of M5005_spy1692 significantly reduced transport rates of radiolabelled maltose and maltotriose, but not glucose, leading us to propose its reannotation as malT for maltose transporter. The ΔmalT, ΔmalE and ΔmalE:malT strains were significantly attenuated in their growth in human saliva and in their ability to catabolize α‐glucans digested by purified human salivary α‐amylase. Compared with wild‐type, the three isogenic mutant strains were significantly impaired in their ability to colonize the mouse oropharynx. Finally, we discovered that the transcript levels of maltodextrin utilization genes are regulated by competitive binding of the maltose repressor MalR and catabolite control protein A. These data provide novel insights into regulation of the GAS maltodextrin genes and their role in GAS host–pathogen interaction, thereby increasing the understanding of links between nutrient acquisition and virulence in common human pathogens.
Yeast mitochondria import ATP through the calcium‐dependent ATP‐Mg/Pi carrier Sal1p, and are ATP consumers during aerobic growth in glucose
Authors: Traba Javier , Froschauer Elisabeth Maria , Wiesenberger Gerlinde , Satrústegui Jorgina , Del Arco Araceli 
Published: May 2008

SummarySal1p, a novel Ca2+‐dependent ATP‐Mg/Pi carrier, is essential in yeast lacking all adenine nucleotide translocases. By targeting luciferase to the mitochondrial matrix to monitor mitochondrial ATP levels, we show in isolated mitochondria that both ATP‐Mg and free ADP are taken up by Sal1p with a Km of 0.20 ± 0.03 mM and 0.28 ± 0.06 mM respectively. Nucleotide transport along Sal1p is strictly Ca2+ dependent. Ca2+ increases the Vmax with a S0.5 of 15 μM, and no changes in the Km for ATP‐Mg. Glucose sensing in yeast generates Ca2+ transients involving Ca2+ influx from the external medium. We find that carbon‐deprived cells respond to glucose with an immediate increase in mitochondrial ATP levels which is not observed in the presence of EGTA or in Sal1p‐deficient cells. Moreover, we now report that during normal aerobic growth on glucose, yeast mitochondria import ATP from the cytosol and hydrolyse it through H+‐ATP synthase. We identify two pathways for ATP uptake in mitochondria, the ADP/ATP carriers and Sal1p. Thus, during exponential growth on glucose, mitochondria are ATP consumers, as those from cells growing in anaerobic conditions or deprived of mitochondrial DNA which depend on cytosolic ATP and mitochondrial ATPase working in reverse to generate a mitochondrial membrane potential. In conclusion, the results show that growth on glucose requires ATP hydrolysis in mitochondria and recruits Sal1p as a Ca2+‐dependent mechanism to import ATP‐Mg from the cytosol. Whether this mechanism is used under similar settings in higher eukaryotes is an open question.
Natural Killer Cell Subpopulations in Putative Resistant Individuals and Patients with Active Mycobacterium tuberculosis Infection
Authors: Barcelos W. , Sathler‐Avelar R. , Martins‐Filho O. A. , Carvalho B. N. , Guimarães T. M. P. D. , Miranda S. S. , Andrade H. M. , Oliveira M. H. P. , Toledo V. P. C. P. 
Published: May 2008

AbstractHerein, we intended to perform flow‐cytometric analyses of peripheral blood NK‐cell subsets in patients with active tuberculosis (TB) and those putative resistant subjects displaying positive tuberculin skin test (TST+) and compared with TST− healthy controls. Our findings demonstrated distinct phenotypic features in TST+ as compared with TB. While lower values of NK‐cells with increased frequency of CD3−CD16+ CD56− and CD3−CD16−CD56+ subsets besides lower frequency of CD3−CD16+ CD56+ NK‐cells was observed in TST+, unaltered levels of NK‐cells with increased levels of CD3−CD16+ CD56− NK‐cells with lower frequency of CD3−CD16+ CD56+ NK‐cells was found in TB. Additional analysis highlighted a shift towards increased levels of CD3−CD16−/+CD56bright NK‐cells as the hallmark of TST+, whereas unaltered frequency was observed in TB. Increased levels of CD3+CD56+ cells were observed in both TST+ and TB. Further focusing on the monocyte/NK‐cell network, we have reported that enhanced frequency of CD14+ CD16+ monocytes particularly observed in TST+. Outstanding were the distinct correlation profiles observed between CD3−CD16−CD56+ NK‐cells and CD3+ CD56+ cells CD14+ CD16+ monocytes for TST+ and TB. These data suggested that high levels of CD3−CD16−CD56+ NK‐cells aside CD14+ CD16+ monocytes as well as non‐concurrent increment of CD3+ CD56+ cells, may be involved in protective mechanisms in putative tuberculosis‐resistant individuals. On the other hand, the basal levels of macrophage‐like monocytes despite its positive correlation with increased levels of CD3+ CD56+ cells may count for the lack of the protective immunity in patients with active tuberculosis. Further studies focusing on the cytokine profiling of peripheral blood innate immunity cells before and after chemotherapic treatment are currently under evaluation.
Gene Array Analysis Comparison between Rat Collagen‐induced Arthritis and Human Rheumatoid Arthritis
Authors: Soto H. , Hevezi P. , Roth R. B. , Pahuja A. , Alleva D. , Acosta H. M. , Martinez C. , Ortega A. , Lopez A. , Araiza‐Casillas R. , Zlotnik A. 
Published: May 2008

AbstractCollagen‐induced arthritis (CIA) is an experimental arthritis model used to study the inflammatory processes in this disease and test potential therapeutics. In order to better characterize this model, we conducted the first comprehensive gene expression analysis of rat CIA. To evaluate how closely the rat model reflects human rheumatoid arthritis (RA), we also analysed gene expression in human RA, using genome‐wide Affymetrix genearrays. By applying multiple strategies, including comparison of the highest induced genes, expression of immunological‐associated genes as well as Ingenuity Pathway Analysis (IPA), we were able to compare the two expression profiles. Among the highest induced genes in RA were several B‐cell‐associated genes, including immunoglobulins, B‐cell markers such as CD20, and cytokines and chemokines that act on B cells such as TNFSF13b/BLyS and CXCL13, none of which was upregulated in CIA. The latter was instead characterized by the upregulation of genes expressed primarily in macrophages and dendritic cells. Of the 22 pathways identified as significant in both diseases by IPA, only three (IL6, chemokine signalling and antigen presentation) were present in both settings. We conclude that there are significant differences in the inflammatory mechanisms between human RA and rat CIA, and that genome‐wide comparative gene expression analyses are useful tools to evaluate the relevance of animal models to human disease.
Absence ofPneumocystis jirovecipneumonia in liver transplantation recipients receiving short‐term (3‐month) prophylaxis
Authors: Trotter J.F. , Levi M. , Steinberg T. , Lancaster J. 
Published: May 2008

Abstract:Pneumocystis jiroveci(formerly known asPneumocystis carinii) is a fungal pathogen that causes pneumonia (PCP) in liver transplant recipients. Consequently, prophylaxis with trimethoprim–sulfamethoxazole (TMP/SMZ) is typically administered for at least 1 year at most liver transplant programs. At our center we have utilized a short‐term (3‐month) prophylactic regimen with TMP/SMZ for the past decade and report our experience and speculate on the potential widespread application of this approach.Methods.For patients transplanted at our center between January 1997 and January 2007, we recorded all documented PCP infections by review of our liver transplant database and hospital‐based electronic medical records system, both of which record all infections and culture results.Results.We recorded no cases of PCP in any of the liver transplant recipients at our center during the study period.Conclusions.We report the absence of PCP in a large cohort of liver transplant recipients receiving a short‐term (3‐month) prophylaxis with TMP/SMZ. These findings provide a rational basis to consider short‐term (3‐month) PCP prophylaxis or avoidance of prophylaxis altogether in selected low‐risk patients.
Dynamics of yolk sac content absorption and intestine development in ducklings fed mixtures with increasing dietary methionine level
Authors: Jamroz D. , Wertelecki T. , Lemme A. , Wiliczkiewicz A. , Orda J. , Skorupińska J. 
Published: May 2008

SummaryThe experiment was carried out with ducklings fed‐control feed mixture (Met level 0.3%) and mixtures supplemented with dl‐methionine at the dose of 0.03 (II); 0.07 (III) 0.12 (IV) and 0.18% (V). In 5 h post‐hatch (12 birds) and on days 3, 4, 6 always 18 birds were taken out from each treatment and killed, then the yolk sac (YS) and intestine were removed. The weight and chemical composition of YS residues (in them also amino acids) were analysed. Moreover on days 1, 3, 4 and 6, the amino acid pattern of YS residual protein was elaborated as well as length and weight of intestine were recorded. Increased doses of supplemental Met improved body weight gain after 4 days of ducklings life. All determined parameters were not affected by treatment. Development of intestines, yolk sac weight and yolk sac composition (DM, fat, protein, amino acid composition) changed with age; however, without any clear effect from dietary methionine level. No differences between sex and analysed parameters were stated.
Phospholipid compositions of sera and synovial fluids from dog, human and horse: a comparison by 31P‐NMR and MALDI‐TOF MS
Authors: Fuchs B. , Bondzio A. , Wagner U. , Schiller J. 
Published: May 2008

SummaryAlterations of the phospholipid (PL) compositions of body fluids are assumed to be indicative of inflammatory diseases, e.g. rheumatoid arthritis (RA). Recently, we have shown that particularly the phosphatidylcholine/lysophosphatidylcholine (PC/LPC) ratio determined in human synovial fluids (SF) and sera represents a reliable measure of the inflammatory state in RA patients. However, it is not yet clear to what extent the PC/LPC ratio is also affected by nutrition habits. In the present study, the PL and the corresponding acyl chain compositions of human body fluids (SF and serum of RA patients as well as serum from healthy volunteers) are compared with those of two other mammalian species (horses and dogs suffering from degenerative joint diseases as well as healthy controls) by high‐resolution 31P‐nuclear magnetic resonance (NMR) spectroscopy and matrix‐assisted laser desorption and ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS). The most important result of this study is that the PL compositions of SF and serum of horse and dog are comparable with those of human body fluids. Compared with humans, however, the horse body fluid contains less PCs with highly unsaturated arachidonoyl residues, while that of dogs possesses the highest content of arachidonoyl‐containing PC. These species‐related differences stem primarily from different nutrition habits (meat vs. plants).
Comparison of three organelle markers for phylogeographic inference in Batrachospermum helminthosum (Batrachospermales, Rhodophyta) from North America
Authors: House Denise L. , Sherwood Alison R. , Vis Morgan L. 
Published: May 2008

SUMMARYPhylogeographic signal provided by the newly developed 23S plastid rRNA marker (universal plastid amplicon, UPA) and the cytochrome oxidase subunit I gene marker (COI) in the freshwater red alga Batrachospermum helminthosum, throughout its range in North America, was investigated. These markers were compared in individuals from a previous study using the cytochrome oxidase 2–3 spacer region (cox2–3), which has yielded the most useful data to date with 13 haplotypes among geographic locations. Five haplotypes were resolved for the UPA, differing by only one to two base pairs (bp), and we conclude that this marker may be more appropriate for studying interspecific variation. In contrast, the COI gene revealed 16 haplotypes, differing from one to 44 base pairs or up to 6.6% sequence variation. The intraspecific variation of COI in this taxon is much greater than that reported thus far for marine red algae (generally <5 bp). The intraspecific variation within B. helminthosum is in accord with levels shown in Batrachospermum macrosporum (48 bp within distant locations in Brazil). The COI gene is comparable to the cox2–3 spacer for phylogeographic studies as the haplotype networks were similar and showed the same geographic patterns. To our knowledge, this is the first comparison of these three regions for phylogeographic research in the red algae.
On the absence of previously reported Japanese and Peruvian species of Prionitis (Halymeniaceae, Rhodophyta) in the northeast Pacific
Authors: Gabrielson Paul W. 
Published: May 2008

SUMMARYPartial rbcL sequences of type specimens, historically significant specimens and recently collected comparative specimens are used to demonstrate that Prionitis decipiens (Montagne) J. Agardh (type locality: Paita, Peru), Prionitis angusta (Harvey) Okamura (type locality: Shimoda, Japan, currently known as Grateloupia angusta (Harvey) Kawaguchi et Wang) and Prionitis cornea (Okamura) E. Y. Dawson (type locality: Shizuoka, Japan, currently known as Grateloupia cornea Okamura), all previously reported from the northeast (NE) Pacific (California, USA and Baja California, Mexico), were not, and currently are not, present. Historically significant specimens from the NE Pacific specifically annotated by E. Y. Dawson as belonging to P. cornea or specifically annotated by I. A. Abbott as belonging to P. angusta were sequenced and shown to belong to either Prionitis linearis Kylin (type locality: La Jolla, California, USA) or to Prionitis filiformis Kylin (type locality: San Francisco, California, USA). The lectotype of Gelidium decipiens Montagne (basionym of Prionitis decipiens) is narrowed to a single specimen illustrated by Montagne, and a lectotype is designated for P. linearis. The utility of partial rbcL sequences (less than 200 base pairs) for determining the identity of specimens is discussed, as is the importance of sequencing type and historically significant specimens.
Haramonas pauciplastida sp. nov. (Raphidophyceae, Heterokontophyta) and phylogenetic analyses of Haramonas species using small subunit ribosomal RNA gene sequences
Authors: Yamaguchi Haruyo , Hoppenrath Mona , Takishita Kiyotaka , Horiguchi Takeo 
Published: May 2008

SUMMARYA new species of the Raphidophyceae, Haramonas pauciplastida sp. nov. from Canada is described. The genus Haramonas has been described based on the type species Haramonas dimorpha and currently only two species are known. This new alga belongs to the genus because it possesses a tubular invagination at the posterior end of the cell, producing a large amount of mucilage and generating both motile and non‐motile phases in its life cycle. The chloroplast color of H. pauciplastida is yellowish green, and is similar to that of Haramonas viridis Horiguchi et Hoppenrath. However, this alga differs from the other species of the genus in that it possesses fewer chloroplasts, which are rarely overlapping. The ultrastructual study shows differences between these two species in the number of thylakoids in the lamella, the presence of a scattered pyrenoid matrix, and the position of the plastoglobuli. The phylogenetic analyses of the small subunit ribosomal RNA gene from the Haramonas species reveal that three species can be distinguished genetically from each other and they form a robust clade in the Raphidophyceae. This result supports the notion that the characteristic features of Haramonas are synapomorphies. This is the first report of molecular data from the Haramonas species.
Microbial community response to a release of neat ethanol onto residual hydrocarbons in a pilot‐scale aquifer tank
Authors: Cápiro Natalie L. , Da Silva Marcio L. B. , Stafford Brent P. , Rixey William G. , Alvarez Pedro J. J. 
Published: May 2008

SummaryThe microbial community response to a neat ethanol release (E100, 76 l) onto residual hydrocarbons in sandy soil was evaluated in a continuous‐flow 8 m3 pilot‐scale aquifer tank, simulating a release at a bulk fuel terminal. Microbial genotypic shifts were assessed using quantitative real‐time PCR analysis. High ethanol concentrations in the capillary fringe at potentially toxic levels, exceeding 100 000 mg l−1, were tolerated by the microbial community. The high biochemical oxygen demand exerted by ethanol rapidly induced anaerobic conditions, and both methane production (up to 1.2 mg l−1) and growth of putative methanogenic Archaea (up to 106 gene copies per g of soil) were observed in shallow groundwater and soil samples 75 cm down gradient from the source. Aerobic conditions returned after ethanol was flushed out of the system, approximately 45 days after the spill (less than 7.5 pore volumes flushed). Total Bacteria growth coincided with ethanol migration and availability, which was restricted to a relatively thin layer at the capillary fringe and water table interface. The concentrations of bacteria harbouring the aerobic catabolic genes dmpN (coding for phenol hydroxylase) and todC1 (coding for toluene dioxygenase) increased (up to 100×) down gradient from the source, likely as a result of both fortuitous growth on ethanol and on aromatic hydrocarbons mobilized by ethanol. Growth of hydrocarbon degraders was corroborated by denaturing gradient gel electrophoresis analysis showing proliferation of Azospirillum and Brevundimonas spp., which are bacteria commonly associated with microaerophilic hydrocarbon degradation. Nevertheless, the relative abundance of hydrocarbon‐specific degraders (as a fraction of total Bacteria) decreased as other bacteria grew to a higher extent. Overall, the observed growth of hydrocarbon degraders suggests a potential enhancement in aerobic natural attenuation in shallow aquifers after ethanol and its degradation by‐products are degraded or flushed from sites impacted by ethanol‐blended fuels.