bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unsuspected Diversity of Arsenite-Oxidizing Bacteria as Revealed by Widespread Distribution of theaoxBGene in Prokaryotes
Authors: Heinrich-Salmeron Audrey , Cordi Audrey , Brochier-Armanet Céline , Halter David , Pagnout Christophe , Abbaszadeh-fard Elham , Montaut Didier , Seby Fabienne , Bertin Philippe N. , Bauda Pascale , Arsène-Ploetze Florence 
Published: May 2011

ABSTRACTIn this study, new strains were isolated from an environment with elevated arsenic levels, Sainte-Marie-aux-Mines (France), and the diversity ofaoxBgenes encoding the arsenite oxidase large subunit was investigated. The distribution of bacterialaoxBgenes is wider than what was previously thought. AoxB subfamilies characterized by specific signatures were identified. An exhaustive analysis of AoxB sequences from this study and from public databases shows that horizontal gene transfer has likely played a role in the spreading ofaoxBin prokaryotic communities.
Ubiquitylation and Developmental Regulation of Invariant Surface Protein Expression in Trypanosomes
Authors: Leung Ka Fai , Riley Fay S. , Carrington Mark , Field Mark C. 
Published: May 2011

ABSTRACT

The cell surface of
Trypanosoma brucei
is dominated by the glycosylphosphatidylinositol-anchored variant surface glycoprotein (VSG), which is essential for immune evasion. VSG biosynthesis, trafficking, and turnover are well documented, but
trans
-membrane domain (TMD) proteins, including the invariant surface glycoproteins (ISGs), are less well characterized. Internalization and degradation of ISG65 depend on ubiquitylation of conserved cytoplasmic lysines. Using epitope-tagged ISG75 and reporter chimeric proteins bearing the cytoplasmic and
trans
-membrane regions of ISG75, together with multiple mutants with lysine-to-arginine mutations, we demonstrate that the cytoplasmic tail of ISG75 is both sufficient and necessary for endosomal targeting and degradation. The ISG75 chimeric reporter protein localized to endocytic organelles, while lysine-null versions were significantly stabilized at the cell surface. Importantly, ISG75 cytoplasmic lysines are modified by extensive oligoubiquitin chains and ubiquitylation is abolished in the lysine-null version. Furthermore, we find evidence for differential modes of turnover of ISG65 and ISG75. Full-length lysine-null ISG65 localization and protein turnover are significantly perturbed, but ISG75 localization and protein turnover are not, while ubiquitin conjugates can be detected for full-length lysine-null ISG75 but not ISG65. We find that the ISG75 ectodomain has a predicted coiled-coil, suggesting that ISG75 could be part of a complex, while ISG65 behaves independently. We also demonstrate a developmental stage-specific mechanism for exclusion of surface ISG expression in insect-stage cells by a ubiquitin-independent mechanism. We suggest that ubiquitylation may be a general mechanism for regulating
trans
-membrane domain surface proteins in trypanosomes.
TbISWI Regulates Multiple Polymerase I (Pol I)-Transcribed Loci and Is Present at Pol II Transcription Boundaries in Trypanosoma brucei
Authors: Stanne Tara M. , Kushwaha Manish , Wand Matthew , Taylor Jesse E. , Rudenko Gloria 
Published: May 2011

ABSTRACT

The unicellular eukaryote
Trypanosoma brucei
is unusual in having very little transcriptional control. The bulk of the
T. brucei
genome is constitutively transcribed by RNA polymerase II (Pol II) as extensive polycistronic transcription units. Exceptions to this rule include several RNA Pol I transcription units such as the
VSG
expression sites (ESs), which are mono-allelically expressed. TbISWI, a member of the SWI2/SNF2 related chromatin remodeling ATPases, plays a role in repression of Pol I-transcribed ESs in both bloodstream- and procyclic-form
T. brucei
. We show that TbISWI binds both active and silent ESs but is depleted from the ES promoters themselves. TbISWI knockdown results in an increase in
VSG
transcripts from the silent
VSG
ESs. In addition to its role in the repression of the silent ESs, TbISWI also contributes to the downregulation of the Pol I-transcribed procyclin loci, as well as nontranscribed
VSG
basic copy arrays and minichromosomes. We also show that TbISWI is enriched at a number of strand switch regions which form the boundaries between Pol II transcription units. These strand switch regions are the presumed sites of Pol II transcription initiation and termination and are enriched in modified histones and histone variants. Our results indicate that TbISWI is a versatile chromatin remodeler that regulates transcription at multiple Pol I loci and is particularly abundant at many Pol II transcription boundaries in
T. brucei
.
The Essentiality of the Fungus-Specific Dam1 Complex Is Correlated with a One-Kinetochore-One-Microtubule Interaction Present throughout the Cell Cycle, Independent of the Nature of a Centromere
Authors: Thakur Jitendra , Sanyal Kaustuv 
Published: May 2011

ABSTRACT

A fungus-specific outer kinetochore complex, the Dam1 complex, is essential in
Saccharomyces cerevisiae
, nonessential in fission yeast, and absent from metazoans. The reason for the reductive evolution of the functionality of this complex remains unknown. Both
Candida albicans
and
Schizosaccharomyces pombe
have regional centromeres as opposed to the short-point centromeres of
S. cerevisiae
. The interaction of one microtubule per kinetochore is established both in
S. cerevisiae
and
C. albicans
early during the cell cycle, which is in contrast to the multiple microtubules that bind to a kinetochore only during mitosis in
S. pombe
. Moreover, the Dam1 complex is associated with the kinetochore throughout the cell cycle in
S. cerevisiae
and
C. albicans
but only during mitosis in
S. pombe
. Here, we show that the Dam1 complex is essential for viability and indispensable for proper mitotic chromosome segregation in
C. albicans
. The kinetochore localization of the Dam1 complex is independent of the kinetochore-microtubule interaction, but the function of this complex is monitored by a spindle assembly checkpoint. Strikingly, the Dam1 complex is required to prevent precocious spindle elongation in premitotic phases. Thus, constitutive kinetochore localization associated with a one-microtubule-one kinetochore type of interaction, but not the length of a centromere, is correlated with the essentiality of the Dam1 complex.
New Cell Surface Protein Involved in Biofilm Formation by Streptococcus parasanguinis
Authors: Liang Xiaobo , Chen Yi-Ywan M. , Ruiz Teresa , Wu Hui 
Published: May 2011

ABSTRACT

Dental biofilm formation is critical for maintaining the healthy microbial ecology of the oral cavity. Streptococci are predominant bacterial species in the oral cavity and play important roles in the initiation of plaque formation. In this study, we identified a new cell surface protein, BapA1, from
Streptococcus parasanguinis
FW213 and determined that BapA1 is critical for biofilm formation. Sequence analysis revealed that BapA1 possesses a typical cell wall-sorting signal for cell surface-anchored proteins from Gram-positive bacteria. No functional orthologue was reported in other streptococci. BapA1 possesses nine putative pilin isopeptide linker domains which are crucial for pilus assembly in a number of Gram-positive bacteria. Deletion of the 3′ portion of
bapA1
generated a mutant that lacks surface-anchored BapA1 and abolishes formation of short fibrils on the cell surface. The mutant failed to form biofilms and exhibited reduced adherence to an
in vitro
tooth model. The BapA1 deficiency also inhibited bacterial autoaggregation. The N-terminal muramidase-released-protein-like domain mediated BapA1-BapA1 interactions, suggesting that BapA1-mediated cell-cell interactions are important for bacterial autoaggregation and biofilm formation. Furthermore, the BapA1-mediated bacterial adhesion and biofilm formation are independent of a fimbria-associated serine-rich repeat adhesin, Fap1, demonstrating that BapA1 is a new streptococcal adhesin.
Scc1 (CP0432) and Scc4 (CP0033) Function as a Type III Secretion Chaperone for CopN of Chlamydia pneumoniae
Authors: Silva-Herzog Eugenia , Joseph Sabrina S. , Avery Ann K. , Coba Jose A. , Wolf Katerina , Fields Kenneth A. , Plano Gregory V. 
Published: May 2011

ABSTRACT

The
Chlamydia pneumoniae
CopN protein is a member of the YopN/TyeA/InvE/MxiC family of secreted proteins that function to regulate the secretion of type III secretion system (T3SS) translocator and effector proteins. In this study, the Scc1 (CP0432) and Scc4 (CP0033) proteins of
C. pneumoniae
AR-39 were demonstrated to function together as a type III secretion chaperone that binds to an N-terminal region of CopN. The Scc1/Scc4 chaperone promoted the efficient secretion of CopN via a heterologous T3SS, whereas, the Scc3 chaperone, which binds to a C-terminal region of CopN, reduced CopN secretion.
Energy-Dependent Stability of Shewanella oneidensis MR-1 Biofilms
Authors: Saville Renee M. , Rakshe Shauna , Haagensen Janus A. J. , Shukla Soni , Spormann Alfred M. 
Published: May 2011

ABSTRACT

Stability and resistance to dissolution are key features of microbial biofilms. How these macroscopic properties are determined by the physiological state of individual biofilm cells in their local physical-chemical and cellular environment is largely unknown. In order to obtain molecular and energetic insight into biofilm stability, we investigated whether maintenance of biofilm stability is an energy-dependent process and whether transcription and/or translation is required for biofilm dissolution. We found that in 12-hour-old
Shewanella oneidensis
MR-1 biofilms, a reduction in cellular ATP concentration, induced either by oxygen deprivation or by addition of the inhibitor of oxidative phosphorylation carbonyl cyanide
m
-chlorophenylhydrazone (CCCP), dinitrophenol (DNP), or CN
−
, resulted in massive dissolution. In 60-hour-old biofilms, the extent of uncoupler-induced cell loss was strongly attenuated, indicating that the integrity of older biofilms is maintained by means other than those operating in younger biofilms. In experiments with 12-hour-old biofilms, the transcriptional and translational inhibitors rifampin, tetracycline, and erythromycin were found to be ineffective in preventing energy starvation-induced detachment, suggesting that neither transcription nor translation is required for this process. Biofilms of
Vibrio cholerae
were also induced to dissolve upon CCCP addition to an extent similar to that in
S. oneidensis
. However,
Pseudomonas aeruginosa
and
P. putida
biofilms remained insensitive to CCCP addition. Collectively, our data show that metabolic energy is directly or indirectly required for maintaining cell attachment, and this may represent a common but not ubiquitous mechanism for stability of microbial biofilms.
The Key Sigma Factor of Transition Phase, SigH, Controls Sporulation, Metabolism, and Virulence Factor Expression in Clostridium difficile
Authors: Saujet Laure , Monot Marc , Dupuy Bruno , Soutourina Olga , Martin-Verstraete Isabelle 
Published: May 2011

ABSTRACT

Toxin synthesis in
Clostridium difficile
increases as cells enter into stationary phase. We first compared the expression profiles of strain 630E during exponential growth and at the onset of stationary phase and showed that genes involved in sporulation, cellular division, and motility, as well as carbon and amino acid metabolism, were differentially expressed under these conditions. We inactivated the
sigH
gene, which encodes an alternative sigma factor involved in the transition to post-exponential phase in
Bacillus subtilis
. Then, we compared the expression profiles of strain 630E and the
sigH
mutant after 10 h of growth. About 60% of the genes that were differentially expressed between exponential and stationary phases, including genes involved in motility, sporulation, and metabolism, were regulated by SigH, which thus appears to be a key regulator of the transition phase in
C. difficile
. SigH positively controls several genes required for sporulation. Accordingly,
sigH
inactivation results in an asporogeneous phenotype. The
spo0A
and
CD2492
genes, encoding the master regulator of sporulation and one of its associated kinases, and the
spoIIA
operon were transcribed from a SigH-dependent promoter. The expression of
tcdA
and
tcdB
, encoding the toxins, and of
tcdR
, encoding the sigma factor required for toxin production, increased in a
sigH
mutant. Finally, SigH regulates the expression of genes encoding surface-associated proteins, such as the Cwp66 adhesin, the S-layer precursor, and the flagellum components. Among the 286 genes positively regulated by SigH, about 40 transcriptional units presenting a SigH consensus in their promoter regions are good candidates for direct SigH targets.
Complete Genome Sequence of Streptococcus suis Serotype 3 Strain ST3
Authors: Hu Pan , Yang Ming , Zhang Anding , Wu Jiayan , Chen Bo , Hua Yafeng , Yu Jun , Chen Huanchun , Xiao Jingfa , Jin Meilin 
Published: May 2011

ABSTRACT

Streptococcus suis
is a zoonotic pathogen causing economic loss in the swine industry and is also a threat to human health. To date, the mechanism of pathogenesis is not fully understood. Here, we report the complete genome sequence of
S. suis
strain ST3 of serotype 3, which provides opportunities to reveal genetic basis of infection of
S. suis
non-serotype 2 strains.
Genome Sequence of Strain IMCC9480, a Xanthorhodopsin-Bearing Betaproteobacterium Isolated from the Arctic Ocean
Authors: Oh Hyun-Myung , Lee Kiyoung , Jang Yoonra , Kang Ilnam , Kim Hee-Jin , Kang Tae-Wook , Kim Seon-Young , Cho Jang-Cheon 
Published: May 2011

ABSTRACT

Strain IMCC9480 is a novel member of the family
Oxalobacteraceae
of the
Betaproteobacteria
, isolated from the Arctic Ocean by dilution-to-extinction culturing. Here we present the draft genome sequence of strain IMCC9480. The genome is predicted to contain genes for xanthorhodopsin, retinoid biosynthesis, carbon monoxide dehydrogenase, and C
1
metabolism.
The role of relationships in improving early diagnosis of prostate cancer
Authors: Forbat L , Hubbard G , Place M , Boyd K , Leung H , Winslow F , Kelly D 
Published: May 2011

AbstractIntroductionEarly diagnosis is critical in reducing mortality in prostate cancer. The extant literature identifies a range of variables which impact on when men present in primary care. For example, recent evidence suggests that men from high deprivation areas are significantly more likely to present with advanced disease and have lower survival rates. Psychosocial theories provide a framework for understanding patterns in the timing of diagnoses, for example, the role of social context and relationships in help-seeking behaviour.AimTo identify how men account for the timing of their presentation and subsequent diagnosis with advanced disease.MethodsEmbedded mixed-method design involving a postal survey (N=320) and semi-structured interviews with a purposive sub-sample of men and partners (N=30). Analysis drew primarily on χ2and spearman's correlation, alongside framework analysis of the qualitative data, informed by Anderson's (1995) model of Total Patient Delay.ResultsData indicate that relationships and experiential knowledge play significant roles in gaining a diagnosis. Notably friends/relatives are key sources of information on prostate cancer and often prompt help-seeking behaviour. Indeed, men's perceptions of risk are not informed by clinical risk factors such as age and family history, but by their own and friends/relatives' experiential knowledge.ConclusionHealth promotion interventions should draw on relational theories, to be cognisant of the important role of relationships in help-seeking behaviour. Adopting a systemic approach has the potential to reach men at higher risk of prostate cancer and contribute to earlier diagnosis.
Evaluation and implementation of an intervention to promote early presentation
Authors: Forster A S , Forbes L J L , Atkins L , Patnick J , Sellars S , Tucker L , Baxter R , Ramirez A J 
Published: May 2011

AbstractIntroduction and aimsOlder women are more likely to delay presentation in breast cancer,1 which in turn contributes to poorer survival.2 We have developed a health professional-delivered intervention to promote early presentation in older women with breast symptoms (Promoting Early Presentation (PEP) Intervention) to be delivered when they attend for their final routine mammogram. We aimed to evaluate its efficacy in an randomized controlled trial (RCT) and adapt it for use in routine clinical practice.MethodsWe randomised 867 women attending for their final round of screening on the NHS Breast Screening Programme to receive either the PEP Intervention delivered by a radiographer or usual care. We measured breast cancer awareness at baseline and 2 years post-randomisation. We are adapting and piloting the PEP Intervention to be suitable for adoption in routine practice across the NHS Breast Screening Programme.ResultsIn the RCT, the PEP Intervention increased the proportion breast cancer aware at 2 years compared with usual care (21% vs 6%, OR: 8.1, 95% CI: 2.7 to 25.0). We have adapted the intervention so that it can be delivered feasibly while maintaining consistent quality.ConclusionsWe have demonstrated the efficacy of the PEP Intervention in an RCT. We plan to evaluate its effectiveness in routine practice by implementing it in three breast screening services, and measuring feasibility, costs and health outcomes (comparing these with health outcomes in control services). Our findings will provide the data needed to inform possible implementation across the entire NHS Breast Screening Programme.
The use of a modified ‘surprise’ question to identify and recruit dying patients into a research project
Authors: Forbes K , Gibbins J , Burcombe M E , Bloor S J , Reid C M , McCoubrie R C , Kinzel C , King S 
Published: May 2011

AbstractIntroduction and aimsTo improve end-of-life care we need good evidence. The challenges of carrying out research with patients who are dying are well documented yet this research is vital to determine whether new interventions improve care. We examined the feasibility of recruiting patients into a study examining their care as they died.MethodsWe performed a prospective mixed-methods observational study of the care given to patients who were dying. All patients on study wards were screened on admission using the question ‘Is this patient so unwell you feel they could die on this admission?’ If the answer was ‘yes’ the patient (and/or family) was approached to give prior consent to being included in the study ‘should they become more unwell’.ResultsOver 2 years, 6703 patients were screened; staff answered ‘yes’ to the screening question for 327 patients (5%). Prior consent (23) or relative assent (94) was obtained for 117 (36%) of these patients. 70 died within the study. Overall, the screening question had a sensitivity of 57% and a specificity of 98%.ConclusionTo our knowledge prior consent for research during the dying process has not been used before within an acute trust. While a large number of patients need to be screened, we have shown that a modified surprise question is helpful in identifying patients who will die during an admission, and it is feasible to gain consent from these patients, or assent from their relatives, for inclusion in a study to examine the dying process.
Education in advanced disease: professionals' knowledge, attitudes and ability
Authors: Flemming K , Closs S J , Foy R , Bennett M I 
Published: May 2011

AbstractIntroduction and aimsThe management of symptoms and lifestyle in advanced disease are essential for the maintenance of patients' quality of life. Health care professionals can facilitate patients to optimise disease management by providing appropriate education. While the provision of education by health professionals for patients with advanced cancer is reasonably well documented, less attention has been paid to other advancing progressive diseases. The aim of this review was to synthesise qualitative research which examined health care professionals' knowledge, attitudes and ability towards delivering educational interventions to patients with the following advanced progressive diseases: heart failure, chronic respiratory disease, end stage renal disease and neuromuscular disorders.MethodsThe synthesis was conducted using meta-ethnography. Systematic searching of five electronic databases (CINAHL, Medline, PsychInfo, Web of Science Social Science Citation Index and EMBASE) occurred. Included papers were data extracted and assessed for quality.ResultsThe searches identified 911 records, of which 17 met the inclusion criteria for the review. Three key themes influencing the delivery of education to patients with advanced disease were identified:Capacity (to educate and aid decision-making)Context (of educational delivery)Timing (of education).ConclusionA range of enablers and barriers identified by health care professionals influence their ability to deliver education at the end of life. Therefore, any interventions to change practice need to have multiple components, rather than targeting sole aspects such as knowledge or motivation alone. Strategies for improving educational practice should explicitly target factors judged as important and potentially amenable to change.
Improving breast and lung cancer services in hospital using experience based co-design (EBCD)
Authors: Wiseman T , Tsianakas V , Maben J , Robert G , Richardson A 
Published: May 2011

AbstractBackground and aimsThis project sought to design better experiences for patients and health care staff from the breast and lung cancer services within two large teaching hospitals in England. Experience based co-design (EBCD) was the chosen action research approach.1 EBCD is a new and innovative methodology combining (1) a user-centred orientation (by adopting a narrative storytelling approach) and (2) a participatory, collaborative change process, allowing staff to ‘see the person in the patient’ and placing patient and staff experience at the centre of service development.Methods and resultsThe project involved an in-depth qualitative study of how care was delivered by staff and received by patients, focusing on patients' emotional ‘journey’. It included 36 filmed patient narratives, capturing the key emotional ‘touch points’, 60 staff interviews about their experience of providing services, and ethnographic observation of clinical areas. Patient and staff interviews were analysed to identify themes and issues for which were feedback to patients and staff at various group events. For example, a composite 30 min film of breast and lung cancer patients’ experiences, was created and used to feedback patient narratives to staff. Through a facilitated three-stage change process which will be described, patients and staff agreed on joint priorities for improvement and then worked together in co-design groups that focused on identified priority areas (for example information provision, day surgery, continuity of care, diagnosis and outpatient care).Discussion and conclusionsThe paper reflects on lessons learned for improving patient/staff experiences through the use of EBCD. It explores the value of the EBCD approach, the use of narratives, observation and film (excerpts will be shown) as a way of humanising health care and engaging staff and patients in a change process to facilitate meaningful and lasting improvements in service provision.