bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phosphate Starvation Induces the Sporulation Killing Factor of
Bacillus subtilis
Authors: Allenby Nicholas E. E. , Watts Carys A. , Homuth Georg , Prágai Zoltán , Wipat Anil , Ward Alan C. , Harwood Colin R. 
Published: June 2006

ABSTRACT

Bacillus subtilis
produces and exports a peptide sporulation killing factor (SkfA) that induces lysis of sibling cells.
skfA
is part of the
skf
operon (
skfA-H
), which is responsible for immunity to SkfA, as well as for production and export of SkfA. Here we report that transcription of
skfA
is markedly induced when cells of
B. subtilis
are subjected to phosphate starvation. The role of PhoP in regulation of the
skf
operon was confirmed by in vitro gel shift assays, which showed that this operon is a new member of the PhoP regulon. A putative stem-loop structure in the
skfA-skfB
intergenic region is proposed to act as a stabilizer of an
skfA
-specific transcript.
Genetic Evidence for the Requirement of RecA Loading Activity in SOS Induction after UV Irradiation inEscherichia coli
Authors: Ivančić-Baće Ivana , Vlašić Ignacija , Salaj-Šmic Erika , Brčić-Kostić Krunoslav 
Published: June 2006

ABSTRACTThe SOS response inEscherichia coliresults in the coordinately induced expression of more than 40 genes which occurs when cells are treated with DNA-damaging agents. This response is dependent on RecA (coprotease), LexA (repressor), and the presence of single-stranded DNA (ssDNA). A prerequisite for SOS induction is the formation of a RecA-ssDNA filament. Depending on the DNA substrate, the RecA-ssDNA filament is produced by either RecBCD, RecFOR, or a hybrid recombination mechansim with specific enzyme activities, including helicase, exonuclease, and RecA loading. In this study we examined the role of RecA loading activity in SOS induction after UV irradiation. We performed a genetic analysis of SOS induction in strains with a mutation which eliminates RecA loading activity in the RecBCD enzyme (recB1080allele). We found that RecA loading activity is essential for SOS induction. In therecB1080mutant RecQ helicase is not important, whereas RecJ nuclease slightly decreases SOS induction after UV irradiation. In addition, we found that therecB1080mutant exhibited constitutive expression of the SOS regulon. Surprisingly, this constitutive SOS expression was dependent on the RecJ protein but not on RecFOR, implying that there is a different mechanism of RecA loading for constitutive SOS expression.
Alanine Dehydrogenase Activity Is Required for Adequate Progression of Phycobilisome Degradation during Nitrogen Starvation in
Synechococcus elongatus
PCC 7942
Authors: Lahmi Roxane , Sendersky Eleonora , Perelman Alexander , Hagemann Martin , Forchhammer Karl , Schwarz Rakefet 
Published: June 2006

ABSTRACT

Degradation of the cyanobacterial light-harvesting antenna, the phycobilisome, is a general acclimation response that is observed under various stress conditions. In this study we identified a novel mutant of
Synechococcus elongatus
PCC 7942 that exhibits impaired phycobilisome degradation specifically during nitrogen starvation, unlike previously described mutants, which exhibit aberrant degradation under nitrogen, sulfur, and phosphorus starvation conditions. The phenotype of the new mutant, AldΩ, results from inactivation of
ald
(encoding alanine dehydrogenase). AldΩ is deficient in transcription induction of a number of genes during nitrogen starvation. These genes include the “general nutrient stress-related” genes,
nblA
and
nblC
, the products of which are essential for phycobilisome degradation. Furthermore, transcripts of several specific nitrogen-responsive genes accumulate at lower levels in AldΩ than in the wild-type strain. In contrast,
ald
inactivation did not decrease the accumulation of transcripts during sulfur starvation. Transcription of
ald
is induced upon nitrogen starvation, which is consistent with the ability of wild-type cells to maintain a low cellular content of alanine under these conditions. Unlike wild-type cells, AldΩ accumulates alanine upon nitrogen starvation. Our analyses suggest that alanine dehydrogenase activity is necessary for an adequate cellular response to nitrogen starvation. Decomposition of alanine may be required to provide a sufficient amount of ammonia. Furthermore, the accumulated alanine, or a related metabolite, may interfere with the cues that modulate acclimation during nitrogen starvation. Taken together, our results provide novel information regarding cellular responses to nitrogen starvation and suggest that mechanisms related to nitrogen-specific responses are involved in modulation of a general acclimation process.
Regulation of LiaRS-Dependent Gene Expression inBacillus subtilis: Identification of Inhibitor Proteins, Regulator Binding Sites, and Target Genes of a Conserved Cell Envelope Stress-Sensing Two-Component System
Authors: Jordan Sina , Junker Anja , Helmann John D. , Mascher Thorsten 
Published: June 2006

ABSTRACTThe regulatory network of the cell envelope stress response inBacillus subtilisinvolves both extracytoplasmic function σ-factors and two-component signal transducing systems. One such system, LiaRS, responds to cell wall antibiotics that interfere with the undecaprenol cycle and to perturbation of the cytoplasmic membrane. It is encoded by the last two genes of theliaIHGFSRlocus. Here, we analyzed the expression of two LiaR-dependent operons,liaIHGFSRandyhcYZ-yhdA, and characterized a palindromic sequence required for LiaR-dependent activation. Since induction of the strongliaIpromoter leads to bothliaIHandliaIHGFRStranscripts, LiaR is positively autoregulated. Systematic deletion analysis of theliaIoperon revealed that LiaF is a potent negative regulator of LiaR-dependent gene expression: a nonpolarliaFdeletion led to constitutive activation of both characterized LiaR-dependent promoters. TheliaFgene is conserved in both sequence and genomic context in theFirmicutesgroup of gram-positive bacteria, located directly upstream ofliaSRorthologs. LiaH, a homolog ofEscherichia coliphage shock protein A, also plays a more subtle role in negatively modulating the bacitracin-inducible expression from LiaR-dependent promoters. Our results support a model in which the LiaFRS module integrates both positive and negative feedback loops to transduce cell envelope stress signals.
GlpD and PlsB Participate in Persister Cell Formation in
Escherichia coli
Authors: Spoering Amy L. , Vulić Marin , Lewis Kim 
Published: June 2006

ABSTRACT

Bacterial populations produce dormant persister cells that are resistant to killing by all antibiotics currently in use, a phenomenon known as multidrug tolerance (MDT). Persisters are phenotypic variants of the wild type and are largely responsible for MDT of biofilms and stationary populations. We recently showed that a
hipBA
toxin/antitoxin locus is part of the MDT mechanism in
Escherichia coli
. In an effort to find additional MDT genes, an
E. coli
expression library was selected for increased survival to ampicillin. A clone with increased persister production was isolated and was found to overexpress the gene for the conserved aerobic
sn
-glycerol-3-phosphate dehydrogenase GlpD. The GlpD overexpression strain showed increased tolerance to ampicillin and ofloxacin, while a strain with
glpD
deleted had a decreased level of persisters in the stationary state. This suggests that GlpD is a component of the MDT mechanism. Further genetic studies of mutants affected in pathways involved in
sn
-glycerol-3-phosphate metabolism have led to the identification of two additional multidrug tolerance loci,
glpABC
, the anaerobic
sn
-glycerol-3-phosphate dehydrogenase, and
plsB
, an
sn
-glycerol-3-phosphate acyltransferase.
Constitutive Activation of Two-Component Response Regulators: Characterization of VirG Activation inAgrobacterium tumefaciens
Authors: Gao Rong , Mukhopadhyay Aindrila , Fang Fang , Lynn David G. 
Published: June 2006

ABSTRACTResponse regulators are the ultimate modulators in two-component signal transduction pathways. The N-terminal receiver domains generally accept phosphates from cognate histidine kinases to control output. VirG for example, the response regulator of the VirA/VirG two-component system inAgrobacterium tumefaciens, mediates the expression of virulence genes in response to plant host signals. Response regulators have a highly conserved structure and share a similar conformational activation upon phosphorylation, yet the sequence and structural features that determine or perturb the cooperative activation events are ill defined. Here we use VirG and the unique features of theAgrobacteriumsystem to extend our understanding of the response regulator activation. Two previously isolated constitutive VirG mutants, VirGN54D and VirGI77V/D52E, provide the foundation for our studies. In vivo phosphorylation patterns establish that VirGN54D is able to accumulate phosphates from small-molecule phosphate donors, such as acetyl phosphate, while the VirGI77V/D52E allele carries conformational changes mimicking the active conformation. Further structural alterations on these two alleles begin to reveal the changes necessary for response regulator activation.
Molecular Characterization of
Pantoea stewartii
subsp.
stewartii
HrpY, a Conserved Response Regulator of the Hrp Type III Secretion System, and its Interaction with the
hrpS
Promoter
Authors: Merighi Massimo , Majerczak Doris R. , Zianni Michael , Tessanne Kimberly , Coplin David L. 
Published: June 2006

ABSTRACT

Pantoea stewartii
subsp.
stewartii
is a bacterial pathogen of corn. Its pathogenicity depends on the translocation of effector proteins into host cells by the Hrp type III secretion system. We previously showed by genetic analysis that the HrpX sensor kinase and the HrpY response regulator are at the head of a complex cascade of regulators controlling
hrp/hrc
secretion and
wts
effector genes. This cascade also includes the HrpS response regulator and the HrpL alternative sigma factor. These regulators are shared among many important plant pathogens in the genera
Pantoea
,
Erwinia
, and
Pseudomonas
. In this study, we dissect the regulatory elements in the
hrpS
promoter region, using genetic and biochemical approaches, and show how it integrates various environmental signals, only some of which are dependent on phosphorylation of HrpY. Primer extension located the transcriptional start site of
hrpS
at a σ
70
promoter 601 bp upstream of the open reading frame. Electrophoretic mobility shift assays and DNase I footprinting analysis demonstrated that HrpY binds to conserved regulatory elements immediately adjacent to this promoter, and its binding affinity was increased by phosphorylation at D57. A consensus sequence for the two direct repeats bound by HrpY is proposed. Deletion analysis of the promoter region revealed that both the HrpY binding site and additional sequences farther upstream, including a putative integration host factor binding site, are required for
hrpS
expression. This finding suggests that other unknown regulatory proteins may act cooperatively with HrpY.
Microvascular proliferation in congenital vascular malformations of skin and soft tissue
Authors: Meijer-Jorna Lorine B , van der Loos Chris M , de Boer Onno J , van der Horst Chantal M A M , van der Wal Allard C 
Published: July 2006

Background:Congenital vascular malformations (VMs) are mass-forming lesions that usually progress slowly, but may become symptomatic because of episodes of sudden growth and pain, particularly those with a substantial component of arteriovenous shunting.Aim:To systematically investigate the features of microvascular proliferation in a large series of surgically treated VMs.Methods:107 resection specimens of clinically and histologically well-documented VMs were screened for the presence and extent of microvascular proliferation, based on morphological parameters, microvessel density (MVD), mast cell density (MCD) and proliferative activity (Ki-67 labelling index) of endothelial cells (ECs) and vascular smooth muscle cells (VSMCs). The extent of microvascular proliferation was correlated with the histological type of VM and clinical characteristics of patients.Results:Microvascular proliferation was observed in 32 (30%) of all VMs, of which 30 cases seemed to be arteriovenous malformations. MVD in areas of microvascular proliferation was 282 (186)/mm2vs 13 (9)/mm2in areas with mature vessels. Both ECs and VSMCs in these areas showed high Ki-67 labelling indexes (mean (SD) 15 (18) and 17 (24)/mm2, respectively). In all lesions, a positive correlation was found between MCD and MVD. Age, sex and location of VM had no predictive value for the occurrence of microvascular proliferation. However, if present, the involved tissue areas were larger and the proliferative activity of EC was higher in male patients than in female patients.Conclusions:Recognition of microvascular proliferation as a not uncommon feature, congenital arteriovenous malformations provide new insight into the growth behaviour and vascular composition of these lesions.
Endobronchial ultrasound-guided fine-needle aspiration and liquid-based thin-layer cytology
Authors: Wallace W A H , Monaghan H M , Salter D M , Gibbons M A , Skwarski K M 
Published: July 2006

Background:Optimal management of patients with lung cancer requires accurate cell typing of tumours and staging at the time of diagnosis. Endobronchial ultrasound-guided lymph node aspiration as a method of diagnosing and staging lung cancer is a relatively new technique.Aim:To report the use of liquid-based-thin-layer cytology for the processing and reporting of these specimens.Methods:The specimens obtained from 80 patients were processed using the ThinPrep system, with the remainder of the samples being processed as a cell block.Results:40 of the 81 procedures yielded malignant cells (30 non-small cell carcinoma, 8 small-cell carcinoma and 2 combined small-cell carcinoma/non-small-cell carcinoma). The cell blocks were found to contain sufficient material to allow the immunohistochemical characterisation of tumour cells with a range of antibodies.Conclusion:The use of liquid-based-thin-layer cytological techniques provides high-quality specimens for diagnostic purposes. When used in conjunction with cell blocks, sufficient material may be obtained to allow immunohistochemical studies to confirm the tumour cell type. Given the current move towards centralisation of pathology services, this approach gives the pathologist high-quality specimens without the need for direct onsite support at the time of the procedure.
Improved clonality assessment in germinal centre/post-germinal centre non-Hodgkin’s lymphomas with high rates of somatic hypermutation
Authors: Catherwood Mark A , Gonzalez David , Patton Caroline , Dobbin Edwina , Venkatraman Lakshmi , Alexander H Denis 
Published: July 2006

Background:PCR detects clonal rearrangements of the Ig gene in lymphoproliferative disorders. False negativity occurs in germinal centre/post-germinal centre lymphomas (GC/PGCLs) as they display a high rate of somatic hypermutation (SHM), which causes primer mismatching when detecting Ig rearrangements by PCR.Aims:To investigate the degree of SHM in a group of GC/PGCLs and assess the rate of false negativity when using BIOMED-2 PCR when compared with previously published strategies.Methods:DNA was isolated from snap-frozen tissue from 49 patients with GC/PGCL (23 diffuse large B cell lymphomas (DLBCLs), 26 follicular lymphomas (FLs)) and PCR-amplified for complete (VDJH), incomplete (DJH) and Igκ/λ rearrangements using the BIOMED-2 protocols, and compared with previously published methods using consensus primers. Germinal centre phenotype was defined by immunohistochemistry based on CD10, Bcl-6 and MUM-1.Results:Clonality detection by amplifying Ig rearrangements using BIOMED-2 family-specific primers was considerably higher than that found using consensus primers (74% DLBCL and 96% FL vs 69% DLBCL and 73% FL). Addition of BIOMED-2 DJH rearrangements increased detection of clonality by 22% in DLBCL. SHM was present in VDJH rearrangements from all patients with DLBCL (median (range) 5.7% (2.5–13.5)) and FL (median (range) 5.3% (2.3–11.9)) with a clonal rearrangement.Conclusions:Use of BIOMED-2 primers has significantly reduced the false negative rate associated with GC/PGCL when compared with consensus primers, and the inclusion of DJH rearrangements represents a potential complementary target for clonality assessment, as SHM is thought not to occur in these types of rearrangements.
Prognostic significance of mucins in colorectal cancer with different DNA mismatch-repair status
Authors: Lugli A , Zlobec I , Baker K , Minoo P , Tornillo L , Terracciano L , Jass J R 
Published: July 2006

Background:Expression of mucin antigen MUC1 and down regulation of MUC2 are associated with adverse prognosis in colorectal cancer (CRC), but their prognostic significance with respect to differing DNA mis- match repair (MMR) status is poorly understood.Objective:To determine the prognostic significance of MUC1 and MUC2 in CRC with different MMR statuses.Methods:Using the tissue microarray (TMA) technique, a series of 1420 unselected, non-consecutive CRC resections was subdivided into three groups: (1) MMR-proficient; (2) MLH1-negative; and (3) presumed hereditary non-polyposis colon cancer (HNPCC). Immunohistochemical analysis of MUC1 and MUC2 expression (>0%) and loss (0%) was performed, and the results were correlated with clinicopathological parameters.Results:In MMR-proficient CRC, MUC1 expression was more frequently found in tumours with higher tumour stage (p = 0.004) and higher tumour grade (p = 0.041) and loss of MUC2 was associated with higher tumour stage (p = 0.028), node stage (p = 0.001), presence of vascular invasion (p = 0.028) and worse survival (p = 0.034). In MLH1-negative CRC, MUC2 loss was associated with the presence of lymph node metastasis (p = 0.028) and worse survival (p = 0.015), but there was no association between MUC1 expression and clinicopathological features. In presumed HNPCC, MUC1 expression and MUC2 loss were not associated with clinicopathological parameters.Conclusions:Mucins have a prognostic significance in sporadic CRC, but not in hereditary CRC. Loss of MUC2 is an adverse prognostic factor in MMR-proficient and MLH1-negative CRC, whereas MUC1 expression is associated with tumour progression in MMR-proficient CRC only.
Do French lay people and health professionals find it acceptable to breach confidentiality to protect a patient’s wife from a sexually transmitted disease?: Figure 1
Authors: Guedj M , Sastre M T Muñoz , Mullet E , Sorum P C 
Published: June 2006

Objective:To determine under what conditions lay people and health professionals find it acceptable for a physician to breach confidentiality to protect the wife of a patient with a sexually transmitted disease (STD).Methods:In a study in France, breaching confidentiality in 48 scenarios were accepted by 144 lay people, 10 psychologists and 7 physicians. The scenarios were all possible combinations of five factors: severity of the disease (severe, lethal); time taken to discuss this with (little time, much time); intent to inform the spouse about the disease (none, one of these days, immediately); intent to adopt protective behaviours (no intent, intent); and decision to consult an expert in STDs (yes, no), 2×2×3×2×2. The importance and interactions of each factor were determined, at the group level, by performing analyses of variance and constructing graphs.Results:The concept of breaching confidentiality to protect a wife from her husband’s STD was favoured much more by lay people and psychologists than by physicians (mean ratings 11.76, 9.28 and 2.90, respectively, on a scale of 0–22). The patient’s stated intentions to protect his wife and to inform her of the disease had the greatest impact on acceptability. A cluster analysis showed groups of lay participants who found breaching confidentiality “always acceptable” (n = 14), “depending on the many circumstances” (n = 87), requiring “consultation with an expert” (n = 30) and “never acceptable (n = 13)”.Conclusions:Most people in France are influenced by situational factors when deciding if a physician should breach confidentiality to protect the spouse of a patient infected with STD.
Privacy and patient–clergy access: perspectives of patients admitted to hospital
Authors: Erde E , Pomerantz S C , Saccocci M , Kramer-Feeley V , Cavalieri T A 
Published: June 2006

Background:For patients admitted to hospital both pastoral care and privacy or confidentiality are important. Rules related to each have come into conflict recently in the US. Federal laws and other rules protect confidentiality in ways that countermand hospitals’ methods for facilitating access to pastoral care. This leads to conflicts and poses an unusual type of dilemma—one of conflicting values and rights. As interests are elements necessary for establishing rights, it is important to explore patients’ interests in privacy compared with their desire for attention from a cleric.Aim:To assess the willingness of patients to have their names and rooms included on a list by religion, having that information given to clergy without their consent, their sense of privacy violation if that were done and their views about patients’ privacy rights.Methods and participants:179 patients, aged 18–92 years, admitted to hospital in an acute care setting, were interviewed and asked about their preferences for confidentiality and pastoral support.Results:Most (57%) patients did not want to be listed by religion; 58% did not think hospitals should give lists to clergy without their consent and 84% welcomed a visit by their own clergy even if triggered from a hospital list.Conclusions:Values related to confidentiality or privacy and pastoral care were found to be inconsistent and more complicated than expected. Balancing the right to privacy and the value of religious support continue to present a challenge for hospitals. Patients’ preferences support the importance of providing balance in a way that protects rights while offering comprehensive services.
Rural and non-rural differences in membership of the American Society of Bioethics and Humanities: Table 1
Authors: Nelson William , Weeks William B 
Published: June 2006

Objective:To determine whether bioethicists are distributed along a rural-to-urban continuum in a way that reflects potential need of those resources as determined by the general population, hospital facilities and hospital beds.Methods:US members of a large, multidisciplinary professional society, the American Society of Bioethics and Humanities (ASBH), the US population, hospital facilities and hospital beds were classified across a four-tier rural-to-urban continuum. The proportion of each group in rural settings was compared with that in urban settings, and odds ratios were calculated with 95% confidence intervals.Results:Although 91% of ASBH members live or work in urban settings, only 66% of the US population did so. In contrast, 2% of ASBH members live or work in rural settings compared with 13% of the population. ASBH members were 10.7 times (95% CI 6.6 to 17.3) as likely to be represented in urban than in rural settings when compared with the general population, 25.6 times (95% CI 15.8 to 41.5) and 6.9 times (95% CI 4.3 to 11.1) as likely with regard to hospital facilities and hospital beds, respectively.Conclusions:Using various comparisons it was found that ASBH members are under-represented in rural as compared with urban settings. Although not all bioethicists are ASBH members, these findings suggest that the availability of professional bioethical resources may be inadequate in rural America. The disparities that were found may have considerable effect on ethics scholarship, research, ethical committees and education, and adds to the argument that rural American communities are under-served.