bluuebunny/crossref_metadata_2025_split huggingface dataset:
The PuhB Protein of
Rhodobacter capsulatus
Functions in Photosynthetic Reaction Center Assembly with a Secondary Effect on Light-Harvesting Complex 1
Authors: Aklujkar Muktak , Prince Roger C. , Beatty J. Thomas 
Published: February 2005

ABSTRACT

The core of the photosynthetic apparatus of purple photosynthetic bacteria such as
Rhodobacter capsulatus
consists of a reaction center (RC) intimately associated with light-harvesting complex 1 (LH1) and the PufX polypeptide. The abundance of the RC and LH1 components was previously shown to depend on the product of the
puhB
gene (formerly known as
orf214
). We report here that disruption of
puhB
diminishes RC assembly, with an indirect effect on LH1 assembly, and reduces the amount of PufX. Under semiaerobic growth conditions, the core complex was present at a reduced level in
puhB
mutants. After transfer of semiaerobically grown cultures to photosynthetic (anaerobic illuminated) conditions, the RC/LH1 complex became only slightly more abundant, and the amount of PufX increased as cells began photosynthetic growth. We discovered that the photosynthetic growth of
puhB
disruption strains of
R. capsulatus
starts after a long lag period, which is due to physiological adaptation rather than secondary mutations. Using a hybrid protein expression system, we determined that the three predicted transmembrane segments of PuhB are capable of spanning a cell membrane and that the second transmembrane segment could mediate self-association of PuhB. We discuss the possible function of PuhB as a dimeric RC assembly factor.
High- and Low-Threshold Genes in the Spo0A Regulon ofBacillus subtilis
Authors: Fujita Masaya , González-Pastor José Eduardo , Losick Richard 
Published: February 2005

ABSTRACTThe master regulator for entry into sporulation inBacillus subtilisis the response regulator Spo0A, which directly governs the expression of about 121 genes. Using cells in which the synthesis of Spo0A was under the control of an inducible promoter or in which production of the regulatory protein was impaired by a promoter mutation, we found that sporulation required a high (threshold) level of Spo0A and that many genes in the regulon differentially responded to high and low doses of the regulator. We distinguished four categories of genes, as follows: (i) those that required a high level of Spo0A to be activated, (ii) those that required a high level of Spo0A to be repressed, (iii) those that were activated at a low level of the regulator, and (iv) those that were repressed at a low dose of the regulator. Genes that required a high dose of Spo0A to be activated were found to have low binding constants for the DNA-binding protein. Some genes that were turned on at a low dose of Spo0A either had a high binding constant for the regulatory protein or were activated by an indirect mechanism involving Spo0A-mediated relief of repression by the repressor protein AbrB. We propose that progressive increases in the level of Spo0A leads to an early phase of transcription in which genes that play auxiliary roles in development, such as cannibalism and biofilm formation, are turned on and a later phase in which genes that play a direct role in sporulation are activated.
Novel Genes of the
dsr
Gene Cluster and Evidence for Close Interaction of Dsr Proteins during Sulfur Oxidation in the Phototrophic Sulfur Bacterium
Allochromatium vinosum
Authors: Dahl Christiane , Engels Sabine , Pott-Sperling Andrea S. , Schulte Andrea , Sander Johannes , Lübbe Yvonne , Deuster Oliver , Brune Daniel C. 
Published: February 2005

ABSTRACT

Seven new genes designated
dsrLJOPNSR
were identified immediately downstream of
dsrABEFHCMK
, completing the
dsr
gene cluster of the phototrophic sulfur bacterium
Allochromatium vinosum
D (DSM 180
T
). Interposon mutagenesis proved an essential role of the encoded proteins for the oxidation of intracellular sulfur, an obligate intermediate during the oxidation of sulfide and thiosulfate. While
dsrR
and
dsrS
encode cytoplasmic proteins of unknown function, the other genes encode a predicted NADPH:acceptor oxidoreductase (DsrL), a triheme
c
-type cytochrome (DsrJ), a periplasmic iron-sulfur protein (DsrO), and an integral membrane protein (DsrP). DsrN resembles cobyrinic acid
a,c
-diamide synthases and is probably involved in the biosynthesis of siro(heme)amide, the prosthetic group of the
dsrAB
-encoded sulfite reductase. The presence of most predicted Dsr proteins in
A. vinosum
was verified by Western blot analysis. With the exception of the constitutively present DsrC, the formation of Dsr gene products was greatly enhanced by sulfide. DsrEFH were purified from the soluble fraction and constitute a soluble α
2
β
2
γ
2
-structured 75-kDa holoprotein. DsrKJO were purified from membranes pointing at the presence of a transmembrane electron-transporting complex consisting of DsrKMJOP. In accordance with the suggestion that related complexes from dissimilatory sulfate reducers transfer electrons to sulfite reductase, the
A. vinosum
Dsr complex is copurified with sulfite reductase, DsrEFH, and DsrC. We therefore now have an ideal and unique possibility to study the interaction of sulfite reductase with other proteins and to clarify the long-standing problem of electron transport from and to sulfite reductase, not only in phototrophic bacteria but also in sulfate-reducing prokaryotes.
A Three-Component Regulatory System Regulates Biofilm Maturation and Type III Secretion inPseudomonas aeruginosa
Authors: Kuchma Sherry L. , Connolly John P. , O'Toole George A. 
Published: February 2005

ABSTRACTBiofilms are structured communities found associated with a wide range of surfaces. Here we report the identification of a three-component regulatory system required for biofilm maturation byPseudomonas aeruginosastrain PA14. A transposon mutation that altered biofilm formation in a 96-well dish assay originally defined this locus, which is comprised of genes for a putative sensor histidine kinase and two response regulators and has been designatedsadARS. Nonpolar mutations in any of thesadARSgenes result in biofilms with an altered mature structure but do not confer defects in growth or early biofilm formation, swimming, or twitching motility. After 2 days of growth under flowing conditions, biofilms formed by the mutants are indistinguishable from those formed by the wild-type (WT) strain. However, by 5 days, mutant biofilms appear to be more homogeneous than the WT in that they fail to form large and distinct macrocolonies and show a drastic reduction in water channels. We propose that thesadARSthree-component system is required for later events in biofilm formation on an abiotic surface. Semiquantitative reverse transcription-PCR analysis showed that there is no detectable change in expression of thesadARSgenes when cells are grown in a planktonic culture versus a biofilm, indicating that this locus is not itself induced during or in response to biofilm formation. DNA microarray studies were used to identify downstream targets of the SadARS system. Among the genes regulated by the SadARS system are those required for type III secretion. Mutations in type III secretion genes result in strains with enhanced biofilm formation. We propose a possible mechanism for the role that the SadARS system plays in biofilm formation.
Alpha-Subunit Positions Methionine 180 and Glutamate 214 of
Pseudomonas stutzeri
OX1 Toluene-
o
-Xylene Monooxygenase Influence Catalysis
Authors: Vardar Gönül , Wood Thomas K. 
Published: February 2005

ABSTRACT

Alpha-subunit position M180 of toluene-
o
-xylene monooxygenase influences the regiospecific oxidation of aromatics (e.g., from
o
-cresol, M180H forms 3-methylcatechol, methylhydroquinone, and 4-methylresorcinol, whereas the wild type forms only 3-methylcatechol). Position E214 influences the rate of reaction (e.g., E214G increases
p-
nitrophenol oxidation 15-fold) by controlling substrate entrance and product efflux as a gate residue.
SOS-Independent Induction ofdinBTranscription by β-Lactam-Mediated Inhibition of Cell Wall Synthesis inEscherichia coli
Authors: Pérez-Capilla Tatiana , Baquero María-Rosario , Gómez-Gómez José-María , Ionel Alina , Martín Soledad , Blázquez Jesús 
Published: February 2005

ABSTRACTTranscription of thedinBgene, encoding DNA polymerase IV, is induced by the inhibition of cell wall synthesis at different levels. Using the β-lactam antibiotic ceftazidime, a PBP3 inhibitor, as a model, we have shown that this induction is independent of the LexA/RecA regulatory system. Induction ofdinBtranscription mediated by ceftazidime produces an increase in the reversion of a +1 Lac frameshift mutation.
Mutational Alterations of the KeycisProline Residue That Cause Accumulation of Enzymatic Reaction Intermediates of DsbA, a Member of the Thioredoxin Superfamily
Authors: Kadokura Hiroshi , Nichols Lorenzo , Beckwith Jon 
Published: February 2005

ABSTRACTThe DsbA-DsbB pathway introduces disulfide bonds into newly translocated proteins. Conversion of the conservedcisproline 151 of DsbA to several hydrophilic residues results in accumulation of mixed disulfides between DsbA and its dedicated oxidant, DsbB. However, only a proline-to-threonine change causes accumulation of mixed disulfides of DsbA with its substrates.
Identification of Genes Involved in the Glyoxylate Regeneration Cycle in
Methylobacterium extorquens
AM1, Including Two New Genes,
meaC
and
meaD
Authors: Korotkova Natalia , Lidstrom Mary E. , Chistoserdova Ludmila 
Published: February 2005

ABSTRACT
The glyoxylate regeneration cycle (GRC) operates in serine cycle methylotrophs to effect the net conversion of acetyl coenzyme A to glyoxylate. Mutants have been generated in several genes involved in the GRC, and phenotypic analysis has been carried out to clarify their role in this cycle.
Contribution of the ATP Binding Site of ParE to Susceptibility to Novobiocin and Quinolones in
Streptococcus pneumoniae
Authors: Dupont Philippe , Aubry Alexandra , Cambau Emmanuelle , Gutmann Laurent 
Published: February 2005

ABSTRACT

In
Streptococcus pneumoniae
, an H103Y substitution in the ATP binding site of the ParE subunit of topoisomerase IV was shown to confer quinolone resistance and hypersensitivity to novobiocin when associated with an S84F change in the A subunit of DNA gyrase. We reconstituted in vitro the wild-type topoisomerase IV and its ParE mutant. The ParE mutant enzyme showed a decreased activity for decatenation at subsaturating ATP levels and was more sensitive to inhibition by novobiocin but was as sensitive to quinolones. These results show that the ParE alteration H103Y alone is not responsible for quinolone resistance and agree with the assumption that it facilitates the open conformation of the ATP binding site that would lead to novobiocin hypersensitivity and to a higher requirement of ATP.
Prolastin, a pharmaceutical preparation of purified human α1-antitrypsin, blocks endotoxin-mediated cytokine release
Authors: Nita Izabela , Hollander Camilla , Westin Ulla , Janciauskiene Sabina-Marija 
Published: February 2005

Abstract
Background
α1-antitrypsin (AAT) serves primarily as an inhibitor of the elastin degrading proteases, neutrophil elastase and proteinase 3. There is ample clinical evidence that inherited severe AAT deficiency predisposes to chronic obstructive pulmonary disease. Augmentation therapy for AAT deficiency has been available for many years, but to date no sufficient data exist to demonstrate its efficacy. There is increasing evidence that AAT is able to exert effects other than protease inhibition. We investigated whether Prolastin, a preparation of purified pooled human AAT used for augmentation therapy, exhibits anti-bacterial effects.

Methods
Human monocytes and neutrophils were isolated from buffy coats or whole peripheral blood by the Ficoll-Hypaque procedure. Cells were stimulated with lipopolysaccharide (LPS) or zymosan, either alone or in combination with Prolastin, native AAT or polymerised AAT for 18 h, and analysed to determine the release of TNFα, IL-1β and IL-8. At 2-week intervals, seven subjects were submitted to a nasal challenge with sterile saline, LPS (25 μg) and LPS-Prolastin combination. The concentration of IL-8 was analysed in nasal lavages performed before, and 2, 6 and 24 h after the challenge.

Results
In vitro, Prolastin showed a concentration-dependent (0.5 to 16 mg/ml) inhibition of endotoxin-stimulated TNFα and IL-1β release from monocytes and IL-8 release from neutrophils. At 8 and 16 mg/ml the inhibitory effects of Prolastin appeared to be maximal for neutrophil IL-8 release (5.3-fold, p < 0.001 compared to zymosan treated cells) and monocyte TNFα and IL-1β release (10.7- and 7.3-fold, p < 0.001, respectively, compared to LPS treated cells). Furthermore, Prolastin (2.5 mg per nostril) significantly inhibited nasal IL-8 release in response to pure LPS challenge.

Conclusion
Our data demonstrate for the first time that Prolastin inhibits bacterial endotoxin-induced pro-inflammatory responses in vitro and in vivo, and provide scientific bases to explore new Prolastin-based therapies for individuals with inherited AAT deficiency, but also for other clinical conditions.
Transient expression analysis of allelic variants of a VNTR in the dopamine transporter gene (DAT1)
Authors: Mill Jonathan , Asherson Philip , Craig Ian , D'Souza Ursula M 
Published: February 2005

Abstract
Background
The 10-repeat allele of a variable number tandem repeat (VNTR) polymorphism in the 3'-untranslated region of the dopamine transporter gene (DAT1) has been associated with a range of psychiatric phenotypes, most notably attention-deficit hyperactivity disorder. The mechanism for this association is not yet understood, although several lines of evidence implicate variation in gene expression. In this study we have characterised the genomic structure of the 9- and 10-repeat VNTR alleles, and directly examined the role of the polymorphism in mediating gene expression by measuring comparative in vitro cellular expression using a reporter-gene assay system.

Results
Differences in the sequence of the 9- and 10- repeat alleles were confirmed but no polymorphic differences were observed between individuals. There was no difference in expression of reporter gene constructs containing the two alleles.

Conclusions
Our data suggests that this VNTR polymorphism may not have a direct effect on DAT1 expression and that the associations observed with psychiatric phenotypes may be mediated via linkage disequilibrium with other functional polymorphisms.
Hesperidin, a citrus bioflavonoid, decreases the oxidative stress produced by carbon tetrachloride in rat liver and kidney
Authors: Tirkey Naveen , Pilkhwal Sangeeta , Kuhad Anurag , Chopra Kanwaljit 
Published: February 2005

Abstract
Background
CCl4 is a well-established hepatotoxin inducing liver injury by producing free radicals. Exposure to CCl4 also induces acute and chronic renal injuries. The present study was designed to establish the protective effect of hesperidin (HDN), a citrus bioflavonoid, on CCl4-induced oxidative stress and resultant dysfunction of rat liver and kidney.

Methods
Animals were pretreated with HDN (100 and 200 mg/kg orally) for one week and then challenged with CCl4 (2 ml/kg/s.c.) in olive oil. Rats were sacrificed by carotid bleeding under ether anesthesia. Liver enzymes, urea and creatinine were estimated in serum. Oxidative stress in liver and kidney tissue was estimated using Thiobarbituric acid reactive substances (TBARS), glutathione (GSH) content, superoxide dismutase(SOD), and Catalase (CAT)

Results
CCl4 caused a marked rise in serum levels of ALT and AST (P < 0.05). TBARS levels were significantly increased whereas GSH, SOD and CAT levels decreased in the liver and kidney homogenates of CCl4 treated rats. HDN (200 mg/kg) successfully attenuated these effects of CCl4

Conclusion
In conclusion, our study demonstrated a protective effect of HDN in CCl4 induced oxidative stress in rat liver and kidney. This protective effect of HDN can be correlated to its direct antioxidant effect.
Autonomic nervous system dysfunction predicts poor prognosis in patients with mild to moderate tetanus
Authors: Wasay Mohammad , Khealani Bhojo A , Talati Naasha , Shamsi Rohmah , Syed Nadir A , Salahuddin Naseem 
Published: February 2005

Abstract
Background
Autonomic nervous system (ANS) dysfunction is present in up to one third of patients with tetanus. The prognostic value of ANS dysfunction is known in severe tetanus but its value is not well established in mild to moderate tetanus.

Methods
Medical records of all patients admitted with tetanus at two academic tertiary care centers in Karachi, Pakistan were reviewed. The demographic, clinical and laboratory data was recorded and analyzed. ANS dysfunction was defined as presence of labile or persistent hypertension or hypotension and sinus tachycardia, tachyarrythmia or bradycardia on EKG. Patients were divided into two groups based on presence of ANS dysfunction (ANS group and non ANS group). Tetanus severity was classified on the basis of Ablett criteria.

Results
Ninety six (64 males; 32 females) patients were admitted with the diagnosis over a period of 10 years. ANS group had 31 (32%) patients while non ANS group comprised of 65 (68%) patients. Both groups matched for age, gender, symptom severity, use of tetanus immunoglobulin and antibiotics. Twelve patients in ANS group had mild to moderate tetanus (Ablett I and II) and 19 patients had severe/very severe tetanus (Ablett III and IV). Fifteen (50%) patients in ANS group required ventilation as compared to 28 (45%) in non-ANS group (p = 0.09). Fourteen (47%) patients died in ANS group as compared to 10 (15%) in non ANS group (p= 0.002). Out of those 14 patients died in ANS group, six patients had mild to moderate tetanus and eight patients had severe/ very severe tetanus. Major cause of death was cardiac arrhythmias (13/14; 93%) in ANS group and respiratory arrest (7/10; 70%) in non ANS group. Ten (33%) patients had complete recovery in ANS group while in non ANS group 35(48%) patients had complete recovery (p= 0.05).

Conclusions
ANS dysfunction was present in one third of our tetanus population. 40% patients with ANS dysfunction had only mild to moderate tetanus. ANS dysfunction, irrespective of the need of mechanical ventilation or severity of tetanus, predicted poor outcome.
Long-term survival rates of laryngeal cancer patients treated by radiation and surgery, radiation alone, and surgery alone : studied by lognormal and Kaplan-Meier survival methods
Authors: Tai Patricia , Yu Edward , Shiels Ross , Tonita Jon 
Published: February 2005

Abstract
Background
Validation of the use of the lognormal model for predicting long-term survival rates using short-term follow-up data.

Methods
907 cases of laryngeal cancer were treated from 1973–1977 by radiation and surgery (248), radiation alone (345), and surgery alone (314), in registries of Connecticut and Metropolitan Detroit of the SEER database, with known survival status up to 1999. Phase 1 of this study used the minimum chi-square test to assess the goodness of fit of the survival times of those who died with disease to a lognormal distribution. Phase 2 used the maximum likelihood method to estimate long-term survival rates using short-term follow-up data. In order to validate the lognormal model, the estimated long-term cancer-specific survival rates (CSSR) were compared with the values calculated by the Kaplan-Meier (KM) method using long-term data.

Results
The 25-year CSSR were predicted to be 72%, 68% and 65% for treatments by radiation and surgery, by radiation alone, and by surgery alone respectively, using short-term follow-up data by the lognormal model. Corresponding results calculated by the KM method were: 72+/-3%, 68+/-3% and 66+/-4% respectively.

Conclusions
The lognormal model was validated for the prediction of the long-term survival rates of laryngeal cancer patients treated by these different methods. The lognormal model may become a useful tool in research on outcomes.
An interactive course to enhance self-efficacy of family practitioners to treat obesity
Authors: Katz Sara , Feigenbaum Amiel , Pasternak Shmuel , Vinker Shlomo 
Published: February 2005

Abstract
Background
Physicians' awareness of their important role in defusing the obesity epidemic has increased. However, the number of family practitioners who treat obesity problems continues to be low. Self-efficacy refers to the belief in one's ability to organize and execute the courses of action required to produce given attainments. Thus, practitioners who judge themselves incapable of managing obesity do not even try. We hypothesized that practitioners' self-efficacy and motivation would be enhanced as a result of participating in an interactive course designed to enrich their knowledge of obesity management.

Methods
Twenty-nine family practitioners participated in the course, which was accompanied by qualitative interviews. The difference between the physicians' pre-course and post-course appraisals was tested by paired t-test. The interviews were analyzed by qualitative methods.

Results
Post-course efficacy appraisals were significantly higher than pre-course appraisals (p < 0.0005). A deeper insight on the practitioners' self-efficacy processes was gained through reflection of the practitioners on their self-efficacy during the interviews.

Conclusions
Up-to-date information and workshops where skills, attitudes and social support were addressed were important in making the program effective.
Claudin-1, -3 and -4 proteins and mRNA expression in benign and malignant breast lesions: a research study
Authors: Tőkés Anna-Mária , Kulka Janina , Paku Sándor , Szik Ágnes , Páska Csilla , Novák Pál Kaposi , Szilák László , Kiss András , Bögi Krisztina , Schaff Zsuzsa 
Published: February 2005

Abstract
Introduction
We compared levels of protein and mRNA expression of three members of the claudin (CLDN) family in malignant breast tumours and benign lesions.

Methods
Altogether, 56 sections from 52 surgically resected breast specimens were analyzed for CLDN1, CLDN3 and CLDN4 expression by immunohistochemistry. mRNA was also analyzed using real-time PCR in 17 of the 52 cases.

Results
CLDNs were rarely observed exclusively at tight junction structures. CLDN1 was present in the membrane of normal duct cells and in some of the cell membranes from ductal carcinoma in situ, and was frequently observed in eight out of nine areas of apocrine metaplasia, whereas invasive tumours were negative for CLDN1 or it was present in a scattered distribution among such tumour cells (in 36/39 malignant tumours). CLDN3 was present in 49 of the 56 sections and CLDN4 was present in all 56 tissue sections. However, CLDN4 was highly positive in normal epithelial cells and was decreased or absent in 17 out of 21 ductal carcinoma grade 1, in special types of breast carcinoma (mucinous, papillary, tubular) and in areas of apocrine metaplasia. CLDN1 mRNA was downregulated by 12-fold in the sample (tumour) group as compared with the control group using GAPDH as the reference gene. CLDN3 and CLDN4 mRNA exhibited no difference in expression between invasive tumours and surrounding tissue.

Conclusions
The significant loss of CLDN1 protein in breast cancer cells suggests that CLDN1 may play a role in invasion and metastasis. The loss of CLDN4 expression in areas of apocrine metaplasia and in the majority of grade 1 invasive carcinomas also suggests a particular role for this protein in mammary glandular cell differentiation and carcinogenesis.