bluuebunny/crossref_metadata_2025_split huggingface dataset:
Symbiotic Autoregulation of
nifA
Expression in
Rhizobium leguminosarum
bv. viciae
Authors: Martínez Marta , Palacios José M. , Imperial Juan , Ruiz-Argüeso Tomás 
Published: September 2004

ABSTRACT

NifA is the general transcriptional activator of nitrogen fixation genes in diazotrophic bacteria. In
Rhizobium leguminosarum
bv. viciae UPM791, the
nifA
gene is part of a gene cluster (
orf71 orf79 fixW orf5 fixABCX nifAB
) separated by 896 bp from an upstream and divergent truncated duplication of
nifH
(Δ
nifH
). Symbiotic expression analysis of genomic
nifA
::
lacZ
fusions revealed that in strain UPM791
nifA
is expressed mainly from a σ
54
-dependent promoter (P

nifA1

) located upstream of
orf71
. This promoter contains canonical NifA upstream activating sequences located 91 bp from the transcription initiation site. The transcript initiated in P

nifA1

spans 5.1 kb and includes
nifA
and
nifB
genes. NifA from
Klebsiella pneumoniae
was able to activate transcription from P

nifA1

in a heterologous
Escherichia coli
system. In
R. leguminosarum
, the P

nifA1

promoter is essential for effective nitrogen fixation in symbiosis with peas. In its absence, partially efficient nitrogen-fixing nodules were produced, and the corresponding bacteroids exhibited only low levels of
nifA
gene expression. The basal level of
nifA
expression resulted from a promoter activity originating upstream of the
fixX-nifA
intergenic region and probably from an incomplete duplication of P

nifA1

located immediately upstream of
fixA
.
Transcription Regulation by the
Mycobacterium tuberculosis
Alternative Sigma Factor SigD and Its Role in Virulence
Authors: Raman Sahadevan , Hazra Rohan , Dascher Christopher C. , Husson Robert N. 
Published: September 2004

ABSTRACT

Mycobacterium tuberculosis
, an obligate mammalian pathogen, adapts to its host during the course of infection via the regulation of gene expression. Of the regulators of transcription that play a role in this response, several alternative sigma factors of
M. tuberculosis
have been shown to control gene expression in response to stresses, and some of these are required for virulence or persistence in vivo. For this study, we examined the role of the alternative sigma factor SigD in
M. tuberculosis
gene expression and virulence. Using microarray analysis, we identified several genes whose expression was altered in a strain with a
sigD
deletion. A small number of these genes, including
sigD
itself, the gene encoding the autocrine growth factor RpfC, and a gene of unknown function, Rv1815, appear to be directly regulated by this sigma factor. By identifying the in vivo promoters of these genes, we have determined a consensus promoter sequence that is putatively recognized by SigD. The expression of several genes encoding PE-PGRS proteins, part of a large family of related genes of unknown function, was significantly increased in the
sigD
mutant. We found that the expression of
sigD
is stable throughout log phase and stationary phase but that it declines rapidly with oxygen depletion. In a mouse infection model, the
sigD
mutant strain was attenuated, with differences in survival and the inflammatory response in the lung between mice infected with the mutant and those infected with the wild type.
Involvement of
exo5
in Production of Surface Polysaccharides in
Rhizobium leguminosarum
and Its Role in Nodulation of
Vicia sativa
subsp.
nigra
Authors: Laus Marc C. , Logman Trudy J. , van Brussel Anton A. N. , Carlson Russell W. , Azadi Parastoo , Gao Mu-Yun , Kijne Jan W. 
Published: September 2004

ABSTRACT

Analysis of two exopolysaccharide-deficient mutants of
Rhizobium leguminosarum
, RBL5808 and RBL5812, revealed independent Tn
5
transposon integrations in a single gene, designated
exo5
. As judged from structural and functional homology, this gene encodes a UDP-glucose dehydrogenase responsible for the oxidation of UDP-glucose to UDP-glucuronic acid. A mutation in
exo5
affects all glucuronic acid-containing polysaccharides and, consequently, all galacturonic acid-containing polysaccharides. Exo5-deficient rhizobia do not produce extracellular polysaccharide (EPS) or capsular polysaccharide (CPS), both of which contain glucuronic acid. Carbohydrate composition analysis and nuclear magnetic resonance studies demonstrated that EPS and CPS from the parent strain have very similar structures. Lipopolysaccharide (LPS) molecules produced by the mutant strains are deficient in galacturonic acid, which is normally present in the core and lipid A portions of the LPS. The sensitivity of
exo5
mutant rhizobia to hydrophobic compounds shows the involvement of the galacturonic acid residues in the outer membrane structure. Nodulation studies with
Vicia sativa
subsp.
nigra
showed that
exo5
mutant rhizobia are impaired in successful infection thread colonization. This is caused by strong agglutination of EPS-deficient bacteria in the root hair curl. Root infection could be restored by simultaneous inoculation with a Nod factor-defective strain which retained the ability to produce EPS and CPS. However, in this case colonization of the nodule tissue was impaired.
Coexistence ofWolbachiawithBuchnera aphidicolaand a Secondary Symbiont in the AphidCinara cedri
Authors: Gómez-Valero Laura , Soriano-Navarro Mario , Pérez-Brocal Vicente , Heddi Abdelaziz , Moya Andrés , García-Verdugo José Manuel , Latorre Amparo 
Published: September 2004

ABSTRACTIntracellular symbiosis is very common in the insect world. For the aphidCinara cedri, we have identified by electron microscopy three symbiotic bacteria that can be characterized by their different sizes, morphologies, and electrodensities. PCR amplification and sequencing of the 16S ribosomal DNA (rDNA) genes showed that, in addition to harboringBuchnera aphidicola, the primary endosymbiont of aphids,C. cedriharbors a secondary symbiont (S symbiont) that was previously found to be associated with aphids (PASS, or R type) and an α-proteobacterium that belongs to theWolbachiagenus. Using in situ hybridization with specific bacterial probes designed for symbiont 16S rDNA sequences, we have shown thatWolbachiawas represented by only a few minute bacteria surrounding the S symbionts. Moreover, the observedB. aphidicolaand the S symbionts had similar sizes and were housed in separate specific bacterial cells, the bacteriocytes. Interestingly, in contrast to the case for all aphids examined thus far, the S symbionts were shown to occupy a similarly sized or even larger bacteriocyte space thanB. aphidicola. These findings, along with the facts thatC. cedriharbors theB. aphidicolastrain with the smallest bacterial genome and that the S symbionts infect allCinaraspp. analyzed so far, suggest the possibility of bacterial replacement in these species.
Substrate Binding Analysis of the 23S rRNA Methyltransferase RrmJ
Authors: Hager Jutta , Staker Bart L. , Jakob Ursula 
Published: September 2004

ABSTRACT
The 23S rRNA methyltransferase RrmJ (FtsJ) is responsible for the 2′-O methylation of the universally conserved U2552 in the A loop of 23S rRNA. This 23S rRNA modification appears to be critical for ribosome stability, because the absence of functional RrmJ causes the cellular accumulation of the individual ribosomal subunits at the expense of the functional 70S ribosomes. To gain insight into the mechanism of substrate recognition for RrmJ, we performed extensive site-directed mutagenesis of the residues conserved in RrmJ and characterized the mutant proteins both in vivo and in vitro. We identified a positively charged, highly conserved ridge in RrmJ that appears to play a significant role in 23S rRNA binding and methylation. We provide a structural model of how the A loop of the 23S rRNA binds to RrmJ. Based on these modeling studies and the structure of the 50S ribosome, we propose a two-step model where the A loop undocks from the tightly packed 50S ribosomal subunit, allowing RrmJ to gain access to the substrate nucleotide U2552, and where U2552 undergoes base flipping, allowing the enzyme to methylate the 2′-O position of the ribose.
Importance of
Rhodospirillum rubrum
H
+
-Pyrophosphatase under Low-Energy Conditions
Authors: García-Contreras Rodolfo , Celis Heliodoro , Romero Irma 
Published: September 2004

ABSTRACT

The physiological role of the membrane-bound pyrophosphatase of
Rhodospirillum rubrum
was investigated by the characterization of a mutant strain. Comparisons of growth levels between the wild type and the mutant under different low-potential conditions and during transitions between different metabolisms indicate that this enzyme provides
R. rubrum
with an alternative energy source that is important for growth in low-energy states.
Major Role of NAD-Dependent Lactate Dehydrogenases in Aerobic Lactate Utilization in
Lactobacillus plantarum
during Early Stationary Phase
Authors: Goffin Philippe , Lorquet Frédérique , Kleerebezem Michiel , Hols Pascal 
Published: September 2004

ABSTRACT

NAD-independent lactate dehydrogenases are commonly thought to be responsible for lactate utilization during the stationary phase of aerobic growth in
Lactobacillus plantarum
. To substantiate this view, we constructed single and double knockout mutants for the corresponding genes,
loxD
and
loxL
. Lactate-to-acetate conversion was not impaired in these strains, while it was completely blocked in mutants deficient in NAD-dependent lactate dehydrogenase activities, encoded by the
ldhD
and
ldhL
genes. We conclude that NAD-dependent but not NAD-independent lactate dehydrogenases are involved in this process.
Recent Genetic Transfer between
Lactococcus lactis
and Enterobacteria
Authors: Bolotin Alexander , Quinquis Benoit , Sorokin Alexei , Ehrlich Dusko S. 
Published: September 2004

ABSTRACT

The genome sequence of
Lactococcus lactis
revealed that the
ycdB
gene was recently exchanged between lactococci and enterobacteria. The present study of
ycdB
orthologs suggests that
L. lactis
was probably the gene donor and reveals three instances of gene transfer to enterobacteria. Analysis of
ycdB
gene transfer between two
L. lactis
subspecies,
L. lactis
subsp.
lactis
and
L. lactis
subsp.
cremoris
, indicates that the gene can be mobilized, possibly by conjugation.
METHANE GAS EMISSIONS FROM LANDFILL: OPPORTUNITIES AND CONSTRAINTS — THE CASE OF AL-RUSSIFA CITY
Authors: MRAYYAN BASSAM 
Published: September 2004

The aim of this study was to illustrate the methane gas impacts on AL-Russifa region, Jordan, in addition to the opportunities and obstacles faced. AL-Russifa city suffers serious health and environmental problems as a result of the methane gas emissions from Al-Russifa Landfill. The uncontrolled methane emissions and the potential of collection, use for producing electricity and the existing activities that include the biogas plant and regulations were analyzed and recommendations presented. The required institutional management and social structure that promote the proper management of solid waste that affect methane emissions need to be advanced through technological exchanges and training programs. Improving the existing biogas project and the establishment of new ones can reduce green house gases while generating electricity; thus reducing Jordan's dependency on imported oil. The lack of financial, technical expertise and awareness among public and private sectors, in addition to the bureaucracy and the short time pay back phenomena are all considered as constraints for achieving such prosperous environmental projects. Establishing upgraded institutions will need to embrace improved capability to generate replicable projects that serve as a vehicle for solving pollution problems and promoting sustainable development.
Inhibition of Akt increases p27Kip1 levels and induces cell cycle arrest in anaplastic large cell lymphoma
Authors: Rassidakis George Z. , Feretzaki Marianna , Atwell Coralyn , Grammatikakis Ioannis , Lin Quan , Lai Raymond , Claret Francois-Xavier , Medeiros L. Jeffrey , Amin Hesham M. 
Published: September 2004

Abstract
Anaplastic large cell lymphoma (ALCL) is a highly proliferative neoplasm that frequently carries the t(2;5)(p23;q35) and aberrantly expresses nucleophosmin–anaplastic lymphoma kinase (NPM-ALK). Previously, NPM-ALK had been shown to activate the phosphatidylinositol 3 kinase (PI3K)/Akt pathway. As the cyclin-dependent kinase (CDK) inhibitor p27Kip1 (p27) is usually not expressed in ALCL, we hypothesized that activated Akt (pAkt) phosphorylates p27 resulting in increased p27 proteolysis and cell cycle progression. Here we demonstrate that inhibition of pAkt activity in ALCL decreases p27 phosphorylation and degradation, resulting in increased p27 levels and cell cycle arrest. Using immunohistochemistry, pAkt was detected in 24 (57%) of 42 ALCL tumors, including 8 (44%) of 18 ALK-positive tumors and 16 (67%) of 24 ALK-negative tumors, and was inversely correlated with p27 levels. The mean percentage of p27-positive tumor cells was 5% in the pAkt-positive group compared with 26% in the pAkt-negative group (P = .0076). These findings implicate that Akt activation promotes cell cycle progression through inactivation of p27 in ALCL.
An integrated 4249 marker FISH/RH map of the canine genome
Authors: Breen Matthew , Hitte Christophe , Lorentzen Travis D , Thomas Rachael , Cadieu Edouard , Sabacan Leah , Scott Allyson , Evanno Gwenaelle , Parker Heidi G , Kirkness Ewen F , Hudson Ruth , Guyon Richard , Mahairas Gregory G , Gelfenbeyn Boris , Fraser Claire M , André Catherine , Galibert Francis , Ostrander Elaine A 
Published: September 2004

Abstract
Background
The 156 breeds of dog recognized by the American Kennel Club offer a unique opportunity to map genes important in genetic variation. Each breed features a defining constellation of morphological and behavioral traits, often generated by deliberate crossing of closely related individuals, leading to a high rate of genetic disease in many breeds. Understanding the genetic basis of both phenotypic variation and disease susceptibility in the dog provides new ways in which to dissect the genetics of human health and biology.

Results
To facilitate both genetic mapping and cloning efforts, we have constructed an integrated canine genome map that is both dense and accurate. The resulting resource encompasses 4249 markers, and was constructed using the RHDF5000-2 whole genome radiation hybrid panel. The radiation hybrid (RH) map features a density of one marker every 900 Kb and contains 1760 bacterial artificial chromosome clones (BACs) localized to 1423 unique positions, 851 of which have also been mapped by fluorescence in situ hybridization (FISH). The two data sets show excellent concordance. Excluding the Y chromosome, the map features an RH/FISH mapped BAC every 3.5 Mb and an RH mapped BAC-end, on average, every 2 Mb. For 2233 markers, the orthologous human genes have been established, allowing the identification of 79 conserved segments (CS) between the dog and human genomes, dramatically extending the length of most previously described CS.

Conclusions
These results provide a necessary resource for the canine genome mapping community to undertake positional cloning experiments and provide new insights into the comparative canine-human genome maps.
Transformation and scattering activities of the receptor tyrosine kinase RON/Stk in rodent fibroblasts and lack of regulation by the jaagsiekte sheep retrovirus receptor, Hyal2
Authors: Miller A Dusty , Van Hoeven Neal S , Liu Shan-Lu 
Published: September 2004

Abstract
Background
The envelope (Env) protein of jaagsiekte sheep retrovirus (JSRV) can transform cells in culture and is likely to be the main factor responsible for lung cancer induction by JSRV in animals. A recent report indicates that the epithelial-cell transforming activity of JSRV Env depends on activation of the cell-surface receptor tyrosine kinase Mst1r (called RON for the human and Stk for the rodent orthologs). In the immortalized line of human epithelial cells used (BEAS-2B cells), the virus receptor Hyal2 was found to bind to and suppress the activity of RON. When Env was expressed it bound to Hyal2 causing its degradation, release of RON activity from Hyal2 suppression, and activation of pathways resulting in cell transformation.

Methods
Due to difficulty with reproducibility of the transformation assay in BEAS-2B cells, we have used more tractable rodent fibroblast models to further study Hyal2 modulation of RON/Stk transforming activity and potential effects of Hyal2 on RON/Stk activation by its natural ligand, macrophage stimulating protein (MSP).

Results
We did not detect transformation of NIH 3T3 cells by plasmids expressing RON or Stk, but did detect transformation of 208F rat fibroblasts by these plasmids at a very low rate. We were able to isolate 208F cell clones that expressed RON or Stk and that showed changes in morphology indicative of transformation. The parental 208F cells did not respond to MSP but 208F cells expressing RON or Stk showed obvious increases in scattering/transformation in response to MSP. Human Hyal2 had no effect on the basal or MSP-induced phenotypes of RON-expressing 208F cells, and human, mouse or rat Hyal2 had no effect on the basal or MSP-induced phenotypes of Stk-expressing 208F cells.

Conclusions
We have shown that RON or Stk expression in 208F rat fibroblasts results in a transformed phenotype that is enhanced by addition of the natural ligand for these proteins, MSP. Hyal2 does not directly modulate the basal or MSP-induced RON/Stk activity, although it is possible that adaptor proteins might mediate such signaling in other cell types.
High-dose ibuprofen therapy associated with esophageal ulceration after pneumonectomy in a patient with cystic fibrosis: a case report
Authors: Mackey Jennifer E , Anbar Ran D 
Published: September 2004

Abstract
Background
Lung disease in patients with cystic fibrosis is thought to develop as a result of airway inflammation, infection, and obstruction. Pulmonary therapies for cystic fibrosis that reduce airway inflammation include corticosteroids, rhDNase, antibiotics, and high-dose ibuprofen. Despite evidence that high-dose ibuprofen slows the progression of lung disease in patients with cystic fibrosis, many clinicians have chosen not to use this therapy because of concerns regarding potential side effects, especially gastrointestinal bleeding. However, studies have shown a low incidence of gastrointestinal ulceration and bleeding in patients with cystic fibrosis who have been treated with high-dose ibuprofen.

Case presentation
The described case illustrates a life-threatening upper gastrointestinal bleed that may have resulted from high-dose ibuprofen therapy in a patient with CF who had undergone a pneumonectomy. Mediastinal shift post-pneumonectomy distorted the patient's esophageal anatomy and may have caused decreased esophageal motility, which led to prolonged contact of the ibuprofen with the esophagus. The concentrated effect of the ibuprofen, as well as its systemic effects, probably contributed to the occurrence of the bleed in this patient.

Conclusions
This report demonstrates that gastrointestinal tract anatomical abnormalities or dysmotility may be contraindications for therapy with high-dose ibuprofen in patients with cystic fibrosis.
Validity and reproducibility of an interviewer-administered food frequency questionnaire for healthy French-Canadian men and women
Authors: Goulet Julie , Nadeau Geneviève , Lapointe Annie , Lamarche Benoît , Lemieux Simone 
Published: September 2004

Abstract
Objective
To evaluate the validity (study 1) and the reproducibility (study 2) of an interviewer-administered food frequency questionnaire (FFQ).

Method
The FFQ was designed at Laval University and contains 91 items and 33 subquestions. Study 1: The FFQ was compared against a 3-day food record (2 week-days and 1 weekend-day), at week 0, 6 and 12 of a nutritional intervention. Study 2: In order to evaluate the reproducibility of the FFQ, 2 registered dietitians administered the FFQ 4-weeks apart among subjects who were not part of the nutritional intervention.

Results
Study 1: Mean values for intake of most nutrients assessed by the FFQ and by the 3-day food record were not statistically different. Energy-adjusted correlation coefficients for major macronutrients ranged from 0.36 for proteins to 0.60 for carbohydrates (p ≤ 0.01). Agreement analysis revealed that on average, 35% of the subjects were classified in the same quartile when nutrients were assessed by either the 3-day food record or the FFQ. Study 2: Significant associations were observed between dietary measurements derived from the two FFQs administered 4 weeks apart. Correlation coefficients for the reproducibility of macronutrients ranged from 0.66 for carbohydrates to 0.83 for lipids after energy adjustment. On average, 46% of the subjects were classified in the same quartile when nutrient intakes were assessed by either FFQ.

Conclusion
These data indicated that the FFQ developed has a good validity and is reproducible.
Anogenital distance in human male and female newborns: a descriptive, cross-sectional study
Authors: Salazar-Martinez Eduardo , Romano-Riquer Patricia , Yanez-Marquez Edith , Longnecker Matthew P , Hernandez-Avila Mauricio 
Published: September 2004

Abstract
Background
In animal studies of the effects of hormonally active agents, measurement of anogenital distance (AGD) is now routine, and serves as a bioassay of fetal androgen action. Although measurement of AGD in humans has been discussed in the literature, to our knowledge it has been measured formally in only two descriptive studies of females. Because AGD has been an easy-to-measure, sensitive outcome in animals studies, we developed and implemented an anthropometric protocol for measurement of AGD in human males as well as females.

Methods
We first evaluated the reliability of the AGD measures in 20 subjects. Then measurements were taken on an additional 87 newborns (42 females, 45 males). All subjects were from Morelos, Mexico.

Results
The reliability (Pearson r) of the AGD measure was, for females 0.50, and for males, 0.64. The between-subject variation in AGD, however, was much greater than the variation due to measurement error. The AGD measure was about two-fold greater in males (mean, 22 mm) than in females (mean, 11 mm), and there was little overlap in the distributions for males and females.

Conclusion
The sexual dimorphism of AGD in humans comprises prima facie evidence that this outcome may respond to in utero exposure to hormonally active agents.
Prevention of non-communicable diseases in Pakistan: an integrated partnership-based model
Authors: Nishtar Sania 
Published: September 2004

AbstractDevelopment and implementation of non-communicable disease (NCD) prevention polices in the developing countries is a multidimensional challenge. This article highlights the evolution of a strategic approach in Pakistan. The model is evidence-based and encompasses a concerted and integrated approach to NCDs. It has been modelled to impact a set of indicators through the combination of a range of actions capitalizing on the strengths of a public-private partnership. The paper highlights the merits and limitations of this approach. The experience outlines a number of clear imperatives for fostering an enabling environment for integrated NCD prevention public health models, which involve roles played by a range of stakeholders. It also highlights the value that such partnership arrangements bring in facilitating the mission and mandates of ministries of health, international agencies with global health mandates, and the non-profit private sector. The experience is of relevance to developing countries that have NCD programs running and those that need to develop them. It provides an empirical basis for enhancing the performance of the health system by fostering partnerships within integrated evidence-based models and permits an analysis of health systems models built on shared responsibility for the purpose of providing sustainable health outcomes.