bluuebunny/crossref_metadata_2025_split huggingface dataset:
CDKN2A promoter methylation is related to the tumor location and histological subtype and associated with Helicobacter pylori flaA(+) strains in gastric adenocarcinomas
Authors: ALVES MARKÊNIA KÉLIA SANTOS , LIMA VALESKA PORTELA , FERRASI ADRIANA CAMARGO , RODRIGUES MARIA APARECIDA , DE MOURA CAMPOS PARDINI MARIA INÊS , RABENHORST SILVIA HELENA BAREM 
Published: February 2010

Alves MKS, Lima VP, Ferrasi AC, Rodrigues MA, de Moura Campos Pardini MI, Rabenhorst SHB. CDKN2A promoter methylation is related to the tumor location and histological subtype and associated with Helicobacter pylori flaA(+) strains in gastric adenocarcinomas. APMIS 2010; 118: 297–307.Promoter hypermethylation of CDKN2A (p16INK4A protein) is the main mechanism of gene inactivation. However, its association with Helicobacter pylori infection is a controversial issue. Therefore, we examined a series of gastric adenocarcinomas to assess the association between p16INK4A inactivation and H. pylori genotype (vacA, cagA, cagE, virB11 and flaA) according to the location and histological subtype of the tumors. p16INK4A expression and CDKN2A promoter methylation were found in 77 gastric adenocarcinoma samples by immunohistochemistry and methylation‐specific PCR, respectively. Helicobacter pylori infection and genotype were determined by PCR. A strong negative correlation between immunostaining and CDKN2A promoter region methylation was found. In diffuse subtype tumors, the inactivation of p16INK4A by promoter methylation was unique in noncardia tumors (p = 0.022). In addition, H. pylori‐bearing flaA was associated with non‐methylation tumors (p = 0.008) and H. pylori strain bearing cagA or vacAs1m1 genes but without flaA was associated with methylated tumors (p = 0.022 and 0.003, respectively). Inactivation of p16INK4A in intestinal and diffuse subtypes showed distinct carcinogenic pathways, depending on the tumor location. Moreover, the process of methylation of the CDKN2A promoter seems to depend on the H. pylori genotype. The present data suggest that there is a differential influence and relevance of H. pylori genotype in gastric cancer development.
NURSE–PATIENT COMMUNICATION WHILE PERFORMING HOME DIALYSIS: THE PATIENTS’ PERCEPTIONS
Authors: Sadala Maria Lúcia Araújo , Miranda Marcelo Guimarães , Lorençon Marisa , De Campos Pereira Estela Pacheco 
Published: February 2010

SUMMARYThis study aimed at describing patients’ perception of their communication with nurses when performing home dialysis. Data were collected from interviews guided by the question: “What is communication like, between you and nurses, during home dialysis treatment?” Results show participants’ perception of treatment during home peritoneal dialysis [Continuous ambulatory peritoneal dialysis (CAPD)]; relationship with nurses and family and the effects of treatment on one's existence. Patients can be self‐caring and they learn to value the autonomy in their own care. However, some are unable to assume the responsibility for self‐care. It was discovered that the connotation of “inspection” that some participants attributed to the nurse's visits, led to an alienation from the education process in the CAPD education. Findings suggest that effective communication and the development of the relationship of a working partnership with patients is crucial. Improvement in the nurses’ communication, aiming at adapting it to the characteristics, limitations and specific needs of each patient, is significant for achieving better outcomes.
WHO CARES…………FOR THE CARERS?
Authors: Kelly Mike 
Published: February 2010

SUMMARYThis paper is about carers; a family member or members who provide unpaid care to a loved one with a chronic condition. Caring for someone who is chronically ill permeates every aspect of life. Dreams may be shattered, plans for the future may have to be radically altered or shelved permanently. Psychological stress is common, but many carers find it difficult to access services. Resources are there to support the person diagnosed, or, on treatment. What resources are directed to the care and support of carers? Drawing on relevant literature and my own clinical experience I give examples of the demands, often unrelenting, and difficulties carers face. I suggest some interventions that can support and facilitate carers, enabling them to continue their role in a healthy, life giving manner.
EXPLORING SYMPTOMS IN PATIENTS MANAGED WITHOUT DIALYSIS: A QUALITATIVE RESEARCH STUDY
Authors: Noble Helen , Meyer Professor Julienne , Bridge Dr Jackie , Johnson Dr Barbara , Kelly Dr Daniel 
Published: February 2010

SUMMARYLittle is known about the prevalence and burden of symptoms in patients managed without dialysis. This study was the result of a larger study exploring the experiences of 30 such patients and their trajectories to death. Data were analysed relating to symptoms once the patients had been referred to a Renal Supportive Care Service based in the East End of London, UK. A high symptom prevalence was found with 30 different symptoms reported at first consultation. Widely reported symptoms impacting on daily living included breathlessness, oedema, pruritus, nausea and vomiting and pain. Findings indicate that as symptoms escalate and death approaches, some symptoms, such as fluid overload and lethargy become difficult to treat indicating that death is close. This new knowledge can help staff as they attempt to determine when the end of life is approaching in order to support and care for patients appropriately. This paper highlights a need for effective identification and management of symptoms as they arise and further exploration of the effects of these symptoms on daily living.
Environmental Determinants of and Impact on Childhood Asthma by the Bacterial Community in Household Dust
Authors: Maier Raina M. , Palmer Michael W. , Andersen Gary L. , Halonen Marilyn J. , Josephson Karen C. , Maier Robert S. , Martinez Fernando D. , Neilson Julia W. , Stern Debra A. , Vercelli Donata , Wright Anne L. 
Published: February 2010

ABSTRACT

Asthma increased dramatically in the last decades of the 20th century and is representative of chronic diseases that have been linked to altered microbial exposure and immune responses. Here we evaluate the effects of environmental exposures typically associated with asthma protection or risk on the microbial community structure of household dust (dogs, cats, and day care). PCR-denaturing gradient gel analysis (PCR-DGGE) demonstrated that the bacterial community structure in house dust is significantly impacted by the presence of dogs or cats in the home (
P
= 0.0190 and 0.0029, respectively) and by whether or not children attend day care (
P
= 0.0037). In addition, significant differences in the dust bacterial community were associated with asthma outcomes in young children, including wheezing (
P
= 0.0103) and specific IgE (
P
= 0.0184). Our findings suggest that specific bacterial populations within the community are associated with either risk or protection from asthma.
Identification and Analysis of the Biosynthetic Gene Cluster Encoding the Thiopeptide Antibiotic Cyclothiazomycin in
Streptomyces hygroscopicus
10-22
Authors: Wang Jiang , Yu Yi , Tang Kexuan , Liu Wen , He Xinyi , Huang Xi , Deng Zixin 
Published: February 2010

ABSTRACT

Thiopeptide antibiotics are an important class of natural products resulting from posttranslational modifications of ribosomally synthesized peptides. Cyclothiazomycin is a typical thiopeptide antibiotic that has a unique bridged macrocyclic structure derived from an 18-amino-acid structural peptide. Here we reported cloning, sequencing, and heterologous expression of the cyclothiazomycin biosynthetic gene cluster from
Streptomyces hygroscopicus
10-22. Remarkably, successful heterologous expression of a 22.7-kb gene cluster in
Streptomyces lividans
1326 suggested that there is a minimum set of 15 open reading frames that includes all of the functional genes required for cyclothiazomycin production. Six genes of these genes,
cltBCDEFG
flanking the structural gene
cltA
, were predicted to encode the enzymes required for the main framework of cyclothiazomycin, and two enzymes encoded by a putative operon,
cltMN
, were hypothesized to participate in the tailoring step to generate the tertiary thioether, leading to the final cyclization of the bridged macrocyclic structure. This rigorous bioinformatics analysis based on heterologous expression of cyclothiazomycin resulted in an ideal biosynthetic model for us to understand the biosynthesis of thiopeptides.
Experimental Adaptation of
Burkholderia cenocepacia
to Onion Medium Reduces Host Range
Authors: Ellis Crystal N. , Cooper Vaughn S. 
Published: February 2010

ABSTRACT

It is unclear whether adaptation to a new host typically broadens or compromises host range, yet the answer bears on the fate of emergent pathogens and symbionts. We investigated this dynamic using a soil isolate of
Burkholderia cenocepacia
, a species that normally inhabits the rhizosphere, is related to the onion pathogen
B. cepacia
, and can infect the lungs of cystic fibrosis patients. We hypothesized that adaptation of
B. cenocepacia
to a novel host would compromise fitness and virulence in alternative hosts. We modeled adaptation to a specific host by experimentally evolving 12 populations of
B. cenocepacia
in liquid medium composed of macerated onion tissue for 1,000 generations. The mean fitness of all populations increased by 78% relative to the ancestor, but significant variation among lines was observed. Populations also varied in several phenotypes related to host association, including motility, biofilm formation, and quorum-sensing function. Together, these results suggest that each population adapted by fixing different sets of adaptive mutations. However, this adaptation was consistently accompanied by a loss of pathogenicity to the nematode
Caenorhabditis elegans
; by 500 generations most populations became unable to kill nematodes. In conclusion, we observed a narrowing of host range as a consequence of prolonged adaptation to an environment simulating a specific host, and we suggest that emergent pathogens may face similar consequences if they become host-restricted.
Characterization of Environmentally Persistent
Escherichia coli
Isolates Leached from an Irish Soil
Authors: Brennan Fiona P. , Abram Florence , Chinalia Fabio A. , Richards Karl G. , O'Flaherty Vincent 
Published: February 2010

ABSTRACT

Soils are typically considered to be suboptimal environments for enteric organisms, but there is increasing evidence that
Escherichia coli
populations can become resident in soil under favorable conditions. Previous work reported the growth of autochthonous
E. coli
in a maritime temperate Luvic Stagnosol soil, and this study aimed to characterize, by molecular and physiological means, the genetic diversity and physiology of environmentally persistent
E. coli
isolates leached from the soil. Molecular analysis (16S rRNA sequencing, enterobacterial repetitive intergenic consensus PCR, pulsed-field gel electrophoresis, and a multiplex PCR method) established the genetic diversity of the isolates (
n
= 7), while physiological methods determined the metabolic capability and environmental fitness of the isolates, relative to those of laboratory strains, under the conditions tested. Genotypic analysis indicated that the leached isolates do not form a single genetic grouping but that multiple genotypic groups are capable of surviving and proliferating in this environment. In physiological studies, environmental isolates grew well across a broad range of temperatures and media, in comparison with the growth of laboratory strains. These findings suggest that certain
E. coli
strains may have the ability to colonize and adapt to soil conditions. The resulting lack of fecal specificity has implications for the use of
E. coli
as an indicator of fecal pollution in the environment.
Role ofGeobacter sulfurreducensOuter Surfacec-Type Cytochromes in Reduction of Soil Humic Acid and Anthraquinone-2,6-Disulfonate
Authors: Voordeckers James W. , Kim Byoung-Chan , Izallalen Mounir , Lovley Derek R. 
Published: February 2010

ABSTRACTDeleting individual genes for outer surfacec-type cytochromes inGeobacter sulfurreducenspartially inhibited the reduction of humic substances and anthraquinone-2,6,-disulfonate. Complete inhibition was obtained only when five of these genes were simultaneously deleted, suggesting that diverse outer surface cytochromes can contribute to the reduction of humic substances and other extracellular quinones.
Fermentation of Glycerol to Succinate by Metabolically Engineered Strains of
Escherichia coli
Authors: Zhang Xueli , Shanmugam K. T. , Ingram Lonnie O. 
Published: February 2010

ABSTRACT

The fermentative metabolism of
Escherichia coli
was reengineered to efficiently convert glycerol to succinate under anaerobic conditions without the use of foreign genes. Formate and ethanol were the dominant fermentation products from glycerol in wild-type
Escherichia coli
ATCC 8739, followed by succinate and acetate. Inactivation of pyruvate formate-lyase (
pflB
) in the wild-type strain eliminated the production of formate and ethanol and reduced the production of acetate. However, this deletion slowed growth and decreased cell yields due to either insufficient energy production or insufficient levels of electron acceptors. Reversing the direction of the gluconeogenic phosphoenolpyruvate carboxykinase reaction offered an approach to solve both problems, conserving energy as an additional ATP and increasing the pool of electron acceptors (fumarate and malate). Recruiting this enzyme through a promoter mutation (
pck*
) to increase expression also increased the rate of growth, cell yield, and succinate production. Presumably, the high NADH/NAD
+
ratio served to establish the direction of carbon flow. Additional mutations were also beneficial. Glycerol dehydrogenase and the phosphotransferase-dependent dihydroxyacetone kinase are regarded as the primary route for glycerol metabolism under anaerobic conditions. However, this is not true for succinate production by engineered strains. Deletion of the
ptsI
gene or any other gene essential for the phosphotranferase system was found to increase succinate yield. Deletion of
pflB
in this background provided a further increase in the succinate yield. Together, these three core mutations (
pck
*,
ptsI
, and
pflB
) effectively redirected carbon flow from glycerol to succinate at 80% of the maximum theoretical yield during anaerobic fermentation in mineral salts medium.
The Second Extracellular Loop of Pore-Forming Subunits of ATP-Binding Cassette Transporters for Basic Amino Acids Plays a Crucial Role in Interaction with the Cognate Solute Binding Protein(s)
Authors: Eckey Viola , Weidlich Daniela , Landmesser Heidi , Bergmann Ulf , Schneider Erwin 
Published: February 2010

ABSTRACT

In the thermophile
Geobacillus stearothermophilus
, the uptake of basic amino acids is mediated by an ABC transporter composed of the substrate binding protein (receptor) ArtJ and a homodimer each of the pore-forming subunit, ArtM, and the nucleotide-binding subunit, ArtP. We recently identified two putative binding sites in ArtJ that might interact with the Art(MP)
2
complex, thereby initiating the transport cycle (A. Vahedi-Faridi et al., J. Mol. Biol. 375:448-459, 2008). Here we investigated the contribution of charged amino acid residues in the second extracellular loop of ArtM to contact with ArtJ. Our results demonstrate a crucial role for residues K177, R185, and E188, since mutations to oppositely charged amino acids or glutamine led to a complete loss of ArtJ-stimulated ATPase activity of the complex variants in proteoliposomes. The defects could not be suppressed by ArtJ variants carrying mutations in site I (K39E and K152E) or II (E163K and D170K), suggesting a more complex interplay than that by a single salt bridge. These findings were supported by cross-linking assays demonstrating physical proximity between ArtJ(N166C) and ArtM(E182C). The importance of positively charged residues for receptor-transporter interaction was underscored by mutational analysis of the closely related transporter HisJ/LAO-HisQMP
2
of
Salmonella enterica
serovar Typhimurium. While transporter variants with mutated positively charged residues in HisQ displayed residual ATPase activities, corresponding mutants of HisM could no longer be stimulated by HisJ/LAO. Interestingly, the ATPase activity of the HisQM(K187E)P
2
variant was inhibited by
l
- and
d
-histidine in detergent, suggesting a role of the residue in preventing free histidine from gaining access to the substrate binding site within HisQM.
Role of FlgT in Anchoring the Flagellum of
Vibrio cholerae
Authors: Martinez Raquel M. , Jude Brooke A. , Kirn Thomas J. , Skorupski Karen , Taylor Ronald K. 
Published: February 2010

ABSTRACT

Flagellar motility has long been regarded as an important virulence factor. In
Vibrio cholerae
, the single polar flagellum is essential for motility as well as for proper attachment and colonization. In this study, we demonstrate that the novel flagellar protein FlgT is involved in anchoring the flagellum to the
V. cholerae
cell. A screen for novel colonization factors by use of Tn
phoA
mutagenesis identified
flgT
. An in-frame deletion of
flgT
established that FlgT is required for attachment, colonization, and motility. Transmission electron microscopy revealed that while the
flgT
mutant is capable of assembling a phenotypically normal flagellum, the
flgT
population is mostly aflagellate compared to the wild-type population. Further analyses indicated that the flagellum of the
flgT
mutant is released into the culture supernatant from the cell upon completion of assembly. Additionally, hook basal body complexes appear to be released along with the filament. These results indicate that FlgT functions to stabilize the flagellar apparatus at the pole of the cell.
Di-Adenosine Tetraphosphate (Ap4A) Metabolism Impacts Biofilm Formation byPseudomonas fluorescensvia Modulation of c-di-GMP-Dependent Pathways
Authors: Monds Russell D. , Newell Peter D. , Wagner Jeffrey C. , Schwartzman Julia A. , Lu Wenyun , Rabinowitz Joshua D. , O'Toole George A. 
Published: February 2010

ABSTRACTDinucleoside tetraphosphates are common constituents of the cell and are thought to play diverse biological roles in organisms ranging from bacteria to humans. In this study we characterized two independent mechanisms by which di-adenosine tetraphosphate (Ap4A) metabolism impacts biofilm formation byPseudomonas fluorescens. Null mutations inapaH, the gene encoding nucleoside tetraphosphate hydrolase, resulted in a marked increase in the cellular level of Ap4A. Concomitant with this increase, Pho regulon activation in low-inorganic-phosphate (Pi) conditions was severely compromised. As a consequence, anapaHmutant was not sensitive to Pho regulon-dependent inhibition of biofilm formation. In addition, we characterized a Pho-independent role for Ap4A metabolism in regulation of biofilm formation. In Pi-replete conditions Ap4A metabolism was found to impact expression and localization of LapA, the major adhesin regulating surface commitment byP. fluorescens. Increases in the level of c-di-GMP in theapaHmutant provided a likely explanation for increased localization of LapA to the outer membrane in response to elevated Ap4A concentrations. Increased levels of c-di-GMP in theapaHmutant were associated with increases in the level of GTP, suggesting that elevated levels of Ap4A may promotede novopurine biosynthesis. In support of this suggestion, supplementation with adenine could partially suppress the biofilm and c-di-GMP phenotypes of theapaHmutant. We hypothesize that changes in the substrate (GTP) concentration mediated by altered flux through nucleotide biosynthetic pathways may be a significant point of regulation for c-di-GMP biosynthesis and regulation of biofilm formation.
Central Role of the Early Colonizer
Veillonella
sp. in Establishing Multispecies Biofilm Communities with Initial, Middle, and Late Colonizers of Enamel
Authors: Periasamy Saravanan , Kolenbrander Paul E. 
Published: February 2010

ABSTRACT

Human dental biofilm communities comprise several species, which can interact cooperatively or competitively. Bacterial interactions influence biofilm formation, metabolic changes, and physiological function of the community. Lactic acid, a common metabolite of oral bacteria, was measured in the flow cell effluent of one-, two- and three-species communities growing on saliva as the sole nutritional source. We investigated single-species and multispecies colonization by using known initial, early, middle, and late colonizers of enamel. Fluorescent-antibody staining and image analysis were used to quantify the biomass in saliva-fed flow cells. Of six species tested, only the initial colonizer
Actinomyces oris
exhibited significant growth. The initial colonizer
Streptococcus oralis
produced lactic acid but showed no significant growth. The early colonizer
Veillonella
sp. utilized lactic acid in two- and three-species biofilm communities. The biovolumes of all two-species biofilms increased when
Veillonella
sp. was present as one of the partners, indicating that this early colonizer promotes mutualistic community development. All three-species combinations exhibited enhanced growth except one, i.e.,
A. oris
,
Veillonella
sp., and the middle colonizer
Porphyromonas gingivalis
, indicating specificity among three-species communities. Further specificity was seen when
Fusobacterium nucleatum
(a middle colonizer),
Aggregatibacter actinomycetemcomitans
(a late colonizer), and
P. gingivalis
did not grow with
S. oralis
in two-species biofilms, but inclusion of
Veillonella
sp. resulted in growth of all three-species combinations. We propose that commensal veillonellae use lactic acid for growth in saliva and that they communicate metabolically with initial, early, middle, and late colonizers to establish multispecies communities on enamel.
Analysis of Protein Expression Regulated by theHelicobacter pyloriArsRS Two-Component Signal Transduction System
Authors: Loh John T. , Gupta Shobhana S. , Friedman David B. , Krezel Andrzej M. , Cover Timothy L. 
Published: February 2010

ABSTRACTPrevious studies have shown that theHelicobacter pyloriArsRS two-component signal transduction system contributes to acid-responsive gene expression. To identify additional members of the ArsRS regulon and further investigate the regulatory role of the ArsRS system, we analyzed protein expression in wild-type andarsSnull mutant strains. Numerous proteins were differentially expressed in anarsSmutant strain compared to a wild-type strain when the bacteria were cultured at pH 5.0 and also when they were cultured at pH 7.0. Genes encoding 14 of these proteins were directly regulated by the ArsRS system, based on observed binding of ArsR to the relevant promoter regions. The ArsRS-regulated proteins identified in this study contribute to acid resistance (urease and amidase), acetone metabolism (acetone carboxylase), resistance to oxidative stress (thioredoxin reductase), quorum sensing (Pfs), and several other functions. These results provide further definition of the ArsRS regulon and underscore the importance of the ArsRS system in regulating expression ofH. pyloriproteins during bacterial growth at both neutral pH and acidic pH.