bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and analysis of in planta expressed genes of Magnaporthe oryzae
Authors: Kim Soonok , Park Jongsun , Park Sook-Young , Mitchell Thomas K , Lee Yong-Hwan 
Published: March 2010

AbstractBackgroundInfection of plants by pathogens and the subsequent disease development involves substantial changes in the biochemistry and physiology of both partners. Analysis of genes that are expressed during these interactions represents a powerful strategy to obtain insights into the molecular events underlying these changes. We have employed expressed sequence tag (EST) analysis to identify rice genes involved in defense responses against infection by the blast fungusMagnaporthe oryzaeand fungal genes involved in infectious growth within the host during a compatible interaction.ResultsA cDNA library was constructed with RNA from rice leaves (Oryza sativacv. Hwacheong) infected withM. oryzaestrain KJ201. To enrich for fungal genes, subtraction library using PCR-based suppression subtractive hybridization was constructed with RNA from infected rice leaves as a tester and that from uninfected rice leaves as the driver. A total of 4,148 clones from two libraries were sequenced to generate 2,302 non-redundant ESTs. Of these, 712 and 1,562 ESTs could be identified to encode fungal and rice genes, respectively. To predict gene function, Gene Ontology (GO) analysis was applied, with 31% and 32% of rice and fungal ESTs being assigned to GO terms, respectively. One hundred uniESTs were found to be specific to fungal infection EST. More than 80 full-length fungal cDNA sequences were used to validateab initioannotated gene model ofM. oryzaegenome sequence.ConclusionThis study shows the power of ESTs to refine genome annotation and functional characterization. Results of this work have advanced our understanding of the molecular mechanisms underpinning fungal-plant interactions and formed the basis for new hypothesis.
Genome dynamics of Bartonella grahamii in micro-populations of woodland rodents
Authors: Berglund Eva C , Ehrenborg Christian , Vinnere Pettersson Olga , Granberg Fredrik , Näslund Kristina , Holmberg Martin , Andersson Siv GE 
Published: March 2010

Abstract

Background
Rodents represent a high-risk reservoir for the emergence of new human pathogens. The recent completion of the 2.3 Mb genome of Bartonella grahamii, one of the most prevalent blood-borne bacteria in wild rodents, revealed a higher abundance of genes for host-cell interaction systems than in the genomes of closely related human pathogens. The sequence variability within the global B. grahamii population was recently investigated by multi locus sequence typing, but no study on the variability of putative host-cell interaction systems has been performed.

Results
To study the population dynamics of B. grahamii, we analyzed the genomic diversity on a whole-genome scale of 27 B. grahamii strains isolated from four different species of wild rodents in three geographic locations separated by less than 30 km. Even using highly variable spacer regions, only 3 sequence types were identified. This low sequence diversity contrasted with a high variability in genome content. Microarray comparative genome hybridizations identified genes for outer surface proteins, including a repeated region containing the fha gene for filamentous hemaggluttinin and a plasmid that encodes a type IV secretion system, as the most variable. The estimated generation times in liquid culture medium for a subset of strains ranged from 5 to 22 hours, but did not correlate with sequence type or presence/absence patterns of the fha gene or the plasmid.

Conclusion
Our study has revealed a geographic microstructure of B. grahamii in wild rodents. Despite near-identity in nucleotide sequence, major differences were observed in gene presence/absence patterns that did not segregate with host species. This suggests that genetically similar strains can infect a range of different hosts.
Chemogenomic and transcriptome analysis identifies mode of action of the chemosensitizing agent CTBT (7-chlorotetrazolo[5,1-c]benzo[1,2,4]triazine)
Authors: Batova Monika , Klobucnikova Vlasta , Oblasova Zuzana , Gregan Juraj , Zahradnik Pavol , Hapala Ivan , Subik Julius , Schüller Christoph 
Published: March 2010

Abstract

Background
CTBT (7-chlorotetrazolo [5,1-c]benzo[1,2,4]triazine) increases efficacy of commonly used antifungal agents by an unknown mechanism. It increases the susceptibility of Saccharomyces cerevisiae, Candida albicans and Candida glabrata cells to cycloheximide, 5-fluorocytosine and azole antimycotic drugs. Here we elucidate CTBT mode of action with a combination of systematic genetic and transcriptome analysis.

Results
To identify the cellular processes affected by CTBT, we screened the systematic haploid deletion mutant collection for CTBT sensitive mutants. We identified 169 hypersensitive deletion mutants. The deleted genes encode proteins mainly involved in mitochondrial functions, DNA repair, transcription and chromatin remodeling, and oxidative stress response. We found that the susceptibility of yeast cells to CTBT depends on molecular oxygen. Transcriptome analysis of the immediate early response to CTBT revealed rapid induction of oxidant and stress response defense genes. Many of these genes depend on the transcription factors Yap1 and Cin5. Yap1 accumulates rapidly in the nucleus in CTBT treated cells suggesting acute oxidative stress. Moreover, molecular calculations supported a superoxide generating activity of CTBT. Superoxide production in vivo by CTBT was found associated to mitochondria as indicated by oxidation of MitoSOX Red.

Conclusion
We conclude that CTBT causes intracellular superoxide production and oxidative stress in fungal cells and is thus enhancing antimycotic drug effects by a secondary stress.
Dynamics of peptidergic secretory granule transport are regulated by neuronal stimulation
Authors: Sobota Jacqueline A , Mohler William A , Cowan Ann E , Eipper Betty A , Mains Richard E 
Published: March 2010

Abstract

Background
Peptidergic neurons store and secrete the contents of large dense core vesicles (LDCVs) from axon terminals and from dendrites. Secretion of peptides requires a highly regulated exocytotic mechanism, plus coordinated synthesis and transport of LDCVs to their sites of release. Although these trafficking events are critical to function, little is known regarding the dynamic behavior of LDCVs and the mechanisms by which their transport is regulated. Sensory neurons also package opiate receptors in peptide-containing LDCVs, which is thought to be important in pain sensation. Since peptide granules cannot be refilled locally after their contents are secreted, it is particularly important to understand how neurons support regulated release of peptides.

Results
A vector encoding soluble peptidylglycine α-hydroxylating monooxygenase fused to green fluorescent protein was constructed to address these questions in cultured primary peptidergic neurons of the trigeminal ganglion using time lapse confocal microscopy. The time course of release differs with secretagogue; the secretory response to depolarization with K+ is rapid and terminates within 15 minutes, while phorbol ester stimulation of secretion is maintained over a longer period. The data demonstrate fundamental differences between LDCV dynamics in axons and growth cones under basal conditions.

Conclusions
Under basal conditions, LDCVs move faster away from the soma than toward the soma, but fewer LDCVs travel anterograde than retrograde. Stimulation decreased average anterograde velocity and increases granule pausing. Data from antibody uptake, quantification of enzyme secretion and appearance of pHluorin fluorescence demonstrate distributed release of peptides all along the axon, not just at terminals.
Hypervariable intronic region in NCX1 is enriched in short insertion-deletion polymorphisms and showed association with cardiovascular traits
Authors: Kepp Katrin , Org Elin , Sõber Siim , Kelgo Piret , Viigimaa Margus , Veldre Gudrun , Tõnisson Neeme , Juhanson Peeter , Putku Margus , Kindmark Andreas , Kožich Viktor , Laan Maris 
Published: March 2010

Abstract

Background
Conserved non-coding regions (CNR) have been shown to harbor gene expression regulatory elements. Genetic variations in these regions may potentially contribute to complex disease susceptibility.

Methods
We targeted CNRs of cardiovascular disease (CVD) candidate gene, Na(+)-Ca(2+) exchanger (NCX1) with polymorphism screening among CVD patients (n = 46) using DHPLC technology. The flanking region (348 bp) of the 14 bp indel in intron 2 was further genotyped by DGGE assay in two Eastern-European CVD samples: essential hypertension (HYPEST; 470 cases, 652 controls) and coronary artery disease, CAD (CADCZ; 257 cases, controls 413). Genotype-phenotype associations were tested by regression analysis implemented in PLINK. Alignments of primate sequences were performed by ClustalW2.

Results
Nine of the identified NCX1 variants were either singletons or targeted by commercial platforms. The 14 bp intronic indel (rs11274804) was represented with substantial frequency in HYPEST (6.82%) and CADCZ (14.58%). Genotyping in Eastern-Europeans (n = 1792) revealed hypervariable nature of this locus, represented by seven alternative alleles. The alignments of human-chimpanzee-macaque sequences showed that the major human variant (allele frequency 90.45%) was actually a human-specific deletion compared to other primates. In humans, this deletion was surrounded by other short (5-43 bp) deletion variants and a duplication (40 bp) polymorphism possessing overlapping breakpoints. This indicates a potential indel hotspot, triggered by the initial deletion in human lineage. An association was detected between the carrier status of 14 bp indel ancestral allele and CAD (P = 0.0016, OR = 2.02; Bonferroni significance level alpha = 0.0045), but not with hypertension. The risk for the CAD development was even higher among the patients additionally diagnosed with metabolic syndrome (P = 0.0014, OR = 2.34). Consistent with the effect on metabolic processes, suggestive evidence for the association with heart rate, serum triglyceride and LDL levels was detected (P = 0.04).

Conclusions
Compared to SNPs targeted by large number of locus-specific and genome-wide assays, considerably less attention has been paid to short indel variants in the human genome. The data of genome dynamics, mutation rate and population genetics of short indels, as well as their impact on gene expressional profile and human disease susceptibility is limited. The characterization of NCX1 intronic hypervariable non-coding region enriched in human-specific indel variants contributes to this gap of knowledge.
The height-, weight-, and BMI-for-age of Polish school-aged children and adolescents relative to international and local growth references
Authors: Kulaga Zbigniew , Litwin Mieczysław , Tkaczyk Marcin , Różdżyńska Agnieszka , Barwicka Katarzyna , Grajda Aneta , Świąder Anna , Gurzkowska Beata , Napieralska Ewelina , Pan Huiqi 
Published: March 2010

Abstract

Background
The growth of children is an indicator of health and society's wellbeing. Growth references are useful in monitoring a child's growth, which is a very important part of child care. Poland's growth references are not updated regularly. Although several growth reference ranges have been developed in Poland over recent years, sampling was restricted to urban populations of major cities. The aim of this study was to assess how well Polish children match with, or diverge from, regional charts and to compare them with international growth references.

Methods
Four Polish and two international (WHO 2007 and USCDC2000) growth references were used to calculate the height, weight and BMI z-scores in a recent, large, population-representative sample of school-aged children and adolescents in Poland. The distributions of z-scores were analysed with descriptive and inferential statistical methods.

Results
Mean height z-scores calculated with the use of the WHO 2007 and USCDC2000 references were positive and significantly different from zero over the entire age range. The mean height z-score was closest to zero in the Poznan reference for boys (0.05) and Warszawa reference for girls (0.01). Median weight z-scores were positive under all weight references over the entire age range with only the exception of 18-year-old girls' weight z-score calculated relative to USCDC2000. Median BMI z-scores were positive in males in early childhood, decreasing with age. In the case of girls, the median BMI z-score calculated using WHO 2007 and USCDC2000 was close to zero in early childhood, decreased in adolescents and reached minimum values at age 18 years. Median BMI z-scores calculated with the use of the Lodz reference fluctuated between 0.05 and 0.2 over the studied age range.

Conclusions
In this contemporary sample of Polish school-aged children, distributions of height, weight and BMI differed from those of children from the international growth references. These differences should be considered when using the references. There exist certain limitations to the analysis of height, weight, and BMI z-scores when Polish regional references are used.
Doxorubicin-induced ovarian toxicity
Authors: Ben-Aharon Irit , Bar-Joseph Hadas , Tzarfaty Galia , Kuchinsky Lital , Rizel Shulamith , Stemmer Salomon M , Shalgi Ruth 
Published: March 2010

Abstract

Background
Young cancer patients may occasionally face infertility and premature gonadal failure. Apart from its direct effect on follicles and oocytes, chemotherapy may induce ovarian toxicity via an impact on the entire ovary. The role of doxorubicin in potential ovarian failure remains obscure. Our intention was to elucidate doxorubicin-related toxicity within ovaries.

Methods
Female mice were injected intraperitoneally with 7.5 or 10 mg/kg doxorubicin and their ovaries were visualized in vivo by high resolution MRI, one day and one month following treatment. Ovaries of other treated mice were excised and weighed at the same post-treatment intervals. Ovarian histological sections were stained for TUNEL or active caspase-3 and follicles were counted and categorized. Ovulation rates were evaluated in superovulated female mice treated with doxorubicin.

Results
A single injection of doxorubicin resulted in a major reduction in both ovarian size and weight that lasted even one month post treatment. A dramatic reduction in ovulation rate was observed one week after treatment, followed by a partial recovery at one month. Histological examination revealed positive staining of TUNEL and active caspase-3. We observed a significant reduction in the population of secondary and primordial follicles one month following treatment.

Conclusions
Our results may imply a mechanism of chemotherapy-induced ovarian toxicity, manifested by reduced ovulation and accompanied by a reduction in ovarian size, caused probably by an acute insult to the ovary.
Monitoring the regulation of gene expression in a growing organ using a fluid mechanics formalism
Authors: Merret Rémy , Moulia Bruno , Hummel Irène , Cohen David , Dreyer Erwin , Bogeat-Triboulot Marie-Béatrice 
Published: March 2010

Abstract

Background
Technological advances have enabled the accurate quantification of gene expression, even within single cell types. While transcriptome analyses are routinely performed, most experimental designs only provide snapshots of gene expression. Molecular mechanisms underlying cell fate or positional signalling have been revealed through these discontinuous datasets. However, in developing multicellular structures, temporal and spatial cues, known to directly influence transcriptional networks, get entangled as the cells are displaced and expand. Access to an unbiased view of the spatiotemporal regulation of gene expression occurring during development requires a specific framework that properly quantifies the rate of change of a property in a moving and expanding element, such as a cell or an organ segment.

Results
We show how the rate of change in gene expression can be quantified by combining kinematics and real-time polymerase chain reaction data in a mechanistic model which considers any organ as a continuum. This framework was applied in order to assess the developmental regulation of the two reference genes Actin11 and Elongation Factor 1-β in the apex of poplar root. The growth field was determined by time-lapse photography and transcript density was obtained at high spatial resolution. The net accumulation rates of the transcripts of the two genes were found to display highly contrasted developmental profiles. Actin11 showed pulses of up and down regulation in the accelerating and decelerating parts of the growth zone while the dynamic of EF1β were much slower. This framework provides key information about gene regulation in a developing organ, such as the location, the duration and the intensity of gene induction/repression.

Conclusions
We demonstrated that gene expression patterns can be monitored using the continuity equation without using mutants or reporter constructions. Given the rise of imaging technologies, this framework in our view opens a new way to dissect the molecular basis of growth regulation, even in non-model species or complex structures.
Membrane attack complex inhibitor CD59a protects against focal cerebral ischemia in mice
Authors: Harhausen Denise , Khojasteh Uldus , Stahel Philip F , Morgan B Paul , Nietfeld Wilfried , Dirnagl Ulrich , Trendelenburg George 
Published: March 2010

AbstractBackgroundThe complement system is a crucial mediator of inflammation and cell lysis after cerebral ischemia. However, there is little information about the exact contribution of the membrane attack complex (MAC) and its inhibitor-protein CD59.MethodsTransient focal cerebral ischemia was induced by middle cerebral artery occlusion (MCAO) in young male and female CD59a knockout and wild-type mice. Two models of MCAO were applied: 60 min MCAO and 48 h reperfusion, as well as 30 min MCAO and 72 h reperfusion. CD59a knockout animals were compared to wild-type animals in terms of infarct size, edema, neurological deficit, and cell death.Results and DiscussionCD59a-deficiency in male mice caused significantly increased infarct volumes and brain swelling when compared to wild-type mice at 72 h after 30 min-occlusion time, whereas no significant difference was observed after 1 h-MCAO. Moreover, CD59a-deficient mice had impaired neurological function when compared to wild-type mice after 30 min MCAO.ConclusionWe conclude that CD59a protects against ischemic brain damage, but depending on the gender and the stroke model used.
Monitoring of clinical signs in goats with transmissible spongiform encephalopathies
Authors: Konold Timm , Bone Gemma E , Phelan Laura J , Simmons Marion M , González Lorenzo , Sisó Sílvia , Goldmann Wilfred , Cawthraw Saira , Hawkins Steve AC 
Published: March 2010

AbstractBackgroundAs there is limited information about the clinical signs of BSE and scrapie in goats, studies were conducted to describe the clinical progression of scrapie and BSE in goats and to evaluate a short clinical protocol for its use in detecting scrapie-affected goats in two herds with previously confirmed scrapie cases. Clinical assessments were carried out in five goats intracerebrally infected with the BSE agent as well as five reported scrapie suspects and 346 goats subject to cull from the two herds, 24 of which were retained for further monitoring. The brain and selected lymphoid tissue were examined by postmortem tests for disease confirmation.ResultsThe sensitivity and specificity of the short clinical protocol in detecting a scrapie case in the scrapie-affected herds was 3.9% and 99.6%, respectively, based on the presence of tremor, positive scratch test, extensive hair loss, ataxia and absent menace response. All BSE- and scrapie-affected goats displayed abnormalities in sensation (over-reactivity to external stimuli, startle responses, pruritus, absent menace response) and movement (ataxia, tremor, postural deficits) at an advanced clinical stage but the first detectable sign associated with scrapie or BSE could vary between animals. Signs of pruritus were not always present despite similar prion protein genotypes. Clinical signs of scrapie were also displayed by two scrapie cases that presented with detectable disease-associated prion protein only in lymphoid tissues.ConclusionsBSE and scrapie may present as pruritic and non-pruritic forms in goats. Signs assessed for the clinical diagnosis of scrapie or BSE in goats should include postural and gait abnormalities, pruritus and visual impairment. However, many scrapie cases will be missed if detection is solely based on the display of clinical signs. PrPdaccumulation in the brain appeared to be related to the severity of clinical disease but not to the display of individual neurological signs.
A systematic review of the use of theory in the design of guideline dissemination and implementation strategies and interpretation of the results of rigorous evaluations
Authors: Davies Philippa , Walker Anne E , Grimshaw Jeremy M 
Published: March 2010

AbstractBackgroundThere is growing interest in the use of cognitive, behavioural, and organisational theories in implementation research. However, the extent of use of theory in implementation research is uncertain.MethodsWe conducted a systematic review of use of theory in 235 rigorous evaluations of guideline dissemination and implementation studies published between 1966 and 1998. Use of theory was classified according to type of use (explicitly theory based, some conceptual basis, and theoretical construct used) and stage of use (choice/design of intervention, process/mediators/moderators, and post hoc/explanation).ResultsFifty-three of 235 studies (22.5%) were judged to have employed theories, including 14 studies that explicitly used theory. The majority of studies (n = 42) used only one theory; the maximum number of theories employed by any study was three. Twenty-five different theories were used. A small number of theories accounted for the majority of theory use including PRECEDE (Predisposing, Reinforcing, and Enabling Constructs in Educational Diagnosis and Evaluation), diffusion of innovations, information overload and social marketing (academic detailing).ConclusionsThere was poor justification of choice of intervention and use of theory in implementation research in the identified studies until at least 1998. Future research should explicitly identify the justification for the interventions. Greater use of explicit theory to understand barriers, design interventions, and explore mediating pathways and moderators is needed to advance the science of implementation research.