bluuebunny/crossref_metadata_2025_split huggingface dataset:
A two-genome microarray for the rice pathogens Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola and its use in the discovery of a difference in their regulation of hrp genes
Authors: Seo Young-Su , Sriariyanun Malinee , Wang Li , Pfeiff Janice , Phetsom Jirapa , Lin Ye , Jung Ki-Hong , Chou Hui Hsien , Bogdanove Adam , Ronald Pamela 
Published: June 2008

Abstract

Background

Xanthomonas oryzae pv. oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc) are bacterial pathogens of the worldwide staple and grass model, rice. Xoo and Xoc are closely related but Xoo invades rice vascular tissue to cause bacterial leaf blight, a serious disease of rice in many parts of the world, and Xoc colonizes the mesophyll parenchyma to cause bacterial leaf streak, a disease of emerging importance. Both pathogens depend on hrp genes for type III secretion to infect their host. We constructed a 50–70 mer oligonucleotide microarray based on available genome data for Xoo and Xoc and compared gene expression in Xoo strains PXO99A and Xoc strain BLS256 grown in the rich medium PSB vs. XOM2, a minimal medium previously reported to induce hrp genes in Xoo strain T7174.

Results
Three biological replicates of the microarray experiment to compare global gene expression in representative strains of Xoo and Xoc grown in PSB vs. XOM2 were carried out. The non-specific error rate and the correlation coefficients across biological replicates and among duplicate spots revealed that the microarray data were robust. 247 genes of Xoo and 39 genes of Xoc were differentially expressed in the two media with a false discovery rate of 5% and with a minimum fold-change of 1.75. Semi-quantitative-RT-PCR assays confirmed differential expression of each of 16 genes each for Xoo and Xoc selected for validation. The differentially expressed genes represent 17 functional categories.

Conclusion
We describe here the construction and validation of a two-genome microarray for the two pathovars of X. oryzae. Microarray analysis revealed that using representative strains, a greater number of Xoo genes than Xoc genes are differentially expressed in XOM2 relative to PSB, and that these include hrp genes and other genes important in interactions with rice. An exception was the rax genes, which are required for production of the host resistance elicitor AvrXa21, and which were expressed constitutively in both pathovars.
Synteny conservation between two distantly-related Rosaceae genomes: Prunus (the stone fruits) and Fragaria(the strawberry)
Authors: Vilanova Santiago , Sargent Daniel J , Arús Pere , Monfort Amparo 
Published: June 2008

AbstractBackgroundThe Rosaceae encompass a large number of economically-important diploid and polyploid fruit and ornamental species in many different genera. The basic chromosome numbers of these genera arex= 7, 8 and 9 and all have compact and relatively similar genome sizes. Comparative mapping between distantly-related genera has been performed to a limited extent in the Rosaceae including a comparison betweenMalus(subfamily Maloideae) andPrunus(subfamily Prunoideae); however no data has been published to date comparingMalusorPrunusto a member of the subfamily Rosoideae. In this paper we compare the genome ofFragaria, a member of the Rosoideae, toPrunus, a member of the Prunoideae.ResultsThe diploid genomes ofPrunus(2n=2x= 16) andFragaria(2n=2x= 14) were compared through the mapping of 71 anchor markers – 40 restriction fragment length polymorphisms (RFLPs), 29 indels or single nucleotide polymorphisms (SNPs) derived from expressed sequence tags (ESTs) and two simple-sequence repeats (SSRs) – on the reference maps of both genera. These markers provided good coverage of thePrunus(78%) andFragaria(78%) genomes, with maximum gaps and average densities of 22 cM and 7.3 cM/marker inPrunusand 32 cM and 8.0 cM/marker inFragaria.ConclusionOur results indicate a clear pattern of synteny, with most markers of each chromosome of one of these species mapping to one or two chromosomes of the other. A large number of rearrangements (36), most of which produced by inversions (27) and the rest (9) by translocations or fission/fusion events could also be inferred. We have provided the first framework for the comparison of the position of genes or DNA sequences of these two economically valuable and yet distantly-related genera of the Rosaceae.
Factors associated with self-rated health status in university students: a cross-sectional study in three European countries
Authors: Mikolajczyk Rafael T , Brzoska Patrick , Maier Claudia , Ottova Veronika , Meier Sabine , Dudziak Urszula , Ilieva Snezhana , El Ansari Walid 
Published: June 2008

Abstract

Background
Self-rated health status (SRHS) is a reliable and valid measure for assessing the subjective and objective health of individuals. Previous studies have either focused predominantly on the elderly or investigated only a narrow range of factors potentially associated with SRHS. In examining student populations, these past studies were limited to single countries. The objectives of this study were to assess which candidate variables were independently associated with SRHS in university students, to compare these variables by country and by gender, and to investigate which of the variables was most important as a rating frame for SRHS.

Methods
The data is from the Cross-National Student Health Survey, conducted in 2005 in universities in Germany, Bulgaria, and Poland (n = 2103; mean age = 20.7 years). SRHS was assessed with a single question using a five-point scale ranging from "excellent" to "poor". The study also measured a wide range of variables including: physical and psychological health, studying, social contacts/social support, and socio-demographic status.

Results
Psychosomatic complaints (considered an aspect of physical health and, adjusted for psychological health) were the most important indicators in forming a rating frame for students' SRHS. There were few differences in the effects of variables associated with SRHS by gender (well-being: a measure of psychological health) and the variables associated with SRHS by country (well-being and self-efficacy). The remaining variables showed homogenous effects for both genders and for all three countries.

Conclusion
The results suggest that SRHS can be reasonably used to compare students' health across countries. SRHS is affected by different physical, psychological and psychosomatic aspects of health; however, its strongest association is with psychosomatic complaints.
Maintenance metabolism and carbon fluxes in Bacillus species
Authors: Tännler Simon , Decasper Seraina , Sauer Uwe 
Published: June 2008

Abstract

Background
Selection of an appropriate host organism is crucial for the economic success of biotechnological processes. A generally important selection criterion is a low maintenance energy metabolism to reduce non-productive consumption of substrate. We here investigated, whether various bacilli that are closely related to Bacillus subtilis are potential riboflavin production hosts with low maintenance metabolism.

Results
While B. subtilis exhibited indeed the highest maintenance energy coefficient, B. licheniformis and B. amyloliquefaciens exhibited only statistically insignificantly reduced maintenance metabolism. Both B. pumilus and B. subtilis (natto) exhibited irregular growth patterns under glucose limitation such that the maintenance metabolism could not be determined. The sole exception with significantly reduced maintenance energy requirements was the B. licheniformis strain T380B. The frequently used spo0A mutation significantly increased the maintenance metabolism of B. subtilis.
At the level of 13C-detected intracellular fluxes, all investigated bacilli exhibited a significant flux through the pentose phosphate pathway, a prerequisite for efficient riboflavin production. Different from all other species, B. subtilis featured high respiratory tricarboxylic acid cycle fluxes in batch and chemostat cultures. In particular under glucose-limited conditions, this led to significant excess formation of NADPH of B. subtilis, while anabolic consumption was rather balanced with catabolic NADPH formation in the other bacilli.

Conclusion
Despite its successful commercial production of riboflavin, B. subtilis does not seem to be the optimal cell factory from a bioenergetic point of view. The best choice of the investigated strains is the sporulation-deficient B. licheniformis T380B strain. Beside a low maintenance energy coefficient, this strain grows robustly under different conditions and exhibits only moderate acetate overflow, hence making it a promising production host for biochemicals and riboflavin in particular.
Antimicrobial resistance in community and nosocomial Escherichia coli urinary tract isolates, London 2005 – 2006
Authors: Bean David C , Krahe Daniel , Wareham David W 
Published: June 2008

Abstract

Background

Escherichia coli is the commonest cause of community and nosocomial urinary tract infection (UTI). Antibiotic treatment is usually empirical relying on susceptibility data from local surveillance studies. We therefore set out to determine levels of resistance to 8 commonly used antimicrobial agents amongst all urinary isolates obtained over a 12 month period.

Methods
Antimicrobial susceptibility to ampicillin, amoxicillin/clavulanate, cefalexin, ciprofloxacin, gentamicin, nitrofurantoin, trimethoprim and cefpodoxime was determined for 11,865 E. coli urinary isolates obtained from community and hospitalised patients in East London.

Results
Nitrofurantoin was the most active agent (94% susceptible), followed by gentamicin and cefpodoxime. High rates of resistance to ampicillin (55%) and trimethoprim (40%), often in combination were observed in both sets of isolates. Although isolates exhibiting resistance to multiple drug classes were rare, resistance to cefpodoxime, indicative of Extended spectrum β-lactamase production, was observed in 5.7% of community and 21.6% of nosocomial isolates.

Conclusion
With the exception of nitrofurantoin, resistance to agents commonly used as empirical oral treatments for UTI was extremely high. Levels of resistance to trimethoprim and ampicillin render them unsuitable for empirical use. Continued surveillance and investigation of other oral agents for treatment of UTI in the community is required.
Oxytocin-Induced Antinociception in the Spinal Cord is Mediated by a Subpopulation of Glutamatergic Neurons in Lamina I-II Which Amplify GABAergic Inhibition
Authors: Breton Jean-Didier , Veinante Pierre , Uhl-Bronner Sandra , Vergnano Angela Maria , Freund-Mercier Marie José , Schlichter Rémy , Poisbeau Pierrick 
Published: June 2008

Background: Recent evidence suggests that oxytocin (OT), secreted in the superficial spinal cord dorsal horn by descending axons of paraventricular hypothalamic nucleus (PVN) neurons, produces antinociception and analgesia. The spinal mechanism of OT is, however, still unclear and requires further investigation. We have used patch clamp recording of lamina II neurons in spinal cord slices and immunocytochemistry in order to identify PVN-activated neurons in the superficial layers of the spinal cord and attempted to determine how this neuronal population may lead to OT-mediated antinociception. Results: We show that OT released during PVN stimulation specifically activates a subpopulation of lamina II glutamatergic interneurons which are localized in the most superficial layers of the dorsal horn of the spinal cord (lamina I-II). This OT-specific stimulation of glutamatergic neurons allows the recruitment of all GABAergic interneurons in lamina II which produces a generalized elevation of local inhibition, a phenomenon which might explain the reduction of incoming Aδ and C primary afferent-mediated sensory messages. Conclusion: Our results obtained in lamina II of the spinal cord provide the first clear evidence of a specific local neuronal network that is activated by OT release to induce antinociception. This OT-specific pathway might represent a novel and interesting therapeutic target for the management of neuropathic and inflammatory pain.
Can single knockouts accurately single out gene functions?
Authors: Deutscher David , Meilijson Isaac , Schuster Stefan , Ruppin Eytan 
Published: June 2008

AbstractBackgroundWhen analyzing complex biological systems, a major objective is localization of function – assessing how much each element contributes to the execution of specific tasks. To establish causal relationships, knockout and perturbation studies are commonly executed. The vast majority of studies perturb a single element at a time, yet one may hypothesize that in non-trivial biological systems single-perturbations will fail to reveal the functional organization of the system, owing to interactions and redundancies.ResultsWe address this fundamental gap between theory and practice by quantifying how misleading the picture arising from classical single-perturbation analysis is, compared with the full multiple-perturbations picture. To this end we use a combination of a novel approach for quantitative, rigorous multiple-knockouts analysis based on the Shapley value from game theory, with an establishedin-silicomodel ofSaccharomyces cerevisiaemetabolism. We find that single-perturbations analysis misses at least 33% of the genes that contribute significantly to the growth potential of this organism, though the essential genes it does find are responsible for most of the growth potential. But when assigning gene contributions for individual metabolic functions, the picture arising from single-perturbations is severely lacking and a multiple-perturbations approach turns out to be essential.ConclusionThe multiple-perturbations investigation yields a significantly richer and more biologically plausible functional annotation of the genes comprising the metabolic network of the yeast.
Time-resolved metabolomics reveals metabolic modulation in rice foliage
Authors: Sato Shigeru , Arita Masanori , Soga Tomoyoshi , Nishioka Takaaki , Tomita Masaru 
Published: June 2008

Abstract

Background
To elucidate the interaction of dynamics among modules that constitute biological systems, comprehensive datasets obtained from "omics" technologies have been used. In recent plant metabolomics approaches, the reconstruction of metabolic correlation networks has been attempted using statistical techniques. However, the results were unsatisfactory and effective data-mining techniques that apply appropriate comprehensive datasets are needed.

Results
Using capillary electrophoresis mass spectrometry (CE-MS) and capillary electrophoresis diode-array detection (CE-DAD), we analyzed the dynamic changes in the level of 56 basic metabolites in plant foliage (Oryza sativa L. ssp. japonica) at hourly intervals over a 24-hr period. Unsupervised clustering of comprehensive metabolic profiles using Kohonen's self-organizing map (SOM) allowed classification of the biochemical pathways activated by the light and dark cycle. The carbon and nitrogen (C/N) metabolism in both periods was also visualized as a phenotypic linkage map that connects network modules on the basis of traditional metabolic pathways rather than pairwise correlations among metabolites. The regulatory networks of C/N assimilation/dissimilation at each time point were consistent with previous works on plant metabolism. In response to environmental stress, glutathione and spermidine fluctuated synchronously with their regulatory targets. Adenine nucleosides and nicotinamide coenzymes were regulated by phosphorylation and dephosphorylation. We also demonstrated that SOM analysis was applicable to the estimation of unidentifiable metabolites in metabolome analysis. Hierarchical clustering of a correlation coefficient matrix could help identify the bottleneck enzymes that regulate metabolic networks.

Conclusion
Our results showed that our SOM analysis with appropriate metabolic time-courses effectively revealed the synchronous dynamics among metabolic modules and elucidated the underlying biochemical functions. The application of discrimination of unidentified metabolites and the identification of bottleneck enzymatic steps even to non-targeted comprehensive analysis promise to facilitate an understanding of large-scale interactions among components in biological systems.
Chromosomal assignment of canine THADA gene to CFA 10q25
Authors: Soller Jan T , Beuing Claudia , Escobar Hugo Murua , Winkler Susanne , Reimann-Berg Nicola , Drieschner Norbert , Dolf Gaudenz , Schelling Claude , Nolte Ingo , Bullerdiek Jörn 
Published: June 2008

AbstractBackgroundChromosomal translocations affecting the chromosome 2p21 cluster in a 450 kb breakpoint region are frequently observed in human benign thyroid adenomas.THADA(thyroid adenoma associated) was identified as the affected gene within this breakpoint region. In contrast to man tumours of the thyroid gland of dogs (Canis lupus familiaris) constitute mainly as follicular cell carcinomas, with malignant thyroid tumours being more frequent than benign thyroid adenomas. In order to elucidate if theTHADAgene is also a target of chromosomal rearrangements in thyroid adenomas of the dog we have physically mapped the canineTHADAgene to canine chromosome 10.A PCR was established to screen a canine genome library for a BAC clone containing the gene sequence of canineTHADA. Further PCR reactions were done using the identified BAC clone as a template in order to verify the corresponding PCR product by sequencing.Canine whole blood was incubated with colcemid in order to arrest the cultured cells in metaphases. The verified BAC DNA was digoxigenin labeled and used as a probe in fluorescencein situhybridization (FISH). Ten well spread metaphases were examined indicating a signal on canine chromosome 10 on both chromatids. A detailed fine mapping was performed indicating the canineTHADAgene locus on the q-arm of chromosome 10.ResultsThe canineTHADAgene locus was mapped on chromosome 10q25. Our mapping results obtained in this study following the previously described nomenclature for the canine karyotype.ConclusionWe analysed whether theTHADAgene locus is a hotspot of canine chromosomal rearrangements in canine neoplastic lesions of the thyroid and in addition might play a role as a candidate gene for a possible malignant transformation of canine thyroid adenomas. Although the available cytogenetic data of canine thyroid adenomas are still insufficient the chromosomal region to which the canineTHADAhas been mapped seems to be no hotspot of chromosomal aberrations seen in canine thyroid adenomas.
In vitro norepinephrine significantly activates isolated platelets from healthy volunteers and critically ill patients following severe traumatic brain injury
Authors: Tschuor Christoph , Asmis Lars M , Lenzlinger Philipp M , Tanner Martina , Härter Luc , Keel Marius , Stocker Reto , Stover John F 
Published: June 2008

Abstract
Introduction
Norepinephrine, regularly used to increase systemic arterial blood pressure and thus improve cerebral perfusion following severe traumatic brain injury (TBI), may activate platelets. This, in turn, could promote microthrombosis formation and induce additional brain damage.

Methods
The objective of this study was to investigate the influence of norepinephrine on platelets isolated from healthy volunteers and TBI patients during the first two post-traumatic weeks. A total of 18 female and 18 male healthy volunteers of different age groups were recruited, while 11 critically ill TBI patients admitted consecutively to our intensive care unit were studied. Arterial and jugular venous platelets were isolated from norepinephrine-receiving TBI patients; peripheral venous platelets were studied in healthy volunteers. Concentration-dependent functional alterations of isolated platelets were analyzed by flow cytometry, assessing changes in surface P-selectin expression and platelet-derived microparticles before and after in vitro stimulation with norepinephrine ranging from 10 nM to 100 μM. The thrombin receptor-activating peptide (TRAP) served as a positive control.

Results
During the first week following TBI, norepinephrine-mediated stimulation of isolated platelets was significantly reduced compared with volunteers (control). In the second week, the number of P-selectin- and microparticle-positive platelets was significantly decreased by 60% compared with the first week and compared with volunteers. This, however, was associated with a significantly increased susceptibility to norepinephrine-mediated stimulation, exceeding changes observed in volunteers and TBI patients during the first week. This pronounced norepinephrine-induced responsiveness coincided with increased arterio-jugular venous difference in platelets, reflecting intracerebral adherence and signs of cerebral deterioration reflected by elevated intracranial pressure and reduced jugular venous oxygen saturation.

Conclusion
Clinically infused norepinephrine might influence platelets, possibly promoting microthrombosis formation. In vitro stimulation revealed a concentration- and time-dependent differential level of norepinephrine-mediated platelet activation, possibly reflecting changes in receptor expression and function. Whether norepinephrine should be avoided in the second post-traumatic week and whether norepinephrine-stimulated platelets might induce additional brain damage warrant further investigations.
Identification of a new transmembrane adaptor protein that constitutively binds Grb2 in B cells
Authors: Liu Yan , Zhang Weiguo 
Published: June 2008

AbstractTransmembrane adaptor proteins couple antigen receptor engagement to downstream signaling cascades in lymphocytes. One example of these proteins is the linker for activation of T cells (LAT), which plays an indispensable role in T cell activation and development. Here, we report identification of a new transmembrane adaptor molecule, namely growth factor receptor-bound protein 2 (Grb2)-binding adaptor protein, transmembrane (GAPT), which is expressed in B cells and myeloid cells. Similar to LAT, GAPT has an extracellular domain, a transmembrane domain, and a cytoplasmic tail with multiple Grb2-binding motifs. In contrast to other transmembrane adaptor proteins, GAPT is not phosphorylated upon BCR ligation but associates with Grb2 constitutively through its proline-rich region. Targeted disruption of the gapt gene in mice affects neither B cell development nor a nitrophenylacetyl-specific antibody response. However, in the absence of GAPT, B cell proliferation after BCR cross-linking is enhanced. In aged GAPT−/− mice, the number of marginal zone (MZ) B cells is increased, and other B cell subsets are normal. The serum concentrations of IgM, IgG2b, and IgG3 are also elevated in these mice. These data indicate that GAPT might play an important role in control of B cell activation and proper maintenance of MZ B cells.
The essential role of the in situ immune reaction in human colorectal cancer
Authors: Pagès Franck , Galon Jérôme , Fridman Wolf H 
Published: June 2008

AbstractColorectal cancer is the second most common cause of cancer-related death. Novel prognostic factors should be identified and validated to refine the present tumor-node-metastasis system. The presence of immune cells infiltrating colorectal cancers is a common phenomenon. However, the current belief is that clinically detectable human tumors escaping immune surveillance are no longer kept in check by the immune cells of the tumor microenvironment. Despite studies showing the influence of immune cell infiltrates on the behavior of colorectal carcinomas, this parameter is not currently recognized as a reliable prognostic factor. We showed that the nature, functional orientation, density, and location of immune cells within distinct tumor regions could provide a prognostic factor superior to and independent of criteria related to the anatomic extent of the tumor. The strength of the immune reaction identified in our studies could advance our understanding of cancer evolution and have important consequences for clinical practice.