bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Genomics of Ethanolamine Utilization
Authors: Tsoy Olga , Ravcheev Dmitry , Mushegian Arcady 
Published: September 2009

ABSTRACT

Ethanolamine can be used as a source of carbon and nitrogen by phylogenetically diverse bacteria. Ethanolamine-ammonia lyase, the enzyme that breaks ethanolamine into acetaldehyde and ammonia, is encoded by the gene tandem
eutBC
. Despite extensive studies of ethanolamine utilization in
Salmonella enterica
serovar Typhimurium, much remains to be learned about EutBC structure and catalytic mechanism, about the evolutionary origin of ethanolamine utilization, and about regulatory links between the metabolism of ethanolamine itself and the ethanolamine-ammonia lyase cofactor adenosylcobalamin. We used computational analysis of sequences, structures, genome contexts, and phylogenies of ethanolamine-ammonia lyases to address these questions and to evaluate recent data-mining studies that have suggested an association between bacterial food poisoning and the diol utilization pathways. We found that EutBC evolution included recruitment of a TIM barrel and a Rossmann fold domain and their fusion to N-terminal α-helical domains to give EutB and EutC, respectively. This fusion was followed by recruitment and occasional loss of auxiliary ethanolamine utilization genes in
Firmicutes
and by several horizontal transfers, most notably from the firmicute stem to the
Enterobacteriaceae
and from
Alphaproteobacteria
to
Actinobacteria
. We identified a conserved DNA motif that likely represents the EutR-binding site and is shared by the ethanolamine and cobalamin operons in several enterobacterial species, suggesting a mechanism for coupling the biosyntheses of apoenzyme and cofactor in these species. Finally, we found that the food poisoning phenotype is associated with the structural components of metabolosome more strongly than with ethanolamine utilization genes or with paralogous propanediol utilization genes per se.
Characterization of the Sporulation Initiation Pathway of
Clostridium difficile
and Its Role in Toxin Production
Authors: Underwood Sarah , Guan Shuang , Vijayasubhash Vinod , Baines Simon D. , Graham Luke , Lewis Richard J. , Wilcox Mark H. , Stephenson Keith 
Published: September 2009

ABSTRACT

Clostridium difficile
is responsible for significant mortality and morbidity in the hospitalized elderly.
C. difficile
spores are infectious and are a major factor contributing to nosocomial transmission. The Spo0A response regulator is the master regulator for sporulation initiation and can influence many other cellular processes. Using the ClosTron gene knockout system, we inactivated genes encoding Spo0A and a putative sporulation-associated sensor histidine kinase in
C. difficile
. Inactivation of
spo0A
resulted in an asporogeneous phenotype, whereas inactivation of the kinase reduced
C. difficle
sporulation capacity by 3.5-fold, suggesting that this kinase also has a role in sporulation initiation. Furthermore, inactivation of either
spo0A
or the kinase resulted in a marked defect in
C. difficile
toxin production. Therefore, Spo0A and the signaling pathway that modulates its activity appear to be involved in regulation of toxin synthesis in
C. difficile
. In addition, Spo0A was directly phosphorylated by a putative sporulation-associated kinase, supporting the hypothesis that sporulation initiation in
C. difficile
is controlled by a two-component signal transduction system rather than a multicomponent phosphorelay. The implications of these findings for
C. difficile
sporulation, virulence, and transmission are discussed.
Evolutionary Dynamics ofompA, the Gene Encoding theChlamydia trachomatisKey Antigen
Authors: Nunes Alexandra , Borrego Maria J. , Nunes Baltazar , Florindo Carlos , Gomes João P. 
Published: September 2009

ABSTRACTChlamydia trachomatisis the trachoma agent and causes most bacterial sexually transmitted infections worldwide. Its major outer membrane protein (MOMP) is a well-known porin and adhesin and is the dominant antigen. So far, investigation of MOMP variability has been focused mainly on molecular epidemiological surveys. In contrast, we aimed to evaluate the impact of the host pressure on this key antigen by analyzing its evolutionary dynamics in 795 isolates from urogenital infections, taking into account the MOMP secondary structure and the sizes/positions of antigenic regions. One-third of the specimens showed a mutational drift from the corresponding genotype, where ∼42% of the mutations had never been described. Amino acid alterations were sixfold more frequent within B-cell epitopes than in the remaining protein (P= 0.027), and some mutations were also found within or close to T-cell antigenic clusters. Interestingly, the two most ecologically successful genotypes, E and F, showed a mutation rate 60.3-fold lower than that of the other genotypes (P< 10−8), suggesting that their efficacy may be the result of a better fitness in dealing with the host immune system rather than of specific virulence factors. Furthermore, the variability exhibited by some genetic variants involved residues that are known to play a critical role during the membrane mechanical movements, contributing to a more stable and flexible porin conformation, which suggests some plasticity to deal with environmental pressure. Globally, these MOMP mutational trends yielded no mosaic structures or important phylogenetic changes, but instead yielded point mutations on specific protein domains, which may enhance pathogen's infectivity, persistence, and transmission.
Distribution and Phylogeny of Light-Oxygen-Voltage-Blue-Light-Signaling Proteins in the Three Kingdoms of Life
Authors: Krauss Ulrich , Minh Bui Quang , Losi Aba , Gärtner Wolfgang , Eggert Thorsten , von Haeseler Arndt , Jaeger Karl-Erich 
Published: September 2009

ABSTRACT

Plants and fungi respond to environmental light stimuli via the action of different photoreceptor modules. One such class, responding to the blue region of light, is constituted by photoreceptors containing so-called
l
ight-
o
xygen-
v
oltage (LOV) domains as sensor modules. Four major LOV families are currently identified in eukaryotes: (i) the plant phototropins, regulating various physiological effects such as phototropism, chloroplast relocation, and stomatal opening; (ii) the aureochromes, mediating photomorphogenesis in photosynthetic stramenopile algae; (iii) the plant circadian photoreceptors of the zeitlupe (ZTL)/adagio (ADO)/flavin-binding Kelch repeat F-box protein 1 (FKF1) family; and (iv) the fungal circadian photoreceptors white-collar 1 (WC-1). Blue-light-sensitive LOV signaling modules are also widespread throughout the prokaryotic world, and physiological responses mediated by bacterial LOV photoreceptors were recently reported. Thus, the question arises as to the evolutionary relationship between the pro- and eukaryotic LOV photoreceptor systems. We used Bayesian and maximum-likelihood tree reconstruction methods to infer evolutionary scenarios that might have led to the widespread appearance of LOV domains among the pro- and eukaryotes. The phylogenetic study presented here suggests a bacterial origin for the LOV domains of the four major eukaryotic LOV photoreceptor families, whereas the LOV sensor domains were most likely recruited from the bacteria in the course of plastid and mitochondrial endosymbiosis.
Dynamics of Two Phosphorelays Controlling Cell Cycle Progression inCaulobacter crescentus
Authors: Chen Y. Erin , Tsokos Christos G. , Biondi Emanuele G. , Perchuk Barrett S. , Laub Michael T. 
Published: September 2009

ABSTRACTInCaulobacter crescentus, progression through the cell cycle is governed by the periodic activation and inactivation of the master regulator CtrA. Two phosphorelays, each initiating with the histidine kinase CckA, promote CtrA activation by driving its phosphorylation and by inactivating its proteolysis. Here, we examined whether the CckA phosphorelays also influence the downregulation of CtrA. We demonstrate that CckA is bifunctional, capable of acting as either a kinase or phosphatase to drive the activation or inactivation, respectively, of CtrA. By identifying mutations that uncouple these two activities, we show that CckA's phosphatase activity is important for downregulating CtrA prior to DNA replication initiation in vivo but that other phosphatases may exist. Our results demonstrate that cell cycle transitions inCaulobacterrequire and are likely driven by the toggling of CckA between its kinase and phosphatase states. More generally, our results emphasize how the bifunctional nature of histidine kinases can help switch cells between mutually exclusive states.
Comparative Genome Analysis ofListeriaBacteriophages Reveals Extensive Mosaicism, Programmed Translational Frameshifting, and a Novel Prophage Insertion Site
Authors: Dorscht Julia , Klumpp Jochen , Bielmann Regula , Schmelcher Mathias , Born Yannick , Zimmer Markus , Calendar Richard , Loessner Martin J. 
Published: September 2009

ABSTRACTThe genomes of sixListeriabacteriophages were sequenced and analyzed. Phages A006, A500, B025, P35, and P40 are members of theSiphoviridaeand contain double-stranded DNA genomes of between 35.6 kb and 42.7 kb. Phage B054 is a unique myovirus and features a 48.2-kb genome. Phage B025 features 3′ overlapping single-stranded genome ends, whereas the other viruses contain collections of terminally redundant, circularly permuted DNA molecules. Phages P35 and P40 have a broad host range and lack lysogeny functions, correlating with their virulent lifestyle. Phages A500, A006, and B025 integrate into bacterial tRNA genes, whereas B054 targets the 3′ end of translation elongation factor genetsf. This is the first reported case of phage integration into such an evolutionarily conserved genetic element. Peptide fingerprinting of viral proteins revealed that both A118 and A500 utilize +1 and −1 programmed translational frameshifting for generating major capsid and tail shaft proteins with C termini of different lengths. In both cases, the unusual +1 frameshift at the 3′ ends of thetshcoding sequences is induced by overlapping proline codons andcis-acting shifty stops. AlthoughListeriaphage genomes feature a conserved organization, they also show extensive mosaicism within the genome building blocks. Of particular interest is B025, which harbors a collection of modules and sequences with relatedness not only to otherListeriaphages but also to viruses infecting other members of theFirmicutes. In conclusion, our results yield insights into the composition and diversity ofListeriaphages and provide new information on their function, genome adaptation, and evolution.
Multiple Two-Component Systems Modulate Alkali Generation inStreptococcus gordoniiin Response to Environmental Stresses
Authors: Liu Yaling , Burne Robert A. 
Published: September 2009

ABSTRACTThe oral commensalStreptococcus gordoniimust adapt to constantly fluctuating and often hostile environmental conditions to persist in the oral cavity. The arginine deiminase system (ADS) ofS. gordoniienables cells to produce, ornithine, ammonia, CO2, and ATP from arginine hydrolysis, augmenting the acid tolerance of the organism. The ADS genes are substrate inducible and sensitive to catabolite repression, mediated through ArcR and CcpA, respectively, but the system also requires low pH and anaerobic conditions for optimal activation. Here, we demonstrate that the CiaRH and ComDE two-component systems (TCS) are required for low-pH-dependent expression of ADS genes inS. gordonii. Further, the VicRK TCS is required for optimal ADS gene expression under anaerobic conditions and enhances the sensitivity of the operon to repression by oxygen. The known anaerobic activator of the ADS, Fnr-like protein (Flp), appeared to act independently of the Vic TCS. Mutants ofS. gordoniilacking components of the CiaRH, ComDE, or VicRK grew more slowly in acidified media and were more sensitive to killing at lethal pH values and to agents that induce oxidative stress. This study provides the first evidence that TCS can regulate the ADS of bacteria in response to specific environmental signals and reveals some notable differences in the contribution of CiaRH, ComDE, and VicRK to viability and stress tolerance between the oral commensalS. gordoniiand the oral pathogenStreptococcus mutans.
Rethinking the History of Philosophy
Authors: Stepanyants Marietta 
Published: September 2009

AbstractBasing herself on Indian and Chinese traditions, the author provides arguments in favour of revising the customary understanding of philosophy per se. The nonexistence of uniformity in the methods of cognition cannot be taken as evidence for the phenomenon of ‘philosophy’ missing outside the Western world. In the East, one can witness fidelity to the broad interpretation of ‘philosophy’, etymologically much nearer to this concept, presuming, along with rationality, the authority of other sources of knowledge. Philosophy came into the world not once but a number of times and in various places. From the outset it bore out, along with common generic traits, its specific ‘patrimonial’ characteristics; in other words, those revealing its own culture. In its turn, each culture is built up around a certain ‘frame’ made up of universal conceptual constituents. The history of philosophy would remain incomplete and one-sided (with a ‘Western bias’) until it ignores the fundamental universals of other cultures. Even the universals and values recognized as common to all mankind are frequently imbued with basically different substance depending on a context of relevant culture. The reappraisal of the history of philosophy should make the teaching system of philosophy multicultural.
The Ethics of Force: Against Aggression and Violence
Authors: Apressyan Ruben G. 
Published: September 2009

AbstractIn opposition to the absolutist ethics of non-violence, the author argues that in response to aggression and violence one has to use every means possible to prevent them. To resist violence is a moral duty of the individual. It would be desirable for violence to be prevented by strength of mind, but if strength of mind is not enough or the aggressor is insensitive to intellectual, spiritual and psychological impacts, one has to employ by accretion all necessary means. Ethics is called upon to set limits to the employment of the means of countering violence.
A Comparative Study of 2 Sustained-Release Morphine Preparations for Pain in Advanced Cancer
Authors: Homsi Jade , Walsh Declan , Lasheen Wael , Nelson Kristine A. , Rybicki Lisa A. , Bast Jane , LeGrand Susan B. 
Published: September 2009

Purpose: Several sustained-release morphine (SRM) formulations are available internationally. This study compared 2 such products available in the United States, SR1 and SR2. Patients and Methods: In an open-label study, patients with advanced cancer pain were randomized to receive SR1 or SR2 every 12 hours around-the-clock (ATC) for 5 days, with immediate release (IR) liquid morphine for rescue dosing (RD). Efficacy, safety, and patient acceptability were determined. Results: A total of 32 patients were evaluable for efficacy and toxicity. Pain scores, RD dosage, RD frequency over 5 days, RD within 3 hours before and after the scheduled SRM, and 8 of the 11 evaluated side effects were higher in the SR1 group. At presumed morphine steady state (day 3), pain scores (P = .05), RD dosage (P = .07), RD frequency (P = .07), and number of RD ±3 hours from scheduled SRM dose (P = .05) were consistently greater in the SR1 group (despite a higher median morphine dose in that group). There was a clinically important and directionally consistent trend that favored SR2, although not all were statistically significant. Patient preference favored SR2 (P < .05). Neither group had difficulty swallowing SR1 or SR2. Conclusions: This is the first study that directly compared two 12-hour SRM formulations. The data suggested, by multiple clinically important measures, that SR2 may provide superior analgesic efficacy and less toxicity compared to SR1. It also supports the concept that it cannot be assumed that different SR formulations of a given opioid are clinically equivalent. A larger study is needed to confirm our findings.
Parental Attributions for Success in Managing the Behavior of Children With ADHD
Authors: Coles Erika K. , Pelham William E. , Gnagy Elizabeth M. 
Published: September 2009

Objective: The current study evaluated the effects of differing intensities of behavior modification and medication on parents’ self-reported success in managing their child’s misbehavior and the attributions parents gave for success or failure. Method: Children were randomized to receive in counterbalanced orders different levels of behavior modification, each for 3-week cycles. In addition, medication was manipulated using a medication assessment procedure. Parents reported daily how successful they were in managing their child’s misbehavior and the attributions for either their success or failure. Results: Parents of children with ADHD generally felt successful in managing their child’s behavior, regardless of treatment condition. In the high behavior modification condition, they were more likely to endorse items that attributed their success to their own effort. Conclusion: In conditions in which parents were given more intensive tools to manage misbehavior they were more likely to attribute their success to their own effort.
CPAP and/or NIV in cardiogenic pulmonary oedema
Authors: Köhnlein T. 
Published: September 2009

Educational aimsDefine the benefits of using CPAP and/or NIV in heart failure.Detail recommendations for the use of ventilators for the clinical treatment of heart failure.Discuss the evidence for and against using ventilators in heart failure.Describe the benefit of using NIV in a pre-clinical setting.SummaryHeart failure is a complex topic which poses difficult decisions for ventilator specialists. Currently available therapies are mechanical ventilation and standard therapy with oxygen or medical intervention. Ventilator specialists face a difficult decision when choosing which of these to use as the evidence for each is not conclusive. The primary aim of the chosen treatment is to improve oxygenation and respiratory acidosis and reduce the work of breathing and dyspnoea. In addition, another goal of treatment is an improvement of cardiac performance. To date, it is difficult to recommend which available treatment is the best at achieving these goals and it is recommended that individual treatment for each patient should be based on their specific needs and circumstances.
Visualization of ribosomal RNA operon copy number distribution
Authors: Rastogi Rajat , Wu Martin , DasGupta Indrani , Fox George E 
Published: September 2009

Abstract

Background
Results of microbial ecology studies using 16S rRNA sequence information can be deceiving due to differences in rRNA operon copy number and genome size of the detected organisms. It therefore will be useful for investigators to have a better understanding of how these two parameters differ in various organism types. In this study, the number of ribosomal operons and genome size were separately mapped onto a Bacterial phylogenetic tree.

Results
A representative Bacterial tree was constructed using 31 marker genes found in 578 bacterial genome sequences. Organism names are displayed on the trees using graduations of color such that similar colors indicate similar numbers of operons or genome size. The resulting images provide an intuitive understanding of how copy number and genome size vary in different Bacterial phyla.

Conclusion
Once the phylogenetic position of a novel organism is known the number of rRNA operons, and to a lesser extent the genome size, can be estimated by examination of the colored maps. Further detail can then be obtained for members of relevant taxa from the rrnDB database.
Locations and patterns of meiotic recombination in two-generation pedigrees
Authors: Ting Jason C , Roberson Elisha DO , Currier Duane G , Pevsner Jonathan 
Published: September 2009

Abstract

Background
Meiotic crossovers are the major mechanism by which haplotypes are shuffled to generate genetic diversity. Previously available methods for the genome-wide, high-resolution identification of meiotic crossover sites are limited by the laborious nature of the assay (as in sperm typing).

Methods
Several methods have been introduced to identify crossovers using high density single nucleotide polymorphism (SNP) array technologies, although programs are not widely available to implement such analyses.

Results
Here we present a two-generation "reverse pedigree analysis" method (analyzing the genotypes of two children relative to each parent) and a web-accessible tool to determine and visualize inheritance differences among siblings and crossover locations on each parental gamete. This approach is complementary to existing methods and uses informative markers which provide high resolution for locating meiotic crossover sites. We introduce a segmentation algorithm to identify crossover sites, and used a synthetic data set to determine that the segmentation algorithm specificity was 92% and sensitivity was 89%. The use of reverse pedigrees allows the inference of crossover locations on the X chromosome in a maternal gamete through analysis of two sons and their father. We further analyzed genotypes from eight multiplex autism families, observing a 1.462 maternal to paternal recombination ratio and no significant differences between affected and unaffected children. Meiotic recombination results from pediSNP can also be used to identify haplotypes that are shared by probands within a pedigree, as we demonstrated with a multiplex autism family.

Conclusion
Using "reverse pedigrees" and defining unique sets of genotype markers within pedigree data, we introduce a method that identifies inherited allelic differences and meiotic crossovers. We implemented the method in the pediSNP software program, and we applied it to several data sets. This approach uses data from two generations to identify crossover sites, facilitating studies of recombination in disease. pediSNP is available online at http://pevsnerlab.kennedykrieger.org/pediSNP.
Association of common variants in mismatch repair genes and breast cancer susceptibility: a multigene study
Authors: Conde João , Silva Susana N , Azevedo Ana P , Teixeira Valdemar , Pina Julieta Esperança , Rueff José , Gaspar Jorge F 
Published: September 2009

Abstract

Background
MMR is responsible for the repair of base-base mismatches and insertion/deletion loops. Besides this, MMR is also associated with an anti-recombination function, suppressing homologous recombination. Losses of heterozygosity and/or microsatellite instability have been detected in a large number of skin samples from breast cancer patients, suggesting a potential role of MMR in breast cancer susceptibility.

Methods
We carried out a hospital-based case-control study in a Caucasian Portuguese population (287 cases and 547 controls) to estimate the susceptibility to non-familial breast cancer associated with some polymorphisms in mismatch repair genes (MSH3, MSH4, MSH6, MLH1, MLH3, PMS1 and MUTYH).

Results
Using unconditional logistic regression we found that MLH3 (L844P, G>A) polymorphism GA (Leu/Pro) and AA (Pro/Pro) genotypes were associated with a decreased risk: OR = 0.65 (0.45-0.95) (p = 0.03) and OR = 0.62 (0.41-0.94) (p = 0.03), respectively.
Analysis of two-way SNP interaction effects on breast cancer revealed two potential associations to breast cancer susceptibility: MSH3 Ala1045Thr/MSH6 Gly39Glu - AA/TC [OR = 0.43 (0.21-0.83), p = 0.01] associated with a decreased risk; and MSH4 Ala97Thr/MLH3 Leu844Pro - AG/AA [OR = 2.35 (1.23-4.49), p = 0.01], GG/AA [OR = 2.11 (1.12-3,98), p = 0.02], and GG/AG [adjusted OR = 1.88 (1.12-3.15), p = 0.02] all associated with an increased risk for breast cancer.

Conclusion
It is possible that some of these common variants in MMR genes contribute significantly to breast cancer susceptibility. However, further studies with a large sample size will be needed to support our results.