bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring QSARs for Binding Affinity of Azoles with CYP2B and CYP3A Enzymes Using GFA and G/PLS Techniques
Authors: Roy Kunal , Roy Partha Pratim 
Published: March 2008

Eighteen azole compounds, including some commercial fungicides, reported by Daisuke Itokawaet al.have been subjected to quantitative structure‐activity relationship (QSAR) analysis for their binding affinity with cytochrome enzymes CYP3A and CYP2B. The analyses were performed using electronic (Charge, FCharge, Apol, Dipole, HOMO, LUMO, and Sr), spatial (Radius of gyration, Jurs descriptors, Shadow indices, Area, PMI‐mag, Density, Vm), different topological parameters (E‐state index, kappa shape index, molecular connectivity index, subgraph cont, information content indices), and thermodynamic (Alog P, Alog P98, Molref) descriptors calculated usingcerius2 version 10 software. Genetic function approximation and genetic partial least squares were used as chemometric tools for modeling. The derived binding affinity models are of high statistical quality (leave‐one‐outQ2ranging from 0.946 to 0.977). The selectivity models also satisfy the statistical significance (Q2ranging from 0.680 to 0.761). The models indicate that the binding affinity of these compounds is related to topological, steric, electronic, and spatial properties of the molecules. The spline‐based genetic models indicate optimum range of different parameters. The models have also been validated by leave‐25%‐out cross‐ validation.
MicroRNAs: Biogenesis and Molecular Functions
Authors: Liu Xuhang , Fortin Kristine , Mourelatos Zissimos 
Published: March 2008

AbstractSmall regulatory RNAs are essential and ubiquitous riboregulators that are the key mediators of RNA interference (RNAi). They include microRNAs (miRNAs) and short‐interfering RNAs (siRNAs), classes of ∼22 nucleotide RNAs. miRNAs and siRNAs bind to Argonaute proteins and form effector complexes that regulate gene expression; in animals, this regulation occurs primarily at the post‐transcriptional level. In this review, we will discuss our current understanding of how miRNA and siRNAs are generated and how they function to silence gene expression, focusing on animal and, in particular, mammalian miRNAs.
Emotional and Physiological Responses to Social‐Evaluative Threat
Authors: Dickerson Sally S. 
Published: March 2008

AbstractSocial‐evaluative threat has been theorized to elicit coordinated psychological and physiological responses, including increases in self‐conscious emotions as well as increases in cortisol and proinflammatory cytokine activity. Acute laboratory stressors with social‐evaluative threat have triggered robust increases in cortisol, whereas equivalent laboratory stressors without this explicit social‐evaluative component have not elicited changes in this physiological parameter. Participants who have reported the greatest increases in self‐conscious emotions have also shown the greatest increases in cortisol activity, suggesting that these physiological changes may occur in concert with self‐conscious states. Other work has shown that social‐evaluative threat and accompanying self‐conscious emotions can influence immune parameters associated with inflammation. These findings have implications for a number of areas of research within social and personality psychology.
The Influence of Children on Their Parents’ Values
Authors: Knafo Ariel , Galansky Neta 
Published: March 2008

AbstractMany parents report that their values are influenced by their children. However, few studies provide direct evidence regarding child–parent value transmission. We review this evidence and propose five main processes of child influence: (i) Passive child influences, causing change in parental values by the mere presence or development of children; (ii) Active child influences, due to children directly attempting to influence their parents’ opinions or providing parents with relevant information; (iii) Differentiation, the emergence of a distinction between parents’ own personal values and their socialization values; (iv) Reciprocal influences; in which parents’ and children’ influences are intertwined; and (v) Counter‐influences, in which parental values change in a direction opposite to that of children's values. A study on child influence illustrates some of these processes. The roles of migration, aging, and parent and child characteristics in child‐to‐parent influences are discussed.
Action Research: A Missing Component in the Emergence of Social and Cross‐Cultural Psychology as a Fully Inter‐Connected Global Enterprise
Authors: Liu James H. , Ng Sik‐hung , Gastardo‐Conaco Ma. Cecilia , Wong Dennis S. W. 
Published: March 2008

AbstractAction research, as envisaged by Lewin, uses research to solve a social problem and provide theoretical knowledge. It involves a cyclical–spiral of planning, action, and evaluation with feedback between parties, taking into account power and value differences and empowering change agents. This has been all but abandoned by social psychologists today. Contemporary ‘participatory’ action research has migrated to fields like education and development and community studies that emphasize a social constructionist epistemology with a qualitative approach of recording bottom‐up processes of social change and community self‐awareness. The globalization of psychology affords new opportunities for a return to more top‐down Lewinian traditions, where academics in the developing world – embedded within a cultural milieu of interconnectedness and relatively exempt from pressures to publish or perish – can work together with academics in wealthy countries to produce a process oriented psychology that is capable of making a difference under conditions of climate change and the end of cheap oil. Asian social psychology, where strongly indigenous psychologies have taken root in growing economies, may take a leading role in this movement.
Is it possible to detect the presence of adenovirus in conjunctiva before the onset of conjunctivitis?
Authors: Kimura Ryoji , Migita Hironori , Kadonosono Kazuaki , Uchio Eiichi 
Published: March 2008

Abstract.Purpose:  It is widely accepted that patients with adenoviral conjunctivitis are contagious approximately as long as 14 days after the onset. However, there is controversy about whether patients with adenoviral conjunctivitis are contagious during the incubation period. We investigated the potential of the eye as a source for spreading infection during the incubation period by analysing the presence of adenovirus (Ad) in contralateral eyes before onset in patients with bilateral adenoviral conjunctivitis using the immunochromatography (IC) test and polymerase chain reaction (PCR).Methods:  Patients with adenoviral conjunctivitis were directed to visit an outpatient clinic at approximately 3‐day intervals until onset in the contralateral eye or 2 weeks after onset in the first eye. Conjunctival scrapings obtained from the first infected eye and the contralateral eye before and after onset were tested to detect Ad antigen using the IC test and PCR.Results:  Out of the 32 cases, 23 (72%) developed conjunctivitis in the contralateral eye. Among these bilateral cases, 18 (78%) were found positive for Ad by PCR after onset in the contralateral eye. However, no specimen obtained before onset showed a positive result for Ad in both tests.Conclusion:  Although there is a possibility that eyes are contagious during the incubation period of adenoviral conjunctivitis in some situations, these results suggest that the possibility of the eye acting as a source for spreading infection during the incubation period is very small.
Survival of Influenza Virus on Banknotes
Authors: Thomas Yves , Vogel Guido , Wunderli Werner , Suter Patricia , Witschi Mark , Koch Daniel , Tapparel Caroline , Kaiser Laurent 
Published: March 2008

ABSTRACT
Successful control of a viral disease requires knowledge of the different vectors that could promote its transmission among hosts. We assessed the survival of human influenza viruses on banknotes given that billions of these notes are exchanged daily worldwide. Banknotes were experimentally contaminated with representative influenza virus subtypes at various concentrations, and survival was tested after different time periods. Influenza A viruses tested by cell culture survived up to 3 days when they were inoculated at high concentrations. The same inoculum in the presence of respiratory mucus showed a striking increase in survival time (up to 17 days). Similarly, B/Hong Kong/335/2001 virus was still infectious after 1 day when it was mixed with respiratory mucus. When nasopharyngeal secretions of naturally infected children were used, influenza virus survived for at least 48 h in one-third of the cases. The unexpected stability of influenza virus in this nonbiological environment suggests that unusual environmental contamination should be considered in the setting of pandemic preparedness.
Collateral Effects of Antibiotics: Carbadox and Metronidazole Induce VSH-1 and Facilitate Gene Transfer among
Brachyspira hyodysenteriae
Strains
Authors: Stanton Thaddeus B. , Humphrey Samuel B. , Sharma Vijay K. , Zuerner Richard L. 
Published: March 2008

ABSTRACT

Brachyspira hyodysenteriae
is an anaerobic spirochete and the etiologic agent of swine dysentery. The genome of this spirochete contains a mitomycin C-inducible, prophage-like gene transfer agent designated VSH-1. VSH-1 particles package random 7.5-kb fragments of the
B. hyodysenteriae
genome and transfer genes between
B. hyodysenteriae
cells. The chemicals and conditions inducing VSH-1 production are largely unknown. Antibiotics used in swine management and stressors inducing traditional prophages might induce VSH-1 and thereby stimulate lateral gene transfer between
B. hyodysenteriae
cells. In these studies, VSH-1 induction was initially detected by a quantitative real-time reverse transcriptase PCR assay evaluating increased transcription of
hvp38
(VSH-1 head protein gene). VSH-1 induction was confirmed by detecting VSH-1-associated 7.5-kb DNA and VSH-1 particles in
B. hyodysenteriae
cultures. Nine antibiotics (chlortetracycline, lincomycin, tylosin, tiamulin, virginiamycin, ampicillin, ceftriaxone, vancomycin, and florfenicol) at concentrations affecting
B. hyodysenteriae
growth did not induce VSH-1 production. By contrast, VSH-1 was detected in
B. hyodysenteriae
cultures treated with mitomycin C (10 μg/ml), carbadox (0.5 μg/ml), metronidazole (0.5 μg/ml), and H
2
O
2
(300 μM). Carbadox- and metronidazole-induced VSH-1 particles transmitted tylosin and chloramphenicol resistance determinants between
B. hyodysenteriae
strains. The results of these studies suggest that certain antibiotics may induce the production of prophage or prophage-like elements by intestinal bacteria and thereby impact intestinal microbial ecology.
Unexpected Importance of Potential Parasites in the Composition of the Freshwater Small-Eukaryote Community
Authors: Lepère Cécile , Domaizon Isabelle , Debroas Didier 
Published: March 2008

ABSTRACT
The diversity of small eukaryotes (0.2 to 5 μm) in a mesotrophic lake (Lake Bourget) was investigated using 18S rRNA gene library construction and fluorescent in situ hybridization coupled with tyramide signal amplification (TSA-FISH). Samples collected from the epilimnion on two dates were used to extend a data set previously obtained using similar approaches for lakes with a range of trophic types. A high level of diversity was recorded for this system with intermediate trophic status, and the main sequences from Lake Bourget were affiliated with ciliates (maximum, 19% of the operational taxonomic units [OTUs]), cryptophytes (33%), stramenopiles (13.2%), and cercozoa (9%). Although the comparison of TSA-FISH results and clone libraries suggested that the level of Chlorophyceae may have been underestimated using PCR with 18S rRNA primers, heterotrophic organisms dominated the small-eukaryote assemblage. We found that a large fraction of the sequences belonged to potential parasites of freshwater phytoplankton, including sequences affiliated with fungi and Perkinsozoa. On average, these sequences represented 30% of the OTUs (40% of the clones) obtained for each of two dates for Lake Bourget. Our results provide information on lacustrine small-eukaryote diversity and structure, adding to the phylogenetic data available for lakes with various trophic types.
Comparative Genomics of “
Dehalococcoides ethenogenes
” 195 and an Enrichment Culture Containing Unsequenced “
Dehalococcoides
” Strains
Authors: West Kimberlee A. , Johnson David R. , Hu Ping , DeSantis Todd Z. , Brodie Eoin L. , Lee Patrick K. H. , Feil Helene , Andersen Gary L. , Zinder Stephen H. , Alvarez-Cohen Lisa 
Published: March 2008

ABSTRACT

Tetrachloroethene (PCE) and trichloroethene (TCE) are prevalent groundwater contaminants that can be completely reductively dehalogenated by some “
Dehalococcoides
” organisms. A
Dehalococcoides
-organism-containing microbial consortium (referred to as ANAS) with the ability to degrade TCE to ethene, an innocuous end product, was previously enriched from contaminated soil. A whole-genome photolithographic microarray was developed based on the genome of “
Dehalococcoides ethenogenes
” 195. This microarray contains probes designed to hybridize to >99% of the predicted protein-coding sequences in the strain 195 genome. DNA from ANAS was hybridized to the microarray to characterize the genomic content of the ANAS enrichment. The microarray results revealed that the genes associated with central metabolism, including an apparently incomplete carbon fixation pathway, cobalamin-salvaging system, nitrogen fixation pathway, and five hydrogenase complexes, are present in both strain 195 and ANAS. Although the gene encoding the TCE reductase,
tceA
, was detected, 13 of the 19 reductive dehalogenase genes present in strain 195 were not detected in ANAS. Additionally, 88% of the genes in predicted integrated genetic elements in strain 195 were not detected in ANAS, consistent with these elements being genetically mobile. Sections of the tryptophan operon and an operon encoding an ABC transporter in strain 195 were also not detected in ANAS. These insights into the diversity of
Dehalococcoides
genomes will improve our understanding of the physiology and evolution of these bacteria, which is essential in developing effective strategies for the bioremediation of PCE and TCE in the environment.
Comparison of Methods for Processing Drinking Water Samples for the Isolation of
Mycobacterium avium
and
Mycobacterium intracellulare
Authors: Thomson Rachel , Carter Robyn , Gilpin Chris , Coulter Chris , Hargreaves Megan 
Published: March 2008

ABSTRACT

Several protocols for isolation of mycobacteria from water exist, but there is no established standard method. This study compared methods of processing potable water samples for the isolation of
Mycobacterium avium
and
Mycobacterium intracellulare
using spiked sterilized water and tap water decontaminated using 0.005% cetylpyridinium chloride (CPC). Samples were concentrated by centrifugation or filtration and inoculated onto Middlebrook 7H10 and 7H11 plates and Lowenstein-Jensen slants and into mycobacterial growth indicator tubes with or without polymyxin, azlocillin, nalidixic acid, trimethoprim, and amphotericin B. The solid media were incubated at 32°C, at 35°C, and at 35°C with CO
2
and read weekly. The results suggest that filtration of water for the isolation of mycobacteria is a more sensitive method for concentration than centrifugation. The addition of sodium thiosulfate may not be necessary and may reduce the yield. Middlebrook M7H10 and 7H11 were equally sensitive culture media. CPC decontamination, while effective for reducing growth of contaminants, also significantly reduces mycobacterial numbers. There was no difference at 3 weeks between the different incubation temperatures.
Occurrence and Expression of Gene Transfer Agent Genes in Marine Bacterioplankton
Authors: Biers Erin J. , Wang Kui , Pennington Catherine , Belas Robert , Chen Feng , Moran Mary Ann 
Published: March 2008

ABSTRACT

Genes with homology to the transduction-like gene transfer agent (GTA) were observed in genome sequences of three cultured members of the marine
Roseobacter
clade. A broader search for homologs for this host-controlled virus-like gene transfer system identified likely GTA systems in cultured
Alphaproteobacteria
, and particularly in marine bacterioplankton representatives. Expression of GTA genes and extracellular release of GTA particles (∼50 to 70 nm) was demonstrated experimentally for the
Roseobacter
clade member
Silicibacter pomeroyi
DSS-3, and intraspecific gene transfer was documented. GTA homologs are surprisingly infrequent in marine metagenomic sequence data, however, and the role of this lateral gene transfer mechanism in ocean bacterioplankton communities remains unclear.
Diverse Responses of the Bivalve-Killing Dinoflagellate
Heterocapsa circularisquama
to Infection by a Single-Stranded RNA Virus
Authors: Mizumoto Hiroyuki , Tomaru Yuji , Takao Yoshitake , Shirai Yoko , Nagasaki Keizo 
Published: March 2008

ABSTRACT

Viruses are believed to be significant pathogens for phytoplankton. Usually, they infect a single algal species, and often their infection is highly strain specific. However, the detailed molecular background of the strain specificity and its ecological significance have not been sufficiently understood. Here, we investigated the temporal changes in viral RNA accumulation and virus-induced cell lysis using a bloom-forming dinoflagellate
Heterocapsa circularisquama
and its single-stranded RNA virus, HcRNAV. We observed at least three host response patterns to virus inoculation: sensitive, resistant, and delayed lysis. In the sensitive response, the host cell culture was permissive for viral RNA replication and apparent cell lysis was observed; in contrast, resistant cell culture was nonpermissive for viral RNA replication and not lysed. In the delayed-lysis response, although viral RNA replication occurred, virus-induced cell lysis was faint and remarkably delayed. In addition, the number of infectious virus particles released to the culture supernatant at 12 days postinoculation was comparable to that of the sensitive strain. By further analysis, a few strains were characterized as variants of the delayed-lysis strain. These observations indicate that the response of
H. circularisquama
to HcRNAV infection is highly diverse.
Bactericidal Effect of Solar Water Disinfection under Real Sunlight Conditions
Authors: Boyle M. , Sichel C. , Fernández-Ibáñez P. , Arias-Quiroz G. B. , Iriarte-Puña M. , Mercado A. , Ubomba-Jaswa E. , McGuigan K. G. 
Published: March 2008

ABSTRACT

Batch solar disinfection (SODIS) inactivation kinetics are reported for suspensions in water of
Campylobacter jejuni
,
Yersinia enterocolitica
, enteropathogenic
Escherichia coli
,
Staphylococcus epidermidis
, and endospores of
Bacillus subtilis
, exposed to strong natural sunlight in Spain and Bolivia. The exposure time required for complete inactivation (at least 4-log-unit reduction and below the limit of detection, 17 CFU/ml) under conditions of strong natural sunlight (maximum global irradiance, ∼1,050 W m
−2
± 10 W m
−2
) was as follows:
C. jejuni
, 20 min;
S. epidermidis
, 45 min; enteropathogenic
E. coli
, 90 min;
Y. enterocolitica
, 150 min. Following incomplete inactivation of
B. subtilis
endospores after the first day, reexposure of these samples on the following day found that 4% (standard error, 3%) of the endospores remained viable after a cumulative exposure time of 16 h of strong natural sunlight. SODIS is shown to be effective against the vegetative cells of a number of emerging waterborne pathogens; however, bacterial species which are spore forming may survive this intervention process.
Phylogenetic Analysis of Members of the
Phycodnaviridae
Virus Family, Using Amplified Fragments of the Major Capsid Protein Gene
Authors: Larsen J. B. , Larsen A. , Bratbak G. , Sandaa R.-A. 
Published: March 2008

ABSTRACT

Algal viruses are considered ecologically important by affecting host population dynamics and nutrient flow in aquatic food webs. Members of the family
Phycodnaviridae
are also interesting due to their extraordinary genome size. Few algal viruses in the
Phycodnaviridae
family have been sequenced, and those that have been have few genes in common and low gene homology. It has hence been difficult to design general PCR primers that allow further studies of their ecology and diversity. In this study, we screened the nine type I core genes of the nucleocytoplasmic large DNA viruses for sequences suitable for designing a general set of primers. Sequence comparison between members of the
Phycodnaviridae
family, including three partly sequenced viruses infecting the prymnesiophyte
Pyramimonas orientalis
and the haptophytes
Phaeocystis pouchetii
and
Chrysochromulina ericina
(
Pyramimonas orientalis
virus 01B [PoV-01B],
Phaeocystis pouchetii
virus 01 [PpV-01], and
Chrysochromulina ericina
virus 01B [CeV-01B], respectively), revealed eight conserved regions in the major capsid protein (MCP). Two of these regions also showed conservation at the nucleotide level, and this allowed us to design degenerate PCR primers. The primers produced 347- to 518-bp amplicons when applied to lysates from algal viruses kept in culture and from natural viral communities. The aim of this work was to use the MCP as a proxy to infer phylogenetic relationships and genetic diversity among members of the
Phycodnaviridae
family and to determine the occurrence and diversity of this gene in natural viral communities. The results support the current legitimate genera in the
Phycodnaviridae
based on alga host species. However, while placing the mimivirus in close proximity to the type species, PBCV-1, of
Phycodnaviridae
along with the three new viruses assigned to the family (PoV-01B, PpV-01, and CeV-01B), the results also indicate that the coccolithoviruses and phaeoviruses are more diverged from this group. Phylogenetic analysis of amplicons from virus assemblages from Norwegian coastal waters as well as from isolated algal viruses revealed a cluster of viruses infecting members of the prymnesiophyte and prasinophyte alga divisions. Other distinct clusters were also identified, containing amplicons from this study as well as sequences retrieved from the Sargasso Sea metagenome. This shows that closely related sequences of this family are present at geographically distant locations within the marine environment.
Correlation between Detection of a Plasmid and High-Level Virulence of
Vibrio nigripulchritudo
, a Pathogen of the Shrimp
Litopenaeus stylirostris
Authors: Reynaud Yann , Saulnier Denis , Mazel Didier , Goarant Cyrille , Le Roux Frédérique 
Published: March 2008

ABSTRACT

Vibrio nigripulchritudo
, the etiological agent of
Litopenaeus stylirostris
summer syndrome, is responsible for mass mortalities of shrimp in New Caledonia. Epidemiological studies led to the suggestion that this disease is caused by an emergent group of pathogenic strains. Genomic subtractive hybridization was carried out between two isolates exhibiting low and high virulence. Our subtraction library was constituted of 521 specific fragments; 55 of these were detected in all virulent isolates from our collection (
n
= 32), and 13 were detected only in the isolates demonstrating the highest pathogenicity (
n
= 19), suggesting that they could be used as genetic markers for high virulence capacity. Interestingly, 10 of these markers are carried by a replicon of 11.2 kbp that contains sequences highly similar to those of a plasmid detected in
Vibrio shilonii
, a coral pathogen. The detection of this plasmid was correlated with the highest pathogenicity status of the isolates from our collection. The origin and consequence of this plasmid acquisition are discussed.