bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Volatilization as a Natural Attenuation Pathway for MTBE
Authors: Lahvis Matthew A. , Baehr Arthur L , Baker Ronald J. 
Published: December 2005

AbstractVolatilization and diffusion through the unsaturated zone can be an important pathway for natural attenuation remediation of methyl tert‐butyl ether (MTBE) at gasoline spill sites. The significance of this pathway depends primarily on the distribution of immiscible product within the unsaturated zone and the relative magnitude of aqueous‐phase advection (ground water recharge) to gaseous‐phase diffusion. At a gasoline spill site in Laurel Bay, South Carolina, rates of MTBE volatilization from ground water downgradient from the source are estimated by analyzing the distribution of MTBE in the unsaturated zone above a solute plume. Volatilization rates of MTBE from ground water determined by transport modeling ranged from 0.0020 to 0.0042 g m‐2/year, depending on the assumed rate of ground water recharge. Although diffusive conditions at the Laurel Bay site are favorable for volatilization, mass loss of MTBE is insignificant over the length (230 m) of the solute plume. Based on this analysis, significant volatilization of MTBE from ground water downgradient from source areas at other sites is not likely. In contrast, model results indicate that volatilization coupled with diffusion to the atmosphere could be a significant mass loss pathway for MTBE in source areas where residual product resides above the capillary zone. Although not documented, mass loss of MTBE at the Laurel Bay site due to volatilization and diffusion to the atmosphere are predicted to be two to three times greater than mass loading of MTBE to ground water due to dissolution and recharge. This result would imply that volatilization in the source zone may be the critical natural attenuation pathway for MTBE at gasoline spill sites, especially when considering capillary zone limitations on volatilization of MTBE from ground water and the relative recalcitrance of MTBE to biodegradation.
Transcriptome Analysis of
Paracoccidioides brasiliensis
Cells Undergoing Mycelium-to-Yeast Transition
Authors: Nunes Luiz R. , Costa de Oliveira Regina , Leite Daniela Batista , da Silva Vivian Schmidt , dos Reis Marques Everaldo , da Silva Ferreira Márcia Eliana , Ribeiro Diógenes Custódio Duarte , de Souza Bernardes Luciano Ângelo , Goldman Maria Helena S. , Puccia Rosana , Travassos Luiz R. , Batista Wagner L. , Nóbrega Marina Pasetto , Nobrega Francisco G. , Yang Ding-Yah , de Bragança Pereira Carlos A. , Goldman Gustavo H. 
Published: December 2005

ABSTRACT

Paracoccidioides brasiliensis
is a thermodimorphic fungus associated with paracoccidioidomycosis (PCM), a systemic mycosis prevalent in South America. In humans, infection starts by inhalation of fungal propagules, which reach the pulmonary epithelium and transform into the yeast parasitic form. Thus, the mycelium-to-yeast transition is of particular interest because conversion to yeast is essential for infection. We have used a
P. brasiliensis
biochip carrying sequences of 4,692 genes from this fungus to monitor gene expression at several time points of the mycelium-to-yeast morphological shift (from 5 to 120 h). The results revealed a total of 2,583 genes that displayed statistically significant modulation in at least one experimental time point. Among the identified gene homologues, some encoded enzymes involved in amino acid catabolism, signal transduction, protein synthesis, cell wall metabolism, genome structure, oxidative stress response, growth control, and development. The expression pattern of 20 genes was independently verified by real-time reverse transcription-PCR, revealing a high degree of correlation between the data obtained with the two methodologies. One gene, encoding 4-hydroxyl-phenyl pyruvate dioxygenase (4-HPPD), was highly overexpressed during the mycelium-to-yeast differentiation, and the use of NTBC [2-(2-nitro-4-trifluoromethylbenzoyl)-cyclohexane-1,3-dione], a specific inhibitor of 4-HPPD activity, as well as that of NTBC derivatives, was able to inhibit growth and differentiation of the pathogenic yeast phase of the fungus in vitro. These data set the stage for further studies involving NTBC and its derivatives as new chemotherapeutic agents against PCM and confirm the potential of array-based approaches to identify new targets for the development of alternative treatments against pathogenic microorganisms.
Genetic and Molecular Analysis of Phytochromes from the Filamentous FungusNeurospora crassa
Authors: Froehlich Allan C. , Noh Bosl , Vierstra Richard D. , Loros Jennifer , Dunlap Jay C. 
Published: December 2005

ABSTRACTPhytochromes (Phys) comprise a superfamily of red-/far-red-light-sensing proteins. Whereas higher-plant Phys that control numerous growth and developmental processes have been well described, the biochemical characteristics and functions of the microbial forms are largely unknown. Here, we describe analyses of the expression, regulation, and activities of two Phys in the filamentous fungusNeurospora crassa. In addition to containing the signature N-terminal domain predicted to covalently associate with a bilin chromophore, PHY-1 and PHY-2 contain C-terminal histidine kinase and response regulator motifs, implying that they function as hybrid two-component sensor kinases activated by light. A bacterially expressed N-terminal fragment of PHY-2 covalently bound either biliverdin or phycocyanobilin in vitro, with the resulting holoprotein displaying red-/far-red-light photochromic absorption spectra and a photocycle in vitro. cDNA analysis ofphy-1andphy-2revealed two splice isoforms for each gene. The levels of thephytranscripts are not regulated by light, but the abundance of thephy-1mRNAs is under the control of the circadian clock. Phosphorylated and unphosphorylated forms of PHY-1 were detected; both species were found exclusively in the cytoplasm, with their relative abundances unaffected by light. Strains containing deletions ofphy-1andphy-2, either singly or in tandem, were not compromised in any known photoresponses inNeurospora, leaving their function(s) unclear.
Identification and Characterization of Cor33p, a Novel Protein Implicated in Tolerance towards Oxidative Stress inCandida albicans
Authors: Sohn K. , Roehm M. , Urban C. , Saunders N. , Rothenstein D. , Lottspeich F. , Schröppel K. , Brunner H. , Rupp S. 
Published: December 2005

ABSTRACTWe applied two-dimensional gel electrophoresis to identify downstream effectors ofCPH1andEFG1under hypha-inducing conditions inCandida albicans. Among the proteins that were expressed in wild-type cells but were strongly downregulated in acph1Δ/efg1Δ double mutant in α-minimal essential medium at 37°C, we could identify not-yet-characterized proteins, including Cor33-1p and Cor33-2p. The two proteins are almost identical (97% identity) and represent products of allelic isoforms of the same gene. Cor33p is highly similar to Cip1p fromCandidasp. but lacks any significant homology to proteins fromSaccharomyces cerevisiae. Strikingly, both proteins share homology with phenylcoumaran benzylic ether reductases and isoflavone reductases from plants. For other hypha-inducing media, like yeast-peptone-dextrose (YPD) plus serum at 37°C, we could not detect any transcription forCOR33in wild-type cells, indicating that Cor33p is not hypha specific. In contrast, we found a strong induction forCOR33when cells were treated with 5 mM hydrogen peroxide. However, under oxidative conditions, transcription ofCOR33was not dependent onEFG1, indicating that other regulatory factors are involved. In fact, upregulation depends onCAP1at least, as transcript levels were clearly reduced in a Δcap1mutant strain under oxidative conditions. Unlike in wild-type cells, transcription ofCOR33in atsa1Δ mutant can be induced by treatment with 0.1 mM hydrogen peroxide. This suggests a functional link betweenCOR33and thiol-specific antioxidant-like proteins that are important in the oxidative-stress response in yeasts. Concordantly,cor33Δ deletion mutants show retarded growth on YPD plates supplemented with hydrogen peroxide, indicating thatCOR33in general is implicated in conferring tolerance toward oxidative stress onCandida albicans.
A Novel, Highly Selective Inhibitor of Pestivirus Replication That Targets the Viral RNA-Dependent RNA Polymerase
Authors: Paeshuyse Jan , Leyssen Pieter , Mabery Eric , Boddeker Nina , Vrancken Robert , Froeyen Matheus , Ansari Israrul H. , Dutartre Hélène , Rozenski Jef , Gil Laura H. V. G. , Letellier Carine , Lanford Robert , Canard Bruno , Koenen Frank , Kerkhofs Pierre , Donis Ruben O. , Herdewijn Piet , Watson Julia , De Clercq Erik , Puerstinger Gerhard , Neyts Johan 
Published: December 2005

ABSTRACT

We
report on the highly potent and selective antipestivirus activity of
5-[(4-bromophenyl)methyl]-2-phenyl-5
H
-imidazo[4,5-c]pyridine
(BPIP). The 50% effective concentration (EC
50
) for
inhibition of bovine viral diarrhea virus (BVDV)-induced cytopathic
effect formation was 0.04 ± 0.01 μM. Comparable
reduction of viral RNA synthesis (EC
50
= 0.12±
0.02 μM) and production of infectious virus
(EC
50
= 0.074 ± 0.003 μM) were
observed. The selectivity index (ratio of 50% cytostatic
concentration/EC
50
) of BPIP was ∼2,000. BPIP was
inactive against the hepatitis C virus subgenomic replicon and yellow
fever virus but demonstrated weak activity against GB
virus. Drug-resistant mutants were at least 300-fold less
susceptible to BPIP than wild-type virus; showed cross-resistance to
N
-propyl-
N
-[2-(2
H
-1,2,4-triazino[5,6-b]indol-3-ylthio)ethyl]-1-propanamine
(VP32947), and carried the F224S mutation in the viral RNA-dependent
RNA polymerase (RdRp). When the F224S mutation was introduced into an
infectious clone, the drug-resistant phenotype was obtained. BPIP did
not inhibit the in vitro activity of recombinant BVDV RdRp, but did
inhibit the activity of replication complexes (RCs). Computational
docking revealed that F224 is located at the top of the finger domain
of the polymerase. Docking of BPIP in the crystal structure of the BVDV
RdRp revealed aromatic ring stacking, some hydrophobic contacts, and a
hydrogen bond. Since two structurally unrelated compounds, i.e., BPIP
and VP32947, target the same region of the BVDV RdRp, this position may
be expected to be critical in the functioning of the polymerase or
assembly of the RC. The potential of BPIP for the treatment of
pestivirus and hepacivirus infections is
discussed.
VP2 Cleavage and the Leucine Ring at the Base of the Fivefold Cylinder Control pH-Dependent Externalization of both the VP1 N Terminus and the Genome of Minute Virus of Mice
Authors: Farr Glen A. , Cotmore Susan F. , Tattersall Peter 
Published: December 2005

ABSTRACT
Cylindrical projections surrounding the fivefold-symmetry axes in minute virus of mice (MVM) harbor central pores that penetrate through the virion shell. In newly released DNA-containing particles, these pores contain residues 28 to 38 belonging to a single copy of VP2, disposed so that its extreme N-terminal domain projects outside the particle. Virions are metastable, initially sequestering internally the N termini of all copies of the minor capsid protein, VP1, that is essential for entry. This VP1 domain can be externalized in vitro in response to limited heating, and we show here that the efficiency of this transition is greatly enhanced by proteolysis of VP2 N termini to yield VP3. This step also renders the VP1 rearrangement pH dependent, indicating that VP2 cleavage is a maturation step required to prime subsequent emergence of the VP1 “entry” domain. The tightest constriction within the cylinder is created by VP2 leucine 172, the five symmetry-related copies of which form a portal that resembles an iris diaphragm across the base of the pore. In MVMp, threonine substitution at this position, L172T, yields infectious particles following transfection at 37°C, but these can initiate infection only at 32°C, and this process can be blocked by exposing virions to a cellular factor(s) at 37°C during the first 8 h after entry. At 32°C, the mutant particle is highly infectious, and it remains stable prior to VP2 cleavage or following cleavage at pH 5.5 or below. However, upon exposure to neutral pH following VP2 cleavage, its VP1-specific sequences and genome are extruded even at room temperature, underscoring the significance of the VP2 cleavage step for MVM particle dynamics.
Identification and Characterization of a
Penaeus monodon
Lymphoid Cell-Expressed Receptor for the Yellow Head Virus
Authors: Assavalapsakul Wanchai , Smith Duncan R. , Panyim Sakol 
Published: December 2005

ABSTRACT

The yellow head virus is a positive-sense, single-stranded RNA virus that causes significant mortality in farmed penaeid shrimp. This study sought to isolate and characterize the receptor protein used by the virus to gain entry into
Penaeus monodon
Oka (lymphoid) organ cells, a primary target of yellow head virus infections. Virus overlay protein binding assay on Oka organ membrane preparations identified a 65-kDa protein, and antibodies raised against this protein inhibited virus entry in primary Oka cell cultures by approximately 80%. N-terminal sequence analysis of the 65-kDa protein generated a 17-amino acid peptide fragment which was used to design degenerate primers that amplified a 1.5-kbp product from Oka organ total RNA, which was cloned and sequenced. Northern analysis and PCR were used to confirm a single RNA transcript that was expressed in most tissues. Subsequently, the mature cDNA was recloned and the expressed protein shown to cross-react with the antibody raised against the original virus binding band. Down regulation of the message through double-stranded RNA-mediated RNA interference silencing resulted in the complete inhibition of virus entry. While the identity of the clone remains unknown, it nevertheless represents the first invertebrate
Nidovirus
receptor isolated to date.
Alternative Sigma Factors and Their Roles in Bacterial Virulence
Authors: Kazmierczak Mark J. , Wiedmann Martin , Boor Kathryn J. 
Published: December 2005

SUMMARY

Sigma factors provide promoter recognition specificity to RNA polymerase holoenzyme, contribute to DNA strand separation, and then dissociate from the core enzyme following transcription initiation. As the regulon of a single sigma factor can be composed of hundreds of genes, sigma factors can provide effective mechanisms for simultaneously regulating expression of large numbers of prokaryotic genes. One newly emerging field is identification of the specific roles of alternative sigma factors in regulating expression of virulence genes and virulence-associated genes in bacterial pathogens. Virulence genes encode proteins whose functions are essential for the bacterium to effectively establish an infection in a host organism. In contrast, virulence-associated genes can contribute to bacterial survival in the environment and therefore may enhance the capacity of the bacterium to spread to new individuals or to survive passage through a host organism. As alternative sigma factors have been shown to regulate expression of both virulence and virulence-associated genes, these proteins can contribute both directly and indirectly to bacterial virulence. Sigma factors are classified into two structurally unrelated families, the σ
70
and the σ
54
families. The σ
70
family includes primary sigma factors (e.g.,
Bacillus subtilis
σ
A
) as well as related alternative sigma factors; σ
54
forms a distinct subfamily of sigma factors referred to as σ
N
in almost all species for which these proteins have been characterized to date. We present several examples of alternative sigma factors that have been shown to contribute to virulence in at least one organism. For each sigma factor, when applicable, examples are drawn from multiple species.
Bacterial Cell Wall Synthesis: New Insights from Localization Studies
Authors: Scheffers Dirk-Jan , Pinho Mariana G. 
Published: December 2005

SUMMARYIn order to maintain shape and withstand intracellular pressure, most bacteria are surrounded by a cell wall that consists mainly of the cross-linked polymer peptidoglycan (PG). The importance of PG for the maintenance of bacterial cell shape is underscored by the fact that, for various bacteria, several mutations affecting PG synthesis are associated with cell shape defects. In recent years, the application of fluorescence microscopy to the field of PG synthesis has led to an enormous increase in data on the relationship between cell wall synthesis and bacterial cell shape. First, a novel staining method enabled the visualization of PG precursor incorporation in live cells. Second, penicillin-binding proteins (PBPs), which mediate the final stages of PG synthesis, have been localized in various model organisms by means of immunofluorescence microscopy or green fluorescent protein fusions. In this review, we integrate the knowledge on the last stages of PG synthesis obtained in previous studies with the new data available on localization of PG synthesis and PBPs, in both rod-shaped and coccoid cells. We discuss a model in which, at least for a subset of PBPs, the presence of substrate is a major factor in determining PBP localization.
Synchronous adenocarcinoma and carcinoid tumor of the terminal ileum in a Crohn's disease patient
Authors: Cioffi Ugo , De Simone Matilde , Ferrero Stefano , Ciulla Michele M , Lemos Alessandro , Avesani Ettore Contessini 
Published: December 2005

Abstract

Background
Several malignancies have been described in association with inflammatory bowel diseases, the most common being adenocarcinoma. Carcinoid tumor and Crohn disease has also been previously reported, however the coexistence of both neoplasms is quite rare and the clinical diagnosis is very difficult. Here we report what we believe to be the fourth case of a mixed adenocarcinoid tumor coexisting with Crohn's disease.

Case report
The patient presented with clinical and radiological features of intestinal obstruction. Laparotomy showed a stricturing lesion in the last 6 cm of the terminal ileum with proximal dilation. Only the histology of the resected surgical specimen proved the presence of a mixed adenocarcinoid tumor involving the terminal ileum.

Conclusion
Carcinoid tumor should be suspected in elderly patients with Crohn's disease presenting with intestinal obstruction and laparotomy should be considered to exclude malignancy.
Rating of personality disorder features in popular movie characters
Authors: Hesse Morten , Schliewe Sanna , Thomsen Rasmus R 
Published: December 2005

AbstractBackgroundTools for training professionals in rating personality disorders are few. We present one such tool: rating of fictional persons. However, before ratings of fictional persons can be useful, we need to know whether raters get the same results, when rating fictional characters.MethodPsychology students at the University of Copenhagen (N = 8) rated four different movie characters from four movies based on three systems: Global rating scales representing each of the 10 personality disorders in the DSM-IV, a criterion list of all criteria for all DSM-IV personality disorders in random order, and the Ten Item Personality Inventory for rating the five-factor model. Agreement was estimated based on intraclass-correlation.ResultsAgreement for rating scales for personality disorders ranged from 0.04 to 0.54. For personality disorder features based on DSM-IV criteria, agreement ranged from 0.24 to 0.89, and agreement for the five-factor model ranged from 0.05 to 0.88. The largest multivariate effect was observed for criteria count followed by the TIPI, followed by rating scales. Raters experienced personality disorder criteria as the easiest, and global personality disorder scales as the most difficult, but with significant variation between movies.ConclusionPsychology students with limited or no clinical experience can agree well on the personality traits of movie characters based on watching the movie. Rating movie characters may be a way to practice assessment of personality.
Skin infection, housing and social circumstances in children living in remote Indigenous communities: testing conceptual and methodological approaches
Authors: Bailie Ross S , Stevens Matthew R , McDonald Elizabeth , Halpin Stephen , Brewster David , Robinson Gary , Guthridge Steven 
Published: December 2005

Abstract

Background
Poor housing conditions in remote Indigenous communities in Australia are a major underlying factor in poor child health, including high rates of skin infections. The aim of this study is to test approaches to data collection, analysis and feedback for a follow-up study of the impact of housing conditions on child health.

Methods
Participation was negotiated in three communities with community councils and individual participants. Data were collected by survey of dwelling condition, interviews, and audit health centre records of children aged under seven years. Community feedback comprised immediate report of items requiring urgent repair followed by a summary descriptive report. Multivariate models were developed to calculate adjusted incidence rate ratios (IRR) for skin infections and their association with aspects of household infrastructure.

Results
There was a high level of participation in all communities. Health centre records were inadequate for audit in one community. The records of 138 children were available for development of multivariate analytic models. Rates of skin infection in dwellings that lacked functioning facilities for removing faeces or which had concrete floors may be up to twice as high as for other dwellings, and the latter association appears to be exacerbated by crowding. Younger children living in older dwellings may also be at approximately two-fold higher risk. A number of socioeconomic and socio-demographic variables also appear to be directly associated with high rates of skin infections.

Conclusion
The methods used in the pilot study were generally feasible, and the analytic approach provides meaningful results. The study provides some evidence that new and modern housing is contributing to a reduction in skin infections in Aboriginal children in remote communities, particularly when this housing leads to a reduction in crowding and the effective removal of human waste.