bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein Folding Failure Sets High-Temperature Limit on Growth of Phage P22 in
Salmonella enterica
Serovar Typhimurium
Authors: Pope Welkin H. , Haase-Pettingell Cameron , King Jonathan 
Published: August 2004

ABSTRACT

The high-temperature limit for growth of microorganisms differs greatly depending on their species and habitat. The importance of an organism's ability to manage thermal stress is reflected in the ubiquitous distribution of the heat shock chaperones. Although many chaperones function to reduce protein folding defects, it has been difficult to identify the specific protein folding pathways that set the high-temperature limit of growth for a given microorganism. We have investigated this for a simple system, phage P22 infection of
Salmonella enterica
serovar Typhimurium. Production of infectious particles exhibited a broad maximum of 150 phage per cell when host cells were grown at between 30 and 39°C in minimal medium. Production of infectious phage declined sharply in the range of 40 to 41°C, and at 42°C, production had fallen to less than 1% of the maximum rate. The host cells maintained optimal division rates at these temperatures. The decrease in phage infectivity was steeper than the loss of physical particles, suggesting that noninfectious particles were formed at higher temperatures. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed a decrease in the tailspike adhesins assembled on phage particles purified from cultures incubated at higher temperatures. The infectivity of these particles was restored by in vitro incubation with soluble tailspike trimers. Examination of tailspike folding and assembly in lysates of phage-infected cells confirmed that the fraction of polypeptide chains able to reach the native state in vivo decreased with increasing temperature, indicating a thermal folding defect rather than a particle assembly defect. Thus, we believe that the folding pathway of the tailspike adhesin sets the high-temperature limit for P22 formation in
Salmonella
serovar Typhimurium.
Characterization of Coliphage PR772 and Evaluation of Its Use for Virus Filter Performance Testing
Authors: Lute Scott , Aranha Hazel , Tremblay Denise , Liang Dehai , Ackermann Hans-W. , Chu Benjamin , Moineau Sylvain , Brorson Kurt 
Published: August 2004

ABSTRACT

Virus filtration is a key clearance unit operation in the manufacture of recombinant protein, monoclonal antibody, and plasma-derived biopharmaceuticals. Recently, a consensus has developed among filter manufacturers and end users about the desirability of a common nomenclature and a standardized test for classifying and identifying virus-retentive filters. The Parenteral Drug Association virus filter task force has chosen PR772 as the model bacteriophage to standardize nomenclature for large-pore-size virus-retentive filters (filters designed to retain viruses larger than 50 to 60 nm in size). Previously, the coliphage PR772 (
Tectiviridae
family) has been used in some filtration studies as a surrogate for mammalian viruses of around 50 to 60 nm. In this report, we describe specific properties of PR772 critical to the support of its use for the standardization of virus filters. The complete genomic sequence of virulent phage PR772 was determined. Its genome contains 14,946 bp with an overall G+C content of 48.3 mol%, and 32 open reading frames of at least 40 codons. Comparison of the PR772 nucleotide sequence with the genome of
Tectiviridae
family prototype phage PRD1 revealed 97.2% identity at the DNA level. By dynamic light-scattering analysis, its hydrodynamic diameter was measured as 82 ± 6 nm, consistent with use in testing large-virus-retentive filters. Finally, dynamic light-scattering analysis of PR772 preparations purified on CsCl gradients showed that the phage preparations are largely monodispersed. In summary, PR772 appears to be an appropriate model bacteriophage for standardization of nomenclature for larger-pore-size virus-retentive filters.
Dominant Microbial Composition and Its Vertical Distribution in Saline Meromictic Lake Kaiike (Japan) as Revealed by Quantitative Oligonucleotide Probe Membrane Hybridization
Authors: Koizumi Yoshikazu , Kojima Hisaya , Fukui Manabu 
Published: August 2004

ABSTRACT

Vertical distributions of dominant bacterial populations in saline meromictic Lake Kaiike were investigated throughout the water column and sediment by quantitative oligonucleotide probe membrane hybridization. Three oligonucleotide probes specific for the small-subunit (SSU) rRNA of three groups of
Chlorobiaceae
were newly designed. In addition, three general domain (
Bacteria
,
Archaea
, and
Eukarya
)-specific probes, two δ-
Proteobacteria
-specific probes, a
Chlorobiaceae
-specific probe, and a
Chloroflexi
-specific probe were used after optimization of their washing conditions. The abundance of the sum of SSU rRNAs hybridizing with probes specific for three groups of
Chlorobiaceae
relative to total SSU rRNA peaked in the chemocline, accounting for up to 68%. The abundance of the δ-proteobacterial SSU rRNA relative to total SSU rRNA rapidly increased just below the chemocline up to 29% in anoxic water and peaked at the 2- to 3-cm sediment depth at ca. 34%. The abundance of SSU rRNAs hybridizing with the probe specific for the phylum
Chloroflexi
relative to total SSU rRNA was highest (31 to 54%) in the top of the sediment but then steeply declined with depth and became stable at 11 to 19%, indicating the robust coexistence of sulfate-reducing bacteria and
Chloroflexi
in the top of the sediment. Any SSU rRNA of
Chloroflexi
in the water column was under the detection limit. The summation of the signals of group-specific probes used in this study accounted for up to 89% of total SSU rRNA, suggesting that the DGGE-oligonucleotide probe hybridization approach, in contrast to conventional culture-dependent approaches, was very effective in covering dominant populations.
Differential Gene Expression To Investigate the Effect of (
5Z
)-4-Bromo- 5-(Bromomethylene)-3-Butyl-2(
5H
)-Furanone on
Bacillus subtilis
Authors: Ren Dacheng , Bedzyk Laura A. , Setlow Peter , England Dacre F. , Kjelleberg Staffan , Thomas Stuart M. , Ye Rick W. , Wood Thomas K. 
Published: August 2004

ABSTRACT

(
5Z
)-4-Bromo-5-(bromomethylene)-3-butyl-2(
5H
)-furanone (furanone) from the red marine alga
Delisea pulchra
was found previously to inhibit the growth, swarming, and biofilm formation of gram-positive bacteria. Using the gram-positive bacterium
Bacillus subtilis
as a test organism, we observed cell killing by 20 μg of furanone per ml, while 5 μg of furanone per ml inhibited growth approximately twofold without killing the cells. To discover the mechanism of this inhibition on a genetic level and to investigate furanone as a novel antibiotic, full-genome DNA microarrays were used to analyze the gene expression profiles of
B. subtilis
grown with and without 5 μg of furanone per ml. This agent induced 92 genes more than fivefold (
P
< 0.05) and repressed 15 genes more than fivefold (
P
< 0.05). The induced genes include genes involved in stress responses (such as the class III heat shock genes
clpC
,
clpE
, and
ctsR
and the class I heat shock genes
groES
, but no class II or IV heat shock genes), fatty acid biosynthesis, lichenan degradation, transport, and metabolism, as well as 59 genes with unknown functions. The microarray results for four genes were confirmed by RNA dot blotting. Mutation of a stress response gene,
clpC
, caused
B. subtilis
to be much more sensitive to 5 μg of furanone per ml (there was no growth in 8 h, while the wild-type strain grew to the stationary phase in 8 h) and confirmed the importance of the induction of this gene as identified by the microarray analysis.
Model System for Growing and Quantifying
Streptococcus pneumoniae
Biofilms In Situ and in Real Time
Authors: Donlan R. M. , Piede J. A. , Heyes C. D. , Sanii L. , Murga R. , Edmonds P. , El-Sayed I. , El-Sayed M. A. 
Published: August 2004

ABSTRACT

Streptococcus pneumoniae
forms biofilms, but little is known about its extracellular polymeric substances (EPS) or the kinetics of biofilm formation. A system was developed to enable the simultaneous measurement of cells and the EPS of biofilm-associated
S. pneumoniae
in situ over time. A biofilm reactor containing germanium coupons was interfaced to an attenuated total reflectance (ATR) germanium cell of a Fourier transform infrared (FTIR) laser spectrometer. Biofilm-associated cells were recovered from the coupons and quantified by total and viable cell count methods. ATR-FTIR spectroscopy of biofilms formed on the germanium internal reflection element (IRE) of the ATR cell provided a continuous spectrum of biofilm protein and polysaccharide (a measure of the EPS). Staining of the biofilms on the IRE surface with specific fluorescent probes provided confirmatory evidence for the biofilm structure and the presence of biofilm polysaccharides. Biofilm protein and polysaccharides were detected within hours after inoculation and continued to increase for the next 141 h. The polysaccharide band increased at a substantially higher rate than did the protein band, demonstrating increasing coverage of the IRE surface with biofilm polysaccharides. The biofilm total cell counts on germanium coupons stabilized after 21 h, at approximately 10
5
cells per cm
2
, while viable counts decreased as the biofilm aged. This system is unique in its ability to detect and quantify biofilm-associated cells and EPS of
S. pneumoniae
over time by using multiple, corroborative techniques. This approach could prove useful for the study of biofilm processes of this or other microorganisms of clinical or industrial relevance.
VdNEP, an Elicitor from
Verticillium dahliae
, Induces Cotton Plant Wilting
Authors: Wang Jian-Ying , Cai Yu , Gou Jin-Ying , Mao Ying-Bo , Xu Yan-Hua , Jiang Wei-Hong , Chen Xiao-Ya 
Published: August 2004

ABSTRACT

Verticillium wilt is a vascular disease of cotton. The causal fungus,
Verticillium dahliae
, secretes elicitors in culture. We have generated ∼1,000 5′-terminal expressed sequence tags (ESTs) from a cultured mycelium of
V. dahliae
. A number of ESTs were found to encode proteins harboring putative signal peptides for secretion, and their cDNAs were isolated. Heterologous expression led to the identification of a protein with elicitor activities. This protein, named
V. dahliae
necrosis- and ethylene-inducing protein (VdNEP), is composed of 233 amino acids and has high sequence identities with fungal necrosis- and ethylene-inducing proteins. Infiltration of the bacterially expressed His-VdNEP into
Nicotiana benthamiana
leaves resulted in necrotic lesion formation. In
Arabidopsis thaliana
, the fusion protein also triggered production of reactive oxygen species and induced the expression of
PR
genes. When added into suspension cultured cells of cotton (
Gossypium arboreum
), the fusion protein elicited the biosynthesis of gossypol and related sesquiterpene phytoalexins at low concentrations, and it induced cell death at higher concentrations. On cotton cotyledons and leaves, His-VdNEP induced dehydration and wilting, similar to symptoms caused by a crude preparation of
V. dahliae
elicitors. Northern blotting showed a low level of
VdNEP
expression in the mycelium during culture. These data suggest that VdNEP is a wilt-inducing factor and that it participates in cotton-
V. dahliae
interactions.
Direct Production of Ethanol from Raw Corn Starch via Fermentation by Use of a Novel Surface-Engineered Yeast Strain Codisplaying Glucoamylase and α-Amylase
Authors: Shigechi Hisayori , Koh Jun , Fujita Yasuya , Matsumoto Takeshi , Bito Yohei , Ueda Mitsuyoshi , Satoh Eiichi , Fukuda Hideki , Kondo Akihiko 
Published: August 2004

ABSTRACT

Direct and efficient production of ethanol by fermentation from raw corn starch was achieved by using the yeast
Saccharomyces cerevisiae
codisplaying
Rhizopus oryzae
glucoamylase and
Streptococcus bovis
α-amylase by using the C-terminal-half region of α-agglutinin and the flocculation functional domain of Flo1p as the respective anchor proteins. In 72-h fermentation, this strain produced 61.8 g of ethanol/liter, with 86.5% of theoretical yield from raw corn starch.
Temporal Transcription Map of the Virulent
Streptococcus thermophilus
Bacteriophage Sfi19
Authors: Ventura Marco , Brüssow Harald 
Published: August 2004

ABSTRACT

A transcription map was developed for the virulent
Streptococcus thermophilus
phage Sfi19 on the basis of systematic Northern blot hybridizations. All deduced 5′ ends were confirmed by primer extension experiments. Three classes of transcripts were detected based on the different times of appearance. Early transcripts were identified in three genome regions; middle transcripts covered
cro
-like, DNA replication, and transcriptional regulation genes; and late genes consisted of structural and lysis genes. Chloramphenicol treatment suppressed the translation of a putative transcriptional factor necessary for the production of late transcripts and shifted middle transcripts to early transcription times.
C-type lectin-like domains in Fugu rubripes
Authors: Zelensky Alex N , Gready Jill E 
Published: August 2004

Abstract
Background
Members of the C-type lectin domain (CTLD) superfamily are metazoan proteins functionally important in glycoprotein metabolism, mechanisms of multicellular integration and immunity. Three genome-level studies on human, C. elegans and D. melanogaster reported previously demonstrated almost complete divergence among invertebrate and mammalian families of CTLD-containing proteins (CTLDcps).

Results
We have performed an analysis of CTLD family composition in Fugu rubripes using the draft genome sequence. The results show that all but two groups of CTLDcps identified in mammals are also found in fish, and that most of the groups have the same members as in mammals. We failed to detect representatives for CTLD groups V (NK cell receptors) and VII (lithostathine), while the DC-SIGN subgroup of group II is overrepresented in Fugu. Several new CTLD-containing genes, highly conserved between Fugu and human, were discovered using the Fugu genome sequence as a reference, including a CSPG family member and an SCP-domain-containing soluble protein. A distinct group of soluble dual-CTLD proteins has been identified, which may be the first reported CTLDcp group shared by invertebrates and vertebrates. We show that CTLDcp-encoding genes are selectively duplicated in Fugu, in a manner that suggests an ancient large-scale duplication event. We have verified 32 gene structures and predicted 63 new ones, and make our annotations available through a distributed annotation system (DAS) server http://anz.anu.edu.au:8080/Fugu_rubripes/ and their sequences as additional files with this paper.

Conclusions
The vertebrate CTLDcp family was essentially formed early in vertebrate evolution and is completely different from the invertebrate families. Comparison of fish and mammalian genomes revealed three groups of CTLDcps and several new members of the known groups, which are highly conserved between fish and mammals, but were not identified in the study using only mammalian genomes. Despite limitations of the draft sequence, the Fugu rubripes genome is a powerful instrument for gene discovery and vertebrate evolutionary analysis. The composition of the CTLDcp superfamily in fish and mammals suggests that large-scale duplication events played an important role in the evolution of vertebrates.
Treating Functional Impairment of Autism with Selective Serotonin-Reuptake Inhibitors
Authors: Moore Malia L , Eichner Samantha F , Jones Jennifer R 
Published: August 2004

OBJECTIVE: To review literature describing use of selective serotonin-reuptake inhibitors (SSRIs) in the management of functional impairments associated with autistic disorder. DATA SOURCES: EMBASE (1980—3rd quarter of 2003), International Pharmaceutical Abstracts (1970–August 2003), and MEDLINE (1966–August 2003) were searched. Search terms included autism, autistic disorder, citalopram, fluoxetine, fluvoxamine, paroxetine, selective serotonin-reuptake inhibitors, and sertraline. DATA SYNTHESIS: Studies and case reports evaluating treatment outcomes associated with the use of SSRIs in managing impairments of autism were reviewed. Multiple SSRI dosing ranges were evaluated in autistic patients of different ages with various functional impairments. No specific SSRI or dose range has been shown to improve a specific autistic symptom although some patients have demonstrated improvements. CONCLUSIONS: Benefits with SSRIs in treating functional impairments in autism have been observed. Response to therapy and adverse effects are individualized. Current evidence does not support selection of one SSRI over another for any impairment associated with autism.
Highly Sensitive Screening Method for Nitroaromatic, Nitramine and Nitrate Ester Explosives by High Performance Liquid Chromatography—Atmospheric Pressure Ionization—Mass Spectrometry (HPLC-API-MS) in Forensic Applications
Authors: Xu X , van de Craats AM , de Bruyn PCAM 
Published: August 2004

Abstract
A highly sensitive screening method based on high performance liquid chromatography atmospheric pressure ionization mass spectrometry (HPLC-API-MS) has been developed for the analysis of 21 nitroaromatic, nitramine and nitrate ester explosives, which include the explosives most commonly encountered in forensic science. Two atmospheric pressure ionization (API) methods, atmospheric pressure chemical ionization (APCI) and electrospray ionization (ESI), and various experimental conditions have been applied to allow for the detection of all 21 explosive compounds. The limit of detection (LOD) in the full-scan mode has been found to be 0.012–1.2 ng on column for the screening of most explosives investigated. For nitrobenzene, an LOD of 10 ng was found with the APCI method in the negative mode. Although the detection of nitrobenzene, 2-, 3-, and 4-nitrotoluene is hindered by the difficult ionization of these compounds, we have found that by forming an adduct with glycine, LOD values in the range of 3–16 ng on column can be achieved. Compared with previous screening methods with thermospray ionization, the API method has distinct advantages, including simplicity and stability of the method applied, an extended screening range and a low detection limit for the explosives studied.
Characterization of Allegedly Musk-Containing Medicinal Products in Taiwan
Authors: Lin DL , Chang HC , Huang SH 
Published: August 2004

Abstract
As a highly valued ingredient of Chinese medicinal remedies, musk is used as a detoxification agent and for treating fever, inflammation and swelling, and pain. Muscone (3-methylcyclopentadecanone-1), an odoriferous secretion from the ventral glands of male musk deer, is believed to be the active ingredient. A small amount of muscopyridine is also found in the secretion from the ventral glands of male musk deer. Common counterfeit ingredients are musk xylene, musk ambrette, musk ketone, and diphenhydramine. An extraction/GC-MS protocol/data evaluation scheme was developed and applied to study allegedly musk-containing Musk-Tiger Bone Plaster preparations and musk pods (or grains) from Chinese medicine stores and an airport customs. The content of muscone in a specific sample was estimated based on the percentage of the amount recovered from the first extraction. No muscone or counterfeit ingredients were found in all musk pod (or grain) samples from the customs and in the majority of Musk-Tiger Bone Plaster preparations, while muscone (alone or with counterfeit ingredients) was found in most of the musk pod (or grain) collected from Chinese medicine stores.
Addressing the Use of Phylogenetics for Identification of Sequences in Error in the SWGDAM Mitochondrial DNA Database
Authors: Budowle B , Polanskey D , Allard MW , Chakraborty R 
Published: August 2004

Abstract
The SWGDAM mtDNA database is a publicly available reference source that is used for estimating the rarity of an evidence mtDNA profile. Because of the current processes for generating population data, it is unlikely that population databases are error free. The majority of the errors are due to human error and are transcriptional in nature. Phylogenetic analysis of data sets can identify some potential errors, and coupled with a review of the sequence data or alignment sheets can be a very useful tool. Seven sequences with errors have been identified by phylogenetic analysis. In addition, two samples were inadvertently modified when placed in the SWGDAM database. The corrected sequences are provided so that users can modify appropriately the current iteration of the SWGDAM database. From a practical perspective, upper bound estimates of the percentage of matching profiles obtained from a database search containing an incorrect sequence and those of a database containing the corrected sequence are not substantially different. Community wide access and review has enabled identification of errors in the SWGDAM data set and will continue to do so. The result of public accessibility is that the quality of the SWGDAM forensic dataset is always improving.
Rasterreflexions-Photogrammetrie zur Messung spiegelnder Oberflächen (Reflection Grating Photogrammetry for the Measurement of Specular Surfaces)
Authors: Petz Marcus , Tutsch Rainer 
Published: July 2004

Abstract
Die berührungslose dreidimensionale Messung spiegelnd reflektierender Freiformflächen bereitet trotz neuerer Fortschritte auf dem Gebiet der Asphärenprüfung noch immer erhebliche Schwierigkeiten. Die in diesem Beitrag vorgestellten geometrisch-optischen Messverfahren nach dem Rasterreflexionsprinzip ermöglichen durch Kombination mit photogrammetrischen Auswertetechniken die punktweise und eindeutige Erfassung nahezu beliebig geformter spiegelnder Oberflächen.
Extension of the age‐of‐fluid method to unsteady and closed‐flow systems
Authors: Jongen T. 
Published: July 2004

AbstractThe age‐of‐fluid method is revisited to evaluate and extend it from its traditional application domain of steady, open‐flow systems to general unsteady and/or closed‐flow systems. The most significant change in the approach comes from the definition of the age of the fluid in a purely kinematic way as a tagging variable, and based solely on the velocity field of the underlying fluid, whereas all the other methods proposed to date somehow determine the age indirectly by tracking an injected tracer material in the flow domain. The resulting mathematical formulation makes it possible to specify the age at arbitrary positions within the flow domain, while being formally very similar to the classical age‐of‐fluid transport equations previously obtained. This has the benefit of clarifying a number of issues such as the treatment of the diffusion coefficient, the definition of suitable boundary conditions, the validation in unsteady flow conditions, and the extension to closed‐flow domains. © 2004 American Institute of Chemical Engineers AIChE J, 50: 2020–2037, 2004