bluuebunny/crossref_metadata_2025_split huggingface dataset:
Consumption of Tropospheric Levels of Methyl Bromide by C
1
Compound-Utilizing Bacteria and Comparison to Saturation Kinetics
Authors: Goodwin Kelly D. , Varner Ruth K. , Crill Patrick M. , Oremland Ronald S. 
Published: July 2002

ABSTRACT

Pure cultures of methylotrophs and methanotrophs are known to oxidize methyl bromide (MeBr); however, their ability to oxidize tropospheric concentrations (parts per trillion by volume [pptv]) has not been tested. Methylotrophs and methanotrophs were able to consume MeBr provided at levels that mimicked the tropospheric mixing ratio of MeBr (12 pptv) at equilibrium with surface waters (≈2 pM). Kinetic investigations using picomolar concentrations of MeBr in a continuously stirred tank reactor (CSTR) were performed using strain IMB-1 and
Leisingeria methylohalidivorans
strain MB2
T
— terrestrial and marine methylotrophs capable of halorespiration. First-order uptake of MeBr with no indication of threshold was observed for both strains. Strain MB2
T
displayed saturation kinetics in batch experiments using micromolar MeBr concentrations, with an apparent
K

s

of 2.4 μM MeBr and a
V
max
of 1.6 nmol h
−1
(10
6
cells)
−1
. Apparent first-order degradation rate constants measured with the CSTR were consistent with kinetic parameters determined in batch experiments, which used 35- to 1 × 10
7
-fold-higher MeBr concentrations.
Ruegeria algicola
(a phylogenetic relative of strain MB2
T
), the common heterotrophs
Escherichia coli
and
Bacillus pumilus
, and a toluene oxidizer,
Pseudomonas mendocina
KR1, were also tested. These bacteria showed no significant consumption of 12 pptv MeBr; thus, the ability to consume ambient mixing ratios of MeBr was limited to C
1
compound-oxidizing bacteria in this study. Aerobic C
1
bacteria may provide model organisms for the biological oxidation of tropospheric MeBr in soils and waters.
Attenuated Nontoxinogenic and Nonencapsulated Recombinant
Bacillus anthracis
Spore Vaccines Protect against Anthrax
Authors: Cohen S. , Mendelson I. , Altboum Z. , Kobiler D. , Elhanany E. , Bino T. , Leitner M. , Inbar I. , Rosenberg H. , Gozes Y. , Barak R. , Fisher M. , Kronman C. , Velan B. , Shafferman A. 
Published: July 2002

ABSTRACT

Several highly attenuated spore-forming nontoxinogenic and nonencapsulated
Bacillus anthracis
vaccines differing in levels of expression of recombinant protective antigen (rPA) were constructed. Biochemical analyses (including electrospray mass spectroscopy and N terminus amino acid sequencing) as well as biological and immunological tests demonstrated that the rPA retains the characteristics of native PA. A single immunization of guinea pigs with 5 × 10
7
spores of one of these recombinant strains, MASC-10, expressing high levels of rPA (≥100 μg/ml) from a constitutive heterologous promoter induced high titers of neutralizing anti-PA antibodies. This immune response was long lasting (at least 12 months) and provided protection against a lethal challenge of virulent (Vollum) anthrax spores. The recombinant
B. anthracis
spore vaccine appears to be more efficacious than the vegetative cell vaccine. Furthermore, while results clearly suggest a direct correlation between the level of expression of PA and the potency of the vaccine, they also suggest that some
B. anthracis
spore-associated antigen(s) may contribute in a significant manner to protective immunity.
Genetic Polymorphisms of Group B StreptococcusscpBAlter Functional Activity of a Cell-Associated Peptidase That Inactivates C5a
Authors: Bohnsack John F. , Takahashi Shinji , Hammitt Laura , Miller Dylan V. , Aly Adrienne A. , Adderson Elisabeth E. 
Published: July 2002

ABSTRACTMany group BStreptococcus agalactiaestrains and other pathogenic streptococci express a cell-associated peptidase that inactivates C5a (C5a-ase), the major neutrophil chemoattractant produced by activation of the complement cascade. Type III group B streptococci (GBS) can be classified genotypically into three restriction digest pattern types. Functional C5a-ase activity of GBS correlates with this genetic typing; therefore, we sought to identify a genetic basis for this phenomenon. Southern hybridization confirms that all type III GBS containscpB, the gene encoding GBS C5a-ase. GBS strains with high C5a-ase functional activity and those with no or very low activity both express immunoreactive C5a-ase. ThescpBsequence of strain I30, which has high C5a-ase activity, is 98.2% homologous to the previously reported serotype II GBSscpBsequence. ThescpBsequences of strains I25 and GW, which have low or no C5a-ase activity, are identical. The predicted I25 and GW C5a-ase proteins share a four-amino-acid deletion affecting the protease histidine active-site consensus motif. Recombinant I30 C5a-ase has good functional activity, whereas recombinant I25 C5a-ase has low activity. These data demonstrate that functional C5a-ase differences between type III GBS strains are attributable to a genetic polymorphism ofscpB. The ubiquitous expression of C5a-ase, irrespective of functional activity, suggests that C5a-ase may have a second, as yet unidentified, function.
Differential Vβ T-Cell Receptor Usage during Chronic Experimental Schistosomiasis Corresponds with Distinct Pathological Presentations
Authors: Secor W. Evan , Freeman George L. 
Published: July 2002

ABSTRACTCBA/J male mice with chronicSchistosoma mansoniinfections display either moderate splenomegaly syndrome (MSS) or hypersplenomegaly syndrome (HSS). As MSS and HSS mice differ in several immunologic characteristics, we investigated T-cell receptor Vβ usage. The groups had significantly different expression of several Vβs, suggesting a relationship between the T-cell repertoire and schistosomiasis pathology.
Mice Lacking T and B Lymphocytes Develop Transient Colitis and Crypt Hyperplasia yet Suffer Impaired Bacterial Clearance during
Citrobacter rodentium
Infection
Authors: Vallance Bruce A. , Deng Wanyin , Knodler Leigh A. , Finlay B. Brett 
Published: July 2002

ABSTRACT

The bacterial pathogen
Citrobacter rodentium
belongs to a family of gastrointestinal pathogens that includes enteropathogenic and enterohemorrhagic
Escherichia coli
and is the causative agent of transmissible colonic hyperplasia in mice. The molecular mechanisms used by these pathogens to colonize host epithelial surfaces and form attaching and effacing (A/E) lesions have undergone intense study. In contrast, little is known about the host's immune response to these infections and its importance in tissue pathology and bacterial clearance. To address these issues, wild-type mice and mice lacking T and B lymphocytes (RAG1 knockout [KO]) were infected with
C. rodentium.
By day 10 postinfection (p.i.), both wild-type and RAG1 KO mice developed colitis and crypt hyperplasia, and these responses became more exaggerated in wild-type mice over the next 2 weeks, as they cleared the infection. By day 24 p.i., bacterial clearance was complete, and the colitis had subsided; however, crypt heights remained increased. In contrast, inflammatory and crypt hyperplastic responses in the RAG1 KO mice were transient, subsiding after 2 weeks. By day 24 p.i., RAG1 KO mice showed no signs of bacterial clearance and infection was often fatal. Surprisingly, despite remaining heavily infected, tissues from RAG1 KO mice surviving the acute colitis showed few signs of disease. These results thus emphasize the important contribution of the host immune response during infection by A/E bacterial pathogens. While T and/or B lymphocytes are essential for host defense against
C. rodentium
, they also mediate much of the tissue pathology and disease symptoms that occur during infection.
Functional Analysis of 14 Genes That Constitute the Purine Catabolic Pathway in
Bacillus subtilis
and Evidence for a Novel Regulon Controlled by the PucR Transcription Activator
Authors: Schultz Anna C. , Nygaard Per , Saxild Hans H. 
Published: July 2002

ABSTRACT

The soil bacterium
Bacillus subtilis
has developed a highly controlled system for the utilization of a diverse array of low-molecular-weight compounds as a nitrogen source when the preferred nitrogen sources, e.g., glutamate plus ammonia, are exhausted. We have identified such a system for the utilization of purines as nitrogen source in
B. subtilis
. Based on growth studies of strains with knockout mutations in genes, complemented with enzyme analysis, we could ascribe functions to 14 genes encoding enzymes or proteins of the purine degradation pathway. A functional xanthine dehydrogenase requires expression of five genes (
pucA, pucB, pucC, pucD
, and
pucE
). Uricase activity is encoded by the
pucL
and
pucM
genes, and a uric acid transport system is encoded by
pucJ
and
pucK
. Allantoinase is encoded by the
pucH
gene, and allantoin permease is encoded by the
pucI
gene. Allantoate amidohydrolase is encoded by
pucF
. In a
pucR
mutant, the level of expression was low for all genes tested, indicating that PucR is a positive regulator of
puc
gene expression. All 14 genes except
pucI
are located in a gene cluster at 284 to 285° on the chromosome and are contained in six transcription units, which are expressed when cells are grown with glutamate as the nitrogen source (limiting conditions), but not when grown on glutamate plus ammonia (excess conditions). Our data suggest that the 14 genes and the
gde
gene, encoding guanine deaminase, constitute a regulon controlled by the
pucR
gene product. Allantoic acid, allantoin, and uric acid were all found to function as effector molecules for PucR-dependent regulation of
puc
gene expression. When cells were grown in the presence of glutamate plus allantoin, a 3- to 10-fold increase in expression was seen for most of the genes. However, expression of the
pucABCDE
unit was decreased 16-fold, while expression of
pucR
was decreased 4-fold in the presence of allantoin. We have identified genes of the purine degradation pathway in
B. subtilis
and showed that their expression is subject to both general nitrogen catabolite control and pathway-specific control.
Lambda Excision Revisited: Testing a Model for Synapsis of Prophage Ends
Authors: Pato Martin L. 
Published: July 2002

ABSTRACT
Excision of lambda prophage was reexamined to test a model for prophage end synapsis. The model proposes that, during in situ prophage replication, following induction, the diverging replication forks are held together. Consequently, prophage DNA is spooled through the replication machinery, drawing the prophage ends together and facilitating synapsis. The model predicts that excision will be slowed if in situ lambda replication is inhibited, and the predicted low rate of excision of a nonreplicating prophage was observed after thermoinduction. However, excision was rapid if additional Int protein was supplied or if the temperature was reduced after induction, showing that (i) Int is partially thermosensitive for excision at 42°C and (ii) in situ replication is not required for rapid excision, a finding that is inconsistent with the model.
Functional Genomic, Biochemical, and Genetic Characterization of the
Salmonella pduO
Gene, an ATP:Cob(I)alamin Adenosyltransferase Gene
Authors: Johnson Celeste L. V. , Pechonick Edith , Park Sanghee D. , Havemann Gregory D. , Leal Nicole A. , Bobik Thomas A. 
Published: July 2002

ABSTRACT

Salmonella enterica
degrades 1,2-propanediol by a pathway dependent on coenzyme B
12
(adenosylcobalamin [AdoCb1]). Previous studies showed that 1,2-propanediol utilization (
pdu
) genes include those for the conversion of inactive cobalamins, such as vitamin B
12
, to AdoCbl. However, the specific genes involved were not identified. Here we show that the
pduO
gene encodes a protein with ATP:cob(I)alamin adenosyltransferase activity. The main role of this protein is apparently the conversion of inactive cobalamins to AdoCbl for 1,2-propanediol degradation. Genetic tests showed that the function of the
pduO
gene was partially replaced by the
cobA
gene (a known ATP:corrinoid adenosyltransferase) but that optimal growth of
S. enterica
on 1,2-propanediol required a functional
pduO
gene. Growth studies showed that
cobA pduO
double mutants were unable to grow on 1,2-propanediol minimal medium supplemented with vitamin B
12
but were capable of growth on similar medium supplemented with AdoCbl. The
pduO
gene was cloned into a T7 expression vector. The PduO protein was overexpressed, partially purified, and, using an improved assay procedure, shown to have cob(I)alamin adenosyltransferase activity. Analysis of the genomic context of genes encoding PduO and related proteins indicated that particular adenosyltransferases tend to be specialized for particular AdoCbl-dependent enzymes or for the de novo synthesis of AdoCbl. Such analyses also indicated that PduO is a bifunctional enzyme. The possibility that genes of unknown function proximal to adenosyltransferase homologues represent previously unidentified AdoCbl-dependent enzymes is discussed.
Functional Role for a 2-Oxo Acid Dehydrogenase in the Halophilic Archaeon
Haloferax volcanii
Authors: Wanner Christian , Soppa Jörg 
Published: July 2002

ABSTRACT

The archaeon
Haloferax volcanii
was previously shown to contain and transcribe the genes for a 2-oxo acid dehydrogenase (OADH) complex, but their presence remained a mystery because no enzymatic activity with any of the known OADH substrates could be found, and an inactivation of one of the genes did not lead to any phenotype. Here we report the identification of an additional
oadh
gene cluster in the genome of
H. volcanii
. In contrast to previously known
oadh
loci, it contains three genes,
oadh2A1
,
oadh2A2
, and
oadh2ld
, with coding capacity for the E1α and E1β subunits and an unattached lipoyl domain, but it is devoid of the genes for a complete E2 and an E3. The genes were isolated by complementation of a nitrate respiration-deficient mutant of
H. volcanii
and therefore were shown to be functional in vivo. Phylogenetic analyses revealed that the deduced E1α and E1β subunits of OADH2 group with bacterial acetoin dehydrogenases but not with the OADH1 subunits, and thus,
H. volcanii
has obtained the two gene groups independently. Comparison of the wild type and the mutant allowed us to exclude a function of OADH2 in the aerobic or anaerobic degradation of acetoin or glucose. Instead, it could be shown that OADH2 is important during nitrate-respirative growth on Casamino Acids. Many physiological and biochemical experiments failed to indicate that OADH2 uses any of the previously known OADH substrates. Growth potentials of the mutant were markedly different in media with a single carbon source versus media with mixed carbon sources.
Extensive Variation in the O-Antigen Gene Cluster within One
Salmonella enterica
Serogroup Reveals an Unexpected Complex History
Authors: Wang Lei , Andrianopoulos Kanella , Liu Dan , Popoff Michel Y. , Reeves Peter R. 
Published: July 2002

ABSTRACT

The 46 serogroups of
Salmonella enterica
have different O-antigens, and each is thought to have a specific form of the O-antigen cluster. Comparison of the 145 serovars of serogroup B revealed much more intraserogroup genetic diversity than expected. The O27 factor, due to an α 1-6 linkage between O units in place of the more common α 1-2 linkage and previously thought to be due to a converting bacteriophage, is now shown to be due to a
wzy

α
(1-6)

gene located within the major gene cluster. Surprisingly a remnant of this gene in all O27
−
serovars shows that the ancestor was O27
+
. There are six distinct gene cluster forms, five apparently derived by a series of deletions and one by an insertion from an ancestral O27
+
form present in 57 serovars. The history of the gene cluster and movement between subspecies I and II can be traced. Two of the derivative forms still have a functional
wzy
α(1-6)
gene, while in three it has been inactivated by deletion or insertion. Two of the forms lacking a functional
wzy
α(1-6)
gene have the
wzy
α(1-2)
gene first described for strain LT2 as
rfc
, whereas for the third the
wzy
gene has not been located.
Identification of the cAD1 Sex Pheromone Precursor in
Enterococcus faecalis
Authors: An Florence Y. , Clewell Don B. 
Published: July 2002

ABSTRACT

The
Enterococcus faecalis
virulence plasmid pAD1 encodes a mating response induced by exposure to an octapeptide sex pheromone, cAD1, secreted by plasmid-free enterococci. The determinant for the pheromone in
E. faecalis
FA2-2, designated
cad
, was found to encode a 309-amino-acid lipoprotein precursor with the last 8 residues of its 22-amino acid signal sequence representing the cAD1 moiety. The lipoprotein moiety contained two 77-amino-acid repeats (70% identity) separated by 45 residues. The nonisogenic
E. faecalis
strain V583 determinant encodes a homologous precursor protein, but it differs at two amino acid positions, both of which are located within the pheromone peptide moiety (positions 2 and 8). Construction of a variant of strain FA2-2 containing the differences present in V583 resulted in cells that did not produce detectable cAD1. The mutant appeared normal under laboratory growth conditions, and while significantly reduced in recipient potential, when carrying pAD1 it exhibited a normal mating response. A mutant of FA2-2 with a truncated lipoprotein moiety appeared normal with respect to recipient potential and, when carrying plasmid DNA, donor potential. A gene encoding a protein designated Eep, believed to be a zinc metalloprotease, had been previously identified as required for pheromone biosynthesis and was believed to be involved in the processing of a pheromone precursor. Our new observation that the pAD1-encoded inhibitor peptide, iAD1, whose precursor is itself a signal sequence, is also dependent on Eep is consistent with the likelihood that such processing occurs at the amino terminus of the cAD1 moiety.
Comparison of Pulsed-Field Gel Electrophoresis and Amplified Fragment Length Polymorphism Techniques for Investigating Outbreaks of Enteritis Due to Campylobacters
Authors: Champion Olivia L. , Best Emma L. , Frost Jennifer A. 
Published: July 2002

ABSTRACT
Campylobacters are the most commonly reported cause of acute bacterial enteritis in the United Kingdom and United States, with poultry, milk, and water implicated as sources or vehicles of infection. The majority of campylobacter infections are sporadic, although outbreaks may occur, and these provide an opportunity to evaluate genotypic fingerprinting techniques. In this study, pulsed-field gel electrophoresis (PFGE) was compared with single-enzyme-amplified fragment length polymorphism (SAFLP). The results for the three separate episodes indicated that SAFLP and PFGE both clustered the strains from the first incident as 100% homologous. The strains from the second and third incidents clustered as distinct from both the first incident and from each other. PFGE is well recognized as a discriminatory fingerprinting technique for campylobacters; however, SAFLP has proven to be equally discriminatory, but far less labor intensive and with the added advantages of less “hands-on” time and inexpensive equipment, it is an excellent alternative to PFGE for investigation of outbreaks.
Alpha/Beta Interferon Promotes Transcription and Inhibits Replication of Borna Disease Virus in Persistently Infected Cells
Authors: Staeheli Peter , Sentandreu Maria , Pagenstecher Axel , Hausmann Jürgen 
Published: July 2002

ABSTRACTBorna disease virus(BDV) is a noncytolytic RNA virus that can replicate in the central nervous system (CNS) of mice. This study shows that BDV multiplication was efficiently blocked in transgenic mice that express mouse alpha-1 interferon (IFN-α1) in astrocytes. To investigate whether endogenous virus-induced IFN might similarly restrict BDV, we usedIFNAR0/0mice, which lack a functional alpha/beta IFN (IFN-α/β) receptor. As would be expected if virus-induced IFN were important to control BDV infection, we found that cultured embryo cells ofIFNAR0/0mice supported viral multiplication, whereas cells from wild-type mice did not. Unexpectedly, however, BDV spread through the CNSs ofIFNAR0/0and wild-type mice with similar kinetics, suggesting that activation of endogenous IFN-α/β genes in BDV-infected brains was too weak or occurred too late to be effective. Surprisingly, Northern blot analysis showed that the levels of the most abundant viral mRNAs in the brains of persistently infectedIFNAR0/0mice were about 20-fold lower than those in wild-type mice. In contrast, genomic viral RNA was produced in about a 10-fold excess in the brains ofIFNAR0/0mice. Human IFN-α2 similarly enhanced transcription and simultaneously repressed replication of the BDV genome in persistently infected Vero cells. Thus, in persistently infected neurons and cultured cells, IFN-α/β appears to freeze the BDV polymerase in the transcriptional mode, resulting in enhanced viral mRNA synthesis and suppressing viral genome replication.
Differentiation-Dependent Chromatin Rearrangement Coincides with Activation of Human Papillomavirus Type 31 Late Gene Expression
Authors: Peña Loren del Mar , Laimins Laimonis A. 
Published: July 2002

ABSTRACT
The life cycle of human papillomaviruses (HPVs) is tightly linked to the differentiation status of the host cell. While early genes are expressed during the initial stages of viral infection, late gene expression occurs in the suprabasal layers of the cervical epithelium. Late genes encode E1^E4, a cytosolic protein, and capsid proteins L1 and L2. We have mapped over 30 initiation sites for late transcripts and show that the transcripts initiate in a 200-nucleotide region within the E7 open reading frame. The mechanisms regulating the activation of late gene expression, however, are not yet understood. DNase I hypersensitivity analysis of HPV-31 chromatin in cell lines that maintain viral genomes extrachromosomally indicates that a major shift in nuclease digestion occurs upon differentiation. In undifferentiated cells, hypersensitive regions exist in the upstream regulatory region proximal to the E6 open reading frame. Upon differentiation, a region between nucleotides 659 and 811 in the E7 open reading frame becomes accessible to DNase I. These results indicate that the late transcript initiation region becomes accessible to transcription factor binding upon differentiation. Several complexes mediate chromatin rearrangement, and we tested whether histone acetylation was sufficient for late transcript activation. Treatment with the histone deacetylase inhibitor trichostatin A was found to be insufficient to activate late gene expression in undifferentiated cells. However, it did activate expression of early transcripts. These results suggest that chromatin remodeling around the late promoter occurs upon epithelial differentiation and that mechanisms in addition to histone deacetylation contribute to activation of late gene expression.