bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uncoupling of the Patterns of Chromatin Association of Different Transcription Elongation Factors by a Histone H3 Mutant in
Saccharomyces cerevisiae
Authors: Lloyd Amanda , Pratt Katie , Siebrasse Erica , Moran Matthew D. , Duina Andrea A. 
Published: December 2008

ABSTRACT

The transcription elongation complexes yFACT, Spt4/Spt5, and Spt6/Iws1 were previously shown to follow similar patterns of association across transcribed genes in
Saccharomyces cerevisiae
. Using a histone H3 mutant, we now provide evidence that the mechanism of association of yFACT across genes is separable from that adopted by Spt4/Spt5 and Spt6/Iws1.
Enhanced Immunogenicity ofPlasmodium falciparumPeptide Vaccines Using a Topical Adjuvant Containing a Potent Synthetic Toll-Like Receptor 7 Agonist, Imiquimod
Authors: Othoro Caroline , Johnston Dean , Lee Rebecca , Soverow Jonathan , Bystryn Jean-Claude , Nardin Elizabeth 
Published: December 2008

ABSTRACTPlasmodium sporozoites injected into the skin by malaria-infected mosquitoes can be effectively targeted by antibodies that block parasite invasion of host hepatocytes and thus prevent the subsequent development of blood stage infections responsible for clinical disease. Malaria subunit vaccines require potent adjuvants, as they lack known pathogen-associated molecular patterns found in attenuated viral or bacterial vaccines that function as Toll-like receptor (TLR) agonists to stimulate dendritic cells and initiate strong adaptive immune responses. A synthetic TLR7 agonist, imiquimod, which is FDA approved for topical treatment of various skin conditions, can function as a potent adjuvant for eliciting T-cell responses to intracellular pathogens and model protein antigens. In the current studies, the topical application of imiquimod at the site of subcutaneously injectedPlasmodium falciparumcircumsporozoite (CS) peptides elicited strong parasite-specific humoral immunity that protected against challenge with transgenic rodent parasites that expressP. falciparumCS repeats. In addition, injection of a simple linear peptide followed by topical imiquimod elicited strong Th1 CD4+T-cell responses, as well as high antibody titers. The correlation of high anti-repeat antibody titers with resistance to sporozoite challenge in vivo and in vitro supports use of this topical TLR7 agonist adjuvant to elicit protective humoral immunity. The safety, simplicity, and economic advantages of a topical synthetic TLR7 agonist adjuvant also apply to other vaccines requiring high antibody titers, such as malaria asexual or sexual blood stage antigens to prevent red blood cell invasion and block transmission to the mosquito vector, and to vaccines to other extracellular pathogens.
The Brucella abortus S19 Δ
vjbR
Live Vaccine Candidate Is Safer than S19 and Confers Protection against Wild-Type Challenge in BALB/c Mice When Delivered in a Sustained-Release Vehicle
Authors: Arenas-Gamboa A. M. , Ficht T. A. , Kahl-McDonagh M. M. , Gomez G. , Rice-Ficht A. C. 
Published: December 2008

ABSTRACT

Brucellosis is an important zoonotic disease of nearly worldwide distribution. Despite the availability of live vaccine strains for bovine (S19, RB51) and small ruminants (Rev-1), these vaccines have several drawbacks, including residual virulence for animals and humans. Safe and efficacious immunization systems are therefore needed to overcome these disadvantages. A
vjbR
knockout was generated in the S19 vaccine and investigated for its potential use as an improved vaccine candidate. Vaccination with a sustained-release vehicle to enhance vaccination efficacy was evaluated utilizing the live S19 Δ
vjbR
::Kan in encapsulated alginate microspheres containing a nonimmunogenic eggshell precursor protein of the parasite
Fasciola hepatica
(vitelline protein B). BALB/c mice were immunized intraperitoneally with either encapsulated or nonencapsulated S19 Δ
vjbR
::Kan at a dose of 1 × 10
5
CFU per animal to evaluate immunogenicity, safety, and protective efficacy. Humoral responses postvaccination indicate that the vaccine candidate was able to elicit an anti-
Brucella
-specific immunoglobulin G response even when the vaccine was administered in an encapsulated format. The safety was revealed by the absence of splenomegaly in mice that were inoculated with the mutant. Finally, a single dose with the encapsulated mutant conferred higher levels of protection compared to the nonencapsulated vaccine. These results suggest that S19 Δ
vjbR
::Kan is safer than S19, induces protection in mice, and should be considered as a vaccine candidate when administered in a sustained-release manner.
Streptococcus pneumoniaeCapsular Serotype 19F Is More Resistant to C3 Deposition and Less Sensitive to Opsonophagocytosis than Serotype 6B
Authors: Melin Merit , Jarva Hanna , Siira Lotta , Meri Seppo , Käyhty Helena , Väkeväinen Merja 
Published: December 2008

ABSTRACTThe polysaccharide capsule is a major virulence mechanism ofStreptococcus pneumoniae, shielding the bacterium from phagocytes. Capsule types may differ in their abilities to resist immune defense. Antibody-mediated complement activation and opsonophagocytosis are crucial in protection against pneumococcus. Conjugate vaccine trials suggest imperfect protection against 19F. We have previously shown that significantly more anti-19F than anti-6B antibody is needed for killing in the opsonophagocytic assay (OPA). In this study, we explored whether the amount of C3 deposited on serotype 6B and 19F pneumococcal strains reflects their sensitivity to opsonophagocytosis. We compared clinical 6B and 19F nasopharyngeal, middle ear, and blood isolates as well as reference OPA strains (n= 16) for their sensitivity to opsonophagocytosis and C3 deposition. Sixfold anticapsular antibody concentrations were required for 50% opsonophagocytic killing of 19F compared to that of 6B strains. Serotype 19F was more resistant to C3 deposition than 6B. Complement deposition and opsonophagocytosis were dependent on the concentration of anticapsular antibodies. Differences between pneumococcal serotypes in antibody-mediated protection may partly be explained by the abilities of the capsules to resist complement deposition. These findings support previous studies suggesting that higher antibody concentrations to the capsular polysaccharide are needed for protection against disease caused by serotype 19F than that caused by 6B.
Host Immune Response and Acute Disease in a Zebrafish Model ofFrancisellaPathogenesis
Authors: Vojtech Lucia N. , Sanders George E. , Conway Carla , Ostland Vaughn , Hansen John D. 
Published: December 2008

ABSTRACTMembers of the bacterial genusFrancisellaare highly virulent and infectious pathogens. New models to studyFrancisellapathogenesis in evolutionarily distinct species are needed to provide comparative insight, as the mechanisms of host resistance and pathogen virulence are not well understood. We took advantage of the recent discovery of a novel species ofFrancisellato establish a zebrafish/Francisellacomparative model of pathogenesis and host immune response. Adult zebrafish were susceptible to acuteFrancisella-induced disease and suffered mortality in a dose-dependent manner. Using immunohistochemical analysis, we localized bacterial antigens primarily to lymphoid tissues and livers of zebrafish following infection by intraperitoneal injection, which corresponded to regions of local cellular necrosis.Francisellasp. bacteria replicated rapidly in these tissues beginning 12 h postinfection, and bacterial titers rose steadily, leveled off, and then decreased by 7 days postinfection. Zebrafish mounted a significant tissue-specific proinflammatory response to infection as measured by the upregulation of interleukin-1β (IL-1β), gamma interferon, and tumor necrosis factor alpha mRNA beginning by 6 h postinfection and persisting for up to 7 days postinfection. In addition, exposure of zebrafish to heat-killed bacteria demonstrated that the significant induction of IL-1β was highly specific to live bacteria. Taken together, the pathology and immune response to acuteFrancisellainfection in zebrafish share many features with those in mammals, highlighting the usefulness of this new model system for addressing both general and specific questions aboutFrancisellahost-pathogen interactions via an evolutionary approach.
Contribution of the Periplasmic Chaperone Skp to Efficient Presentation of the Autotransporter IcsA on the Surface ofShigella flexneri
Authors: Wagner Jennifer K. , Heindl Jason E. , Gray Andrew N. , Jain Sumita , Goldberg Marcia B. 
Published: December 2008

ABSTRACTIcsA is an outer membrane protein in the autotransporter family that is required forShigella flexneripathogenesis. Following its secretion through the Sec translocon, IcsA is incorporated into the outer membrane in a process that depends on YaeT, a component of an outer membrane β-barrel insertion machinery. We investigated the role of the periplasmic chaperone Skp in IcsA maturation. Skp is required for the presentation of the mature amino terminus (alpha-domain) of IcsA on the bacterial surface and contributes to cell-to-cell spread ofS. flexneriin cell culture. A mutation inskpdoes not prevent the insertion of the β-barrel into the outer membrane, suggesting that the primary role of Skp is the folding of the IcsA alpha-domain. In addition, the requirement forskpcan be partially bypassed by disruptingicsP, an ortholog ofEscherichia coli ompT, which encodes the protease that processes IcsA between the mature amino terminus and the β-barrel outer membrane anchor. These findings are consistent with a model in which Skp plays a critical role in the chaperoning of the alpha-domain of IcsA during transit through the periplasm.
The
d
-2-Hydroxyacid Dehydrogenase Incorrectly Annotated PanE Is the Sole Reduction System for Branched-Chain 2-Keto Acids in
Lactococcus lactis
Authors: Chambellon Emilie , Rijnen Liesbeth , Lorquet Frédérique , Gitton Christophe , van Hylckama Vlieg Johan E. T. , Wouters Jeroen A. , Yvon Mireille 
Published: December 2008

ABSTRACT

Hydroxyacid dehydrogenases of lactic acid bacteria, which catalyze the stereospecific reduction of branched-chain 2-keto acids to 2-hydroxyacids, are of interest in a variety of fields, including cheese flavor formation via amino acid catabolism. In this study, we used both targeted and random mutagenesis to identify the genes responsible for the reduction of 2-keto acids derived from amino acids in
Lactococcus lactis
. The gene
panE
, whose inactivation suppressed hydroxyisocaproate dehydrogenase activity, was cloned and overexpressed in
Escherichia coli
, and the recombinant His-tagged fusion protein was purified and characterized. The gene annotated
panE
was the sole gene responsible for the reduction of the 2-keto acids derived from leucine, isoleucine, and valine, while
ldh
, encoding
l
-lactate dehydrogenase, was responsible for the reduction of the 2-keto acids derived from phenylalanine and methionine. The kinetic parameters of the His-tagged PanE showed the highest catalytic efficiencies with 2-ketoisocaproate, 2-ketomethylvalerate, 2-ketoisovalerate, and benzoylformate (
V
max
/

K
m

ratios of 6,640, 4,180, 3,300, and 2,050 U/mg/mM, respectively), with NADH as the exclusive coenzyme. For the reverse reaction, the enzyme accepted
d
-2-hydroxyacids but not
l
-2-hydroxyacids. Although PanE showed the highest degrees of identity to putative NADP-dependent 2-ketopantoate reductases (KPRs), it did not exhibit KPR activity. Sequence homology analysis revealed that, together with the
d
-mandelate dehydrogenase of
Enterococcus faecium
and probably other putative KPRs, PanE belongs to a new family of
d
-2-hydroxyacid dehydrogenases which is unrelated to the well-described
d
-2-hydroxyisocaproate dehydrogenase family. Its probable physiological role is to regenerate the NAD
+
necessary to catabolize branched-chain amino acids, leading to the production of ATP and aroma compounds.
Functional Analysis of the
Streptomyces coelicolor
NrdR ATP-Cone Domain: Role in Nucleotide Binding, Oligomerization, and DNA Interactions
Authors: Grinberg Inna , Shteinberg Tatyana , Hassan A. Quamrul , Aharonowitz Yair , Borovok Ilya , Cohen Gerald 
Published: December 2008

ABSTRACT

Ribonucleotide reductases (RNRs) are essential enzymes in all living cells, providing the only known de novo pathway for the biosynthesis of deoxyribonucleotides (dNTPs), the immediate precursors of DNA synthesis and repair. RNRs catalyze the controlled reduction of all four ribonucleotides to maintain a balanced pool of dNTPs during the cell cycle.
Streptomyces
species contain genes,
nrdAB
and
nrdJ
, coding for oxygen-dependent class I and oxygen-independent class II RNRs, either of which is sufficient for vegetative growth. Both sets of genes are transcriptionally repressed by NrdR. NrdR contains a zinc ribbon DNA-binding domain and an ATP-cone domain similar to that present in the allosteric activity site of many class I and class III RNRs. Purified NrdR contains up to 1 mol of tightly bound ATP or dATP per mol of protein and binds to tandem 16-bp sequences, termed NrdR-boxes, present in the upstream regulatory regions of bacterial RNR operons. Previously, we showed that the ATP-cone domain alone determines nucleotide binding and that an NrdR mutant defective in nucleotide binding was unable to bind to DNA probes containing NrdR-boxes. These observations led us to propose that when NrdR binds ATP/dATP it undergoes a conformational change that affects DNA binding and hence RNR gene expression. In this study, we analyzed a collection of ATP-cone mutant proteins containing changes in residues inferred to be implicated in nucleotide binding and show that they result in pleiotrophic effects on ATP/dATP binding, on protein oligomerization, and on DNA binding. A model is proposed to integrate these observations.
Preferential Reduction of the Thermodynamically Less Favorable Electron Acceptor, Sulfate, by a Nitrate-Reducing Strain of the Sulfate-Reducing Bacterium
Desulfovibrio desulfuricans
27774
Authors: Marietou Angeliki , Griffiths Lesley , Cole Jeff 
Published: December 2008

ABSTRACT

Desulfovibrio desulfuricans
strain 27774 is one of a relative small group of sulfate-reducing bacteria that can also grow with nitrate as an alternative electron acceptor, but how nitrate reduction is regulated in any sulfate-reducing bacterium is controversial. Strain 27774 grew more rapidly and to higher yields of biomass with nitrate than with sulfate or nitrite as the only electron acceptor. In the presence of both sulfate and nitrate, sulfate was used preferentially, even when cultures were continuously gassed with nitrogen and carbon dioxide to prevent sulfide inhibition of nitrate reduction. The
napC
transcription start site was identified 112 bases upstream of the first base of the translation start codon. Transcripts initiated at the
napC
promoter that were extended across the
napM-napA
boundary were detected by reverse transcription-PCR, confirming that the six
nap
genes can be cotranscribed as a single operon. Real-time PCR experiments confirmed that
nap
operon expression is regulated at the level of mRNA transcription by at least two mechanisms: nitrate induction and sulfate repression. We speculate that three almost perfect inverted-repeat sequences located upstream of the transcription start site might be binding sites for one or more proteins of the CRP/FNR family of transcription factors that mediate nitrate induction and sulfate repression of nitrate reduction by
D. desulfuricans
.
Activation of Dormant Bacterial Genes byNonomuraeasp. Strain ATCC 39727 Mutant-Type RNA Polymerase
Authors: Talà Adelfia , Wang Guojun , Zemanova Martina , Okamoto Susumu , Ochi Kozo , Alifano Pietro 
Published: December 2008

ABSTRACTThere is accumulating evidence that the ability of actinomycetes to produce antibiotics and other bioactive secondary metabolites has been underestimated due to the presence of cryptic gene clusters. The activation of dormant genes is therefore one of the most important areas of experimental research for the discovery of drugs in these organisms. The recent observation that several actinomycetes possess two RNA polymerase β-chain genes (rpoB) has opened up the possibility, explored in this study, of developing a new strategy to activate dormant gene expression in bacteria. TworpoBparalogs,rpoB(S) andrpoB(R), provideNonomuraeasp. strain ATCC 39727 with two functionally distinct and developmentally regulated RNA polymerases. The product ofrpoB(R), the expression of which increases after transition to stationary phase, is characterized by five amino acid substitutions located within or close to the so-called rifampin resistance clusters that play a key role in fundamental activities of RNA polymerase. Here, we report thatrpoB(R) markedly activated antibiotic biosynthesis in the wild-typeStreptomyces lividansstrain 1326 and also in strain KO-421, a relaxed (rel) mutant unable to produce ppGpp. Site-directed mutagenesis demonstrated that therpoB(R)-specific missense H426N mutation was essential for the activation of secondary metabolism. Our observations also indicated that mutant-type or duplicated,rpoBoften exists in nature among rare actinomycetes and will thus provide a basis for further basic and applied research.
Transcription of
clpP
Is Enhanced by a Unique Tandem Repeat Sequence in
Streptococcus mutans
Authors: Zhang Jiaqin , Banerjee Anirban , Biswas Indranil 
Published: December 2008

ABSTRACT

Streptococcus mutans
, the primary causative agent of human dental caries, contains a single copy of the gene encoding ClpP, the chief intracellular protease responsible for tolerance to various environmental stresses. To better understand the role of ClpP in stress response, we investigated the regulation of
clpP
expression in
S. mutans
. Using semiquantitative reverse transcription-PCR analysis, we observed that, under nonstressed conditions,
clpP
expression is somewhat constant throughout the growth phases, although it gradually decreases as cells enter the late stationary phase. The half-life of the
clpP
transcript was found to be less than 1 minute. Sequence analysis of the
clpP
locus reveals the presence of a 50-bp tandem repeat sequence located immediately upstream of the
clpP
promoter (P
clpP
). PCR and DNA sequence analyses suggest that the number of tandem repeat units can vary from as few as two to as many as nine, depending on the particular
S. mutans
isolate. Further analysis, using a transcriptional reporter fusion consisting of P
clpP
fused to a promoterless
gusA
gene, indicates that the presence of the repeat sequence region within P
clpP
results in an approximately fivefold increase in expression from P
clpP
compared to the repeat-free transcriptional reporter fusion. CtsR, a transcriptional repressor that negatively regulates
clpP
expression, has no effect on this repeat-mediated induction of
clpP
transcription. Furthermore, the repeat sequence is not necessary for the induction of
clpP
under stress conditions. Database searches indicate that the region containing the tandem repeats is absent in the
clpP
loci in other bacteria, including other closely related
Streptococcus
spp., suggesting that the repeat sequences are specific for the induction of
clpP
expression in
S. mutans
. We speculate that a host-specific transcriptional activator might be involved in the upregulation of
clpP
expression in
S. mutans
.
Extracytoplasmic Function σ Factors Regulate Expression of the
Bacillus subtilis yabE
Gene via a
cis
-Acting Antisense RNA
Authors: Eiamphungporn Warawan , Helmann John D. 
Published: December 2008

ABSTRACT

Bacillus subtilis yabE
encodes a predicted resuscitation-promoting factor/stationary-phase survival (Rpf/Sps) family autolysin. Here, we demonstrate that
yabE
is negatively regulated by a
cis
-acting antisense RNA which, in turn, is regulated by two extracytoplasmic function σ factors: σ
X
and σ
M
.
FRACTAL, A MICROSCOPIC CROWD MODEL
Authors: WIDYARTO SETYAWAN , LATIFF M. S. ABD. 
Published: December 2008

The core of this research is related to the human crowd problem. Some major problems are congestion, emergency evacuation, and fatal catastrophe. In fact, it has been realized that many crowd related problems can be resolved by influencing (controlling) human flow with providing various control measures. Thus, the problem itself becomes the motivation for this research and the solution is approached through model and simulation within the virtual environment. The relationship between fractal pattern and crowd behavior is produced with respect to the crowd behavior model. It exposes a comparison between the crowd paths resulting from the model developed and the fractal formation created to imitate the crowd paths. A new approach for crowd behavior modeling is proposed based on fractal features and, thus, gives new understanding about a relationship between fractal pattern and crowd behavior. Several innovations of fractal patterns that can be used in crowd behavior model applications adds to the novelty of the research contribution. Ultimately, the new method of modeling the crowd can be obtained and at the same time the new direction of crowd modeling research can be directed.
Another Look at Early Chan: Daoxuan, Bodhidharma, and the Three Levels Movement
Authors: Greene Eric 
Published: December 2008

AbstractAs one of the earliest records pertaining to Bodhidharma, Daoxuan's Xu gaoseng zhuan is a crucial text in the study of so-called Early Chan. Though it is often thought that Daoxuan was attempting to promote the Bodhidharma lineage, recent studies have suggested that he was actually attacking Bodhidharma and his later followers. The present article suggests that such readings are in correct and that Daoxuan was in fact attacking the followers of the Three Levels (Sanjie) movement founded by Xinxing, whose role in defining the meaning of chan during the seventh century has not been sufficiently appreciated. Étant un des premiers documents à parler de Bodhidharma, le Xu Gaoseng zhuan de Daoxuan constitue une source cruciale pour l'étude du "Chan primitif". Même si l'on considère le plus souvent que Daoxuan s'efforçait de promouvoir la lignée de Bodhidharma, plusieurs études récentes suggèrent qu'en fait il attaquait Bodhidharma et ses héritiers. L'auteur suggère que cette interprétation n'est pas correcte: en réalité Daoxuan s'attaquait aux adhérents du mouvement des "Trois niveaux" (Sanjie) fondé par Xinxing, dont la contribution à la définition du sens du chan pendant le VIIe siècle n'a pas encore été suffisamment appréciée.