bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adaptation and Antibiotic Tolerance of Anaerobic Burkholderia pseudomallei
Authors: Hamad Mohamad A. , Austin Chad R. , Stewart Amanda L. , Higgins Mike , Vázquez-Torres Andrés , Voskuil Martin I. 
Published: May 2011

ABSTRACT

The Gram-negative bacterium
Burkholderia pseudomallei
is the etiological agent of melioidosis and is remarkably resistant to most classes of antibacterials. Even after months of treatment with antibacterials that are relatively effective
in vitro
, there is a high rate of treatment failure, indicating that this pathogen alters its patterns of antibacterial susceptibility in response to cues encountered in the host. The pathology of melioidosis indicates that
B. pseudomallei
encounters host microenvironments that limit aerobic respiration, including the lack of oxygen found in abscesses and in the presence of nitric oxide produced by macrophages. We investigated whether
B. pseudomallei
could survive in a nonreplicating, oxygen-deprived state and determined if this physiological state was tolerant of conventional antibacterials.
B. pseudomallei
survived initial anaerobiosis, especially under moderately acidic conditions similar to those found in abscesses. Microarray expression profiling indicated a major shift in the physiological state of hypoxic
B. pseudomallei
, including induction of a variety of typical anaerobic-environment-responsive genes and genes that appear specific to anaerobic
B. pseudomallei
. Interestingly, anaerobic
B. pseudomallei
was unaffected by antibacterials typically used in therapy. However, it was exquisitely sensitive to drugs used against anaerobic pathogens. After several weeks of anaerobic culture, a significant loss of viability was observed. However, a stable subpopulation that maintained complete viability for at least 1 year was established. Thus, during the course of human infection, if a minor subpopulation of bacteria inhabited an oxygen-restricted environment, it might be indifferent to traditional therapy but susceptible to antibiotics frequently used to treat anaerobic infections.
Novel Diamidines with Activity against Babesia divergens
In Vitro
and Babesia microti
In Vivo
Authors: Nehrbass-Stuedli Angela , Boykin David , Tidwell Richard R. , Brun Reto 
Published: May 2011

ABSTRACT

Dicationic diamidines, such as diminazene and pentamidine, are well-studied chemotherapeutic agents with significant activity against parasitic diseases. The
in vitro
activities of novel diamidine compounds against the
Babesia divergens
strains 1903B and 4201 were investigated. The most potent compound, a diphenyl furan, had a 50% inhibitory concentration (IC
50
) of 1.5 ng/ml. In a murine model, several test compounds were effective enough to cure mice infected with
Babesia microti
at a dose of 12.5 and/or 25 mg/kg of body weight given by the subcutaneous route for 4 days. The best antibabesial properties were exhibited by terphenyls, benzimidazoles, diphenyl furans, pentamidine, and pentamidine analogues.
Inducible
l
-Alanine Exporter Encoded by the Novel Gene
ygaW
(
alaE
) in Escherichia coli
Authors: Hori Hatsuhiro , Yoneyama Hiroshi , Tobe Ryuta , Ando Tasuke , Isogai Emiko , Katsumata Ryoichi 
Published: April 2011

ABSTRACT

We previously isolated a mutant hypersensitive to
l
-alanyl-
l
-alanine from a non-
l
-alanine-metabolizing
Escherichia coli
strain and found that it lacked an inducible
l
-alanine export system. Consequently, this mutant showed a significant accumulation of intracellular
l
-alanine and a reduction in the
l
-alanine export rate compared to the parent strain. When the mutant was used as a host to clone a gene(s) that complements the dipeptide-hypersensitive phenotype, two uncharacterized genes,
ygaW
and
ytfF
, and two characterized genes,
yddG
and
yeaS
, were identified. Overexpression of each gene in the mutant resulted in a decrease in the intracellular
l
-alanine level and enhancement of the
l
-alanine export rate in the presence of the dipeptide, suggesting that their products function as exporters of
l
-alanine. Since
ygaW
exhibited the most striking impact on both the intra- and the extracellular
l
-alanine levels among the four genes identified, we disrupted the
ygaW
gene in the non-
l
-alanine-metabolizing strain. The resulting isogenic mutant showed the same intra- and extracellular
l
-alanine levels as observed in the dipeptide-hypersensitive mutant obtained by chemical mutagenesis. When each gene was overexpressed in the wild-type strain, which does not intrinsically excrete alanine, only the
ygaW
gene conferred on the cells the ability to excrete alanine. In addition, expression of the
ygaW
gene was induced in the presence of the dipeptide. On the basis of these results, we concluded that YgaW is likely to be the physiologically most relevant exporter for
l
-alanine in
E. coli
and proposed that the gene be redesignated
alaE
for
ala
nine
e
xport.
Identification of Mycoparasitism-Related Genes in Trichoderma atroviride
Authors: Reithner Barbara , Ibarra-Laclette Enrique , Mach Robert L. , Herrera-Estrella Alfredo 
Published: April 2011

ABSTRACT

A high-throughput sequencing approach was utilized to carry out a comparative transcriptome analysis of
Trichoderma atroviride
IMI206040 during mycoparasitic interactions with the plant-pathogenic fungus
Rhizoctonia solani
. In this study, transcript fragments of 7,797
Trichoderma
genes were sequenced, 175 of which were host responsive. According to the functional annotation of these genes by KOG (eukaryotic orthologous groups), the most abundant group during direct contact was “metabolism.” Quantitative reverse transcription (RT)-PCR confirmed the differential transcription of 13 genes (including
swo1
, encoding an expansin-like protein;
axe1
, coding for an acetyl xylan esterase; and homologs of genes encoding the aspartyl protease
papA
and a trypsin-like protease,
pra1
) in the presence of
R. solani
. An additional relative gene expression analysis of these genes, conducted at different stages of mycoparasitism against
Botrytis cinerea
and
Phytophthora capsici
, revealed a synergistic transcription of various genes involved in cell wall degradation. The similarities in expression patterns and the occurrence of regulatory binding sites in the corresponding promoter regions suggest a possible analog regulation of these genes during the mycoparasitism of
T. atroviride
. Furthermore, a chitin- and distance-dependent induction of
pra1
was demonstrated.
Molecular Characterization of Cronobacter Lipopolysaccharide O-Antigen Gene Clusters and Development of Serotype-Specific PCR Assays
Authors: Jarvis K. G. , Grim C. J. , Franco A. A. , Gopinath G. , Sathyamoorthy V. , Hu L. , Sadowski J. A. , Lee C. S. , Tall B. D. 
Published: April 2011

ABSTRACT

Cronobacter
(formerly
Enterobacter sakazakii
) is a recently defined genus consisting of six species,
C. sakazakii
,
C. malonaticus
,
C. dublinensis
,
C. muytjensii
,
C. turicensis
, and
Cronobacter
genomospecies 1. In this study, MboII restriction fragment length polymorphism (RFLP) patterns of O-antigen gene clusters, located between
galF
and
gnd
, were used to identify serotypes in
Cronobacter
spp. Seven O-antigen RFLP clusters were generated, including three
C. sakazakii
clusters, previously identified as serotypes O1, O2, and O3. The O-antigen regions of six strains with unique RFLP patterns, including two
C. sakazakii
strains, two
C. malonaticus
strains, one
C. turicensis
strain, and one
C. muytjensii
strain, revealed three O-antigen gene clusters shared among
Cronobacter
species. PCR assays were developed, targeting the
wzx
O-antigen polymerase gene, and used to screen 231
Cronobacter
strains to determine the frequency of these newly identified serotypes.
Bacterial Subfamily of LuxR Regulators That Respond to Plant Compounds
Authors: Subramoni Sujatha , Gonzalez Juan F. , Johnson Aaron , Péchy-Tarr Maria , Rochat Laurène , Paulsen Ian , Loper Joyce E. , Keel Christoph , Venturi Vittorio 
Published: April 2011

ABSTRACT

Pseudomonas fluorescens
are rhizobacteria known for their biocontrol properties. Several antimicrobial functions are crucial for this process, and the experiments described here investigate the modulation of their expression during the plant-bacterium interaction. The role of a LuxR family regulator in interkingdom signaling has been investigated using genome-scale transcriptome analysis, gene promoter studies
in vivo
and
in vitro
, biocontrol assays, and response to plant compounds. PsoR, a LuxR solo or orphan regulator of
P. fluorescens
, was identified. PsoR is solubilized and activates a
lux
-box-containing promoter only in the presence of macerated plants, suggesting the presence of a plant molecule(s) that most likely binds to PsoR. Gene expression profiles revealed that genes involved in the inhibition of plant pathogens were affected by PsoR, including a chitinase gene, iron metabolism genes, and biosynthetic genes of antifungal compounds. 2,4-Diacetylphloroglucinol production is PsoR dependent both
in vitro
and
in vivo
.
psoR
mutants were significantly reduced for their ability to protect wheat plants from root rot, and damping-off caused by
Pythium ultimum
infection. PsoR most likely senses a molecule(s) in the plant and modulates expression of genes that have a role in biocontrol. PsoR and related proteins form a subfamily of LuxR family regulators in plant-associated bacteria.
Squalene-Hopene Cyclases
Authors: Siedenburg Gabriele , Jendrossek Dieter 
Published: April 2011

ABSTRACTHopanoids and sterols are members of a large group of cyclic triterpenoic compounds that have important functions in many prokaryotic and eukaryotic organisms. They are biochemically synthesized from linear precursors (squalene, 2,3-oxidosqualene) in only one enzymatic step that is catalyzed by squalene-hopene cyclase (SHC) or oxidosqualene cyclase (OSC). SHCs and OSCs are related in amino acid sequences and probably are derived from a common ancestor. The SHC reaction requires the formation of five ring structures, 13 covalent bonds, and nine stereo centers and therefore is one of the most complex one-step enzymatic reactions. We summarize the knowledge of the properties of triterpene cyclases and details of the reaction mechanism ofAlicyclobacillus acidocaldariusSHC. Properties of other SHCs are included.
Increased Fitness and Alteration of Metabolic Pathways during Bacillus subtilis Evolution in the Laboratory
Authors: Maughan Heather , Nicholson Wayne L. 
Published: April 2011

ABSTRACT

Five batch cultures of
Bacillus subtilis
were subjected to evolution in the laboratory for 6,000 generations under conditions repressing sporulation in complex liquid medium containing glucose. Between generations 1,000 and 2,000, variants with a distinct small-colony morphology arose and swept through four of the five populations that had been previously noted for their loss of sporulation (H. Maughan et al., Genetics 177:937-948, 2007). To better understand the nature of adaptation in these variants, individual strains were isolated from one population before (WN715) and after (WN716) the sweep. In addition to colony morphology, strains WN715 and WN716 differed in their motility, aerotaxis, and cell morphology. Competition experiments showed that strain WN716 had evolved a distinct fitness advantage over the ancestral strain and strain WN715 during growth and the transition to the postexponential growth phase, which was more pronounced when WN715 was present in the coculture. Microarray analyses revealed candidate genes in which mutations may have produced some of the observed phenotypes. For example, loss of motility in WN716 was accompanied by decreased transcription of all flagellar, motility, and chemotaxis genes on the microarray. Transcription of
alsS
and
alsD
was also lower in strain WN716, and the predicted loss of acetoin production and enhanced acetate production was confirmed by high-performance liquid chromatography (HPLC) analysis. The results suggested that the derived colony morphology of strain WN716 was associated with increased fitness, the alteration of several metabolic pathways, and the loss of a typical postexponential-phase response.
Modular Synthase-Encoding Gene Involved in α-Olefin Biosynthesis in Synechococcus sp. Strain PCC 7002
Authors: Mendez-Perez Daniel , Begemann Matthew B. , Pfleger Brian F. 
Published: April 2011

ABSTRACT

A gene involved in the production of medium-chain α-olefins was identified in the cyanobacterium
Synechococcus
sp. strain PCC 7002. The gene encodes a large multidomain protein with homology to type I polyketide synthases, suggesting a route for hydrocarbon biosynthesis from fatty acids via an elongation decarboxylation mechanism.
BTI1, an Azoreductase with pH-Dependent Substrate Specificity
Authors: Johansson Hans E. , Johansson Mary K. , Wong Albert C. , Armstrong Eliana S. , Peterson Erik J. , Grant Richard E. , Roy Margaret A. , Reddington Mark V. , Cook Ronald M. 
Published: April 2011

ABSTRACT
The group II azoreductase BTI1 utilizes NADPH to directly cleave azo bonds in water-soluble azo dyes, including quenchers of fluorescence. Unexpectedly, optimal reduction was dye specific, ranging from a pH of <5.5 for Janus green B, to pH 6.0 for methyl red, methyl orange, and BHQ-10, to pH >8.3 for flame orange.
Effects of Bacterial Microflora of the Lower Digestive Tract of Free-Range Waterfowl on Influenza Virus Activation
Authors: King Marcus D. , Guentzel M. Neal , Arulanandam Bernard P. , Bodour Adria A. , Brahmakshatriya Vinayak , Lupiani Blanca , Chambers James P. 
Published: April 2011

ABSTRACTProteolytic cleavage activation of influenza virus hemagglutinin (HA0) is required for cell entry via receptor-mediated endocytosis. Despite numerous studies describing bacterial protease-mediated influenza A viral activation in mammals, very little is known about the role of intestinal bacterial flora of birds in hemagglutinin cleavage/activation. Therefore, the cloaca of wild waterfowl was examined for (i) representative bacterial types and (ii) their ability to cleave in a “trypsin-like” manner the precursor viral hemagglutinin molecule (HA0). Using radiolabeled HA0, bacterial secretion-mediated trypsin-like conversion of HA0 to HA1 and HA2 peptide products was observed to various degrees in 42 of 44 bacterial isolates suggestive of influenza virus activation in the cloaca of wild waterfowl. However, treatment of uncleaved virus with all bacterial isolates gave rise to substantially reduced emergent virus progeny compared with what was expected. Examination of two isolates exhibiting pronounced trypsin-like conversion of HA0 to HA1 and HA2 peptide products and low infectivity revealed lipase activity to be present. Because influenza virus possesses a complex lipid envelope, the presence of lipid hydrolase activity could in part account for the observed less-than-expected level of viable progeny. A thorough characterization of respective isolate protease HA0 hydrolysis products as well as other resident activities (i.e., lipase) is ongoing such that the role of these respective contributors in virus activation/inactivation can be firmly established.
Diversity of Somatic Coliphages in Coastal Regions with Different Levels of Anthropogenic Activity in São Paulo State, Brazil
Authors: Burbano-Rosero E. M. , Ueda-Ito M. , Kisielius J. J. , Nagasse-Sugahara T. K. , Almeida B. C. , Souza C. P. , Markman C. , Martins G. G. , Albertini L. , Rivera I. N. G. 
Published: April 2011

ABSTRACTBacteriophages are the most abundant and genetically diverse viruses on Earth, with complex ecology in both quantitative and qualitative terms. Somatic coliphages (SC) have been reported to be good indicators of fecal pollution in seawater. This study focused on determining the concentration of SC and their diversity by electron microscopy of seawater, plankton, and bivalve samples collected at three coastal regions in São Paulo, Brazil. The SC counts varied from <1 to 3.4 × 103PFU/100 ml in seawater (73 samples tested), from <1 to 4.7 × 102PFU/g in plankton (46 samples tested), and from <1 to 2.2 × 101PFU/g in bivalves (11 samples tested). In seawater samples, a relationship between the thermotolerant coliforms andEscherichia coliand SC was observed at the three regions (P= 0.0001) according to the anthropogenic activities present at each region. However, SC were found in plankton samples from three regions: Baixada Santista (17/20), Canal de São Sebastião (6/14), and Ubatuba (3/12). In seawater samples collected from Baixada Santista, four morphotypes were observed: A1 (4.5%), B1 (50%), C1 (36.4%), and D1 (9.1%). One coliphage,Siphoviridaetype T1, had the longest tail: between 939 and 995 nm. In plankton samples,Siphoviridae(65.8%),Podoviridae(15.8%),Microviridae(15.8%), andMyoviridae(2.6%) were found. In bivalves, only the morphotype B1 was observed. These SC were associated with enteric hosts: enterobacteria,E. coli,Proteus,Salmonella, andYersinia. Baixada Santista is an area containing a high level of fecal pollution compared to those in the Canal de São Sebastião and Ubatuba. This is the first report of coliphage diversity in seawater, plankton, and bivalve samples collected from São Paulo coastal regions. A better characterization of SC diversity in coastal environments will help with the management and evaluation of the microbiological risks for recreation, seafood cultivation, and consumption.
Bacterial Diversity across Individual Lichens
Authors: Mushegian Alexandra A. , Peterson Celeste N. , Baker Christopher C. M. , Pringle Anne 
Published: April 2011

ABSTRACT
Symbioses are unique habitats for bacteria. We surveyed the spatial diversity of bacterial communities across multiple individuals of closely related lichens using terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing. Centers of lichens house richer, more consistent assemblages than species-poor and compositionally disparate lichen edges, suggesting that ecological succession plays a role in structuring these communities.
Simple Enrichment System for Hydrogen Producers
Authors: Tolvanen Katariina E. S. , Mangayil Rahul K. , Karp Matti T. , Santala Ville P. 
Published: April 2011

ABSTRACT

This study presents a simple enrichment system where gas pressure produced by microbes performs functions that are normally done by labor. The system was tested with
Escherichia coli
strains with different hydrogen production and growth capabilities. The results show that the system can enrich the best hydrogen producer.
Type II Toxoplasma gondiiKU80Knockout Strains Enable Functional Analysis of Genes Required for Cyst Development and Latent Infection
Authors: Fox Barbara A. , Falla Alejandra , Rommereim Leah M. , Tomita Tadakimi , Gigley Jason P. , Mercier Corinne , Cesbron-Delauw Marie-France , Weiss Louis M. , Bzik David J. 
Published: April 2011

ABSTRACTType IIToxoplasma gondiiKU80knockouts (Δku80) deficient in nonhomologous end joining were developed to delete the dominant pathway mediating random integration of targeting episomes. Gene targeting frequency in the type II Δku80Δhxgprtstrain measured at the orotate (OPRT) and the uracil (UPRT) phosphoribosyltransferase loci was highly efficient. To assess the potential of the type II Δku80Δhxgprtstrain to examine gene function affecting cyst biology and latent stages of infection, we targeted the deletion of four parasite antigen genes (GRA4,GRA6,ROP7, andtgd057) that encode characterized CD8+T cell epitopes that elicit corresponding antigen-specific CD8+T cell populations associated with control of infection. Cyst development in these type II mutant strains was not found to be strictly dependent on antigen-specific CD8+T cell host responses. In contrast, a significant biological role was revealed for the dense granule proteins GRA4 and GRA6 in cyst development since brain tissue cyst burdens were drastically reduced specifically in mutant strains withGRA4and/orGRA6deleted. Complementation of the Δgra4and Δgra6mutant strains using a functional allele of the deletedGRAcoding region placed under the control of the endogenousUPRTlocus was found to significantly restore brain cyst burdens. These results reveal that GRA proteins play a functional role in establishing cyst burdens and latent infection. Collectively, our results suggest that a type II Δku80Δhxgprtgenetic background enables a higher-throughput functional analysis of the parasite genome to reveal fundamental aspects of parasite biology controlling virulence, pathogenesis, and transmission.
Three Mitochondrial DNA Polymerases Are Essential for Kinetoplast DNA Replication and Survival of Bloodstream Form Trypanosoma brucei
Authors: Bruhn David F. , Sammartino Mark P. , Klingbeil Michele M. 
Published: April 2011

ABSTRACT

Trypanosoma brucei
, the causative agent of human African trypanosomiasis, has a complex life cycle that includes multiple life cycle stages and metabolic changes as the parasite switches between insect vector and mammalian host. The parasite's single mitochondrion contains a unique catenated mitochondrial DNA network called kinetoplast DNA (kDNA) that is composed of minicircles and maxicircles. Long-standing uncertainty about the requirement of kDNA in bloodstream form (BF)
T. brucei
has recently eroded, with reports of posttranscriptional editing and subsequent translation of kDNA-encoded transcripts as essential processes for BF parasites. These studies suggest that kDNA and its faithful replication are indispensable for this life cycle stage. Here we demonstrate that three kDNA replication proteins (mitochondrial DNA polymerases IB, IC, and ID) are required for BF parasite viability. Silencing of each polymerase was lethal, resulting in kDNA loss, persistence of prereplication DNA monomers, and collapse of the mitochondrial membrane potential. These data demonstrate that kDNA replication is indeed crucial for BF
T. brucei
. The contributions of mitochondrial DNA polymerases IB, IC, and ID to BF parasite viability suggest that these and other kDNA replication proteins warrant further investigation as a new class of targets for the development of antitrypanosomal drugs.
Characterization, Localization, Essentiality, and High-Resolution Crystal Structure of Glucosamine 6-Phosphate
N
-Acetyltransferase from Trypanosoma brucei
Authors: Mariño Karina , Güther M. Lucia Sampaio , Wernimont Amy K. , Qiu Wei , Hui Raymond , Ferguson Michael A. J. 
Published: April 2011

ABSTRACT

A gene predicted to encode
Trypanosoma brucei
glucosamine 6-phosphate
N
-acetyltransferase (
TbGNA1
; EC 2.3.1.4) was cloned and expressed in
Escherichia coli
. The recombinant protein was enzymatically active, and its high-resolution crystal structure was obtained at 1.86 Å. Endogenous TbGNA1 protein was localized to the peroxisome-like microbody, the glycosome. A bloodstream-form
T. brucei
GNA1
conditional null mutant was constructed and shown to be unable to sustain growth
in vitro
under nonpermissive conditions, demonstrating that there are no metabolic or nutritional routes to UDP-GlcNAc other than via GlcNAc-6-phosphate. Analysis of the protein glycosylation phenotype of the
TbGNA1
mutant under nonpermissive conditions revealed that poly-
N
-acetyllactosamine structures were greatly reduced in the parasite and that the glycosylation profile of the principal parasite surface coat component, the variant surface glycoprotein (VSG), was modified. The significance of results and the potential of TbGNA1 as a novel drug target for African sleeping sickness are discussed.