bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of Tetracycline-Resistant
Streptococcus thermophilus
Isolates from Italian Soft Cheeses
Authors: Rizzotti Lucia , La Gioia Federica , Dellaglio Franco , Torriani Sandra 
Published: April 2009

ABSTRACT

Tetracycline-resistant
Streptococcus thermophilus
isolates from soft cheeses harbored the genes
tet
(S),
tet
(M), and
tet
(L). Molecular analysis of these genes revealed their expression, localization on plasmids or Tn
916
-Tn
1545
family transposons, and their similarity with published sequences. The study highlights the importance of an accurate safety assessment of using
S. thermophilus
as a starter culture.
Widespread Abundance of Functional Bacterial Amyloid in Mycolata and Other Gram-Positive Bacteria
Authors: Jordal Peter Bruun , Dueholm Morten Simonsen , Larsen Poul , Petersen Steen Vang , Enghild Jan Johannes , Christiansen Gunna , Højrup Peter , Nielsen Per Halkjær , Otzen Daniel Erik 
Published: April 2009

ABSTRACTUntil recently, extracellular functional bacterial amyloid (FuBA) has been detected and characterized in only a few bacterial species, includingEscherichia coli,Salmonella, and the gram-positive organismStreptomyces coelicolor. Here we probed gram-positive bacteria with conformationally specific antibodies and revealed the existence of FuBA in 12 of 14 examined mycolata species, as well as six other distantly related species examined belonging to the phylaActinobacteriaandFirmicutes. Most of the bacteria produced extracellular fimbriae, sometimes copious amounts of them, and in two cases large extracellular fibrils were also produced. In three cases, FuBA was revealed only after extensive removal of extracellular material by saponification, indicating that there is integrated attachment within the cellular envelope. Spores of species in the generaStreptomyces,Bacillus, andNocardiawere all coated with amyloids. FuBA was purified fromGordonia amarae(from the cell envelope) andGeodermatophilus obscurus, and they had the morphology, tinctorial properties, and β-rich structure typical of amyloid. The presence of approximately 9-nm-wide amyloids in the cell envelope ofG. amaraewas visualized by transmission electron microscopy analysis. We conclude that amyloid is widespread among gram-positive bacteria and may in many species constitute a hitherto overlooked integral part of the spore and the cellular envelope.
Aldouronate Utilization in
Paenibacillus
sp. Strain JDR-2: Physiological and Enzymatic Evidence for Coupling of Extracellular Depolymerization and Intracellular Metabolism
Authors: Nong Guang , Rice John D. , Chow Virginia , Preston James F. 
Published: April 2009

ABSTRACT

Paenibacillus
sp. strain JDR-2, an aggressively xylanolytic bacterium isolated from decaying sweet gum wood, secretes a multimodular glycohydrolase family GH10 endoxylanase (XynA1) anchored to the cell surface. The gene encoding XynA1 is part of a xylan utilization regulon that includes an aldouronate utilization gene cluster with genes encoding a GH67 α-glucuronidase (AguA), a GH10 endoxylanase (XynA2), and a GH43 arabinofuranosidase/β-xylosidase (XynB). Here we show that this
Paenibacillus
sp. strain is able to utilize methylglucuronoxylose (MeGAX
1
), an aldobiuronate product that accumulates during acid pretreatment of lignocellulosic biomass, and methylglucuronoxylotriose (MeGAX
3
), the product of the extracellular XynA1 acting on methylglucuronoxylan (MeGAX
n
). The average rates of utilization of MeGAX
n
, MeGAX
1
, and MeGAX
3
were 149.8, 59.4, and 54.3 μg xylose equivalents·ml
−1
·h
−1
, respectively, and were proportional to the specific growth rates on the substrates. AguA was active with MeGAX
1
and MeGAX
3
, releasing 4-
O
-methyl-
d
-glucuronate α-1,2 linked to a nonreducing terminal xylose residue. XynA2 converted xylotriose, generated by the action of AguA on MeGAX
3
, to xylose and xylobiose. The ability to utilize MeGAX
1
provides a novel metabolic potential for bioconversion of acid hydrolysates of lignocellulosics. The 2.8-fold-greater rate of utilization of polymeric MeGAX
n
than that of MeGAX
3
indicates that there is coupling of extracellular depolymerization, assimilation, and intracellular metabolism, allowing utilization of lignocellulosics with minimal pretreatment. Along with adjacent genes encoding transcriptional regulators and ABC transporter proteins, the
aguA
and
xynA2
genes in the cluster described above contribute to the efficient utilization of aldouronates derived from dilute acid and/or enzyme pretreatment protocols applied to the conversion of hemicellulose to biofuels and chemicals.
Toward Cloning of the Magnetotactic Metagenome: Identification of Magnetosome Island Gene Clusters in Uncultivated Magnetotactic Bacteria from Different Aquatic Sediments
Authors: Jogler Christian , Lin Wei , Meyerdierks Anke , Kube Michael , Katzmann Emanuel , Flies Christine , Pan Yongxin , Amann Rudolf , Reinhardt Richard , Schüler Dirk 
Published: April 2009

ABSTRACTIn this report, we describe the selective cloning of large DNA fragments from magnetotactic metagenomes from various aquatic habitats. This was achieved by a two-step magnetic enrichment which allowed the mass collection of environmental magnetotactic bacteria (MTB) virtually free of nonmagnetic contaminants. Four fosmid libraries were constructed and screened by end sequencing and hybridization analysis using heterologous magnetosome gene probes. A total of 14 fosmids were fully sequenced. We identified and characterized two fosmids, most likely originating from two different alphaproteobacterial strains of MTB that contain several putative operons with homology to the magnetosome island (MAI) of cultivated MTB. This is the first evidence that uncultivated MTB exhibit similar yet differing organizations of the MAI, which may account for the diversity in biomineralization and magnetotaxis observed in MTB from various environments.
Phenotypic and Transcriptomic Analyses of Mildly and Severely Salt-Stressed
Bacillus cereus
ATCC 14579 Cells
Authors: den Besten Heidy M. W. , Mols Maarten , Moezelaar Roy , Zwietering Marcel H. , Abee Tjakko 
Published: April 2009

ABSTRACT

Bacteria are able to cope with the challenges of a sudden increase in salinity by activating adaptation mechanisms. In this study, exponentially growing cells of the pathogen
Bacillus cereus
ATCC 14579 were exposed to both mild (2.5% [wt/vol] NaCl) and severe (5% [wt/vol] NaCl) salt stress conditions.
B. cereus
continued to grow at a slightly reduced growth rate when it was shifted to mild salt stress conditions. Exposure to severe salt stress resulted in a lag period, and after 60 min growth had resumed, with cells displaying a filamentous morphology. Whole-genome expression analyses of cells exposed to 2.5% salt stress revealed that the expression of these cells overlapped with the expression of cells exposed to 5% salt stress, suggesting that the corresponding genes were involved in a general salt stress response. Upregulation of osmoprotectant, Na
+
/H
+
, and di- and tripeptide transporters and activation of an oxidative stress response were noticeable aspects of the general salt stress transcriptome response. Activation of this response may confer cross-protection against other stresses, and indeed, increased resistance to heat and hydrogen peroxide could be demonstrated after preexposure to salt. A temporal shift between the transcriptome response and several phenotypic responses of severely salt-stressed cells was observed. After resumption of growth, these cells showed cellular filamentation, reduced chemotaxis, increased catalase activity, and optimal oxidative stress resistance, which corresponded to the transcriptome response displayed in the initial lag period. The linkage of transcriptomes and phenotypic characteristics can contribute to a better understanding of cellular stress adaptation strategies and possible cross-protection mechanisms.
In Silico Prediction of Horizontal Gene Transfer Events in
Lactobacillus bulgaricus
and
Streptococcus thermophilus
Reveals Protocooperation in Yogurt Manufacturing
Authors: Liu Mengjin , Siezen Roland J. , Nauta Arjen 
Published: April 2009

ABSTRACT

Lactobacillus bulgaricus
and
Streptococcus thermophilus
, used in yogurt starter cultures, are well known for their stability and protocooperation during their coexistence in milk. In this study, we show that a close interaction between the two species also takes place at the genetic level. We performed an in silico analysis, combining gene composition and gene transfer mechanism-associated features, and predicted horizontally transferred genes in both
L. bulgaricus
and
S. thermophilus
. Putative horizontal gene transfer (HGT) events that have occurred between the two bacterial species include the transfer of exopolysaccharide (EPS) biosynthesis genes, transferred from
S. thermophilus
to
L. bulgaricus
, and the gene cluster
cbs-cblB
(
cglB
)-
cysE
for the metabolism of sulfur-containing amino acids, transferred from
L. bulgaricus
or
Lactobacillus helveticus
to
S. thermophilus
. The HGT event for the
cbs-cblB
(
cglB
)-
cysE
gene cluster was analyzed in detail, with respect to both evolutionary and functional aspects. It can be concluded that during the coexistence of both yogurt starter species in a milk environment, agonistic coevolution at the genetic level has probably been involved in the optimization of their combined growth and interactions.
Reverse Transcription of 16S rRNA To Monitor Ribosome-Synthesizing Bacterial Populations in the Environment
Authors: Lu Ting , Stroot Peter G. , Oerther Daniel B. 
Published: April 2009

ABSTRACT

Identification and quantification of phylogenetically defined bacterial populations in the environment are often performed using molecular tools targeting 16S rRNA. Fluorescence in situ hybridization has been used to monitor the expression and processing of rRNA by targeting the 3′ tail of precursor 16S rRNA. To expand this approach, we employed reverse transcription of total RNA using primer S-D-Bact-0338-a-A-18. Length heterogeneity detected by slab gel analysis, denaturing high-performance liquid chromatography (DHPLC) was used to differentiate the 5′ tail of the precursor from mature 16S rRNA, and the relative abundance of the precursor compared to the abundance of mature 16S rRNA was shown to be a sensitive indicator of the physiologic state of
Acinetobacter calcoaceticus
ATCC 23055
T
. Our results demonstrate that this is a sensitive and reliable method with a detection limit of 10 ng of single-stranded DNA. The assay was also used to differentiate among precursor 16S rRNA levels with mixed pure cultures, as well as to examine the response of a mixed activated sludge culture exposed to fresh growth medium and the antibiotic chloramphenicol. The results of this study demonstrate that this assay is a novel reverse transcription assay that simultaneously measures the mature and precursor 16S rRNA pools for mixed bacterial populations in an engineered environment. Furthermore, collection of the reverse transcription products derived from activated sludge samples by the DHPLC approach enabled identification of the active bacterial genera. Comparison of 16S and precursor 16S rRNA clone library results indicated that the precursor 16S rRNA library is a more sensitive indicator for active bacteria in engineered environmental samples.
Identification of the
Candida albicans
Cap1p Regulon
Authors: Znaidi Sadri , Barker Katherine S. , Weber Sandra , Alarco Anne-Marie , Liu Teresa T. , Boucher Geneviève , Rogers P. David , Raymond Martine 
Published: April 2009

ABSTRACT

Cap1p, a transcription factor of the basic region leucine zipper family, regulates the oxidative stress response (OSR) in
Candida albicans
. Alteration of its C-terminal cysteine-rich domain (CRD) results in Cap1p nuclear retention and transcriptional activation. To better understand the function of Cap1p in
C. albicans
, we used genome-wide location profiling (chromatin immunoprecipitation-on-chip) to identify its transcriptional targets in vivo. A triple-hemagglutinin (HA
3
) epitope was introduced at the C terminus of wild-type Cap1p (Cap1p-HA
3
) or hyperactive Cap1p with an altered CRD (Cap1p-CSE-HA
3
). Location profiling using whole-genome oligonucleotide tiling microarrays identified 89 targets bound by Cap1p-HA
3
or Cap1p-CSE-HA
3
(the binding ratio was at least twofold;
P
≤ 0.01). Strikingly, Cap1p binding was detected not only at the promoter region of its target genes but also at their 3′ ends and within their open reading frames, suggesting that Cap1p may associate with the transcriptional or chromatin remodeling machinery to exert its activity. Overrepresented functional groups of the Cap1p targets (
P
≤ 0.02) included 11 genes involved in the OSR (
CAP1
,
GLR1
,
TRX1
,
SOD1
,
CAT1
, and others), 13 genes involved in response to drugs (
PDR16
,
MDR1
,
FLU1
,
YCF1
,
FCR1
, and others), 4 genes involved in phospholipid transport (
PDR16
,
GIT1
,
RTA2
, and orf19.932), and 3 genes involved in the regulation of nitrogen utilization (
GST3
, orf19.2693, and orf19.3121), suggesting that Cap1p has other cellular functions in addition to the OSR. Bioinformatic analyses of the bound sequences suggest that Cap1p recognizes the DNA motif 5′-MTKASTMA. Finally, transcriptome analyses showed that increased expression generally accompanies Cap1p binding at its targets, indicating that Cap1p functions as a transcriptional activator.
Comparative Genomics Using Microarrays Reveals Divergence and Loss of Virulence-Associated Genes in Host-Specific Strains of the Insect PathogenMetarhizium anisopliae
Authors: Wang Sibao , Leclerque Andreas , Pava-Ripoll Monica , Fang Weiguo , St. Leger Raymond J. 
Published: April 2009

ABSTRACTMany strains ofMetarhizium anisopliaehave broad host ranges, but others are specialists and adapted to particular hosts. Patterns of gene duplication, divergence, and deletion in three generalist and three specialist strains were investigated by heterologous hybridization of genomic DNA to genes from the generalist strain Ma2575. As expected, major life processes are highly conserved, presumably due to purifying selection. However, up to 7% of Ma2575 genes were highly divergent or absent in specialist strains. Many of these sequences are conserved in other fungal species, suggesting that there has been rapid evolution and loss in specialistMetarhiziumgenomes. Some poorly hybridizing genes in specialists were functionally coordinated, indicative of reductive evolution. These included several involved in toxin biosynthesis and sugar metabolism in root exudates, suggesting that specialists are losing genes required to live in alternative hosts or as saprophytes. Several components of mobile genetic elements were also highly divergent or lost in specialists. Exceptionally, the genome of the specialist cricket pathogen Ma443 contained extra insertion elements that might play a role in generating evolutionary novelty. This study throws light on the abundance of orphans in genomes, as 15% of orphan sequences were found to be rapidly evolving in the Ma2575 lineage.
Induction of Follicular Gastritis following Postthymectomy Autoimmune Gastritis inHelicobacter pylori-Infected BALB/c Mice
Authors: Oshima Chikashi , Okazaki Kazuichi , Matsushima Yumi , Sawada Mitsutaka , Chiba Tsutomu , Takahashi Kiyoyuki , Hiai Hiroshi , Katakai Tomoya , Kasakura Shinpei , Masuda Tohru 
Published: May 2009

ABSTRACTHelicobacter pyloriis the major causative agent of chronic antral gastritis and is thought to be involved in the pathogenesis of mucosa-associated lymphoid tissue lymphoma (MALToma) developing in the human stomach. The aim of this study was to clarify whether corporal autoimmune gastritis (AIG), which is known to decrease acidity due to destruction of parietal cells, predisposes mice toH. pyloriinfection, thereby leading to MALToma-like pathology. BALB/c mice in which AIG had been induced by thymectomy 3 days after birth (AIG mice) were used. The AIG mice were orally administered mouse-adaptedH. pyloriat the age of 6 weeks and were examined histologically and serologically after 2 to 12 months. The results were compared with those obtained from uninfected AIG mice and infected normal mice. Germinal centers were induced in the corpus in 57% of theH. pylori-infected AIG mice, which elicited anti-H. pyloriantibody responses in association with upregulation of interleukin-4 (IL-4) mRNA. In these mice, parietal cells remained in the corpus mucosa. These findings were in contrast to those with the uninfected AIG mice: fundic gland atrophy due to disappearance of parietal cells associated with upregulation of gamma interferon, but not IL-4, mRNA and no germinal center formation in the corpus. These observations suggest that AIG alters the infectivity ofH. pylori, leading to MALToma-like follicular gastritis, at an early stage afterH. pyloriinfection.
Differential Binding of Clonal Variants ofPlasmodium falciparumto Allelic Forms of Intracellular Adhesion Molecule 1 Determined by Flow Adhesion Assay
Authors: Adams S. , Turner G. D. H. , Nash G. B. , Micklem K. , Newbold C. I. , Craig A. G. 
Published: May 2009

ABSTRACTAdhesion ofPlasmodium falciparum-infected erythrocytes to the endothelial ligand intercellular adhesion molecule 1 (ICAM-1) has been implicated in the pathogenesis of cerebral malaria. Recently, a high-frequency coding polymorphism in the N-terminal domain of ICAM-1 (ICAM-1Kilifi) that is associated with susceptibility to cerebral disease in Kenya has been described. Preliminary static adhesion assays suggested that two different selectedP. falciparumlines, ITO4-A4 (A4) and ItG-ICAM (ItG), have different properties of binding to the natural variant proteins ICAM-1 and ICAM-1Kilifi. Using a flow adhesion assay system, we have confirmed differences between the two lines in binding of parasitized erythrocytes to the variant ICAM-1 proteins. Total adhesion of ItG-infected erythrocytes to ICAM-1 and ICAM-1Kilifiis greater than that of A4-infected erythrocytes, and erythrocytes infected by both parasite strains show reduced binding to ICAM-1Kilifi. However, under these physiologically relevant flow conditions, we have shown differences between A4 and ItG strains in dynamic rolling behavior on ICAM-1Kilifi. The percentage of erythrocytes infected with A4 that roll on both ICAM-1 and ICAM-1Kilifiis greater than that of those infected with ItG. Also, the rolling velocity of A4-infected erythrocytes on ICAM-1Kilifiis markedly increased compared to that on ICAM-1, in contrast to the rolling velocity of ItG-infected erythrocytes, which is similar on both proteins. These findings suggest that different parasite lines can vary in their avidity for the same host ligand, which may have important consequences for the pathophysiology ofP. falciparummalaria.
Interleukin-12 as an Adjuvant Promotes Immunoglobulin G and Type 1 Cytokine Recall Responses to Major Surface Protein 2 of the Ehrlichial PathogenAnaplasma marginale
Authors: Tuo Wenbin , Palmer Guy H. , McGuire Travis C. , Zhu Daming , Brown Wendy C. 
Published: May 2009

ABSTRACTAnaplasma marginaleis a tick-transmitted pathogen of cattle closely related to the human ehrlichiae,Ehrlichia chaffeensisand the agent of human granulocytic ehrlichiosis (HGE). These pathogens have in common a structurally conserved outer membrane protein (OMP) designated the major surface protein 2 (MSP-2) inA. marginaleand HGE and OMP-1 inE. chaffeensis. Protective immunity against ehrlichial pathogens is believed to require induction of gamma interferon (IFN-γ) and opsonizing immunoglobulin (Ig) subclasses directed against OMP epitopes that, in concert, activate macrophages for phagocytosis and killing. Because interleukin-12 (IL-12) acts as an adjuvant for protein immunization to induce IFN-γ and protective immunity against intracellular pathogens, we hypothesized that as an adjuvant with MSP-2, IL-12 would augment type 1 recall responses toA. marginale. IL-12 was coadsorbed with MSP-2 to alum and shown to significantly enhance IFN-γ production by lymph node cells (LNC) and LNC-derived CD4+T-cell lines from immunized calves following recall stimulation withA. marginale. LNC proliferation and IL-2 production were also enhanced in IL-12-treated calves. Elevated recall proliferative responses by peripheral blood mononuclear cells were still evident 9 months after immunization. Serum IgG levels were consistently increased in IL-12 immunized calves, predominantly due to higher IgG1 responses. The results support the use of IL-12 coadsorbed with OMP of ehrlichial pathogens in alum to amplify both antibody and type-1 cytokine responses important for protective immunity.
Comparative Analysis of the Mucosal Adjuvanticity of the Type II Heat-Labile Enterotoxins LT-IIa and LT-IIb
Authors: Martin Michael , Metzger Daniel J. , Michalek Suzanne M. , Connell Terry D. , Russell Michael W. 
Published: May 2009

ABSTRACTCholera toxin (CT) and the heat-labile enterotoxin ofEscherichia coli(LT-I) are members of the serogroup I heat-labile enterotoxins (HLT) and can serve as systemic and mucosal adjuvants. However, information is lacking with respect to the structurally related but antigenically distinct serogroup II HLT, LT-IIa and LT-IIb, which have different binding specificities for ganglioside receptors. The purpose of this study was to assess the effectiveness of LT-IIa and LT-IIb as mucosal adjuvants in comparison to the prototypical type I HLT, CT. BALB/c mice were immunized by the intranasal (i.n.) route with the surface protein adhesin AgI/II ofStreptococcus mutansalone or supplemented with an adjuvant amount of CT, LT-IIa, or LT-IIb. Antigen-specific antibody responses in saliva, vaginal wash, and plasma were assayed by enzyme-linked immunosorbent assay. Mice given AgI/II with LT-IIa or LT-IIb by the i.n. route had significantly higher mucosal and systemic antibody responses than mice immunized with AgI/II alone. Anti-AgI/II immunoglobulin A (IgA) antibody activity in saliva and vaginal secretions of mice given AgI/II with LT-IIa or LT-IIb was statistically similar in magnitude to that seen in mice given AgI/II and CT. LT-IIb significantly enhanced the number of AgI/II-specific antibody-secreting cells in the draining superficial cervical lymph nodes compared to LT-IIa and CT. LT-IIb and CT induced significantly higher plasma anti-AgI/II IgG titers compared to LT-IIa. When LT-IIb was used as adjuvant, the proportion of plasma IgG2a relative to IgG1 anti-AgI/II antibody was elevated in contrast to the predominance of IgG1 antibodies promoted by AgI/II alone or when CT or LT-IIa was used. In vitro stimulation of AgI/II-specific cells from the superficial lymph nodes and spleen revealed that LT-IIa and LT-IIb induced secretion of interleukin-4 and significantly higher levels of gamma interferon compared to CT. These results demonstrate that the type II HLT LT-IIa and LT-IIb exhibit potent and distinct adjuvant properties for stimulating immune responses to a noncoupled protein immunogen after mucosal immunization.
Isolation of
Bacteroides fragilis
Mutants with In Vivo Growth Defects by Using Tn
4400
′, a Modified Tn
4400
Transposition System, and a New Screening Method
Authors: Tang Yixin P. , Malamy Michael H. 
Published: May 2009

ABSTRACT

A modified version of the
Bacteroides fragilis
transposon Tn
4400
, designated Tn
4400
′, enabling rapid isolation and analysis of
B. fragilis
mutants has been constructed. To identify potential virulence factors, Tn
4400
′-generated mutants were screened by a new method; this resulted in the isolation of 21 mutant strains with impaired growth characteristics on tissue culture monolayers but normal growth in rich medium anaerobically.