bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of Molecular Resolution on Sequence-Based Discovery of Ecological Diversity among
Synechococcus
Populations in an Alkaline Siliceous Hot Spring Microbial Mat
Authors: Melendrez Melanie C. , Lange Rachel K. , Cohan Frederick M. , Ward David M. 
Published: December 2010

ABSTRACT

Previous research has shown that sequences of 16S rRNA genes and 16S-23S rRNA internal transcribed spacer regions may not have enough genetic resolution to define all ecologically distinct
Synechococcus
populations (ecotypes) inhabiting alkaline, siliceous hot spring microbial mats. To achieve higher molecular resolution, we studied sequence variation in three protein-encoding loci sampled by PCR from 60°C and 65°C sites in the Mushroom Spring mat (Yellowstone National Park, WY). Sequences were analyzed using the ecotype simulation (ES) and AdaptML algorithms to identify putative ecotypes. Between 4 and 14 times more putative ecotypes were predicted from variation in protein-encoding locus sequences than from variation in 16S rRNA and 16S-23S rRNA internal transcribed spacer sequences. The number of putative ecotypes predicted depended on the number of sequences sampled and the molecular resolution of the locus. Chao estimates of diversity indicated that few rare ecotypes were missed. Many ecotypes hypothesized by sequence analyses were different in their habitat specificities, suggesting different adaptations to temperature or other parameters that vary along the flow channel.
Lateral Transfer of the Denitrification Pathway Genes among
Thermus thermophilus
Strains
Authors: Alvarez Laura , Bricio Carlos , José Gómez Manuel , Berenguer José 
Published: December 2010

ABSTRACT

Nitrate respiration is a common and strain-specific property in
Thermus thermophilus
encoded by the nitrate respiration conjugative element (NCE) that can be laterally transferred by conjugation. In contrast, nitrite respiration and further denitrification steps are restricted to a few isolates of this species. These later steps of the denitrification pathway are under the regulatory control of an NCE-encoded transcription factor, but nothing is known about their coding sequences or its putative genetic linkage to the NCE. In this study we examine the genetic linkage between nitrate and nitrite respiration through lateral gene transfer (LGT) assays and describe a cluster of genes encoding the nitrite-nitric oxide respiration in
T. thermophilus
PRQ25. We show that the whole denitrification pathway can be transferred from the denitrificant strain PRQ25 to an aerobic strain, HB27, and that the genes coding for nitrite and nitric oxide respiration are encoded near the NCE. Sequence data from the draft genome of PRQ25 confirmed these results and allowed us to describe the most compact
nor-nir
cluster known thus far and to demonstrate the expression and activities of the encoded enzymes in the HB27 denitrificant derivatives obtained by LGT. We conclude that this NCE
nor-nir
supercluster constitutes a whole denitrification island that can be spread by lateral transfer among
Thermus thermophilus
strains.
Differential Regulation of the Cellulase Transcription Factors XYR1, ACE2, and ACE1 in Trichoderma reesei Strains Producing High and Low Levels of Cellulase
Authors: Portnoy Thomas , Margeot Antoine , Seidl-Seiboth Verena , Le Crom Stéphane , Ben Chaabane Fadhel , Linke Rita , Seiboth Bernhard , Kubicek Christian P. 
Published: December 2010

ABSTRACT

Due to its capacity to produce large amounts of cellulases,
Trichoderma reesei
is increasingly being investigated for second-generation biofuel production from lignocellulosic biomass. The induction mechanisms of
T. reesei
cellulases have been described recently, but the regulation of the genes involved in their transcription has not been studied thoroughly. Here we report the regulation of expression of the two activator genes
xyr1
and
ace2
, and the corepressor gene
ace1
, during the induction of cellulase biosynthesis by the inducer lactose in
T. reesei
QM 9414, a strain producing low levels of cellulase (low producer). We show that all three genes are induced by lactose.
xyr1
was also induced by
d
-galactose, but this induction was independent of
d
-galactose metabolism. Moreover,
ace1
was carbon catabolite repressed, whereas full induction of
xyr1
and
ace2
in fact required CRE1. Significant differences in these regulatory patterns were observed in the high-producer strain RUT C30 and the hyperproducer strain
T. reesei
CL847. These observations suggest that a strongly elevated basal transcription level of
xyr1
and reduced upregulation of
ace1
by lactose may have been important for generating the hyperproducer strain and that thus, these genes are major control elements of cellulase production.
The Putative Hydrolase YycJ (WalJ) Affects the Coordination of Cell Division with DNA Replication inBacillus subtilisand May Play a Conserved Role in Cell Wall Metabolism
Authors: Biller Steven J. , Wayne Kyle J. , Winkler Malcolm E. , Burkholder William F. 
Published: December 2010

ABSTRACTBacteria must accurately replicate and segregate their genetic information to ensure the production of viable daughter cells. The high fidelity of chromosome partitioning is achieved through mechanisms that coordinate cell division with DNA replication. We report that YycJ (WalJ), a predicted member of the metallo-β-lactamase superfamily found in most low-G+C Gram-positive bacteria, contributes to the fidelity of cell division inBacillus subtilis. B. subtilisΔwalJ(ΔwalJBsu) mutants divide over unsegregated chromosomes more frequently than wild-type cells, and this phenotype is exacerbated when DNA replication is inhibited. Two lines of evidence suggest that WalJBsuand its ortholog in the Gram-positive pathogenStreptococcus pneumoniae, WalJSpn(VicX), play a role in cell wall metabolism: (i) strains ofB. subtilisandS. pneumoniaelackingwalJexhibit increased sensitivity to a narrow spectrum of cephalosporin antibiotics, and (ii) reducing the expression of a two-component system that regulates genes involved in cell wall metabolism, WalRK (YycFG), renderswalJessential for growth inB. subtilis, as observed previously withS. pneumoniae. Together, these results suggest that the enzymatic activity of WalJ directly or indirectly affects cell wall metabolism and is required for accurate coordination of cell division with DNA replication.
Inerolysin, a Cholesterol-Dependent Cytolysin Produced by
Lactobacillus
iners
Authors: Rampersaud Ryan , Planet Paul J. , Randis Tara M. , Kulkarni Ritwij , Aguilar Jorge L. , Lehrer Robert I. , Ratner Adam J. 
Published: December 2010

ABSTRACT

Lactobacillus
iners
is a common constituent of the human vaginal microbiota. This species was only recently characterized due to its fastidious growth requirements and has been hypothesized to play a role in the pathogenesis of bacterial vaginosis. Here we present the identification and molecular characterization of a protein toxin produced by
L
.
iners
. The
L
.
iners
genome encodes an open reading frame with significant primary sequence similarity to intermedilysin (ILY; 69.2% similarity) and vaginolysin (VLY; 68.4% similarity), the cholesterol-dependent cytolysins from
Streptococcus
intermedius
and
Gardnerella
vaginalis
, respectively. Clinical isolates of
L
.
iners
produce this protein, inerolysin (INY), during growth
in
vitro
, as assessed by Western analysis. INY is a pore-forming toxin that is activated by reducing agents and inhibited by excess cholesterol. It is active across a pH range of 4.5 to 6.0 but is inactive at pH 7.4. At sublytic concentrations, INY activates p38 mitogen-activated protein kinase and allows entry of fluorescent phalloidin into the cytoplasm of epithelial cells. Unlike VLY and ILY, which are human specific, INY is active against cells from a broad range of species. INY represents a new target for studies directed at understanding the role of
L
.
iners
in states of health and disease at the vaginal mucosal surface.
The Sensor Kinase CbrA Is a Global Regulator That Modulates Metabolism, Virulence, and Antibiotic Resistance in
Pseudomonas aeruginosa
Authors: Yeung Amy T. Y. , Bains Manjeet , Hancock Robert E. W. 
Published: December 2010

ABSTRACT

Pseudomonas aeruginosa
is an opportunistic pathogen that possesses a large arsenal of virulence factors enabling the pathogen to cause serious infections in immunocompromised patients, burn victims, and cystic fibrosis patients. CbrA is a sensor kinase that has previously been implied to play a role with its cognate response regulator CbrB in the metabolic regulation of carbon and nitrogen utilization in
P. aeruginosa
. Here it is demonstrated that CbrA and CbrB play an important role in various virulence and virulence-related processes of the bacteria, including swarming, biofilm formation, cytotoxicity, and antibiotic resistance. The
cbrA
deletion mutant was completely unable to swarm while exhibiting an increase in biofilm formation, supporting the inverse regulation of swarming and biofilm formation in
P. aeruginosa
. The
cbrA
mutant also exhibited increased cytotoxicity to human lung epithelial cells as early as 4 and 6 h postinfection. Furthermore, the
cbrA
mutant demonstrated increased resistance toward a variety of clinically important antibiotics, including polymyxin B, ciprofloxacin, and tobramycin. Microarray analysis revealed that under swarming conditions, CbrA regulated the expression of many genes, including
phoPQ
,
pmrAB
,
arnBCADTEF
,
dnaK
, and
pvdQ
, consistent with the antibiotic resistance and swarming impairment phenotypes of the
cbrA
mutant. Phenotypic and real-time quantitative PCR (RT-qPCR) analyses of a PA14
cbrB
mutant suggested that CbrA may be modulating swarming, biofilm formation, and cytotoxicity via CbrB and that the CrcZ small RNA is likely downstream of this two-component regulator. However, as CbrB did not have a resistance phenotype, CbrA likely modulates antibiotic resistance in a manner independent of CbrB.
Pseudomonas aeruginosa
Enhances Production of an Antimicrobial in Response to
N
-Acetylglucosamine and Peptidoglycan
Authors: Korgaonkar Aishwarya K. , Whiteley Marvin 
Published: December 2010

ABSTRACT

Pseudomonas aeruginosa
is an opportunistic pathogen often associated with chronic lung infections in individuals with the genetic disease cystic fibrosis (CF). Previous work from our laboratory revealed that five genes predicted to be important for catabolism of
N
-acetylglucosamine (GlcNAc) are induced during
in vitro
growth in CF lung secretions (sputum). Here, we demonstrate that these genes comprise an operon (referred to as the
nag
operon) and that NagE, a putative component of the GlcNAc phosphotransferase system, is required for growth on and uptake of GlcNAc. Using primer extension analysis, the promoter of the
nag
operon was mapped and shown to be inducible by GlcNAc and regulated by the transcriptional regulator NagR. Transcriptome analysis revealed that in addition to induction of the
nag
operon, several
P. aeruginosa
genes encoding factors critical for extracellular antimicrobial production are also induced by GlcNAc. Finally, we show that the GlcNAc-containing polymer peptidoglycan induces production of the antimicrobial pyocyanin. Based on this data, we propose a model in which
P. aeruginosa
senses surrounding bacteria by monitoring exogenous peptidoglycan and responds to this cue through enhanced production of an antimicrobial.
Identification of Two Feruloyl Esterases in
Dickeya dadantii
3937 and Induction of the Major Feruloyl Esterase and of Pectate Lyases by Ferulic Acid
Authors: Hassan Susan , Hugouvieux-Cotte-Pattat Nicole 
Published: December 2010

ABSTRACT

The plant-pathogenic bacterium
Dickeya dadantii
(formerly
Erwinia chrysanthemi
) produces a large array of plant cell wall-degrading enzymes. Using an
in situ
detection test, we showed that it produces two feruloyl esterases, FaeD and FaeT. These enzymes cleave the ester link between ferulate and the pectic or xylan chains. FaeD and FaeT belong to the carbohydrate esterase family CE10, and they are the first two feruloyl esterases to be identified in this family. Cleavage of synthetic substrates revealed strong activation of FaeD and FaeT by ferulic acid. The gene
faeT
appeared to be weakly expressed, and its product, FaeT, is a cytoplasmic protein. In contrast, the gene
faeD
is strongly induced in the presence of ferulic acid, and FaeD is an extracellular protein secreted by the Out system, responsible for pectinase secretion. The product of the adjacent gene
faeR
is involved in the positive control of
faeD
in response to ferulic acid. Moreover, ferulic acid acts in synergy with polygalacturonate to induce pectate lyases, the main virulence determinant of soft rot disease. Feruloyl esterases dissociate internal cross-links in the polysaccharide network of the plant cell wall, suppress the polysaccharide esterifications, and liberate ferulic acid, which contributes to the induction of pectate lyases. Together, these effects of feruloyl esterases could facilitate soft rot disease caused by pectinolytic bacteria.
Integrated cone-beam CT and fluoroscopic navigation in treatment of head and neck vascular malformations and tumors
Authors: Nesbit Gary M , Nesbit Eric G , Hamilton Bronwyn E 
Published: December 2010

Background and aimAccurate direct puncture access to vascular malformations and tumors of the head and neck is critical to successful embolization treatment and avoidance of complications. The primary focus of this project was to evaluate the accuracy and ease of needle placement using integrated 3D cone-beam CT and fluoroscopic guidance in accessing head and neck vascular malformations and tumors, and to determine its contribution to lesion treatment.MethodsA total of 27 patients, 14 female and 13 male, aged 4–63 years, were included in this study. The lesions included 11 venous malformations, 5 arteriovenous malformations, 5 juvenile nasopharyngeal angiofibromas, 2 lymphovenous malformations, 1 lymphatic malformation, 1 capillary malformation, 1 nasal cavity leiomyoma, and 1 dural arteriovenous fistula. A total of 65 needle placements in 33 procedures were performed using an integrated 3D cone-beam CT and fluoroscopic guidance system.ResultsTargeting was successful with a single pass in 62 of 65 planned needle placements to a superficial location in 24, the hypopharynx, retro-pharyngeal, pyriform sinus, or paratracheal spaces in 21, the sphenoid sinus and upper nasal cavity via trans-nasal approach in 5, intra-orbital in 5, intra-laryngeal in 4, pterygo-palatine fossa in 4, external auditory canal in 1, and intracranial via a juxta-torcular burr hole in 1. Needle placement was within 2 mm of the planned target in 11 locations in the 8 patients where post needle-placement cone-beam CT was obtained.ConclusionThis integrated 3D cone-beam CT and fluoroscopic guidance allowed access to deep, difficult to access, locations with ease using a single needle pass in most cases, resulting in improved treatment with decreased procedure times.
Vascular inflammation in central nervous system diseases: adhesion receptors controlling leukocyte–endothelial interactions
Authors: Rossi Barbara , Angiari Stefano , Zenaro Elena , Budui Simona Luciana , Constantin Gabriela 
Published: December 2010

ABSTRACTLeukocyte trafficking from the blood into the tissues represents a key process during inflammation and requires multiple steps mediated by adhesion molecules and chemoattractants. Inflammation has a detrimental role in several diseases, and in such cases, the molecular mechanisms controlling leukocyte migration are potential therapeutic targets. Over the past 20 years, leukocyte migration in the CNS has been investigated almost exclusively in the context of stroke and MS. Experimental models of ischemic stroke have led to the characterization of adhesion molecules controlling leukocyte migration during acute inflammation, whereas EAE, the animal model of MS, has provided similar data for chronic inflammation. Such experiments have led to clinical trials of antileukocyte adhesion therapy, with consistently positive outcomes in human subjects with MS, showing that interference with leukocyte adhesion can ameliorate chronic inflammatory CNS diseases. This review summarizes our current understanding of the roles of adhesion molecules controlling leukocyte–endothelial interactions in stroke and MS, focusing on recently discovered, novel migration mechanisms. We also discuss the growing evidence suggesting a role for vascular inflammation and leukocyte trafficking in neurodegenerative diseases such as AD. Moreover, we highlight recent findings suggesting a role for leukocyte–endothelial interactions in the pathogenesis of seizures and epilepsy, thus linking endothelial activation and leukocyte trafficking to neuronal electrical hyperactivity. These emerging roles for leukocytes and leukocyte adhesion mechanisms in CNS diseases provide insight into the mechanisms of brain damage and may contribute to the development of novel therapeutic strategies.
Applications of myeloid-specific promoters in transgenic mice support in vivo imaging and functional genomics but do not support the concept of distinct macrophage and dendritic cell lineages or roles in immunity
Authors: Hume David A 
Published: December 2010

ABSTRACTMyeloid lineage cells contribute to innate and acquired immunity, homeostasis, wound repair, and inflammation. There is considerable interest in manipulation of their function in transgenic mice using myeloid-specific promoters. This review considers the applications and specificity of some of the most widely studied transgenes, driven by promoter elements of the lysM, csf1r, CD11c, CD68, macrophage SRA, and CD11b genes, as well as several others. Transgenes have been used in mice to generate myeloid lineage-specific cell ablation, expression of genes of interest, including fluorescent reporters, or deletion via recombination. In general, the specificity of such transgenes has been overinterpreted, and none of them provide well-documented, reliable, differential expression in any specific myeloid cell subset, macrophages, granulocytes, or myeloid DCs. Nevertheless, they have proved valuable in cell isolation, functional genomics, and live imaging of myeloid cell behavior in many different pathologies.
Macrophage phagocytosis of neutrophils at inflammatory/infectious foci: a cooperative mechanism in the control of infection and infectious inflammation
Authors: Silva Manuel T 
Published: December 2010

ABSTRACTMacrophages and neutrophils possess overlapping and complementary features associated to their common origin and subsequent specialization during myelopoiesis. That specialization results in macrophage lineage being limited in antimicrobial capacity and cytotoxicity comparatively with the neutrophil lineage. These and other features of mature macrophages and neutrophils, like different lifespan and tissue localization, promote their particular lifestyles and prompt a functional partnership for cooperation in the protective antimicrobial host defense. This partnership includes reciprocal recruitment to infected sites, cooperative effector antimicrobial activities, and pro-resolving anti-inflammatory effects. One modality of the cooperative effector antimicrobial activities involves the phagocytosis by the macrophage of apoptosing neutrophils and of nonapoptosing neutrophils expressing “eat-me” signals. This cooperative interaction results in the enhancement of the comparatively limited macrophage antimicrobial capacity by the acquisition and use of potent neutrophil microbicidal molecules. Here, data are reviewed that suggest that this is a process actively engaging the two professional phagocytes. Phagocytosis of neutrophils by macrophages at inflammatory/infectious foci accumulates two effects beneficial to the protective host immune response: help in the control of the infection and prevention of neutrophil autolysis, effects that converge to accelerate the resolution of the infection-associated inflammation.
Macrophage-derived BAFF induces AID expression through the p38MAPK/CREB and JNK/AP-1 pathways
Authors: Kim Hyun-A , Seo Goo-Young , Kim Pyeung-Hyeun 
Published: December 2010

ABSTRACT
BAFF is expressed primarily by macrophages and DCs. BAFF stimulates the differentiation and survival of B cells and induces Ig production. We have demonstrated previously that murine macrophages treated with TGF-β1 or IFN-γ express membrane-bound and soluble forms of BAFF. The ability of these two forms of BAFF to induce expression of AID, which plays a critical role in Ig CSR in B cells, was investigated. Both forms of BAFF, derived from macrophages activated by IFN-γ or TGF-β1, can increase AID expression. Subsequent analysis of BAFF signaling suggested that BAFF induces AID through BCMA, a BAFF-receptor, and p38MAPK and CREB act as intermediates in AID expression. In addition, JNK and AP-1 have similar activities. Our findings suggest that macrophage-derived BAFF stimulates B cells to express AID through BCMA and at least two different pathways, including the p38MAPK/CREB and the JNK/AP-1 pathways.
Antimicrobial activity of some synthesized glucopyranosyl-pyrimidine carbonitrile and fused pyrimidine systems
Authors: Sayed Hayam , Abbas Hebat-Allah , Morsi Eman , Amr Abd , Abdelwahad Nayera 
Published: December 2010

Antimicrobial activity of some synthesized glucopyranosyl-pyrimidine carbonitrile and fused pyrimidine systems
3-Amino-5-(4-chlorophenylamino)-4-cyanofuran-2-carboxamide (2) was used as the key molecule for preparation of various furopyrimidines 3-9 and formation of spiro-cycloalkane furopyrimidines 10, 11. Also, poly fused heterocyclic compounds 13-17 were prepared from compound 2. The synthesized compounds were screened for their antimicrobial activity.
Silymarin-solid dispersions: Characterization and influence of preparation methods on dissolution
Authors: Sonali Dalwadi , Tejal Soni , Vaishali Thakkar , Tejal Gandhi 
Published: December 2010

Silymarin-solid dispersions: Characterization and influence of preparation methods on dissolution
The influence of preparation methodology of silymarin solid dispersions using a hydrophilic polymer on the dissolution performance of silymarin was investigated. Silymarin solid dispersions were prepared using HPMC E 15LV by kneading, spray drying and co-precipitation methods and characterized by FTIR, DSC, XRPD and SEM. Dissolution profiles were compared by statistical and model independent methods. The FTIR and DSC studies revealed weak hydrogen bond formation between the drug and polymer, while XRPD and SEM confirmed the amorphous nature of the drug in co-precipitated solid dispersion. Enhanced dissolution compared to pure drug was found in the following order: co-precipitation > spray drying > kneading methodology (p < 0.05). All preparation methods enhanced silymarin dissolution from solid dispersions of different characteristics. The co-precipitation method proved to be best and provided a stable amorphous solid dispersion with 2.5 improved dissolution compared to the pure drug.