bluuebunny/crossref_metadata_2025_split huggingface dataset:
Moxifloxacin Pharmacokinetics/Pharmacodynamics and Optimal Dose and Susceptibility Breakpoint Identification for Treatment of DisseminatedMycobacterium aviumInfection
Authors: Deshpande Devyani , Srivastava Shashikant , Meek Claudia , Leff Richard , Hall Gerri S. , Gumbo Tawanda 
Published: April 2010

ABSTRACTOrganisms of theMycobacterium avium-intracellularecomplex (MAC) have been demonstrated to be susceptible to moxifloxacin. However, clinical data on how to utilize moxifloxacin to treat disseminated MAC are scanty. In addition, there have been no moxifloxacin pharmacokinetic-pharmacodynamic (PK/PD) studies performed for MAC infection. We utilized anin vitroPK/PD model of intracellular MAC to study moxifloxacin PK/PD for disseminated disease. Moxifloxacin doses, based on a serum half-life of 12 h, were administered, and the 0- to 24-h area under the concentration-time curve (AUC0-24) to MIC ratios associated with 1.0 log10CFU/ml per week kill and 90% of maximal kill (EC90) were identified. The AUC0-24/MIC ratio associated with 1.0 log10CFU/ml kill was 17.12, and that with EC90was 391.56 (r2= 0.97). Next, the moxifloxacin MIC distribution in 102 clinical isolates of MAC was identified. The median MIC was 1 to 2 mg/liter. Monte Carlo simulations of 10,000 patients with disseminated MAC were performed to determine the probability that daily moxifloxacin doses of 400 and 800 mg/day would achieve or exceed 1.0 log10CFU/ml per week kill or EC90. Doses of 400 and 800 mg/day achieved the AUC0-24/MIC ratio of 17.12 in 64% and 92% of patients, respectively. The critical concentration of moxifloxacin against MAC was identified as 0.25 mg/liter in Middlebrook media. The proposed susceptibility breakpoint means that a larger proportion of clinical isolates is resistant to moxifloxacin prior to therapy. For patients infected with susceptible isolates, however, 800 mg a day should be examined for safety and efficacy for disseminatedM. aviumdisease.
phrR
-Like Gene
praR
of
Azorhizobium caulinodans
ORS571 Is Essential for Symbiosis with
Sesbania rostrata
and Is Involved in Expression of
reb
Genes
Authors: Akiba Noriko , Aono Toshihiro , Toyazaki Hiroki , Sato Satoru , Oyaizu Hiroshi 
Published: April 2010

ABSTRACT

This study focuses on the function of the gene
praR
that encodes a putative transcription factor in
Azorhizobium caulinodans
ORS571, a microsymbiont of
Sesbania rostrata
. The
praR
gene is a homolog of the
phrR
gene of
Sinorhizobium medicae
WSM419, and the
praR
and
phrR
homologs are distributed throughout the class
Alphaproteobacteria
. The growth and nitrogen fixation activity of an
A. caulinodans praR
deletion mutant in the free-living state were not significantly different from those of the wild-type strain. However, the stem nodules formed by the
praR
mutant showed lower nitrogen fixation activity than the wild-type stem nodules. Microscopy revealed that infected host cells with an oval or elongated shape were observed at early stages in the nodules formed by the
praR
mutant, but these infected cells gradually fell into two types. One maintained an oval or elongated shape, but the vacuoles in these cells gradually enlarged and the bacteria gradually disappeared. The other cells were shrunken with bacteria remaining inside. Microarrays revealed that genes homologous to the
reb
genes of
Caedibacter taeniospiralis
were highly expressed in the
praR
mutant. Furthermore, the stem nodules formed by an
A. caulinodans
mutant with a deletion of
praR
and
reb
-homologous genes showed high nitrogen fixation activity, comparable to that of the wild-type stem nodules, and were filled with oval or elongated host cells. These results suggest that PraR controls the expression of the
reb
-homologous genes and that high expression of
reb
-homologous genes causes aberrance in
A. caulinodans
-
S. rostrata
symbiosis.
Nonstarch Polysaccharides Modulate Bacterial Microbiota, Pathways for Butyrate Production, and Abundance of Pathogenic
Escherichia coli
in the Pig Gastrointestinal Tract
Authors: Metzler-Zebeli Barbara U. , Hooda Seema , Pieper Robert , Zijlstra Ruurd T. , van Kessel Andrew G. , Mosenthin Rainer , Gänzle Michael G. 
Published: April 2010

ABSTRACT

The impact of nonstarch polysaccharides (NSP) differing in their functional properties on intestinal bacterial community composition, prevalence of butyrate production pathway genes, and occurrence of
Escherichia coli
virulence factors was studied for eight ileum-cannulated growing pigs by use of terminal restriction fragment length polymorphism (TRFLP) and quantitative PCR. A cornstarch- and casein-based diet was supplemented with low-viscosity, low-fermentability cellulose (CEL), with high-viscosity, low-fermentability carboxymethylcellulose (CMC), with low-viscosity, high-fermentability oat β-glucan (LG), and with high-viscosity, high-fermentability oat β-glucan (HG). Only minor effects of NSP fractions on the ileal bacterial community were observed, but NSP clearly changed the digestion in the small intestine. Compared to what was observed for CMC, more fermentable substrate was transferred into the large intestine with CEL, LG, and HG, resulting in higher levels of postileal dry-matter disappearance. Linear discriminant analysis of NSP and TRFLP profiles and 16S rRNA gene copy numbers for major bacterial groups revealed that CMC resulted in a distinctive bacterial community in comparison to the other NSP, which was characterized by higher gene copy numbers for total bacteria,
Bacteroides-Prevotella-Porphyromonas
,
Clostridium
cluster XIVa, and
Enterobacteriaceae
and increased prevalences of
E. coli
virulence factors in feces. The numbers of butyryl-coenzyme A (CoA) CoA transferase gene copies were higher than those of butyrate kinase gene copies in feces, and these quantities were affected by NSP. The present results suggest that the NSP fractions clearly and distinctly affected the taxonomic composition and metabolic features of the fecal microbiota. However, the effects were more linked to the individual NSP and to their effect on nutrient flow into the large intestine than to their shared functional properties.
Growth of Bacteria on 3-Nitropropionic Acid as a Sole Source of Carbon, Nitrogen, and Energy
Authors: Nishino Shirley F. , Shin Kwanghee A. , Payne Rayford B. , Spain Jim C. 
Published: April 2010

ABSTRACT

3-Nitropropionic acid (3NPA) is a widespread nitroaliphatic toxin found in a variety of legumes and fungi. Several enzymes have been reported that can transform the compound, but none led to the mineralization of 3NPA. We report here the isolation of bacteria that grow on 3NPA and its anion, propionate-3-nitronate (P3N), as the sole source of carbon, nitrogen, and energy. Experiments with resting cells, cell extracts, and purified enzymes indicate that the pathway involves conversion of 3NPA to P3N, which upon denitration yields malonic semialdehyde, nitrate, nitrite, and traces of H
2
O
2
. Malonic semialdehyde is decarboxylated to acetyl coenzyme A. The gene that encodes the enzyme responsible for the denitration of P3N was cloned and expressed, and the enzyme was purified. Stoichiometry of the reaction indicates that the enzyme is a monooxygenase. The gene sequence is related to a large group of genes annotated as 2-nitropropane dioxygenases, but the P3N monooxygenase and closely related enzymes form a cluster within COG2070 that differs from previously characterized 2-nitropropane dioxygenases by their substrate specificities and reaction products. The results suggest that the P3N monooxygenases enable bacteria to exploit 3NPA in natural habitats as a growth substrate.
Paenibacillus
sp. Strain E18 Bifunctional Xylanase-Glucanase with a Single Catalytic Domain
Authors: Shi Pengjun , Tian Jian , Yuan Tiezheng , Liu Xin , Huang Huoqing , Bai Yingguo , Yang Peilong , Chen Xiaoyan , Wu Ningfeng , Yao Bin 
Published: April 2010

ABSTRACT

Xylanases are utilized in a variety of industries for the breakdown of plant materials. Most native and engineered bifunctional/multifunctional xylanases have separate catalytic domains within the same polypeptide chain. Here we report a new bifunctional xylanase (XynBE18) produced by
Paenibacillus
sp. E18 with xylanase and β-1,3-1,4-glucanase activities derived from the same active center by substrate competition assays and site-directed mutagenesis of xylanase catalytic Glu residues (E129A and E236A). The gene consists of 981 bp, encodes 327 amino acids, and comprises only one catalytic domain that is highly homologous to the glycoside hydrolase family 10 xylanase catalytic domain. Recombinant XynBE18 purified from
Escherichia coli
BL21(DE3) showed specificity toward oat spelt xylan and birchwood xylan and β-1,3-1,4-glucan (barley β-glucan and lichenin). Homology modeling and molecular dynamic simulation were used to explore structure differences between XynBE18 and the monofunctional xylanase XynE2, which has enzymatic properties similar to those of XynBE18 but does not hydrolyze β-1,3-1,4-glucan. The cleft containing the active site of XynBE18 is larger than that of XynE2, suggesting that XynBE18 is able to bind larger substrates such as barley β-glucan and lichenin. Further molecular docking studies revealed that XynBE18 can accommodate xylan and β-1,3-1,4-glucan, but XynE2 is only accessible to xylan. These results indicate a previously unidentified structure-function relationship for substrate specificities among family 10 xylanases.
Rapid Functional Screening of
Streptomyces coelicolor
Regulators by Use of a pH Indicator and Application to the MarR-Like Regulator AbsC
Authors: Yang Yung-Hun , Song Eunjung , Lee Bo-Rahm , Kim Eun-jung , Park Sung-Hee , Kim Yun-Gon , Lee Chang-Soo , Kim Byung-Gee 
Published: April 2010

ABSTRACT

To elucidate the function of an unknown regulator in
Streptomyces
, differences in phenotype and antibiotic production between a deletion mutant and a wild-type strain (WT) were compared. These differences are easily hidden by complex media. To determine the specific nutrient conditions that reveal such differences, we used a multiwell method containing different nutrients along with bromothymol blue. We found several nutrients that provide key information on characterization conditions. By comparing the growth of wild-type and mutant strains on screened nutrients, we were able to measure growth, organic acid production, and antibiotic production for the elucidation of regulator function. As a result of this method, a member of the MarR-like regulator family, SCO5405 (AbsC), was newly characterized to control pyruvate dehydrogenase in
Streptomyces coelicolor
. Deletion of SCO5405 increased the pH of the culture broth due to decreased production of organic acids such as pyruvate and α-ketoglutarate and increased extracellular actinorhodin (ACT) production in minimal medium containing glucose and alanine (MMGA). This method could therefore be a high-throughput method for the characterization of unknown regulators.
Diversity of Bacteria and Glycosyl Hydrolase Family 48 Genes in Cellulolytic Consortia Enriched from Thermophilic Biocompost
Authors: Izquierdo Javier A. , Sizova Maria V. , Lynd Lee R. 
Published: April 2010

ABSTRACT

The enrichment from nature of novel microbial communities with high cellulolytic activity is useful in the identification of novel organisms and novel functions that enhance the fundamental understanding of microbial cellulose degradation. In this work we identify predominant organisms in three cellulolytic enrichment cultures with thermophilic compost as an inoculum. Community structure based on 16S rRNA gene clone libraries featured extensive representation of clostridia from cluster III, with minor representation of clostridial clusters I and XIV and a novel
Lutispora
species cluster. Our studies reveal different levels of 16S rRNA gene diversity, ranging from 3 to 18 operational taxonomic units (OTUs), as well as variability in community membership across the three enrichment cultures. By comparison, glycosyl hydrolase family 48 (GHF48) diversity analyses revealed a narrower breadth of novel clostridial genes associated with cultured and uncultured cellulose degraders. The novel GHF48 genes identified in this study were related to the novel clostridia
Clostridium straminisolvens
and
Clostridium clariflavum
, with one cluster sharing as little as 73% sequence similarity with the closest known relative. In all, 14 new GHF48 gene sequences were added to the known diversity of 35 genes from cultured species.
Variation of Physiochemical Properties and Cell Association Activity of Membrane Vesicles with Growth Phase in
Pseudomonas aeruginosa
Authors: Tashiro Yosuke , Ichikawa Sosaku , Shimizu Motoyuki , Toyofuku Masanori , Takaya Naoki , Nakajima-Kambe Toshiaki , Uchiyama Hiroo , Nomura Nobuhiko 
Published: April 2010

ABSTRACT

Pseudomonas aeruginosa
and other Gram-negative bacteria release membrane vesicles (MVs) from their surfaces, and MVs have an ability to interact with bacterial cells. Although it has been known that many bacteria have mechanisms that control their phenotypes with the transition from exponential phase to stationary phase, changes of properties in released MVs have been poorly understood. Here, we demonstrate that MVs released by
P. aeruginosa
during the exponential and stationary phases possess different physiochemical properties. MVs purified from the stationary phase had higher buoyant densities than did those purified from the exponential phase. Surface charge, characterized by zeta potential, of MVs tended to be more negative as the growth shifted to the stationary phase, although the charges of PAO1 cells were not altered.
Pseudomonas
quinolone signal (PQS), one of the regulators related to MV production in
P. aeruginosa
, was lower in MVs purified from the exponential phase than in those from the stationary phase. MVs from the stationary phase more strongly associated with
P. aeruginosa
cells than did those from the exponential phase. Our findings suggest that properties of MVs are altered to readily interact with bacterial cells along with the growth transition in
P. aeruginosa
.
Huanglongbing, a Systemic Disease, Restructures the Bacterial Community Associated with Citrus Roots
Authors: Trivedi Pankaj , Duan Yongping , Wang Nian 
Published: April 2010

ABSTRACT

To examine the effect of pathogens on the diversity and structure of plant-associated bacterial communities, we carried out a molecular analysis using citrus and huanglongbing as a host-disease model. 16S rRNA gene clone library analysis of citrus roots revealed shifts in microbial diversity in response to pathogen infection. The clone library of the uninfected root samples has a majority of phylotypes showing similarity to well-known plant growth-promoting bacteria, including
Caulobacter
,
Burkholderia
,
Lysobacter
,
Pantoea
,
Pseudomonas
,
Stenotrophomonas
,
Bacillus
, and
Paenibacillus
. Infection by “
Candidatus
Liberibacter asiaticus” restructured the native microbial community associated with citrus roots and led to the loss of detection of most phylotypes while promoting the growth of bacteria such as
Methylobacterium
and
Sphingobacterium
. In pairwise comparisons, the clone library from uninfected roots contained significantly higher 16S rRNA gene diversity, as reflected in the higher Chao 1 richness estimation (
P
≤ 0.01) of 237.13 versus 42.14 for the uninfected and infected clone libraries, respectively. Similarly, the Shannon index of the uninfected clone library (4.46) was significantly higher than that of the infected clone library (2.61). Comparison of the uninfected clone library with the infected clone library using LIBSHUFF statistics showed a significant difference (
P
≤ 0.05). Quantitative PCR analysis revealed that the bacterial community changes not only qualitatively but also quantitatively. The relative proportions of different groups of bacteria changed significantly after infection with the pathogen. These data indicate that infection of citrus by “
Ca
. Liberibacter asiaticus” has a profound effect on the structure and composition of the bacterial community associated with citrus roots.
Moderately Thermophilic Magnetotactic Bacteria from Hot Springs in Nevada
Authors: Lefèvre Christopher T. , Abreu Fernanda , Schmidt Marian L. , Lins Ulysses , Frankel Richard B. , Hedlund Brian P. , Bazylinski Dennis A. 
Published: April 2010

ABSTRACT

Populations of a moderately thermophilic magnetotactic bacterium were discovered in Great Boiling Springs, Nevada, ranging from 32 to 63°C. Cells were small, Gram-negative, vibrioid to helicoid in morphology, and biomineralized a chain of bullet-shaped magnetite magnetosomes. Phylogenetically, based on 16S rRNA gene sequencing, the organism belongs to the phylum
Nitrospirae
.
Identification of Diverse Antimicrobial Resistance Determinants Carried on Bacterial, Plasmid, or Viral Metagenomes from an Activated Sludge Microbial Assemblage
Authors: Parsley Larissa C. , Consuegra Erin J. , Kakirde Kavita S. , Land Andrew M. , Harper Willie F. , Liles Mark R. 
Published: April 2010

ABSTRACT

Using both sequence- and function-based metagenomic approaches, multiple antibiotic resistance determinants were identified within metagenomic libraries constructed from DNA extracted from bacterial chromosomes, plasmids, or viruses within an activated sludge microbial assemblage. Metagenomic clones and a plasmid that in
Escherichia coli
expressed resistance to chloramphenicol, ampicillin, or kanamycin were isolated, with many cloned DNA sequences lacking any significant homology to known antibiotic resistance determinants.
Study of Matrix Additives for Sensitive Analysis of Lipid A by Matrix-Assisted Laser Desorption Ionization Mass Spectrometry
Authors: Zhou Ping , Altman Eleonora , Perry Malcolm B. , Li Jianjun 
Published: April 2010

ABSTRACT

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been widely used for structural characterization of bacterial endotoxins (lipid A). However, the mass spectrometric behavior of the lipid A molecule is highly dependent on the matrix. Furthermore, this dependence is strongly linked to phosphorylation patterns. Using lipid A from
Escherichia coli
O116 as a model system, we have investigated the effects of different matrices and comatrix compounds on the analysis of lipid A. In this paper, we report a highly sensitive matrix system for lipid A analysis, which consists of 5-chloro-2-mercaptobenzothiazole matrix and EDTA ammonium salt comatrix. This matrix system enhances the sensitivity of the analysis of diphosphorylated lipid A species by more than 100-fold and in addition provides tolerance to high concentrations of sodium dodecyl sulfate (SDS) and tolerance to sodium chloride and calcium chloride at 10 μM, 100 μM, and 10 μM concentrations. The method was further evaluated for analysis of lipid A species with different phosphorylation patterns and from different bacteria, including
Helicobacter pylori
,
Salmonella enterica
serovar Riogrande, and
Francisella novicida
.
Translocation of NopP by
Sinorhizobium fredii
USDA257 into
Vigna unguiculata
Root Nodules
Authors: Schechter Lisa M. , Guenther Jeanette , Olcay Elizabeth A. , Jang Sungchan , Krishnan Hari B. 
Published: April 2010

ABSTRACT

Sinorhizobium fredii
is a nitrogen-fixing legume symbiont that stimulates the formation of root nodules.
S. fredii
nodulation of roots is influenced by Nop proteins, which are secreted through a type III secretion system (T3SS). We demonstrate that
S. fredii
injects NopP into
Vigna unguiculata
nodules in a T3SS-dependent manner.
Localization and Targeting of an Unusual Pyridine Nucleotide Transhydrogenase in Entamoeba histolytica
Authors: Yousuf Mohammad Abu , Mi-ichi Fumika , Nakada-Tsukui Kumiko , Nozaki Tomoyoshi 
Published: April 2010

ABSTRACT

Pyridine nucleotide transhydrogenase (PNT) catalyzes the direct transfer of a hydride-ion equivalent between NAD(H) and NADP(H) in bacteria and the mitochondria of eukaryotes. PNT was previously postulated to be localized to the highly divergent mitochondrion-related organelle, the mitosome, in the anaerobic/microaerophilic protozoan parasite
Entamoeba histolytica
based on the potential mitochondrion-targeting signal. However, our previous proteomic study of isolated phagosomes suggested that PNT is localized to organelles other than mitosomes. An immunofluorescence assay using anti-
E. histolytica
PNT (
Eh
PNT) antibody raised against the NADH-binding domain showed a distribution to the membrane of numerous vesicles/vacuoles, including lysosomes and phagosomes. The domain(s) required for the trafficking of PNT to vesicles/vacuoles was examined by using amoeba transformants expressing a series of carboxyl-terminally truncated PNTs fused with green fluorescent protein or a hemagglutinin tag. All truncated PNTs failed to reach vesicles/vacuoles and were retained in the endoplasmic reticulum. These data indicate that the putative targeting signal is not sufficient for the trafficking of PNT to the vesicular/vacuolar compartments and that full-length PNT is necessary for correct transport. PNT displayed a smear of >120 kDa on SDS-PAGE gels. PNGase F and tunicamycin treatment, chemical degradation of carbohydrates, and heat treatment of PNT suggested that the apparent aberrant mobility of PNT is likely attributable to its hydrophobic nature. PNT that is compartmentalized to the acidic compartments is unprecedented in eukaryotes and may possess a unique physiological role in
E. histolytica
.
Cryptococcal Interactions with the Host Immune System
Authors: Voelz Kerstin , May Robin C. 
Published: April 2010

ABSTRACTOpportunistic pathogens have become of increasing medical importance over the last decade due to the AIDS pandemic. Not only is cryptococcosis the fourth-most-common fatal infectious disease in sub-Saharan Africa, but alsoCryptococcusis an emerging pathogen of immunocompetent individuals. The interaction betweenCryptococcusand the host's immune system is a major determinant for the outcome of disease. Despite initial infection in early childhood withCryptococcus neoformansand frequent exposure toC. neoformanswithin the environment, immunocompetent individuals are generally able to contain the fungus or maintain the yeast in a latent state. However, immune deficiencies lead to disseminating infections that are uniformly fatal without rapid clinical intervention. This review will discuss the innate and adaptive immune responses toCryptococcusand cryptococcal strategies to evade the host's defense mechanisms. It will also address the importance of these strategies in pathogenesis and the potential of immunotherapy in cryptococcosis treatment.
Pho85 Kinase, a Cyclin-Dependent Kinase, Regulates Nuclear Accumulation of the Rim101 Transcription Factor in the Stress Response of Saccharomyces cerevisiae
Authors: Nishizawa Masafumi , Tanigawa Mirai , Hayashi Michio , Maeda Tatsuya , Yazaki Yoshiaki , Saeki Yasushi , Toh-e Akio 
Published: April 2010

ABSTRACT

The budding yeast
Saccharomyces cerevisiae
alters its gene expression profile in response to changing environmental conditions. The Pho85 kinase, one of the yeast cyclin-dependent kinases (CDK), is known to play an important role in the cellular response to alterations in parameters such as nutrient levels and salinity. Several genes whose expression is regulated, either directly or indirectly, by the Rim101 transcription factor become constitutively activated when Pho85 function is absent,. Because Rim101 is responsible for adaptation to alkaline conditions, this observation suggests an interaction between Pho85 and Rim101 in the response to alkaline stress. We have found that Pho85 affects neither
RIM101
transcription, the proteolytic processing that is required for Rim101 activation, nor Rim101 stability. Rather, Pho85 regulates the nuclear accumulation of active Rim101, possibly via phosphorylation. Additionally, we report that Pho85 and the transcription factor Pho4 are necessary for adaptation to alkaline conditions and that
PTK2
activation by Pho4 is involved in this process. These findings illustrate novel roles for the regulators of the
PHO
system when yeast cells cope with various environmental stresses potentially threatening their survival.