bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic and Functional Analysis of the Cellulase System Expressed by Postia placenta during Brown Rot of Solid Wood
Authors: Ryu Jae San , Shary Semarjit , Houtman Carl J. , Panisko Ellen A. , Korripally Premsagar , St. John Franz J. , Crooks Casey , Siika-aho Matti , Magnuson Jon K. , Hammel Kenneth E. 
Published: September 2011

ABSTRACT

Brown rot basidiomycetes have an important ecological role in lignocellulose recycling and are notable for their rapid degradation of wood polymers via oxidative and hydrolytic mechanisms. However, most of these fungi apparently lack processive (
exo
-acting) cellulases, such as cellobiohydrolases, which are generally required for efficient cellulolysis. The recent sequencing of the
Postia placenta
genome now permits a proteomic approach to this longstanding conundrum. We grew
P. placenta
on solid aspen wood, extracted proteins from the biodegrading substrate, and analyzed tryptic digests by shotgun liquid chromatography-tandem mass spectrometry. Comparison of the data with the predicted
P. placenta
proteome revealed the presence of 34 likely glycoside hydrolases, but only four of these—two in glycoside hydrolase family 5, one in family 10, and one in family 12—have sequences that suggested possible activity on cellulose. We expressed these enzymes heterologously and determined that they all exhibited endoglucanase activity on phosphoric acid-swollen cellulose. They also slowly hydrolyzed filter paper, a more crystalline substrate, but the soluble/insoluble reducing sugar ratios they produced classify them as nonprocessive. Computer simulations indicated that these enzymes produced soluble/insoluble ratios on reduced phosphoric acid-swollen cellulose that were higher than expected for random hydrolysis, which suggests that they could possess limited
exo
activity, but they are at best 10-fold less processive than cellobiohydrolases. It appears likely that
P. placenta
employs a combination of oxidative mechanisms and
endo
-acting cellulases to degrade cellulose efficiently in the absence of a significant processive component.
Evaluation of a Transposase Protocol for Rapid Generation of Shotgun High-Throughput Sequencing Libraries from Nanogram Quantities of DNA
Authors: Marine Rachel , Polson Shawn W. , Ravel Jacques , Hatfull Graham , Russell Daniel , Sullivan Matthew , Syed Fraz , Dumas Michael , Wommack K. Eric 
Published: September 2011

ABSTRACT

Construction of DNA fragment libraries for next-generation sequencing can prove challenging, especially for samples with low DNA yield. Protocols devised to circumvent the problems associated with low starting quantities of DNA can result in amplification biases that skew the distribution of genomes in metagenomic data. Moreover, sample throughput can be slow, as current library construction techniques are time-consuming. This study evaluated Nextera, a new transposon-based method that is designed for quick production of DNA fragment libraries from a small quantity of DNA. The sequence read distribution across nine phage genomes in a mock viral assemblage met predictions for six of the least-abundant phages; however, the rank order of the most abundant phages differed slightly from predictions.
De novo
genome assemblies from Nextera libraries provided long contigs spanning over half of the phage genome; in four cases where full-length genome sequences were available for comparison, consensus sequences were found to match over 99% of the genome with near-perfect identity. Analysis of areas of low and high sequence coverage within phage genomes indicated that GC content may influence coverage of sequences from Nextera libraries. Comparisons of phage genomes prepared using both Nextera and a standard 454 FLX Titanium library preparation protocol suggested that the coverage biases according to GC content observed within the Nextera libraries were largely attributable to bias in the Nextera protocol rather than to the 454 sequencing technology. Nevertheless, given suitable sequence coverage, the Nextera protocol produced high-quality data for genomic studies. For metagenomics analyses, effects of GC amplification bias would need to be considered; however, the library preparation standardization that Nextera provides should benefit comparative metagenomic analyses.
Correlation of Genomic and Physiological Traits of Thermoanaerobacter Species with Biofuel Yields
Authors: Hemme Christopher L. , Fields Matthew W. , He Qiang , Deng Ye , Lin Lu , Tu Qichao , Mouttaki Housna , Zhou Aifen , Feng Xueyang , Zuo Zheng , Ramsay Bradley D. , He Zhili , Wu Liyou , Van Nostrand Joy , Xu Jian , Tang Yinjie J. , Wiegel Juergen , Phelps Tommy J. , Zhou Jizhong 
Published: September 2011

ABSTRACT

Thermophilic anaerobic noncellulolytic
Thermoanaerobacter
species are of great biotechnological importance in cellulosic ethanol production due to their ability to produce high ethanol yields by simultaneous fermentation of hexose and pentose. Understanding the genome structure of these species is critical to improving and implementing these bacteria for possible biotechnological use in consolidated bioprocessing schemes (CBP) for cellulosic ethanol production. Here we describe a comparative genome analysis of two ethanologenic bacteria,
Thermoanaerobacter
sp. X514 and
Thermoanaerobacter pseudethanolicus
39E. Compared to 39E, X514 has several unique key characteristics important to cellulosic biotechnology, including additional alcohol dehydrogenases and xylose transporters, modifications to pentose metabolism, and a complete vitamin B
12
biosynthesis pathway. Experimental results from growth, metabolic flux, and microarray gene expression analyses support genome sequencing-based predictions which help to explain the distinct differences in ethanol production between these strains. The availability of whole-genome sequence and comparative genomic analyses will aid in engineering and optimizing
Thermoanaerobacter
strains for viable CBP strategies.
Recovery of As-Yet-Uncultured Soil Acidobacteria on Dilute Solid Media
Authors: George Isabelle F. , Hartmann Manuela , Liles Mark R. , Agathos Spiros N. 
Published: September 2011

ABSTRACT

A growing number of
Acidobacteria
strains have been isolated from environments worldwide, with most isolates derived from acidic samples and affiliated with subdivision 1. We recovered 18
Acidobacteria
strains from an alkaline soil, among which 11 belonged to the previously uncultured subdivision 6. Various medium formulations were tested for their effects on
Acidobacteria
growth.
Nostophycin Biosynthesis Is Directed by a Hybrid Polyketide Synthase-Nonribosomal Peptide Synthetase in the Toxic Cyanobacterium Nostoc sp. Strain 152
Authors: Fewer David P. , Österholm Julia , Rouhiainen Leo , Jokela Jouni , Wahlsten Matti , Sivonen Kaarina 
Published: September 2011

ABSTRACT

Cyanobacteria are a rich source of natural products with interesting pharmaceutical properties. Here, we report the identification, sequencing, annotation, and biochemical analysis of the nostophycin (
npn
) biosynthetic gene cluster. The
npn
gene cluster spans 45.1 kb and consists of three open reading frames encoding a polyketide synthase, a mixed polyketide nonribosomal peptide synthetase, and a nonribosomal peptide synthetase. The genetic architecture and catalytic domain organization of the proteins are colinear in arrangement, with the putative order of the biosynthetic assembly of the cyclic heptapeptide. NpnB contains an embedded monooxygenase domain linking nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) catalytic domains and predicted here to hydroxylate the nostophycin during assembly. Expression of the adenylation domains and subsequent substrate specificity assays support the involvement of this cluster in nostophycin biosynthesis. Biochemical analyses suggest that the loading substrate of NpnA is likely to be a phenylpropanoic acid necessitating deletion of a carbon atom to explain the biosynthesis of nostophycin. Biosyntheses of nostophycin and microcystin resemble each other, but the phylogenetic analyses suggest that they are distantly related to one another.
Identification and Characterization of a Novel Class of Extracellular Poly(3-Hydroxybutyrate) Depolymerase from Bacillus sp. Strain NRRL B-14911
Authors: Ma Wan-Ting , Lin Ju-Hui , Chen Hui-Ju , Chen Syuan-Yi , Shaw Gwo-Chyuan 
Published: September 2011

ABSTRACT

The catalytic, linker, and denatured poly(3-hydroxybutyrate) (dPHB)-binding domains of bacterial extracellular PHB depolymerases (PhaZs) are classified into several different types. We now report a novel class of extracellular PHB depolymerase from
Bacillus
sp. strain NRRL B-14911. Its catalytic domain belongs to type 1, whereas its putative linker region neither possesses the sequence features of the three known types of linker domains nor exhibits significant amino acid sequence similarity to them. Instead, this putative linker region can be divided into two distinct linker domains of novel types: LD1 and LD2. LD1 shows significant amino acid sequence similarity to certain regions of a large group of PHB depolymerase-unrelated proteins. LD2 and its homologs are present in a small group of PhaZs. The remaining C-terminal portion of this PhaZ can be further divided into two distinct domains: SBD1 and SBD2. Each domain showed strong binding to dPHB, and there is no significant sequence similarity between them. Each domain neither possesses the sequence features of the two known types of dPHB-binding domains nor shows significant amino acid sequence similarity to them. These unique features indicate the presence of two novel and distinct types of dPHB-binding domains. Homologs of these novel domains also are present in the extracellular PhaZ of
Bacillus megaterium
and the putative extracellular PhaZs of
Bacillus pseudofirmus
and
Bacillus
sp. strain SG-1. The
Bacillus
sp. NRRL B-14911 PhaZ appears to be a representative of a novel class of extracellular PHB depolymerases.
Identification and Characterization of Leucocyclicin Q, a Novel Cyclic Bacteriocin Produced by Leuconostoc mesenteroides TK41401
Authors: Masuda Yoshimitsu , Ono Hiroshi , Kitagawa Hiroshi , Ito Haruo , Mu Fuqin , Sawa Naruhiko , Zendo Takeshi , Sonomoto Kenji 
Published: September 2011

ABSTRACT

The culture supernatant of
Leuconostoc mesenteroides
TK41401, isolated from Japanese pickles, possessed antimicrobial activity against broad range of a bacterial genera and particularly strong activity against
Bacillus coagulans
, the major contaminant of pickles. An antimicrobial peptide was purified in three chromatographic steps, and its molecular mass was determined to be 6,115.59 Da by electrospray ionization time-of-flight mass spectrometry (ESI-TOF MS). The primary structure of this peptide was determined by amino acid and DNA sequencing, and these analyses revealed that it was translated as a 63-residue precursor. This precursor showed high similarity to the precursor of lactocyclicin Q, a cyclic bacteriocin produced by
Lactococcus
sp. strain QU 12. The molecular weight calculated after cyclization, which was presumed to involve the same process as in lactocyclicin Q (between L3 and W63), agreed with that estimated by ESI-TOF MS. This peptide was proved to be a novel cyclic bacteriocin, and it was termed leucocyclicin Q. The antimicrobial spectrum of this bacteriocin clearly differed from that of lactocyclicin Q, even though their primary structures were quite similar. This is the first report of a cyclic bacteriocin produced by a strain of the genus
Leuconostoc
.
Cloning-Independent and Counterselectable Markerless Mutagenesis System in Streptococcus mutans
Authors: Xie Zhoujie , Okinaga Toshinori , Qi Fengxia , Zhang Zhijun , Merritt Justin 
Published: September 2011

ABSTRACT

Insertion duplication mutagenesis and allelic replacement mutagenesis are among the most commonly utilized approaches for targeted mutagenesis in bacteria. However, both techniques are limited by a variety of factors that can complicate mutant phenotypic studies. To circumvent these limitations, multiple markerless mutagenesis techniques have been developed that utilize either temperature-sensitive plasmids or counterselectable suicide vectors containing both positive- and negative-selection markers. For many species, these techniques are not especially useful due to difficulties of cloning with
Escherichia coli
and/or a lack of functional negative-selection markers. In this study, we describe the development of a novel approach for the creation of markerless mutations. This system employs a cloning-independent methodology and should be easily adaptable to a wide array of Gram-positive and Gram-negative bacterial species. The entire process of creating both the counterselection cassette and mutation constructs can be completed using overlapping PCR protocols, which allows extremely quick assembly and eliminates the requirement for either temperature-sensitive replicons or suicide vectors. As a proof of principle, we used
Streptococcus mutans
reference strain UA159 to create markerless in-frame deletions of 3 separate bacteriocin genes as well as triple mutants containing all 3 deletions. Using a panel of 5 separate wild-type
S. mutans
strains, we further demonstrated that the procedure is nearly 100% efficient at generating clones with the desired markerless mutation, which is a considerable improvement in yield compared to existing approaches.
Analysis of the LIV System of Campylobacter jejuni Reveals Alternative Roles for LivJ and LivK in Commensalism beyond Branched-Chain Amino Acid Transport
Authors: Ribardo Deborah A. , Hendrixson David R. 
Published: September 2011

ABSTRACT

Campylobacter jejuni
is a leading cause of diarrheal disease in humans and an intestinal commensal in poultry and other agriculturally important animals. These zoonotic infections result in significant amounts of
C. jejuni
present in the food supply to contribute to disease in humans. We previously found that a transposon insertion in
Cjj81176_1038
, encoding a homolog of the
Escherichia coli
LivJ periplasmic binding protein of the leucine, isoleucine, and valine (LIV) branched-chain amino acid transport system, reduced the commensal colonization capacity of
C. jejuni
81-176 in chicks.
Cjj81176_1038
is the first gene of a six-gene locus that encodes homologous components of the
E. coli
LIV system. By analyzing mutants with in-frame deletions of individual genes or pairs of genes, we found that this system constitutes a LIV transport system in
C. jejuni
responsible for a high level of leucine acquisition and, to a lesser extent, isoleucine and valine acquisition. Despite each LIV protein being required for branched-chain amino acid transport, only the LivJ and LivK periplasmic binding proteins were required for wild-type levels of commensal colonization of chicks. All LIV permease and ATPase components were dispensable for
in vivo
growth. These results suggest that the biological functions of LivJ and LivK for colonization are more complex than previously hypothesized and extend beyond a role for binding and acquiring branched-chain amino acids during commensalism. In contrast to other studies indicating a requirement and utilization of other specific amino acids for colonization, acquisition of branched-chain amino acids does not appear to be a determinant for
C. jejuni
during commensalism.
Estimated prevalence of theGYS‐1mutation in healthy Austrian Haflingers
Authors: Schwarz B. , Ertl R. , Zimmer S. , Netzmann Y. , Klein D. , Schwendenwein I. , Hoven R. V. D. 
Published: September 2011

The aim of this study was to determine the occurrence and frequency of a mutation in the gene coding for skeletal muscle glycogen synthase type 1 (GYS‐1), which is the cause of equine polysaccharide storage myopathy (PSSM) type 1 in a population of 50 Haflingers.GYS‐1genotyping of 50 Haflingers was performed with a validated restriction fragment length polymorphism (RFLP) assay. The second aim was to compare resting and post‐exercise muscle enzyme activities as well as parameters of glucose metabolism in blood between horses with and without the mutation. Nine of the 50 Haflingers were identified to be heterozygous for the mutation (HR). None was homozygous (HH). The estimated HR prevalence was 18 per cent in this herd. Mean aspartate aminotransferase (AST) activity at rest and mean creatine kinase and AST activity after exercise were significantly higher in HR compared with RR (homozygote normal) horses. No significant differences could be found in the other parameters.
Combined Blockade of Integrin-α4β1 Plus Cytokines SDF-1α or IL-1β Potently Inhibits Tumor Inflammation and Growth
Authors: Schmid Michael C. , Avraamides Christie J. , Foubert Philippe , Shaked Yuval , Kang Sang Won , Kerbel Robert S. , Varner Judith A. 
Published: September 2011

Abstract
Tumor-associated macrophages promote tumor growth by stimulating angiogenesis and suppressing antitumor immunity. Thus, therapeutics that inhibit macrophage recruitment to tumors may provide new avenues for cancer therapy. In this study, we showed how chemoattractants stromal cell-derived growth factor 1 alpha (SDF-1α) and interleukin 1 beta (IL-1β) collaborate with myeloid cell integrin-α4β1 to promote tumor inflammation and growth. We found that SDF-1α and IL-1β are highly expressed in the microenvironments of murine lung, pancreatic, and breast tumors; surprisingly, SDF-1α was expressed only by tumor cells, whereas IL-1β was produced only by tumor-derived granulocytes and macrophages. In vivo, both factors directly recruited proangiogenic macrophages to tissues, whereas antagonists of both factors suppressed tumor inflammation, angiogenesis, and growth. Signals induced by IL-1β and SDF-1α promoted the interaction of talin and paxillin with the cytoplasmic tails of integrin-α4β1, thereby stimulating myeloid cell adhesion to endothelium in vitro and in vivo. Inhibition of integrin-α4β1, SDF-1α, or IL-1β was sufficient to block tumor inflammation and growth, and the combined blockade of these molecules greatly accentuated these effects. Furthermore, antagonists of integrin-α4β1 inhibited chemotherapy-induced tumor inflammation and acted synergistically with chemotherapeutic agents to suppress tumor inflammation and growth. These results show that targeting myeloid cell recruitment mechanisms can be an effective approach to suppress tumor progression. Cancer Res; 71(22): 6965–75. ©2011 AACR.
Rapid Detection of Coronary Artery Stenoses With Real-Time Perfusion Echocardiography During Regadenoson Stress
Authors: Porter Thomas R. , Adolphson Mary , High Robin R. , Smith Lynette M. , Olson Joan , Erdkamp Michelle , Xie Feng , O'Leary Edward , Wong Benjamin F. , Eifert-Rain Susan , Hagen Mary E. , Abdelmoneim Sahar S. , Mulvagh Sharon L. 
Published: September 2011

Background—
Real-time myocardial contrast echocardiography permits the detection of myocardial perfusion abnormalities during stress echocardiography, which may improve the accuracy of the test in detecting coronary artery stenoses. We hypothesized that this technique could be used after a bolus injection of the selective A2A receptor agonist regadenoson to rapidly and safely detect coronary artery stenoses.

Methods and Results—

In 100 patients referred for quantitative coronary angiography, real-time myocardial contrast echocardiography was performed during a continuous intravenous infusion of 3% Definity at baseline and at 2-minute intervals for up to 6 minutes after a regadenoson bolus injection (400 μg). Myocardial perfusion was assessed by examination of myocardial contrast replenishment after brief high mechanical index impulses. A perfusion defect was defined as a delay (>2 seconds) in myocardial contrast replenishment in 2 contiguous segments. Wall motion was also analyzed. The overall sensitivity/specificity/accuracy for myocardial perfusion analysis in detecting a >50% diameter stenosis was 80%/74%/78%, whereas for wall motion analysis it was 60%/72%/66% (
P
<0.001 for differences in sensitivity). Sensitivity for myocardial perfusion analysis was highest on images obtained during the first 2 minutes after regadenoson bolus (
P
<0.001 compared with wall motion), whereas wall motion sensitivity was highest at the 4-to-6–minute period after the bolus. No significant side effects occurred after regadenoson bolus injection.

Conclusions—
Regadenoson real-time myocardial contrast echocardiography appears to be a feasible, safe, and rapid noninvasive method for the detection of significant coronary artery stenoses.

Clinical Trial Registration—

URL:
http://www.clinicaltrials.gov
. Unique identifier: NCT0087369.
Continuity of care for people with psychotic illness: Its relationship to clinical and social functioning
Authors: Catty Jocelyn , White Sarah , Clement Sarah , Cowan Naomi , Geyer Connie , Harvey Kate , Jones Ian Rees , McLaren Susan , Poole Zoe , Rose Diana , Wykes Til , Burns Tom 
Published: September 2011

Background: The relationship between continuity of care and user characteristics or outcomes has rarely been explored. The ECHO study operationalized and tested a multi-axial definition of continuity of care, producing a seven-factor model used here. Aims: To assess the relationship between user characteristics and established components of continuity of care, and the impact of continuity on clinical and social functioning. Methods: The sample comprised 180 community mental health team users with psychotic disorders who were interviewed at three annual time-points, to assess their experiences of continuity of care and clinical and social functioning. Scores on seven continuity factors were tested for association with user-level variables. Results: Improvement in quality of life was associated with better Experience & Relationship continuity scores (better user-rated continuity and therapeutic relationship) and with lower Meeting Needs continuity factor scores. Higher Meeting Needs scores were associated with a decrease in symptoms. Conclusion: Continuity is a dynamic process, influenced significantly by care structures and organizational change.
Olfactory hallucinations in primary headache disorders: Case series and literature review
Authors: Coleman Elisheva R , Grosberg Brian M , Robbins Matthew S 
Published: September 2011

Background: Olfactory hallucinations (phantosmias) have rarely been reported in migraine patients. Unlike visual, sensory, language, brainstem, and motor symptoms, they are not recognized as a form of aura by the International Classification of Headache Disorders. Methods: We examined the clinical features of 39 patients (14 new cases and 25 from the literature) with olfactory hallucinations in conjunction with their primary headache disorders. Results: In a 30-month period, the prevalence of phantosmias among all patients seen at our headache center was 0.66%. Phantosmias occurred most commonly in women with migraine, although they were also seen in several patients with other primary headache diagnoses. The typical hallucination lasted 5–60 minutes, occurred shortly before or simultaneous with the onset of head pain, and was of a highly specific and unpleasant odor, most commonly a burning smell. In the majority of patients, phantosmias diminished or disappeared with initiation of prophylactic therapy for headaches. Conclusions: We propose that olfactory hallucinations are probably an uncommon but distinctive form of migraine aura, based on their semiology, timing and response to headache prophylaxis.