bluuebunny/crossref_metadata_2025_split huggingface dataset:
Equine Stomachs Harbor an Abundant and Diverse Mucosal Microbiota
Authors: Perkins G. A. , den Bakker H. C. , Burton A. J. , Erb H. N. , McDonough S. P. , McDonough P. L. , Parker J. , Rosenthal R. L. , Wiedmann M. , Dowd S. E. , Simpson K. W. 
Published: February 2012

ABSTRACTLittle is known about the gastric mucosal microbiota in healthy horses, and its role in gastric disease has not been critically examined. The present study used a combination of 16S rRNA bacterial tag-encoded pyrosequencing (bTEFAP) and fluorescencein situhybridization (FISH) to characterize the composition and spatial distribution of selected gastric mucosal microbiota of healthy horses. Biopsy specimens of the squamous, glandular, antral, and any ulcerated mucosa were obtained from 6 healthy horses by gastroscopy and from 3 horses immediately postmortem. Pyrosequencing was performed on biopsy specimens from 6 of the horses and yielded 53,920 reads in total, with 631 to 4,345 reads in each region per horse. The microbiome segregated into two distinct clusters comprised of horses that were stabled, fed hay, and sampled at postmortem (cluster 1) and horses that were pastured on grass, fed hay, and biopsied gastroscopically after a 12-h fast (cluster 2). The types of bacteria obtained from different anatomic regions clustered by horse rather than region. The dominant bacteria in cluster 1 wereFirmicutes(>83% reads/sample), mainlyStreptococcusspp.,Lactobacillusspp. and,Sarcinaspp. Cluster 2 was more diverse, with predominantlyProteobacteria,Bacteroidetes, andFirmicutes, consisting ofActinobacillusspp.Moraxellaspp.,Prevotellaspp., andPorphyromonasspp.Helicobactersp. sequences were not identified in any of 53,920 reads. FISH (n= 9) revealed bacteria throughout the stomach in close apposition to the mucosa, with significantly moreStreptococcusspp. present in the glandular region of the stomach. The equine stomach harbors an abundant and diverse mucosal microbiota that varies by individual.
NAD(P)
+
-Malic Enzyme Mutants of Sinorhizobium sp. Strain NGR234, but Not Azorhizobium caulinodans ORS571, Maintain Symbiotic N
2
Fixation Capabilities
Authors: Zhang Ye , Aono Toshihiro , Poole Phillip , Finan Turlough M. 
Published: February 2012

ABSTRACT

C
4
-dicarboxylic acids appear to be metabolized via the tricarboxylic acid (TCA) cycle in N
2
-fixing bacteria (bacteroids) within legume nodules. In
Sinorhizobium meliloti
bacteroids from alfalfa, NAD
+
-malic enzyme (DME) is required for N
2
fixation, and this activity is thought to be required for the anaplerotic synthesis of pyruvate. In contrast, in the pea symbiont
Rhizobium leguminosarum
, pyruvate synthesis occurs via either DME or a pathway catalyzed by phosphoenolpyruvate carboxykinase (PCK) and pyruvate kinase (PYK). Here we report that
dme
mutants of the broad-host-range
Sinorhizobium
sp. strain NGR234 formed nodules whose level of N
2
fixation varied from 27 to 83% (plant dry weight) of the wild-type level, depending on the host plant inoculated. NGR234 bacteroids had significant PCK activity, and while single
pckA
and single
dme
mutants fixed N
2
at reduced rates, a
pckA dme
double mutant had no N
2
-fixing activity (Fix
−
). Thus, NGR234 bacteroids appear to synthesize pyruvate from TCA cycle intermediates via DME or PCK pathways. These NGR234 data, together with other reports, suggested that the completely Fix
−
phenotype of
S. meliloti dme
mutants may be specific to the alfalfa-
S. meliloti
symbiosis. We therefore examined the ME-like genes
azc3656
and
azc0119
from
Azorhizobium caulinodans
, as
azc3656
mutants were previously shown to form Fix
−
nodules on the tropical legume
Sesbania rostrata
. We found that purified AZC3656 protein is an NAD(P)
+
-malic enzyme whose activity is inhibited by acetyl-coenzyme A (acetyl-CoA) and stimulated by succinate and fumarate. Thus, whereas DME is required for symbiotic N
2
fixation in
A. caulinodans
and
S. meliloti
, in other rhizobia this activity can be bypassed via another pathway(s).
Identification and Characterization of γ-Aminobutyric Acid Uptake System GabP

Cg

(NCgl0464) in Corynebacterium glutamicum
Authors: Zhao Zhi , Ding Jiu-Yuan , Ma Wen-hua , Zhou Ning-Yi , Liu Shuang-Jiang 
Published: February 2012

ABSTRACT

Corynebacterium glutamicum
is widely used for industrial production of various amino acids and vitamins, and there is growing interest in engineering this bacterium for more commercial bioproducts such as γ-aminobutyric acid (GABA). In this study, a
C. glutamicum
GABA-specific transporter (GabP

Cg

) encoded by
ncgl0464
was identified and characterized. GabP

Cg

plays a major role in GABA uptake and is essential to
C. glutamicum
growing on GABA. GABA uptake by GabP

Cg

was weakly competed by
l
-Asn and
l
-Gln and stimulated by sodium ion (Na
+
). The

K
m

and
V
max
values were determined to be 41.1 ± 4.5 μM and 36.8 ± 2.6 nmol min
−1
(mg dry weight [DW])
−1
, respectively, at pH 6.5 and 34.2 ± 1.1 μM and 67.3 ± 1.0 nmol min
−1
(mg DW)
−1
, respectively, at pH 7.5. GabP

Cg

has 29% amino acid sequence identity to a previously and functionally identified aromatic amino acid transporter (TyrP) of
Escherichia coli
but low identities to the currently known GABA transporters (17% and 15% to
E. coli
GabP and
Bacillus subtilis
GabP, respectively). The mutant RES167 Δ
ncgl0464
/pGXKZ9 with the GabP

Cg

deletion showed 12.5% higher productivity of GABA than RES167/pGXKZ9. It is concluded that GabP

Cg

represents a new type of GABA transporter and is potentially important for engineering GABA-producing
C. glutamicum
strains.
Investigations of Salmonella enterica Serovar Newport Infections of Oysters by Using Immunohistochemistry and Knockout Mutagenesis
Authors: Morrison Christopher M. , Dial Sharon M. , Day William A. , Joens Lynn A. 
Published: February 2012

ABSTRACTThe consumption of raw oysters is an important risk factor in the acquisition of food-borne disease, withSalmonellabeing one of a number of pathogens that have been found in market oysters. Previous work by our lab found thatSalmonellawas capable of surviving in oysters for over 2 months under laboratory conditions, and this study sought to further investigateSalmonella's tissue affinity and mechanism of persistence within the oysters. Immunohistochemistry was used to show thatSalmonellawas capable of breaching the epithelial barriers, infecting the deeper connective tissues of the oysters, and evading destruction by the oysters' phagocytic hemocytes. To further investigate the mechanism of these infections, genes vital to the function ofSalmonella's two main type III secretion systems were disrupted and the survivability of these knockout mutants within oysters was assayed. When theSalmonellapathogenicity island 1 and 2 mutant strains were exposed to oysters, there were no detectable deficiencies in their abilities to survive, suggesting thatSalmonella's long-term infection of oysters does not rely upon these two important pathogenicity islands and must be due to some other, currently unknown, mechanism.
Functional Assignment of YvgO, a Novel Set of Purified and Chemically Characterized Proteinaceous Antifungal Variants Produced by Bacillus thuringiensis SF361
Authors: Manns David C. , Churey John J. , Worobo Randy W. 
Published: February 2012

ABSTRACTThis study reports a novel class of antifungal protein derived from bacterial origin.Bacillus thuringiensisSF361, the strain also responsible for producing the novel bacteriocin thurincin H, exhibits broad antifungal activity against select members of several fungal genera, includingAspergillus,Byssochlamys, andPenicillium, as well as the pathogenic yeastCandida albicans. Optimal antifungal production and secretion were observed after-log phase growth when incubated at 37°C in a carbohydrate-free growth medium. High-performance liquid chromatography purification was performed after pH-selective ammonium sulfate precipitation and size-exclusion chromatography. Intact mass analysis and peptide mass fingerprinting identified the 13,484-Da protein to be a mass homolog to the YvgO protein construct sequenced fromBacillus cereusAH 1134. Further analysis via amino-terminal sequencing also revealed the existence of four distinct yet equally efficacious YvgO variants differing only within the first four N-terminal residues. YvgO was found to be remarkably stable, maintaining its antifungal activity under a wide pH and temperature range. When assayed against the toxigenic speciesByssochlamys fulvaH25, the selected primary filamentous fungal indicator, the MIC was estimated to be 1.5 ppm.Candida albicans3153 was more resistant, exhibiting MICs between 25 and 800 ppm, depending on growth conditions. YvgO is unique among antifungals, showing no known sequential or functional homology to the typical classes of antifungal proteins, including common membrane-acting agents such as cellulases and glucanases. Due to its activity against an array of pathogenic and spoilage fungi, the potentials for clinical, agricultural, and food-processing applications are encouraging.
Quantification of Human Fecal Bifidobacterium Species by Use of Quantitative Real-Time PCR Analysis Targeting the
groEL
Gene
Authors: Junick Jana , Blaut Michael 
Published: February 2012

ABSTRACT

Quantitative real-time PCR assays targeting the
groEL
gene for the specific enumeration of 12 human fecal
Bifidobacterium
species were developed. The housekeeping gene
groEL
(
HSP60
in eukaryotes) was used as a discriminative marker for the differentiation of
Bifidobacterium adolescentis
,
B. angulatum
,
B. animalis
,
B. bifidum
,
B. breve
,
B. catenulatum
,
B. dentium
,
B. gallicum
,
B. longum
,
B. pseudocatenulatum
,
B. pseudolongum
, and
B. thermophilum
. The bifidobacterial chromosome contains a single copy of the
groEL
gene, allowing the determination of the cell number by quantification of the
groEL
copy number. Real-time PCR assays were validated by comparing fecal samples spiked with known numbers of a given
Bifidobacterium
species. Independent of the
Bifidobacterium
species tested, the proportion of
groEL
copies recovered from fecal samples spiked with 5 to 9 log
10
cells/g feces was approximately 50%. The quantification limit was 5 to 6 log
10
groEL
copies/g feces. The interassay variability was less than 10%, and variability between different DNA extractions was less than 23%. The method developed was applied to fecal samples from healthy adults and full-term breast-fed infants. Bifidobacterial diversity in both adults and infants was low, with mostly ≤3
Bifidobacterium
species and
B. longum
frequently detected. The predominant species in infant and adult fecal samples were
B. breve
and
B. adolescentis
, respectively. It was possible to distinguish
B. catenulatum
and
B. pseudocatenulatum
. We conclude that the
groEL
gene is a suitable molecular marker for the specific and accurate quantification of human fecal
Bifidobacterium
species by real-time PCR.
Establishment of Characteristic Gut Bacteria during Development of the Honeybee Worker
Authors: Martinson Vincent G. , Moy Jamie , Moran Nancy A. 
Published: February 2012

ABSTRACTPrevious surveys have shown that adult honeybee (Apis mellifera) workers harbor a characteristic gut microbiota that may play a significant role in bee health. For three major phylotypes within this microbiota, we have characterized distributions and abundances across the life cycle and among gut organs. These distinctive phylotypes, called Beta, Firm-5, and Gamma-1 (BFG), were assayed using quantitative PCR, fluorescentin situhybridization (FISH) microscopy, and the experimental manipulation of inoculation routes within developing bees. Adult workers (9 to 30 days posteclosion) contained a large BFG microbiota with a characteristic distribution among gut organs. The crop and midgut were nearly devoid of these phylotypes, while the ileum and rectum together contained more than 95% of the total BFG microbiota. The ileum contained a stratified community in which the Beta and Gamma-1 phylotypes dominated, filling the longitudinal folds of this organ. Deep sequencing of 16S rRNA genes showed clear differences among communities in midgut, ileum, and rectum. In contrast with older workers, larvae and newly emerged workers contain few or no bacteria, and their major food source, bee bread, lacks most characteristic phylotypes. In experiments aimed at determining the route of inoculation, newly emerged workers (NEWs) sometimes acquired the typical phylotypes through contact with older workers, contact with the hive, and emergence from the brood cell; however, transmission was patchy in these assays. Our results outline a colonization pattern for the characteristic phylotypes throughA. melliferaontogeny. We propose the names “CandidatusSnodgrassella alvi” and “CandidatusGilliamella apicola” for the Beta and Gamma-1 phylotypes, respectively.
Bul Proteins, a Nonredundant, Antagonistic Family of Ubiquitin Ligase Regulatory Proteins
Authors: Novoselova Tatiana V. , Zahira Kiran , Rose Ruth-Sarah , Sullivan James A. 
Published: February 2012

ABSTRACT

Like other Nedd4 ligases,
Saccharomyces cerevisiae
E3 Rsp5p utilizes adaptor proteins to interact with some substrates. Previous studies have indentified Bul1p and Bul2p as adaptor proteins that facilitate the ligase-substrate interaction. Here, we show the identification of a third member of the Bul family, Bul3p, the product of two adjacent open reading frames separated by a stop codon that undergoes readthrough translation. Combinatorial analysis of
BUL
gene deletions reveals that they regulate some, but not all, of the cellular pathways known to involve Rsp5p. Surprisingly, we find that Bul proteins can act antagonistically to regulate the same ubiquitin-dependent process, and the nature of this antagonistic activity varies between different substrates. We further show, using
in vitro
ubiquitination assays, that the Bul proteins have different specificities for WW domains and that the two forms of Bul3p interact differently with Rsp5p, potentially leading to alternate functional outcomes. These data introduce a new level of complexity into the regulatory interactions that take place between Rsp5p and its adaptors and substrates and suggest a more critical role for the Bul family of proteins in controlling adaptor-mediated ubiquitination.
Streptococcus pneumoniae Can Utilize Multiple Sources of Hyaluronic Acid for Growth
Authors: Marion Carolyn , Stewart Jason M. , Tazi Mia F. , Burnaugh Amanda M. , Linke Caroline M. , Woodiga Shireen A. , King Samantha J. 
Published: February 2012

ABSTRACT

The mechanisms by which
Streptococcus pneumoniae
obtains carbohydrates for growth during airway colonization remain to be elucidated. The low concentration of free carbohydrates in the normal human airway suggests that pneumococci must utilize complex glycan structures for growth. The glycosaminoglycan hyaluronic acid is present on the apical surface of airway epithelial cells. As pneumococci express a hyaluronate lyase (Hyl) that cleaves hyaluronic acid into disaccharides, we hypothesized that during colonization pneumococci utilize the released carbohydrates for growth. Hyaluronic acid supported significant pneumococcal growth in an
hyl
-dependent manner. A phosphoenolpyruvate-dependent phosphotransferase system (PTS) and an unsaturated glucuronyl hydrolase (Ugl) encoded downstream of
hyl
are also essential for growth on hyaluronic acid. This genomic arrangement is present in several other organisms, suggesting conservation of the utilization mechanism between species.
In vivo
experiments support the hypothesis that
S. pneumoniae
utilizes hyaluronic acid as a carbon source during colonization. We also demonstrate that pneumococci can utilize the hyaluronic acid capsule of other bacterial species for growth, suggesting an alternative carbohydrate source for pneumococcal growth. Together, these data support a novel function for pneumococcal degradation of hyaluronic acid
in vivo
and provide mechanistic details of growth on this glycosaminoglycan.
Signal Perception by the Secretion Stress-Responsive CssRS Two-Component System in Bacillus subtilis
Authors: Noone David , Botella Eric , Butler Clodagh , Hansen Annette , Jende Inga , Devine Kevin M. 
Published: February 2012

ABSTRACT

The CssRS two-component system responds to heat and secretion stresses in
Bacillus subtilis
by controlling expression of HtrA and HtrB chaperone-type proteases and positively autoregulating its own expression. Here we report on the features of the CssS extracellular loop domain that are involved in signal perception and on CssS subcellular localization. Individual regions of the CssS extracellular loop domain contribute differently to signal perception and activation. The conserved hydrophilic 26-amino-acid segment juxtaposed to transmembrane helix 1 is involved in the switch between the deactivated and activated states, while the conserved 19-amino-acid hydrophobic segment juxtaposed to transmembrane 2 is required for signal perception and/or transduction. Perturbing the size of the extracellular loop domain increases CssS kinase activity and makes it unresponsive to secretion stress. CssS is localized primarily at the septum but is also found in a punctate pattern with lower intensity throughout the cell cylinder. Moreover, the CssRS-controlled HtrA and HtrB proteases are randomly distributed in foci throughout the cell surface, with more HtrB than HtrA foci in unstressed cells.
A disjointed effort: paediatric musculoskeletal examination
Authors: Gill Irwin , Sharif Farhana 
Published: February 2012

BackgroundMusculoskeletal (MSK) symptoms are a frequent cause of emergency department attendance for children, and while most often indicative of benign or self-limiting disease, such symptoms can occasionally be the first presentation of serious illness such as leukaemia or juvenile idiopathic arthritis. MSK examination, however, is often not included as part of the routine paediatric examination. The authors aimed to evaluate how often and how thoroughly MSK examination was performed during admissions to the paediatric ward and to compare it with the examination of other symptoms in relation to the presenting complaint and eventual diagnosis.ResultsMedical records for 100 consecutive patients were reviewed. A poster campaign to increase awareness was then commenced along with oral and written presentations to staff regarding MSK examination. A further 100 consecutive patients were then reviewed. Only 9% of children in the initial group had routine MSK examination, rising to 32% in the second group. Where performed, MSK examination was often incomplete. Frequent errors included only examining the reported site of injury and only examining a single limb or single joint when limpness/stiffness was the presenting complaint. Non-limb joints were very rarely examined.ConclusionsMSK examination is not performed routinely during paediatric admissions in contrast to the examination of other symptoms regardless of the presenting complaint. This may need to be addressed by local audit and increased undergraduate teaching.
Eliciting views on antibiotic prescribing and resistance among hospital and outpatient care physicians in Berlin, Germany: results of a qualitative study
Authors: Velasco Edward , Ziegelmann Antina , Eckmanns Tim , Krause Gérard 
Published: February 2012

ObjectiveTo better understand physicians' views on factors of influence for the prescribing of antibiotics and on antibiotic resistance in the Berlin region, Germany.DesignQualitative study with focus groups.SettingOutpatient care and hospital care practice in the Berlin region, Germany.Participants7 General practitioners, two urologists, one paediatrician from outpatient care and eight internists, two paediatricians, two ear, nose and throat specialists and two urologists from hospital care.ResultsPhysicians showed differential interest in topics related to antibiotic prescribing and antibiotic resistance. Outpatient care physicians were interested in topics around their own prescribing, such as being able to diagnose and prescribe precisely, and topics about patient demand and non-compliance. Hospital care physicians were interested in hygiene challenges, limited consult time and multi-resistant pathogens.ConclusionsPhysicians considered the development of resistance to be more in the domain of clinical treatment than that of the patient. Major challenges related to antibiotic resistance for this group of physicians are access to and clarity of treatment recommendations, implementation of hygienic measures, as well as increased outsourcing of laboratory services. Results raise questions about whether meeting physicians' expectations should be a focus when developing intervention that aims to influence antibiotic resistance in this and other areas of Germany.
Computerised lung sound analysis to improve the specificity of paediatric pneumonia diagnosis in resource-poor settings: protocol and methods for an observational study
Authors: Ellington Laura E , Gilman Robert H , Tielsch James M , Steinhoff Mark , Figueroa Dante , Rodriguez Shalim , Caffo Brian , Tracey Brian , Elhilali Mounya , West James , Checkley William 
Published: February 2012

IntroductionWHO case management algorithm for paediatric pneumonia relies solely on symptoms of shortness of breath or cough and tachypnoea for treatment and has poor diagnostic specificity, tends to increase antibiotic resistance. Alternatives, including oxygen saturation measurement, chest ultrasound and chest auscultation, exist but with potential disadvantages. Electronic auscultation has potential for improved detection of paediatric pneumonia but has yet to be standardised. The authors aim to investigate the use of electronic auscultation to improve the specificity of the current WHO algorithm in developing countries.MethodsThis study is designed to test the hypothesis that pulmonary pathology can be differentiated from normal using computerised lung sound analysis (CLSA). The authors will record lung sounds from 600 children aged ≤5 years, 100 each with consolidative pneumonia, diffuse interstitial pneumonia, asthma, bronchiolitis, upper respiratory infections and normal lungs at a children's hospital in Lima, Peru. The authors will compare CLSA with the WHO algorithm and other detection approaches, including physical exam findings, chest ultrasound and microbiologic testing to construct an improved algorithm for pneumonia diagnosis.DiscussionThis study will develop standardised methods for electronic auscultation and chest ultrasound and compare their utility for detection of pneumonia to standard approaches. Utilising signal processing techniques, the authors aim to characterise lung sounds and through machine learning, develop a classification system to distinguish pathologic sounds. Data will allow a better understanding of the benefits and limitations of novel diagnostic techniques in paediatric pneumonia.