bluuebunny/crossref_metadata_2025_split huggingface dataset:
The CSF tap test in normal pressure hydrocephalus: evaluation time, reliability and the influence of pain
Authors: Virhammar J. , Cesarini K. G. , Laurell K. 
Published: July 2011

Background:  The cerebrospinal fluid tap test (TT) is a diagnostic tool used to select patients with idiopathic normal pressure hydrocephalus (iNPH) for shunt surgery. The procedure and the evaluation of the TT vary between centres. We aimed to describe the evaluation time after the TT, to assess the variability between repeated measurements, the interrater agreement of the gait tests chosen and finally to investigate whether pain affects the gait performance post‐TT.Methods:  Forty patients (21 men and 19 women) under evaluation for iNPH underwent a TT. Standardized gait analyses were performed before and 2, 4, 6, 8 and 24 h after the TT and repeated twice on every occasion. Independent of each other, two investigators evaluated the quality of gait. At each assessment time, the patients graded headache and back pain on a visual analogue scale.Results:  Twenty‐seven patients (15 men and 12 women) responded to TT. Improvements in gait speed and number of steps were significant at every assessment time post‐TT. The variability between two measurements was low (Intra class correlation coefficient = 0.97), and the inter‐rater agreement was good with a κ = 0.74. Pain correlated negatively with improvement in gait speed (r = −0.40, P < 0.05).Conclusions:  We suggest that the TT can be evaluated at any time within the first 24 h and should be repeated if the patient does not initially improve. Gait analysis appears reliable between two evaluators. Further, it is indicated that post‐lumbar puncture pain negatively affects the gait and should be minimized.
Low antioxidant status of serum uric acid, bilirubin and albumin in patients with neuromyelitis optica
Authors: Peng F. , Yang Y. , Liu J. , Jiang Y. , Zhu C. , Deng X. , Hu X. , Chen X. , Zhong X. 
Published: July 2011

Background:  Oxidative stress plays a central role in neuropathology of multiple sclerosis (MS). The patients with MS have low antioxidant status. Antioxidant therapy may represent an attractive treatment of MS. However, the relationship between neuromyelitis optica (NMO), a distinct nosologic entity or a form of MS, and antioxidant status has not fully been investigated.Objectives:  To investigate the correlation between NMO and serum antioxidant status of uric acid (UA), bilirubin and albumin.Methods:  The serum levels of antioxidant molecules UA, bilirubin (Tbil and Ibil) and albumin were measured in 236 individuals comprising healthy subjects and patients with NMO or MS.Results:  We found that serum levels of UA, Tbil, Ibil and albumin in patients with NMO were significantly lower than those in healthy control group. Moreover, these results were also observed when the male and female cohorts were investigated separately. Likewise, the serum levels of UA, Tbil, Ibil and albumin in patients with NMO were also lower than those of patients with MS. In all groups, women had lower serum UA, Tbil, Ibil and albumin levels than men. In UA groups, women had significantly lower serum UA levels than men.Conclusion:  We concluded that there were reducing serum levels of UA, bilirubin and albumin in patients with NMO. The study showed patients with NMO had low antioxidant status. As a replacement therapy to patients, administration of albumin, bilirubin and UA or theirs precursors, such as inosine of UA precursor, may be beneficial to the patients with NMO.
Little impact of hatchery supplementation that uses native broodstock on the genetic structure and diversity of steelhead trout revealed by a large‐scale spatio‐temporal microsatellite survey
Authors: Gow Jennifer L. , Tamkee Patrick , Heggenes Jan , Wilson Greg A. , Taylor Eric B. 
Published: July 2011

AbstractArtificial breeding programs initiated to enhance the size of animal populations are often motivated by the desire to increase harvest opportunities. The introduction of non‐native genotypes, however, can have negative evolutionary impacts. These may be direct, such as introgressive hybridization, or indirect via competition. Less is known about the effects of stocking with native genotypes. We assayed variation at nine microsatellite loci in 902 steelhead trout (Oncorhynchus mykiss) from five rivers in British Columbia, Canada. These samples were collected over 58 years, a time period that spanned the initiation of native steelhead trout broodstock hatchery supplementation in these rivers. We detected no changes in estimates of effective population size, genetic variation or temporal genetic structure within any population, nor of altered genetic structure among them. Genetic interactions with nonmigratoryO. mykiss, the use of substantial numbers of primarily native broodstock with an approximate 1:1 male‐to‐female ratio, and/or poor survival and reproductive success of hatchery fish may have minimized potential genetic changes. Although no genetic changes were detected, ecological effects of hatchery programs still may influence wild population productivity and abundance. Their effects await the design and implementation of a more comprehensive evaluation program.
Induction of Attachment-Independent Biofilm Formation and Repression ofhfqExpression by Low-Fluid-Shear Culture of Staphylococcus aureus
Authors: Castro Sarah L. , Nelman-Gonzalez Mayra , Nickerson Cheryl A. , Ott C. Mark 
Published: July 2011

ABSTRACTThe opportunistic pathogenStaphylococcus aureusencounters a wide variety of fluid shear levels within the human host, and they may play a key role in dictating whether this organism adopts a commensal interaction with the host or transitions to cause disease. By using rotating-wall vessel bioreactors to create a physiologically relevant, low-fluid-shear environment,S. aureuswas evaluated for cellular responses that could impact its colonization and virulence.S. aureuscells grown in a low-fluid-shear environment initiated a novel attachment-independent biofilm phenotype and were completely encased in extracellular polymeric substances. Compared to controls, low-shear-cultured cells displayed slower growth and repressed virulence characteristics, including decreased carotenoid production, increased susceptibility to oxidative stress, and reduced survival in whole blood. Transcriptional whole-genome microarray profiling suggested alterations in metabolic pathways. Further genetic expression analysis revealed downregulation of the RNA chaperone Hfq, which parallels low-fluid-shear responses of certain Gram-negative organisms. This is the first study to report an Hfq association with fluid shear in a Gram-positive organism, suggesting an evolutionarily conserved response to fluid shear among structurally diverse prokaryotes. Collectively, our results suggestS. aureusresponds to a low-fluid-shear environment by initiating a biofilm/colonization phenotype with diminished virulence characteristics, which could lead to insight into key factors influencing the divergence between infection and colonization during the initial host-pathogen interaction.
Predominant Effect of Host Genetics on Levels of Lactobacillus johnsonii Bacteria in the Mouse Gut
Authors: Buhnik-Rosenblau Keren , Danin-Poleg Yael , Kashi Yechezkel 
Published: July 2011

ABSTRACT

The gut microbiota is strongly associated with the well-being of the host. Its composition is affected by environmental factors, such as food and maternal inoculation, while the relative impact of the host's genetics have been recently uncovered. Here, we studied the effect of the host genetic background on the composition of intestinal bacteria in a murine model, focusing on lactic acid bacteria (LAB) as an important group that includes many probiotic strains. Based on 16S rRNA gene genotyping, variation was observed in fecal LAB populations of BALB/c and C57BL/6J mouse lines.
Lactobacillus johnsonii
, a potentially probiotic bacterium, appeared at significantly higher levels in C57BL/6J versus BALB/c mouse feces. In the BALB/c gut, the
L. johnsonii
level decreased rapidly after oral administration, suggesting that some selective force does not allow its persistence at higher levels. The genetic inheritance of
L. johnsonii
levels was further tested in reciprocal crosses between the two mouse lines. The resultant F1 offspring presented similar
L. johnsonii
levels, confirming that mouse genetics plays a major role in determining these levels compared to the smaller maternal effect. Our findings suggest that mouse genetics has a major effect on the composition of the LAB population in general and on the persistence of
L. johnsonii
in the gut in particular. Concentrating on a narrow spectrum of culturable LAB enables the isolation and characterization of such potentially probiotic bacterial strains, which might be specifically oriented to the genetic background of the host as part of a personalized-medicine approach.
Flavobacterium johnsoniae as a Model Organism for Characterizing Biopolymer Utilization in Oligotrophic Freshwater Environments
Authors: Sack Eveline L. W. , van der Wielen Paul W. J. J. , van der Kooij Dick 
Published: July 2011

ABSTRACT

Biopolymers are important substrates for heterotrophic bacteria in oligotrophic freshwater environments, but information on bacterial growth kinetics with biopolymers is scarce. The objective of this study was to characterize bacterial biopolymer utilization in these environments by assessing the growth kinetics of
Flavobacterium johnsoniae
strain A3, which is specialized in utilizing biopolymers at μg liter
−1
levels. Growth of strain A3 with amylopectin, xyloglucan, gelatin, maltose, or fructose at 0 to 200 μg C liter
−1
in tap water followed Monod or Teissier kinetics, whereas growth with laminarin followed Teissier kinetics. Classification of the specific affinity of strain A3 for the tested substrates resulted in the following affinity order: laminarin (7.9 × 10
−2
liter·μg
−1
of C·h
−1
) ≫ maltose > amylopectin ≈ gelatin ≈ xyloglucan > fructose (0.69 × 10
−2
liter·μg
−1
of C·h
−1
). No specific affinity could be determined for proline, but it appeared to be high. Extracellular degradation controlled growth with amylopectin, xyloglucan, or gelatin but not with laminarin, which could explain the higher affinity for laminarin. The main degradation products were oligosaccharides or oligopeptides, because only some individual monosaccharides and amino acids promoted growth. A higher yield and a lower ATP cell
−1
level was achieved at ≤10 μg C liter
−1
than at >10 μg C liter
−1
with every substrate except gelatin. The high specific affinities of strain A3 for different biopolymers confirm that some representatives of the classes
Cytophagia
-
Flavobacteria
are highly adapted to growth with these compounds at μg liter
−1
levels and support the hypothesis that
Cytophagia-Flavobacteria
play an important role in biopolymer degradation in (ultra)oligotrophic freshwater environments.
The Pentose Moiety of Adenosine and Inosine Is an Important Energy Source for the Fermented-Meat Starter Culture Lactobacillus sakei CTC 494
Authors: Rimaux T. , Vrancken G. , Vuylsteke B. , De Vuyst L. , Leroy F. 
Published: July 2011

ABSTRACT

The genome sequence of
Lactobacillus sakei
23K has revealed that the species
L. sakei
harbors several genes involved in the catabolism of energy sources other than glucose in meat, such as glycerol, arginine, and nucleosides. In this study, a screening of 15
L. sakei
strains revealed that arginine, inosine, and adenosine could be used as energy sources by all strains. However, no glycerol catabolism occurred in any of the
L. sakei
strains tested. A detailed kinetic analysis of inosine and adenosine catabolism in the presence of arginine by
L. sakei
CTC 494, a fermented-meat starter culture, was performed. It showed that nucleoside catabolism occurred as a mixed-acid fermentation in a pH range (pH 5.0 to 6.5) relevant for sausage fermentation. This resulted in the production of a mixture of acetic acid, formic acid, and ethanol from ribose, while the nucleobase (hypoxanthine and adenine in the case of fermentations with inosine and adenosine, respectively) was excreted into the medium stoichiometrically. This indicates that adenosine deaminase activity did not take place. The ratios of the different fermentation end products did not vary with environmental pH, except for the fermentation with inosine at pH 5.0, where lactic acid was produced too. In all cases, no other carbon-containing metabolites were found; carbon dioxide was derived only from arginine catabolism. Arginine was cometabolized in all cases and resulted in the production of both citrulline and ornithine. Based on these results, a pathway for inosine and adenosine catabolism in
L. sakei
CTC 494 was presented, whereby both nucleosides are directly converted into their nucleobase and ribose, the latter entering the heterolactate pathway. The present study revealed that the pentose moiety (ribose) of the nucleosides inosine and adenosine is an effective fermentable substrate for
L. sakei
. Thus, the ability to use these energy sources offers a competitive advantage for this species in a meat environment.
Comparison of Real-Time PCR, Reverse Transcriptase Real-Time PCR, Loop-Mediated Isothermal Amplification, and the FDA Conventional Microbiological Method for the Detection of Salmonella spp. in Produce
Authors: Zhang Guodong , Brown Eric W. , González-Escalona Narjol 
Published: July 2011

ABSTRACT

Contamination of foods, especially produce, with
Salmonella
spp. is a major concern for public health. Several methods are available for the detection of
Salmonella
in produce, but their relative efficiency for detecting
Salmonella
in commonly consumed vegetables, often associated with outbreaks of food poisoning, needs to be confirmed. In this study, the effectiveness of three molecular methods for detection of
Salmonella
in six produce matrices was evaluated and compared to the FDA microbiological detection method. Samples of cilantro (coriander leaves), lettuce, parsley, spinach, tomato, and jalapeno pepper were inoculated with
Salmonella
serovars at two different levels (10
5
and <10
1
CFU/25 g of produce). The inoculated produce was assayed by the FDA
Salmonella
culture method (
Bacteriological Analytical Manual
) and by three molecular methods: quantitative real-time PCR (qPCR), quantitative reverse transcriptase real-time PCR (RT-qPCR), and loop-mediated isothermal amplification (LAMP). Comparable results were obtained by these four methods, which all detected as little as 2 CFU of
Salmonella
cells/25 g of produce. All control samples (not inoculated) were negative by the four methods. RT-qPCR detects only live
Salmonella
cells, obviating the danger of false-positive results from nonviable cells. False negatives (inhibition of either qPCR or RT-qPCR) were avoided by the use of either a DNA or an RNA amplification internal control (IAC). Compared to the conventional culture method, the qPCR, RT-qPCR, and LAMP assays allowed faster and equally accurate detection of
Salmonella
spp. in six high-risk produce commodities.
Interesting Starter Culture Strains for Controlled Cocoa Bean Fermentation Revealed by Simulated Cocoa Pulp Fermentations of Cocoa-Specific Lactic Acid Bacteria
Authors: Lefeber Timothy , Janssens Maarten , Moens Frédéric , Gobert William , De Vuyst Luc 
Published: July 2011

ABSTRACT

Among various lactic acid bacterial strains tested, cocoa-specific strains of
Lactobacillus fermentum
were best adapted to the cocoa pulp ecosystem. They fermented glucose to lactic acid and acetic acid, reduced fructose to mannitol, and converted citric acid into lactic acid and 2,3-butanediol.
Plasmids of Raw Milk Cheese Isolate Lactococcus lactis subsp. lactis Biovar diacetylactis DPC3901 Suggest a Plant-Based Origin for the Strain
Authors: Fallico Vincenzo , McAuliffe Olivia , Fitzgerald Gerald F. , Ross R. Paul 
Published: July 2011

ABSTRACT

The four-plasmid complement of the raw milk cheese isolate
Lactococcus lactis
subsp.
lactis
biovar diacetylactis DPC3901 was sequenced, and some genetic features were functionally analyzed. The complete sequences of pVF18 (18,977 bp), pVF21 (21,739 bp), pVF22 (22,166 bp), and pVF50 (53,876 bp) were obtained. Each plasmid contained genes not previously described for
Lactococcus
, in addition to genes associated with plant-derived lactococcal strains. Most of the novel genes were found on pVF18 and encoded functions typical of bacteria associated with plants, such as activities of plant cell wall modification (
orf11
and
orf25
). In addition, a predicted high-affinity regulated system for the uptake of cobalt was identified (
orf19
to
orf21
[
orf19
-
21]
), which has a single database homolog on a plant-derived
Leuconostoc
plasmid and whose functionality was demonstrated following curing of pVF18. pVF21 and pVF22 encode additional metal transporters, which, along with
orf19
-
21
of pVF18, could enhance host ability to uptake growth-limiting amounts of biologically essential ions within the soil. In addition, vast regions from pVF50 and pVF21 share significant homology with the plant-derived lactococcal plasmid pGdh442, which is indicative of extensive horizontal gene transfer and recombination between these plasmids and suggests a common plant niche for their hosts. Phenotypes associated with these regions include glutamate dehydrogenase activity and Na
+
and K
+
transport. The presence of numerous plant-associated markers in
L. lactis
DPC3901 suggests a plant origin for the raw milk cheese isolate and provides for the first time the genetic basis to support the concept of the plant-milk transition for
Lactococcus
strains.
Detection of Viable Cryptosporidium parvum in Soil by Reverse Transcription–Real-Time PCR Targeting
hsp70
mRNA
Authors: Liang Zhanbei , Keeley Ann 
Published: July 2011

ABSTRACT

Extraction of high-quality mRNA from
Cryptosporidium parvum
is a key step in PCR detection of viable oocysts in environmental samples. Current methods for monitoring oocysts are limited to water samples; therefore, the goal of this study was to develop a rapid and sensitive procedure for
Cryptosporidium
detection in soil samples. The efficiencies of five RNA extraction methods were compared (mRNA extraction with the Dynabeads mRNA Direct kit after chemical and physical sample treatments, and total RNA extraction methods using the FastRNA Pro Soil-Direct, PowerSoil Total RNA, E.Z.N.A. soil RNA, and Norgen soil RNA purification kits) for the direct detection of
Cryptosporidium
with oocyst-spiked sandy, loamy, and clay soils by using TaqMan reverse transcription-PCR. The study also evaluated the presence of inhibitors by synthesis and incorporation of an internal positive control (IPC) RNA into reverse transcription amplifications, used different facilitators (bovine serum albumin, yeast RNA, salmon DNA, skim milk powder, casein, polyvinylpyrrolidone, sodium hexametaphosphate, and
Salmonella enterica
serovar Typhi) to mitigate RNA binding on soil components, and applied various treatments (β-mercaptoethanol and bead beating) to inactivate RNase and ensure the complete lysis of oocysts. The results of spiking studies showed that
Salmonella
cells most efficiently relieved binding of RNA. With the inclusion of
Salmonella
during extraction, the most efficient mRNA method was Dynabeads, with a detection limit of 6 × 10
2
oocysts g
−1
of sandy soil. The most efficient total RNA method was PowerSoil, with detection limits of 1.5 × 10
2
, 1.5 × 10
3
, and 1.5 × 10
4
C. parvum
oocysts g
−1
soil for sandy, loamy, and clay samples, respectively.
Novel Pathway for the Degradation of 2-Chloro-4-Nitrobenzoic Acid by Acinetobacter sp. Strain RKJ12
Authors: Prakash Dhan , Kumar Ravi , Jain R. K. , Tiwary B. N. 
Published: July 2011

ABSTRACTThe organismAcinetobactersp. RKJ12 is capable of utilizing 2-chloro-4-nitrobenzoic acid (2C4NBA) as a sole source of carbon, nitrogen, and energy. In the degradation of 2C4NBA by strain RKJ12, various metabolites were isolated and identified by a combination of chromatographic, spectroscopic, and enzymatic activities, revealing a novel assimilation pathway involving both oxidative and reductive catabolic mechanisms. The metabolism of 2C4NBA was initiated by oxidativeorthodehalogenation, leading to the formation of 2-hydroxy-4-nitrobenzoic acid (2H4NBA), which subsequently was metabolized into 2,4-dihydroxybenzoic acid (2,4-DHBA) by a mono-oxygenase with the concomitant release of chloride and nitrite ions. Stoichiometric analysis indicated the consumption of 1 mol O2per conversion of 2C4NBA to 2,4-DHBA, ruling out the possibility of two oxidative reactions. Experiments with labeled H218O and18O2indicated the involvement of mono-oxygenase-catalyzed initial hydrolytic dechlorination and oxidative denitration mechanisms. The further degradation of 2,4-DHBA then proceeds via reductive dehydroxylation involving the formation of salicylic acid. In the lower pathway, the organism transformed salicylic acid into catechol, which was mineralized by theorthoring cleavage catechol-1,2-dioxygenase tocis, cis-muconic acid, ultimately forming tricarboxylic acid cycle intermediates. Furthermore, the studies carried out on a 2C4NBA−derivative and a 2C4NBA+transconjugant demonstrated that the catabolic genes for the 2C4NBA degradation pathway possibly reside on the ∼55-kb transmissible plasmid present in RKJ12.
Time Course of Gene Expression during Porphyromonas gingivalis Strain ATCC 33277 Biofilm Formation
Authors: Yamamoto Reiko , Noiri Yuichiro , Yamaguchi Mikiyo , Asahi Yoko , Maezono Hazuki , Ebisu Shigeyuki 
Published: July 2011

ABSTRACT

Chronological gene expression patterns of biofilm-forming cells are important to understand bioactivity and pathogenicity of biofilms. For
Porphyromonas gingivalis
ATCC 33277 biofilm formation, the number of genes differentially regulated by more than 1.5-fold was highest during the growth stage (312/2,090 genes), and some pathogen-associated genes were time-dependently controlled.
Nucleotide Polymorphism-Based Single-Tube Test for Robust Molecular Identification of All Currently Described Brucella Species
Authors: Wattiau Pierre , Whatmore Adrian M. , Van Hessche Mieke , Godfroid Jacques , Fretin David 
Published: July 2011

ABSTRACT

Among the numerous molecular methods described during the last 20 years to identify
Brucella
, multiplexed amplification methods offer the cheapest and simplest technical solution for molecular identification. However, one disadvantage of such methods is their need to undergo technical revalidation each time a new marker is added to the system. Moreover, polymorphic markers cannot be assessed at the single-nucleotide level in these assays. Since new
Brucella
species are continuously being described, open methodologies able to accommodate new markers while preserving all other system parameters have an obvious advantage. We present a ligase chain reaction (LCR)-based method that simultaneously assesses multiple genetic markers at the single-nucleotide level. Most of the selected markers originate from a multilocus sequence typing (MLST) database that has been extensively validated on hundreds of different
Brucella
strains. When assayed on both reference and field strains, the method yields characteristic capillary electrophoresis profiles for each of the 10
Brucella
species described to date and displays discriminatory potential below the species level for some. Since the LCR methodology is insensitive to interference resulting from the use of multiple oligonucleotides in a single mixture, the way is open for smooth future updates of the proposed system. Such updates are inevitable, given the pending description of new
Brucella
species.