bluuebunny/crossref_metadata_2025_split huggingface dataset:
The plastid‐specific ribosomal proteins of Arabidopsis thaliana can be divided into non‐essential proteins and genuine ribosomal proteins
Authors: Tiller Nadine , Weingartner Magdalena , Thiele Wolfram , Maximova Eugenia , Schöttler Mark A. , Bock Ralph 
Published: September 2011

SummaryPlastid translation occurs on bacterial‐type 70S ribosomes consisting of a large (50S) subunit and a small (30S) subunit. The vast majority of plastid ribosomal proteins have orthologs in bacteria. In addition, plastids also possess a small set of unique ribosomal proteins, so‐called plastid‐specific ribosomal proteins (PSRPs). The functions of these PSRPs are unknown, but, based on structural studies, it has been proposed that they may represent accessory proteins involved in translational regulation. Here we have investigated the functions of five PSRPs using reverse genetics in the model plant Arabidopsis thaliana. By analyzing T‐DNA insertion mutants and RNAi lines, we show that three PSRPs display characteristics of genuine ribosomal proteins, in that down‐regulation of their expression led to decreased accumulation of the 30S or 50S subunit of the plastid ribosomes, resulting in plastid translational deficiency. In contrast, two other PSRPs can be knocked out without visible or measurable phenotypic consequences. Our data suggest that PSRPs fall into two types: (i) PSRPs that have a structural role in the ribosome and are bona fide ribosomal proteins, and (ii) non‐essential PSRPs that are not required for stable ribosome accumulation and translation under standard greenhouse conditions.
The effects of dietary weight loss with or without exercise training on liver enzymes in obese metabolic syndrome subjects
Authors: Straznicky N. E. , Lambert E. A. , Grima M. T. , Eikelis N. , Nestel P. J. , Dawood T. , Schlaich M. P. , Masuo K. , Chopra R. , Sari C. I. , Dixon J. B. , Tilbrook A. J. , Lambert G. W. 
Published: September 2011

Aim: Insulin resistance and visceral adiposity are predisposing factors for fatty liver disease. The main objectives of this study were (i) to compare the effects of caloric restriction (CR) alone or together with moderate‐intensity aerobic exercise training (CR+EX) on liver enzymes, a surrogate marker of liver injury, in obese metabolic syndrome (MetS) subjects and (ii) to identify anthropometric, metabolic, cardiovascular and dietary predictors of changes in liver enzymes.Methods: Sedentary men and women (n = 63), aged 55 ± 6 (s.d.) years with body mass index 32.7 ± 4.1 kg/m2 and confirmed MetS, were randomized to 12‐week CR, CR+EX or no treatment (Control).Results: Weight loss averaged 7.6% in the CR and 9.1% in the CR+EX group (time effect, p < 0.001; group effect, p = 0.11); insulin sensitivity improved by 49 and 45%, respectively (both p < 0.001). Fitness (maximal oxygen consumption) increased by 19% in the CR+EX group only (p < 0.001). Alanine aminotransferase (ALT) levels decreased by 20% in the CR and 24% in the CR+EX group (time effect, both p < 0.001; group effect, p = 0.68); corresponding values for γ‐glutamyltransferase (GGT) were −28 and −33%, respectively (time effect, both p < 0.001; group effect, p = 0.28). Reduction in abdominal fat mass (measured by DXA from L1 to L4) independently predicted ΔALT (r = 0.42, p = 0.005) and ΔGGT (r = 0.55, p < 0.001), whereas change in dietary saturated fat intake was independently associated with ΔALT (r = 0.35, p = 0.03).Conclusions: Reductions in central adiposity and saturated fat intake are key drivers of improvement in liver enzymes during lifestyle interventions. Exercise training did not confer significant incremental benefits in this study.
An analytical technique for measuring protein carbonyl in the stratum corneum using surface plasmon resonance
Authors: Date A. , Shimakura T. , Sasaki M. , Yamaguchi M. 
Published: September 2011

SynopsisProtein carbonyl groups in the stratum corneum may be used as a biomarker for skin photo‐stress. To evaluate the relationship between the protein carbonyl to total protein (TP) ratio (carbonylation ratio) and skin photo‐stress, the authors established a methodology by which protein carbonyl can be easily and highly sensitively analysed using an optical technique based on surface plasmon resonance (SPR). To collect the stratum corneum, tape stripping was employed. Firstly, the protein carbonyl was reacted with 2,4‐dinitrobenzenesulfonic acid dihydrate, and the quantity of dinitrophenylated (DNP)‐protein carbonyl was determined using an anti‐dinitrophenyl (anti‐DNP) antibody. The mass of DNP‐protein carbonyl was measured using SPR. A truncated sampling‐reporting cycle of <5 min allowed speedy reporting of DNP‐protein carbonyl levels. A significant difference was observed in the protein carbonyl/TP ratio (carbonylation ratio) between a sun‐protected area (mid‐ventral arm) and a sun‐exposed area (upper cheek, P < 0.05). Additionally, the carbonylation ratio of the sun‐exposed area showed a higher value than that of the sun‐protected area. It was suggested that the carbonylation ratio might be a useful index of skin photo‐stress.
The process leading to affirmation of life with cleft lip and cleft palate: The importance of acquiring coherence
Authors: OMIYA Tomoko , ITO Mikiko , YAMAZAKI Yoshihiko 
Published: September 2011

AbstractAims:  The objectives of this study were to understand the experiences of people with cleft lip and cleft palate (CLCP) and to describe the processes and factors leading to the acquisition of high self‐esteem.Methods:  Semi‐structured interviews were conducted of 19 subjects with CLCP recruited via hospitals and through snowball sampling, and the results were analyzed qualitatively, comparing high and low self‐esteem groups.Results:  Participants with high self‐esteem had gone through the phases of “noticing their difference from others”, “knowing about and deepening their understanding of CLCP”, “no denial of their life with CLCP” and “affirmation of life with CLCP”. Seven factor categories including “received sufficient explanation of CLCP condition (from parents) in the early stage”, “have not received negative messages about CLCP” and “feeling the presence of someone who accepts their feelings and supports them” were extracted as factors promoting these processes.Conclusions:  Knowing about and understanding CLCP enables individuals to acquire a sense of coherence in their lives, which may be related to gaining a feeling of control over their cleft condition, acquiring a sense of autonomy, and finding a meaning for their lives. Thus, medical professionals should provide explanations that enable patients to understand CLCP, and also facilitate interaction between patients with the same condition.
Detection of outlier loci and their utility for fisheries management
Authors: Russello Michael A. , Kirk Stephanie L. , Frazer Karen K. , Askey Paul J. 
Published: September 2011

AbstractGenetics‐based approaches have informed fisheries management for decades, yet remain challenging to implement within systems involving recently diverged stocks or where gene flow persists. In such cases, genetic markers exhibiting locus‐specific (‘outlier’) effects associated with divergent selection may provide promising alternatives to loci that reflect genome‐wide (‘neutral’) effects for guiding fisheries management. Okanagan Lake kokanee (Oncorhynchus nerka), a fishery of conservation concern, exhibits two sympatric ecotypes adapted to different reproductive environments; however, previous research demonstrated the limited utility of neutral microsatellites for assigning individuals. Here, we investigated the efficacy of an outlier‐based approach to fisheries management by screening >11 000 expressed sequence tags for linked microsatellites and conducting genomic scans for kokanee sampled across seven spawning sites. We identified eight outliers among 52 polymorphic loci that detected ecotype‐level divergence, whereas there was no evidence of divergence at neutral loci. Outlier loci exhibited the highest self‐assignment accuracy to ecotype (92.1%), substantially outperforming 44 neutral loci (71.8%). Results were robust among‐sampling years, with assignment and mixed composition estimates for individuals sampled in 2010 mirroring baseline results. Overall, outlier loci constitute promising alternatives for informing fisheries management involving recently diverged stocks, with potential applications for designating management units across a broad range of taxa.
Microbial Communities Show Parallels at Sites with Distinct Litter and Soil Characteristics
Authors: Sagova-Mareckova Marketa , Omelka Marek , Cermak Ladislav , Kamenik Zdenek , Olsovska Jana , Hackl Evelyn , Kopecky Jan , Hadacek Franz 
Published: September 2011

ABSTRACTPlant and microbial community composition in connection with soil chemistry determines soil nutrient cycling. The study aimed at demonstrating links between plant and microbial communities and soil chemistry occurring among and within four sites: two pine forests with contrasting soil pH and two grasslands of dissimilar soil chemistry and vegetation. Soil was characterized by C and N content, particle size, and profiles of low-molecular-weight compounds determined by high-performance liquid chromatography (HPLC) of soil extracts. Bacterial and actinobacterial community composition was assessed by terminal restriction fragment length polymorphism (T-RFLP) and cloning followed by sequencing. Abundances of bacteria, fungi, and actinobacteria were determined by quantitative PCR. In addition, a pool of secondary metabolites was estimated byermresistance genes coding for rRNA methyltransferases. The sites were characterized by a stable proportion of C/N within each site, while on a larger scale, the grasslands had a significantly lower C/N ratio than the forests. A Spearman's test showed that soil pH was correlated with bacterial community composition not only among sites but also within each site. Bacterial, actinobacterial, and fungal abundances were related to carbon sources while T-RFLP-assessed microbial community composition was correlated with the chemical environment represented by HPLC profiles. Actinobacteria community composition was the only studied microbial characteristic correlated to all measured factors. It was concluded that the microbial communities of our sites were influenced primarily not only by soil abiotic characteristics but also by dominant litter quality, particularly, by percentage of recalcitrant compounds.
Increased Persistence of Salmonella enterica Serovar Typhi in the Presence of Acanthamoeba castellanii
Authors: Douesnard-Malo Frédéric , Daigle France 
Published: September 2011

ABSTRACT

Salmonella enterica
serovar Typhi (
S
. Typhi) is the etiological agent of the systemic disease typhoid fever. Transmission occurs via ingestion of contaminated food or water.
S
. Typhi is specific to humans, and no animal or environmental reservoirs are known. As the free-living amoeba
Acanthamoeba castellanii
is an environmental host for many pathogenic bacteria, this study investigates interactions between
S
. Typhi and
A. castellanii
by using cocultures. Growth of both organisms was estimated by cell count, viable count, flow cytometry, and fluorescence microscopy. Results indicate that
S
. Typhi can survive at least 3 weeks when grown with
A. castellanii
, as opposed to less than 10 days when grown as singly cultured bacteria under the same conditions. Interestingly, growth rates of amoebae after 14 days were similar in cocultures or when amoebae were singly cultured, suggesting that
S
. Typhi is not cytotoxic to
A. castellanii
. Bacteria surviving in coculture were not intracellular and did not require a physical contact with amoebae for their survival. These results suggest that
S
. Typhi may have a selective advantage when it is associated with
A. castellanii
and that amoebae may contribute to
S
. Typhi persistence in the environment.
Naturally Occurring Motility-Defective Mutants of Salmonella enterica Serovar Enteritidis Isolated Preferentially from Nonhuman Rather than Human Sources
Authors: Yim Lucía , Betancor Laura , Martínez Arací , Bryant Clare , Maskell Duncan , Chabalgoity José A. 
Published: September 2011

ABSTRACT

Salmonellosis represents a worldwide health problem because it is one of the major causes of food-borne disease. Although motility is postulated as an important
Salmonella
virulence attribute, there is little information about variation in motility in natural isolates. Here we report the identification of a point mutation (T551 → G) in
motA
, a gene essential for flagellar rotation, in several
Salmonella enterica
serovar Enteritidis field isolates. This mutation results in bacteria that can biosynthesize structurally normal but paralyzed flagella and are impaired in their capacity to invade human intestinal epithelial cells. Introduction of a wild-type copy of
motA
into one of these isolates restored both motility and cell invasiveness. The
motA
mutant triggered higher proinflammatory transcriptional responses than an aflagellate isolate in differentiated Caco-2 cells, suggesting that the paralyzed flagella are able to signal through pattern recognition receptors. A specific PCR was designed to screen for the T551 → G mutation in a collection of 266
S
. Enteritidis field isolates from a nationwide epidemic, comprising 194 from humans and 72 from other sources. We found that 72 of the 266 (27%) isolates were nonmotile, including 24.7% (48/194) of human and 33.3% (24/72) of food isolates. Among nonmotile isolates, 15 carried the T551 → G mutation and, significantly, 13 were recovered from food, including 7 from eggs, but only 2 were from human sources. These results suggest that the presence of paralyzed flagella may impair the ability of
S
. Enteritidis to cause disease in the human host but does not prevent its ability to colonize chickens and infect eggs.
Geographical Location Determines the Population Structure in Phyllosphere Microbial Communities of a Salt-Excreting Desert Tree
Authors: Finkel Omri M. , Burch Adrien Y. , Lindow Steven E. , Post Anton F. , Belkin Shimshon 
Published: September 2011

ABSTRACT

The leaf surfaces of
Tamarix
, a salt-secreting desert tree, harbor a diverse community of microbial epiphytes. This ecosystem presents a unique combination of ecological characteristics and imposes a set of extreme stress conditions. The composition of the microbial community along ecological gradients was studied from analyses of microbial richness and diversity in the phyllosphere of three
Tamarix
species in the Mediterranean and Dead Sea regions in Israel and in two locations in the United States. Over 200,000 sequences of the 16S V6 and 18S V9 hypervariable regions revealed a diverse community, with 788 bacterial and 64 eukaryotic genera but only one archaeal genus. Both geographic location and tree species were determinants of microbial community structures, with the former being more dominant. Tree leaves of all three species in the Mediterranean region were dominated by
Halomonas
and
Halobacteria
, whereas trees from the Dead Sea area were dominated by
Actinomycetales
and
Bacillales
. Our findings demonstrate that microbial phyllosphere communities on different
Tamarix
species are highly similar in the same locale, whereas trees of the same species that grow in different climatic regions host distinct microbial communities.
Complete Genome Sequence of the Fish Pathogen Flavobacterium branchiophilum
Authors: Touchon Marie , Barbier Paul , Bernardet Jean-François , Loux Valentin , Vacherie Benoit , Barbe Valérie , Rocha Eduardo P. C. , Duchaud Eric 
Published: September 2011

ABSTRACT

Members of the genus
Flavobacterium
occur in a variety of ecological niches and represent an interesting diversity of lifestyles.
Flavobacterium branchiophilum
is the main causative agent of bacterial gill disease, a severe condition affecting various cultured freshwater fish species worldwide, in particular salmonids in Canada and Japan. We report here the complete genome sequence of strain FL-15 isolated from a diseased sheatfish (
Silurus glanis
) in Hungary. The analysis of the
F. branchiophilum
genome revealed putative mechanisms of pathogenicity strikingly different from those of the other, closely related fish pathogen
Flavobacterium psychrophilum
, including the first cholera-like toxin in a non-
Proteobacteria
and a wealth of adhesins. The comparison with available genomes of other
Flavobacterium
species revealed a small genome size, large differences in chromosome organization, and fewer rRNA and tRNA genes, in line with its more fastidious growth. In addition, horizontal gene transfer shaped the evolution of
F. branchiophilum
, as evidenced by its virulence factors, genomic islands, and CRISPR (clustered regularly interspaced short palindromic repeats) systems. Further functional analysis should help in the understanding of host-pathogen interactions and in the development of rational diagnostic tools and control strategies in fish farms.
Prevention of Gordonia and Nocardia Stabilized Foam Formation by Using Bacteriophage GTE7
Authors: Petrovski Steve , Seviour Robert J. , Tillett Daniel 
Published: September 2011

ABSTRACT

Most activated sludge treatment plants suffer from the presence of foams on the surfaces of their aeration reactors. These are often stabilized by hydrophobic mycolic acid-synthesizing actinobacterial species. A polyvalent
Siphoviridae
phage, GTE7, which lysed several
Gordonia
and
Nocardia
species, is described here. Its genome has a modular structure similar to that described for
Rhodococcus
phage ReqiDocB7. In laboratory-scale experiments, we showed that GTE7 prevents stabilization of foams by these
Gordonia
and
Nocardia
species.
Characterization of Single-Nucleotide-Polymorphism Markers for Plasmopara viticola, the Causal Agent of Grapevine Downy Mildew
Authors: Delmotte F. , Machefer V. , Giresse X. , Richard-Cervera S. , Latorse M. P. , Beffa R. 
Published: September 2011

ABSTRACT

We report 34 new nuclear single-nucleotide-polymorphism (SNP) markers that have been developed from an expressed sequence tag library of
Plasmopara viticola
, the causal agent of grapevine downy mildew. This newly developed battery of markers will provide useful additional genetic tools for population genetic studies of this important agronomic species.
Cross-Sectional and Longitudinal Comparisons of the Predominant Fecal Microbiota Compositions of a Group of Pediatric Patients with Cystic Fibrosis and Their Healthy Siblings
Authors: Duytschaever Gwen , Huys Geert , Bekaert Maarten , Boulanger Linda , De Boeck Kris , Vandamme Peter 
Published: September 2011

ABSTRACT

Although only poorly documented, it can be assumed that intensive antibiotic treatments of chronic lung infections in patients with cystic fibrosis (CF) also affect the diversity and metabolic functioning of the gastrointestinal microbiota and potentially lead to a state of dysbiosis. A better knowledge of the differences in gut microbiota composition and stability between patients with CF and healthy subjects could lead to optimization of current antibiotic therapies and/or development of add-on therapies. Using conventional culturing and population fingerprinting by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA amplicons, we compared the predominant fecal microbiota of 21 patients with CF and 24 healthy siblings in a cross-sectional study. General medium counts, as well as counts on media specific for lactic acid bacteria, clostridia,
Bifidobacterium
spp.,
Veillonella
spp., and
Bacteroides-Prevotella
spp., were consistently higher in sibling samples than in CF samples, whereas the reverse was found for enterobacterial counts. DGGE fingerprinting uncovered large intersubject variations in both study groups. On the other hand, the cross-sectional data indicated that the predominant fecal microbiota of patients and siblings had comparable species richness. In addition, a longitudinal study was performed on 7 or 8 consecutive samples collected over a 2-year period from two patients and their respective siblings. For these samples, DGGE profiling indicated an overall trend toward lower temporal stability and lower species richness in the predominant fecal CF microbiota. The observed compositional and dynamic perturbations provide the first evidence of a general dysbiosis in children with CF compared to their siblings.
Direct and Indirect Influence of Parental Bedrock on Streambed Microbial Community Structure in Forested Streams
Authors: Mosher Jennifer J. , Findlay Robert H. 
Published: September 2011

ABSTRACT

A correlative study was performed to determine if variation in streambed microbial community structure in low-order forested streams can be directly or indirectly linked to the chemical nature of the parental bedrock of the environments through which the streams flow. Total microbial and photosynthetic biomass (phospholipid phosphate [PLP] and chlorophyll
a
), community structure (phospholipid fatty acid analysis), and physical and chemical parameters were measured in six streams, three located in sandstone and three in limestone regions of the Bankhead National Forest in northern Alabama. Although stream water flowing through the two different bedrock types differed significantly in chemical composition, there were no significant differences in total microbial and photosynthetic biomass in the sediments. In contrast, sedimentary microbial community structure differed between the bedrock types and was significantly correlated with stream water ion concentrations. A pattern of seasonal variation in microbial community structure was also observed. Further statistical analysis indicated dissolved organic matter (DOM) quality, which was previously shown to be influenced by geological variation, correlated with variation in bacterial community structure. These results indicate that the geology of underlying bedrock influences benthic microbial communities directly via changes in water chemistry and also indirectly via stream water DOM quality.
Two Large, Related, Cryptic Plasmids from Geographically Distinct Isolates of Sulfobacillus thermotolerans
Authors: Deane S. M. , Rawlings D. E. 
Published: September 2011

ABSTRACT

Two large cryptic plasmids (59.2 and 65.9 kb) from isolates of
Sulfobacillus thermotolerans
from Yellowstone National Park (United States) and the Caribbean island of Montserrat were isolated and sequenced. This analysis revealed a common “backbone” region coding for a potential plasmid stability system plus a nonpheromone conjugation system containing homologues of both type IV and type II (tight adherence, or Tad-like) secretion systems.
Secreted Factors from Bifidobacterium animalis subsp.
lactis
Inhibit NF-κB-Mediated Interleukin-8 Gene Expression in Caco-2 Cells
Authors: Wang Zhonggui , Wang Jinfeng , Cheng Yi , Liu Xin , Huang Ying 
Published: September 2011

ABSTRACT

The objective of the present study was to evaluate the anti-inflammatory effects of
Bifidobacterium animalis
subsp.
lactis
strain BB12 in stimulated Caco-2 cells and to characterize the factors responsible for these anti-inflammatory effects. Characterization and purification studies indicate that BB12's anti-inflammatory factors might include a 50-kDa proteinaceous compound that is stable under a variety of heat and pH conditions.
Rapid Screening Method for Compounds That Affect the Growth and Germination of Candida albicans, Using a Real-Time PCR Thermocycler
Authors: Jarosz Lucja M. , Krom Bastiaan P. 
Published: September 2011

ABSTRACT

We propose a screening method for compounds affecting growth and germination in
Candida albicans
using a real-time PCR thermocycler to quantify green fluorescent protein (GFP) fluorescence. Using P

ACT1
-GFP

and P

HWP1
-GFP

reporter strains, the effects of a wide range of compounds on growth and hyphal formation were quantitatively assessed within 3 h after inoculation.