bluuebunny/crossref_metadata_2025_split huggingface dataset:
Upregulation of skeletal muscle inflammatory genes links inflammation with insulin resistance in women with the metabolic syndrome
Authors: Poelkens Fleur , Lammers Gerwen , Pardoel Elisabeth M. , Tack Cees J. , Hopman Maria T. E. 
Published: June 2013

New Findings
What is the central question of this study?There is a close relationship between insulin resistance and inflammation, but it is largely unknown how these processes are linked in skeletal muscle tissue.
What is the main finding and its importance?Gene expression microarray analysis identified three inflammatory genes the expression level of which was highly correlated with insulin resistance in women with the metabolic syndrome. This suggests an important role for these genes in the development of skeletal muscle insulin resistance.
The metabolic syndrome, a combination of interrelated metabolic risk factors, is associated with insulin resistance and promotes the development of cardiovascular diseases and type 2 diabetes mellitus. There is a close link between inflammation and metabolic disease, but the responsible mechanisms remain elusive. The aim of this study was to identify differentially expressed genes in insulin‐resistant skeletal muscle tissue of women with the metabolic syndrome compared with healthy control women. Women with the metabolic syndrome (n= 19) and healthy control women (n= 20) were extensively phenotyped, insulin sensitivity was measured using a hyperinsulinaemic euglycaemic clamp, and a skeletal muscle biopsy was obtained. Gene expression levels were compared between the two groups by microarrays. The upregulated genes in skeletal muscle of the women with the metabolic syndrome were primarily enriched for inflammatory response‐associated genes. The three most significantly upregulated of this group, interleukin 6 receptor (IL6R), histone deacetylase 9 (HDAC9) and CD97 molecule (CD97), were significantly correlated with insulin resistance. Taken together, these findings suggest an important role for a number of inflammatory‐related genes in the development of skeletal muscle insulin resistance.
Molecular Characterization of “Candidatus Similichlamydia latridicola” gen. nov., sp. nov. (Chlamydiales: “Candidatus Parilichlamydiaceae”), a Novel Chlamydia-Like Epitheliocystis Agent in the Striped Trumpeter, Latris lineata (Forster)
Authors: Stride M. C. , Polkinghorne A. , Miller T. L. , Nowak B. F. 
Published: June 2013

ABSTRACTHistological analysis of gill samples taken from individuals ofLatris lineatareared in aquaculture in Tasmania, Australia, and those sampled from the wild revealed the presence of epitheliocystis-like basophilic inclusions. Subsequent morphological,in situhybridization, and molecular analyses were performed to confirm the presence of this disease and discovered aChlamydia-like organism associated with this condition, and the criteria set by Fredericks and Relman's postulates were used to establish disease causation. Three distinct 16S rRNA genotypes were sequenced from 16 fish, and phylogenetic analyses of the nearly full-length 16S rRNA sequences generated for this bacterial agent indicated that they were nearly identical novel members of the orderChlamydiales. This new taxon formed a well-supported clade with “CandidatusParilichlamydia carangidicola” from the yellowtail kingfish (Seriola lalandi). On the basis of sequence divergence over the 16S rRNA region relative to all other members of the orderChlamydiales, a new genus and species are proposed here for theChlamydia-like bacterium fromL. lineata, i.e., “CandidatusSimilichlamydia latridicola” gen. nov., sp. nov.
Litter Supply as a Driver of Microbial Activity and Community Structure on Decomposing Leaves: a Test in Experimental Streams
Authors: Frossard Aline , Gerull Linda , Mutz Michael , Gessner Mark O. 
Published: June 2013

ABSTRACT

Succession of newly created landscapes induces profound changes in plant litter supplied to streams. Grasses dominate inputs into open-land streams, whereas tree litter is predominant in forested streams. We set out to elucidate whether the activity and structure of microbial communities on decomposing leaves are determined by litter quality (i.e., grass or tree leaves colonized) or whether changes during riparian succession affecting litter standing stocks on the stream bed play an overriding role. We used 15 outdoor experimental streams to simulate changes in litter supplies reflecting five stages of riparian succession: (i) a biofilm stage with no litter, (ii) an open-land stage characterized by grass litter inputs, (iii) a transitional stage with a mix of grass and tree litter, (iv) an early forested stage with tree litter, and (v) an advanced forested stage with 2.5 times the amount of tree litter. Microbial activities on tree (
Betula pendula
) and grass (
Calamagrostis epigejos
) litter were unaffected by either the quantity or type of litter supplied to the experimental streams (i.e., litter standing stock) but differed between the two litter types. This was in stark contrast with bacterial and fungal community structure, which markedly differed on grass and tree litter and, to a lesser extent, also among streams receiving different litter inputs. These patterns reveal distinct responses of microbial community structure and activity to the bulk litter available in streams but consistent responses to the litter type colonized.
Oxygen Consumption Rates of Bacteria under Nutrient-Limited Conditions
Authors: Riedel Timothy E. , Berelson William M. , Nealson Kenneth H. , Finkel Steven E. 
Published: June 2013

ABSTRACTMany environments on Earth experience nutrient limitation and as a result have nongrowing or very slowly growing bacterial populations. To better understand bacterial respiration under environmentally relevant conditions, the effect of nutrient limitation on respiration rates of heterotrophic bacteria was measured. The oxygen consumption and population density of batch cultures ofEscherichia coliK-12,Shewanella oneidensisMR-1, andMarinobacter aquaeoleiVT8 were tracked for up to 200 days. The oxygen consumption per CFU (QO2) declined by more than 2 orders of magnitude for all three strains as they transitioned from nutrient-abundant log-phase growth to the nutrient-limited early stationary phase. The large reduction in QO2from growth to stationary phase suggests that nutrient availability is an important factor in considering environmental respiration rates. Following the death phase, during the long-term stationary phase (LTSP), QO2values of the surviving population increased with time and more cells were respiring than formed colonies. Within the respiring population, a subpopulation of highly respiring cells increased in abundance with time. Apparently, as cells enter LTSP, there is a viable but not culturable population whose bulk community and per cell respiration rates are dynamic. This result has a bearing on how minimal energy requirements are met, especially in nutrient-limited environments. The minimal QO2rates support the extension of Kleiber's law to the mass of a bacterium (100-fg range).
Aquacultured Rainbow Trout (Oncorhynchus mykiss) Possess a Large Core Intestinal Microbiota That Is Resistant to Variation in Diet and Rearing Density
Authors: Wong Sandi , Waldrop Thomas , Summerfelt Steven , Davidson John , Barrows Frederic , Kenney P. Brett , Welch Timothy , Wiens Gregory D. , Snekvik Kevin , Rawls John F. , Good Christopher 
Published: June 2013

ABSTRACT

As global aquaculture fish production continues to expand, an improved understanding of how environmental factors interact in fish health and production is needed. Significant advances have been made toward economical alternatives to costly fishmeal-based diets, such as grain-based formulations, and toward defining the effect of rearing density on fish health and production. Little research, however, has examined the effects of fishmeal- and grain-based diets in combination with alterations in rearing density. Moreover, it is unknown whether interactions between rearing density and diet impact the composition of the fish intestinal microbiota, which might in turn impact fish health and production. We fed aquacultured adult rainbow trout (
Oncorhynchus mykiss
) fishmeal- or grain-based diets, reared them under high- or low-density conditions for 10 months in a single aquaculture facility, and evaluated individual fish growth, production, fin indices, and intestinal microbiota composition using 16S rRNA gene sequencing. We found that the intestinal microbiotas were dominated by a shared core microbiota consisting of 52 bacterial lineages observed across all individuals, diets, and rearing densities. Variations in diet and rearing density resulted in only minor changes in intestinal microbiota composition despite significant effects of these variables on fish growth, performance, fillet quality, and welfare. Significant interactions between diet and rearing density were observed only in evaluations of fin indices and the relative abundance of the bacterial genus
Staphylococcus
. These results demonstrate that aquacultured rainbow trout can achieve remarkable consistency in intestinal microbiota composition and suggest the possibility of developing novel aquaculture strategies without overtly altering intestinal microbiota composition.
Whole-Genome Transcriptional Analysis of Escherichia coli during Heat Inactivation Processes Related to Industrial Cooking
Authors: Guernec A. , Robichaud-Rincon P. , Saucier L. 
Published: June 2013

ABSTRACT

Escherichia coli
K-12 was grown to the stationary phase, for maximum physiological resistance, in brain heart infusion (BHI) broth at 37°C. Cells were then heated at 58°C or 60°C to reach a process lethality value

(

F

o

70

10

)

of 2 or 3 or to a core temperature of 71°C (control industrial cooking temperature). Growth recovery and cell membrane integrity were evaluated immediately after heating, and a global transcription analysis was performed using gene expression microarrays. Only cells heated at 58°C with
F

o

= 2 were still able to grow on liquid or solid BHI broth after heat treatment. However, their transcriptome did not differ from that of bacteria heated at 58°C with
F

o

= 3 (
P
value for the false discovery rate [P-FDR] > 0.01), where no growth recovery was observed posttreatment. Genome-wide transcriptomic data obtained at 71°C were distinct from those of the other treatments without growth recovery. Quantification of heat shock gene expression by real-time PCR revealed that
dnaK
and
groEL
mRNA levels decreased significantly above 60°C to reach levels similar to those of control cells at 37°C (
P
< 0.0001). Furthermore, despite similar levels of cell inactivation measured by growth on BHI media after heating, 132 and 8 genes were differentially expressed at 71°C compared to 58°C and 60°C at
F

o

= 3, respectively (P-FDR < 0.01). Among them, genes such as
aroA
,
citE
,
glyS
,
oppB
, and
asd
, whose expression was upregulated at 71°C, may be worth investigating as good biomarkers for accurately determining the efficiency of heat treatments, especially when cells are too injured to be enumerated using growth media.
l
-Amino Acid Ligase from Pseudomonas syringae Producing Tabtoxin Can Be Used for Enzymatic Synthesis of Various Functional Peptides
Authors: Arai Toshinobu , Arimura Yasuhiro , Ishikura Shun , Kino Kuniki 
Published: June 2013

ABSTRACT

Functional peptides are expected to be beneficial compounds that improve our quality of life. To address the growing need for functional peptides, we have examined peptide synthesis by using microbial enzymes.
l
-Amino acid ligase (Lal) catalyzes the condensation of unprotected amino acids in an ATP-dependent manner and is applicable to fermentative production. Hence, Lal is a promising enzyme to achieve cost-effective synthesis. To obtain a Lal with novel substrate specificity, we focused on the putative Lal involved in the biosynthesis of the dipeptidic phytotoxin designated tabtoxin. The
tabS
gene was cloned from
Pseudomonas syringae
NBRC14081 and overexpressed in
Escherichia coli
cells. The recombinant TabS protein produced showed the broadest substrate specificity of any known Lal; it detected 136 of 231 combinations of amino acid substrates when dipeptide synthesis was examined. In addition, some new substrate specificities were identified and unusual amino acids, e.g.,
l
-pipecolic acid, hydroxy-
l
-proline, and β-alanine, were found to be acceptable substrates. Furthermore, kinetic analysis and monitoring of the reactions over a short time revealed that TabS showed distinct substrate selectivity at the N and C termini, which made it possible to specifically synthesize a peptide without by-products such as homopeptides and heteropeptides with the reverse sequence. TabS specifically synthesized the following functional peptides, including their precursors:
l
-arginyl-
l
-phenylalanine (antihypertensive effect; yield, 62%),
l
-leucyl-
l
-isoleucine (antidepressive effect; yield, 77%),
l
-glutaminyl-
l
-tryptophan (precursor of
l
-glutamyl-
l
-tryptophan, which has antiangiogenic activity; yield, 54%),
l
-leucyl-
l
-serine (enhances saltiness; yield, 83%), and
l
-glutaminyl-
l
-threonine (precursor of
l
-glutamyl-
l
-threonine, which enhances saltiness; yield, 96%). Furthermore, our results also provide new insights into tabtoxin biosynthesis.
Biosynthesis of the Osmoprotectant Ectoine, but Not Glycine Betaine, Is Critical for Survival of Osmotically Stressed Vibrio parahaemolyticus Cells
Authors: Ongagna-Yhombi Serge Y. , Boyd E. Fidelma 
Published: June 2013

ABSTRACT

Vibrio parahaemolyticus
is a halophile present in marine and estuarine environments, ecosystems characterized by fluctuations in salinity and temperature. One strategy to thrive in such environments is the synthesis and/or uptake of compatible solutes. The
V. parahaemolyticus
genome contains biosynthesis systems for both ectoine and glycine betaine, which are known to act as compatible solutes in other species. We showed that
V. parahaemolyticus
had a 6% NaCl tolerance when grown in M9 minimal medium with 0.4% glucose (M9G) with a >5-h lag phase. By using
1
H nuclear magnetic resonance spectroscopy (
1
H-NMR) analysis, we determined that cells synthesized ectoine and glutamate in a NaCl-dependent manner. The most effective compatible solutes as measured by a reduction in lag-phase growth in M9G with 6% NaCl (M9G 6% NaCl) were in the order glycine betaine > choline > proline = glutamate > ectoine. However,
V. parahaemolyticus
could use glutamate or proline as the sole carbon source, but not ectoine or glycine betaine, which suggests that these are bona fide compatible solutes. Expression analysis showed that the
ectA
and
betA
genes were more highly expressed in log-phase cells, and expression of both genes was induced by NaCl up-shock. Under all conditions examined, the
ectA
gene was more highly expressed than the
betA
gene. Analysis of in-frame deletions in
betA
and
ectB
and in a double mutant showed that the
ectB
mutant was defective for growth, and this defect was rescued by the addition of glycine betaine, proline, ectoine, and glutamate, indicating that these compounds are compatible solutes for this species. The presence of both synthesis systems was the predominant distribution pattern among members of the
Vibrionaceae
family, suggesting this is the ancestral state.
Evidence of Metabolic Switching and Implications for Food Safety from the Phenome(s) of Salmonella enterica Serovar Typhimurium DT104 Cultured at Selected Points across the Pork Production Food Chain
Authors: Martins Marta , McCusker Matthew P. , McCabe Evonne M. , O'Leary Denis , Duffy Geraldine , Fanning Séamus 
Published: June 2013

ABSTRACT

Salmonella enterica
serovar Typhimurium DT104 is a recognized food-borne pathogen that displays a multidrug-resistant phenotype and that is associated with systemic infections. At one extreme of the food chain, this bacterium can infect humans, limiting the treatment options available and thereby contributing to increased morbidity and mortality. Although the antibiotic resistance profile is well defined, little is known about other phenotypes that may be expressed by this pathogen at key points across the pork production food chain. In this study, 172
Salmonella enterica
serovar Typhimurium DT104/DT104b isolated from an extensive “farm-to-fork” surveillance study, focusing on the pork food chain, were characterized in detail. Isolates were cultured from environmental, processing, retail, and clinical sources, and the study focused on phenotypes that may have contributed to persistence/survival in these different niches. Molecular subtypes, along with antibiotic resistance profiles, tolerance to biocides, motility, and biofilm formation, were determined. As a basis for human infection, acid survival and the ability to utilize a range of energy sources and to adhere to and/or invade Caco-2 cells were also studied. Comparative alterations to biocide tolerance were observed in isolates from retail.
l
-Tartaric acid and
d
-mannose-1-phosphate induced the formation of biofilms in a preselected subset of strains, independent of their origin. All clinical isolates were motile and demonstrated an enhanced ability to survive in acidic conditions. Our data report on a diverse phenotype, expressed by
S
. Typhimurium isolates cultured from the pork production food chain. Extending our understanding of the means by which this pathogen adapts to environmental niches along the “farm-to-fork” continuum will facilitate the protection of vulnerable consumers through targeted improvements in food safety measures.
Adherence to and Invasion of Human Intestinal Cells by Arcobacter Species and Their Virulence Genotypes
Authors: Levican Arturo , Alkeskas Aldukali , Günter Claudia , Forsythe Stephen J. , Figueras María José 
Published: June 2013

ABSTRACT

The genus
Arcobacter
is composed of 17 species which have been isolated from various sources. Of particular interest are
A. butzleri
,
A. cryaerophilus
, and
A. skirrowii
, as these have been associated with human cases of diarrhea, the probable transmission routes being through the ingestion of contaminated drinking water and food. To date, only limited studies of virulence traits in this genus have been undertaken. The present study used 60
Arcobacter
strains isolated from different sources, representing 16 of the 17 species of the genus, to investigate their ability to adhere to and invade the human intestinal cell line Caco-2. In addition, the presence of five putative virulence genes (
ciaB
,
cadF
,
cj1349
,
hecA
, and
irgA
) was screened for in these strains by PCR. All
Arcobacter
species except
A. bivalviorum
and
Arcobacter
sp. strain W63 adhered to Caco-2 cells, and most species (10/16) were invasive. The most invasive species were
A. skirrowii
,
A. cryaerophilus
,
A. butzleri
, and
A. defluvii
. All invasive strains were positive for
ciaB
(encoding a putative invasion protein). Other putative virulence genes were present in other species, i.e.,
A. butzleri
(
cadF
,
cj1349
,
irgA
, and
hecA
),
A. trophiarum
(
cj1349
),
A. ellisii
(
cj1349
), and
A. defluvii
(
irgA
). No virulence genes were detected in strains which showed little or no invasion of Caco-2 cells. These results indicate that many
Arcobacter
species are potential pathogens of humans and animals.
Isolation of Optically Targeted Single Bacteria by Application of Fluidic Force Microscopy to Aerobic Anoxygenic Phototrophs from the Phyllosphere
Authors: Stiefel Philipp , Zambelli Tomaso , Vorholt Julia A. 
Published: June 2013

ABSTRACT

In their natural environment, bacteria often behave differently than they do under laboratory conditions. To gain insight into the physiology of bacteria
in situ
, dedicated approaches are required to monitor their adaptations and specific behaviors under environmental conditions. Optical microscopy is crucial for the observation of fundamental characteristics of bacteria, such as cell shape, size, and marker gene expression. Here, fluidic force microscopy (FluidFM) was exploited to isolate optically selected bacteria for subsequent identification and characterization. In this study, bacteriochlorophyll-producing bacteria, which can be visualized due to their characteristic fluorescence in the infrared range, were isolated from leaf washes. Bacterial communities from the phyllosphere were investigated because they harbor genes indicative of aerobic anoxygenic photosynthesis. Our data show that different species of
Methylobacterium
express their photosystem
in planta
, and they show a distinct pattern of bacteriochlorophyll production under laboratory conditions that is dependent on supplied carbon sources.
Sequence Variability of P2-Like Prophage Genomes Carrying the Cytolethal Distending Toxin V Operon in Escherichia coli O157
Authors: Sváb Domonkos , Horváth Balázs , Maróti Gergely , Dobrindt Ulrich , Tóth István 
Published: June 2013

ABSTRACT

Cytolethal distending toxins (CDT) are potent cytotoxins of several Gram-negative pathogenic bacteria, including
Escherichia coli
, in which five types (CDT-I to CDT-V) have been identified so far. CDT-V is frequently associated with Shiga-toxigenic
E. coli
(STEC), enterohemorrhagic
E. coli
(EHEC) O157 strains, and strains not fitting any established pathotypes. In this study, we were the first to sequence and annotate a 31.2-kb-long, noninducible P2-like prophage carrying the
cdt-V
operon from an
stx
- and
eae
-negative
E. coli
O157:H43 strain of bovine origin. The
cdt-V
operon is integrated in the place of the
tin
and
old
phage immunity genes (termed the TO region) of the prophage, and the prophage itself is integrated into the bacterial chromosome between the housekeeping genes
cpxP
and
fieF
. The presence of P2-like genes (
n
= 20) was investigated in a further five CDT-V-positive bovine
E. coli
O157 strains of various serotypes, three EHEC O157:NM strains, four strains expressing other variants of CDT, and eight CDT-negative strains. All but one CDT-V-positive atypical O157 strain uniformly carried all the investigated genomic regions of P2-like phages, while the EHEC O157 strains missed three regions and the CDT-V-negative strains carried only a few P2-like sequences. Our results suggest that P2-like phages play a role in the dissemination of
cdt-V
between
E. coli
O157 strains and that after integration into the bacterial chromosome, they adapted to the respective hosts and became temperate.