bluuebunny/crossref_metadata_2025_split huggingface dataset:
Snf1 Is a Regulator of Lipid Accumulation in Yarrowia lipolytica
Authors: Seip John , Jackson Raymond , He Hongxian , Zhu Quinn , Hong Seung-Pyo 
Published: September 2013

ABSTRACT

In the oleaginous yeast
Yarrowia lipolytica
,
de novo
lipid synthesis and accumulation are induced under conditions of nitrogen limitation (or a high carbon-to-nitrogen ratio). The regulatory pathway responsible for this induction has not been identified. Here we report that the SNF1 pathway plays a key role in the transition from the growth phase to the oleaginous phase in
Y. lipolytica
. Strains with a
Y. lipolytica
snf1
(
Ylsnf1
) deletion accumulated fatty acids constitutively at levels up to 2.6-fold higher than those of the wild type. When introduced into a
Y. lipolytica
strain engineered to produce omega-3 eicosapentaenoic acid (EPA),
Ylsnf1
deletion led to a 52% increase in EPA titers (7.6% of dry cell weight) over the control. Other components of the
Y. lipolytica
SNF1 pathway were also identified, and their function in limiting fatty acid accumulation is suggested by gene deletion analyses. Deletion of the gene encoding YlSnf4, YlGal83, or YlSak1 significantly increased lipid accumulation in both growth and oleaginous phases compared to the wild type. Furthermore, microarray and quantitative reverse transcription-PCR (qRT-PCR) analyses of the
Ylsnf1
mutant identified significantly differentially expressed genes during
de novo
lipid synthesis and accumulation in
Y. lipolytica
. Gene ontology analysis found that these genes were highly enriched with genes involved in lipid metabolism. This work presents a new role for Snf1/AMP-activated protein kinase (AMPK) pathways in lipid accumulation in this oleaginous yeast.
Wastewater Effluent Impacts Ammonia-Oxidizing Prokaryotes of the Grand River, Canada
Authors: Sonthiphand Puntipar , Cejudo Eduardo , Schiff Sherry L. , Neufeld Josh D. 
Published: September 2013

ABSTRACT

The Grand River (Ontario, Canada) is impacted by wastewater treatment plants (WWTPs) that release ammonia (NH
3
and NH
4
+
) into the river. In-river microbial communities help transform this ammonia into more oxidized compounds (e.g., NO
3
−
or N
2
), although the spatial distribution and relative abundance of freshwater autotrophic ammonia-oxidizing prokaryotes (AOP) are not well characterized. This study investigated freshwater N cycling within the Grand River, focusing on sediment and water columns, both inside and outside a WWTP effluent plume. The diversity, relative abundance, and nitrification activity of AOP were investigated by denaturing gradient gel electrophoresis (DGGE), quantitative real-time PCR (qPCR), and reverse transcriptase qPCR (RT-qPCR), targeting both 16S rRNA and functional genes, together with activity assays. The analysis of bacterial 16S rRNA gene fingerprints showed that the WWTP effluent strongly affected autochthonous bacterial patterns in the water column but not those associated with sediment nucleic acids. Molecular and activity data demonstrated that ammonia-oxidizing archaea (AOA) were numerically and metabolically dominant in samples taken from outside the WWTP plume, whereas ammonia-oxidizing bacteria (AOB) dominated numerically within the WWTP effluent plume. Potential nitrification rate measurements supported the dominance of AOB activity in downstream sediment. Anaerobic ammonia-oxidizing (anammox) bacteria were detected primarily in sediment nucleic acids. In-river AOA patterns were completely distinct from effluent AOA patterns. This study demonstrates the importance of combined molecular and activity-based studies for disentangling molecular signatures of wastewater effluent from autochthonous prokaryotic communities.
Occurrence of Pepper Mild Mottle Virus in Drinking Water Sources in Japan
Authors: Haramoto Eiji , Kitajima Masaaki , Kishida Naohiro , Konno Yoshiaki , Katayama Hiroyuki , Asami Mari , Akiba Michihiro 
Published: September 2013

ABSTRACT

Pepper mild mottle virus (PMMoV) is a plant virus that has been recently proposed as a potential indicator of human fecal contamination of environmental waters; however, information on its geographical occurrence in surface water is still limited. We aimed to determine the seasonal and geographic occurrence of PMMoV in drinking water sources all over Japan. Between July 2008 and February 2011, 184 source water samples were collected from 30 drinking water treatment plants (DWTPs); viruses from 1 to 2 liters of each sample were concentrated by using an electronegative membrane, followed by RNA extraction and reverse transcription. Using quantitative PCR, PMMoV was detected in 140 (76%) samples, with a concentration ranging from 2.03 × 10
3
to 2.90 × 10
6
copies/liter. At least one of the samples from 27 DWTPs (
n
= 4 or 8) was positive for PMMoV; samples from 10 of these DWTPs were always contaminated. There was a significant difference in the occurrence of PMMoV among geographical regions but not a seasonal difference. PMMoV was frequently detected in samples that were negative for human enteric virus or
Escherichia coli
. A phylogenetic analysis based on the partial nucleotide sequences of the PMMoV coat protein gene in 12 water samples from 9 DWTPs indicated that there are genetically diverse PMMoV strains present in drinking water sources in Japan. To our knowledge, this is the first study to demonstrate the occurrence of PMMoV in environmental waters across wide geographical regions.
An Efficient Method Using Gluconacetobacter europaeus To Reduce an Unfavorable Flavor Compound, Acetoin, in Rice Vinegar Production
Authors: Akasaka Naoki , Sakoda Hisao , Hidese Ryota , Ishii Yuri , Fujiwara Shinsuke 
Published: September 2013

ABSTRACT

Gluconacetobacter europaeus
, one of the microorganisms most commonly used for vinegar production, produces the unfavorable flavor compound acetoin. Since acetoin reduction is important for rice vinegar production, a genetic approach was attempted to reduce acetoin produced by
G. europaeus
KGMA0119 using specific gene knockout without introducing exogenous antibiotic resistance genes. A uracil-auxotrophic mutant with deletion of the orotate phosphoribosyltransferase gene (
pyrE
) was first isolated by positive selection using 5-fluoroorotic acid. The
pyrE
disruptant designated KGMA0704 (Δ
pyrE
) showed 5-fluoroorotic acid resistance. KGMA0704 and the
pyrE
gene were used for further gene disruption experiments as a host cell and a selectable marker, respectively. Targeted disruption of
aldC
or
als
, which encodes α-acetolactate decarboxylase or α-acetolactate synthase, was attempted in KGMA0704. The disruption of these genes was expected to result in a decrease in acetoin levels. A disruption vector harboring the
pyrE
marker within the targeted gene was constructed for double-crossover recombination. The cells of KGMA0704 were transformed with the exogenous DNA using electroporation, and genotypic analyses of the transformants revealed the unique occurrence of targeted
aldC
or
als
gene disruption. The
aldC
disruptant KGMA4004 and the
als
disruptant KGMA5315 were cultivated, and the amount of acetoin was monitored. The acetoin level in KGMA4004 culture was significantly reduced to 0.009% (wt/vol) compared with KGMA0119 (0.042% [wt/vol]), whereas that of KGMA5315 was not affected (0.037% [wt/vol]). This indicates that
aldC
disruption is critical for acetoin reduction.
G. europaeus
KGMA4004 has clear application potential in the production of rice vinegar with less unfavorable flavor.
Impact of Logging and Forest Conversion to Oil Palm Plantations on Soil Bacterial Communities in Borneo
Authors: Lee-Cruz Larisa , Edwards David P. , Tripathi Binu M. , Adams Jonathan M. 
Published: September 2013

ABSTRACT
Tropical forests are being rapidly altered by logging and cleared for agriculture. Understanding the effects of these land use changes on soil bacteria, which constitute a large proportion of total biodiversity and perform important ecosystem functions, is a major conservation frontier. Here we studied the effects of logging history and forest conversion to oil palm plantations in Sabah, Borneo, on the soil bacterial community. We used paired-end Illumina sequencing of the 16S rRNA gene, V3 region, to compare the bacterial communities in primary, once-logged, and twice-logged forest and land converted to oil palm plantations. Bacteria were grouped into operational taxonomic units (OTUs) at the 97% similarity level, and OTU richness and local-scale α-diversity showed no difference between the various forest types and oil palm plantations. Focusing on the turnover of bacteria across space, true β-diversity was higher in oil palm plantation soil than in forest soil, whereas community dissimilarity-based metrics of β-diversity were only marginally different between habitats, suggesting that at large scales, oil palm plantation soil could have higher overall γ-diversity than forest soil, driven by a slightly more heterogeneous community across space. Clearance of primary and logged forest for oil palm plantations did, however, significantly impact the composition of soil bacterial communities, reflecting in part the loss of some forest bacteria, whereas primary and logged forests did not differ in composition. Overall, our results suggest that the soil bacteria of tropical forest are to some extent resilient or resistant to logging but that the impacts of forest conversion to oil palm plantations are more severe.
Dynamics of the Saccharomyces cerevisiae Transcriptome during Bread Dough Fermentation
Authors: Aslankoohi Elham , Zhu Bo , Rezaei Mohammad Naser , Voordeckers Karin , De Maeyer Dries , Marchal Kathleen , Dornez Emmie , Courtin Christophe M. , Verstrepen Kevin J. 
Published: September 2013

ABSTRACTThe behavior of yeast cells during industrial processes such as the production of beer, wine, and bioethanol has been extensively studied. In contrast, our knowledge about yeast physiology during solid-state processes, such as bread dough, cheese, or cocoa fermentation, remains limited. We investigated changes in the transcriptomes of three genetically distinctSaccharomyces cerevisiaestrains during bread dough fermentation. Our results show that regardless of the genetic background, all three strains exhibit similar changes in expression patterns. At the onset of fermentation, expression of glucose-regulated genes changes dramatically, and the osmotic stress response is activated. The middle fermentation phase is characterized by the induction of genes involved in amino acid metabolism. Finally, at the latest time point, cells suffer from nutrient depletion and activate pathways associated with starvation and stress responses. Further analysis shows that genes regulated by the high-osmolarity glycerol (HOG) pathway, the major pathway involved in the response to osmotic stress and glycerol homeostasis, are among the most differentially expressed genes at the onset of fermentation. More importantly, deletion ofHOG1and other genes of this pathway significantly reduces the fermentation capacity. Together, our results demonstrate that cells embedded in a solid matrix such as bread dough suffer severe osmotic stress and that a proper induction of the HOG pathway is critical for optimal fermentation.
Development of a Tetracycline-Inducible Gene Expression System for the Study of Helicobacter pylori Pathogenesis
Authors: Debowski Aleksandra W. , Verbrugghe Phebe , Sehnal Miriam , Marshall Barry James , Benghezal Mohammed 
Published: September 2013

ABSTRACT

Deletion mutants and animal models have been instrumental in the study of
Helicobacter pylori
pathogenesis. Conditional mutants, however, would enable the study of the temporal gene requirement during
H. pylori
colonization and chronic infection. To achieve this goal, we adapted the
Escherichia coli
Tn
10
-derived tetracycline-inducible expression system for use in
H. pylori
. The
ureA
promoter was modified by inserting one or two
tet
operators to generate tetracycline-responsive promoters, named
uPtetO
, and these promoters were then fused to the reporter
gfp
mut2 and inserted into different loci. The expression of the tetracycline repressor (
tetR
) was placed under the control of one of three promoters and inserted into the chromosome. Conditional expression of green fluorescent protein (GFP) in strains harboring
tetR
and
uPtetO-GFP
was characterized by measuring GFP activity and by immunoblotting. The two
tet
-responsive
uPtetO
promoters differ in strength, and induction of these promoters was inducer concentration and time dependent, with maximum expression achieved after induction for 8 to 16 h. Furthermore, the chromosomal location of the
uPtetO-GFP
construct and the nature of the promoter driving expression of
tetR
influenced the strength of the
uPtetO
promoters upon induction. Integration of
uPtetO-GFP
and
tetR
constructs at different genomic loci was stable
in vivo
and did not affect colonization. Finally, we demonstrate tetracycline-dependent induction of GFP expression
in vivo
during chronic infection. These results open new experimental avenues for dissecting
H. pylori
pathogenesis using animal models and for testing the roles of specific genes in colonization of, adaptation to, and persistence in the host.
Evidence of Intraflagellar Transport and Apical Complex Formation in a Free-Living Relative of the Apicomplexa
Authors: Portman Neil , Foster Christie , Walker Giselle , Šlapeta Jan 
Published: September 2013

ABSTRACT

Since its first description,
Chromera velia
has attracted keen interest as the closest free-living relative of parasitic Apicomplexa. The life cycle of this unicellular alga is complex and involves a motile biflagellate form. Flagella are thought to be formed in the cytoplasm, a rare phenomenon shared with
Plasmodium
in which the canonical mode of flagellar assembly, intraflagellar transport, is dispensed with. Here we demonstrate the expression of intraflagellar transport components in
C. velia
, answering the question of whether this organism has the potential to assemble flagella via the canonical route. We have developed and characterized a culturing protocol that favors the generation of flagellate forms. From this, we have determined a marked shift in the mode of daughter cell production from two to four daughter cells per division as a function of time after passage. We conduct an ultrastructural examination of the
C. velia
flagellate form by using serial TEM and show that flagellar biogenesis in
C. velia
occurs prior to cytokinesis. We demonstrate a close association of the flagellar apparatus with a complex system of apical structures, including a micropore, a conoid, and a complex endomembrane system reminiscent of the apical complex of parasitic apicomplexans. Recent work has begun to elucidate the possible flagellar origins of the apical complex, and we show that in
C. velia
these structures are contemporaneous within a single cell and share multiple connections. We propose that
C. velia
therefore represents a vital piece in the puzzle of the origins of the apical complex.
Cerebral Blood Flow and Apoptosis-Associated Factor with Electroacupuncture in a Traumatic Brain Injury Rat Model
Authors: Chuang Chih Hsiang , Hsu Yao Chin , Wang Che Chuan , Hu ChoYa , Kuo Jinn Rung 
Published: September 2013

Objective Electroacupuncture (EA) has been widely used for treatment of stroke, but there is little information on the effect of EA on the neuroprotective function in traumatic brain injury (TBI). The aim of the present study was to investigate the protective effects and mechanisms of EA treatment in a TBI rat model. Methods Male Sprague–Dawley rats were randomly divided into four groups: sham operation, TBI control, TBI+EA treated for 30 min or TBI+EA treated for 60 min. The animals were treated with EA immediately after TBI. The EA was applied at acupuncture points GV20, GV26, LI4 and KI1 with a dense-dispersed wave, frequencies of 0.2 and 1 Hz, and amplitude of 1 mA for 30 or 60 min. Regional blood flow, cell infarction volume, extent of neuronal apoptosis, expression of cell apoptosis-associated factor transforming growth-interacting factor (TGIF) were studied, and functional outcome was assessed by running speed test. All tests except regional blood flow were performed 72 h after TBI onset. Results Immediately after TBI, compared with the TBI control groups, the regional blood flow was significantly increased by EA treatment for 60 min. Compared with the TBI controls 72 h after TBI, the TBI-induced run speed impairment, infarction volume, neuronal apoptosis and apoptosis-associated TGIF expression were significantly improved by EA treatment. Conclusions The treatment of TBI in the acute stage with EA for 60 min could increase the regional blood flow and attenuate the levels of TGIF in the injured cortex, might lead to a decrease in neuronal apoptosis and cell infarction volume, and might represent one mechanism by which functional recovery may occur.
Body composition in sport: a comparison of a novel ultrasound imaging technique to measure subcutaneous fat tissue compared with skinfold measurement
Authors: Müller Wolfram , Horn Martin , Fürhapter-Rieger Alfred , Kainz Philipp , Kröpfl Julia M , Maughan Ronald J , Ahammer Helmut 
Published: September 2013

BackgroundExtremely low weight and rapid changes in weight and body composition have become major concerns in many sports, but sufficiently accurate field methods for body composition assessment in athletes are missing. This study aimed to explore the use of ultrasound methods for assessment of body fat content in athletes.Methods19 female athletes (stature: 1.67(±0.06) m, weight: 59.6(±7.6) kg; age: 19.5(±3.3) years) were investigated by three observers using a novel ultrasound method for thickness measurement of uncompressed subcutaneous adipose tissue and of embedded structures. Two observers also measured skinfold thickness at eight International Society for the Advancement of Kinanthrometry (ISAK) sites; mean skinfold values were compared to mean subcutaneous adipose tissue thicknesses measured by ultrasound. Interobserver reliability of imaging and evaluation obtained by this ultrasound technique: intraclass correlation coefficient ICC=0.968 (95% CI 0.957 to 0.977); evaluation of given images: ICC=0.997 (0.993 to 0.999).ResultsSkinfold compared to ultrasound thickness showed that compressibility of subcutaneous adipose tissue depends largely on the site and the person: regression slopes ranged from 0.61 (biceps) to 1.59 (thigh) and CIs were large. Limits of agreement ranged from 2.6 to 8.6 mm. Regression lines did not intercept the skinfold axis at zero because of the skin thickness being included in the skinfold. The four ISAK trunk sites caused ultrasound imaging problems in 13 of 152 sites (8 ISAK sites, 19 athletes).ConclusionsThe ultrasound method allows measurement ofuncompressedsubcutaneous adipose tissue thickness with an accuracy of 0.1–0.5 mm, depending on the probe frequency. Compressibility of the skinfold depends on the anatomical site, and skin thickness varies by a factor of two. This inevitably limits the skinfold methods for body fat estimation. Ultrasound accuracy for subcutaneous adipose tissue measurement is limited by the plasticity of fat and furrowed tissue borders. Comparative US measurements show that skinfold measurements do not allow accurate assessment of subcutaneous adipose tissue thickness.
Current hydration guidelines are erroneous: dehydration does not impair exercise performance in the heat
Authors: Wall Bradley A , Watson Greig , Peiffer Jeremiah J , Abbiss Chris R , Siegel Rodney , Laursen Paul B 
Published: September 2013

BackgroundLaboratory studies that support the hydration guidelines of leading governing bodies have shown that dehydration to only −2% of body mass can lead to increase in body temperature and heart rate during exercise, and decrease in performance. These studies, however, have been conducted in relatively windless environments (ie, wind speed <12.9 km/h), without participants being blinded to their hydration status.AimTo investigate the effect of blinded hydration status on cycling time-trial performance in the heat with ecologically valid facing wind speed conditions.MethodsDuring three experimental trials, 10 cyclists were dehydrated to −3% body mass by performing 2 h of submaximal exercise (walking and cycling) in the heat, before being reinfused with saline to replace 100%, 33% or 0% of fluid losses, leaving them 0%, −2% or −3% hypohydrated, respectively. Participants then completed a 25 km time trial in the heat (33°C, 40% relative humidity; wind speed 32 km/h) during which their starting hydration status was maintained by infusing saline at a rate equal to their sweat rate. The treatment was participant-blinded and the order was randomised. Completion time, power output, heart rate, rectal temperature and perceptual variables were measured.ResultsWhile rectal temperature was higher beyond 17 km of the time trial in the −3% vs 0% conditions (38.9±0.3°C vs 38.6±0.3°C; p<0.05), no other differences between trials were shown.ConclusionWhen well-trained cyclists performed a 25 km cycling time trial under ecologically valid conditions and were blinded to their hydration status, performance, physiological and perceptual variables were not different between trials. These data do not support the residing basis behind many of the current hydration guidelines.
The role of International Sport Federations in the protection of the athlete's health and promotion of sport for health of the general population
Authors: Mountjoy Margo , Junge Astrid 
Published: September 2013

ObjectiveTo determine the priorities and activities of International Sport Federations (IFs) with respect to the promotion of health in their sport and for the general population.MethodsAll 35 IFs participating in Olympic Games in 2014 or in 2016 were asked to rate the importance of 10 indicated topics, and to report their programmes, guidelines or research activities on 16 health-related topics using an online questionnaire (response rate 97%).ResultsOn average, the ‘fight against doping’ had the highest priority followed by ‘health of their elite athlete’ and ‘image as a safe sport’. The topics with the lowest importance ratings were ‘health of their recreational athlete’, ‘increasing the number of recreational athletes’ and ‘health of the general population’. All except one IF reported to have health-related programmes/guidelines/research activities; most IFs had 7 or 8 of the listed activities. Eight IFs (23.5%) stated to have activities for ‘prevention of chronic diseases in the general population’ but only FIFA and FINA reported related projects.ConclusionsIFs aimed to protect the health of their elite athletes through a variety of activities, however the health and number of their recreational athletes was of low importance for them. Thus, IFs are missing an important opportunity to increase the popularity of their sport, and to contribute to the health of the general population by encouraging physical activity through their sport. FIFA’s ‘Football for Health’ and FINA’s ‘Swim for All’ projects could serve as role models.