bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nitrogen starvation‐induced accumulation of triacylglycerol in the green algae: evidence for a role forROC40, a transcription factor involved in circadian rhythm
Authors: Goncalves Elton C. , Koh Jin , Zhu Ning , Yoo Mi‐Jeong , Chen Sixue , Matsuo Takuya , Johnson Jodie V. , Rathinasabapathi Bala 
Published: February 2016

SummaryMicroalgal triacylglycerol (TAG), a promising source of biofuel, is induced upon nitrogen starvation (−N), but the proteins and genes involved in this process are poorly known. We performed isobaric tagging for relative and absolute quantification (iTRAQ)‐based quantitative proteomics to identifyChlorellaproteins with modulated expression under short‐term −N. Out of 1736 soluble proteins and 2187 membrane‐associated proteins identified, 288 and 56, respectively, were differentially expressed under −N. Gene expression analysis on select genes confirmed the same direction ofmRNAmodulation for most proteins. TheMYB‐related transcription factorROC40 was the most induced protein, with a 9.6‐fold increase upon −N. In a previously generatedChlamydomonasmutant, gravimetric measurements of crude total lipids revealed thatroc40was impaired in its ability to increase the accumulation ofTAGupon −N, and this phenotype was complemented when wild‐type Roc40 was expressed. Results from radiotracer experiments were consistent with theroc40mutant being comparable to the wild type in recycling membrane lipids toTAGbut being impaired in additionalde novosynthesis ofTAGduring −N stress. In this study we provide evidence to support the hypothesis that transcription factorROC40 has a role in −N‐induced lipid accumulation, and uncover multiple previously unknown proteins modulated by short‐term −N in green algae.
Renal biomarkers in domestic species
Authors: Hokamp Jessica A. , Nabity Mary B. 
Published: February 2016

AbstractCurrent conventional tests of kidney damage and function in blood (serum creatinine and urea nitrogen) and urine (urine protein creatinine ratio and urine specific gravity) are widely used for diagnosis and monitoring of kidney disease. However, they all have important limitations, and additional markers of glomerular filtration rate and glomerular and tubular damage are desirable, particularly for earlier detection of renal disease when therapy is most effective. Additionally, urinary markers of kidney damage and function may help localize damage to the affected portion of the kidney. In general, the presence of high‐ and intermediate‐molecular weight proteins in the urine are indicative of glomerular damage, while low‐molecular weight proteins and enzymes in the urine suggest tubular damage due to decreased reabsorption of proteins, direct tubular damage, or both. This review aims to discuss many of these new blood and urinary biomarkers in domestic veterinary species, focusing primarily on dogs and cats, how they may be used for diagnosis of renal disease, and their limitations. Additionally, a brief discussion of serum creatinine is presented, highlighting its limitations and important considerations for its improved interpretation in domestic species based on past literature and recent studies.
Sysmex XT‐2000iV scattergram analysis in a cat with basophilia
Authors: Stranieri Angelica , Ferrari Roberta , Zanzani Sergio , Rossi Gabriele 
Published: February 2016

AbstractA 13‐year‐old female Domestic Shorthair cat was presented to the Veterinary Teaching Hospital of the University of Milan for an interscapular mass suspected to be a mesenchymal malignant tumor. A preoperative CBC performed with Sysmex XT‐2000iV showed leukocytosis with neutrophilia and eosinophilia. The Sysmex WBC/DIFF scattergram showed an additional, well‐separated cluster of events between the neutrophil, eosinophil, and lymphocyte clusters. Blood smear evaluation revealed the presence of a significant number of basophils; thus, it was hypothesized that the additional cluster could represent the basophilic population. A second CBC, 24 days later, showed the same pattern on the WBC/DIFF scattergram in the absence of leukocytosis and neutrophilia. After surgical excision of the mass, a definitive diagnosis of feline injection site sarcoma was made. To the author's knowledge, there are no previous reports about the identification of feline basophils in the WBC/DIFF scattergram of Sysmex XT‐2000iV.
The ageing neuromuscular system and sarcopenia: a mitochondrial perspective
Authors: Rygiel Karolina A. , Picard Martin , Turnbull Doug M. 
Published: February 2016

AbstractSkeletal muscles undergo structural and functional decline with ageing, culminating in sarcopenia. The underlying neuromuscular mechanisms have been the subject of intense investigation, revealing mitochondrial abnormalities as potential culprits within both nerve and muscle cells. Implicated mechanisms involve impaired mitochondrial dynamics, reduced organelle biogenesis and quality control via mitophagy, accumulation of mitochondrial DNA (mtDNA) damage and respiratory chain defect, metabolic disturbance, pro‐apoptotic signalling, and oxidative stress. This article provides an overview of the cellular mechanisms whereby mitochondria may promote maladaptive changes within motor neurons, the neuromuscular junction (NMJ) and muscle fibres. Lifelong physical activity, which promotes mitochondrial health across tissues, is emerging as an effective countermeasure for sarcopenia.
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Application of systems and control theory‐based hazard analysis to radiation oncology
Authors: Pawlicki Todd , Samost Aubrey , Brown Derek W. , Manger Ryan P. , Kim Gwe‐Ya , Leveson Nancy G. 
Published: February 2016

Purpose:Both humans and software are notoriously challenging to account for in traditional hazard analysis models. The purpose of this work is to investigate and demonstrate the application of a new, extended accident causality model, called systems theoretic accident model and processes (STAMP), to radiation oncology. Specifically, a hazard analysis technique based on STAMP, system‐theoretic process analysis (STPA), is used to perform a hazard analysis.Methods:The STPA procedure starts with the definition of high‐level accidents for radiation oncology at the medical center and the hazards leading to those accidents. From there, the hierarchical safety control structure of the radiation oncology clinic is modeled, i.e., the controls that are used to prevent accidents and provide effective treatment. Using STPA, unsafe control actions (behaviors) are identified that can lead to the hazards as well as causal scenarios that can lead to the identified unsafe control. This information can be used to eliminate or mitigate potential hazards. The STPA procedure is demonstrated on a new online adaptive cranial radiosurgery procedure that omits the CT simulation step and uses CBCT for localization, planning, and surface imaging system during treatment.Results:The STPA procedure generated a comprehensive set of causal scenarios that are traced back to system hazards and accidents. Ten control loops were created for the new SRS procedure, which covered the areas of hospital and department management, treatment design and delivery, and vendor service. Eighty three unsafe control actions were identified as well as 472 causal scenarios that could lead to those unsafe control actions.Conclusions:STPA provides a method for understanding the role of management decisions and hospital operations on system safety and generating process design requirements to prevent hazards and accidents. The interaction of people, hardware, and software is highlighted. The method of STPA produces results that can be used to improve safety and prevent accidents and warrants further investigation.
Functional Analysis of an S-Layer-Associated Fibronectin-Binding Protein in Lactobacillus acidophilus NCFM
Authors: Hymes Jeffrey P. , Johnson Brant R. , Barrangou Rodolphe , Klaenhammer Todd R. 
Published: February 2016

ABSTRACT

Bacterial surface layers (S-layers) are crystalline arrays of self-assembling proteinaceous subunits called S-layer proteins (Slps) that comprise the outermost layer of the cell envelope. Many additional proteins that are associated with or embedded within the S-layer have been identified in
Lactobacillus acidophilus
NCFM, an S-layer-forming bacterium that is widely used in fermented dairy products and probiotic supplements. One putative S-layer-associated protein (SLAP), LBA0191, was predicted to mediate adhesion to fibronectin based on the
in silico
detection of a fibronectin-binding domain. Fibronectin is a major component of the extracellular matrix (ECM) of intestinal epithelial cells. Adhesion to intestinal epithelial cells is considered an important trait for probiotic microorganisms during transit and potential association with the intestinal mucosa. To investigate the functional role of LBA0191 (designated FbpB) in
L. acidophilus
NCFM, an
fbpB
-deficient strain was constructed. The
L. acidophilus
mutant with a deletion of
fbpB
lost the ability to adhere to mucin and fibronectin
in vitro
. Homologues of
fbpB
were identified in five additional putative S-layer-forming species, but no homologues were detected in species outside the
L. acidophilus
homology group.
Mutations in Novel Lipopolysaccharide Biogenesis Genes Confer Resistance to Amoebal Grazing in Synechococcus elongatus
Authors: Simkovsky Ryan , Effner Emily E. , Iglesias-Sánchez Maria José , Golden Susan S. 
Published: February 2016

ABSTRACT

In natural and artificial aquatic environments, population structures and dynamics of photosynthetic microbes are heavily influenced by the grazing activity of protistan predators. Understanding the molecular factors that affect predation is critical for controlling toxic cyanobacterial blooms and maintaining cyanobacterial biomass production ponds for generating biofuels and other bioproducts. We previously demonstrated that impairment of the synthesis or transport of the O-antigen component of lipopolysaccharide (LPS) enables resistance to amoebal grazing in the model predator-prey system consisting of the heterolobosean amoeba HGG1 and the cyanobacterium
Synechococcus elongatus
PCC 7942 (R. S. Simkovsky et al., Proc Natl Acad Sci U S A 109:16678–16683, 2012,
http://dx.doi.org/10.1073/pnas.1214904109
). In this study, we used this model system to identify additional gene products involved in the synthesis of O antigen, the ligation of O antigen to the lipid A-core conjugated molecule (including a novel ligase gene), the generation of GDP-fucose, and the incorporation of sugars into the lipid A core oligosaccharide of
S. elongatus
. Knockout of any of these genes enables resistance to HGG1, and of these, only disruption of the genes involved in synthesis or incorporation of GDP-fucose into the lipid A-core molecule impairs growth. Because these LPS synthesis genes are well conserved across the diverse range of cyanobacteria, they enable a broader understanding of the structure and synthesis of cyanobacterial LPS and represent mutational targets for generating resistance to amoebal grazers in novel biomass production strains.
A New Strategy for Production of 5-Aminolevulinic Acid in Recombinant Corynebacterium glutamicum with High Yield
Authors: Yang Peng , Liu Wenjing , Cheng Xuelian , Wang Jing , Wang Qian , Qi Qingsheng 
Published: February 2016

ABSTRACT

5-Aminolevulinic acid (ALA), a nonprotein amino acid involved in tetrapyrrole synthesis, has been widely applied in agriculture, medicine, and food production. Many engineered metabolic pathways have been constructed; however, the production yields are still low. In this study, several 5-aminolevulinic acid synthases (ALASs) from different sources were evaluated and compared with respect to their ALA production capacities in an engineered
Corynebacterium glutamicum
CgS1 strain that can accumulate succinyl-coenzyme A (CoA). A codon-optimized ALAS from
Rhodobacter capsulatus
SB1003 displayed the best potential. Recombinant strain CgS1/pEC-SB produced 7.6 g/liter ALA using a mineral salt medium in a fed-batch fermentation mode. Employing two-stage fermentation, 12.46 g/liter ALA was produced within 17 h, with a productivity of 0.73 g/liter/h, in recombinant
C. glutamicum
. Through overexpression of the heterologous nonspecific ALA exporter RhtA from
Escherichia coli
, the titer was further increased to 14.7 g/liter. This indicated that strain CgS1/pEC-SB-rhtA holds attractive industrial application potential for the future.

IMPORTANCE
In this study, a two-stage fermentation strategy was used for production of the value-added nonprotein amino acid 5-aminolevulinic acid from glucose and glycine in a generally recognized as safe (GRAS) host,
Corynebacterium glutamicum
. The ALA titer represented the highest in the literature, to our knowledge. This high production capacity, combined with the potential easy downstream processes, made the recombinant strain an attractive candidate for industrial use in the future.
Relationship of Enhanced Butyrate Production by Colonic Butyrate-Producing Bacteria to Immunomodulatory Effects in Normal Mice Fed an Insoluble Fraction of Brassica rapa L
Authors: Tanaka Sachi , Yamamoto Kana , Yamada Kazuki , Furuya Kanon , Uyeno Yutaka 
Published: February 2016

ABSTRACTThis study was performed to determine the effects of feeding a fiber-rich fraction ofBrassicavegetables on the immune response through changes in enteric bacteria and short-chain fatty acid (SCFA) production in normal mice. The boiled-water-insoluble fraction ofBrassica rapaL. (nozawana), which consists mainly of dietary fiber, was chosen as a test material. A total of 31 male C57BL/6J mice were divided into two groups and housed in a specific-pathogen-free facility. The animals were fed either a control diet or the control diet plus the insolubleB. rapaL. fraction for 2 weeks and sacrificed to determine microbiological and SCFA profiles in lower-gut samples and immunological molecules. rRNA-based quantification indicated that the relative population ofBacteroideteswas markedly lower in the colon samples of the insolubleB. rapaL. fraction-fed group than that in the controls. Populations of theEubacterium rectalegroup andFaecalibacterium prausnitzii, both of which are representative butyrate-producing bacteria, doubled after 2 weeks of fraction intake, accompanying a marginal increase in the proportion of colonic butyrate. In addition, feeding with the fraction significantly increased levels of the anti-inflammatory cytokine interleukin-10 (IL-10) and tended to increase splenic regulatory T cell numbers but significantly reduced the population of cells expressing activation markers. We demonstrated that inclusion of the boiled-water-insoluble fraction ofB. rapaL. can alter the composition of the gut microbiota to decrease the numbers ofBacteroidetesand to increase the numbers of butyrate-producing bacteria, either of which may be involved in the observed shift in the production of splenic IL-10.
Visualizing the Translocation and Localization of Bacterial Type III Effector Proteins by Using a Genetically Encoded Reporter System
Authors: Gawthorne Jayde A. , Audry Laurent , McQuitty Claire , Dean Paul , Christie John M. , Enninga Jost , Roe Andrew J. 
Published: February 2016

ABSTRACT

Bacterial type III secretion system (T3SS) effector proteins are critical determinants of infection for many animal and plant pathogens. However, monitoring of the translocation and delivery of these important virulence determinants has proved to be technically challenging. Here, we used a genetically engineered LOV (light-oxygen-voltage) sensing domain derivative to monitor the expression, translocation, and localization of bacterial T3SS effectors. We found the
Escherichia coli
O157:H7 bacterial effector fusion Tir-LOV was functional following its translocation and localized to the host cell membrane in discrete foci, demonstrating that LOV-based reporters can be used to visualize the effector translocation with minimal manipulation and interference. Further evidence for the versatility of the reporter was demonstrated by fusing LOV to the C terminus of the
Shigella flexneri
effector IpaB. IpaB-LOV localized preferentially at bacterial poles before translocation. We observed the rapid translocation of IpaB-LOV in a T3SS-dependent manner into host cells, where it localized at the bacterial entry site within membrane ruffles.
Packaging of Campylobacter jejuni into Multilamellar Bodies by the Ciliate Tetrahymena pyriformis
Authors: Trigui Hana , Paquet Valérie E. , Charette Steve J. , Faucher Sébastien P. 
Published: February 2016

ABSTRACT

Campylobacter jejuni
is the leading cause of bacterial gastroenteritis worldwide. Transmission to humans occurs through consumption of contaminated food or water. The conditions affecting the persistence of
C. jejuni
in the environment are poorly understood. Some protozoa package and excrete bacteria into multilamellar bodies (MLBs). Packaged bacteria are protected from deleterious conditions, which increases their survival. We hypothesized that
C. jejuni
could be packaged under aerobic conditions by the amoeba
Acanthamoeba castellanii
or the ciliate
Tetrahymena pyriformis
, both of which are able to package other pathogenic bacteria.
A. castellanii
did not produce MLBs containing
C. jejuni
. In contrast, when incubated with
T. pyriformis
,
C. jejuni
was ingested, packaged in MLBs, and then expelled into the milieu. The viability of the bacteria inside MLBs was confirmed by microscopic analyses. The kinetics of
C. jejuni
culturability showed that packaging increased the survival of
C. jejuni
up to 60 h, in contrast to the strong survival defect seen in ciliate-free culture. This study suggests that
T. pyriformis
may increase the risk of persistence of
C. jejuni
in the environment and its possible transmission between different reservoirs in food and potable water through packaging.
Versatile Vectors for Efficient Mutagenesis of Bradyrhizobium diazoefficiens and Other Alphaproteobacteria
Authors: Ledermann Raphael , Strebel Silvan , Kampik Clara , Fischer Hans-Martin 
Published: February 2016

ABSTRACT

Analysis of bacterial gene function commonly relies on gene disruption or replacement followed by phenotypic characterization of the resulting mutant strains. Deletion or replacement of targeted regions is commonly achieved via two homologous recombination (HR) events between the bacterial genome and a nonreplicating plasmid carrying DNA fragments flanking the region to be deleted. The counterselection of clones that have integrated the entire plasmid in their genome via a single HR event is crucial in this procedure. Various genetic tools and well-established protocols are available for this type of mutagenesis in model bacteria; however, these methods are not always efficiently applicable in less established systems. Here we describe the construction and application of versatile plasmid vectors pREDSIX and pTETSIX for marker replacement and markerless mutagenesis, respectively. Apart from an array of restriction sites optimized for cloning of GC-rich DNA fragments, the vector backbone contains a constitutively expressed gene for mCherry, enabling the rapid identification of clones originating from single or double HR events by fluorescence-assisted cell sorting (FACS). In parallel, we constructed a series of plasmids from which gene cassettes providing resistance against gentamicin, kanamycin, hygromycin B, streptomycin and spectinomycin, or tetracycline were excised for use with pREDSIX-based marker replacement mutagenesis. In proof-of-concept mutagenesis experiments, we demonstrated the potential for the use of the developed tools for gene deletion mutagenesis in the nitrogen-fixing soybean symbiont
Bradyrhizobium diazoefficiens
(formerly
Bradyrhizobium japonicum
) and three additional members of the alphaproteobacteria.

IMPORTANCE
Mutation and phenotypic analysis are essential to the study of gene function. Efficient mutagenesis protocols and tools are available for many bacterial species, including various model organisms; however, genetic analysis of less-well-characterized organisms is often impaired by the lack of efficient methods. Here we describe a set of novel genetic tools for facilitated mutagenesis of the nitrogen-fixing soybean symbiont
Bradyrhizobium diazoefficiens
and related alphaproteobacteria. We demonstrated their usefulness by generating several mutant strains lacking defined genes. Isolation of both antibiotic resistance gene-containing and markerless deletion mutants is greatly facilitated because undesired clones which contain the entire mutagenic plasmid integrated in the genome can be identified on the basis of their fluorescent phenotype derived from the
mCherry
gene carried by the vector backbone. The possibility to generate markerless mutants assists with the isolation of strains carrying multiple deletions, which can be crucial while studying functionally redundant genes.
Association of screen time with self-perceived attention problems and hyperactivity levels in French students: a cross-sectional study
Authors: Montagni Ilaria , Guichard Elie , Kurth Tobias 
Published: February 2016

ObjectiveTo investigate whether high levels of screen time exposure are associated with self-perceived levels of attention problems and hyperactivity in higher education students.DesignCross-sectional study among participants of the i-Share cohort.SettingFrench-speaking students of universities and higher education institutions.Participants4816 graduate students who were at least 18 years old.ExposureScreen time was assessed by self-report of the average time spent on five different screen activities on smartphone, television, computer and tablet and categorised into quartiles.Main outcome measureWe used the Attention Deficit Hyperactivity Disorder Self-Report Scale (ASRS-v1.1) concerning students’ behaviour over the past 6 months to measure self-perceived levels of attention problems and hyperactivity. Responses were summarised into a global score as well as scores for attention problems and hyperactivity.ResultsThe 4816 participants of this study had a mean age of 20.8 years and 75.5% were female. Multivariable ordinary regression models showed significant associations of screen time exposure with quintiles of the total score of self-perceived attention problems and hyperactivity levels as well as the individual domains. Compared to the lowest screen time exposure category, the ORs (95% CI) were 1.58 (1.37 to 1.82) for each increasing level of quintiles of the global score, 1.57 (1.36 to 1.81) for increasing quintiles of attention levels and 1.25 (1.09 to 1.44) for increasing quartiles of hyperactivity.ConclusionsResults of this large cross-sectional study among French university and higher education students show dose-dependent associations between screen time and self-perceived levels of attention problems and hyperactivity. Further studies are warranted to evaluate whether interventions could positively influence these associations.