bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biosynthesis of the β-Methylarginine Residue of Peptidyl Nucleoside Arginomycin in Streptomyces arginensis NRRL 15941
Authors: Feng Jun , Wu Jun , Gao Jie , Xia Zhigui , Deng Zixin , He Xinyi 
Published: June 2014

ABSTRACT

The peptidyl nucleoside arginomycin is active against Gram-positive bacteria and fungi but displays much lower toxicity to mice than its analog blasticidin S. It features a rare amino acid, β-methylarginine, which is attached to the deoxyhexose moiety via a 4′-aminoacyl bond. We here report cloning of the complete biosynthetic gene cluster for arginomycin from
Streptomyces arginensis
NRRL 15941. Among the 14 putative essential open reading frames,
argM
, encoding an aspartate aminotransferase (AAT), and adjacent
argN
, encoding an
S
-adenosyl methionine (SAM)-dependent methyltransferase, are coupled to catalyze arginine and yield β-methylarginine in
Escherichia coli
. Purified ArgM can transfer the α-amino group of
l
-arginine to α-ketoglutaric acid to give glutamate and thereby converts
l
-arginine to 5-guanidino-2-oxopentanoic acid, which is methylated at the C-3 position by ArgN to form 5-guanidino-3-methyl-2-oxopentanoic acid. Iteratively, ArgM specifically catalyzes transamination from the donor
l
-aspartate to the resulting 5-guanidino-3-methyl-2-oxopentanoic acid, generating β-methylarginine. The complete and concise biosynthetic pathway for the rare and bioactive amino acid revealed by this study may pave the way for the production of β-methylarginine either by enzymatic conversion or by engineered living cells.
Elucidation of Insertion Elements Carried on Plasmids and
In Vitro
Construction of Shuttle Vectors from the Toxic Cyanobacterium Planktothrix
Authors: Christiansen Guntram , Goesmann Alexander , Kurmayer Rainer 
Published: June 2014

ABSTRACT

Several gene clusters that are responsible for toxin synthesis in bloom-forming cyanobacteria have been found to be associated with transposable elements (TEs). In particular, insertion sequence (IS) elements were shown to play a role in the inactivation or recombination of the genes responsible for cyanotoxin synthesis. Plasmids have been considered important vectors of IS element distribution to the host. In this study, we aimed to elucidate the IS elements propagated on the plasmids and the chromosome of the toxic cyanobacterium
Planktothrix agardhii
NIVA-CYA126/8 by means of high-throughput sequencing. In total, five plasmids (pPA5.5, pPA14, pPA50, pPA79, and pPA115, of 5, 6, 50, 79, and 120 kbp, respectively) were elucidated, and two plasmids (pPA5.5, pPA115) were found to propagate full IS element copies. Large stretches of shared DNA information between plasmids were constituted of TEs. Two plasmids (pPA5.5, pPA14) were used as candidates to engineer shuttle vectors (named pPA5.5SV and pPA14SV, respectively)
in vitro
by PCR amplification and the subsequent transposition of the Tn
5 cat
transposon containing the R6Kγ origin of replication of
Escherichia coli
. While pPA5.5SV was found to be fully segregated, pPA14SV consistently co-occurred with its wild-type plasmid even under the highest selective pressure. Interestingly, the Tn
5 cat
transposon became transferred by homologous recombination into another plasmid, pPA50. The availability of shuttle vectors is considered to be of relevance in investigating genome plasticity as a consequence of homologous recombination events. Combining the potential of high-throughput sequencing and
in vitro
production of shuttle vectors makes it simple to produce species-specific shuttle vectors for many cultivable prokaryotes.
Identification and Characterization of a Halotolerant, Cold-Active Marine Endo-β-1,4-Glucanase by Using Functional Metagenomics of Seaweed-Associated Microbiota
Authors: Martin Marjolaine , Biver Sophie , Steels Sébastien , Barbeyron Tristan , Jam Murielle , Portetelle Daniel , Michel Gurvan , Vandenbol Micheline 
Published: June 2014

ABSTRACT

A metagenomic library was constructed from microorganisms associated with the brown alga
Ascophyllum nodosum
. Functional screening of this library revealed 13 novel putative esterase loci and two glycoside hydrolase loci. Sequence and gene cluster analysis showed the wide diversity of the identified enzymes and gave an idea of the microbial populations present during the sample collection period. Lastly, an endo-β-1,4-glucanase having less than 50% identity to sequences of known cellulases was purified and partially characterized, showing activity at low temperature and after prolonged incubation in concentrated salt solutions.
Rubber Oxygenase and Latex Clearing Protein Cleave Rubber to Different Products and Use Different Cleavage Mechanisms
Authors: Birke Jakob , Jendrossek Dieter 
Published: June 2014

ABSTRACT

Two types of enzyme for oxidative cleavage of poly(
cis
-1,4-isoprene) are known. One is rubber oxygenase (RoxA) that is secreted by
Xanthomonas
sp. strain 35Y and a few other Gram-negative rubber-degrading bacteria during growth on polyisoprene. RoxA was studied in the past, and the recently solved structure showed a structural relationship to bacterial cytochrome
c
peroxidases (J. Seidel et al., Proc. Natl. Acad. Sci. U. S. A. 110:13833–13838, 2013,
http://dx.doi.org/10.1073/pnas.1305560110
). The other enzyme is latex-clearing protein (Lcp) that is secreted by rubber-degrading actinomycetes, but Lcp has not yet been purified. Here, we expressed Lcp of
Streptomyces
sp. strain K30 in a Δ
roxA
background of
Xanthomonas
sp. strain 35Y and purified native (untagged) Lcp. The specific activities of Lcp and RoxA were 0.70 and 0.48 U/mg, respectively. Lcp differed from RoxA in the absence of heme groups and other characteristics. Notably, Lcp degraded polyisoprene via endo-type cleavage to tetra-C
20
and higher oligo-isoprenoids with aldehyde and keto end groups, whereas RoxA used an exo-type cleavage mechanism to give the main end product 12-oxo-4,8-dimethyltrideca-4,8-diene-1-al (ODTD). RoxA was able to cleave isolated Lcp-derived oligo-isoprenoid molecules to ODTD. Inhibitor studies, spectroscopic investigations and metal analysis gave no indication for the presence of iron, other metals, or cofactors in Lcp. Our results suggest that Lcp could be a member of the growing group of cofactor-independent oxygenases and differs in the cleavage mechanism from heme-dependent RoxA. In conclusion, RoxA and Lcp represent two different answers to the same biochemical problem, the cleavage of polyisoprene, a polymer that has carbon-carbon double bonds as the only functional groups for enzymatic attack.
VibA, a Homologue of a Transcription Factor for Fungal Heterokaryon Incompatibility, Is Involved in Antifungal Compound Production in the Plant-Symbiotic Fungus Epichloë festucae
Authors: Niones Jennifer T. , Takemoto Daigo 
Published: June 2014

ABSTRACT

Symbiotic association of epichloae endophytes (
Epichloë/Neotyphodium
species) with cool-season grasses of the subfamily Pooideae confers bioprotective benefits to the host plants against abiotic and biotic stresses. While the production of fungal bioprotective metabolites is a well-studied mechanism of host protection from insect herbivory, little is known about the antibiosis mechanism against grass pathogens by the mutualistic endophyte. In this study, an
Epichloë festucae
mutant defective in antimicrobial substance production was isolated by a mutagenesis approach. In an isolated mutant that had lost antifungal activity, the exogenous DNA fragment was integrated into the promoter region of the
vibA
gene, encoding a homologue of the transcription factor VIB-1. VIB-1 in
Neurospora crassa
is a regulator of genes essential in vegetative incompatibility and promotion of cell death. Here we show that deletion of the
vibA
gene severely affected the antifungal activity of the mutant against the test pathogen
Drechslera erythrospila
. Further analyses showed that overexpressing
vibA
enhanced the antifungal activity of the wild-type isolate against test pathogens. Transformants overexpressing
vibA
showed an inhibitory activity on test pathogens that the wild-type isolate could not. Moreover, overexpressing
vibA
in a nonantifungal
E. festucae
wild-type Fl1 isolate enabled the transformant to inhibit the mycelial and spore germination of
D. erythrospila
. These results demonstrate that enhanced expression of
vibA
is sufficient for a nonantifungal isolate to obtain antifungal activity, implicating the critical role of VibA in antifungal compound production by epichloae endophytes.
PFP1
, a Gene Encoding an Epc-N Domain-Containing Protein, Is Essential for Pathogenicity of the Barley Pathogen Rhynchosporium commune
Authors: Siersleben Sylvia , Penselin Daniel , Wenzel Claudia , Albert Sylvie , Knogge Wolfgang 
Published: June 2014

ABSTRACT

Scald caused by
Rhynchosporium commune
is an important foliar disease of barley. Insertion mutagenesis of
R. commune
generated a nonpathogenic fungal mutant which carries the inserted plasmid in the upstream region of a gene named
PFP1
. The characteristic feature of the gene product is an Epc-N domain. This motif is also found in homologous proteins shown to be components of histone acetyltransferase (HAT) complexes of fungi and animals. Therefore, PFP1 is suggested to be the subunit of a HAT complex in
R. commune
with an essential role in the epigenetic control of fungal pathogenicity. Targeted
PFP1
disruption also yielded nonpathogenic mutants which showed wild-type-like growth
ex planta
, except for the occurrence of hyphal swellings. Complementation of the deletion mutants with the wild-type gene reestablished pathogenicity and suppressed the hyphal swellings. However, despite wild-type-level
PFP1
expression, the complementation mutants did not reach wild-type-level virulence. This indicates that the function of the protein complex and, thus, fungal virulence are influenced by a position-affected long-range control of
PFP1
expression.
The Volatome of Aspergillus fumigatus
Authors: Heddergott C. , Calvo A. M. , Latgé J. P. 
Published: June 2014

ABSTRACT

Early detection of invasive aspergillosis is absolutely required for efficient therapy of this fungal infection. The identification of fungal volatiles in patient breath can be an alternative for the detection of
Aspergillus fumigatus
that still remains problematic. In this work, we investigated the production of volatile organic compounds (VOCs) by
A. fumigatus
in vitro
, and we show that volatile production depends on the nutritional environment.
A. fumigatus
produces a multiplicity of VOCs, predominantly terpenes and related compounds. The production of sesquiterpenoid compounds was found to be strongly induced by increased iron concentrations and certain drugs, i.e., pravastatin. Terpenes that were always detectable in large amounts were α-pinene, camphene, and limonene, as well as sesquiterpenes, identified as α-bergamotene and β-
trans
-bergamotene. Other substance classes that were found to be present in the volatome, such as 1-octen-3-ol, 3-octanone, and pyrazines, were found only under specific growth conditions. Drugs that interfere with the terpene biosynthesis pathway influenced the composition of the fungal volatome, and most notably, a block of sesquiterpene biosynthesis by the bisphosphonate alendronate fundamentally changed the VOC composition. Using deletion mutants, we also show that a terpene cyclase and a putative kaurene synthase are essential for the synthesis of volatile terpenes by
A. fumigatus
. The present analysis of
in vitro
volatile production by
A. fumigatus
suggests that VOCs may be used in the diagnosis of infections caused by this fungus.
Interaction of Cryptococcus neoformans Extracellular Vesicles with the Cell Wall
Authors: Wolf Julie M. , Espadas-Moreno Javier , Luque-Garcia Jose L. , Casadevall Arturo 
Published: June 2014

ABSTRACT

Cryptococcus neoformans
produces extracellular vesicles containing a variety of cargo, including virulence factors. To become extracellular, these vesicles not only must be released from the plasma membrane but also must pass through the dense matrix of the cell wall. The greatest unknown in the area of fungal vesicles is the mechanism by which these vesicles are released to the extracellular space given the presence of the fungal cell wall. Here we used electron microscopy techniques to image the interactions of vesicles with the cell wall. Our goal was to define the ultrastructural morphology of the process to gain insights into the mechanisms involved. We describe single and multiple vesicle-leaving events, which we hypothesized were due to plasma membrane and multivesicular body vesicle origins, respectively. We further utilized melanized cells to “trap” vesicles and visualize those passing through the cell wall. Vesicle size differed depending on whether vesicles left the cytoplasm in single versus multiple release events. Furthermore, we analyzed different vesicle populations for vesicle dimensions and protein composition. Proteomic analysis tripled the number of proteins known to be associated with vesicles. Despite separation of vesicles into batches differing in size, we did not identify major differences in protein composition. In summary, our results indicate that vesicles are generated by more than one mechanism, that vesicles exit the cell by traversing the cell wall, and that vesicle populations exist as a continuum with regard to size and protein composition.
Normal Telomere Length Maintenance in Saccharomyces cerevisiae Requires Nuclear Import of the Ever Shorter Telomeres 1 (Est1) Protein via the Importin Alpha Pathway
Authors: Hawkins Charlene , Friedman Katherine L. 
Published: June 2014

ABSTRACT

The Est1 (ever shorter telomeres 1) protein is an essential component of yeast telomerase, a ribonucleoprotein complex that restores the repetitive sequences at chromosome ends (telomeres) that would otherwise be lost during DNA replication. Previous work has shown that the telomerase RNA component (
TLC1
) transits through the cytoplasm during telomerase biogenesis, but mechanisms of protein import have not been addressed. Here we identify three nuclear localization sequences (NLSs) in Est1p. Mutation of the most N-terminal NLS in the context of full-length Est1p reduces Est1p nuclear localization and causes telomere shortening—phenotypes that are rescued by fusion with the NLS from the simian virus 40 (SV40) large-T antigen. In contrast to that of the
TLC1
RNA, Est1p nuclear import is facilitated by Srp1p, the yeast homolog of importin α. The reduction in telomere length observed at the semipermissive temperature in a
srp1
mutant strain is rescued by increased Est1p expression, consistent with a defect in Est1p nuclear import. These studies suggest that at least two nuclear import pathways are required to achieve normal telomere length homeostasis in yeast.
Reality check: the cost–effectiveness of removing body checking from youth ice hockey
Authors: Lacny Sarah , Marshall Deborah A , Currie Gillian , Kulin Nathalie A , Meeuwisse Willem H , Kang Jian , Emery Carolyn A 
Published: June 2014

Background/aimThe risk of injury among Pee Wee (ages 11–12 years) ice hockey players in leagues that allow body checking is threefold greater than in leagues that do not allow body checking. We estimated the cost–effectiveness of a no body checking policy versus a policy that allows body checking in Pee Wee ice hockey.MethodsCost–effectiveness analysis alongside a prospective cohort study during the 2007–2008 season, including players in Quebec (n=1046), where policy did not allow body checking, and in Alberta (n=1108), where body checking was allowed. Injury incidence rates (injuries/1000 player-hours) and incidence proportions (injuries/100 players), adjusted for cluster using Poisson regression, allowed for standardised comparisons and meaningful translation to community stakeholders. Based on Alberta fee schedules, direct healthcare costs (physician visits, imaging, procedures) were adjusted for cluster using bootstrapping. We examined uncertainty in our estimates using cost–effectiveness planes.ResultsAssociated with significantly higher injury rates, healthcare costs where policy allowed body checking were over 2.5 times higher than where policy disallowed body checking ($C473/1000 player-hours (95% CI $C358 to $C603) vs $C184/1000 player-hours (95% CI $C120 to $C257)). The difference in costs between provinces was $C289/1000 player-hours (95% CI $C153 to $C432). Projecting results onto Alberta Pee Wee players registered in the 2011–2012 season, an estimated 1273 injuries and $C213 280 in healthcare costs would be avoided during just one season with the policy change.ConclusionOur study suggests that a policy disallowing body checking in Pee Wee ice hockey is cost-saving (associated with fewer injuries and lower costs) compared to a policy allowing body checking. As we did not account for long-term outcomes, our results underestimate the economic impact of these injuries.
Study protocol for the nutritional route in oesophageal resection trial: a single-arm feasibility trial (NUTRIENT trial)
Authors: Weijs Teus J , Nieuwenhuijzen Grard A P , Ruurda Jelle P , Kouwenhoven Ewout A , Rosman Camiel , Sosef Meindert , v Hillegersberg Richard , Luyer Misha D P 
Published: June 2014

IntroductionThe best route of feeding for patients undergoing an oesophagectomy is unclear. Concerns exist that early oral intake would increase the incidence and severity of pneumonia and anastomotic leakage. However, in studies including patients after many other types of gastrointestinal surgery and in animal experiments, early oral intake has been shown to be beneficial and enhance recovery. Therefore, we aim to determine the feasibility of early oral intake after oesophagectomy.Methods and analysisThis study is a feasibility trial in which 50 consecutive patients will start oral intake directly following oesophagectomy. Primary outcomes will be the frequency and severity of anastomotic leakage and (aspiration) pneumonia. Clinical parameters will be registered prospectively and nutritional requirements and intake will be assessed by a dietician. Surgical complications will be registered.Ethics and disseminationApproval for this study has been obtained from the Medical Ethical Committee of the Catharina Hospital Eindhoven and the study has been registered at the Dutch Trial Register, NTR4136. Results will be published and presented at international congresses.DiscussionWe hypothesise that the oral route of feeding is safe and feasible following oesophagectomy, as has been shown previously for other types of gastrointestinal surgery. It is expected that early oral nutrition will result in enhanced recovery. Furthermore, complications related to artificial feeding, such as jejunostomy tube feeding, are believed to be reduced. However, (aspiration) pneumonia and anastomotic leakage are potential risks that are carefully monitored.Trial registration numberNTR4136.
An instrument for the assessment of diarrhoeal severity based on a longitudinal community-based study
Authors: Lee Gwenyth , Peñataro Yori Pablo , Paredes Olortegui Maribel , Caulfield Laura E , Sack David A , Fischer-Walker Christa , Black Robert E , Kosek Margaret 
Published: June 2014

ObjectiveDiarrhoea is a significant contributer to morbidity and is among the leading causes of death of children living in poverty. As such, the incidence, duration and severity of diarrhoeal episodes in the household are often key variables of interest in a variety of community-based studies. However, there currently exists no means of defining diarrhoeal severity that are (A) specifically designed and adapted for community-based studies, (B) associated with poorer child outcomes and (C) agreed on by the majority of researchers. Clinical severity scores do exist and are used in healthcare settings, but these tend to focus on relatively moderate-to-severe dehydrating and dysenteric disease, require trained observation of the child and, given the variability of access and utilisation of healthcare, fail to sufficiently describe the spectrum of disease in the community setting.DesignLongitudinal cohort study.SettingSanta Clara de Nanay, a rural community in the Northern Peruvian Amazon.Participants442 infants and children 0–72 months of age.Main outcome measuresChange in weight over 1-month intervals and change in length/height over 9-month intervals.ResultsDiarrhoeal episodes with symptoms of fever, anorexia, vomiting, greater number of liquid stools per day and greater number of total stools per day were associated with poorer weight gain compared with episodes without these symptoms. An instrument to measure the severity was constructed based on the duration of these symptoms over the course of a diarrhoeal episode.ConclusionsIn order to address limitations of existing diarrhoeal severity scores in the context of community-based studies, we propose an instrument comprised of diarrhoea-associated symptoms easily measured by community health workers and based on the association of these symptoms with poorer child growth. This instrument can be used to test the impact of interventions on the burden of diarrhoeal disease.
How weight change is modelled in population studies can affect research findings: empirical results from a large-scale cohort study
Authors: Paige E , Korda R J , Banks E , Rodgers B 
Published: June 2014

ObjectivesTo investigate how results of the association between education and weight change vary when weight change is defined and modelled in different ways.DesignLongitudinal cohort study.Participants60 404 men and women participating in the Social, Environmental and Economic Factors (SEEF) subcomponent of the 45 and Up Study—a population-based cohort study of people aged 45 years or older, residing in New South Wales, Australia.Outcome measuresThe main exposure was self-reported education, categorised into four groups. The outcome was annual weight change, based on change in self-reported weight between the 45 and Up Study baseline questionnaire and SEEF questionnaire (completed an average of 3.3 years later). Weight change was modelled in four different ways: absolute change (kg) modelled as (1) a continuous variable and (2) a categorical variable (loss, maintenance and gain), and relative (%) change modelled as (3) a continuous variable and (4) a categorical variable. Different cut-points for defining weight-change categories were also tested.ResultsWhen weight change was measured categorically, people with higher levels of education (compared with no school certificate) were less likely to lose or to gain weight. When weight change was measured as the average of a continuous measure, a null relationship between education and annual weight change was observed. No material differences in the education and weight-change relationship were found when comparing weight change defined as an absolute (kg) versus a relative (%) measure. Results of the logistic regression were sensitive to different cut-points for defining weight-change categories.ConclusionsUsing average weight change can obscure important directional relationship information and, where possible, categorical outcome measurements should be included in analyses.