bluuebunny/crossref_metadata_2025 huggingface dataset:
Incentives in a Stage‐Gate Process
Authors: Chao Raul O. , Lichtendahl Kenneth C. , Grushka‐Cockayne Yael
Published: August 2013

Many large organizations use a stage‐gate process to manage new product development projects. In a typical stage‐gate process project managers learn about potential ideas from research and exert effort in development while senior executives make intervening go/no‐go decisions. This decentralized decision making results in an agency problem because the idea quality in early stages is unknown to the executive and the project manager must exert unobservable development effort in later stages. In light of these challenges, how should the firm structure incentives to ensure that project managers reveal relevant information and invest the appropriate effort to create value? In this study, we develop a model of adverse selection in research and moral hazard in development with a go/no‐go decision at the intervening gate. Our results show that the principal's uncertainty regarding early‐stage idea quality—a term we refer to as idea risk—alters the effect of late‐stage development risk. The presence of idea risk can alter the incentives offered to the agent and may lead the principal to reject projects that otherwise seem favorable in terms of positive net present value. A simulation of early‐stage ideas, found through search on a complex landscape, shows that the firm can mitigate the negative effects of idea risk by encouraging breadth of search and high tolerance for failure.
Expression of Adrenergic Receptors in Bovine and Rabbit Oocytes and Preimplantation Embryos
Authors: Čikoš Š , Czikková S , Chrenek P , Makarevich AV , Burkuš J , Janštová Ž , Fabian D , Koppel J
Published: August 2013

Contents

Catecholamines play an important role in embryogenesis, and data obtained in the rodent model indicate that they can act even during the preimplantation period of development. Using RT‐PCR with specific oligonucleotide primers distinguishing among all members of the adrenergic receptor family, we examined expression of adrenergic receptors in bovine and rabbit oocytes, morulas and blastocysts. We found several profiles of adrenoceptor mRNA expression. Transcripts for some receptor subtypes (bovine alpha 2 receptors, rabbit α2A, α2C, β1 and β2 receptors) were detected at all examined stages, which suggests receptor expression throughout (or at most stages) the preimplantation developmental period. Expression in oocytes but not at later stages was found in only one adrenoceptor subtype (rabbit α1B). In contrast, mRNA for several adrenoceptors was found in embryos but not in oocytes (bovine beta adrenoceptors and rabbit α1A). Nucleotide sequences of our PCR products amplified in rabbit oocytes, and preimplantation embryos represent the first published mRNA sequences (partial sequences coding at least one transmembrane region) of rabbit α2C, β1 and β2 adrenoceptors. Our results suggest that the expression of adrenergic receptors can be a general feature of mammalian oocytes and preimplantation embryos. On the other hand, comparison of three mammalian species (cattle, rabbit and mouse) revealed possible interspecies differences in the expression of particular adrenoceptor subtypes. Our results support the opinion that stress mediators can act directly in cells of preimplantation embryos.
A new look at variance estimation based on low, high and closing prices taking into account the drift
Authors: Fiszeder Piotr , Perczak Grzegorz
Published: August 2013

The joint distribution of low, high and closing prices of the arithmetic Brownian motion is used to evaluate the properties of the most popular estimators of the variance constructed on the basis of high, low and closing prices. The expected values and mean square errors of the Parkinson, Garman–Klass and Rogers–Satchell estimators for the process with a zero drift and a non‐zero drift are derived. Moreover, new volatility estimators, more efficient in the majority of financial applications than the Rogers–Satchell estimator, are proposed. The considered estimators are applied to the estimation of the volatility of the Polish stock index WIG20.
Cutaneous Listeriosis in a Veterinarian with the Evidence of Zoonotic Transmission – A Case Report
Authors: Zelenik K. , Avberšek J. , Pate M. , Lušicky M. , Krt B. , Ocepek M. , Zdovc I.
Published: August 2013

A case of Listeria monocytogenes skin infection in a man is presented. A 54‐year‐old male veterinary practitioner developed pustular changes on the skin of arms and hands after assisting with the delivery of a stillborn calf. Listeria monocytogenes was isolated from the skin lesions on the arms and from the bovine placenta. Listeria monocytogenes isolates were serotyped and genotyped with pulsed‐field gel electrophoresis (PFGE) to confirm the suspected transmission of the pathogen from animal to human. All isolates were of serotype 4b with identical pulsotype. To the best of our knowledge, this is the first case of cutaneous listeriosis in which the evidence for zoonotic transmission of L. monocytogenes is supported by genotyping methods.
Differential vasomotor effects of insulin on gastrocnemius and soleus feed arteries in the OLETF rat model: role of endothelin‐1
Authors: Jenkins Nathan T. , Padilla Jaume , Martin Jeffrey S. , Crissey Jacqueline M. , Thyfault John P. , Rector R. Scott , Laughlin M. Harold
Published: August 2013

New findings

What is the central question of this study?

This study investigated the influence of obesity on insulin‐induced vasomotor reactivity in rat skeletal muscle feed arteries.

What is the main finding and its importance?

Irrespective of obesity, the gastrocnemius feed artery displayed diminished insulin‐induced vasodilatory response compared to the soleus feed artery. This difference between the arteries was abolished in the presence of an endothelin‐1 receptor antagonist. Therefore, our findings demonstrate that insulin‐induced endothelin‐1 production is not uniform among all skeletal muscle resistance vessels.

The vascular actions of insulin are complex, because it can stimulate both nitric oxide‐mediated dilatation and endothelin (ET)‐1‐mediated constriction. We examined vasoreactivity to insulin in isolated feed arteries of the gastrocnemius (GFA) and soleus muscles (SFA) of 32‐week‐old Long–Evans Tokushima Otsuka (LETO) and Otsuka Long–Evans Tokushima fatty (OLETF) rats, a hyperphagic rodent model of obesity and insulin resistance. The insulin‐induced vasoreactivity of SFA and GFA was similar in LETO (healthy) and OLETF (obese/insulin‐resistant) rats. However, examination of between‐vessel effects revealed a number of novel insights into the heterogeneous vascular effects of insulin. Soleus feed arteries dilated more than GFA in LETO at 100 and 1000 μIU ml−1 insulin (23 versus 6 and 28 versus 0%, respectively; P < 0.05 for between‐vessel differences). Likewise, in OLETF rats there was significantly greater dilatation in SFA than GFA at 10, 100 and 1000 μIU ml−1 insulin (28 versus 3, 30 versus 0 and 34 versus 0%, respectively; all P < 0.05). In the presence of 3 μm tezosentan, a non‐specific endothelin‐1 receptor blocker, insulin‐induced dilatation of the GFA was enhanced such that differences between vessels were largely abolished in both groups. Furthermore, acetylecholine‐induced dilatation was significantly greater in SFA than GFA within each group, whereas sodium nitroprusside‐induced dilatory responses were greater in the GFA compared with the SFA. Overall, our findings indicate that the insulin/endothelin‐1 vasoconstrictor pathway is more active in GFA than in SFA, independent of obesity in the OLETF rat model.
Autonomic control of the heart during exercise in humans: role of skeletal muscle afferents
Authors: Fisher James P.
Published: August 2013

New findings

What is the topic of this review?

The autonomic nervous system plays a key role in bringing about the cardiovascular responses to exercise necessitated by the increased metabolic requirements of the active skeletal muscle. The complex interaction of central and peripheral neural control mechanisms evokes a decrease in parasympathetic activity and an increase sympathetic activity to the heart during exercise.

What advances does it highlight?

This review presents some of the recent insights provided by human studies into the role of mechanically and metabolically sensitive skeletal muscle afferents in the regulation of cardiac autonomic control during exercise.

The autonomic responses to exercise are orchestrated by the interactions of several central and peripheral neural mechanisms. This report focuses on the role of peripheral feedback from skeletal muscle afferents in the autonomic control of the heart during exercise in humans. Heart rate responses to passive calf stretch are abolished with cardiac parasympathetic blockade, indicating that the activation of mechanically sensitive skeletal muscle afferents (muscle mechanoreceptors) can inhibit cardiac parasympathetic activity and is likely to contribute to the increase in heart rate at the onset of exercise. Recent experiments show that the partial restriction of blood flow to the exercising skeletal muscles, to augment the activation of metabolically sensitive skeletal muscle afferents (muscle metaboreceptors) in humans, evokes an increase in heart rate that is attenuated with β1‐adrenergic blockade, thus suggesting that this response is principally mediated via an increase in cardiac sympathetic activity. Heart rate remains at resting levels during isolated activation of muscle metaboreceptors with postexercise ischaemia following hand grip, unless cardiac parasympathetic activity is inhibited, whereupon a sympathetically mediated increase in heart rate is unmasked. During postexercise ischaemia following leg cycling exercise, heart rate appears to remain elevated due to withdrawal of parasympathetic tone and/or the activation of sympathetic activity to the heart. Although the importance of skeletal muscle afferent feedback to the autonomic control of the heart during exercise is incontrovertible, the complexity of cardiac sympathetic–parasympathetic interactions and the absence of direct intraneural recordings in humans mean that it remains incompletely understood.
Modeling Polysiloxane Volume and Viscosity Variations With Molecular Structure and Thermodynamic State
Authors: Zolper Thomas J. , Jungk Manfred , Marks Tobin J. , Chung Yip-Wah , Wang Qian
Published: August 2013

Siloxane-based polymers (polysiloxanes) exhibit a range of volume, viscosity, and pressure-viscosity behaviors that are strongly influenced by the macromolecular structure. In this report, a combination of extant rheological models is applied to develop a molecular-rheological modeling formalism that predicts polysiloxane rheological properties, such as specific volume, which means density, viscosity, and pressure-viscosity index variations with macromolecular structure, pressure, and temperature. Polysiloxane molecular features are described in terms of alkyl branch length L, pendant type J, density of branch functional monomers Q, and degree of polymerization DP. Both new and published data are used for model parameter determination and validation. Several siloxane-based polymers with alkyl, aryl, alkyl-aryl, cycloalkyl, and halogenated branches were synthesized to examine the modeled relationship between their molecular structures and rheological behaviors.
Variable-Length Link-Spring Model for Kink Formation During Wire Bonding
Authors: Wang Fuliang , Tang Weidong , Li Junhui , Han Lei
Published: August 2013

Kinks have a strong influence on the structural performance of wire bonds. In this study, a variable-length link-spring model has been developed to better understand kink formation. In this model, a gold wire was decomposed into segments that were represented by a link and a torsional spring. One end of the gold wire was fixed, and the other end was free. The friction and air tension forces at the wire ends were considered a function of the capillary position, and the wire segments and moment balance equations were added at the free end as the wire length increased. By using this model, the wire profile, moment, and curvature diagrams at the reverse motion stage were obtained to study the dynamical kink formation and wire-length increasing processes. The analysis result was verified experimentally. Good agreement is obtained between the analytical and the experimental wire profiles. This study indicates that a moment magnitude of several hundred mN·μm is required to form a kink, and the wire profile is the result of the residual curvature and the instantaneous bending moment.
Flows Through Real Porous Media: X-Ray Computed Tomography, Experiments, and Numerical Simulations
Authors: Breugem Wim-Paul , van Dijk Vincent , Delfos René
Published: August 2013

Two different direct-forcing immersed boundary methods (IBMs) were applied for the purpose of simulating slow flow through a real porous medium: the volume penalization IBM and the stress IBM. The porous medium was a random close packing of about 9000 glass beads in a round tube. The packing geometry was determined from an X-ray computed tomography (CT) scan in terms of the distribution of the truncated solid volume fraction (either 0 or 1) on a three-dimensional Cartesian grid. The scan resolution corresponded to 19.3 grid cells over the mean bead diameter. A facility was built to experimentally determine the permeability of the packing. Numerical simulations were performed for the same packing based on the CT scan data. For both IBMs the numerically determined permeability based on the Richardson extrapolation was just 10% lower than the experimentally found value. As expected, at finite grid resolution the stress IBM appeared to be the most accurate IBM.
Impact of Land Use on Arbuscular Mycorrhizal Fungal Communities in Rural Canada
Authors: Dai Mulan , Bainard Luke D. , Hamel Chantal , Gan Yantai , Lynch Derek
Published: August 2013

The influence of land use on soil bio-resources is largely unknown. We examined the communities of arbuscular mycorrhizal (AM) fungi in wheat-growing cropland, natural areas, and seminatural areas along roads. We sampled the Canadian prairie extensively (317 sites) and sampled 20 sites in the Atlantic maritime ecozone for comparison. The proportions of the different AM fungal taxa in the communities found at these sites varied with land use type and ecozones, based on pyrosequencing of 18S rRNA gene (rDNA) amplicons, but the lists of AM fungal taxa obtained from the different land use types and ecozones were very similar. In the prairie, the Glomeraceae family was the most abundant and diverse family of Glomeromycota, followed by the Claroideoglomeraceae, but in the Atlantic maritime ecozone, the Claroideoglomeraceae family was most abundant. In the prairie, species richness and Shannon's diversity index were highest in roadsides, whereas cropland had a higher degree of species richness than roadsides in the Atlantic maritime ecozone. The frequencies of occurrence of the different AM fungal taxa in croplands in the prairie and Atlantic maritime ecozones were highly correlated, but the AM fungal communities in these ecozones had different structures. We conclude that the AM fungal resources of soils are resilient to disturbance and that the richness of AM fungi under cropland management has been maintained, despite evidence of a structural shift imposed by this type of land use. Roadsides in the Canadian prairie are a good repository for the conservation of AM fungal diversity.
Gains of Bacterial Flagellar Motility in a Fungal World
Authors: Pion Martin , Bshary Redouan , Bindschedler Saskia , Filippidou Sevasti , Wick Lukas Y. , Job Daniel , Junier Pilar
Published: August 2013

The maintenance of energetically costly flagella by bacteria in non-water-saturated media, such as soil, still presents an evolutionary conundrum. Potential explanations have focused on rare flooding events allowing dispersal. Such scenarios, however, overlook bacterial dispersal along mycelia as a possible transport mechanism in soils. The hypothesis tested in this study is that dispersal along fungal hyphae may lead to an increase in the fitness of flagellated bacteria and thus offer an alternative explanation for the maintenance of flagella even in unsaturated soils. Dispersal along fungal hyphae was shown for a diverse array of motile bacteria. To measure the fitness effect of dispersal, additional experiments were conducted in a model system mimicking limited dispersal, usingPseudomonas putidaKT2440 and its nonflagellated (ΔfliM) isogenic mutant in the absence or presence ofMorchella crassipesmycelia. In the absence of the fungus, flagellar motility was beneficial solely under conditions of water saturation allowing dispersal, while under conditions limiting dispersal, the nonflagellated mutant exhibited a higher level of fitness than the wild-type strain. In contrast, in the presence of a mycelial network under conditions limiting dispersal, the flagellated strain was able to disperse using the mycelial network and had a higher level of fitness than the mutant. On the basis of these results, we propose that the benefit of mycelium-associated dispersal helps explain the persistence of flagellar motility in non-water-saturated environments.
From Green to Red: Horizontal Gene Transfer of the Phycoerythrin Gene Cluster between Planktothrix Strains
Authors: Tooming-Klunderud Ave , Sogge Hanne , Rounge Trine Ballestad , Nederbragt Alexander J. , Lagesen Karin , Glöckner Gernot , Hayes Paul K. , Rohrlack Thomas , Jakobsen Kjetill S.
Published: August 2013

Horizontal gene transfer is common in cyanobacteria, and transfer of large gene clusters may lead to acquisition of new functions and conceivably niche adaption. In the present study, we demonstrate that horizontal gene transfer between closely related
Planktothrix
strains can explain the production of the same oligopeptide isoforms by strains of different colors. Comparison of the genomes of eight
Planktothrix
strains revealed that strains producing the same oligopeptide isoforms are closely related, regardless of color. We have investigated genes involved in the synthesis of the photosynthetic pigments phycocyanin and phycoerythrin, which are responsible for green and red appearance, respectively. Sequence comparisons suggest the transfer of a functional phycoerythrin gene cluster generating a red phenotype in a strain that is otherwise more closely related to green strains. Our data show that the insertion of a DNA fragment containing the 19.7-kb phycoerythrin gene cluster has been facilitated by homologous recombination, also replacing a region of the phycocyanin operon. These findings demonstrate that large DNA fragments spanning entire functional gene clusters can be effectively transferred between closely related cyanobacterial strains and result in a changed phenotype. Further, the results shed new light on the discussion of the role of horizontal gene transfer in the sporadic distribution of large gene clusters in cyanobacteria, as well as the appearance of red and green strains.
Bifidobacterium animalis subsp. lactis ATCC 27673 Is a Genomically Unique Strain within Its Conserved Subspecies
Authors: Loquasto Joseph R. , Barrangou Rodolphe , Dudley Edward G. , Stahl Buffy , Chen Chun , Roberts Robert F.
Published: August 2013

Many strains of
Bifidobacterium animalis
subsp.
lactis
are considered health-promoting probiotic microorganisms and are commonly formulated into fermented dairy foods. Analyses of previously sequenced genomes of
B. animalis
subsp.
lactis
have revealed little genetic diversity, suggesting that it is a monomorphic subspecies. However, during a multilocus sequence typing survey of
Bifidobacterium
, it was revealed that
B. animalis
subsp.
lactis
ATCC 27673 gave a profile distinct from that of the other strains of the subspecies. As part of an ongoing study designed to understand the genetic diversity of this subspecies, the genome of this strain was sequenced and compared to other sequenced genomes of
B. animalis
subsp.
lactis
and
B. animalis
subsp.
animalis
. The complete genome of ATCC 27673 was 1,963,012 bp, contained 1,616 genes and 4 rRNA operons, and had a G+C content of 61.55%. Comparative analyses revealed that the genome of ATCC 27673 contained six distinct genomic islands encoding 83 open reading frames not found in other strains of the same subspecies. In four islands, either phage or mobile genetic elements were identified. In island 6, a novel clustered regularly interspaced short palindromic repeat (CRISPR) locus which contained 81 unique spacers was identified. This type I-E CRISPR-
cas
system differs from the type I-C systems previously identified in this subspecies, representing the first identification of a different system in
B. animalis
subsp.
lactis
. This study revealed that ATCC 27673 is a strain of
B. animalis
subsp.
lactis
with novel genetic content and suggests that the lack of genetic variability observed is likely due to the repeated sequencing of a limited number of widely distributed commercial strains.
Visualization of Imbalances in Sulfur Assimilation and Synthesis of Sulfur-Containing Amino Acids at the Single-Cell Level
Authors: Hoffmann Kristina , Grünberger Alexander , Lausberg Frank , Bott Michael , Eggeling Lothar
Published: August 2013

We describe genetically encoded sensors which transmit elevated cytosolic concentrations of O-acetyl serine (OAS) and O-acetyl homoserine (OAH)—intermediates of
l
-cysteine and
l
-methionine synthesis—into an optical output. The sensor pSenOAS3 elicits 7.5-fold-increased fluorescence in cultures of a
Corynebacterium glutamicum
strain that excrete
l
-cysteine. Determination of the cytosolic OAS concentration revealed an increase to 0.13 mM, whereas the concentration in the reference strain was below the detection limit, indicating that incorporation of assimilatory sulfur is limited in the strain studied. In another strain, overexpression of
metX
encoding homoserine acetyltransferase resulted in an 8-fold increase in culture fluorescence at a cytosolic OAH concentration of 0.76 mM. We also assayed for consequences of extracellular sulfur supply and observed a graded fluorescence increase at decreasing sulfur concentrations below 400 μM. Overall, this demonstrates the usefulness of the sensors for monitoring intracellular sulfur availability. The sensors also enable monitoring at the single-cell level, and since related and close homologs of the transcription factor used in the constructed sensors are widespread among bacteria, this technology offers a new possibility of assaying
in vivo
for sulfur limitation and of doing this at the single-cell level.
Phylogenetic and Chemical Diversity of a Hybrid-Isoprenoid-Producing Streptomycete Lineage
Authors: Gallagher Kelley A. , Rauscher Kristin , Pavan Ioca Laura , Jensen Paul R.
Published: August 2013

Streptomyces
species dedicate a large portion of their genomes to secondary metabolite biosynthesis. A diverse and largely marine-derived lineage within this genus has been designated MAR4 and identified as a prolific source of hybrid isoprenoid (HI) secondary metabolites. These terpenoid-containing compounds are common in nature but rarely observed as bacterial secondary metabolites. To assess the phylogenetic diversity of the MAR4 lineage, complementary culture-based and culture-independent techniques were applied to marine sediment samples collected off the Channel Islands, CA. The results, including those from an analysis of publically available sequence data and strains isolated as part of prior studies, placed 40 new strains in the MAR4 clade, of which 32 originated from marine sources. When combined with sequences cloned from environmental DNA, 28 MAR4 operational taxonomic units (0.01% genetic distance) were identified. Of these, 82% consisted exclusively of either cloned sequences or cultured strains, supporting the complementarity of these two approaches. Chemical analyses of diverse MAR4 strains revealed the production of five different HI structure classes. All 21 MAR4 strains tested produced at least one HI class, with most strains producing from two to four classes. The two major clades within the MAR4 lineage displayed distinct patterns in the structural classes and the number and amount of HIs produced, suggesting a relationship between taxonomy and secondary metabolite production. The production of HI secondary metabolites appears to be a phenotypic trait of the MAR4 lineage, which represents an emerging model with which to study the ecology and evolution of HI biosynthesis.
Effect of Electropermeabilization by Ohmic Heating for Inactivation of Escherichia coli O157:H7, Salmonella enterica Serovar Typhimurium, and Listeria monocytogenes in Buffered Peptone Water and Apple Juice
Authors: Park Il-Kyu , Kang Dong-Hyun
Published: August 2013

The effect of electric field-induced ohmic heating for inactivation of
Escherichia coli
O157:H7,
Salmonella enterica
serovar Typhimurium, and
Listeria monocytogenes
in buffered peptone water (BPW) (pH 7.2) and apple juice (pH 3.5; 11.8 °Brix) was investigated in this study. BPW and apple juice were treated at different temperatures (55°C, 58°C, and 60°C) and for different times (0, 10, 20, 25, and 30 s) by ohmic heating compared with conventional heating. The electric field strength was fixed at 30 V/cm and 60 V/cm for BPW and apple juice, respectively. Bacterial reduction resulting from ohmic heating was significantly different (
P
< 0.05) from that resulting from conventional heating at 58°C and 60°C in BPW and at 55°C, 58°C, and 60°C in apple juice for intervals of 0, 10, 20, 25, and 30 s. These results show that electric field-induced ohmic heating led to additional bacterial inactivation at sublethal temperatures. Transmission electron microscopy (TEM) observations and the propidium iodide (PI) uptake test were conducted after treatment at 60°C for 0, 10, 20, 25 and 30 s in BPW to observe the effects on cell permeability due to electroporation-caused cell damage. PI values when ohmic and conventional heating were compared were significantly different (
P
< 0.05), and these differences increased with increasing levels of inactivation of three food-borne pathogens. These results demonstrate that ohmic heating can more effectively reduce bacterial populations at reduced temperatures and shorter time intervals, especially in acidic fruit juices such as apple juice. Therefore, loss of quality can be minimized in a pasteurization process incorporating ohmic heating.
Probing the Functional Diversity of Global Pristine Soil Communities with 3-Chlorobenzoate Reveals that Communities of Generalists Dominate Catabolic Transformation
Authors: Rhodes Albert N. , Fulthorpe Roberta R. , Tiedje James M.
Published: August 2013

Understanding of functional diversity of microbial populations has lagged description of their molecular diversity. Differences in substrate specificity, kinetics, products, and regulation can dramatically influence phenotypic variation among closely related strains, features that are missed when the strains studied are the fastest-growing and most easily isolated from serial enrichments. To investigate the broader bacterial diversity underlying degradation of anthropogenic chemicals in nature, we studied the 3-chlorobenzoate (3-CBA) degradation rate in a collection of aerobic 3-CBA degraders previously isolated from undisturbed soils in two representative ecosystems: (i) Mediterranean sclerophyllous woodlands in California, Chile, South Africa, and Australia and (ii) boreal forests in Canada and Russia. The majority of isolates degraded 3-CBA slowly and did not completely mineralize 1.0 mM 3-CBA within 1 week. Those with intermediate degradation rates had incomplete degradation pathways and produced colored intermediates indicative of chlorocatechol, a product likely metabolized by other members of the community. About 10% of the isolates grew rapidly and mineralized greater than 90% of the 3-CBA, but because of population heterogeneity in soil, they are likely not large contributors to a soil's total transformation capacity. This suggests that xenobiotic degradation in nature is carried out by a community of cometabolic generalists and not by the efficient specialists that have been traditionally studied in the laboratory. A subset of 58 genotypically distinct strains able to degrade >80% of the 3-CBA was examined for their catabolic versatility using 45 different compounds: mono- and dichlorinated benzoates, phenols, anilines, toluenes, nitrobenzenes, chlorobenzenes, and 2,4-dichlorophenoxyacetic acid. The isolates degraded from 2 to more than 30 compounds with a median of 7, but there was no correlation to habitat of isolation or 3-CBA activity. However, these findings were indicative of finer-scale functional diversity.
The Genome of the Alga-Associated Marine Flavobacterium Formosa agariphila KMM 3901
T
Reveals a Broad Potential for Degradation of Algal Polysaccharides
Authors: Mann Alexander J. , Hahnke Richard L. , Huang Sixing , Werner Johannes , Xing Peng , Barbeyron Tristan , Huettel Bruno , Stüber Kurt , Reinhardt Richard , Harder Jens , Glöckner Frank Oliver , Amann Rudolf I. , Teeling Hanno
Published: August 2013

In recent years, representatives of the
Bacteroidetes
have been increasingly recognized as specialists for the degradation of macromolecules.
Formosa
constitutes a
Bacteroidetes
genus within the class
Flavobacteria
, and the members of this genus have been found in marine habitats with high levels of organic matter, such as in association with algae, invertebrates, and fecal pellets. Here we report on the generation and analysis of the genome of the type strain of
Formosa agariphila
(KMM 3901
T
), an isolate from the green alga
Acrosiphonia sonderi
.
F. agariphila
is a facultative anaerobe with the capacity for mixed acid fermentation and denitrification. Its genome harbors 129 proteases and 88 glycoside hydrolases, indicating a pronounced specialization for the degradation of proteins, polysaccharides, and glycoproteins. Sixty-five of the glycoside hydrolases are organized in at least 13 distinct polysaccharide utilization loci, where they are clustered with TonB-dependent receptors, SusD-like proteins, sensors/transcription factors, transporters, and often sulfatases. These loci play a pivotal role in bacteroidetal polysaccharide biodegradation and in the case of
F. agariphila
revealed the capacity to degrade a wide range of algal polysaccharides from green, red, and brown algae and thus a strong specialization of toward an alga-associated lifestyle. This was corroborated by growth experiments, which confirmed usage particularly of those monosaccharides that constitute the building blocks of abundant algal polysaccharides, as well as distinct algal polysaccharides, such as laminarins, xylans, and κ-carrageenans.
Cloning and Heterologous Expression of the Thioviridamide Biosynthesis Gene Cluster from Streptomyces olivoviridis
Authors: Izawa Masumi , Kawasaki Takashi , Hayakawa Yoichi
Published: August 2013

Thioviridamide is a unique peptide antibiotic containing five thioamide bonds from
Streptomyces olivoviridis
. Draft genome sequencing revealed a gene (the
tvaA
gene) encoding the thioviridamide precursor peptide. The thioviridamide biosynthesis gene cluster was identified by heterologous production of thioviridamide in
Streptomyces lividans
.
An Improved PCR-Restriction Fragment Length Polymorphism (RFLP) Method for the Identification of
cry1
-Type Genes
Authors: Shu Changlong , Liu Dongming , Zhou Zishan , Cai Jilin , Peng Qi , Gao Jiguo , Song Fuping , Zhang Jie
Published: August 2013

The
cry1
-type genes of
Bacillus thuringiensis
represent the largest
cry
gene family, which contains 50 distinct holotypes. It is becoming more and more difficult to identify
cry1
-type genes using current methods because of the increasing number of
cry1
-type genes. In the present study, an improved PCR-restriction fragment length polymorphism (PCR-RFLP) method which can distinguish 41 holotypes of
cry1
-type genes was developed. This improved method was used to identify
cry1
-type genes in 20
B. thuringiensis
strains that are toxic to lepidoptera. The results showed that the improved method can efficiently identify single and clustered
cry1
-type genes and can be used to evaluate
cry1
-type genes in novel strain collections of
B. thuringiensis
. Among the detected
cry1
-type genes, we identified four novel genes,
cry1Ai
,
cry1Bb
,
cry1Ja
, and
cry1La
. The bioassay results from the expressed products of the four novel
cry
genes showed that Cry1Ai2, Cry1Bb2, and Cry1Ja2 were highly toxic against
Plutella xylostella
, whereas Cry1La2 exhibited no activity. Moreover, Cry1Ai2 had good lethal activity against
Ostrinia furnacalis
,
Hyphantria cunea
,
Chilo suppressalis
, and
Bombyx mori
larvae and considerable weight loss activity against
Helicoverpa armigera
.
Pseudoalteromonas spp. Serve as Initial Bacterial Attractants in Mesocosms of Coastal Waters but Have Subsequent Antifouling Capacity in Mesocosms and when Embedded in Paint
Authors: Bernbom Nete , Ng Yoke Yin , Olsen Stefan Møller , Gram Lone
Published: August 2013

The purpose of the present study was to determine if the monoculture antifouling effect of several pigmented pseudoalteromonads was retained in
in vitro
mesocosm systems using natural coastal seawater and when the bacteria were embedded in paint used on surfaces submerged in coastal waters.
Pseudoalteromonas piscicida
survived on a steel surface and retained antifouling activity for at least 53 days in sterile seawater, whereas
P. tunicata
survived and had antifouling activity for only 1 week. However, during the first week, all
Pseudoalteromonas
strains facilitated rather than prevented bacterial attachment when used to coat stainless steel surfaces and submerged in mesocosms with natural seawater. The bacterial density on surfaces coated with sterile growth medium was 10
5
cells/cm
2
after 7 days, whereas counts on surfaces precoated with
Pseudoalteromonas
were significantly higher, at 10
6
to 10
8
cells/cm
2
. However, after 53 days, seven of eight
Pseudoalteromonas
strains had reduced total bacterial adhesion compared to the control.
P. piscicida
,
P. antarctica
, and
P. ulvae
remained on the surface, at levels similar to those in the initial coating, whereas
P. tunicata
could not be detected. Larger fouling organisms were observed on all plates precoated with
Pseudoalteromonas
; however, plates coated only with sterile growth medium were dominated by a bacterial biofilm. Suspensions of a
P. piscicida
strain and a
P. tunicata
strain were incorporated into ship paints (Hempasil x3 87500 and Hempasil 77500) used on plates that were placed at the Hempel A/S test site in Jyllinge Harbor. For the first 4 months, no differences were observed between control plates and treated plates, but after 5 to 6 months, the control plates were more fouled than the plates with pseudoalteromonad-based paint. Our study demonstrates that no single laboratory assay can predict antifouling effects and that a combination of laboratory and real-life methods must be used to determine the potential antifouling capability of new agents or organisms.
Development of Fatty Acid-Producing Corynebacterium glutamicum Strains
Authors: Takeno Seiki , Takasaki Manami , Urabayashi Akinobu , Mimura Akinori , Muramatsu Tetsuhiro , Mitsuhashi Satoshi , Ikeda Masato
Published: August 2013

To date, no information has been made available on the genetic traits that lead to increased carbon flow into the fatty acid biosynthetic pathway ofCorynebacterium glutamicum. To develop basic technologies for engineering, we employed an approach that begins by isolating a fatty acid-secreting mutant without depending on mutagenic treatment. This was followed by genome analysis to characterize its genetic background. The selection of spontaneous mutants resistant to the palmitic acid ester surfactant Tween 40 resulted in the isolation of a desired mutant that produced oleic acid, suggesting that a single mutation would cause increased carbon flow down the pathway and subsequent excretion of the oversupplied fatty acid into the medium. Two additional rounds of selection of spontaneous cerulenin-resistant mutants led to increased production of the fatty acid in a stepwise manner. Whole-genome sequencing of the resulting best strain identified three specific mutations (fasR20,fasA63up, andfasA2623). Allele-specific PCR analysis showed that the mutations arose in that order. Reconstitution experiments with these mutations revealed that onlyfasR20gave rise to oleic acid production in the wild-type strain. The other two mutations contributed to an increase in oleic acid production. Deletion offasRfrom the wild-type strain led to oleic acid production as well. Reverse transcription-quantitative PCR analysis revealed that thefasR20mutation brought about upregulation of thefasAandfasBgenes encoding fatty acid synthases IA and IB, respectively, by 1.31-fold ± 0.11-fold and 1.29-fold ± 0.12-fold, respectively, and of theaccD1gene encoding the β-subunit of acetyl-CoA carboxylase by 3.56-fold ± 0.97-fold. On the other hand, thefasA63upmutation upregulated thefasAgene by 2.67-fold ± 0.16-fold. In flask cultivation with 1% glucose, thefasR20 fasA63upfasA2623triple mutant produced approximately 280 mg of fatty acids/liter, which consisted mainly of oleic acid (208 mg/liter) and palmitic acid (47 mg/liter).
Transcriptional Response of the Archaeal Ammonia Oxidizer Nitrosopumilus maritimus to Low and Environmentally Relevant Ammonia Concentrations
Authors: Nakagawa Tatsunori , Stahl David A.
Published: August 2013

The ability of chemoautotrophic ammonia-oxidizing archaea to compete for ammonia among marine microorganisms at low ambient concentrations has been in part attributed to their extremely high affinity for ammonia, but as yet there is no mechanistic understanding of supporting metabolism. We examined transcription of selected genes for anabolic functions (CO
2
fixation, ammonia transport, and cell wall synthesis) and a central catabolic function (ammonia oxidation) in the thaumarchaeon
Nitrosopumilus maritimus
SCM1 growing at two ammonia concentrations, as measured by combined ammonia and ammonium, one well above the

K
m

for ammonia oxidation (∼500 μM) and the other well below the

K
m

(<10 nM). Transcript levels were generally immediately and differentially repressed when cells transitioned from ammonia-replete to ammonia-limiting conditions. Transcript levels for ammonia oxidation, CO
2
fixation, and one of the ammonia transport genes were approximately the same at high and low ammonia availability. Transcripts for all analyzed genes decreased with time in the complete absence of ammonia, but with various rates of decay. The new steady-state mRNA levels established are presumably more reflective of the natural physiological state of ammonia-oxidizing archaea and offer a reference for interpreting message abundance patterns in the natural environment.
Structural Features of Sugars That Trigger or Support Conidial Germination in the Filamentous Fungus Aspergillus niger
Authors: Hayer Kimran , Stratford Malcolm , Archer David B.
Published: August 2013

The asexual spores (conidia) of
Aspergillus niger
germinate to produce hyphae under appropriate conditions. Germination is initiated by conidial swelling and mobilization of internal carbon and energy stores, followed by polarization and emergence of a hyphal germ tube. The effects of different pyranose sugars, all analogues of
d
-glucose, on the germination of
A. niger
conidia were explored, and we define germination as the transition from a dormant conidium into a germling. Within germination, we distinguish two distinct stages, the initial swelling of the conidium and subsequent polarized growth. The stage of conidial swelling requires a germination trigger, which we define as a compound that is sensed by the conidium and which leads to catabolism of
d
-trehalose and isotropic growth. Sugars that triggered germination and outgrowth included
d
-glucose,
d
-mannose, and
d
-xylose. Sugars that triggered germination but did not support subsequent outgrowth included
d
-tagatose,
d
-lyxose, and 2-deoxy-
d
-glucose. Nontriggering sugars included
d
-galactose,
l
-glucose, and
d
-arabinose. Certain nontriggering sugars, including
d
-galactose, supported outgrowth if added in the presence of a complementary triggering sugar. This division of functions indicates that sugars are involved in two separate events in germination, triggering and subsequent outgrowth, and the structural features of sugars that support each, both, or none of these events are discussed. We also present data on the uptake of sugars during the germination process and discuss possible mechanisms of triggering in the absence of apparent sugar uptake during the initial swelling of conidia.
Substrate-Induced Transcriptional Activation of the MoCel7C Cellulase Gene Is Associated with Methylation of Histone H3 at Lysine 4 in the Rice Blast Fungus Magnaporthe oryzae
Authors: Vu Ba Van , Pham Kieu Thi Minh , Nakayashiki Hitoshi
Published: August 2013

The mechanisms involved in substrate-dependent regulation of a
Magnaporthe oryzae
gene encoding a cellulase which we designate MoCel7C (MGG_14954) were investigated. The levels of MoCel7C transcript were dramatically increased more than 1,000-fold, 16 to 24 h after transfer to a medium containing 2% carboxymethylcellulose (CMC), while levels were very low or undetectable in conventional rich medium. Green fluorescent protein reporter assays showed that the MoCel7C promoter was activated by cello-oligosaccharides larger than a pentamer. CMC-induced activation of the MoCel7C promoter was suppressed by glucose and cellobiose. Chromatin immunoprecipitation assays revealed that histone H3 methylation on lysine 4 (H3K4) at the MoCel7C locus was associated with activation of the gene by CMC. Consistently, CMC-induced MoCel7C gene activation was drastically diminished in a knockout (KO) mutant of the MoSET1 gene, which encodes a histone lysine methyltransferase that catalyzes H3K4 methylation in
M. oryzae
. Interestingly, however, MoCel7C transcript levels under noninducing conditions were significantly increased in the MoSET1 KO mutant, suggesting that MoSET1 directly or indirectly plays a role in both activation and suppression of the MoCel7C gene in response to environmental signals. In addition, gene expression and silencing vectors using the MoCel7C promoter were constructed.
Arabinoxylan Oligosaccharide Hydrolysis by Family 43 and 51 Glycosidases from Lactobacillus brevis DSM 20054
Authors: Michlmayr Herbert , Hell Johannes , Lorenz Cindy , Böhmdorfer Stefan , Rosenau Thomas , Kneifel Wolfgang
Published: August 2013

Due to their potential prebiotic properties, arabinoxylan-derived oligosaccharides [(A)XOS] are of great interest as functional food and feed ingredients. While the (A)XOS metabolism of
Bifidobacteriaceae
has been extensively studied, information regarding lactic acid bacteria (LAB) is still limited in this context. The aim of the present study was to fill this important gap by characterizing candidate (A)XOS hydrolyzing glycoside hydrolases (GHs) identified in the genome of
Lactobacillus brevis
DSM 20054. Two putative GH family 43 xylosidases (XynB1 and XynB2) and a GH family 43 arabinofuranosidase (Abf3) were heterologously expressed and characterized. While the function of XynB1 remains unclear, XynB2 could efficiently hydrolyze xylooligosaccharides. Abf3 displayed high specific activity for arabinobiose but could not release arabinose from an (A)XOS preparation. However, two previously reported GH 51 arabinofuranosidases from
Lb. brevis
were able to specifically remove α-1,3-linked arabinofuranosyl residues from arabino-xylooligosaccharides (AXHm3 specificity). These results imply that
Lb. brevis
is at least genetically equipped with functional enzymes in order to hydrolyze the depolymerization products of (arabino)xylans and arabinans. The distribution of related genes in
Lactobacillales
genomes indicates that GH 43 and, especially, GH 51 glycosidase genes are rare among LAB and mainly occur in obligately heterofermentative
Lactobacillus
spp.,
Pediococcus
spp., members of the
Leuconostoc/Weissella
branch, and
Enterococcus
spp. Apart from the prebiotic viewpoint, this information also adds new perspectives on the carbohydrate (i.e., pentose-oligomer) metabolism of LAB species involved in the fermentation of hemicellulose-containing substrates.
Diversity and Ecophysiology of New Isolates of Extremely Acidophilic CS
2
-Converting Acidithiobacillus Strains
Authors: Smeulders Marjan J. , Pol Arjan , Zandvoort Marcel H. , Jetten Mike S. M. , Op den Camp Huub J. M.
Published: August 2013

Biofiltration of industrial carbon disulfide (CS
2
)-contaminated waste air streams results in the acidification of biofilters and therefore reduced performance, high water use, and increased costs. To address these issues, we isolated 16 extremely acidophilic CS
2
-converting
Acidithiobacillus thiooxidans
strains that tolerated up to 6% (vol/vol) sulfuric acid. The ecophysiological properties of five selected strains (2Bp, Sts 4-3, S1p, G8, and BBW1) were compared. These five strains had pH optima between 1 (2Bp) and 2 (S1p). Their affinities for CS
2
ranged between 80 (G8) and 130 (2Bp) μM. Strains S1p, G8, and BBW1 had more hydrophobic cell surfaces and produced less extracellular polymeric substance than did strains 2Bp and Sts 4-3. All five strains converted about 80% of the S added as CS
2
to S
0
when CS
2
was supplied in excess. The rate of S
0
consumption varied between 7 (Sts 4-3) and 63 (S1p) nmol O
2
min
−1
ml culture
−1
. Low S
0
consumption rates correlated partly with low levels of cell attachment to externally produced S
0
globules. During chemostat growth, the relative amount of CS
2
hydrolase in the cell increased with decreasing growth rates. This resulted in more S
0
accumulation during CS
2
overloads at low growth rates. Intermittent interruptions of the CS
2
supply affected all five strains. Strains S1p, G8, and BBW1 recovered from 24 h of starvation within 4 h, and strains 2Bp and Sts 4-3 recovered within 24 h after CS
2
was resupplied. We recommend the use of mixtures of
Acidithiobacillus
strains in industrial biofilters.
Novel Mono-, Di-, and Trimethylornithine Membrane Lipids in Northern Wetland Planctomycetes
Authors: Moore Eli K. , Hopmans Ellen C. , Rijpstra W. Irene C. , Villanueva Laura , Dedysh Svetlana N. , Kulichevskaya Irina S. , Wienk Hans , Schoutsen Frans , Sinninghe Damsté Jaap S.
Published: August 2013

Northern peatlands represent a significant global carbon store and commonly originate from
Sphagnum
moss-dominated wetlands. These ombrotrophic ecosystems are rain fed, resulting in nutrient-poor, acidic conditions. Members of the bacterial phylum
Planctomycetes
are highly abundant and appear to play an important role in the decomposition of
Sphagnum
-derived litter in these ecosystems. High-performance liquid chromatography coupled to high-resolution accurate-mass mass spectrometry (HPLC-HRAM/MS) analysis of lipid extracts of four isolated planctomycetes from wetlands of European north Russia revealed novel ornithine membrane lipids (OLs) that are mono-, di-, and trimethylated at the ε-nitrogen position of the ornithine head group. Nuclear magnetic resonance (NMR) analysis of the isolated trimethylornithine lipid confirmed the structural identification. Similar fatty acid distributions between mono-, di-, and trimethylornithine lipids suggest that the three lipid classes are biosynthetically linked, as in the sequential methylation of the terminal nitrogen in phosphatidylethanolamine to produce phosphatidylcholine. The mono-, di-, and trimethylornithine lipids described here represent the first report of methylation of the ornithine head groups in biological membranes. Various bacteria are known to produce OLs under phosphorus limitation or fatty-acid-hydroxylated OLs under thermal or acid stress. The sequential methylation of OLs, leading to a charged choline-like moiety in the trimethylornithine lipid head group, may be an adaptation to provide membrane stability under acidic conditions without the use of scarce phosphate in nutrient-poor ombrotrophic wetlands.