bluuebunny/crossref_metadata_2025_split huggingface dataset:
Flow Characteristics of Porous Metal Structures for Specified Permeability Manufactured by Laser Beam Melting Technology
Authors: Benra F.-K. , Dohmen H. J. , Clauss S. , Sehrt J. T. , Witt G. 
Published: March 2015

The characteristic additive build-up at the laser beam melting technology provides the opportunity to freeform porous and defined structures at specific areas in one part. By adjusting the process parameters specific characteristics of the manufactured part such as density, permeability, pore size, porosity and shear strength can be realized. The manufacturing process of a test body is described in detail.
The permeability of the manufactured parts is investigated experimentally. In addition a numerical model is build and the flow structure inside of the test body is illustrated. The numerically obtained results are compared to the experimentally obtained results.
To show the advantages of this technology for future applications a numerical model of a porous blade surrounded by a hot gas flow and cooled from inside of the porous structure is investigated. The results show that the method to define the characteristics during the laser beam melting process has to be optimized.
Ion chamber absorbed dose calibration coefficients, ND,w, measured at ADCLs: Distribution analysis and stability
Authors: Muir B. R. 
Published: March 2015

Purpose:To analyze absorbed dose calibration coefficients, ND,w, measured at accredited dosimetry calibration laboratories (ADCLs) for client ionization chambers to study (i) variability among ND,w coefficients for chambers of the same type calibrated at each ADCL to investigate ion chamber volume fluctuations and chamber manufacturing tolerances; (ii) equivalency of ion chamber calibration coefficients measured at different ADCLs by intercomparing ND,w coefficients for chambers of the same type; and (iii) the long‐term stability of ND,w coefficients for different chamber types by investigating repeated chamber calibrations.Methods:Large samples of ND,w coefficients for several chamber types measured over the time period between 1998 and 2014 were obtained from the three ADCLs operating in the United States. These are analyzed using various graphical and numerical statistical tests for the four chamber types with the largest samples of calibration coefficients to investigate (i) and (ii) above. Ratios of calibration coefficients for the same chamber, typically obtained two years apart, are calculated to investigate (iii) above and chambers with standard deviations of old/new ratios less than 0.3% meet stability requirements for accurate reference dosimetry recommended in dosimetry protocols.Results:It is found that ND,w coefficients for a given chamber type compared among different ADCLs may arise from differing probability distributions potentially due to slight differences in calibration procedures and/or the transfer of the primary standard. However, average ND,w coefficients from different ADCLs for given chamber types are very close with percent differences generally less than 0.2% for Farmer‐type chambers and are well within reported uncertainties.Conclusions:The close agreement among calibrations performed at different ADCLs reaffirms the Calibration Laboratory Accreditation Subcommittee process of ensuring ADCL conformance with National Institute of Standards and Technology standards. This study shows that ND,w coefficients measured at different ADCLs are statistically equivalent, especially considering reasonable uncertainties. This analysis of ND,w coefficients also allows identification of chamber types that can be considered stable enough for accurate reference dosimetry.
Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps
Authors: Vigneron Adrien , L'Haridon Stéphane , Godfroy Anne , Roussel Erwan G. , Cragg Barry A. , Parkes R. John , Toffin Laurent 
Published: March 2015

ABSTRACT

In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
Integrated Cryptosporidium Assay To Determine Oocyst Density, Infectivity, and Genotype for Risk Assessment of Source and Reuse Water
Authors: King Brendon , Fanok Stella , Phillips Renae , Swaffer Brooke , Monis Paul 
Published: March 2015

ABSTRACT

Cryptosporidium
continues to be problematic for the water industry, with risk assessments often indicating that treatment barriers may fail under extreme conditions. However, risk analyses have historically used oocyst densities and not considered either oocyst infectivity or species/genotype, which can result in an overestimation of risk if the oocysts are not human infective. We describe an integrated assay for determining oocyst density, infectivity, and genotype from a single-sample concentrate, an important advance that overcomes the need for processing multiple-grab samples or splitting sample concentrates for separate analyses. The assay incorporates an oocyst recovery control and is compatible with standard primary concentration techniques. Oocysts were purified from primary concentrates using immunomagnetic separation prior to processing by an infectivity assay. Plate-based cell culture was used to detect infectious foci, with a monolayer washing protocol developed to allow recovery and enumeration of oocysts. A simple DNA extraction protocol was developed to allow typing of any wells containing infectious
Cryptosporidium
. Water samples from a variety of source water and wastewater matrices, including a semirural catchment, wastewater, an aquifer recharge site, and storm water, were analyzed using the assay. Results demonstrate that the assay can reliably determine oocyst densities, infectivity, and genotype from single-grab samples for a variety of water matrices and emphasize the varying nature of
Cryptosporidium
risk extant throughout source waters and wastewaters. This assay should therefore enable a more comprehensive understanding of
Cryptosporidium
risk for different water sources, assisting in the selection of appropriate risk mitigation measures.
Sharing a Host Plant (Wheat [Triticum aestivum]) Increases the Fitness of Fusarium graminearum and the Severity of Fusarium Head Blight but Reduces the Fitness of Grain Aphids (Sitobion avenae)
Authors: Drakulic Jassy , Caulfield John , Woodcock Christine , Jones Stephen P. T. , Linforth Robert , Bruce Toby J. A. , Ray Rumiana V. 
Published: March 2015

ABSTRACT

We hypothesized that interactions between fusarium head blight-causing pathogens and herbivores are likely to occur because they share wheat as a host plant. Our aim was to investigate the interactions between the grain aphid,
Sitobion avenae
, and
Fusarium graminearum
on wheat ears and the role that host volatile chemicals play in mediating interactions. Wheat ears were treated with aphids and
F. graminearum
inoculum, together or separately, and disease progress was monitored by visual assessment and by quantification of pathogen DNA and mycotoxins. Plants exposed to both aphids and
F. graminearum
inoculum showed accelerated disease progression, with a 2-fold increase in disease severity and 5-fold increase in mycotoxin accumulation over those of plants treated only with
F. graminearum
. Furthermore, the longer the period of aphid colonization of the host prior to inoculation with
F. graminearum
, the greater the amount of pathogen DNA that accumulated. Headspace samples of plant volatiles were collected for use in aphid olfactometer assays and were analyzed by gas chromatography-mass spectrometry (GC-MS) and GC-coupled electroantennography. Disease-induced plant volatiles were repellent to aphids, and 2-pentadecanone was the key semiochemical underpinning the repellent effect. We measured aphid survival and fecundity on infected wheat ears and found that both were markedly reduced on infected ears. Thus, interactions between
F. graminearum
and grain aphids on wheat ears benefit the pathogen at the expense of the pest. Our findings have important consequences for disease epidemiology, because we show increased spread and development of host disease, together with greater disease severity and greater accumulation of pathogen DNA and mycotoxin, when aphids are present.
Using Total Internal Reflection Fluorescence Microscopy To Visualize Rhodopsin-Containing Cells
Authors: Keffer J. L. , Sabanayagam C. R. , Lee M. E. , DeLong E. F. , Hahn M. W. , Maresca J. A. 
Published: March 2015

ABSTRACT

Sunlight is captured and converted to chemical energy in illuminated environments. Although (bacterio)chlorophyll-based photosystems have been characterized in detail, retinal-based photosystems, rhodopsins, have only recently been identified as important mediators of light energy capture and conversion. Recent estimates suggest that up to 70% of cells in some environments harbor rhodopsins. However, because rhodopsin autofluorescence is low—comparable to that of carotenoids and significantly less than that of (bacterio)chlorophylls—these estimates are based on metagenomic sequence data, not direct observation. We report here the use of ultrasensitive total internal reflection fluorescence (TIRF) microscopy to distinguish between unpigmented, carotenoid-producing, and rhodopsin-expressing bacteria.
Escherichia coli
cells were engineered to produce lycopene, β-carotene, or retinal. A gene encoding an uncharacterized rhodopsin, actinorhodopsin, was cloned into retinal-producing
E. coli
. The production of correctly folded and membrane-incorporated actinorhodopsin was confirmed via development of pink color in
E. coli
and SDS-PAGE. Cells expressing carotenoids or actinorhodopsin were imaged by TIRF microscopy. The 561-nm excitation laser specifically illuminated rhodopsin-containing cells, allowing them to be differentiated from unpigmented and carotenoid-containing cells. Furthermore, water samples collected from the Delaware River were shown by PCR to have rhodopsin-containing organisms and were examined by TIRF microscopy. Individual microorganisms that fluoresced under illumination from the 561-nm laser were identified. These results verify the sensitivity of the TIRF microscopy method for visualizing and distinguishing between different molecules with low autofluorescence, making it useful for analyzing natural samples.
Pseudomycoicidin, a Class II Lantibiotic from Bacillus pseudomycoides
Authors: Basi-Chipalu Shradha , Dischinger Jasmin , Josten Michaele , Szekat Christiane , Zweynert Annegret , Sahl Hans-Georg , Bierbaum Gabriele 
Published: March 2015

ABSTRACT

Lantibiotics are ribosomally synthesized antimicrobial peptides with substantial posttranslational modifications. They are characterized by the unique amino acids lanthionine and methyllanthionine, which are introduced by dehydration of Ser/Thr residues and linkage of the resulting dehydrated amino acids with Cys residues. BLAST searches using the mersacidin biosynthetic enzyme (MrsM) in the NCBI database revealed a new class II lantibiotic gene cluster in
Bacillus pseudomycoides
DSM 12442. Production of an antimicrobial substance with activity against Gram-positive bacteria was detectable in a cell wash extract of this strain. The substance was partially purified, and mass spectrometric analysis predicted a peptide of 2,786 Da in the active fraction. In order to characterize the putative lantibiotic further, heterologous expression of the predicted biosynthetic genes was performed in
Escherichia coli
. Coexpression of the prepeptide (PseA) along with the corresponding modification enzyme (PseM) resulted in the production of a modified peptide with the corresponding mass, carrying four out of eight possible dehydrations and supporting the presence of four thioether and one disulfide bridge. After the proteolytic removal of the leader, the core peptide exhibited antimicrobial activity. In conclusion, pseudomycoicidin is a novel lantibiotic with antimicrobial activity that was heterologously produced in
E. coli
.
Nitrite Control over Dissimilatory Nitrate/Nitrite Reduction Pathways in Shewanella loihica Strain PV-4
Authors: Yoon Sukhwan , Sanford Robert A. , Löffler Frank E. 
Published: March 2015

ABSTRACT

Shewanella loihica
strain PV-4 harbors both a functional denitrification (NO
3
−
→N
2
) and a respiratory ammonification (NO
3
−
→NH
4
+
) pathway. Batch and chemostat experiments revealed that NO
2
−
affects pathway selection and the formation of reduced products. Strain PV-4 cells grown with NO
2
−
as the sole electron acceptor produced exclusively NH
4
+
. With NO
3
−
as the electron acceptor, denitrification predominated and N
2
O accounted for ∼90% of reduced products in the presence of acetylene. Chemostat experiments demonstrated that the NO
2
−
:NO
3
−
ratio affected the distribution of reduced products, and respiratory ammonification dominated at high NO
2
−
:NO
3
−
ratios, whereas low NO
2
−
:NO
3
−
ratios favored denitrification. The NO
2
−
:NO
3
−
ratios affected
nirK
transcript abundance, a measure of denitrification activity, in the chemostat experiments, and cells grown at a NO
2
−
:NO
3
−
ratio of 3 had ∼37-fold fewer
nirK
transcripts per cell than cells grown with NO
3
−
as the sole electron acceptor. In contrast, the transcription of
nrfA
, implicated in NO
2
−
-to-NH
4
+
reduction, remained statistically unchanged under continuous cultivation conditions at NO
2
−
:NO
3
−
ratios below 3. At NO
2
−
:NO
3
−
ratios above 3, both
nirK
and
nrfA
transcript numbers decreased and the chemostat culture washed out, presumably due to NO
2
−
toxicity. These findings implicate NO
2
−
as a relevant modulator of NO
3
−
fate in
S. loihica
strain PV-4, and, by extension, suggest that NO
2
−
is a relevant determinant for N retention (i.e., ammonification) versus N loss and greenhouse gas emission (i.e., denitrification).
Organic Amendments to Avocado Crops Induce Suppressiveness and Influence the Composition and Activity of Soil Microbial Communities
Authors: Bonilla Nuria , Vida Carmen , Martínez-Alonso Maira , Landa Blanca B. , Gaju Nuria , Cazorla Francisco M. , de Vicente Antonio 
Published: March 2015

ABSTRACT

One of the main avocado diseases in southern Spain is white root rot caused by the fungus
Rosellinia necatrix
Prill. The use of organic soil amendments to enhance the suppressiveness of natural soil is an inviting approach that has successfully controlled other soilborne pathogens. This study tested the suppressive capacity of different organic amendments against
R. necatrix
and analyzed their effects on soil microbial communities and enzymatic activities. Two-year-old avocado trees were grown in soil treated with composted organic amendments and then used for inoculation assays. All of the organic treatments reduced disease development in comparison to unamended control soil, especially yard waste (YW) and almond shells (AS). The YW had a strong effect on microbial communities in bulk soil and produced larger population levels and diversity, higher hydrolytic activity and strong changes in the bacterial community composition of bulk soil, suggesting a mechanism of general suppression. Amendment with AS induced more subtle changes in bacterial community composition and specific enzymatic activities, with the strongest effects observed in the rhizosphere. Even if the effect was not strong, the changes caused by AS in bulk soil microbiota were related to the direct inhibition of
R. necatrix
by this amendment, most likely being connected to specific populations able to recolonize conducive soil after pasteurization. All of the organic amendments assayed in this study were able to suppress white root rot, although their suppressiveness appears to be mediated differentially.
Processing Environment and Ingredients Are Both Sources of Leuconostoc gelidum, Which Emerges as a Major Spoiler in Ready-To-Eat Meals
Authors: Pothakos Vasileios , Stellato Giuseppina , Ercolini Danilo , Devlieghere Frank 
Published: March 2015

ABSTRACT

Mesophilic and psychrotrophic organism viable counts, as well as high-throughput 16S rRNA gene-based pyrosequencing, were performed with the aim of elucidating the origin of psychrotrophic lactic acid bacteria (LAB) in a ready-to-eat (RTE) meal manufacturing plant. The microbial counts of the products at the end of the shelf life were greatly underestimated when mesophilic incubation was implemented due to overlooked, psychrotrophic members of the LAB.
Pseudomonas
spp.,
Enterobacteriaceae
,
Streptococcaceae
, and
Lactobacillus
spp. constituted the most widespread operational taxonomic units (OTUs), whereas
Leuconostoc
gelidum
was detected as a minor member of the indigenous microbiota of the food ingredients and microbial community of the processing environment, albeit it colonized samples at almost every sampling point on the premises. However,
L. gelidum
became the most predominant microbe at the end of the shelf life. The ability of
L. gelidum
to outgrow notorious, spoilage-related taxa like
Pseudomonas
,
Brochothrix
, and
Lactobacillus
underpins its high growth dynamics and severe spoilage character under refrigeration temperatures. The use of predicted metagenomes was useful for observation of putative gene repertoires in the samples analyzed in this study. The end products grouped in clusters characterized by gene profiles related to carbohydrate depletion presumably associated with a fast energy yield, a finding which is consistent with the fastidious nature of highly competitive LAB that dominated at the end of the shelf life. The present study showcases the detrimental impact of contamination with psychrotrophic LAB on the shelf life of packaged and cold-stored foodstuffs and the long-term quality implications for production batches once resident microbiota are established in the processing environment.
Phosphate Limitation Induces Drastic Physiological Changes, Virulence-Related Gene Expression, and Secondary Metabolite Production in Pseudovibrio sp. Strain FO-BEG1
Authors: Romano Stefano , Schulz-Vogt Heide N. , González José M. , Bondarev Vladimir 
Published: March 2015

ABSTRACT

Phosphorus is a vital nutrient for living organisms and is obtained by bacteria primarily via phosphate uptake. However, phosphate is often scarcely accessible in nature, and there is evidence that in many areas of the ocean, its concentration limits bacterial growth. Surprisingly, the phosphate starvation response has been extensively investigated in different model organisms (e.g.,
Escherichia coli
), but there is a dearth of studies on heterotrophic marine bacteria. In this work, we describe the response of
Pseudovibrio
sp. strain FO-BEG1, a metabolically versatile alphaproteobacterium and potential symbiont of marine sponges, to phosphate limitation. We compared the physiology, protein expression, and secondary metabolite production under phosphate-limited conditions to those under phosphate surplus conditions. We observed that phosphate limitation had a pleiotropic effect on the physiology of the strain, triggering cell elongation, the accumulation of polyhydroxyalkanoate, the degradation of polyphosphate, and the exchange of membrane lipids in favor of phosphorus-free lipids such as sulfoquinovosyl diacylglycerols. Many proteins involved in the uptake and degradation of phospho-organic compounds were upregulated, together with subunits of the ABC transport system for phosphate. Under conditions of phosphate limitation, FO-BEG1 secreted compounds into the medium that conferred an intense yellow coloration to the cultures. Among these compounds, we identified the potent antibiotic tropodithietic acid. Finally, toxin-like proteins and other proteins likely involved in the interaction with the eukaryotic host were also upregulated. Altogether, our data suggest that phosphate limitation leads to a pronounced reorganization of FO-BEG1 physiology, involving phosphorus, carbon, and sulfur metabolism; cell morphology; secondary metabolite production; and the expression of virulence-related genes.
Efficient Production of 2,5-Diketo-
d
-Gluconate via Heterologous Expression of 2-Ketogluconate Dehydrogenase in Gluconobacter japonicus
Authors: Kataoka Naoya , Matsutani Minenosuke , Yakushi Toshiharu , Matsushita Kazunobu 
Published: March 2015

ABSTRACT

2,5-Diketo-
d
-gluconate (2,5DKG) is a compound that can be the intermediate for
d
-tartrate and also vitamin C production. Although
Gluconobacter oxydans
NBRC3293 produces 2,5DKG from
d
-glucose via
d
-gluconate and 2-keto-
d
-gluconate (2KG), with accumulation of the product in the culture medium, the efficiency of 2,5DKG production is unsatisfactory because there is a large amount of residual
d
-gluconate at the end of the biotransformation process. Oxidation of 2KG to 2,5DKG is catalyzed by a membrane-bound flavoprotein-cytochrome
c
complex: 2-keto-gluconate dehydrogenase (2KGDH). Here, we studied the
kgdSLC
genes encoding 2KGDH in
G. oxydans
NBRC3293 to improve 2,5DKG production by
Gluconobacter
spp. The
kgdS
,
kgdL
, and
kgdC
genes correspond to the small, large, and cytochrome subunits of 2KGDH, respectively. The
kgdSLC
genes were cloned into a broad-host-range vector carrying a DNA fragment of the putative promoter region of the membrane-bound alcohol dehydrogenase gene of
G. oxydans
for expression in
Gluconobacter
spp. According to our results, 2KGDH that was purified from the recombinant
Gluconobacter
cells showed characteristics nearly the same as those reported previously. We also expressed the
kgdSLC
genes in a mutant strain of
Gluconobacter japonicus
NBRC3271 (formerly
Gluconobacter dioxyacetonicus
IFO3271) engineered to produce 2KG efficiently from a mixture of
d
-glucose and
d
-gluconate. This mutant strain consumed almost all of the starting materials (
d
-glucose and
d
-gluconate) to produce 2,5DKG quantitatively as a seemingly unique metabolite. To our knowledge, this is the first report of a
Gluconobacter
strain that produces 2,5DKG efficiently and homogeneously.