bluuebunny/crossref_metadata_2025_split huggingface dataset:
Understanding
Interior Ballistic Processes in a Flash Tube
Authors: Houim Ryan
W. , Kuo Kenneth
K. 
Published: October 2010

Abstract
Vented flash tubes have often been used in the ignition train of medium and large caliber weapon systems. Despite their long history of ballistic usage, there are undesirable features associated with uneven venting of the combustion products. Pressure measurements at various locations from the flash tube have shown severe variations with time, which is associated with spatially nonuniform mass discharging rate from the vent holes. Measured pressure profiles in the flash tube show counterintuitive, nonmonotonic pressure distributions with the lowest pressure in the middle of the venting section of the flash tube. A model of the flash tube venting process was developed to explain these phenomena using modern, high-order numerical schemes. Source terms accounting for mass addition from the black powder pellets, mass loss through the vent holes, wall friction, differential area changes, and volume changes from surface regression of black powder pellets were fully coupled in the model. The numerical results of this model reproduced the severe pressure variations and nonmonotonic pressure profiles observed in experiments. In general, they are caused by gas dynamic effects from a slowly moving normal shock wave in the middle portion of the venting section of the flash tube. As the driving pressure from the burning black powder pellets changes, the location of the normal shock wave jumps from one vent hole set to another, producing pressure variations observed in experiments. The physical understanding gained from this model solution has provided guidance for achieving more uniform mass discharging rate by varying the vent hole sizes as a function of distance along the flash tube.
Detection and Confirmation of
Clostridium botulinum
in Water Used for Cooling at a Plant Producing Low-Acid Canned Foods
Authors: Sachdeva Amita , Defibaugh-Chávez Stephanie L. H. , Day James B. , Zink Donald , Sharma Shashi K. 
Published: October 2010

ABSTRACT

Our laboratory tested water samples used for cooling low-acid canned foods at a canning facility under investigation by the U.S. Food and Drug Administration. We used an enzyme-linked immunosorbent assay with digoxigenin-labeled antibodies (DIG-ELISA) and real-time PCR as screening methods and confirmed the presence of neurotoxin-producing
Clostridium botulinum
in the samples by mouse bioassay.
Oxalate Efflux Transporter from the Brown Rot Fungus
Fomitopsis palustris
Authors: Watanabe Tomoki , Shitan Nobukazu , Suzuki Shiro , Umezawa Toshiaki , Shimada Mikio , Yazaki Kazufumi , Hattori Takefumi 
Published: October 2010

ABSTRACT

An oxalate-fermenting brown rot fungus,
Fomitopsis palustris
, secretes large amounts of oxalic acid during wood decay. Secretion of oxalic acid is indispensable for the degradation of wood cell walls, but almost nothing is known about the transport mechanism by which oxalic acid is secreted from
F. palustris
hyphal cells. We characterized the mechanism for oxalate transport using membrane vesicles of
F. palustris
. Oxalate transport in
F. palustris
was ATP dependent and was strongly inhibited by several inhibitors, such as valinomycin and NH
4
+
, suggesting the presence of a secondary oxalate transporter in this fungus. We then isolated a cDNA,
FpOAR
(

F

omitopsis

p

alustris
o
xalic
a
cid
r
esistance), from
F. palustris
by functional screening of yeast transformants with cDNAs grown on oxalic acid-containing plates. FpOAR is predicted to be a membrane protein that possesses six transmembrane domains but shows no similarity with known oxalate transporters. The yeast transformant possessing
FpOAR
(
FpOAR
-transformant) acquired resistance to oxalic acid and contained less oxalate than the control transformant. Biochemical analyses using membrane vesicles of the
FpOAR
-transformant showed that the oxalate transport property of FpOAR was consistent with that observed in membrane vesicles of
F. palustris
. The quantity of
FpOAR
transcripts was correlated with increasing oxalic acid accumulation in the culture medium and was induced when exogenous oxalate was added to the medium. These results strongly suggest that FpOAR plays an important role in wood decay by acting as a secondary transporter responsible for secretion of oxalate by
F. palustris
.
Wide Distribution among Halophilic Archaea of a Novel Polyhydroxyalkanoate Synthase Subtype with Homology to Bacterial Type III Synthases
Authors: Han Jing , Hou Jing , Liu Hailong , Cai Shuangfeng , Feng Bo , Zhou Jian , Xiang Hua 
Published: October 2010

ABSTRACTPolyhydroxyalkanoates (PHAs) are accumulated as intracellular carbon and energy storage polymers by various bacteria and a few haloarchaea. In this study, 28 strains belonging to 15 genera in the familyHalobacteriaceaewere investigated with respect to their ability to synthesize PHAs and the types of their PHA synthases. Fermentation results showed that 18 strains from 12 genera could synthesize polyhydroxybutyrate (PHB) or poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). For most of these haloarchaea, selected regions of thephaEandphaCgenes encoding PHA synthases (type III) were cloned via PCR with consensus-degenerate hybrid oligonucleotide primers (CODEHOPs) and were sequenced. The PHA synthases were also examined by Western blotting using haloarchaealHaloarcula marismortuiPhaC (PhaCHm) antisera. Phylogenetic analysis showed that the type III PHA synthases from species of theHalobacteriaceaeand theBacteriadomain clustered separately. Comparison of their amino acid sequences revealed that haloarchaeal PHA synthases differed greatly in both molecular weight and certain conserved motifs. The longer C terminus of haloarchaeal PhaC was found to be indispensable for its enzymatic activity, and two additional amino acid residues (C143 and C190) of PhaCHmwere proved to be important for itsin vivofunction. Thus, we conclude that a novel subtype (IIIA) of type III PHA synthase with unique features that distinguish it from the bacterial subtype (IIIB) is widely distributed in haloarchaea and appears to be involved in PHA biosynthesis.
Mixed-Culture Transcriptome Analysis Reveals the Molecular Basis of Mixed-Culture Growth in
Streptococcus thermophilus
and
Lactobacillus bulgaricus
Authors: Sieuwerts Sander , Molenaar Douwe , van Hijum Sacha A. F. T. , Beerthuyzen Marke , Stevens Marc J. A. , Janssen Patrick W. M. , Ingham Colin J. , de Bok Frank A. M. , de Vos Willem M. , van Hylckama Vlieg Johan E. T. 
Published: October 2010

ABSTRACT

Many food fermentations are performed using mixed cultures of lactic acid bacteria. Interactions between strains are of key importance for the performance of these fermentations. Yogurt fermentation by
Streptococcus thermophilus
and
Lactobacillus bulgaricus
(basonym,
Lactobacillus delbrueckii
subsp.
bulgaricus
) is one of the best-described mixed-culture fermentations. These species are believed to stimulate each other's growth by the exchange of metabolites such as folic acid and carbon dioxide. Recently, postgenomic studies revealed that an upregulation of biosynthesis pathways for nucleotides and sulfur-containing amino acids is part of the global physiological response to mixed-culture growth in
S. thermophilus
, but an in-depth molecular analysis of mixed-culture growth of both strains remains to be established. We report here the application of mixed-culture transcriptome profiling and a systematic analysis of the effect of interaction-related compounds on growth, which allowed us to unravel the molecular responses associated with batch mixed-culture growth in milk of
S. thermophilus
CNRZ1066 and
L. bulgaricus
ATCC BAA-365. The results indicate that interactions between these bacteria are primarily related to purine, amino acid, and long-chain fatty acid metabolism. The results support a model in which formic acid, folic acid, and fatty acids are provided by
S. thermophilus
. Proteolysis by
L. bulgaricus
supplies both strains with amino acids but is insufficient to meet the biosynthetic demands for sulfur and branched-chain amino acids, as becomes clear from the upregulation of genes associated with these amino acids in mixed culture. Moreover, genes involved in iron uptake in
S. thermophilus
are affected by mixed-culture growth, and genes coding for exopolysaccharide production were upregulated in both organisms in mixed culture compared to monocultures. The confirmation of previously identified responses in
S. thermophilus
using a different strain combination demonstrates their generic value. In addition, the postgenomic analysis of the responses of
L. bulgaricus
to mixed-culture growth allows a deeper understanding of the ecology and interactions of this important industrial food fermentation process.
Interference of
Mycoplasma
Infection in a Gene Expression Study: It Was the Environment and Not the Gene
Authors: Hoermann Gregor , Spergser Joachim , Einwallner Elisa , Makristathis Athanasios , Perne Andrea , Willinger Birgit , Schwarzinger Ilse 
Published: October 2010

ABSTRACT

We show that short-term exposure to doxycycline, as used in tetracycline-inducible gene expression models, protects cells from stress-induced death in cultures infected with
Mycoplasma arginini
. Coinciding with the expected maximum level of gene activity, antimicrobial effects of tetracyclines might be mistaken for antiapoptotic properties of the expressed gene product.
Evidence for Different Contributions of Archaea and Bacteria to the Ammonia-Oxidizing Potential of Diverse Oregon Soils
Authors: Taylor Anne E. , Zeglin Lydia H. , Dooley Sandra , Myrold David D. , Bottomley Peter J. 
Published: October 2010

ABSTRACT

A method was developed to determine the contributions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) to the nitrification potentials (NPs) of soils taken from forest, pasture, cropped, and fallowed (19 years) lands. Soil slurries were exposed to acetylene to irreversibly inactivate ammonia monooxygenase, and upon the removal of acetylene, the recovery of nitrification potential (RNP) was monitored in the presence and absence of bacterial or eukaryotic protein synthesis inhibitors. For unknown reasons, and despite measureable NPs, RNP did not occur consistently in forest soil samples; however, pasture, cropped, and fallowed soil RNPs commenced after lags that ranged from 12 to 30 h after acetylene removal. Cropped soil RNP was completely prevented by the bacterial protein synthesis inhibitor kanamycin (800 μg/ml), whereas a combination of kanamycin plus gentamicin (800 μg/ml each) only partially prevented the RNP (60%) of fallowed soils. Pasture soil RNP was completely insensitive to either kanamycin, gentamicin, or a combination of the two. Unlike cropped soil, pasture and fallowed soil RNPs occurred at both 30°C and 40°C and without supplemental NH
4
+
(≤10 μM NH
4
+
in solution), and pasture soil RNP demonstrated ∼50% insensitivity to 100 μM allyl thiourea (ATU). In addition, fallowed and pasture soil RNPs were insensitive to the fungal inhibitors nystatin and azoxystrobin. This combination of properties suggests that neither fungi nor AOB contributed to pasture soil RNP and that AOA were responsible for the RNP of the pasture soils. Both AOA and AOB may contribute to RNP in fallowed soil, while RNP in cropped soils was dominated by AOB.
Inhibition of Cellulase-Catalyzed Lignocellulosic Hydrolysis by Iron and Oxidative Metal Ions and Complexes
Authors: Tejirian Ani , Xu Feng 
Published: October 2010

ABSTRACT
Enzymatic lignocellulose hydrolysis plays a key role in microbially driven carbon cycling and energy conversion and holds promise for bio-based energy and chemical industries. Cellulases (key lignocellulose-active enzymes) are prone to interference from various noncellulosic substances (e.g., metal ions). During natural cellulolysis, these substances may arise from other microbial activities or abiotic events, and during industrial cellulolysis, they may be derived from biomass feedstocks or upstream treatments. Knowledge about cellulolysis-inhibiting reactions is of importance for the microbiology of natural biomass degradation and the development of biomass conversion technology. Different metal ions, including those native to microbial activity or employed for biomass pretreatments, are often tested for enzymatic cellulolysis. Only a few metal ions act as inhibitors of cellulases, which include ferrous and ferric ions as well as cupric ion. In this study, we showed inhibition by ferrous/ferric ions as part of a more general effect from oxidative (or redox-active) metal ions and their complexes. The correlation between inhibition and oxidation potential indicated the oxidative nature of the inhibition, and the dependence on air established the catalytic role that iron ions played in mediating the dioxygen inhibition of cellulolysis. Individual cellulases showed different susceptibilities to inhibition. It is likely that the inhibition exerted its effect more on cellulose than on cellulase. Strong iron ion chelators and polyethylene glycols could mitigate the inhibition. Potential microbiological and industrial implications of the observed effect of redox-active metal ions on enzymatic cellulolysis, as well as the prevention and mitigation of this effect in industrial biomass conversion, are discussed.
Participation of Valine 171 in α-Helix 5 of
Bacillus thuringiensis
Cry1Ab δ-Endotoxin in Translocation of Toxin into
Lymantria dispar
Midgut Membranes
Authors: Alzate Oscar , Osorio Cristina , Florez Alvaro M. , Dean Donald H. 
Published: October 2010

ABSTRACT

The Cry1Ab δ-endotoxin V171C mutant protein exhibits a 25-fold increase in toxicity against
Lymantria dispar
, which correlates with a faster rate of partitioning into the midgut membrane and slightly decreased protein stability. This is an insect-specific mechanism; similar results were not observed in
Manduca sexta
, another Cry1Ab δ-endotoxin-susceptible insect.
Comparison of the Pathogenic Potentials of Environmental and Clinical
Vibrio parahaemolyticus
Strains Indicates a Role for Temperature Regulation in Virulence
Authors: Mahoney Jennifer C. , Gerding Matthew J. , Jones Stephen H. , Whistler Cheryl A. 
Published: October 2010

ABSTRACT

Although the presence of pathogenic
Vibrio
spp. in estuarine environments of northern New England has been known for some time (C. H. Bartley and L. W. Slanetz, Appl. Microbiol. 21: 965-966, 1971, and K. R. O'Neil, S. H. Jones, and D. J. Grimes, FEMS Microbiol. Lett. 60:163-167, 1990), their virulence and the relative threat they may pose to human health has yet to be evaluated. In this study, the virulence potential of 33
Vibrio parahaemolyticus
isolates collected from the Great Bay Estuary of New Hampshire was assessed in comparison to that of clinical strains. The environmental isolates lack thermostable direct hemolysin (TDH) and TDH-related hemolysin (TRH), which are encoded by
tdh
and
trh
, respectively. Though not hemolytic, they do possess putative virulence factors, such type III secretion system 1, and are highly cytotoxic to human gastrointestinal cells. The expression of known and putative virulence-associated traits, including hemolysin, protease, motility, biofilm formation, and cytotoxicity, by clinical reference isolates correlated with increased temperature from 28°C to 37°C. In contrast, the environmental isolates did not induce their putative virulence-associated traits in response to a temperature of 37°C. We further identified a significant correlation between hemolytic activity and growth phase among clinical strains, whereby hemolysin production decreases with increasing cell density. The introduction of a
tdh
::
gfp
promoter fusion into the environmental strains revealed that they regulate this virulence-associated gene appropriately in response to temperature, indicating that their existing regulatory mechanisms are primed to manage newly acquired virulence genes.
Increased Ethanol Productivity in Xylose-Utilizing
Saccharomyces cerevisiae
via a Randomly Mutagenized Xylose Reductase
Authors: Runquist David , Hahn-Hägerdal Bärbel , Bettiga Maurizio 
Published: October 2010

ABSTRACT

Baker's yeast (
Saccharomyces cerevisiae
) has been genetically engineered to ferment the pentose sugar xylose present in lignocellulose biomass. One of the reactions controlling the rate of xylose utilization is catalyzed by xylose reductase (XR). In particular, the cofactor specificity of XR is not optimized with respect to the downstream pathway, and the reaction rate is insufficient for high xylose utilization in
S. cerevisiae.
The current study describes a novel approach to improve XR for ethanol production in
S. cerevisiae
. The cofactor binding region of XR was mutated by error-prone PCR, and the resulting library was expressed in
S. cerevisiae
. The
S. cerevisiae
library expressing the mutant XR was selected in sequential anaerobic batch cultivation. At the end of the selection process, a strain (TMB 3420) harboring the XR mutations N272D and P275Q was enriched from the library. The
V
max
of the mutated enzyme was increased by an order of magnitude compared to that of the native enzyme, and the NADH/NADPH utilization ratio was increased significantly. The ethanol productivity from xylose in TMB 3420 was increased ∼40 times compared to that of the parent strain (0.32 g/g [dry weight {DW}] × h versus 0.007 g/g [DW] × h), and the anaerobic growth rate was increased from ∼0 h
−1
to 0.08 h
−1
. The improved traits of TMB 3420 were readily transferred to the parent strain by reverse engineering of the mutated XR gene. Since integrative vectors were employed in the construction of the library, transfer of the improved phenotype does not require multicopy expression from episomal plasmids.
Importance of SigB for
Listeria monocytogenes
Static and Continuous-Flow Biofilm Formation and Disinfectant Resistance
Authors: van der Veen Stijn , Abee Tjakko 
Published: October 2010

ABSTRACT

Listeria monocytogenes
is a food-borne pathogen that is able to form biofilms in food processing facilities. Biofilms are generally more resistant to antimicrobial agents, making it difficult to eradicate them during cleanup procedures. So far, little is known about the function of stress resistance mechanisms in biofilm formation and their resistance to disinfectants. In this study, we investigated the role of
sigB
, which encodes a major transcriptional regulator of stress response genes, in
L. monocytogenes
static and continuous-flow biofilm formation and its function in the resistance of biofilm cells to the disinfectants benzalkonium chloride and peracetic acid. Quantitative real-time PCR and promoter reporter studies showed that
sigB
is activated in static and continuous-flow biofilms. Biofilm formation studies using an in-frame
sigB
deletion mutant and complementation mutant showed that the presence of SigB is required to obtain wild-type levels of both static and continuous-flow biofilms. Finally, disinfection treatments of planktonically grown cells and cells dispersed from static and continuous-flow biofilms showed that SigB is involved in the resistance of both planktonic cells and biofilms to the disinfectants benzalkonium chloride and peracetic acid.
Quantification of the Emetic Toxin Cereulide in Food Products by Liquid Chromatography-Mass Spectrometry Using Synthetic Cereulide as a Standard
Authors: Biesta-Peters Elisabeth G. , Reij Martine W. , Blaauw Richard H. , in ′t Veld Paul H. , Rajkovic Andreja , Ehling-Schulz Monika , Abee Tjakko 
Published: October 2010

ABSTRACT

Bacillus cereus
produces the emetic toxin cereulide, a cyclic dodecadepsipeptide that can act as a K
+
ionophore, dissipating the transmembrane potential in mitochondria of eukaryotic cells. Because pure cereulide has not been commercially available, cereulide content in food samples has been expressed in valinomycin equivalents, a highly similar cyclic potassium ionophore that is commercially available. This research tested the biological activity of synthetic cereulide and validated its use as a standard in the quantification of cereulide contents in food samples. The synthesis route consists of 10 steps that result in a high yield of synthetic cereulide that showed biological activity in the HEp-2 cell assay and the boar sperm motility assay. The activity is different in both methods, which may be attributed to differences in K
+
content of the test media used. Using cereulide or valinomycin as a standard to quantify cereulide based on liquid chromatography-mass spectrometry (LC-MS), the concentration determined with cereulide as a standard was on average 89.9% of the concentration determined using valinomycin as a standard. The recovery experiments using cereulide-spiked food products and acetonitrile as extraction solute showed that the LC-MS method with cereulide as a standard is a reliable and accurate method to quantify cereulide in food, because the recovery rate was close to 100% over a wide concentration range.
Surface Display of a Functional Minicellulosome by Intracellular Complementation Using a Synthetic Yeast Consortium and Its Application to Cellulose Hydrolysis and Ethanol Production
Authors: Tsai Shen-Long , Goyal Garima , Chen Wilfred 
Published: October 2010

ABSTRACT

In this paper, we report the surface assembly of a functional minicellulosome by using a synthetic yeast consortium. The basic design of the consortium consisted of four different engineered yeast strains capable of either displaying a trifunctional scaffoldin, Scaf-ctf (SC), carrying three divergent cohesin domains from
Clostridium thermocellum
(t),
Clostridium cellulolyticum
(c), and
Ruminococcus flavefaciens
(f), or secreting one of the three corresponding dockerin-tagged cellulases (endoglucanase [AT], exoglucanase [EC/CB], or β-glucosidase [BF]). The secreted cellulases were docked onto the displayed Scaf-ctf in a highly organized manner based on the specific interaction of the three cohesin-dockerin pairs employed, resulting in the assembly of a functional minicellulosome on the yeast surface. By exploiting the modular nature of each population to provide a unique building block for the minicellulosome structure, the overall cellulosome assembly, cellulose hydrolysis, and ethanol production were easily fine-tuned by adjusting the ratio of different populations in the consortium. The optimized consortium consisted of a SC:AT:CB:BF ratio of 7:2:4:2 and produced almost twice the level of ethanol (1.87 g/liter) as a consortium with an equal ratio of the different populations. The final ethanol yield of 0.475 g of ethanol/g of cellulose consumed also corresponded to 93% of the theoretical value. This result confirms the use of a synthetic biology approach for the synergistic saccharification and fermentation of cellulose to ethanol by using a yeast consortium displaying a functional minicellulosome.