bluuebunny/crossref_metadata_2025_split huggingface dataset:
Blagovest Sendov – Pioneer of Mathematical Modeling in Bulgaria
Authors: Markov Svetoslav 
Published: December 2012

In February 2012 Prof. Blagovest Sendov turned 80. I first met him in 1963 as a student in mathematics at the Department of Physics and Mathematics of Sofia University. I was fascinated by his lectures in Numerical Methods. His first lecture was devoted to Mathematical modeling. On several realistic case studies Prof. Sendov revealed what was to me the philosophy of science.В . . .
“Candidatus Hepatobacter penaei,” an Intracellular Pathogenic Enteric Bacterium in the Hepatopancreas of the Marine Shrimp Penaeus vannamei (Crustacea: Decapoda)
Authors: Nunan Linda M. , Pantoja Carlos R. , Gomez-Jimenez Silvia , Lightner Donald V. 
Published: December 2012

ABSTRACT

The bacteria that cause necrotizing hepatopancreatitis in
Penaeus vannamei
adversely affect penaeid shrimp cultured in the western hemisphere. 16S rRNA and gyrase B gene analyses determined the taxonomic position of these bacteria. The name “
Candidatus
Hepatobacter penaei” is proposed for these pathogenic bacteria, which are members of the
Rickettsiales
order.
Novel Platform for the Detection of Staphylococcus aureus Enterotoxin B in Foods
Authors: Tallent Sandra M. , DeGrasse Jeffrey A. , Wang Ningyan , Mattis Daiva M. , Kranz David M. 
Published: December 2012

ABSTRACT

Staphylococcal contamination of food products and staphylococcal food-borne illnesses continue to be a problem worldwide. Screening of food for the presence of
Staphylococcus aureus
and/or enterotoxins using traditional methods is laborious. Reliable and rapid multiplex detection methods from a single food extract or culture supernatant would simplify testing. A fluorescence-based cytometric bead array was developed for the detection of staphylococcal enterotoxin B (SEB), using magnetic microspheres coupled with either an engineered, enterotoxin-specific Vβ domain of the T-cell receptor (Vβ-TCR) or polyclonal antibodies. The binding affinity of the Vβ-TCR for SEB has been shown to be in the picomolar range, comparable to the best monoclonal antibodies. The coupled beads were validated with purified enterotoxins and tested in a variety of food matrices spiked with enterotoxins. The Vβ-TCR or antibody was shown to specifically bind SEB in four different food matrices, including milk, mashed potatoes, vanilla pudding, and cooked chicken. The use of traditional polyclonal antibodies and Vβ-TCR provides a redundant system that ensures accurate identification of the enterotoxin, and the use of labeled microspheres permits simultaneous testing of multiple enterotoxins from a single sample.
Engineering of Corynebacterium glutamicum for High-Yieldl-Valine Production under Oxygen Deprivation Conditions
Authors: Hasegawa Satoshi , Suda Masako , Uematsu Kimio , Natsuma Yumi , Hiraga Kazumi , Jojima Toru , Inui Masayuki , Yukawa Hideaki 
Published: December 2012

ABSTRACTWe previously demonstrated efficientl-valine production by metabolically engineeredCorynebacterium glutamicumunder oxygen deprivation. To achieve the high productivity, a NADH/NADPH cofactor imbalance during the synthesis ofl-valine was overcome by engineering NAD-preferring mutant acetohydroxy acid isomeroreductase (AHAIR) and using NAD-specific leucine dehydrogenase fromLysinibacillus sphaericus. Lactate as a by-product was largely eliminated by disrupting the lactate dehydrogenase geneldhA. Nonetheless, a few other by-products, particularly succinate, were still produced and acted to suppress thel-valine yield. Eliminating these by-products therefore was deemed key to improving thel-valine yield. By additionally disrupting the phosphoenolpyruvate carboxylase geneppc, succinate production was effectively suppressed, but both glucose consumption andl-valine production dropped considerably due to the severely elevated intracellular NADH/NAD+ratio. In contrast, this perturbed intracellular redox state was more than compensated for by deletion of three genes associated with NADH-producing acetate synthesis and overexpression of five glycolytic genes, includinggapA, encoding NADH-inhibited glyceraldehyde-3-phosphate dehydrogenase. Inserting feedback-resistant mutant acetohydroxy acid synthase and NAD-preferring mutant AHAIR in the chromosome resulted in higherl-valine yield and productivity. Deleting the alanine transaminase geneavtAsuppressed alanine production. The resultant strain produced 1,280 mMl-valine at a yield of 88% mol mol of glucose−1after 24 h under oxygen deprivation, a vastly improved yield over our previous best.
Efficient Plant Biomass Degradation by Thermophilic Fungus Myceliophthora heterothallica
Authors: van den Brink Joost , van Muiswinkel Gonny C. J. , Theelen Bart , Hinz Sandra W. A. , de Vries Ronald P. 
Published: December 2012

ABSTRACT

Rapid and efficient enzymatic degradation of plant biomass into fermentable sugars is a major challenge for the sustainable production of biochemicals and biofuels. Enzymes that are more thermostable (up to 70°C) use shorter reaction times for the complete saccharification of plant polysaccharides compared to hydrolytic enzymes of mesophilic fungi such as
Trichoderma
and
Aspergillus
species. The genus
Myceliophthora
contains four thermophilic fungi producing industrially relevant thermostable enzymes. Within this genus, isolates belonging to
M. heterothallica
were recently separated from the well-described species
M. thermophila
. We evaluate here the potential of
M. heterothallica
isolates to produce efficient enzyme mixtures for biomass degradation. Compared to the other thermophilic
Myceliophthora
species, isolates belonging to
M. heterothallica
and
M. thermophila
grew faster on pretreated spruce, wheat straw, and giant reed. According to their protein profiles and
in vitro
assays after growth on wheat straw, (hemi-)cellulolytic activities differed strongly between
M. thermophila
and
M. heterothallica
isolates. Compared to
M. thermophila
,
M. heterothallica
isolates were better in releasing sugars from mildly pretreated wheat straw (with 5% HCl) with a high content of xylan. The high levels of residual xylobiose revealed that enzyme mixtures of
Myceliophthora
species lack sufficient β-xylosidase activity. Sexual crossing of two
M. heterothallica
showed that progenies had a large genetic and physiological diversity. In the future, this will allow further improvement of the plant biomass-degrading enzyme mixtures of
M. heterothallica
.
Distribution and Environmental Persistence of the Causative Agent of White-Nose Syndrome, Geomyces destructans, in Bat Hibernacula of the Eastern United States
Authors: Lorch Jeffrey M. , Muller Laura K. , Russell Robin E. , O'Connor Michael , Lindner Daniel L. , Blehert David S. 
Published: December 2012

ABSTRACT

White-nose syndrome (WNS) is an emerging disease of hibernating bats caused by the recently described fungus
Geomyces destructans
. First isolated in 2008, the origins of this fungus in North America and its ability to persist in the environment remain undefined. To investigate the correlation between manifestation of WNS and distribution of
G. destructans
in the United States, we analyzed sediment samples collected from 55 bat hibernacula (caves and mines) both within and outside the known range of WNS using a newly developed real-time PCR assay.
Geomyces destructans
was detected in 17 of 21 sites within the known range of WNS at the time when the samples were collected; the fungus was not found in 28 sites beyond the known range of the disease at the time when environmental samples were collected. These data indicate that the distribution of
G. destructans
is correlated with disease in hibernating bats and support the hypothesis that the fungus is likely an exotic species in North America. Additionally, we examined whether
G. destructans
persists in infested bat hibernacula when bats are absent. Sediment samples were collected from 14 WNS-positive hibernacula, and the samples were screened for viable fungus by using a culture technique. Viable
G. destructans
was cultivated from 7 of the 14 sites sampled during late summer, when bats were no longer in hibernation, suggesting that the fungus can persist in the environment in the absence of bat hosts for long periods of time.
Surface Orientation Affects the Direction of Cone Growth by Leptolyngbya sp. Strain C1, a Likely Architect of Coniform Structures Octopus Spring (Yellowstone National Park)
Authors: Reyes Kristina , Gonzalez Nicolas I. , Stewart Joshua , Ospino Frank , Nguyen Dickie , Cho David T. , Ghahremani Nahal , Spear John R. , Johnson Hope A. 
Published: December 2012

ABSTRACT

Laminated, microbially produced stromatolites within the rock record provide some of the earliest evidence for life on Earth. The chemical, physical, and biological factors that lead to the initiation of these organosedimentary structures and shape their morphology are unclear. Modern coniform structures with morphological features similar to stromatolites are found on the surface of cyanobacterial/microbial mats. They display a vertical element of growth, can have lamination, can be lithified, and observably grow with time. To begin to understand the microbial processes and interactions required for cone formation, we determined the phylogenetic composition of the microbial community of a coniform structure from a cyanobacterial mat at Octopus Spring, Yellowstone National Park, and reconstituted coniform structures
in vitro
. The 16S rRNA clone library from the coniform structure was dominated by
Leptolyngbya
sp. Other cyanobacteria and heterotrophic bacteria were present in much lower abundance. The same
Leptolyngbya
sp. identified in the clone library was also enriched in the laboratory and could produce cones
in vitro
. When coniform structures were cultivated in the laboratory, the initial incubation conditions were found to influence coniform morphology. In addition, both the angle of illumination and the orientation of the surface affected the angle of cone formation demonstrating how external factors can influence coniform, and likely, stromatolite morphology.
Transmission Dynamics of Bartonella sp. Strain OE 1-1 in Sundevall's Jirds (Meriones crassus)
Authors: Morick Danny , Krasnov Boris R. , Khokhlova Irina S. , Gottlieb Yuval , Harrus Shimon 
Published: December 2012

ABSTRACT

A high prevalence of
Bartonella
infection is found in many natural systems; however, the transmission dynamics leading to observations of these infections is not fully understood. The capability of
Xenopsylla ramesis
fleas to serve as competent vectors of
Bartonella
sp. OE 1-1 (a strain closely related to the zoonotic
Bartonella elizabethae
) to
Meriones crassus
jirds was investigated. Naïve
X. ramesis
fleas were placed for 72 h on naïve jirds or jirds that were either experimentally or naturally infected with
Bartonella
sp. strain OE 1-1, after which they were placed on naïve jirds. Postfeeding, 69 to 100% of the fleas collected from each
Bartonella
-positive jird contained
Bartonella
DNA, and all naïve jirds became positive for
Bartonella
sp. OE 1-1 after infestation with the infected fleas. In addition, maternal transmission of
Bartonella
sp. OE 1-1 in jirds was tested by mating 5
Bartonella
-positive and 5 naïve female jirds with 10 naïve male jirds in the absence of fleas. Fifteen offspring were delivered by each group. Cultures of blood drawn from all offspring on days 35 and 47 postdelivery were found to be negative for
Bartonella
. A single spleen sample from the offspring of a
Bartonella
-positive mother was found molecularly positive for
Bartonella
sp. OE 1-1. This study demonstrates that
X. ramesis
fleas are competent vectors of
Bartonella
sp. OE 1-1 to
M. crassus
jirds and indicates that maternal transmission is probably not the major transmission route from female jirds to their offspring. We suggest that the dynamics of
Bartonella
sp. OE 1-1 in the
M. crassus
jird population in nature is mostly dependent on its vectors.
Catabolism of Serine by Pediococcus acidilactici and Pediococcus pentosaceus
Authors: Irmler Stefan , Bavan Tharmatha , Oberli Andrea , Roetschi Alexandra , Badertscher René , Guggenbühl Barbara , Berthoud Hélène 
Published: December 2012

ABSTRACT

The ability to produce diacetyl from pyruvate and
l
-serine was studied in various strains of
Pediococcus pentosaceus
and
Pediococcus acidilactici
isolated from cheese. After being incubated on both substrates, only
P. pentosaceus
produced significant amounts of diacetyl. This property correlated with measurable serine dehydratase activity in cell extracts. A gene encoding the serine dehydratase (
dsdA
) was identified in
P. pentosaceus
, and strains that showed no serine dehydratase activity carried mutations that rendered the gene product inactive. A functional
dsdA
was cloned from
P. pentosaceus
FAM19132 and expressed in
Escherichia coli
. The purified recombinant enzyme catalyzed the formation of pyruvate from
l
- and
d
-serine and was active at low pH and elevated NaCl concentrations, environmental conditions usually present in cheese. Analysis of the amino acid profiles of culture supernatants from
dsdA
wild-type and
dsdA
mutant strains of
P. pentosaceus
did not show differences in serine levels. In contrast,
P. acidilactici
degraded serine. Moreover, this species also catabolized threonine and produced alanine and α-aminobutyrate.
Methanogens and Methanogenesis in the Rumens and Ceca of Lambs Fed Two Different High-Grain-Content Diets
Authors: Popova M. , Morgavi D. P. , Martin C. 
Published: December 2012

ABSTRACT

The amount and nature of dietary starch are known to influence the extent and site of feed digestion in ruminants. However, how starch degradability may affect methanogenesis and methanogens along the ruminant's digestive tract is poorly understood. This study examined the diversity and metabolic activity of methanogens in the rumen and cecum of lambs receiving wheat or corn high-grain-content diets. Methane production
in vivo
and
ex situ
was also monitored.
In vivo
daily methane emissions (CH
4
g/day) were 36% (
P
< 0.05) lower in corn-fed lambs than in wheat-fed lambs.
Ex situ
methane production (μmol/h) was 4-fold higher for ruminal contents than for cecal contents (
P
< 0.01), while methanogens were 10-fold higher in the rumen than in the cecum (
mcrA
copy numbers;
P
< 0.01). Clone library analysis indicated that
Methanobrevibacter
was the dominant genus in both sites. Diet induced changes at the species level, as the
Methanobrevibacter millerae-M. gottschalkii-M. smithii
clade represented 78% of the sequences from the rumen of wheat-fed lambs and just about 52% of the sequences from the rumen of the corn-fed lambs. Diet did not affect
mcrA
expression in the rumen. In the cecum, however, expression was 4-fold and 2-fold lower than in the rumen for wheat- and corn-fed lambs, respectively. Though we had no direct evidence for compensation of reduced rumen methane production with higher cecum methanogenesis, the ecology of methanogens in the cecum should be better considered.
Reconciliation of Sequence Data and Updated Annotation of the Genome of Agrobacterium tumefaciens C58, and Distribution of a Linear Chromosome in the Genus Agrobacterium
Authors: Slater Steven , Setubal João C. , Goodner Brad , Houmiel Kathryn , Sun Jian , Kaul Rajinder , Goldman Barry S. , Farrand Stephen K. , Almeida Nalvo , Burr Thomas , Nester Eugene , Rhoads David M. , Kadoi Ryosuke , Ostheimer Trucian , Pride Nicole , Sabo Allison , Henry Erin , Telepak Erin , Cromes Lindsey , Harkleroad Alana , Oliphant Louis , Pratt-Szegila Phil , Welch Roy , Wood Derek 
Published: December 2012

ABSTRACT

Two groups independently sequenced the
Agrobacterium tumefaciens
C58 genome in 2001. We report here consolidation of these sequences, updated annotation, and additional analysis of the evolutionary history of the linear chromosome, which is apparently limited to the biovar I group of
Agrobacterium
.
Use of a Novel Escherichia coli-Leuconostoc Shuttle Vector for Metabolic Engineering of Leuconostoc citreum To Overproduce
d
-Lactate
Authors: Chae Han Seung , Lee Seung Hwan , Lee Ju-Hoon , Park Si Jae , Lee Pyung Cheon 
Published: December 2012

ABSTRACT

Determination of the complete nucleotide sequence of a cryptic plasmid, pMBLT00, from
Leuconostoc mesenteroides
subsp.
mesenteroides
KCTC13302 revealed that it contains 20,721 bp, a G+C content of 38.7%, and 18 open reading frames. Comparative sequence and mung been nuclease analyses of pMBLT00 showed that pMBLT00 replicates via the theta replication mechanism. A new, stable
Escherichia coli-Leuconostoc
shuttle vector, pMBLT02, which was constructed from a theta-replicating pMBLT00 replicon and an erythromycin resistance gene of pE194, was successfully introduced into
Leuconostoc
,
Lactococcus lactis
, and
Pediococcus
. This shuttle vector was used to engineer
Leuconostoc citreum
95 to overproduce
d
-lactate. The
L. citreum
95 strain engineered using plasmid pMBLT02, which overexpresses
d
-lactate dehydrogenase, exhibited enhanced production of optically pure
d
-lactate (61 g/liter, which is 6 times greater than the amount produced by the control strain) when cultured in a reactor supplemented with 140 g/liter glucose. Therefore, the shuttle vector pMBLT02 can serve as a useful and stable plasmid vector for further development of a
d
-lactate overproduction system in other
Leuconostoc
strains and
Lactococcus lactis
.
Protective Mechanisms of Respiratory Tract Streptococci against Streptococcus pyogenes Biofilm Formation and Epithelial Cell Infection
Authors: Fiedler Tomas , Riani Catur , Koczan Dirk , Standar Kerstin , Kreikemeyer Bernd , Podbielski Andreas 
Published: December 2012

ABSTRACT

Streptococcus pyogenes
(group A streptococci [GAS]) encounter many streptococcal species of the physiological microbial biome when entering the upper respiratory tract of humans, leading to the question how GAS interact with these bacteria in order to establish themselves at this anatomic site and initiate infection. Here we show that
S. oralis
and
S. salivarius
in direct contact assays inhibit growth of GAS in a strain-specific manner and that
S. salivarius
, most likely via bacteriocin secretion, also exerts this effect in transwell experiments. Utilizing scanning electron microscopy documentation, we identified the tested strains as potent biofilm producers except for GAS M49. In mixed-species biofilms,
S. salivarius
dominated the GAS strains, while
S. oralis
acted as initial colonizer, building the bottom layer in mixed biofilms and thereby allowing even GAS M49 to form substantial biofilms on top. With the exception of
S. oralis
, artificial saliva reduced single-species biofilms and allowed GAS to dominate in mixed biofilms, although the overall two-layer structure was unchanged. When covered by
S. oralis
and
S. salivarius
biofilms, epithelial cells were protected from GAS adherence, internalization, and cytotoxic effects. Apparently, these species can have probiotic effects. The use of Affymetrix array technology to assess HEp-2 cell transcription levels revealed modest changes after exposure to
S. oralis
and
S. salivarius
biofilms which could explain some of the protective effects against GAS attack. In summary, our study revealed a protection effect of respiratory tract bacteria against an important airway pathogen and allowed a first
in vitro
insight into local environmental processes after GAS enter the respiratory tract.
Reducing Biogenic-Amine-Producing Bacteria, Decarboxylase Activity, and Biogenic Amines in Raw Milk Cheese by High-Pressure Treatments
Authors: Calzada Javier , del Olmo Ana , Picón Antonia , Gaya Pilar , Nuñez Manuel 
Published: December 2012

ABSTRACT
Biogenic amines may reach concentrations of public health concern in some cheeses. To minimize biogenic amine buildup in raw milk cheese, high-pressure treatments of 400 or 600 MPa for 5 min were applied on days 21 and 35 of ripening. On day 60, counts of lactic acid bacteria, enterococci, and lactobacilli were 1 to 2 log units lower in cheeses treated at 400 MPa and 4 to 6 log units lower in cheeses treated at 600 MPa than in control cheese. At that time, aminopeptidase activity was 16 to 75% lower in cheeses treated at 400 MPa and 56 to 81% lower in cheeses treated at 600 MPa than in control cheese, while the total free amino acid concentration was 35 to 53% higher in cheeses treated at 400 MPa and 3 to 15% higher in cheeses treated at 600 MPa, and decarboxylase activity was 86 to 96% lower in cheeses treated at 400 MPa and 93 to 100% lower in cheeses treated at 600 MPa. Tyramine, putrescine, and cadaverine were the most abundant amines in control cheese. The total biogenic amine concentration on day 60, which reached a maximum of 1.089 mg/g dry matter in control cheese, was 27 to 33% lower in cheeses treated at 400 MPa and 40 to 65% lower in cheeses treated at 600 MPa. On day 240, total biogenic amines attained a concentration of 3.690 mg/g dry matter in control cheese and contents 11 to 45% lower in cheeses treated at 400 MPa and 73 to 76% lower in cheeses treated at 600 MPa. Over 80% of the histidine and 95% of the tyrosine had been converted into histamine and tyramine in control cheese by day 60. Substrate depletion played an important role in the rate of biogenic amine buildup, becoming a limiting factor in the case of some amino acids.
Functional Gene Differences in Soil Microbial Communities from Conventional, Low-Input, and Organic Farmlands
Authors: Xue Kai , Wu Liyou , Deng Ye , He Zhili , Van Nostrand Joy , Robertson Philip G. , Schmidt Thomas M. , Zhou Jizhong 
Published: December 2012

ABSTRACT

Various agriculture management practices may have distinct influences on soil microbial communities and their ecological functions. In this study, we utilized GeoChip, a high-throughput microarray-based technique containing approximately 28,000 probes for genes involved in nitrogen (N)/carbon (C)/sulfur (S)/phosphorus (P) cycles and other processes, to evaluate the potential functions of soil microbial communities under conventional (CT), low-input (LI), and organic (ORG) management systems at an agricultural research site in Michigan. Compared to CT, a high diversity of functional genes was observed in LI. The functional gene diversity in ORG did not differ significantly from that of either CT or LI. Abundances of genes encoding enzymes involved in C/N/P/S cycles were generally lower in CT than in LI or ORG, with the exceptions of genes in pathways for lignin degradation, methane generation/oxidation, and assimilatory N reduction, which all remained unchanged. Canonical correlation analysis showed that selected soil (bulk density, pH, cation exchange capacity, total C, C/N ratio, NO
3
−
, NH
4
+
, available phosphorus content, and available potassium content) and crop (seed and whole biomass) variables could explain 69.5% of the variation of soil microbial community composition. Also, significant correlations were observed between NO
3
−
concentration and denitrification genes, NH
4
+
concentration and ammonification genes, and N
2
O flux and denitrification genes, indicating a close linkage between soil N availability or process and associated functional genes.