bluuebunny/crossref_metadata_2025 huggingface dataset:
Temporal, spatial and ecological dynamics of speciation among amphi‐Beringian small mammals
Authors: Hope Andrew G. , Takebayashi Naoki , Galbreath Kurt E. , Talbot Sandra L. , Cook Joseph A.
Published: December 2012

Aim

Quaternary climate cycles played an important role in promoting diversification across the Northern Hemisphere, although details of the mechanisms driving evolutionary change are still poorly resolved. In a comparative phylogeographical framework, we investigate temporal, spatial and ecological components of evolution within a suite of Holarctic small mammals. We test a hypothesis of simultaneous divergence among multiple taxon pairs, investigating time to coalescence and demographic change for each taxon in response to a combination of climate and geography.

Location

Beringia, the nexus of the northern continents.

Methods

We used approximate Bayesian computation methods to test for simultaneous divergence among eight pairs of taxa, using cytochrome b gene sequences. We calculated coalescence times for eastern and western components of each pair and for the combined pairs, and relate dates to Quaternary climatic periodicity and combinations of environmental events and physical barriers. Population growth and expansion statistics were used to test evolutionary responses among taxa, including range shifts, persistence or periodic extirpation. Species distribution models (SDMs) for each taxon were used to predict their geographical ranges during the present interglacial, Last Glacial Maximum and previous interglacial.

Results

Multiple divergence events across Beringia were primarily coincident with extreme glacial cycles of the late Quaternary. Structure within Beringia is spatially consistent with at least three environmental barriers arising at different times: the Kolyma Uplands, Bering Strait and portions of the Bering Isthmus. Levels of divergence varied substantially, indicating evolutionary processes spanning deep and shallow time‐scales. The different demographics among taxa reflect their distinct ecological responses. SDMs predicted regional distributional changes through time and different spatial responses among taxa.

Main conclusions

Beringia predominantly constituted a dispersal corridor during the early Quaternary and a major centre of endemism in the late Quaternary. Coincident with severe glacial cycles, small mammal species were ‘caught’ in Beringia and diversified over multiple climatic phases. Relative genetic differentiation across Beringia appears to be related to ecological differences reflecting a gradual adaptation to Beringian environments through time. Some methodological constraints associated with resolving recent (late Quaternary) isolation events or drawing inferences from a single locus are discussed.
Characteristics of Porphyromonas gingivalis lipopolysaccharide in co‐culture with Fusobacterium nucleatum
Authors: Lee S.H. , Baek D.H.
Published: December 2012

Porphyromonas gingivalis is associated with chronic periodontitis and forms multi‐species biofilms. They can communicate within species as well as with other species found in the subgingiva, which may induce changes in the growth ratio and virulence of periodontopathogens. The lipopolysaccharide (LPS) of P. gingivalis shows different virulence by growth condition. The purpose of this study was to investigate the characteristics of P. gingivalis LPS when co‐cultured with Fusobacterium nucleatum. After culture of P. gingivalis in the presence or absence of F. nucleatum, P. gingivalis LPS was extracted. THP‐1 cells were treated with the LPS and induction of cytokine expression was investigated using real‐time reverse transcription polymerase chain reaction (RT‐PCR) and enzyme‐linked immunosorbent assay (ELISA). For the analysis of P. gingivalis LPS, LPS biosynthesis‐related genes such as lpxA and lpxD were evaluated with real‐time RT‐PCR. Finally, molecular mass of lipid A was measured by mass spectrometry after hydrolysis of the LPS. Co‐cultured P. gingivalis LPS exhibited higher induction of expression of interleukin 1β, 6, and 8 than single‐cultured P. gingivalis LPS. These symptoms may be caused by an increase in m/z 1689 lipid A through the upregulation of lpxA and lpxD expression by communication between P. gingivalis and F. nucleatum.
Minimal models for rational functions in a dynamical setting
Authors: Bruin Nils , Molnar Alexander
Published: December 2012

We present a practical algorithm to compute models of rational functions with minimal resultant under conjugation by fractional linear transformations. We also report on a search for rational functions of degrees 2 and 3 with rational coefficients that have many integers in a single orbit. We find several minimal quadratic rational functions with eight integers in an orbit and several minimal cubic rational functions with ten integers in an orbit. We also make some elementary observations on possibilities of an analogue of Szpiro’s conjecture in a dynamical setting and on the structure of the set of minimal models for a given rational function.
Intracerebroventricular losartan infusion modulates angiotensin II type 1 receptor expression in the subfornical organ and drinking behaviour in bile‐duct‐ligated rats
Authors: Walch Joseph D. , Carreño Flávia Regina , Cunningham J. Thomas
Published: December 2012

New Findings

What is the central question of this study?

Dilutional hyponatraemia increases morbidity and mortality associated with heart or liver failure. Vasopressin release and increased fluid intake contribute to hyposmolality, but the underlying mechanisms are poorly understood. Our study tests the role of the central renin–angiotensin system in hyposmolality in a rat model of liver failure.

What is the main finding and its importance?

Hepatic cirrhosis produced hyposmolality, with increased water intake and increased angiotensin receptors in the subfornical organ, a forebrain circumventricular organ. Central infusions of the angiotensin receptor blocker losartan normalized both water intake and the increase in angiotensin receptors. However, the rats remained hyposmotic, suggesting a selective role for the central renin–angiotensin system.

Bile duct ligation (BDL) causes congestive liver failure that initiates haemodynamic changes, including peripheral vasodilatation and generalized oedema. Peripheral vasodilatation is hypothesized to activate compensatory mechanisms, including increased drinking behaviour and neurohumoral activation. This study tested the hypothesis that changes in the expression of angiotensin II type 1 receptor (AT1R) mRNA and protein in the lamina terminalis are associated with BDL‐induced hyposmolality in the rat. All rats received either BDL or sham‐ligation surgery. The rats were housed in metabolic chambers for measurement of fluid and food intake and urine output. Expression of AT1R in the lamina terminalis was assessed by Western blot and quantitative real‐time PCR (RT‐qPCR). Average baseline water intake increased significantly in BDL rats compared with sham‐operated rats, and upregulation of AT1R protein and AT1aR mRNA were observed in the subfornical organ of BDL rats. Separate groups of BDL and sham‐ligated rats were instrumented with minipumps filled with either losartan (2.0 μg μl−1) or 0.9% saline for chronic intracerebroventricular or chronic subcutaneous infusion. Chronic intracerebroventricular losartan infusion attenuated the increased drinking behaviour and prevented the increased abundance of AT1R protein in the subfornical organ in BDL rats. Chronic subcutaneous infusion did not affect water intake or AT1R abundance in the subfornical organ. The data presented here indicate a possible role of increased central AT1R expression in the regulation of drinking behaviour during congestive cirrhosis.
Modeling of Viral Dynamics after Liver Transplantation in Patients with Chronic Hepatitis B and D
Authors: Filmann Natalie , Herrmann Eva
Published: December 2012

Viral kinetic models have become an important tool for understanding the main biological processes behind the dynamics of chronic viral diseases and optimizing effectiveness of anti-viral therapy. We analyzed the dynamics of hepatitis B and D co-infection (HBV/HDV) and the pharmacokinetics/pharmacodynamics of the reinfection prophylaxis with polyclonal antibodies after liver transplantation. Therefore we developed a mechanistic model consisting of a system of ordinary differential equations. This model was fitted by analyzing the kinetics of HBV/HDV viremia after liver transplantation in patient data and correlated with the reinfection prophylaxis dosing schemes. The results suggest that this modeling approach may help to optimize reinfection prophylaxis.
Exploring Family Relations between International Patent Applications
Authors: Hingley Peter
Published: December 2012

In the international system for granting patents for inventions, first patent filings can be followed by subsequent filings at other patent offices within one year. Each such group of related filings constitutes a patent family. Tests are developed as to whether the observed number of first filings that leads to subsequent filings (r) is in agreement with a random process of assignment of the hits from the subsequent filings. An exact expression for the random distribution can be used for small sized data sets. Its behaviour and also the behaviour of an asymptotic Poisson approximation as well as a censored binomial distribution for r are assessed. The approach is stimulated by the Fisher-Wright model in population genetics and possible parallel applications to other biological processes are sought, such as transformations of stem cells and cancer.
Model and Simulations of a Wood Frog Population
Authors: Al-Asuoad Nofe , Anguelov Roumen , Berven Keith , Shillor Meir
Published: December 2012

This work presents and simulates a mathematical model В for the dynamics of a population of Wood Frogs. The model consists of a system of five coupled impulsive differential equations for the larvae, juveniles (early, middle, and late) and the mature adult populations. A simulation result depicts possible dynamics of the frogs' population when during one year the larvae population dies out. This provides a tool for the study of the resilience of the population and the conditions that may lead to its survival and flourishing or extinction.
Constructing One-Dimensional Continuous Models from Two-Dimensional Discrete Models of Medical Implants
Authors: Prieto-Langarica Alicia , Kojouharov Hristo V , Tang Liping
Published: December 2012

Medically implanted devices are becoming increasingly important in medical practice. Over 4 million people in the United States have long-term biomedical implants. However, many medical implants have to be removed because of infection or because their protein coating causes excessive inflammation and decrease in the immune system response. In this work, a discrete two-dimensional model of blood cells and bacteria interactions on the surface of a medical implant is transformed into a discrete one-dimensional model. This one-dimensional model is then upscaled into a partial differential equation model. The results from the discrete two-dimensional model and the continuous one-dimensional model are then compared for different protein coating mixtures. Two medical treatment alternatives are also explored and the two models are compared again.
An Upstream Finite Volume Scheme for a Bone Healing Model
Authors: Uzureau Alexandre , Coudiere Yves , Saad Mazen
Published: December 2012

This paper is devoted to the introduction of a numerical scheme for a bone healing model and simulation of skull fractures. The mathematical model describes the evolution of mesenchymal stem cells, osteoblasts, bone matrix and osteogenic growth factor. WeВ propose a numerical scheme based on an implicit finite volume method constructed on an orthogonal mesh. The efficiency and robustness of the scheme are shown in simulating a skull fracture in rats.
Structure of the Global Attractors in a Model for Ectoparasite Borne Diseases
Authors: Dénes Attila , Röst Gergely
Published: December 2012

We delineate a mathematical model for the dynamics of the spread of ectoparasites and the diseases transmitted by them. We present how the dynamics of the system depends on the three reproduction numbers belonging to three of the four possible equilibria and give a complete characterization of the structure of the global attractor in each possible case depending on the reproduction numbers.
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  . . .
From the Guest Editor
Authors: Markov Svetoslav
Published: December 2012

The BIOMATH 2012 International Conference on Mathematical Methods and Models in Biosciences was held at the Academy of Sciences in Sofia, Bulgaria, in June 17–22, 2012, http://www.biomath.bg/2012/. We were happy to meet more than 70 participants from twenty different countries. More than 40 contributions were submitted for publication in the present BIOMATH proceedings.
Ontology-Based Knowledge Representation for Obsolescence Forecasting
Authors: Zheng Liyu , Nelson Raymond , Terpenny Janis , Sandborn Peter
Published: December 2012

The impact and pervasiveness of diminishing manufacturing sources and material shortages (DMSMS) obsolescence are increasing due to rapidly advancing technologies which shorten the procurement lives of high-tech parts. For long field-life systems, this has led to an increasing disparity in the life cycle of parts as compared to the life cycle of the overall system. This disparity is challenging since obsolescence dates of parts are important to product life cycle planning. While proposed obsolescence forecasting methods have demonstrated some effectiveness, obsolescence management is a continuing challenge since current methods are very difficult to integrate with other tools and lack clear, complete, and consistent information representation. This paper presents an ontology framework to support the needs of knowledge representation for obsolescence forecasting. The formalized obsolescence forecasting method is suitable for products with a life cycle that can be represented with a Gaussian distribution. Classical product life cycle models can be represented using the logic of ontological constructs. The forecasted life cycle curve and zone of obsolescence are obtained by fitting sales data with the Gaussian distribution. Obsolescence is forecasted by executing semantic queries. The knowledge representation for obsolescence forecasting is realized using web ontology language (OWL) and semantic web rule language (SWRL) in the ontology editor Protégé-OWL. A flash memory example is included to demonstrate the obsolescence forecasting procedure. Discussion of future work is included with a focus on extending the ontology beyond the initial representation for obsolescence forecasting to a comprehensive knowledge representation scheme and management system that can facilitate information sharing and collaboration for obsolescence management.
“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

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

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

We 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

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

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

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

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

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

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

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

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

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

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

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.
Mechanisms of Human Adenovirus Inactivation by Sunlight and UVC Light as Examined by Quantitative PCR and Quantitative Proteomics
Authors: Bosshard Franziska , Armand Florence , Hamelin Romain , Kohn Tamar
Published: December 2012

Human adenoviruses (HAdV) are important pathogens in both industrialized and developing nations. HAdV has been shown to be relatively resistant to monochromatic UVC light. Polychromatic UVC light, in contrast, is a more effective means of disinfection, presumably due to the involvement of viral proteins in the inactivation mechanism. Solar disinfection of HAdV, finally, is only poorly understood. In this paper, the kinetics and mechanism of HAdV inactivation by UVC light and direct and indirect solar disinfection are elucidated. PCR and mass spectrometry were employed to quantify the extent of genome and protein degradation and to localize the affected regions in the HAdV proteins. For this purpose, we used for the first time an approach involving stable isotope labeling by amino acids in cell culture (SILAC) of a human virus. Inactivation by UVC light and the full sunlight spectrum were found to efficiently inactivate HAdV, whereas UVA-visible light only caused inactivation in the presence of external sensitizers (indirect solar disinfection). Genome damage was significant for UVC but was less important for solar disinfection. In contrast, indirect solar disinfection exhibited extensive protein degradation. In particular, the fiber protein and the amino acids responsible for host binding within the fiber protein were shown to degrade. In addition, the central domain of the penton protein was damaged, which may inhibit interactions with the fiber protein and lead to a disruption of the initial stages of infection. Damage to the hexon protein, however, appeared to affect only regions not directly involved in the infectious cycle.
Heterologous Expression of a Bioactive β-Hexosyltransferase, an Enzyme Producer of Prebiotics, from Sporobolomyces singularis
Authors: Dagher Suzanne F. , Azcarate-Peril M. Andrea , Bruno-Bárcena José M.
Published: December 2012

Galacto-oligosaccharides (GOS) are indigestible dietary fibers that are able to reach the lower gastrointestinal tract to be selectively fermented by health-promoting bacteria. In this report, we describe the heterologous expression of an optimized synthetically produced version of the β-hexosyltransferase gene (Bht) fromSporobolomyces singularis. TheBhtgene encodes a glycosyl hydrolase (EC 3.2.1.21) that acts as galactosyltransferase, able to catalyze a one-step conversion of lactose to GOS. Expression of the enzyme inEscherichia coliyielded an inactive insoluble protein, while the methylotrophic yeastPichia pastorisGS115 produced a bioactive β-hexosyltransferase (rBHT). The enzyme exhibited faster kinetics at pHs between 3.5 and 6 and at temperatures between 40 and 50°C. Enzyme stability improved at temperatures lower than 40°C, and glucose was found to be a competitive inhibitor of enzymatic activity.P. pastorissecreted a fraction of the bioactive rBHT into the fermentation broth, while the majority of the enzyme remained associated with the outer membrane. Both the secreted and the membrane-associated forms were able to efficiently convert lactose to GOS. Additionally, resting cells with membrane-bound enzyme converted 90% of the initial lactose into GOS at 68% yield (g/g) (the maximum theoretical is 75%) with no secondary residual (glucose or galactose) products. This is the first report of a bioactive BHT fromS. singularisthat has been heterologously expressed.
Quantification of IncP-1 Plasmid Prevalence in Environmental Samples
Authors: Jechalke Sven , Dealtry Simone , Smalla Kornelia , Heuer Holger
Published: December 2012

To study the role of broad-host-range IncP-1 plasmids in bacterial adaptability to irregular environmental challenges, a quantitative real-time PCR assay was developed that specifically detects the
korB
gene, which is conserved in all IncP-1 plasmids, in environmental samples. IncP-1 plasmid dynamics in a biopurification system for pesticide wastes were analyzed.
Surface Stress Induces a Conserved Cell Wall Stress Response in the Pathogenic Fungus Candida albicans
Authors: Heilmann Clemens J. , Sorgo Alice G. , Mohammadi Sepehr , Sosinska Grazyna J. , de Koster Chris G. , Brul Stanley , de Koning Leo J. , Klis Frans M.
Published: December 2012

The human fungal pathogenCandida albicanscan grow at temperatures of up to 45°C. Here, we show that at 42°C substantially less biomass was formed than at 37°C. The cells also became more sensitive to wall-perturbing compounds, and the wall chitin levels increased, changes that are indicative of wall stress. Quantitative mass spectrometry of the wall proteome using15N metabolically labeled wall proteins as internal standards revealed that at 42°C the levels of the β-glucan transglycosylases Phr1 and Phr2, the predicted chitin transglycosylases Crh11 and Utr2, and the wall maintenance protein Ecm33 increased. Consistent with our previous results for fluconazole stress, this suggests that a wall-remodeling response is mounted to relieve wall stress. Thermal stress as well as different wall and membrane stressors led to an increased phosphorylation of the mitogen-activated protein (MAP) kinase Mkc1, suggesting activation of the cell wall integrity (CWI) pathway. Furthermore, all wall and membrane stresses tested resulted in diminished cell separation. This was accompanied by decreased secretion of the major chitinase Cht3 and the endoglucanase Eng1 into the medium. Consistent with this,cht3cells showed a similar phenotype. When treated with exogenous chitinase, cell clusters both from stressed cells and mutant strains were dispersed, underlining the importance of Cht3 for cell separation. We propose that surface stresses lead to a conserved cell wall remodeling response that is mainly governed by Mkc1 and is characterized by chitin reinforcement of the wall and the expression of remedial wall remodeling enzymes.
Translational Control in Plasmodium and Toxoplasma Parasites
Authors: Zhang Min , Joyce Bradley R. , Sullivan William J. , Nussenzweig Victor
Published: December 2012

The life cycles of apicomplexan parasites such as
Plasmodium
spp. and
Toxoplasma gondii
are complex, consisting of proliferative and latent stages within multiple hosts. Dramatic transformations take place during the cycles, and they demand precise control of gene expression at all levels, including translation. This review focuses on the mechanisms that regulate translational control in
Plasmodium
and
Toxoplasma
, with a particular emphasis on the phosphorylation of the α subunit of eukaryotic translation initiation factor 2 (eIF2α). Phosphorylation of eIF2α (eIF2α∼P) is a conserved mechanism that eukaryotic cells use to repress global protein synthesis while enhancing gene-specific translation of a subset of mRNAs. Elevated levels of eIF2α∼P have been observed during latent stages in both
Toxoplasma
and
Plasmodium
, indicating that translational control plays a role in maintaining dormancy. Parasite-specific eIF2α kinases and phosphatases are also required for proper developmental transitions and adaptation to cellular stresses encountered during the life cycle. Identification of small-molecule inhibitors of apicomplexan eIF2α kinases may selectively interfere with parasite translational control and lead to the development of new therapies to treat malaria and toxoplasmosis.
Fierce Competition between Toxoplasma and Chlamydia for Host Cell Structures in Dually Infected Cells
Authors: Romano Julia D. , de Beaumont Catherine , Carrasco Jose A. , Ehrenman Karen , Bavoil Patrik M. , Coppens Isabelle
Published: December 2012

The prokaryote
Chlamydia trachomatis
and the protozoan
Toxoplasma gondii
, two obligate intracellular pathogens of humans, have evolved a similar
modus operandi
to colonize their host cell and salvage nutrients from organelles. In order to gain fundamental knowledge on the pathogenicity of these microorganisms, we have established a cell culture model whereby single fibroblasts are coinfected by
C. trachomatis
and
T. gondii
. We previously reported that the two pathogens compete for the same nutrient pools in coinfected cells and that
Toxoplasma
holds a significant competitive advantage over
Chlamydia
. Here we have expanded our coinfection studies by examining the respective abilities of
Chlamydia
and
Toxoplasma
to co-opt the host cytoskeleton and recruit organelles. We demonstrate that the two pathogen-containing vacuoles migrate independently to the host perinuclear region and rearrange the host microtubular network around each vacuole. However,
Toxoplasma
outcompetes
Chlamydia
to the host microtubule-organizing center to the detriment of the bacterium, which then shifts to a stress-induced persistent state. Solely in cells preinfected with
Chlamydia
, the centrosomes become associated with the chlamydial inclusion, while the
Toxoplasma
parasitophorous vacuole displays growth defects. Both pathogens fragment the host Golgi apparatus and recruit Golgi elements to retrieve sphingolipids. This study demonstrates that the productive infection by both
Chlamydia
and
Toxoplasma
depends on the capability of each pathogen to successfully adhere to a finely tuned developmental program that aims to remodel the host cell for the pathogen's benefit. In particular, this investigation emphasizes the essentiality of host organelle interception by intravacuolar pathogens to facilitate access to nutrients.