bluuebunny/crossref_metadata_2025 huggingface dataset:
Decreased Immunoglobulin A Concentrations in Feces, Duodenum, and Peripheral Blood Mononuclear Cells of Dogs with Inflammatory Bowel Disease
Authors: Maeda S. , Ohno K. , Uchida K. , Nakashima K. , Fukushima K. , Tsukamoto A. , Nakajima M. , Fujino Y. , Tsujimoto H.
Published: December 2012

Background

Although immunoglobulin A (IgA) plays a key role in regulating gut homeostasis, its role in canine inflammatory bowel disease (IBD) is unknown.

Hypothesis

IgA expression may be altered in dogs withIBD, unlike that observed in healthy dogs and dogs with other gastrointestinal diseases.

Animals

Thirty‐seven dogs withIBD, 10 dogs with intestinal lymphoma, and 20 healthy dogs.

Methods

Prospective study. IgA and IgG concentrations in serum, feces, and duodenal samples were measured by ELISA. IgA+cells in duodenal lamina propria and IgA+CD21+peripheral blood mononuclear cells (PBMCs) were examined by immunohistochemistry and flow cytometry, respectively. Duodenal expression of the IgA‐inducing cytokine transforming growth factor β (TGF‐β), B cell activating factor (BAFF), and a proliferation‐inducing ligand (APRIL) was quantified by real‐timeRT‐PCR.

Results

Compared to healthy dogs, dogs withIBDhad significantly decreased concentrations of IgA in fecal and duodenal samples. The number of IgA+CD21+PBMCs and IgA+cells in duodenal lamina propria was significantly lower in dogs withIBDthan in healthy dogs or dogs with intestinal lymphoma. DuodenalBAFFandAPRILmRNAexpression was significantly higher inIBDdogs than in the healthy controls. DuodenalTGF‐β mRNAexpression was significantly lower in dogs withIBDthan in healthy dogs and dogs with intestinal lymphoma.

Conclusions and Clinical Importance

IBDdogs have decreased IgA concentrations in feces and duodenum and fewer IgA+PBMCs, which might contribute to development of chronic enteritis in dogs withIBD.
The origin of chondrules and chondrites: Debris from low‐velocity impacts between molten planetesimals?
Authors: SANDERS Ian S. , SCOTT Edward R. D.
Published: December 2012

Abstract–We investigate the hypothesis that many chondrules are frozen droplets of spray from impact plumes launched when thin‐shelled, largely molten planetesimals collided at low speed during accretion. This scenario, here dubbed “splashing,” stems from evidence that such planetesimals, intensely heated by26Al, were abundant in the protoplanetary disk when chondrules were being formed approximately 2 Myr after calcium‐aluminum‐rich inclusions (CAIs), and that chondrites, far from sampling the earliest planetesimals, are made from material that accreted later, when26Al could no longer induce melting. We show how “splashing” is reconcilable with many features of chondrules, including their ages, chemistry, peak temperatures, abundances, sizes, cooling rates, indented shapes, “relict” grains, igneous rims, and metal blebs, and is also reconcilable with features that challenge the conventional view that chondrules are flash‐melted dust‐clumps, particularly the high concentrations of Na and FeO in chondrules, but also including chondrule diversity, large phenocrysts, macrochondrules, scarcity of dust‐clumps, and heating. We speculate that type I (FeO‐poor) chondrules come from planetesimals that accreted early in the reduced, partially condensed, hot inner nebula, and that type II (FeO‐rich) chondrules come from planetesimals that accreted in a later, or more distal, cool nebular setting where incorporation of water‐ice with high Δ17O aided oxidation during heating. We propose that multiple collisions and repeated re‐accretion of chondrules and other debris within restricted annular zones gave each chondrite group its distinctive properties, and led to so‐called “complementarity” and metal depletion in chondrites. We suggest that differentiated meteorites are numerically rare compared with chondrites because their initially plentiful molten parent bodies were mostly destroyed during chondrule formation.
Oxygen isotopic composition of the solar nebula gas inferred from high‐precision isotope imaging of melilite crystals in an Allende CAI
Authors: PARK Changkun , WAKAKI Shigeyuki , SAKAMOTO Naoya , KOBAYASHI Sachio , YURIMOTO Hisayoshi
Published: December 2012

Abstract– High‐precision isotope imaging analyses of reversely zoned melilite crystals in the gehlenitic mantle of Type A CAI ON01 of the Allende carbonaceous chondrite reveal that there are four types of oxygen isotopic distributions within melilite single crystals: (1) uniform depletion of 16O (δ18O ≈ −10‰), (2) uniform enrichment of 16O (δ18O ≈ −40‰), (3) variations in isotopic composition from 16O‐poor core to 16O‐rich rim (δ18O ≈ −10‰ to −30‰, −20‰ to −45‰, and −10‰ to −35‰) with decreasing åkermanite content, and (4) 16O‐poor composition (δ18O ≥ −10‰) along the crystal rim. Hibonite, spinel, and perovskite grains are 16O‐rich (δ18O ≈ −45‰), and adjoin 16O‐poor melilites. Gas‐solid or gas‐melt isotope exchange in the nebula is inconsistent with both the distinct oxygen isotopic compositions among the minerals and the reverse zoning of melilite. Fluid‐rock interaction on the parent body resulted in 16O‐poor compositions of limited areas near holes, cracks, or secondary phases, such as anorthite or grossular. We conclude that reversely zoned melilites mostly preserve the primary oxygen isotopic composition of either 16O‐enriched or 16O‐depleted gas from which they were condensed. The correlation between oxygen isotopic composition and åkermanite content may indicate that oxygen isotopes of the solar nebula gas changed from 16O‐poor to 16O‐rich during melilite crystal growth. We suggest that the radial excursions of the inner edge of the protoplanetary disk gas simultaneously resulted in both the reverse zoning and oxygen isotopic variation of melilite, due to mixing of 16O‐poor disk gas and 16O‐rich coronal gas. Gas condensates aggregated to form the gehlenite mantle of the Type A CAI ON01.
Comparability of GDP estimates in Sub‐Saharan Africa: The effect of Revisions in Sources and Methods Since Structural Adjustment
Authors: Jerven Morten
Published: December 2012

The unreliability of African income estimates was highlighted when Ghana announced that GDP estimates were revised upwards by 60.3 percent in November 2010. Similar revisions are to be expected in other countries. Many statistical offices are currently using outdated base years. It is argued that with the current uneven application of methods and poor availability of data, any ranking of countries according to GDP levels is misleading. The paper emphasizes the challenges for “data users” in light of these revisions. GDP data are disseminated through international organizations, but without any detailed data descriptions. It is argued that many statistical offices in Sub‐Saharan Africa struggled to recover from the structural adjustment period, and the offices have not had the capacity to handle other challenges such as providing data to monitor the Millennium Development Goals. Currently, neither data users nor data producers are getting the assistance they need.
Fluidelastic Instability Modeling of Loosely Supported Multispan U-Tubes in Nuclear Steam Generators
Authors: Hassan Marwan , Mohany Atef
Published: December 2012

Steam generators in nuclear power plants have experienced tube failures caused by flow-induced vibrations. Two excitation mechanisms are responsible for such failures; random turbulence excitation and fluidelastic instability. The random turbulence excitation mechanism results in long-term failures due to fretting-wear damage at the tube supports, while fluidelastic instability results in short-term failures due to excessive vibration of the tubes. Such failures may require shutdowns, which result in production losses, and pose potential threats to human safety and the environment. Therefore, it is imperative to predict the nonlinear tube response and the associated fretting-wear damage to tubes due to fluid excitation. In this paper, a numerical model is developed to predict the nonlinear dynamic response of a steam generator with multispan U-tubes and anti-vibration bar supports, and the associated fretting wear due to fluid excitation. Both the crossflow turbulence and fluidelastic instability forces are considered in this model. The finite element method is utilized to model the vibrations and impact dynamics. The tube bundle geometry is similar to the geometry used in CANDU steam generators. Eight sets of flat-bar supports are considered. Moreover, the effect of clearances between the tubes and their supports, and axial offset between the supports are investigated. The results are presented and comparisons are made for the parameters influencing the fretting-wear damage, such as contact ratio, impact forces, and normal work rate. It is clear that tubes in loose flat-bar supports have complex dynamics due to a combination of geometry, tube-to-support clearance, offset, and misalignment. However, the results of the numerical simulation along with the developed model provide new insight into the flow-induced vibration mechanism and fretting wear of multispan U-tubes that can be incorporated into future design guidelines for steam generators and large heat exchangers.
A Hybrid Approach for the Simulation of the Thermal Motion of a Nearly Neutrally Buoyant Nanoparticle in an Incompressible Newtonian Fluid Medium
Authors: Uma B. , Radhakrishnan R. , Eckmann D. M. , Ayyaswamy P. S.
Published: December 2012

A hybrid approach consisting of a Markovian fluctuating hydrodynamics of the fluid and a non-Markovian Langevin dynamics with the Ornstein–Uhlenbeck noise perturbing the translational and rotational equations of motion of a nanoparticle is employed to study the thermal motion of a nearly neutrally buoyant nanoparticle in an incompressible Newtonian fluid medium. A direct numerical simulation adopting an arbitrary Lagrangian–Eulerian based finite element method is employed for the simulation of the hybrid approach. The instantaneous flow around the particle and the particle motion are fully resolved. The numerical results show that (a) the calculated temperature of the nearly neutrally buoyant Brownian particle in a quiescent fluid satisfies the equipartition theorem; (b) the translational and rotational decay of the velocity autocorrelation functions result in algebraic tails, over long time; (c) the translational and rotational mean square displacements of the particle obey Stokes–Einstein and Stokes–Einstein–Debye relations, respectively; and (d) the parallel and perpendicular diffusivities of the particle closer to the wall are consistent with the analytical results, where available. The study has important implications for designing nanocarriers for targeted drug delivery. A major advantage of our novel hybrid approach employed in this paper as compared to either the fluctuating hydrodynamics approach or the generalized Langevin approach by itself is that only the hybrid method has been shown to simultaneously preserve both hydrodynamic correlations and equilibrium statistics in the incompressible limit.
Strain‐encoded breast MRI in phantom and ex vivo specimens with histological validation: Preliminary results
Authors: Haruoni Ahmed A. , Hossain Jakir , El Khouli Riham , Matsuda Kant M. , Bluemke David A. , Osman Nael F. , Jacobs Michael A.
Published: December 2012

Purpose:

To evaluate the feasibility of using strain‐encoded (SENC) breast magnetic resonance images (MRI) for breast cancer detection by examining the compression and relaxation response properties in phantoms andex vivo breast samples.

Methods:

A tissue phantom was constructed to mimic different sizes of breast masses and tissue stiffness. In addition, five humanex vivo whole breast specimens with and without masses were studied. MR data was acquired on a 3T scanner consisting of T1‐weighted, fat suppressed spin echo T2‐weighted, and SENC breast images. Mechanical tissue characteristics (strain) of the phantoms and breast tissue samples were measured using SENC imaging in both compression and relaxation modes. The breast tissue specimens were sectioned and stained in the same plane as the MRI for histological evaluation.

Results:

For the phantom, SENC images showed soft masses with quantitative strain values between 35% and 50%, while harder masses had strain values between 0% and 20%. Combined compression (CMP) and relaxation (REX) breast SENC images separately categorized all masses into three different groups. For breast SENC, the signal intensities betweenex vivo breast mass and breast glandular tissue were significantly different (−7.6 ± 2.6 verses −20.6 ± 5.4 for SENC‐CMP, and 4.2 ± 1.5 verses 22.6 ± 5 for SENC‐REX, p < 0.05).

Conclusions:

We have demonstrated that SENC breast MRI can be used to obtain mechanical tissue properties and give quantitative estimates of strain in tumors. This feasibility study provides the basis for future clinical studies.
Global Decline in Large Old Trees
Authors: Lindenmayer David B. , Laurance William F. , Franklin Jerry F.
Published: December 2012

The loss of large old trees in many ecosystems around the world poses a threat to ecosystem integrity.
Development of Novel Sugar Isomerases by Optimization of Active Sites in Phosphosugar Isomerases for Monosaccharides
Authors: Yeom Soo-Jin , Kim Yeong-Su , Oh Deok-Kun
Published: December 2012

Phosphosugar isomerases can catalyze the isomerization of not only phosphosugar but also of monosaccharides, suggesting that the phosphosugar isomerases can be used as sugar isomerases that do not exist in nature. Determination of active-site residues of phosphosugar isomerases, including ribose-5-phosphate isomerase from
Clostridium difficile
(CDRPI), mannose-6-phosphate isomerase from
Bacillus subtilis
(BSMPI), and glucose-6-phosphate isomerase from
Pyrococcus furiosus
(PFGPI), was accomplished by docking of monosaccharides onto the structure models of the isomerases. The determinant residues, including Arg133 of CDRPI, Arg192 of BSMPI, and Thr85 of PFGPI, were subjected to alanine substitutions and found to act as phosphate-binding sites. R133D of CDRPI, R192 of BSMPI, and T85Q of PFGPI displayed the highest catalytic efficiencies for monosaccharides at each position. These residues exhibited 1.8-, 3.5-, and 4.9-fold higher catalytic efficiencies, respectively, for the monosaccharides than the wild-type enzyme. However, the activities of these 3 variant enzymes for phosphosugars as the original substrates disappeared. Thus, R133D of CDRPI, R192 of BSMPI, and T85Q of PFGPI are no longer phosphosugar isomerases; instead, they are changed to a
d
-ribose isomerase, an
l
-ribose isomerase, and an
l
-talose isomerase, respectively. In this study, we used substrate-tailored optimization to develop novel sugar isomerases which are not found in nature based on phosphosugar isomerases.
Processivity and Enzymatic Mode of a Glycoside Hydrolase Family 5 Endoglucanase from Volvariella volvacea
Authors: Zheng Fei , Ding Shaojun
Published: December 2012

EG1 is a modular glycoside hydrolase family 5 endoglucanase from
Volvariella volvacea
consisting of an N-terminal carbohydrate-binding module (CBM1) and a catalytic domain (CD). The ratios of soluble to insoluble reducing sugar produced from filter paper after 8 and 24 h of exposure to EG1 were 6.66 and 8.56, respectively, suggesting that it is a processive endoglucanase. Three derivatives of EG1 containing a core domain only or additional CBMs were constructed in order to evaluate the contribution of the CBM to the processivity and enzymatic mode of EG1 under stationary and agitated conditions. All four enzymatic forms exhibited the same mode of action on both soluble and insoluble cellulosic substrates with cellobiose as a main end product. An additional CBM fused at either the N or C terminus reduced specific activity toward soluble and insoluble celluloses under stationary reaction conditions. Deletion of the CBM significantly decreased enzyme processivity. Insertion of an additional CBM also resulted in a dramatic decrease in processivity in enzyme-substrate reaction mixtures incubated for 0.5 h, but this effect was reversed when reactions were allowed to proceed for longer periods (24 h). Further significant differences were observed in the substrate adsorption/desorption patterns of EG1 and enzyme derivatives equipped with an additional CBM under agitated reaction conditions. An additional family 1 CBM improved EG1 processivity on insoluble cellulose under highly agitated conditions. Our data indicate a strong link between high adsorption levels and low desorption levels in the processivity of EG1 and possibly other processive endoglucanses.
Proteome Analyses of Strains ATCC 51142 and PCC 7822 of the Diazotrophic Cyanobacterium Cyanothece sp. under Culture Conditions Resulting in Enhanced H
2
Production
Authors: Aryal Uma K. , Callister Stephen J. , Mishra Sujata , Zhang Xiaohui , Shutthanandan Janani I. , Angel Thomas E. , Shukla Anil K. , Monroe Matthew E. , Moore Ronald J. , Koppenaal David W. , Smith Richard D. , Sherman Louis
Published: December 2012

Cultures of the cyanobacterial genus
Cyanothece
have been shown to produce high levels of biohydrogen. These strains are diazotrophic and undergo pronounced diurnal cycles when grown under N
2
-fixing conditions in light-dark cycles. We seek to better understand the way in which proteins respond to these diurnal changes, and we performed quantitative proteome analysis of
Cyanothece
sp. strains ATCC 51142 and PCC 7822 grown under 8 different nutritional conditions. Nitrogenase expression was limited to N
2
-fixing conditions, and in the absence of glycerol, nitrogenase gene expression was linked to the dark period. However, glycerol induced expression of nitrogenase during part of the light period, together with cytochrome
c
oxidase (Cox), glycogen phosphorylase (Glp), and glycolytic and pentose phosphate pathway (PPP) enzymes. This indicated that nitrogenase expression in the light was facilitated via higher levels of respiration and glycogen breakdown. Key enzymes of the Calvin cycle were inhibited in
Cyanothece
ATCC 51142 in the presence of glycerol under H
2
-producing conditions, suggesting a competition between these sources of carbon. However, in
Cyanothece
PCC 7822, the Calvin cycle still played a role in cofactor recycling during H
2
production. Our data comprise the first comprehensive profiling of proteome changes in
Cyanothece
PCC 7822 and allow an in-depth comparative analysis of major physiological and biochemical processes that influence H
2
production in both strains. Our results revealed many previously uncharacterized proteins that may play a role in nitrogenase activity and in other metabolic pathways and may provide suitable targets for genetic manipulation that would lead to improvement of large-scale H
2
production.
Isolation of Acetobacterium sp. Strain AG, Which Reductively Debrominates Octa- and Pentabrominated Diphenyl Ether Technical Mixtures
Authors: Ding Chang , Chow Wai Ling , He Jianzhong
Published: December 2012

Polybrominated diphenyl ethers (PBDEs) are a class of environmental pollutants that have been classified as persistent organic pollutants since 2009. In this study, a sediment-free enrichment culture (culture G) was found to reductively debrominate octa- and penta-BDE technical mixtures to less-brominated congeners (tetra-, tri-, and di-BDEs) via a
para
-dominant debromination pattern for the former and a strict
para
debromination pattern for the latter. Culture G could debrominate 96% of 280 nM PBDEs in an octa-BDE mixture to primarily tetra-BDEs in 21 weeks. Continuous transferring of culture G with octa-/penta-BDEs dissolved in
n
-nonane or trichloroethene (TCE) yielded two strains (
Acetobacterium
sp. strain AG and
Dehalococcoides
sp. strain DG) that retained debromination capabilities. In the presence of lactate but without TCE, strain AG could cometabolically debrominate 75% of 275 nM PBDEs in a penta-BDE mixture in 33 days. Strain AG shows 99% identity to its closest relative,
Acetobacterium malicum
. In contrast to strain AG, strain DG debrominated PBDEs only in the presence of TCE. In addition, 18 out of 19 unknown PBDE debromination products were successfully identified from octa- and penta-BDE mixtures and revealed, for the first time, a comprehensive microbial PBDE debromination pathway. As an acetogenic autotroph that rapidly debrominates octa- and penta-BDE technical mixtures,
Acetobacterium
sp. strain AG adds to the still-limited understanding of PBDE debromination by microorganisms.
Adaptation and Heterogeneity of Escherichia coli MC1000 Growing in Complex Environments
Authors: Puentes-Téllez Pilar Eliana , Hansen Martin Asser , Sørensen Søren Johannes , van Elsas Jan Dirk
Published: December 2012

In a study aiming to assess bacterial evolution in complex growth media, we evaluated the long-term adaptive response ofEscherichia coliMC1000 in Luria-Bertani (LB) medium. Seven parallel populations were founded and followed over 150 days in sequential batch cultures under three different oxygen conditions (defined environments), and 19 evolved forms were isolated. The emergence of forms with enhanced fitness was evident in competition experiments of all evolved forms versus the ancestral strain. The evolved forms were then subjected to phenotypic and genomic analyses relative to the ancestor. Profound changes were found in their phenotypes as well as whole-genome sequences. Interestingly, considerable heterogeneity was found at the intrapopulational level. However, consistently occurring parallel adaptive responses were found across all populations. The evolved forms all contained a mutation ingalR, a repressor of the galactose operon. Concomitantly, the new forms revealed enhanced growth on galactose as well as galactose-containing disaccharides. This response was likely driven by the LB medium.
HbzF Catalyzes Direct Hydrolysis of Maleylpyruvate in the Gentisate Pathway of Pseudomonas alcaligenes NCIMB 9867
Authors: Liu Kun , Liu Ting-Ting , Zhou Ning-Yi
Published: December 2012

HbzF from
Pseudomonas alcaligenes
NCIMB 9867 was purified to homogeneity as a His-tagged protein and likely a dimer by SDS-PAGE and gel filtration. This protein was demonstrated to be a novel maleylpyruvate hydrolase, catalyzing direct hydrolysis of maleylpyruvate to maleate and pyruvate, and belongs to the fumarylacetoacetate hydrolase superfamily. This study reveals the genetic determinate for the direct maleylpyruvate hydrolysis in the gentisate pathway, complementary to the well-studied maleylpyruvate isomerization route.
Significance of Heme-Based Respiration in Meat Spoilage Caused by Leuconostoc gasicomitatum
Authors: Jääskeläinen Elina , Johansson Per , Kostiainen Olli , Nieminen Timo , Schmidt Georg , Somervuo Panu , Mohsina Marzia , Vanninen Paula , Auvinen Petri , Björkroth Johanna
Published: December 2012

Leuconostoc gasicomitatum
is a psychrotrophic lactic acid bacterium (LAB) which causes spoilage in cold-stored modified-atmosphere-packaged (MAP) meat products. In addition to the fermentative metabolism,
L. gasicomitatum
is able to respire when exogenous heme and oxygen are available. In this study, we investigated the respiration effects on growth rate, biomass, gene expression, and volatile organic compound (VOC) production in laboratory media and pork loin. The meat samples were evaluated by a sensory panel every second or third day for 29 days. We observed that functional respiration increased the growth (rate and yield) of
L. gasicomitatum
in laboratory media with added heme and
in situ
meat with endogenous heme. Respiration increased enormously (up to 2,600-fold) the accumulation of acetoin and diacetyl, which are buttery off-odor compounds in meat. Our transcriptome analyses showed that the gene expression patterns were quite similar, irrespective of whether respiration was turned off by excluding heme from the medium or mutating the
cydB
gene, which is essential in the respiratory chain. The respiration-based growth of
L. gasicomitatum
in meat was obtained in terms of population development and subsequent development of sensory characteristics. Respiration is thus a key factor explaining why
L. gasicomitatum
is so well adapted in high-oxygen packed meat.
Analagous Population Structures for Two Alphabaculoviruses Highlight a Functional Role for Deletion Mutants
Authors: Serrano Amaya , Williams Trevor , Simón Oihane , López-Ferber Miguel , Caballero Primitivo , Muñoz Delia
Published: December 2012

A natural
Spodoptera exigua
multiple nucleopolyhedrovirus (SeMNPV) isolate from Florida shares a strikingly similar genotypic composition to that of a natural
Spodoptera frugiperda
MNPV (SfMNPV) isolate from Nicaragua. Both isolates comprise a high proportion of large-deletion genotypes that lack genes that are essential for viral replication or transmission. To determine the likely origins of such genotypically similar population structures, we performed genomic and functional analyses of these genotypes. The homology of nucleotides in the deleted regions was as high as 79%, similar to those of other colinear genomic regions, although some SfMNPV genes were not present in SeMNPV. In addition, no potential consensus sequences were shared between the deletion flanking sequences. These results indicate an evolutionary mechanism that independently generates and sustains deletion mutants within each virus population. Functional analyses using different proportions of complete and deletion genotypes were performed with the two viruses in mixtures of occlusion bodies (OBs) or co-occluded virions. Ratios greater than 3:1 of complete/deletion genotypes resulted in reduced pathogenicity (expressed as median lethal dose), but there were no significant changes in the speed of kill. In contrast, OB yields increased only in the 1:1 mixture. The three phenotypic traits analyzed provide a broader picture of the functional significance of the most extensively deleted SeMNPV genotype and contribute toward the elucidation of the role of such mutants in baculovirus populations.
Bioluminescence Imaging Study of Spatial and Temporal Persistence of Lactobacillus plantarum and Lactococcus lactis in Living Mice
Authors: Daniel Catherine , Poiret Sabine , Dennin Véronique , Boutillier Denise , Pot Bruno
Published: December 2012

Lactic acid bacteria, especially lactobacilli, are common inhabitants of the gastrointestinal tract of mammals, for which they have received considerable attention due to their putative health-promoting properties. In this study, we describe the development and application of luciferase-expressing
Lactobacillus plantarum
and
Lactococcus lactis
strains for noninvasive
in vivo
monitoring in the digestive tract of mice. We report for the first time the functional
in vitro
expression in
Lactobacillus plantarum
NCIMB8826 and in
Lactococcus lactis
MG1363 of the click beetle luciferase (CBluc), as well as
Gaussia
and bacterial luciferases, using a combination of vectors, promoters, and codon-optimized genes. We demonstrate that a CBluc construction is the best-performing luciferase system for the noninvasive
in vivo
detection of lactic acid bacteria after oral administration. The persistence and viability of both strains was studied by bioluminescence imaging in anesthetized mice and in mouse feces.
In vivo
bioluminescence imaging confirmed that after a single or multiple oral administrations,
L. lactis
has shorter survival times in the mouse gastrointestinal tract than
L. plantarum
, and it also revealed the precise gut compartments where both strains persisted. The application of luciferase-labeled bacteria has significant potential to allow the
in vivo
and
ex vivo
study of the interactions of lactic acid bacteria with their mammalian host.
Enterohemorrhagic Escherichia coli O157:H7 Survival in an
In Vitro
Model of the Human Large Intestine and Interactions with Probiotic Yeasts and Resident Microbiota
Authors: Thévenot Jonathan , Etienne-Mesmin Lucie , Denis Sylvain , Chalancon Sandrine , Alric Monique , Livrelli Valérie , Blanquet-Diot Stéphanie
Published: December 2012

This is the first report on the fate of enterohemorrhagic
Escherichia coli
O157:H7 in simulated human colonic conditions. The pathogen was progressively eliminated from the bioreactor and did not modify the major populations of resident microbiota. The coadministration of the
Saccharomyces cerevisiae
CNCM I-3856 probiotic strain led to a significant increase in acetate production but did not reduce pathogen viability.
Two Doses of Bovine Viral Diarrhea Virus DNA Vaccine Delivered by Electroporation Induce Long-Term Protective Immune Responses
Authors: van Drunen Littel-van den Hurk Sylvia , Lawman Zoe , Snider Marlene , Wilson Don , van den Hurk Jan V. , Ellefsen Barry , Hannaman Drew
Published: December 2012

Bovine viral diarrhea virus (BVDV) is a pathogen of major importance in cattle, so there is a need for new effective vaccines. DNA vaccines induce balanced immune responses and are relatively inexpensive and thus promising for both human and veterinary applications. In this study, newborn calves with maternal antibodies were vaccinated intramuscularly (i.m.) with a BVDV E2 DNA vaccine with the TriGrid Delivery System for i.m. delivery (TDS-IM). Two doses of this vaccine spaced 6 or 12 weeks apart were sufficient to induce significant virus-neutralizing antibody titers, numbers of activated T cells, and reduction in viral shedding and clinical presentations after BVDV-2 challenge. In contrast to the placebo-treated animals, the vaccinated calves did not lose any weight, which is an excellent indicator of the well-being of an animal and has a significant economic impact. Furthermore, the interval between the two vaccinations did not influence the magnitude of the immune responses or degree of clinical protection, and a third immunization was not necessary or beneficial. Since electroporation may enhance not only the magnitude but also the duration of immunity after DNA immunization, the interval between vaccination and challenge was extended in a second trial, which showed that two doses of this E2 DNA vaccine again significantly reduced clinical disease against BVDV for several months. These results are promising and support this technology for use against infectious diseases in cattle and large species, including humans, in general.
Morphogenetic Circuitry Regulating Growth and Development in the Dimorphic Pathogen Penicillium marneffei
Authors: Boyce Kylie J. , Andrianopoulos Alex
Published: December 2012

Penicillium marneffeiis an emerging human-pathogenic fungus endemic to Southeast Asia. Like a number of other fungal pathogens,P. marneffeiexhibits temperature-dependent dimorphic growth and grows in two distinct cellular morphologies, hyphae at 25°C and yeast cells at 37°C. Hyphae can differentiate to produce the infectious agents, asexual spores (conidia), which are inhaled into the host lung, where they are phagocytosed by pulmonary alveolar macrophages. Within macrophages, conidia germinate into unicellular yeast cells, which divide by fission. This minireview focuses on the current understanding of the genes required for the morphogenetic control of conidial germination, hyphal growth, asexual development, and yeast morphogenesis inP. marneffei.
Septin Phosphorylation and Coiled-Coil Domains Function in Cell and Septin Ring Morphology in the Filamentous Fungus Ashbya gossypii
Authors: Meseroll Rebecca A. , Occhipinti Patricia , Gladfelter Amy S.
Published: December 2012

Septins are a class of GTP-binding proteins conserved throughout many eukaryotes. Individual septin subunits associate with one another and assemble into heteromeric complexes that form filaments and higher-order structures
in vivo
. The mechanisms underlying the assembly and maintenance of higher-order structures in cells remain poorly understood. Septins in several organisms have been shown to be phosphorylated, although precisely how septin phosphorylation may be contributing to the formation of high-order septin structures is unknown. Four of the five septins expressed in the filamentous fungus,
Ashbya gossypii
, are phosphorylated, and we demonstrate here the diverse roles of these phosphorylation sites in septin ring formation and septin dynamics, as well as cell morphology and viability. Intriguingly, the alteration of specific sites in Cdc3p and Cdc11p leads to a complete loss of higher-order septin structures, implicating septin phosphorylation as a regulator of septin structure formation. Introducing phosphomimetic point mutations to specific sites in Cdc12p and Shs1p causes cell lethality, highlighting the importance of normal septin modification in overall cell function and health. In addition to discovering roles for phosphorylation, we also present diverse functions for conserved septin domains in the formation of septin higher-order structure. We previously showed the requirement for the Shs1p coiled-coil domain in limiting septin ring size and reveal here that, in contrast to Shs1p, the coiled-coil domains of Cdc11p and Cdc12p are required for septin ring formation. Our results as a whole reveal novel roles for septin phosphorylation and coiled-coil domains in regulating septin structure and function.
Analyses of Extracellular Carbohydrates in Oomycetes Unveil the Existence of Three Different Cell Wall Types
Authors: Mélida Hugo , Sandoval-Sierra Jose V. , Diéguez-Uribeondo Javier , Bulone Vincent
Published: December 2012

Some of the most devastating plant and animal pathogens belong to the oomycete class. The cell walls of these microorganisms represent an excellent target for disease control, but their carbohydrate composition is elusive. We have undertaken a detailed cell wall analysis in 10 species from 2 major oomycete orders, the Peronosporales and the Saprolegniales, thereby unveiling the existence of 3 clearly different cell wall types: type I is devoid of
N
-acetylglucosamine (GlcNAc) but contains glucuronic acid and mannose; type II contains up to 5% GlcNAc and residues indicative of cross-links between cellulose and 1,3-β-glucans; type III is characterized by the highest GlcNAc content (>5%) and the occurrence of unusual carbohydrates that consist of 1,6-linked GlcNAc residues. These 3 cell wall types are also distinguishable by their cellulose content and the fine structure of their 1,3-β-glucans. We propose a cell wall paradigm for oomycetes that can serve as a basis for the establishment of cell wall architectural models and the further identification of cell wall subtypes. This paradigm is complementary to morphological and molecular criteria for taxonomic grouping and provides useful information for unraveling poorly understood cell wall carbohydrate biosynthetic pathways through the identification and characterization of the corresponding enzymes.
Individual and Combined Roles of the Master Regulators AphA and LuxR in Control of the Vibrio harveyi Quorum-Sensing Regulon
Authors: van Kessel Julia C. , Rutherford Steven T. , Shao Yi , Utria Alan F. , Bassler Bonnie L.
Published: December 2012

Bacteria use a chemical communication process called quorum sensing to control transitions between individual and group behaviors. In theVibrio harveyiquorum-sensing circuit, two master transcription factors, AphA and LuxR, coordinate the quorum-sensing response. Here we show that AphA regulates 167 genes, LuxR regulates 625 genes, and they coregulate 77 genes. LuxR strongly controls genes at both low cell density and high cell density, suggesting that it is the major quorum-sensing regulator. In contrast, AphA is absent at high cell density and acts to fine-tune quorum-sensing gene expression at low cell density. We examined two loci as case studies of coregulation by AphA and LuxR. First, AphA and LuxR directly regulate expression of the genes encoding the quorum-regulatory small RNAs Qrr2, Qrr3, and Qrr4, the consequence of which is a specifically timed transition between the individual and the group life-styles. Second, AphA and LuxR repress type III secretion system genes but at different times and to different extents. The consequence of this regulation is that type III secretion is restricted to a peak at mid-cell density. Thus, the asymmetric production of AphA and LuxR coupled with differences in their strengths and timing of target gene regulation generate a precise temporal pattern of gene expression.
Sequential Triplex Real-Time PCR Assay for Detecting 21 Pneumococcal Capsular Serotypes That Account for a High Global Disease Burden
Authors: Pimenta Fabiana C. , Roundtree Alexis , Soysal Ahmet , Bakir Mustafa , du Plessis Mignon , Wolter Nicole , von Gottberg Anne , McGee Lesley , Carvalho Maria da Gloria , Beall Bernard
Published: December 2012

We developed and validated a real-time PCR assay consisting of 7 triplexed reactions to identify 11 individual serotypes plus 10 small serogroups representing the majority of disease-causing isolates of
Streptococcus pneumoniae
. This assay targets the 13 serotypes included within the 13-valent conjugate vaccine and 8 additional key serotypes or serogroups. Advantages over other serotyping assays are described. The assay will be expanded to 40 serotypes/serogroups. We will provide periodic updates at our protocol website.
Rapid Hepatitis C Virus Divergence among Chronically Infected Individuals
Authors: Cruz-Rivera Mayra , Carpio-Pedroza Juan Carlos , Escobar-Gutiérrez Alejandro , Lozano Daniela , Vergara-Castaneda Arely , Rivera-Osorio Pilar , Martinez-Guarneros Armando , Chacon Carlos A. Vazquez , Fonseca-Coronado Salvador , Vaughan Gilberto
Published: December 2012

Here, we analyze the viral divergence among hepatitis C virus (HCV) chronic cases infected with genotype 1. The intrahost viral evolution was assessed by deep sequencing using the 454 Genome Sequencer platform. The results showed a rapid nucleotide sequence divergence. This notorious short-term viral evolution is of the utmost importance for the study of HCV transmission, because direct links between related samples were virtually lost. Thus, rapid divergence of HCV significantly affects genetic relatedness studies and outbreak investigations.
Bacterial Calligraphy: A Memento for Undergraduate Research Students
Authors: Ng Wenfa
Published: December 2012

The research project is a major assignment for final-year undergraduate students. As part of the project’s learning outcomes, undergraduate students are exposed to research methodology, design, and execution of experiments, as well as to data interpretation and presentation. Given the intense nature of the research experience in time and in effort, and the close working relationships and camaraderie that develop, a memento would be fitting at the conclusion of the research project. This activity describes how to create such a memento by using a purple pigment-producing soil bacterium, Chromobacterium violaceum, as an “ink” to inscribe the initials of each student’s name on an agar plate in a process named “bacterial calligraphy.”
Online Genome Analysis Resources for Educators, a Comparative ReviewReviews of:
Carolina Biological Supply Company,
www.carolina.com;
Bio-Rad,
www.bio-rad.com;
Edvotek Inc.,
www.edvotek.com;
Hiram Genomics Store,
www.hiramgenomicsstore.com; and
23andMe,
www.23andme.com.
Authors: Prescott Sarah Grace
Published: December 2012

A comparative review of several companies that offer similar kits or services that allow students to isolate DNA (human and others), amplify it by PCR, and in some cases sequence the resulting sample. The companies include:
Carolina® Biological Supply Company, Bio-Rad®, Edvotek® Inc.,
Hiram Genomics Store, and 23andMe.
New Face of an Old FriendReview of:	Microbiology: A Human Perspective,	7th ed.;	NesterEugeneAndersonDeniseEvans RobertsC.Jr.; (	2011).	McGraw-Hill Science/Engineering/Math,	New York, NY.	864 pages.
Authors: Tawde Mangala , Trujillo Monica
Published: December 2012

Review of:
Microbiology: A Human Perspective, 7th ed.;
Eugene Nester, Denise Anderson, and C. Evans Roberts Jr.; (2011). McGraw-Hill Science/Engineering/Math, New York, NY. 864 pages.
Longevity and Patau syndrome: what determines survival?
Authors: Peroos Sherina , Forsythe Elizabeth , Pugh Jennifer Harriet , Arthur-Farraj Peter , Hodes Deborah
Published: December 2012

The authors report of an 8-year-old girl with non-mosaic Patau syndrome. The median life expectancy of Patau syndrome is 7–10 days, and 90% die in the first year of life. Survival is often attributed to mosaicism and the severity of associated malformations. We delineate the developing phenotype and review the literature discussing potential contributory factors to longevity.
Page kidney in a 17-year-old renal allograft
Authors: Gandhi Vanita , Khosravi Maryam , Burns Aine
Published: December 2012

Page kidney is a condition where extrinsic renal compression from a haematoma or mass results in hypertension and loss of renal function. Most cases are caused by a subcapsular haematoma following blunt trauma or invasive procedures (eg, renal biopsy). We report a patient who spontaneously developed Page kidney 17 years after renal transplantation. This case represents the oldest renal allograft to develop non-traumatic Page kidney.
Synergistic prognostic values of cardiac sympathetic innervation with left ventricular hypertrophy and left atrial size in heart failure patients without reduced left ventricular ejection fraction: a cohort study
Authors: Doi Takahiro , Nakata Tomoaki , Hashimoto Akiyoshi , Yuda Satoshi , Wakabayashi Takeru , Kouzu Hidemichi , Kaneko Naofumi , Hase Mamoru , Tsuchihashi Kazufumi , Miura Tetsuji
Published: December 2012

Objectives

This study tested whether cardiac sympathetic innervation assessed by metaiodobenzylguanidine (MIBG) activity has long-term prognostic value in combination with left ventricular hypertrophy (LVH) and left atrial size in heart failure (HF) patients without reduced left ventricular ejection fraction (LVEF).

Design

A single-centre prospective cohort study.

Setting/participants

With primary endpoints of cardiac death and rehospitalisation due to HF progression, 178 consecutive symptomatic HF patients with 74% men, mean age of 56 years and mean LVEF of 64.5% were followed up for 80 months. The entry criteria consisted of LVEF more than 50%, completion of predischarge clinical evaluations including cardiac MIBG and echocardiographic studies and at least more than 1-year follow-up when survived.

Results

Thirty-four patients with cardiac evens had larger left atrial dimension (LAD), increased LV mass index, reduced MIBG activity quantified as heart-to-mediastinum ratio (HMR) than did the others. Multivariable Cox analysis showed that LAD and HMR were significant predictors (HR of 1.080 (95% CI 1.00 to 1.16, p=0.044) and 0.107 (95% CI 0.01 to 0.61, p=0.012, respectively). Thresholds of HMR (1.65) and LAD (37 mm) were closely related to identification of high-risk patients. In particular, HMR was a significant determinant of cardiac events in both patients with and without LV hypertrophy. Reduced HMR with enlarged LAD or LV hypertrophy identified patients at most increased risk; overall log-rank value, 11.5, p=0.0032 for LAD and 17.5, p=0.0002, respectively.

Conclusions

In HF patients without reduced LV ejection fraction, impairment of cardiac sympathetic innervation is related to cardiac outcomes independently and synergistically with LA size and LV hypertrophy. Cardiac sympathetic innervation assessment can contribute to better risk-stratification in combination with evaluation of LA size and LV mass but is needed to be evaluated for establishing aetiology-based risk assessment in HF patients at increased risk.
Those who can, teach. Assessing medical students’ perception of a finals revision programme delivered by foundation and core trainees: a cross-sectional study
Authors: Mole Guy , Gillespie Liam
Published: December 2012

Objective

To determine whether medical students perceive a foundation and core trainee finals revision programme as useful.

Design

Questionnaires were used to assess students’ perception of the teaching programme.

Setting

A medical school in the South of England.

Participants

There were 106 final year medical students in the cohort.

Results

The teaching scored well in all facets analysed and scored best on enthusiasm, interactivity and communication.

Conclusions

We provide a framework for how foundation and core trainees could provide a very well received teaching programme benefiting medical students, the doctors and the medical school.
Cause of death in MS: long-term follow-up of a randomised cohort, 21 years after the start of the pivotal IFNβ-1b study
Authors: Goodin Douglas S , Ebers George C , Cutter Gary , Cook Stuart D , O'Donnell Timothy , Reder Anthony T , Kremenchutzky Marcelo , Oger Joel , Rametta Mark , Beckmann Karola , Knappertz Volker
Published: December 2012

Objectives

Compared with controls, multiple sclerosis (MS) patients die, on average, 7–14 years prematurely. Previously, we reported that, 21 years after their participation in the pivotal randomised, controlled trial (RCT) of interferon β-1b, mortality was reduced by 46–47% in the two groups who received active therapy during the RCT. To determine whether the excessive deaths observed in placebo-treated patients was due to MS-related causes, we analysed the causes-of-death (CODs) in these three, randomised, patient cohorts.

Design

Long-term follow-up (LTF) of the pivotal RCT of interferon β-1b.

Setting

Eleven North American MS-centres participated.

Participants

In the original RCT, 372 patients participated, of whom 366 (98.4%) were identified after a median of 21.1 years from RCT enrolment.

Interventions

Using multiple information sources, we attempted to establish COD and its relationship to MS in deceased patients.

Primary outcome

An independent adjudication committee, masked to treatment assignment and using prespecified criteria, determined the likely CODs and their MS relationships.

Results

Among the 366 MS patients included in this LTF study, 81 deaths were recorded. Mean age-at-death was 51.7 (±8.7) years. COD, MS relationship, or both were determined for 88% of deaths (71/81). Patients were assigned to one of nine COD categories: cardiovascular disease/stroke; cancer; pulmonary infections; sepsis; accidents; suicide; death due to MS; other known CODs; and unknown COD. Of the 69 patients for whom information on the relationship of death to MS was available, 78.3% (54/69) were adjudicated to be MS related. Patients randomised to receive placebo during the RCT (compared with patients receiving active treatment) experienced an excessive number of MS-related deaths.

Conclusions

In this long-term, randomised, cohort study, MS patients receiving placebo during the RCT experienced greater all-cause mortality compared to those on active treatment. The excessive mortality in the original placebo group was largely from MS-related causes, especially, MS-related pulmonary infections.