bluuebunny/crossref_metadata_2025 huggingface dataset:
The Transposon impala Is Activated by Low Temperatures: Use of a Controlled Transposition System To Identify Genes Critical for Viability of Aspergillus fumigatus
Authors: Carr Paul D. , Tuckwell Danny , Hey Peter M. , Simon Laurence , d'Enfert Christophe , Birch Mike , Oliver Jason D. , Bromley Michael J.
Published: January 2010

Genes that are essential for viability represent potential targets for the development of anti-infective agents. However, relatively few have been determined in the filamentous fungal pathogen
Aspergillus fumigatus
. A novel solution employing parasexual genetics coupled with transposon mutagenesis using the
Fusarium oxysporum
transposon
impala
had previously enabled the identification of 20 essential genes from
A. fumigatus
; however, further use of this system required a better understanding of the mode of action of the transposon itself. Examination of a range of conditions indicated that
impala
is activated by prolonged exposure to low temperatures. This newly identified property was then harnessed to identify 96 loci that are critical for viability in
A. fumigatus
, including genes required for RNA metabolism, organelle organization, protein transport, ribosome biogenesis, and transcription, as well as a number of noncoding RNAs. A number of these genes represent potential targets for much-needed novel antifungal drugs.
Role of Transcription Factor CaNdt80p in Cell Separation, Hyphal Growth, and Virulence in Candida albicans
Authors: Sellam Adnane , Askew Christopher , Epp Elias , Tebbji Faiza , Mullick Alaka , Whiteway Malcolm , Nantel André
Published: January 2010

The NDT80/PhoG transcription factor family includes ScNdt80p, a key modulator of the progression of meiotic division in
Saccharomyces cerevisiae
. In
Candida albicans
, a member of this family, CaNdt80p, modulates azole sensitivity by controlling the expression of ergosterol biosynthesis genes. We previously demonstrated that CaNdt80p promoter targets, in addition to
ERG
genes, were significantly enriched in genes related to hyphal growth. Here, we report that CaNdt80p is indeed required for hyphal growth in response to different filament-inducing cues and for the proper expression of genes characterizing the filamentous transcriptional program. These include noteworthy genes encoding cell wall components, such as
HWP1
,
ECE1
,
RBT4
, and
ALS3
. We also show that CaNdt80p is essential for the completion of cell separation through the direct transcriptional regulation of genes encoding the chitinase Cht3p and the cell wall glucosidase Sun41p. Consistent with their hyphal defect,
ndt80
mutants are avirulent in a mouse model of systemic candidiasis. Interestingly, based on functional-domain organization, CaNdt80p seems to be a unique regulator characterizing fungi from the CTG clade within the subphylum Saccharomycotina. Therefore, this study revealed a new role of the novel member of the fungal NDT80 transcription factor family as a regulator of cell separation, hyphal growth, and virulence.
The Aspergillus fumigatus P-Type Golgi Apparatus Ca
2+
/Mn
2+
ATPase PmrA Is Involved in Cation Homeostasis and Cell Wall Integrity but Is Not Essential for Pathogenesis
Authors: Pinchai Nadthanan , Juvvadi Praveen Rao , Fortwendel Jarrod R. , Perfect B. Zachary , Rogg Luise E. , Asfaw Yohannes G. , Steinbach William J.
Published: January 2010

The
Aspergillus fumigatus
Δ
pmrA
(Golgi apparatus Ca
2+
/Mn
2+
P-type ATPase) strain has osmotically suppressible basal growth defects and cationic tolerance associated with increased expression of calcineurin pathway genes. Despite increased β-glucan and chitin content, it is hypersensitive to cell wall inhibitors but remains virulent, suggesting a role for PmrA in cation homeostasis and cell wall integrity.
Activation of ExoU Phospholipase Activity Requires Specific C-Terminal Regions
Authors: Schmalzer Katherine M. , Benson Marc A. , Frank Dara W.
Published: January 2010

Pseudomonas aeruginosa
is a Gram-negative opportunistic pathogen that utilizes a type III secretion system to subvert host innate immunity. Of the 4 known effector proteins injected into eukaryotic cells, ExoS and ExoU are cytotoxic. The cytotoxic phenotype of ExoU depends on the enzymatic activity of the patatin-like phospholipase A
2
domain localized to the N-terminal half of the protein. Amino acid residues located within the C-terminal region of ExoU are postulated to be required for trafficking or localization to the plasma membrane of eukaryotic cells. This report describes the characterization of a transposon-based linker insertion library in ExoU. Utilizing an unbiased screening approach and sensitive methods for measuring enzymatic activity, we identified regions of ExoU that are critical for activation of the phospholipase activity by the only known cofactor, SOD1. Insertions at D572 and L618 reduced the rate of substrate cleavage. Enzymatic activity could be restored to almost parental levels when SOD1 concentrations were increased, suggesting that the linker insertion disrupted the interaction between ExoU and SOD1. An enzyme-linked immunosorbent assay (ELISA)-based binding test was developed to measure ExoU-SOD1 binding. These experiments suggest that ExoU activation by SOD1 is hampered by linker insertion. ExoU derivatives harboring minimal phospholipase activity retained biological activity in tissue culture assays. These proteins affected primarily cellular architecture in a manner similar to that of ExoT. Our studies suggest that conformational changes in ExoU are facilitated by SOD1. Importantly, the level of phospholipase activity influences the biological outcome of ExoU intoxication.
Precise Excision of IS
5
from the Intergenic Region between the
fucPIK
and the
fucAO
Operons and Mutational Control of
fucPIK
Operon Expression in
Escherichia coli
Authors: Zhang Zhongge , Yen Ming Ren , Saier Milton H.
Published: January 2010

Excision of transposable genetic elements from host DNA occurs at low frequencies and is usually imprecise. A common insertion sequence element in
Escherichia coli
, IS
5
, has been shown to provide various benefits to its host by inserting into specific sites. Precise excision of this element had not previously been demonstrated. Using a unique system, the fucose (
fuc
) regulon, in which IS
5
insertion and excision result in two distinct selectable phenotypes, we have demonstrated that IS
5
can precisely excise from its insertion site, restoring the wild-type phenotype. In addition to precise excision, several “suppressor” insertion, deletion, and point mutations restore the wild-type Fuc
+
phenotype to various degrees without IS
5
excision. The possible bases for these observations are discussed.
Pyruvate Carboxylase Plays a Crucial Role in Carbon Metabolism of Extra- and Intracellularly ReplicatingListeria monocytogenes
Authors: Schär Jennifer , Stoll Regina , Schauer Kristina , Loeffler Daniela I. M. , Eylert Eva , Joseph Biju , Eisenreich Wolfgang , Fuchs Thilo M. , Goebel Werner
Published: January 2010

The human pathogenL. monocytogenesis a facultatively intracellular bacterium that survives and replicates in the cytosol of many mammalian cells. The listerial metabolism, especially under intracellular conditions, is still poorly understood. Recent studies analyzed the carbon metabolism ofL. monocytogenesby the13C isotopologue perturbation method in a defined minimal medium containing [U-13C6]glucose. It was shown that these bacteria produce oxaloacetate mainly by carboxylation of pyruvate due to an incomplete tricarboxylic acid cycle. Here, we report that apycAinsertion mutant defective in pyruvate carboxylase (PYC) still grows, albeit at a reduced rate, in brain heart infusion (BHI) medium but is unable to multiply in a defined minimal medium with glucose or glycerol as a carbon source. Aspartate and glutamate of thepycAmutant, in contrast to the wild-type strain, remain unlabeled when [U-13C6]glucose is added to BHI, indicating that the PYC-catalyzed carboxylation of pyruvate is the predominant reaction leading to oxaloacetate inL. monocytogenes. ThepycAmutant is also unable to replicate in mammalian cells and exhibits high virulence attenuation in the mouse sepsis model.
Thermosensing Function of theEscherichia coliRedox Sensor Aer
Authors: Nishiyama So-ichiro , Ohno Shinji , Ohta Noriko , Inoue Yuichi , Fukuoka Hajime , Ishijima Akihiko , Kawagishi Ikuro
Published: January 2010

Escherichia colichemoreceptors can sense changes in temperature for thermotaxis. Here we found that the aerotaxis transducer Aer, a homolog of chemoreceptors lacking a periplasmic domain, mediates thermoresponses. We propose that thermosensing by the chemoreceptors is a general attribute of their highly conserved cytoplasmic domain (or their less conserved transmembrane domain).
Pseudomonas aeruginosaIncreases Formation of Multidrug-Tolerant Persister Cells in Response to Quorum-Sensing Signaling Molecules
Authors: Möker Nina , Dean Charles R. , Tao Jianshi
Published: January 2010

Bacterial persister cells constitute a small portion of a culture which is tolerant to killing by lethal doses of bactericidal antibiotics. These phenotypic variants are formed in numerous bacterial species, including those with clinical relevance like the opportunistic pathogenPseudomonas aeruginosa. Although persisters are believed to contribute to difficulties in the treatment of many infectious diseases, the underlying mechanisms affecting persister formation are not well understood. Here we show that even thoughP. aeruginosacultures have a significantly smaller fraction of multidrug-tolerant persister cells than cultures ofEscherichia coliorStaphylococcus aureus, they can increase persister numbers in response to quorum-sensing-related signaling molecules. The phenazine pyocyanin (and the closely related molecule paraquat) and the acyl-homoserine lactone 3-OC12-HSL significantly increased the persister numbers in logarithmicP. aeruginosaPAO1 or PA14 cultures but not inE. coliorS. aureuscultures.
The Zur-Regulated ZinT Protein Is an Auxiliary Component of the High-Affinity ZnuABC Zinc Transporter That Facilitates Metal Recruitment during Severe Zinc Shortage
Authors: Petrarca Patrizia , Ammendola Serena , Pasquali Paolo , Battistoni Andrea
Published: January 2010

The pathways ensuring the efficient uptake of zinc are crucial for the ability of bacteria to multiply in the infected host. To better understand bacterial responses to zinc deficiency, we have investigated the role of the periplasmic protein ZinT in
Salmonella enterica
serovar Typhimurium. We have found that
zinT
expression is regulated by Zur and parallels that of ZnuA, the periplasmic component of the zinc transporter ZnuABC. Despite the fact that ZinT contributes to
Salmonella
growth in media containing little zinc, disruption of
zinT
does not significantly affect virulence in mice. The role of ZinT became clear using strains expressing a mutated form of ZnuA lacking a characteristic histidine-rich domain. In fact,
Salmonella
strains producing this modified form of ZnuA exhibited a ZinT-dependent capability to import zinc either
in vitro
or in infected mice, suggesting that ZinT and the histidine-rich region of ZnuA have redundant function. The hypothesis that ZinT and ZnuA cooperate in the process of zinc recruitment is supported by the observation that they form a stable binary complex
in vitro
. Although the presence of ZinT is not strictly required to ensure the functionality of the ZnuABC transporter, our data suggest that ZinT facilitates metal acquisition during severe zinc shortage.
Binding of Azole Antibiotics to
Staphylococcus aureus
Flavohemoglobin Increases Intracellular Oxidative Stress
Authors: Nobre Lígia S. , Todorovic Smilja , Tavares Ana Filipa N. , Oldfield Eric , Hildebrandt Peter , Teixeira Miguel , Saraiva Lígia M.
Published: January 2010

In this work, we report that flavohemoglobin contributes to the azole susceptibility of
Staphylococcus aureus
. We first observed that deletion of the flavohemoglobin gene leads to an increase in the viability of imidazole-treated
S. aureus
cells and that reversion to the wild-type phenotype occurs upon expression of flavohemoglobin from a multicopy plasmid. Further spectroscopic analyses showed that miconazole, the most efficient azole antibiotic against
S. aureus
, ligates to heme of both oxidized and reduced flavohemoglobin. The binding of miconazole to oxidized flavohemoglobin, with an association constant of 1.7 × 10
6
M
−1
, typical of a tight, specific binding equilibrium, results in augmentation of the superoxide production by the enzyme. These results are corroborated by
in vivo
studies showing that imidazole-treated
S. aureus
cells expressing flavohemoglobin contain a larger amount of reactive oxygen species. Moreover, it was observed that the survival of miconazole-treated
S. aureus
internalized by murine macrophages is higher for cells lacking flavohemoglobin. Altogether, the present data revealed that in
S. aureus
, flavohemoglobin enhances the antimicrobial activity of imidazoles via an increase of intracellular oxidative stress.
The ArcB Sensor Kinase of
Escherichia coli
Autophosphorylates by an Intramolecular Reaction
Authors: Peña-Sandoval Gabriela R. , Georgellis Dimitris
Published: January 2010

The Arc two-component system, comprising the ArcB sensor kinase and the ArcA response regulator, modulates the expression of numerous genes in response to the respiratory conditions of growth. ArcB is a tripartite histidine kinase whose activity is regulated by the oxidation of two cytosol-located redox-active cysteine residues that participate in intermolecular disulfide bond formation. Here we show that ArcB autophosphorylates through an intramolecular reaction which diverges from the usually envisaged intermolecular autophosphorylation of homodimeric histidine kinases.
Microscopic Cords, a Virulence-Related Characteristic of
Mycobacterium tuberculosis
, Are Also Present in Nonpathogenic Mycobacteria
Authors: Julián Esther , Roldán Mónica , Sánchez-Chardi Alejandro , Astola Oihane , Agustí Gemma , Luquin Marina
Published: January 2010

The aggregation of mycobacterial cells in a definite order, forming microscopic structures that resemble cords, is known as cord formation, or cording, and is considered a virulence factor in the
M
ycobacterium tuberculosis
complex and the species
M
ycobacterium marinum
. In the 1950s, cording was related to a trehalose dimycolate lipid that, consequently, was named the cord factor. However, modern techniques of microbial genetics have revealed that cording can be affected by mutations in genes not directly involved in trehalose dimycolate biosynthesis. Therefore, questions such as “How does mycobacterial cord formation occur?” and “Which molecular factors play a role in cord formation?” remain unanswered. At present, one of the problems in cording studies is the correct interpretation of cording morphology. Using optical microscopy, it is sometimes difficult to distinguish between cording and clumping, which is a general property of mycobacteria due to their hydrophobic surfaces. In this work, we provide a new way to visualize cords in great detail using scanning electron microscopy, and we show the first scanning electron microscopy images of the ultrastructure of mycobacterial cords, making this technique the ideal tool for cording studies. This technique has enabled us to affirm that nonpathogenic mycobacteria also form microscopic cords. Finally, we demonstrate that a strong correlation exists between microscopic cords, rough colonial morphology, and increased persistence of mycobacteria inside macrophages.
The Ribosomal Protein L2 Interacts with the RNA Polymerase α Subunit and Acts as a Transcription Modulator in
Escherichia coli
Authors: Rippa Valentina , Cirulli Claudia , Di Palo Benedetta , Doti Nunzianna , Amoresano Angela , Duilio Angela
Published: January 2010

Identification of interacting proteins in stable complexes is essential to understand the mechanisms that regulate cellular processes at the molecular level. Transcription initiation in prokaryotes requires coordinated protein-protein and protein-DNA interactions that often involve one or more transcription factors in addition to RNA polymerase (RNAP) subunits. The RNAP α subunit (RNAPα) is a key regulatory element in gene transcription and functions through direct interaction with other proteins to control all stages of this process. A clear description of the RNAPα protein partners should greatly increase our understanding of transcription modulation. A functional proteomics approach was employed to investigate protein components that specifically interact with RNAPα. A tagged form of
Escherichia coli
RNAPα was used as bait to determine the molecular partners of this subunit in a whole-cell extract. Among other interacting proteins, 50S ribosomal protein L2 (RPL2) was clearly identified by mass spectrometry. The direct interaction between RNAPα and RPL2 was confirmed both
in vivo
and
in vitro
by performing coimmunoprecipitation and bacterial two-hybrid experiments. The functional role of this interaction was also investigated in the presence of a ribosomal promoter by using a β-galactosidase gene reporter assay. The results clearly demonstrated that RPL2 was able to increase β-galactosidase expression only in the presence of a specific ribosomal promoter, whereas it was inactive when it was assayed with an unrelated promoter. Interestingly, other ribosomal proteins (L1, L3, L20, and L27) did not have any effect on rRNA expression. The findings reported here strongly suggest that in addition to its role in ribosome assembly the highly conserved RPL2 protein plays a specific and direct role in regulation of transcription.
Direct Evidence for Control of the Pheromone-InducibleprgQOperon ofEnterococcus faecalisPlasmid pCF10 by a Countertranscript-Driven Attenuation Mechanism
Authors: Johnson Christopher M. , Manias Dawn A. , Haemig Heather A. H. , Shokeen Sonia , Weaver Keith E. , Henkin Tina M. , Dunny Gary M.
Published: January 2010

The mating response ofEnterococcus faecaliscells carrying the conjugative plasmid pCF10 is controlled by multiple regulatory circuits. Initiation of transcription of theprgQconjugation operon is controlled by the peptide receptor protein PrgX; binding of the pheromone peptide cCF10 to PrgX abolishes PrgX repression, while binding of the inhibitor peptide iCF10 enhances repression. The results of molecular analysis ofprgQtranscripts and genetic studies suggested that the elongation ofprgQtranscripts past a putative terminator (IRS1) may be controlled by the interaction of nascentprgQmRNAs with a small antisense RNA (Anti-Q) encoded withinprgQ. Direct evidence for interaction of these RNAs, as well as the resulting effects on readthrough ofprgQtranscription, has been limited. Here we report the results of experiments that (i) determine the inherent termination properties ofprgQtranscripts in the absence of Anti-Q; (ii) determine the direct effects of the interaction of Anti-Q with nascentprgQtranscripts in the absence of complicating effects of the PrgX protein; and (iii) begin to dissect the structural components involved in these interactions. The results confirm the existence of alternative terminating and antiterminating forms of nascentprgQtranscriptsin vivoand demonstrate that the interaction of Anti-Q with these transcripts leads to termination via inhibition of antiterminator formation.In vitrotranscription assays support the major results of thein vivostudies. The data support a model for Anti-Q function suggested from recent studies of these RNAs and their interactionsin vitro(S. Shokeen, C. M. Johnson, T. J. Greenfield, D. A. Manias, G. M. Dunny, and K. E. Weaver, submitted for publication).
SufU Is an Essential Iron-Sulfur Cluster Scaffold Protein in
Bacillus subtilis
Authors: Albrecht Alexander G. , Netz Daili J. A. , Miethke Marcus , Pierik Antonio J. , Burghaus Olaf , Peuckert Florian , Lill Roland , Marahiel Mohamed A.
Published: January 2010

Bacteria use three distinct systems for iron-sulfur (Fe/S) cluster biogenesis: the ISC, SUF, and NIF machineries. The ISC and SUF systems are widely distributed, and many bacteria possess both of them. In
Escherichia coli
, ISC is the major and constitutive system, whereas SUF is induced under iron starvation and/or oxidative stress. Genomic analysis of the Fe/S cluster biosynthesis genes in
Bacillus subtilis
suggests that this bacterium's genome encodes only a SUF system consisting of a
sufCDSUB
gene cluster and a distant
sufA
gene. Mutant analysis of the putative Fe/S scaffold genes
sufU
and
sufA
revealed that
sufU
is essential for growth under minimal standard conditions, but not
sufA
. The drastic growth retardation of a conditional mutant depleted of SufU was coupled with a severe reduction of aconitase and succinate dehydrogenase activities in total-cell lysates, suggesting a crucial function of SufU in Fe/S protein biogenesis. Recombinant SufU was devoid of Fe/S clusters after aerobic purification. Upon
in vitro
reconstitution, SufU bound an Fe/S cluster with up to ∼1.5 Fe and S per monomer. The assembled Fe/S cluster could be transferred from SufU to the
apo
form of isopropylmalate isomerase Leu1, rapidly forming catalytically active [4Fe-4S]-containing
holo
-enzyme. In contrast to native SufU, its D43A variant carried a Fe/S cluster after aerobic purification, indicating that the cluster is stabilized by this mutation. Further, we show that
apo
-SufU is an activator of the cysteine desulfurase SufS by enhancing its activity about 40-fold
in vitro
. SufS-dependent formation of
holo
-SufU suggests that SufU functions as an Fe/S cluster scaffold protein tightly cooperating with the SufS cysteine desulfurase.
Specificity of the Type II Secretion Systems of Enterotoxigenic
Escherichia coli
and
Vibrio cholerae
for Heat-Labile Enterotoxin and Cholera Toxin
Authors: Mudrak Benjamin , Kuehn Meta J.
Published: January 2010

The Gram-negative type II secretion (T2S) system is a multiprotein complex mediating the release of virulence factors from a number of pathogens. While an understanding of the function of T2S components is emerging, little is known about what identifies substrates for export. To investigate T2S substrate recognition, we compared mutations affecting the secretion of two highly homologous substrates: heat-labile enterotoxin (LT) from enterotoxigenic
Escherichia coli
(ETEC) and cholera toxin (CT) from
Vibrio cholerae
. Each toxin consists of one enzymatic A subunit and a ring of five B subunits mediating the toxin's secretion. Here, we report two mutations in LT's B subunit (LTB) that reduce its secretion from ETEC without global effects on the toxin. The Q3K mutation reduced levels of secreted LT by half, and as with CT (T. D. Connell, D. J. Metzger, M. Wang, M. G. Jobling, and R. K. Holmes, Infect. Immun. 63:4091-4098, 1995), the E11K mutation impaired LT secretion. Results
in vitro
and
in vivo
show that these mutants are not degraded more readily than wild-type LT. The Q3K mutation did not significantly affect CT B subunit (CTB) secretion from
V. cholerae
, and the E11A mutation altered LT and CTB secretion to various extents, indicating that these toxins are identified as secretion substrates in different ways. The levels of mutant LTB expressed in
V. cholerae
were low or undetectable, but each CTB mutant expressed and secreted at wild-type levels in ETEC. Therefore, ETEC's T2S system seems to accommodate mutations in CTB that impair the secretion of LTB. Our results highlight the exquisitely fine-tuned relationship between T2S substrates and their coordinate secretion machineries in different bacterial species.
A flowline map of glaciated Canada based on remote sensing dataThis paper is accompanied by a large foldout map entitled A flowline map of glaciated Canada based on remote sensing data (see pocket on back cover).
Authors: Shaw John , Sharpe Davis , Harris Jeff
Published: January 2010

The map A flowline map of glaciated Canada based on remote sensing data presents flowlines for the former Laurentide and Cordilleran ice sheets based on flow indicators derived from aggregated, flow-parallel landforms — drumlins and crag and tails, fluting, sinuous ridges and furrows, and rises. An extensive review introduces the concepts and evolution of flowline mapping at continental-ice-sheet and regional scales, emphasizing the use of new remote sensing data. Coherent, glaciologically plausible sets of flowlines mapped as flow tracts reflect large-scale flow structure in the paleo-ice sheets and demarcate fields of flow-parallel bedforms. In addition to flow reconstruction, mapped distributions of fields of glacial terrain types — hummocky terrain, Rogen terrain, and bedrock-dominant terrain — increase our power to interpret flowlines and, in turn, give evidence on the genesis of these terrains. End moraines and eskers also aid map interpretation. Landsat 7 Enhanced Thematic Mapper+ (ETM+) satellite images and Shuttle Radar Topography Mission (SRTM) hill shades provide the basic information for this flowline mapping in a Geographical Information System (ArcMap). Information on the Flowline Map allows us to develop conceptual models of ice sheets and to appreciate regional constraints on applications in mineral exploration, in aggregate and groundwater discovery and assessment, in soil and landform genesis, and in glaciology, paleoclimatology, and paleoceanography.
Paleoproterozoic subduction in northwestern Canada from near-vertical and wide-angle seismic reflection data
Authors: Oueity Jounada , Clowes Ron M.
Published: January 2010

Near-vertical incidence and refraction – wide-angle reflection seismic data, recorded as part of Lithoprobe studies in the Paleoproterozoic–Archean domains of Canada’s Northwest Territories, show remarkable reflections from within the upper mantle. A parallel pair of reflectors imaged by the near-vertical data can be traced from Moho levels (∼33 km) down to ∼70 km depth. In a previous study, the reflectors were interpreted as the top and bottom of an ∼1.8 Ga subducted oceanic crust beneath the Hottah terrane. Further inboard, where the seismic line changes its direction from east–west to nearly north–south, another pair of reflectors extends subhorizontally for about 100 km at ∼70 km depth before dipping downward. The subhorizontal reflectors were not correlated with the dipping slab; instead they were interpreted as a separate feature. However, they roughly coincide with a horizontal interface modeled from wide-angle data by an earlier study. Considering the crooked line acquisition geometry, we re-examined both near-vertical incidence and wide-angle reflection data using 2-dimensional (2-D) and 3-D forward and inverse modeling algorithms. Our results demonstrate that the subhorizontal reflectors are the continuation of the relict subducted slab, which now extends laterally for 300 km. Its base is the source of the wide-angle data. The apparent flattening for the near-vertical data is most likely an artifact of projecting a 3-D geometry onto a 2-D cross section. The shallowly subducted slab probably contributed to the thickening and stabilization of the subcrustal lithosphere below the Wopmay orogen.
No evidence for large differences in genomic methylation between wild and hatchery steelhead (Oncorhynchus mykiss)
Authors: Blouin Michael S. , Thuillier Virginie , Cooper Becky , Amarasinghe Vindhya , Cluzel Laura , Araki Hitoshi , Grunau Christoph
Published: January 2010

When salmonid fish that have been raised in hatcheries spawn in the wild, they often produce fewer surviving adult offspring than wild fish. Recent data from steelhead ( Oncorhynchus mykiss ) in the Hood River (Oregon, USA) show that even one or two generations of hatchery culture can result in dramatic declines in fitness. Although intense domestication selection could cause such declines, it is worth considering alternative explanations. One possibility is heritable epigenetic changes induced by the hatchery environment. Here, we show, using methylation-sensitive amplified fragment length polymorphism, that hatchery and wild adult steelhead from the Hood River do not appear to differ substantially in overall levels of genomic methylation. Thus, although altered methylation of specific DNA sites or other epigenetic processes could still be important, the hatchery environment does not appear to cause a global hypo- or hypermethylation of the genome or create a large number of sites that are differentially methylated.
Integration of growth hormone gene constructs in transgenic strains of coho salmon (Oncorhynchus kisutch) at centromeric or telomeric sites
Authors: Phillips Ruth B. , Devlin Robert H.
Published: January 2010

Very little information is currently available regarding the sites of integration of transgenes in genetically engineered fish. We examined the chromosomal location of growth hormone gene constructs containing GH1 in three different strains of transgenic coho salmon produced by microinjection into pronuclei of fertilized eggs. The constructs were labeled and used as probes in fluorescence in situ hybridization experiments on chromosome preparations from the M77, MT5750A, and H3D0474 strains of transgenic coho salmon. The constructs were localized at 1–3 different sites in different strains. In the M77 strain the construct was found at a single centromeric site on a medium-sized metacentric chromosome, while in the MT5750A strain, the construct was found at a single telomeric site on the short arm of chromosome pair 21, a subtelocentric chromosome with a large band of repetitive DNA on the short arm. In the H3D0474 strain, the construct was found at telomeric sites on the long arms of three metacentric chromosomes that appear to represent one pair of homologous chromosomes and one chromosome containing the homeologous long arm (recently duplicated chromosome arm) corresponding to the long arm of the first pair. This suggests transfer of the construct may have occurred by homologous and homeologous crossing over. All of the constructs incorporated at restricted sites characterized by the presence of tandem DNA repeats.
Identification of new winter wheat – winter barley addition lines (6HS and 7H) using fluorescence in situ hybridization and the stability of the whole ‘Martonvásári 9 kr1’ – ‘Igri’ addition set
Authors: Szakács É. , Molnár-Láng M.
Published: January 2010

A previous paper reported the development of disomic addition lines (2H, 3H, 4H, and 1HS isochromosomic) from hybrids between the winter wheat ‘Martonvásári 9 kr1’ and the two-rowed winter barley cultivar ‘Igri’. The present paper describes the isolation of two new additions, the 7H disomic and 6HS ditelosomic additions, using fluorescence in situ hybridization with the repetitive DNA probes Afa-family and HvT01. The identification of the barley chromosomes in the wheat genome was confirmed with simple sequence repeat markers. The morphological characterization of the new addition lines is also discussed. Studies of the genetic stability of the whole set (2H, 3H, 4H, 7H, 1HS iso, 6HS) of ‘Martonvásári 9 kr1’ – ‘Igri’ additions revealed that the most stable disomic additions are 2H and 3H and the most unstable line is the 1HS isochromosomic addition.
The use of instability to train the core musculature
Authors: Behm David G. , Drinkwater Eric J. , Willardson Jeffrey M. , Cowley Patrick M.
Published: January 2010

Training of the trunk or core muscles for enhanced health, rehabilitation, and athletic performance has received renewed emphasis. Instability resistance exercises have become a popular means of training the core and improving balance. Whether instability resistance training is as, more, or less effective than traditional ground-based resistance training is not fully resolved. The purpose of this review is to address the effectiveness of instability resistance training for athletic, nonathletic, and rehabilitation conditioning. The anatomical core is defined as the axial skeleton and all soft tissues with a proximal attachment on the axial skeleton. Spinal stability is an interaction of passive and active muscle and neural subsystems. Training programs must prepare athletes for a wide variety of postures and external forces, and should include exercises with a destabilizing component. While unstable devices have been shown to be effective in decreasing the incidence of low back pain and increasing the sensory efficiency of soft tissues, they are not recommended as the primary exercises for hypertrophy, absolute strength, or power, especially in trained athletes. For athletes, ground-based free-weight exercises with moderate levels of instability should form the foundation of exercises to train the core musculature. Instability resistance exercises can play an important role in periodization and rehabilitation, and as alternative exercises for the recreationally active individual with less interest or access to ground-based free-weight exercises. Based on the relatively high proportion of type I fibers, the core musculature might respond well to multiple sets with high repetitions (e.g., >15 per set); however, a particular sport may necessitate fewer repetitions.
Communication between the AAA+ ring and microtubule-binding domain of dyneinThis paper is one of a selection of papers published in this special issue entitled 8th International Conference on AAA Proteins and has undergone the Journal's usual peer review process.
Authors: Carter Andrew P. , Vale Ronald D.
Published: January 2010

Dyneins are microtubule motors, the core of which consists of a ring of AAA+ domains. ATP-driven conformational changes of the AAA+ ring are used to drive the movement of a mechanical element (termed the linker domain) that provides the motor’s powerstroke and to change the affinity of the motor for microtubules (strong binding during the power stroke and weak binding to allow stepping and recocking of the linker domain). Dynein’s microtubule-binding domain (MTBD) is located at the end of a 10 nm long anti-parallel coiled coil (the stalk) and conformational changes that alter the affinity for microtubules must propagate through this coiled coil. A recent crystal structure of dynein’s MTBD sheds new light on how this long-range communication along a coiled coil might occur.
Cytotoxic phenolic compounds in leaf buds of Populus tremuloides
Authors: Pichette André , Eftekhari Azadeh , Georges Patricia , Lavoie Serge , Mshvildadze Vakhtang , Legault Jean
Published: January 2010

Phytochemical investigations of the EtOH extract of Populus tremuloides leaf buds led to the isolation of 19 phenolic compounds. Among them, (1S,2S)-1-[4-O-E-coumaroyl-β-d-glucopyranosyloxy]cyclohexanediol was reported for the first time, and its structure was determined by spectroscopic (NMR and MS) and chemical methods. Seventeen of the isolated compounds were tested for their cytotoxicity against lung carcinoma (A549) and colorectal adenocarcinoma (DLD-1) human cell lines. Antibacterial activity was also evaluated against Escherichia coli and Staphylococcus aureus .
Role of the RhoA/Rho-kinase pathway in the regulation of pulmonary vasoconstrictor function
Authors: Nossaman Bobby D. , Nossaman Vaughn E. , Murthy Subramanyam N. , Kadowitz Philip J.
Published: January 2010

Calcium is the major intracellular messenger that triggers smooth muscle contraction. The study of calcium-binding proteins, such as calmodulin and its downstream effectors, reveals critical regulation of smooth muscle contraction by protein kinases and phosphatases. Moreover, the small GTP-binding protein RhoA and its downstream effector protein, Rho-kinase, have been shown to play a novel role in the regulation of smooth muscle contraction. Studies have shown that the activation of Rho-kinase is involved in the development of endothelial dysfunction, inflammation, restenosis, and increased vascular tone in a number of cardiovascular disorders. Because inhibitors of this pathway promote vasodilation independent of the mechanism that increases vasoconstrictor tone, it is our hypothesis that Rho-kinase is constitutively active in regulating vasoconstrictor tone in the pulmonary and systemic vascular beds. Studies in the literature suggest that the RhoA/Rho-kinase pathway has an important role in the pathogenesis of pulmonary hypertension.
Leflunomide induces immunosuppression in collagen-induced arthritis rats by upregulating CD4+CD25+regulatory T cells
Authors: Wang Ting-Yu , Li Jun , Li Chang-Yu , Jin Yong , Lü Xiong-Wen , Wang Xiao-Hua , Zhou Qian
Published: January 2010

This study was to investigate the effect of leflunomide on the immunosuppressive CD4+CD25+regulatory T cells (CD4+CD25+Tregs) in collagen-induced arthritis (CIA) rats. CIA was induced by collagen type II in Wistar rats. Immunofluorescence flow cytometry and RT-PCR were used to determine the proportion of CD4+CD25+Tregs and the expression of Foxp3 mRNA, respectively. Proliferation of T lymphocytes was assayed with MTT reagent, and the level of transforming growth factor β1 (TGF-β1) in the supernatant of concanavalin A (Con A)-induced T lymphocytes was determined by ELISA kit. Our investigations demonstrated that inhibition of arthritis by leflunomide was related to changes in CD4+CD25+Tregs. In addition, A771726, which is the active metabolite of leflunomide, promoted the differentiation of spleen lymphocytes into CD4+CD25+Tregs, increased antiinflammatory cytokine TGF-β1 secretion, and adjusted the activity of Con A-induced lymphocytes in vitro.
Role of glucagon-like peptide-1 analogues on insulin receptor regulation in diabetic rat hearts
Authors: Hantouche Christine M. , Bitar Khalil M. , Nemer Georges M. , Obeid Mounir Y. , Kadi Lina N. , Der-Boghossian Asdghig H. , Bikhazi Anwar B.
Published: January 2010

This study focused on the regulation and affinity modulation of the insulin receptor of coronary endothelium and cardiomyocytes in nondiabetic and STZ-induced type 1 diabetic rats. Male rats were divided into the following 9 groups: nondiabetic (N), nondiabetic treated with exendin-4 (NE), nondiabetic treated with dipeptidyl peptidase IV (DPP-IV) inhibitor (NDp), diabetic (D), diabetic treated with insulin (DI), diabetic treated with exendin-4 (DE), diabetic co-treated with insulin and exendin-4 (DIE), diabetic treated with DPP-IV inhibitor (DDp), and diabetic co-treated with insulin and DPP-IV inhibitor (DIDp). After the rats were treated for 1 month, a first-order Bessel function was employed to estimate the insulin binding affinity (with time constant τ = 1/k−n) to its receptors on the coronary endothelium and cardiomyocytes using CHAPS-untreated and CHAPS-treated heart perfusion, respectively. The results showed that diabetes (D) decreased the τ value on the coronary endothelium and increased it on cardiomyocytes compared with the nondiabetic group (N). Treatment with insulin and (or) exendin-4, a glucagon-like peptide-1 (GLP-1) analogue, increased τ on the coronary endothelium only. On the coronary endothelium, τ values of DI and DIDp were normalized. Western blots of the insulin receptor showed upregulation in D, downregulation in DI, and normalization in DE and DDp. Immunohistochemistry and RT-PCR findings indicated atrial natriuretic factor (ANF) in all diabetic ventricles, thus ascertaining hypertrophy. Therefore, negative myocardial effects related to the insulin receptor were diminished in diabetic rats treated with DPP-IV inhibitor and, more efficiently, by exendin-4.
The effect of prey availability on metabolism and activity in the tarantulaPhormictopus cancerides
Authors: Philip B. N. , Shillington C.
Published: January 2010

Spiders typically exhibit very low resting metabolic rates (RMR) and altered feeding behaviors as mechanisms to survive extended periods of limited food availability. We examined the effect of different periods of food deprivation on RMR and foraging activities in the Hispaniolan giant tarantula ( Phormictopus cancerides (Latreille, 1806)) (Araneae: Theraphosidae). Juvenile tarantulas were separated into two feeding groups and fed once either every 5 or 30 days. Monthly feeding trials were preceded by RMR measurements. During feeding trials, we compared differences between the two groups in (i) prey capture frequency, (ii) time to prey capture, (iii) locomotory activity, and (iv) the predator’s prey detection distance. Metabolic rates increased for the well-fed group but remained constant for individuals fed once a month. Time to prey capture decreased for food-limited individuals and the proportion of individuals that ate during each feeding trial was significantly higher in the 30-day group. Conversely, results for locomotory activity and detection distances were inconclusive.
DISAPPEARANCE OF SCHWINGER'S STRING AT THE CHARGE–MONOPOLE "MOLECULE"
Authors: KORENBLIT S. E. , LEE KIEUN
Published: January 2010

An equivalence of total angular momentum operator of charge–monopole system to the momentum operator of a symmetrical quantum top is observed. This explicitly shows the string independence of Dirac's quantization condition leading to disappearance of Schwinger's string and reveals some properties of diatomic molecule for this system.
A CRITERION FOR SELECTING RELEVANT INTRINSIC MODE FUNCTIONS IN EMPIRICAL MODE DECOMPOSITION
Authors: AYENU-PRAH ALBERT , ATTOH-OKINE NII
Published: January 2010

Information extraction from time series has traditionally been done with Fourier analysis, which use stationary sines and cosines as basis functions. However, data that come from most natural phenomena are mostly nonstationary. A totally adaptive alternative method has been developed called the Hilbert–Huang transform (HHT), which involves generating basis functions called the intrinsic mode functions (IMFs) via the empirical mode decomposition (EMD). The EMD is a numerical procedure that is prone to numerical errors that may persist in the decomposition as extra IMFs. In this study, results of numerical experiments are presented, which would establish a stringent threshold by which relevant IMFs are distinguished from IMFs that may have been generated by numerical errors. The threshold is dependent on the correlation coefficient between the IMFs and the original signal. Finally, the threshold is applied to IMFs of earthquake signals from five accelerometers located in a building.
Semantic clustering of XML documents
Authors: Tagarelli Andrea , Greco Sergio
Published: January 2010

Dealing with structure and content semantics underlying semistructured documents is challenging for any task of document management and knowledge discovery conceived for such data. In this work we address the novel problem of clustering semantically related XML documents according to their structure and content features. XML features are generated by enriching syntactic with semantic information based on a lexical knowledge base. The backbone of the proposed framework for the semantic clustering of XML documents is a data representation model that exploits the notion of tree tuple to identify semantically cohesive substructures in XML documents and represent them as transactional data. This framework is equipped with two clustering algorithms based on different paradigms, namely centroid-based partitional clustering and frequent-itemset-based hierarchical clustering. An extensive experimental evaluation was conducted on real data sets from various domains, showing the significance of our approach as a solution for the semantic clustering of XML documents.
Therapeutics Development for Cystic Fibrosis: A Successful Model for a Multisystem Genetic Disease
Authors: Ashlock Melissa A. , Olson Eric R.
Published: January 2010

Cystic fibrosis (CF) is a progressive genetic disease primarily involving the respiratory and gastrointestinal tracts. Multiple therapies directed at CF symptoms and clinical management strategies have emerged from iterative cycles of therapeutics development, helping to change the face of CF from a fatal childhood affliction to a disease in which nearly 50% of U.S. patients are adults. However, as a consequence of therapeutic advances, the burden of CF care is high, and despite progress, most patients succumb to respiratory failure. Addressing the basic defect in CF with systemic small molecules is evolving as a promising approach. A successful collaboration between a voluntary health organization and a pharmaceutical company, complemented by academic investigators and patients, has led to the clinical development of investigational drugs that restore function to defective CFTR protein in various tissues in CF patients. Important activities, leverage points, and challenges in this exemplary collaboration are reviewed with hope that the CF and other genetic disease communities can benefit from the lessons learned in generating new therapeutic approaches in CF.
Early Events in Sexual Transmission of HIV and SIV and Opportunities for Interventions
Authors: Haase Ashley T.
Published: January 2010

To constrain the growth of the HIV/AIDS pandemic and ultimately end it, effective measures must be developed to prevent sexual mucosal transmission, the major route by which new infections are acquired. I review sexual mucosal transmission of HIV and SIV, with a focus on vaginal transmission in the SIV rhesus macaque animal model, and the evidence for small founder populations of infected cells and the local expansion at the portal of entry necessary to establish systemic infection. These early events represent windows of maximum opportunity for interventions to prevent systemic infection. I highlight the paradoxical role the innate immune response plays in actually facilitating transmission, and a novel microbicide strategy that targets this innate response to prevent systemic infection, and I conclude with an agenda for future research that emphasizes mucosal immunology, virology and pathogenesis studies at each anatomic site of entry.
Increased interstitial loading reduces the effect of microstructural variations in cardiac tissue
Authors: Hubbard Marjorie Letitia , Henriquez Craig S.
Published: January 2010

Electrical propagation in diseased and aging hearts is strongly influenced by structural changes that occur in both the intracellular and interstitial spaces of cardiac tissue; however, very few studies have investigated how interactions between the two spaces affect propagation at the microscale. In this study, we used one-dimensional microstructural computer models of interconnected ventricular myocytes to systematically investigate how increasing the effective interstitial resistivity (ρoeff) influences action potential propagation in fibers with variations in intracellular properties such as cell coupling and cell length. Changes in ρoeff were incorporated into a monodomain model using a correction to the intracellular properties that was based on bidomain simulations. The results showed that increasing ρoeff in poorly coupled one-dimensional fibers alters the distribution of electrical load at the microscale and causes propagation to become more continuous. In the poorly coupled fiber, this continuous state is characterized by decreased gap junction delay, sustained conduction velocity, increased sodium current, reduced maximum upstroke velocity, and increased safety factor. Long, poorly coupled cells experience greater loading effects than short cells and show the greatest initial response to changes in ρoeff. In inhomogeneous fibers with adjacent well-coupled and poorly coupled regions, increasing ρoeff in the poorly coupled region also reduces source-load mismatch, which delays the onset of conduction block and reduces the dispersion of repolarization at the transition between the two regions. Increasing the ρoeff minimizes the effect of cell-to-cell variations and may influence the pattern of activation in critical regimes characterized by low intercellular coupling, microstructural heterogeneity, and reduced or abnormal membrane excitability.