bluuebunny/crossref_metadata_2025_split huggingface dataset:
TheMycobacterium aviumsubsp.paratuberculosisMAP3464 Gene Encodes an Oxidoreductase Involved in Invasion of Bovine Epithelial Cells through the Activation of Host Cell Cdc42
Authors: Alonso-Hearn Marta , Patel Dilip , Danelishvili Lia , Meunier-Goddik Lisbeth , Bermudez Luiz E. 
Published: October 2007

ABSTRACTMycobacterium aviumsubsp.paratuberculosisinfection of cattle takes place through the intestinal mucosa. To identifyM.aviumsubsp.paratuberculosisgenes associated with the invasion of bovine epithelial cells in vitro, we screened a library of transposon mutants. Several mutants ofM.aviumsubsp.paratuberculosiswere identified which invaded Madin-Darby bovine kidney (MDBK) epithelial cells less efficiently than wild-type (wt)M.aviumsubsp.paratuberculosis. The ΔOx mutant had the transposon located in the MAP3464 gene, a putative oxidoreductase gene whose expression is upregulated upon bacterial contact with MDBK cells. Complete restoration of invasion comparable to that for the wt bacterium was achieved by introducing a copy of the complete oxidoreductase operon into the ΔOx mutant. Immunoprecipitation and Western blot analysis indicated that wtM.aviumsubsp.paratuberculosisactivates Cdc42 and RhoA pathways of internalization 15 and 60 min after infection of the host cell, respectively. The ΔOx mutant, however, failed to activate the Cdc42 pathway. To determine whether anM.aviumsubsp.paratuberculosisprotein delivered to the host cell mediates the entry of the wt bacterium by activation of the Cdc42 pathway, affinity precipitation of active Cdc42 from MDBK-infected cells followed by mass spectrometry was carried out. We identified a 17-amino-acid bacterial peptide associated with the Cdc42 of cells infected with wtM.aviumsubsp.paratuberculosisbut not with the ΔOx mutant. The sequence of the peptide matches MAP3985c, a hypothetical protein, possibly functioning as a putative Cdc42 effector. These findings reveal a novel signaling pathway activated duringM.aviumsubsp.paratuberculosisentry that links the product of MAP3464 gene to activation of Cdc42 in the host cell.
Genetic and Functional Analyses of PptA, a Phospho-Form Transferase Targeting Type IV Pili inNeisseria gonorrhoeae
Authors: Næssan Cecilia L. , Egge-Jacobsen Wolfgang , Heiniger Ryan W. , Wolfgang Matthew C. , Aas Finn Erik , Røhr Åsmund , Winther-Larsen Hanne C. , Koomey Michael 
Published: October 2007

ABSTRACTThe PilE pilin subunit protein ofNeisseria gonorrhoeaeundergoes unique covalent modifications with phosphoethanolamine (PE) and phosphocholine (PC). Thepilinphospho-formtransferase A (PptA) protein, required for these modifications, shows sequence relatedness with and architectural similarities to lipopolysaccharide PE transferases. Here, we used regulated expression and mutagenesis as means to better define the relationships between PptA structure and function, as well as to probe the mechanisms by which other factors impact the system. We show here thatpptAexpression is coupled at the level of transcription to its distal gene,murF, in a division/cell wall gene operon and that PptA can act in a dose-dependent fashion in PilE phospho-form modification. Molecular modeling and site-directed mutagenesis provided the first direct evidence that PptA is a member of the alkaline phosphatase superfamily of metalloenzymes with similar metal-binding sites and conserved structural folds. Through phylogenetic analyses and sequence alignments, these conclusions were extended to include the lipopolysaccharide PE transferases, including members of the disparate Lpt6 subfamily, and the MdoB family of phosphoglycerol transferases. Each of these enzymes thus likely acts as a phospholipid head group transferase whose catalytic mechanism involves atrans-esterification step generating a protein-phospho-form ester intermediate. Coexpression of PptA with PilE inPseudomonas aeruginosaresulted in high levels of PE modification but was not sufficient for PC modification. This and other findings show that PptA-associated PC modification is governed by as-yet-undefined ancillary factors unique toN. gonorrhoeae.
O-Linked Glycosylation Ensures the Normal Conformation of the Autotransporter Adhesin Involved in Diffuse Adherence
Authors: Charbonneau Marie-Ève , Girard Victoria , Nikolakakis Anastasia , Campos Manuel , Berthiaume Frédéric , Dumas France , Lépine François , Mourez Michael 
Published: October 2007

ABSTRACT

The
Escherichia coli
adhesin involved in diffuse adherence (AIDA-I) is one of the few glycosylated proteins found in
Escherichia coli
. Glycosylation is mediated by a specific heptosyltransferase encoded by the
aah
gene, but little is known about the role of this modification and the mechanism involved. In this study, we identified several peptides of AIDA-I modified by the addition of heptoses by use of mass spectrometry and N-terminal sequencing of proteolytic fragments of AIDA-I. One threonine and 15 serine residues were identified as bearing heptoses, thus demonstrating for the first time that AIDA-I is O-glycosylated. We observed that unglycosylated AIDA-I is expressed in smaller amounts than its glycosylated counterpart and shows extensive signs of degradation upon heat extraction. We also observed that unglycosylated AIDA-I is more sensitive to proteases and induces important extracytoplasmic stress. Lastly, as was previously shown, we noted that glycosylation is required for AIDA-I to mediate adhesion to cultured epithelial cells, but purified mature AIDA-I fused to GST was found to bind in vitro to cells whether or not it was glycosylated. Taken together, our results suggest that glycosylation is required to ensure a normal conformation of AIDA-I and may be only indirectly necessary for its cell-binding function.
Transient Erythromycin Resistance Phenotype Associated with Peptidyl-tRNA Drop-Off on Early UGG and GGG Codons
Authors: Mačvanin Mirjana , Gonzalez de Valdivia Ernesto I. , Ardell David H. , Isaksson Leif A. 
Published: October 2007

ABSTRACTExpression of minigenes encoding tetra- or pentapeptides MXLX or MXLXV (E peptides), where X is a nonpolar amino acid, renders cells erythromycin resistant whereas expression of minigenes encoding tripeptide MXL does not. By using a 3A′ reporter gene system beginning with an E-peptide-encoding sequence, we asked whether the codons UGG and GGG, which are known to promote peptidyl-tRNA drop-off at early positions in mRNA, would result in a phenotype of erythromycin resistance if located after this sequence. We find that UGG or GGG, at either position +4 or +5, without a following stop codon, is associated with an erythromycin resistance phenotype upon gene induction. Our results suggest that, while a stop codon at +4 gives a tripeptide product (MIL) and erythromycin sensitivity, UGG or GGG codons at the same position give a tetrapeptide product (MILW or MILG) and phenotype of erythromycin resistance. Thus, the drop-off event on GGG or UGG codons occurs after incorporation of the corresponding amino acid into the growing peptide chain. Drop-off gives rise to a peptidyl-tRNA where the peptide moiety functionally mimics a minigene peptide product of the type previously associated with erythromycin resistance. Several genes inEscherichia colifulfill the requirements of high mRNA expression and an E-peptide sequence followed by UGG or GGG at position +4 or +5 and should potentially be able to give an erythromycin resistance phenotype.
Characterization of the Arsenate Respiratory Reductase from
Shewanella
sp. Strain ANA-3
Authors: Malasarn Davin , Keeffe Jennifer R. , Newman Dianne K. 
Published: October 2007

ABSTRACT

Microbial arsenate respiration contributes to the mobilization of arsenic from the solid to the soluble phase in various locales worldwide. To begin to predict the extent to which As(V) respiration impacts arsenic geochemical cycling, we characterized the expression and activity of the
Shewanella
sp. strain ANA-3 arsenate respiratory reductase (ARR), the key enzyme involved in this metabolism. ARR is expressed at the beginning of the exponential phase and persists throughout the stationary phase, at which point it is released from the cell. In intact cells, the enzyme localizes to the periplasm. To purify ARR, a heterologous expression system was developed in
Escherichia coli
. ARR requires anaerobic conditions and molybdenum for activity. ARR is a heterodimer of ∼131 kDa, composed of one ArrA subunit (∼95 kDa) and one ArrB subunit (∼27 kDa). For ARR to be functional, the two subunits must be expressed together. Elemental analysis of pure protein indicates that one Mo atom, four S atoms associated with a
bis
-molybdopterin guanine dinucleotide cofactor, and four to five [4Fe-4S] are present per ARR. ARR has an apparent melting temperature of 41°C, a
K

m

of 5 μM, and a
V
max
of 11,111 μmol of As(V) reduced min
−1
mg of protein
−1
and shows no activity in the presence of alternative electron acceptors such as antimonite, nitrate, selenate, and sulfate. The development of a heterologous overexpression system for ARR will facilitate future structural and/or functional studies of this protein family.
HasB, theSerratia marcescensTonB Paralog, Is Specific to HasR
Authors: Benevides-Matos Najla , Wandersman Cécile , Biville Francis 
Published: October 2007

ABSTRACTSerratia marcescenspossesses two functional TonB paralogs, TonBSmand HasB, for energizing TonB-dependent transport receptors (TBDT). Previous work had shown that HasB is specific to heme uptake in the natural host and inEscherichia coliexpressing theS. marcescensTBDT receptor HasR, whereas theS. marcescensTonB andE. coliTonB proteins function equally well with various TBDT receptors for heme and siderophores. This has raised the question of the target of this specificity. HasB could be specific either to heme TBDT receptors or only to HasR. To resolve this question, we have cloned inE. colianotherS. marcescensheme receptor, HemR, and we show here that this receptor is TonB dependent and does not work with HasB. This demonstrates that HasB is not dedicated to heme TBDT receptors but rather forms a specific pair with HasR. This is the first reported case of a specific TonB protein working with only one TBDT receptor in one given species. We discuss the occurrence, possible molecular mechanisms, and selective advantages of such dedicated TonB paralogs.
Role of RelA of
Streptococcus mutans
in Global Control of Gene Expression
Authors: Nascimento Marcelle M. , Lemos José A. , Abranches Jacqueline , Lin Vanessa K. , Burne Robert A. 
Published: October 2007

ABSTRACT

The production of (p)ppGpp by
Streptococcus mutans
UA159 is catalyzed by three gene products: RelA, RelP, and RelQ. Here, we investigate the role of the RelA (Rel) homologue of
S. mutans
in the stringent response and in the global control of gene expression. RelA of
S. mutans
was shown to synthesize pppGpp in vitro from GTP and ATP in the absence of added ribosomes, as well as in vivo in an
Escherichia coli relA-spoT
mutant. Mupirocin (MUP) was shown to induce high levels of (p)ppGpp production in
S. mutans
in a
relA
-dependent manner, with a concomitant reduction in GTP pools. Transcription profiling after MUP treatment of
S. mutans
revealed that 104 genes were upregulated and 130 were downregulated (
P
≤ 0.001); mainly, genes for macromolecular biosynthesis, translation, and energy metabolism were downregulated. When a derivative of UA159 carrying a complete deletion of the
relA
gene was treated with MUP, 72 genes were upregulated and 52 were downregulated (
P
≤ 0.001). The expression of 50 genes (
P
≤ 0.001) was commonly affected by MUP treatment in the two strains, suggesting that
S. mutans
can mount a
relA
-independent response to MUP. Consistent with the gene expression profiling, RelA was shown to play major roles in the regulation of phenotypic traits that are required for establishment, persistence, and virulence expression by this oral pathogen. Thus, RelA is the major (p)ppGpp synthase controlling the stringent response in
S. mutans
, and it coordinates the expression of genes and phenotypes that contribute to the pathogenic potential of the organism.
Variation in the histopathological features of patients with ascending aortic aneurysms: a study of 111 surgically excised cases
Authors: Collins M J , Dev V , Strauss B H , Fedak P W M , Butany J 
Published: October 2007

Background:Ascending aortic aneurysms (AA) are a common, though poorly understood medical condition.Aims:To document the histological changes in a large series of human ascending AA, and to correlate these changes with clinical variables.Methods:111 ascending AA were excised at surgery over a 3 year period. Each aneurysm was received as a continuous ring of tissue. Sections were taken from the anterior, posterior, greater and lesser curvature of the aorta and graded in a semi-quantitative fashion for the degree of elastin fragmentation, elastin loss, smooth muscle cell (SMC) loss, intimal changes and inflammation.Results:Mean patient age at surgery was 58.7 (15.6) years; there were 70 men and 41 women. 12 patients had Marfan syndrome, 34 (30.6%) had a bicuspid aortic valve (BAV), while 71 (64.0%) had a tricuspid aortic valve (TAV). Inflammatory cells were present in 28 cases (25.2%) and were confined to the adventitia. No particular region of the aortic circumference was more severely affected, however a BAV was associated with significantly less intimal change, and less fragmentation and loss of elastic tissue compared with patients with a TAV. Advanced age (>65 years), female gender and Marfan syndrome were all associated with more severe elastin degeneration and smooth muscle cell loss (p<0.05 for all).Conclusion:Results indicate a wide variation in the histological appearance in ascending AA, depending on patient characteristics. They suggest that the underlying aneurysm pathogenesis may also be highly variable; this warrants further investigation.
Expression of periostin in human breast cancer
Authors: Puglisi F , Puppin C , Pegolo E , Andreetta C , Pascoletti G , D’Aurizio F , Pandolfi M , Fasola G , Piga A , Damante G , Di Loreto C 
Published: October 2007

Background:Periostin is a secreted adhesion protein, normally expressed in mesenchime-derived cells. Aberrant expression of the periostin gene in epithelial tumours seems to play a role in angiogenesis and metastases.Aims:To investigate periostin expression in a consecutive series of breast carcinomas and correlate it with established biological and prognostic factors.Methods:A consecutive series of 206 breast carcinomas was investigated by immunohistochemistry with a specific antiperiostin antibody. Immunohistochemical expression of oestrogen and progesterone receptors, Ki-67 (MIB-1), HER-2/neu, VEGF-A, VEGFR-1 and VEGFR-2 was analysed. Periostin expression was also investigated in MCF-7 and MDA-468 cell lines by immunohistochemistry, western blot and quantitative RT-PCR. Localisation of periostin was investigated in MCF-7 cells by the green fluorescent protein (GFP) approach.Results:Periostin was highly expressed in carcinoma cells, but not in normal breast tissues. The pattern of expression was mainly cytoplasmic. However, in 12% of cases a nuclear reactivity was observed. Nuclear periostin significantly correlated with tumour size, and with expression of oestrogen receptor, progesterone receptor, VEGF-A, VEGFR-1 and VEGFR-2. A nuclear localisation of periostin was also observed in MCF-7 and MDA-468 cell lines. In MCF-7 cells the nuclear localisation of periostin was also shown by transfection of a vector expressing a GFP-periostin chimeric protein.Conclusions:Results indicate that the aberrant gene expression of periostin in breast cancer cells is associated with an abnormal nuclear localisation of the protein. The nuclear localisation of periostin in breast cancer may induce significant biological effects.
Ecological and hydrological aspects of peat formation
Authors: Moore P. D. 
Published: October 2007

Abstract
Peat formation is dependent upon an imbalance in the energetic relations of an ecosystem such that the total energy fixation by photosynthesis exceeds the total respiration on the part of the plants, animal consumers, detritivores and microbial components of the ecosystem. The imbalance comes about through the impedence of some detritivore and microbial activity as a result of the waterlogging of the environment. A knowledge of hydrological relationships in different types of mire (any freshwater wetland ecosystem in which soil organic matter accumulates) is necessary for the understanding of the rate of formation and the nature of the peat formed.
A hydrological scheme for mire classification is discussed in relation to the type of peat developed from the mire types described, particularly the proportion of inorganic material incorporated into various peatland types. Two major hydrological divisions can be distinguished—those depending entirely upon rainfall for their water intake and those receiving water both by rainfall and overland drainage. The differentiation is of profound importance in terms of the inorganic (loss on ignition; ash) content of the peat, since the rain-based (ombrotrophic) system generally has a far more limited supply of inorganic material than the flow-fed (rheotrophic) one.
One must seek models for coal-forming systems among ombrogenous tropical mires. Elevated peat-forming surfaces equivalent to the temperate raised mires are recorded from tropical areas and some of these bear vegetation whose physiognomy (general form and structure) resembles that of reconstructed coal forests. In these bog forests, peats of low ash content accumulate and such mires may prove to be the closest modern analogy to coalforming systems.
Lycopod succession in coals: an example from the Low Barnsley Seam (Westphalian B), Yorkshire, England
Authors: Bartram K. M. 
Published: October 2007

Abstract

Lycopsid megaspores processed from petrologically defined samples of the Low Barnsley Seam, Westphalian B, Upper Carboniferous have vertical distributions arranged in repeated successions of phases. A total of six phases was distinguished producing a more detailed pattern of succession than has previously been identified using miospores. Two important phases were recognized for the first time, designated: Phase 0, characterized by the species
Cystosporites verrucosus
Dijkstra,
Lagenicula horrida
Zerndt,
Pseudovalvisisporites nigrozonalis
(Stach & Zerndt) Lachkar and
Cystosporites giganteus
(Zerndt) Schopf, interpreted as a colonizing assemblage, and Phase 2, characterized by the species
Triangulatisporites tertius
Potonié & Kremp and
Valvisisporites auritus
(Zerndt) Potonié & Kremp which is considered to represent an association of non-arborescent lycopods.

Phases are broadly related to petrographic type(s) but changes in phases and petrography are not necessarily coincident. Phasal changes of the kind described are believed to result from the formation of a raised bog.
Gondwana coal basins of Australia and South Africa: tectonic setting, depositional systems and resources
Authors: Hobday D. K. 
Published: October 2007

Abstract
Upper Carboniferous and Permian coals of eastern Australia (Bowen, Sydney, Cooper, Galilee and satellite basins) and southern Africa (Karoo Basin) resemble one another in their general composition and associated clastic facies. The Australian examples, however, show more petrographic and geometric variability than their southern African Gondwana counterparts.

Critical controls on the distribution and quality of coal in both regions appear to have been (1) a near-polar location with accompanying periglacial conditions, (2) Permian through early Triassic warming independent of any significant change in palaeolatitude, (3) associated floral changes from tundra vegetation to swamps and deciduous
Glossopteris
forests, (4) variable subsidence and sedimentation rates in foredeep, rift, and epicratonic basin settings, (5) local palaeotopographic effects, (6) eustatically induced changes in base level and marine transgression, and (7) a range of depositional systems from proximal conglomeratic alluvial fans through fluvial, delta-plain, lake-margin, back-barrier, and blanket peat mires in sediment-starved basins.

In most cases, palaeotopography and depositional environment were the most important factors in determining coal seam geometry, and had considerable influence on coal quality, specifically its maceral content. Most of the commercial seams are contained in fluvial and delta-plain sequences, with thick, dip-elongate interchannel seams and really extensive coals typically overlying abandoned delta lobes. However, some important seams are juxtaposed with conglomerates of wet alluvial-fan origin or are associated with quartzose barrier sandstones; others originated in clastic-starved systems bordering shallow lakes or in blanket swamps that received moisture from groundwater discharge or direct rainfall.
Some seams display characteristics that were primarily controlled by other more regional factors such as rapid tectonic subsidence, changes in groundwater regime, or gradual marine transgression. While influencing the thickness and areal extent of seams, these factors were even more important in determining microlithotypes, maceral content, and inorganic composition of the coals.
Not only is coal mining crucial to the economies of both Australia and S Africa, with further expansion likely in the coming decades, but coal and dispersed coal particles have generated billions of barrels of commercial oil reserves along with large volumes of gas. Australian petroleum reserves are predominantly of land-plant origin, and source-reservoir relationships provide important analogues for exploring other non-marine basins.
A global assay of haemostasis which uses recombinant tissue factor and tissue-type plasminogen activator to measure the rate of fibrin formation and fibrin degradation in plasma
Authors: Zhu Kun , Skeppholm Mika , Vedin Jenny , Svensson Jan , Egberg Nils , Blombäck Margareta , He Shu 
Published: October 2007

SummaryThe global assay of Overall Haemostasis Potential we previously described has been refined. The coagulation cascade in plateletpoor plasma is triggered by adding a minimal dose of recombinant tissue factor together with purified phospholipids and calcium; fibrinolysis is initiated by adding recombinant tissue type-plasminogen activator in a concentration similar to what can be obtained during thrombolysis. Numerical differentials of optical densities reflecting rates of fibrin formation and degradation are calculated by a new software, and the Coagulation Profile (Cp) and the Fibrinolysis Profile (Fp) are determined. The combined effect of these counteractive systems is expressed as a ratio of Cp to Fp, called the Overall Haemostasis Index. Commercially available coagulant-deficient patient plasma samples and plasma with various amounts of added PAI-1 are examined; changes of fibrin turbidity demonstrate that this assay can determine Cp and Fp in a physiologically relevant way. Increased Cp and decreased Fp in prothrombotic patients, as well as expected effects of heparin or a thrombin inhibitor on Cp and Fp, suggest that our method can detect hypercoagulability and assist in monitoring antithrombotic treatment. Ongoing studies will show whether this simple assay can be of value in clinical routine.