bluuebunny/crossref_metadata_2025_split huggingface dataset:
INTEGRATED GRAVITY AND SEISMIC INVESTIGATION OVER THE JABAL HAFIT STRUCTURE: IMPLICATIONS FOR BASEMENT CONFIGURATION OF THE FRONTAL FOLD‐AND‐THRUST BELT OF THE NORTHERN OMAN MOUNTAINS
Authors: Ali M. Y. , Sirat M. , Small J. 
Published: December 2008

A gravity survey was conducted over and around Jabal Hafit, located on the border between the United Arab Emirates (UAE) and Oman on the western edge of the northern Oman Mountains, as part of a study to investigate the subsurface structures and sedimentary sequences of the area. This new data, together with outcrop geology, well data and measurements of physical properties of rock samples, was integrated with a new interpretation of reprocessed commercial seismic reflection profiles recorded across the Jabal Hafit anticline.We recognize five major tectonostratigraphic sequences in the seismic profiles: Mesozoic shelf carbonates; Upper Cretaceous foreland (primarily Fiqa Formation); the Hawasina allochthon; and Upper Cretaceous to Lower Tertiary, and Upper Tertiary sequences. The seismic sections suggest that Jabal Hafit represents a backfolded anticline associated with a steep east‐vergent thrust that probably lies above a blind thrust fault along the base of the foreland basin sequence at depth. The lack of onlapping and thinning in the Lower Tertiary sequence suggests that the initiation of folding may have started after the Oligocene‐Miocene and corresponds to the beginning of the collision of Arabia and central Iran along the Zagros suture in Iran. In addition, the seismic sections suggest a pop‐up structure beneath the Jabal Hafit structure at the base of the foreland basin sequence. The structure is bounded by high‐angle listric reverse faults that cut downward through the Mesozoic shelf carbonates and are interpreted to be related to the inversion of deep structures.NNW to SSE trending positive residual gravity anomalies of up to +8 mGal occur on the Jabal Hafit and Al‐Ain anticlines. These positive gravity highs are attributed to uplifted basement structures which probably resulted from the reactivation of deep‐seated fault blocks. The residual Bouguer anomaly values decline gradually to the east and west of Jabal Hafit probably due to the deepening of the basement. A large negative gravity anomaly of <−5 mGal is observed east of Jabal Hafit and coincides with a syncline which caused thickening of the Upper Cretaceous and Tertiary sequences.
AN INTEGRATED STUDY OF DIAGENESIS AND DEPOSITIONAL FACIES IN TIDAL SANDSTONES: HAWAZ FORMATION (MIDDLE ORDOVICIAN), MURZUQ BASIN, LIBYA
Authors: Abouessa A. , Morad S. 
Published: December 2008

Studies of the impact of diagenesis on reservoir quality in tidal sandstones can be of great importance in successful hydrocarbon exploration. The study reported here shows that diagenetic alterations and bioturbation have induced considerable deterioration and heterogeneity in the reservoir quality of the sand‐dominated tidal deposits of the Middle Ordovician Hawaz Formation in the Muruq Basin, Libya. Comparison is made between the diagenetic evolution of samples from the subsurface (present‐day depth 1500 m) and from surface outcrops in order to study the impact of burial and uplift on the spatial and temporal distribution of reservoir quality in the Hawaz Formation sandstones.Eogenetic alterations, which were mediated by meteoric water circulation, included kaolinitization and dissolution of framework silicates and mechanical compaction. Mesogenetic alterations (T > 70°C; depth > 2 km) included pressure dissolution of quartz grains and concomitant quartz cementation, conversion of kaolinite into dickite, illitization of kaolinite and of grain‐coating clays, and the precipitation of Mg‐rich siderite cement. Reduction of intergranular porosity was due more to compaction than to cementation, yet quartz overgrowths are up to 16% in some of the sandstones. Bioturbation has resulted in a greater reduction in sandstone permeability in the lower part of the formation than the upper part. A higher ratio of dickite to kaolinite in subsurface samples than in outcrop samples is attributed to the longer residence time of the former sandstones under mesogenetic conditions. Telodiagenesis has not resulted in enhancement of reservoir quality of the Hawaz Formation Sandstones but in pseudomorphic calcitization of siderite and oxidation of pyrite to goethite.This study shows that the reservoir‐quality evolution of tidal sandstones can best be elucidated when linked to depositional facies and distribution of diagenetic alterations.
A FUZZY LOGIC APPROACH TO ESTIMATING HYDRAULIC FLOW UNITS FROM WELL LOG DATA: A CASE STUDY FROM THE AHWAZ OILFIELD, SOUTH IRAN
Authors: Kadkhodaie‐Ilkhchi A. , Amini A. 
Published: December 2008

Porosity‐permeability relationships in the framework of hydraulic flow units can be used to characterize heterogeneous reservoir rocks. Porosity is a volumetric parameter whereas permeability is a measure of a rock's flow properties and depends on pore distribution and connectivity. Thus zonation of a reservoir using flow zone indicators and the identification of flow units can be used to evaluate reservoir quality based on porosity‐permeability relationships.In the present study, we attempt to make a quantitative correlation between flow units and well log responses using fuzzy logic in the mixed carbonate‐clastic Asmari Formation at the Ahwaz oilfield, South Iran. A hybrid neuro‐fuzzy approach was used to verify the results of fuzzy modelling. For this purpose, well log and core data from three wells at Ahwaz were used to make an intelligent formulation between core‐derived flow units and well log responses. Data from a separate well was used for evaluation and validation of the results.The results of this study demonstrate that there is a good agreement between core‐derived and fuzzy‐logic derived flow units. Fuzzy logic was successful in modelling flow units from well logs at well locations for which no core data was available.
IMPACT OF DIAGENESIS ON RESERVOIR‐QUALITY EVOLUTION IN FLUVIAL AND LACUSTRINE‐DELTAIC SANDSTONES: EVIDENCE FROM JURASSIC AND TRIASSIC SANDSTONES FROM THE ORDOS BASIN, CHINA
Authors: Luo J.L. , Morad S. , Salem A. , Ketzer J.M. , Lei X.L. , Guo D.Y. , Hlal O. 
Published: December 2008

The reservoir quality of Jurassic and Triassic fluvial and lacustrine‐deltaic sandstones in the intracratonic Ordos Basin is strongly influenced by depositional facies and various types of diagenetic modifications. The fluvial sandstones have higher average He‐porosity and permeability (14.8% and 12.7 mD, respectively) than the deltaic sandstones (9.8% and 5.8 mD, respectively). In addition to extensive mechanical compaction, eodiagenesis (220–97 Ma; depth < 2000 m; T < 70°C) has resulted in dissolution and kaolinitization of detrital silicates in the Jurassic fluvial sandstones, and in smectite infiltration and minor cementation by calcite and siderite in the Triassic fluvial and deltaic sandstones. Pervasive eogenetic carbonate cementation (> 20 vol.%) occurred in Triassic deltaic siltstones and very fine‐grained sandstones which are closely associated with organic‐rich mudstones. Mesodiagenesis (97–65 Ma), which occurred during rapid subsidence to depths of 3700–4400 m, resulted in the albitization of plagioclase, checmical compaction, the conversion of kaolinite into dickite, and cementation by quartz overgrowths, chlorite, illite, ankerite (δ13CVPDB=−2.4‰ to +2.6‰; δ18OVPDB=−21.5‰ to −10‰) and calcite (δ13CVPDB=−4.7‰ to +3.7‰; δ18OVPDB=−21.8‰ to −13.4‰). Oil emplacement (95 Ma) retarded cementation by mesogenetic quartz and carbonate but had little influence on dickite, illite and chlorite formation. Retardation of quartz cementation was also due to the presence of chlorite fringes around detrital quartz grains. Dickitization of eogenetic kaolinite together with the short residence time at maximum burial temperatures (105–124°C) has retarded the albitization of K‐feldspars and illite formation and hence prevented severe permeability destruction. Telodiagenesis, which occurred after uplift (Eocene to end‐Neogene), caused slight dissolution and kaolinitization of feldspars.This study demonstrates that despite complex patterns of diagenetic modifications in the Triassic and Jurassic successions, depositional porosity and permeability are better preserved in fluvial meandering channel sandstones than in deltaic sandstones. These results should be important for modelling of reservoir‐quality distribution and exploration risk evaluation in the basin.
Spinal Cord Neuronal Pathology in Multiple Sclerosis
Authors: Gilmore Christopher P. , DeLuca Gabriele C. , Bö Lars , Owens Trudy , Lowe James , Esiri Margaret M. , Evangelou Nikos 
Published: December 2008

AbstractThe objective of this study was to assess neuronal pathology in the spinal cord in multiple sclerosis (MS), both within myelinated and demyelinated tissue. Autopsy material was obtained from 38 MS cases and 21 controls. Transverse sections were taken from three spinal cord levels and stained using Luxol Fast Blue/Cresyl Violet and myelin protein immunohistochemistry. Measurements of neuronal number and size were made for all neurons within the anterior horns of the gray matter. Neurons were classified as motoneurons or interneurons according to size criteria. In comparison with controls, both motoneuron and interneuron number were reduced in MS cases at the upper cervical (interneuron P = 0.0549; motoneuron P = 0.0073) and upper thoracic (interneuron P = 0.0507; motoneuron P = 0.0144), but not the lumbar level. Interneuron cross‐sectional area was reduced in MS cases at all levels (upper cervical, P = 0.0000; upper thoracic, P = 0.0002; lumbar, P = 0.0337). Neuronal loss appears to be predominantly related to local gray matter plaques, whereas interneuron atrophy occurs in both myelinated and demyelinated areas.
Potential To Reduce
Escherichia coli
Shedding in Cattle Feces by Using Sainfoin (
Onobrychis viciifolia
) Forage, Tested In Vitro and In Vivo
Authors: Berard Natalie C. , Holley Richard A. , McAllister Tim A. , Ominski Kim H. , Wittenberg Karin M. , Bouchard Kristen S. , Bouchard Jenelle J. , Krause Denis O. 
Published: December 2008

ABSTRACT

There is a growing concern about the presence of pathogens in cattle manure and its implications on human and environmental health. The phytochemical-rich forage sainfoin (
Onobrychis viciifolia
) and purified phenolics (
trans
-cinnamic acid,
p
-coumaric acid, and ferulic acid) were evaluated for their ability to reduce the viability of pathogenic
Escherichia coli
strains, including
E. coli
O157:H7. MICs were determined using purified phenolics and acetone extracts of sainfoin and alfalfa (
Medicago sativa
), a non-tannin-containing legume. Ground sainfoin or pure phenolics were mixed with fresh cattle feces and inoculated with a ciprofloxacin-resistant strain of
E. coli
, O157:H7, to assess its viability at −20°C, 5°C, or 37°C over 14 days. Forty steers were fed either a sainfoin (hay or silage) or alfalfa (hay or silage) diet over a 9-week period. In the in vitro study, the MICs for coumaric (1.2 mg/ml) and cinnamic (1.4 mg/ml) acids were 10- to 20-fold lower than the MICs for sainfoin and alfalfa extracts. In the inoculated feces, the −20°C treatment had death rates which were at least twice as high as those of the 5°C treatment, irrespective of the additive used. Sainfoin was less effective than coumaric acid in reducing
E. coli
O157:H7 Cip
r
in the inoculated feces. During the animal trial, fecal
E. coli
numbers declined marginally in the presence of sainfoin (silage and hay) and alfalfa silage but not in the presence of hay, indicating the presence of other phenolics in alfalfa. In conclusion, phenolic-containing forages can be used as a means of minimally reducing
E. coli
shedding in cattle without affecting animal production.
How Diverse Is the GenusWolbachia? Multiple-Gene Sequencing Reveals a Putatively NewWolbachiaSupergroup Recovered from Spider Mites (Acari: Tetranychidae)
Authors: Ros Vera I. D. , Fleming Vicki M. , Feil Edward J. , Breeuwer Johannes A. J. 
Published: December 2008

ABSTRACTAt least 20% of all arthropods and some nematode species are infected with intracellular bacteria of the genusWolbachia. This highly diverse genus has been subdivided into eight “supergroups” (A to H) on the basis of nucleotide sequence data. Here, we report the discovery of a newWolbachiasupergroup recovered from the spider mite speciesBryobiaspecies V (Acari: Tetranychidae), based on the sequences of three protein-coding genes (ftsZ,gltA, andgroEL) and the 16S rRNA gene. Other tetranychid mites possess supergroup BWolbachiastrains. The discovery of anotherWolbachiasupergroup expands the known diversity ofWolbachiaand emphasizes the high variability of the genus. Our data also clarify the existing supergroup structure and highlight the use of multiple gene sequences for robust phylogenetic analysis. In addition to previous reports of recombination between the arthropod-infecting supergroups A and B, we provide evidence for recombination between the nematode-infecting supergroups C and D. Robust delineation of supergroups is essential for understanding the origin and spread of this common reproductive parasite and for unraveling mechanisms of host adaptation and manipulation across a wide range of hosts.
Pseudomonas savastanoi
pv. savastanoi Contains Two
iaaL
Paralogs, One of Which Exhibits a Variable Number of a Trinucleotide (TAC) Tandem Repeat
Authors: Matas Isabel M. , Pérez-Martínez Isabel , Quesada José M. , Rodríguez-Herva José J. , Penyalver Ramón , Ramos Cayo 
Published: December 2008

ABSTRACT

In this study,
Pseudomonas savastanoi
pv. savastanoi isolates were demonstrated to contain two
iaaL
paralogs, which are both chromosomally located in most strains. Comparative analysis of
iaaL
nucleotide sequences amplified from these two paralogs revealed that one paralog,
iaaL
Psn
, is 100% identical to
iaaL
from
P. savastanoi
pv. nerii, while the other paralog,
iaaL
Psv
, exhibited 93% identity to
iaaL
from
Pseudomonas syringae
pv. tomato (
iaaL
Pto
). A 3-nucleotide motif (TAC) comprised of 3 to 15 repeats, which remained stable after propagation of the strains in olive plants, was found in
iaaL
Psv
. Based on the observed nucleotide sequence variations, a restriction fragment length polymorphism assay was developed that allowed differentiation among
iaaL
Psn
,
iaaL
Psv
, and
iaaL
Pto
.
In addition, reverse transcriptase PCR on total RNA from
P. savastanoi
pv. savastanoi strains demonstrated that both
iaaL
Psv
and
iaaL
Psn
containing 14 or fewer TAC repeats are transcribed. Capillary electrophoresis analysis of PCR-amplified DNA fragments containing the TAC repeats from
iaaL
Psv
allowed the differentiation of
P. savastanoi
pv. savastanoi isolates.
Bovine
Campylobacter jejuni
Strains Differ from Human and Chicken Strains in an Analysis of Certain Molecular Genetic Markers
Authors: Gonzalez Manuel , Hakkinen Marjaana , Rautelin Hilpi , Hänninen Marja-Liisa 
Published: December 2008

ABSTRACT

The association of four new genetic markers with a chicken, bovine, or human host was studied among 645
Campylobacter jejuni
isolates. The γ-glutamate transpeptidase gene and
dmsA
were common in human and chicken isolates but uncommon among bovine isolates. In the
t
test, bovine isolates differed significantly (
P
< 0.05) from human and chicken isolates.
Environmental Isolates of
Burkholderia pseudomallei
in Ceará State, Northeastern Brazil
Authors: Rolim Dione B. , Rocha Marcos F. G. , Brilhante Raimunda S. N. , Cordeiro Rossana A. , Leitão-Junior Natanael P. , Inglis Timothy J. J. , Sidrim José J. C. 
Published: December 2008

ABSTRACT

Melioidosis has been considered an emerging disease in Brazil since the first cases were reported to occur in the northeast region. This study investigated two municipalities in Ceará state where melioidosis cases have been confirmed to occur.
Burkholderia pseudomallei
was isolated in 26 (4.3%) of 600 samples in the dry and rainy seasons.
Detection of an Allele Conferring Resistance to
Bacillus sphaericus
Binary Toxin in
Culex quinquefasciatus
Populations by Molecular Screening
Authors: Chalegre Karlos Diogo de Melo , Romão Tatiany Patrícia , Amorim Liliane Barbosa , Anastacio Daniela Bandeira , de Barros Rosineide Arruda , de Oliveira Cláudia Maria Fontes , Regis Lêda , de-Melo-Neto Osvaldo Pompílio , Silva-Filha Maria Helena Neves Lobo 
Published: December 2008

ABSTRACT

The activity of the
Bacillus sphaericus
binary (Bin) toxin on
Culex quinquefasciatus
larvae depends on its specific binding to the Cqm1 receptor, a midgut membrane-bound α-glucosidase. A 19-nucleotide deletion in the
cqm1
gene (
cqm1

REC

) mediates high-level resistance to Bin toxin. Here, resistance in nontreated and
B. sphaericus
-treated field populations of
C. quinquefasciatus
was assessed through bioassays as well as a specific PCR assay designed to detect the
cqm1

REC

allele in individual larvae. Resistance ratios at 90% lethal concentration, gathered through bioassays, were close to 1 and indicate that the selected populations had similar levels of susceptibility to
B. sphaericus
, comparable to that of a laboratory colony. A diagnostic PCR assay detected the
cqm1

REC

allele in all populations investigated, and its frequency in two nontreated areas was 0.006 and 0.003, while the frequency in the
B. sphaericus
-treated population was significantly higher. Values of 0.053 and 0.055 were detected for two distinct sets of samples, and homozygote resistant larvae were found. Evaluation of Cqm1 expression in individual larvae through α-glucosidase assays corroborated the allelic frequency revealed by PCR. The data from this study indicate that the
cqm1

REC

allele was present at a detectable frequency in nontreated populations, while the higher frequency in samples from the treated area is, perhaps, correlated with the exposure to
B. sphaericus
. This is the first report of the molecular detection of a biolarvicide resistance allele in mosquito populations, and it confirms that the PCR-based approach is suitable to track such alleles in target populations.
Cytosine Deaminase as a Negative Selection Marker for Gene Disruption and Replacement in the Genus
Streptomyces
and Other Actinobacteria
Authors: Dubeau Marie-Pierre , Ghinet Mariana Gabriela , Jacques Pierre-Étienne , Clermont Nancy , Beaulieu Carole , Brzezinski Ryszard 
Published: December 2008

ABSTRACT

We developed a novel negative selection system for actinobacteria based on cytosine deaminase (CodA). We constructed vectors that include a synthetic gene encoding the CodA protein from
Escherichia coli
optimized for expression in
Streptomyces
species. Gene disruption and the introduction of an unmarked in-frame deletion were successfully achieved with these vectors.
Characterization of the Complete Zwittermicin A Biosynthesis Gene Cluster fromBacillus cereus
Authors: Kevany Brian M. , Rasko David A. , Thomas Michael G. 
Published: December 2008

ABSTRACTBacillus cereusUW85 produces the linear aminopolyol antibiotic zwittermicin A (ZmA). This antibiotic has diverse biological activities, such as suppression of disease in plants caused by protists, inhibition of fungal and bacterial growth, and amplification of the insecticidal activity of the toxin protein fromBacillus thuringiensis. ZmA has an unusual chemical structure that includes adamino acid and ethanolamine and glycolyl moieties, as well as having an unusual terminal amide that is generated from the modification of the nonproteinogenic amino acid β-ureidoalanine. The diverse biological activities and unusual structure of ZmA have stimulated our efforts to understand how this antibiotic is biosynthesized. Here, we present the identification of the complete ZmA biosynthesis gene cluster fromB. cereusUW85. A nearly identical gene cluster is identified on a plasmid fromB. cereusAH1134, and we show that this strain is also capable of producing ZmA. Bioinformatics and biochemical analyses of the ZmA biosynthesis enzymes strongly suggest that ZmA is initially biosynthesized as part of a larger metabolite that is processed twice, resulting in the formation of ZmA and two additional metabolites. Additionally, we propose that the biosynthesis gene cluster for the production of the amino sugar kanosamine is contained within the ZmA biosynthesis gene cluster inB. cereusUW85.
Gene Expression Profiling in the Human Pathogenic Dermatophyte
Trichophyton rubrum
during Growth on Proteins
Authors: Zaugg Christophe , Monod Michel , Weber Johann , Harshman Keith , Pradervand Sylvain , Thomas Jerome , Bueno Manuel , Giddey Karin , Staib Peter 
Published: December 2008

ABSTRACT

Dermatophytes are highly specialized filamentous fungi which cause the majority of superficial mycoses in humans and animals. The high secreted proteolytic activity of these microorganisms during growth on proteins is assumed to be linked to their particular ability to exclusively infect keratinized host structures such as the skin stratum corneum, hair, and nails. Individual secreted dermatophyte proteases were recently described and linked with the in vitro digestion of keratin. However, the overall adaptation and transcriptional response of dermatophytes during protein degradation are largely unknown. To address this question, we constructed a cDNA microarray for the human pathogenic dermatophyte
Trichophyton rubrum
that was based on transcripts of the fungus grown on proteins. Profiles of gene expression during the growth of
T. rubrum
on soy and keratin protein displayed the activation of a large set of genes that encode secreted endo- and exoproteases. In addition, other specifically induced factors potentially implicated in protein utilization were identified, including heat shock proteins, transporters, metabolic enzymes, transcription factors, and hypothetical proteins with unknown functions. Of particular interest is the strong upregulation of key enzymes of the glyoxylate cycle in
T. rubrum
during growth on soy and keratin, namely, isocitrate lyase and malate synthase. This broad-scale transcriptional analysis of dermatophytes during growth on proteins reveals new putative pathogenicity-related host adaptation mechanisms of these human pathogenic fungi.
Global Gene Expression Analysis during Germination in the Chytridiomycete
Blastocladiella emersonii
Authors: Salem-Izacc Silvia M. , Koide Tie , Vêncio Ricardo Z. N. , Gomes Suely L. 
Published: December 2008

ABSTRACT

Blastocladiella emersonii
is an aquatic fungus of the Chytridiomycete class. During germination, the zoospore, a motile nongrowing cell, goes through a cascade of morphological changes that culminates with its differentiation into the germling cell, capable of coenocytic vegetative growth. Transcriptome analyses of
B. emersonii
cells were carried out during germination induced under various environmental conditions. Microarray data analyzing 3,563 distinct
B. emersonii
genes revealed that 26% of them are differentially expressed during germination in nutrient medium at at least one of the time points investigated. Over 500 genes are upregulated during the time course of germination under those conditions, most being related to cell growth, including genes involved in protein biosynthesis, DNA transcription, energetic metabolism, carbohydrate and oligopeptide transport, and cell cycle control. On the other hand, several transcripts stored in the zoospores are downregulated during germination in nutrient medium, such as genes involved in signal transduction, amino acid transport, and chromosome organization. In addition, germination induced in the presence of nutrients was compared with that triggered either by adenine or potassium ions in inorganic salt solution. Several genes involved in cell growth, induced during germination in nutrient medium, do not show increased expression when
B. emersonii
zoospores germinate in inorganic solution, suggesting that nutrients exert a positive effect on gene transcription. The transcriptome data also revealed that most genes involved in cell signaling show the same expression pattern irrespective of the initial germination stimulus.