bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metatranscriptome Analysis of the Human Fecal Microbiota Reveals Subject-Specific Expression Profiles, with Genes Encoding Proteins Involved in Carbohydrate Metabolism Being Dominantly Expressed
Authors: Booijink Carien C. G. M. , Boekhorst Jos , Zoetendal Erwin G. , Smidt Hauke , Kleerebezem Michiel , de Vos Willem M. 
Published: June 2010

ABSTRACT

The human gastrointestinal (GI) tract provides home to a complex microbial community, collectively termed microbiota. Although major efforts have been made to describe the diversity and stability of the microbiota, functional studies have been largely restricted to intestinal isolates and include few community studies. The aim of this study was to explore the
in situ
gene expression of the fecal microbiota and to evaluate the RNA fingerprinting method cDNA-AFLP (cDNA amplified fragment length polymorphism) for this purpose. To this end, cDNA-AFLP analysis of enriched mRNA revealed that two healthy subjects showed highly divergent expression profiles with considerable fluctuations in time. Subsequent excision and sequence determination of bands from the mRNA-enriched profiles resulted in 122 identifiable sequences (transcripts and rRNAs). The classification of retrieved transcripts into functional clusters based on COG (cluster of orthologous genes) annotation showed that most assigned transcripts belonged to the metabolism cluster (26% of all sequences), underlining that even at the very end of the intestinal tract the microbiota is still very active. This study furthermore revealed that cDNA-AFLP is a useful tool to compare gene expression profiles in time in complex microbial communities.
Novel High-Throughput Detection Method To Assess Bacterial Surfactant Production
Authors: Burch Adrien Y. , Shimada Briana K. , Browne Patrick J. , Lindow Steven E. 
Published: June 2010

ABSTRACTA novel biosurfactant detection assay was developed for the observation of surfactants on agar plates. By using an airbrush to apply a fine mist of oil droplets, surfactants can be observed instantaneously as halos around biosurfactant-producing colonies. This atomized oil assay can detect a wide range of different synthetic and bacterially produced surfactants. This method could detect much lower concentrations of many surfactants than a commonly used water drop collapse method. It is semiquantitative and therefore has broad applicability for uses such as high-throughput mutagenesis screens of biosurfactant-producing bacterial strains. The atomized oil assay was used to screen for mutants of the plant pathogenPseudomonas syringaepv. syringae B728a that were altered in the production of biosurfactants. Transposon mutants displaying significantly altered surfactant halos were identified and further analyzed. All mutants identified displayed altered swarming motility, as would be expected of surfactant mutants. Additionally, measurements of the transcription of the syringafactin biosynthetic cluster in the mutants, the principal biosurfactant known to be produced by B728a, revealed novel regulators of this pathway.
Transcriptomic Responses ofSalmonella entericaSerovars Enteritidis and Typhimurium to Chlorine-Based Oxidative Stress
Authors: Wang Siyun , Phillippy Adam M. , Deng Kaiping , Rui Xiaoqian , Li Zengxin , Tortorello Mary Lou , Zhang Wei 
Published: June 2010

ABSTRACTSalmonella entericaserovars Enteritidis and Typhimurium are the leading causative agents of salmonellosis in the United States.S.Enteritidis is predominantly associated with contamination of shell eggs and egg products, whereasS.Typhimurium is frequently linked to tainted poultry meats, fresh produce, and recently, peanut-based products. Chlorine is an oxidative disinfectant commonly used in the food industry to sanitize the surfaces of foods and food processing facilities (e.g., shell eggs and poultry meats). However, chlorine disinfection is not always effective, as someS. entericastrains may resist and survive the disinfection process. To date, little is known about the underlying mechanisms of howS. entericaresponds to chlorine-based oxidative stress. In this study, we designed a custom bigenome microarray that consists of 385,000 60-mer oligonucleotide probes and targets 4,793 unique gene features in the genomes ofS.Enteritidis strain PT4 andS.Typhimurium strain LT2. We explored the transcriptomic responses of both strains to two different chlorine treatments (130 ppm of chlorine for 30 min and 390 ppm of chlorine for 10 min) in brain heart infusion broth. We identified 209S. entericacore genes associated with Fe-S cluster assembly, cysteine biosynthesis, stress response, ribosome formation, biofilm formation, and energy metabolism that were differentially expressed (>1.5-fold;P< 0.05). In addition, we found that serovars Enteriditis and Typhimurium differed in the responses of 33 stress-related genes and 19 virulence-associated genes to the chlorine stress. Findings from this study suggest that the oxidative-stress response may renderS. entericaresistant or susceptible to certain types of environmental stresses, which in turn promotes the development of more effective hurdle interventions to reduce the risk ofS. entericacontamination in the food supply.
Inhibition of
Salmonella
Host Cell Invasion by Dimethyl Sulfide
Authors: Antunes L. Caetano M. , Buckner Michelle M. C. , Auweter Sigrid D. , Ferreira Rosana B. R. , Lolić Petra , Finlay B. Brett 
Published: June 2010

ABSTRACT

We show that dimethyl sulfoxide (DMSO) inhibits
Salmonella hilA
expression and that this inhibition is stronger under anaerobiosis. Because DMSO can be reduced to dimethyl sulfide (DMS) during anaerobic growth, we hypothesized that DMS was responsible for
hilA
inhibition. Indeed, DMS strongly inhibited the expression of
hilA
and multiple
Salmonella
pathogenicity island 1 (SPI-1)-associated genes as well as the invasion of cultured epithelial cells. Because DMSO and DMS are widespread in nature, we hypothesize that this phenomenon may contribute to environmental sensing by
Salmonella
.
Rapid Method for Isolation of Desiccation-Tolerant Strains and Xeroprotectants
Authors: Narváez-Reinaldo J. J. , Barba I. , González-López J. , Tunnacliffe A. , Manzanera M. 
Published: June 2010

ABSTRACT
A novel biotechnological process has been developed for the isolation of desiccation-tolerant microorganisms and their xeroprotectants, i.e., compatible solutes involved in long-term stability of biomolecules in the dry state. Following exposure of soil samples to chloroform, we isolated a collection of desiccation-tolerant microorganisms. This collection was screened for the production of xeroprotectants by a variation of the bacterial milking (osmotic downshock) procedure and by a novel air-drying/rehydration (“dry milking”) incubation method. The resultant solutes were shown to protect both proteins and living cells against desiccation damage, thereby validating them as xeroprotectants. Nuclear magnetic resonance (NMR) analytical studies were performed to identify the xeroprotectants; synthetic mixtures of these compounds were shown to perform similarly to natural isolates in drying experiments with proteins and cells. This new approach has biotechnological and environmental implications for the identification of new xeroprotectants of commercial and therapeutic value.
The LysR-Type Virulence Activator AphB Regulates the Expression of Genes in
Vibrio cholerae
in Response to Low pH and Anaerobiosis
Authors: Kovacikova Gabriela , Lin Wei , Skorupski Karen 
Published: June 2010

ABSTRACT

AphB is a LysR-type activator that initiates the expression of the virulence cascade in
Vibrio cholerae
by cooperating with the quorum-sensing-regulated activator AphA at the
tcpPH
promoter on the
Vibrio
pathogenicity island (VPI). To identify the ancestral chromosomal genes in
V. cholerae
regulated by AphB, we carried out a microarray analysis and show here that AphB influences the expression of a number of genes that are not associated with the VPI. One gene strongly activated by AphB is
cadC
, which encodes the ToxR-like transcriptional activator responsible for activating the expression of lysine decarboxylase, which plays an important role in survival at low pH. Other genes activated by AphB encode a Na
+
/H
+
antiporter, a carbonic anhydrase, a member of the ClC family of chloride channels, and a member of the Gpr1/Fun34/YaaH family. AphB influences each of these genes directly by recognizing a conserved binding site within their promoters, as determined by gel mobility shift assays. Transcriptional
lacZ
fusions indicate that AphB activates the expression of these genes under aerobic conditions in response to low pH and also under anaerobic conditions at neutral pH. Further experiments show that the regulation of
cadC
by AphB in response to low pH and anaerobiosis is mirrored in the heterologous organism
Escherichia coli
, is independent of the global regulators Fnr and ArcAB, and depends upon the region of the promoter that contains the AphB binding site. These results raise the possibility that the activity of AphB is influenced by the pH and oxygen tension of the environment.
Target Immunity of the Tn
3
-Family Transposon Tn
4430
Requires Specific Interactions between the Transposase and the Terminal Inverted Repeats of the Transposon
Authors: Nicolas Emilien , Lambin Michaël , Hallet Bernard 
Published: June 2010

ABSTRACT

Specificity of the Tn
4430
target immunity signal was examined by fusing the transposase TnpA to the LacI repressor of
Escherichia coli
. The resulting chimeric proteins failed to impose immunity to DNA targets carrying copies of the
lacO
operator, though they were proficient in
lacO
binding
in vivo
and remained responsive to wild-type immunity conferred by the Tn
4430
inverted repeat end. Intriguingly, the presence of
lacO
repeats within the target was found to strongly influence target site selection by Tn
4430
, but in a LacI-independent manner.
Progressive fold and fabric evolution associated with regional strain gradients: a case study from across a Scandian ductile thrust nappe, Scottish Caledonides
Authors: Alsop G. I. , Cheer D. A. , Strachan R. A. , Krabbendam M. , Kinny P. D. , Holdsworth R. E. , Leslie A. G. 
Published: June 2010

Abstract

Fold and fabric patterns developed within a major Caledonian thrust nappe in NW Scotland reflect a progressive increase in regional D
2
strain towards the basal ductile detachment. Within the upper greenschist to lower amphibolite facies thrust sheet, the main gently east-dipping foliations and SE-plunging transport-parallel lineations maintain a broadly similar orientation over
c
. 600 km
2
. Associated main phase, thrust-related folds (F
2
) are widely developed, and towards the base of the thrust sheet display progressive tightening and increasing curvilinearity of fold hinges ultimately resulting in sheath folds. Secondary folds (F
3
) are largely restricted to high-strain zones and are interpreted as flow perturbation folds formed during non-coaxial, top-to-the-NW ductile thrusting. These features are consistent with a structural model that incorporates plane strain pure-shear flattening with a superimposed and highly variable simple shear component focused into high-strain zones. The increase in strain over a distance of 30 km across strike is similar to the increasing deformation observed when structures are traced along strike to the north, and which are apparently related to proximity to basement-cover contacts. A U–Pb zircon age of 415±6 Ma obtained from a syn-D
2
meta-granite confirms that regional deformation occurred during the Scandian phase of the Caledonian orogeny.
Lateral variations and linkages in thrust geometry: the Traligill Transverse Zone, Assynt Culmination, Moine Thrust Belt, NW Scotland
Authors: Krabbendam M. , Leslie A. G. 
Published: June 2010

Abstract
Abrupt lateral changes in thrust geometry occur in many fold-and-thrust belts along so-called transverse zones, commonly related to pre-existing basement faults. However, the causative structures are usually concealed. We analyse here the Traligill Transverse Zone in the Assynt Culmination of the Caledonian Moine Thrust Belt, NW Scotland. This transverse zone trends sub-parallel to the WNW transport direction and is associated with en echelon faults cutting thrusts, discontinuity of thrust architecture and oblique fold-and-thrust structures. Thick thrust sheets north of the Transverse Zone contain thick basement slices; thrust sheets to the south are thin and involve a thin-bedded sequence. The Traligill Transverse Zone developed above the Loch Assynt Fault, a basement cross-fault, and reactivated Proterozoic ductile shearzone. Piercing point analysis shows that the cross-fault was active both before and after thrusting. Thrusting thus affected strata that were already disrupted by steep faults. The amplitude of the disturbance in fold-and-thrust architecture along the Traligill Transverse Zone is much greater than the vertical displacement along the fault; this is attributed to localized transpressional thrust-stacking. Other basement cross-faults and their relationship with lateral variations within the Moine Thrust Belt and in other thrust belts are discussed.
Regional-scale lateral variation and linkage in ductile thrust architecture: the Oykel Transverse Zone, and mullions, in the Moine Nappe, NW Scotland
Authors: Leslie A. G. , Krabbendam M. , Kimbell G. S. , Strachan R. A. 
Published: June 2010

Abstract
Sharp lateral changes in structural geometry of ductile thrust stacks are not widely reported. A regional-scale lateral culmination wall forms the southern boundary of the Cassley Culmination in Moine rocks in the Caledonides of Sutherland, Northern Scotland. This culmination wall is part of the Oykel Transverse Zone (OTZ), a kilometre-scale shear zone characterized by constrictional finite strain fabrics aligned sub-parallel to the regional WNW-directed thrust transport direction. Main phase folds and fabrics in the transverse zone hanging wall are folded by main phase folds and fabrics in the footwall, thus recording foreland-propagating ductile deformation. South of the Cassley Culmination, shortening occurred uniformly, without development of discrete subsidiary thrusts; distributed deformation (fold development) alternated with localized thrusting within the culmination. The classic ESE-plunging mullions at Oykel Bridge are an integral part of the OTZ and were generated by constriction aligned sub-parallel to the transport direction. Constriction is attributed to differential, transtensional movement across the OTZ during culmination development. Subsequent formation of the underlying Assynt Culmination further accentuated upward-bulging of the Cassley Culmination, amplifying the lateral change across the transverse zone. The OTZ aligns with a pronounced gravity gradient on the south-western side of the Lairg gravity low. Interpretive modelling relates this gradient to a buried basement ramp that possibly controlled the location of the transverse zone.
Relationships between the Loch Ailsh and Borralan alkaline intrusions and thrusting in the Moine Thrust zone, southern Assynt culmination, NW Scotland
Authors: Searle M. P. , Law R. D. , Dewey J. F. , Streule M. J. 
Published: June 2010

Abstract

The Moine Thrust zone of NW Scotland marks the Caledonian orogenic front and in the Assynt region consists of several west-vergent major thrust sheets (Moine, Ben More, Glencoul and Sole Thrust sheets) that place allochthonous rocks onto the Lewisian basement and Torridon Group cover in the west. Here we present two new balanced and restored sections across the Moine Thrust zone in the region of the Loch Ailsh and Loch Borralan alkali intrusions. Syenites and alkaline pyroxenites intrude up to Durness Group carbonates. Syenites are interpreted as cut by the Moine and Ben More Thrusts and therefore their intrusion age (
c
. 430 Ma) provides a maximum age constraint on cessation of motion along the Moine Thrust. We review and discuss several controversies, notably: (1) relationships between folding in the Ben More Thrust sheet (Sgonnan Mor folds) and fabric development associated with intrusion of the Loch Ailsh pluton and initiation of the Moine and Ben More Thrusts; (2) structural relationships around the Borralan intrusion, particularly the nature of its basal and lateral margins (intrusive or thrust-ramp); (3) the structural relationships of the Cam Loch and Benn Fhuarain klippen; and (4) the timing of motion of all thrust sheets in the southern Assynt culmination.
The Geological Structure of the North-West Highlands of Scotland
– revisited: Peach
et al.
100 years on
Authors: Butler Robert W. H. 
Published: June 2010

Abstract
Following years of sporadic debate, in the early 1880s consensus was reached that thrust tectonics explained hitherto controversial geological field relationships in NW Scotland. This spawned a major research effort there by the Geological Survey of Great Britain that culminated in a series of highly detailed geological maps, preliminary research papers and, eventually, the publication of a memoir to the region. These works became highly influential to early-20th century geoscience, especially structural geology. Not only did they provide the first major synthesis of thrust belt structure, they also provided the basis for descriptions of fault and shear zone processes and deductive methods for unravelling tectonic histories in metamorphic basement. A common misconception is that the results arose from mapping alone, without regard to extant models and theory and this approach is held up as an ideal for fieldwork. Yet the notebooks and writings of the surveyors show the application of learning not only from other research groups but also between themselves. As with modern mapping, the Survey team created interpretations that built on contemporary knowledge. This work in turn has driven subsequent research for over 100 years, in the NW Highlands and in deformed rocks throughout the world.
Predicting seismic properties from three-dimensional microstructures: a new look at an old quartzite
Authors: Lloyd Geoffrey E. , Law Richard D. , Mainprice David 
Published: June 2010

Abstract
The mylonitic Cambrian quartzites, Moine Thrust Zone, NW Scotland, have long been used to study microstructural and petrofabric evolution and to develop understanding of grain-scale processes accommodating large-scale displacements. Today, structural geology is entering a new age of understanding of the basic processes involved in microstructural evolution due to the emergence of novel instrumental techniques and theoretical models. It seems apposite therefore to re-evaluate the microstructure of one example of this classic quartz mylonite from the Stack of Glencoul, Assynt, using arguably the most important of these new techniques, electron backscattered diffraction (EBSD). The three-dimensional (3D) microstructure and petrofabric of this rock was analysed using EBSD, to: 1) corroborate previous optical and X-ray texture goniometry measurements; 2) investigate the potential for sampling and/or tectonic sectioning bias that may be introduced inadvertently into any petrofabric analysis; and 3) predict its seismic properties. It is found that microstructures do differ between orthogonal structural sections, leading to variations in strengths of different components in the overall petrofabric that might impact on seismic properties. The results emphasize the true 3D nature of microstructures and petrofabrics, which can be recognized and accommodated more readily by this new generation of analytical techniques.
Inclined transpression at the toe of an arcuate thrust: an example from the Precambrian ‘Mylonite Zone’ of the Sveconorwegian orogen
Authors: Viola Giulio , Henderson Iain C. 
Published: June 2010

Abstract
The ‘Mylonite Zone’ (MZ) forms a major, arcuate terrane boundary in the Precambrian Sveconorwegian orogen of SW Scandinavia. SE-directed thrusting along this curvilinear shear zone emplaced the higher-grade Idefjorden Terrane to the west onto the lower-grade Eastern Segment terrane to the east. Detailed structural characterization of the MZ mylonites in two different localities (Värmlandsnäs and Bua peninsulas) reveals a complex three-dimensional strain pattern. Inclined transpression is inferred on the basis of coexisting (and broadly coeval) foliation-parallel oblique shearing (resolvable in a strike-slip and dip-slip component) and across-foliation shortening. The former accommodated the transpressive component of the MZ, and its kinematics is either sinistral or dextral depending on the local strike of the MZ with respect to the regional thrust shortening vector. The latter led to pure-shear shortening perpendicular to the thrust sheet and subsequent lateral extrusion parallel to the mylonitic foliation via the development of antithetic displacements. No significant strain partitioning is observed at the meso-scale and strain is thus truly triclinic. The example described is an outstanding case of triclinic deformation, confirms theoretical analyses of complex strain models and adds valuable natural field constraints to our knowledge of deformation in the crust.
Peach and Horne: the British Association excursion to Assynt September 1912
Authors: Barber A. J. 
Published: June 2010

Abstract

At the meeting of the British Association held in Dundee in September 1912 a group of eminent European geologists, including most of the leading Alpine tectonic experts of the day, intrigued by the account of the structure of the NW Highlands given in the 1907 memoir, expressed a wish to see these structures for themselves. Peach and Horne were approached, and agreed to lead an excursion to the Assynt area following the meeting. The programme for the excursion followed an itinerary that many geological parties still follow today. On the final evening of the excursion Albert Heim (Zurich), the doyen of Alpine geologists, gave a vote of thanks to the leaders and Maurice Lugeon (Lausanne) composed
La Chanson du Moine Thrust
which the participants sung with great enthusiasm. Brief biographies are given of the participants, many of whom were already distinguished, while most of the junior participants, particularly those from the British Geological Survey, went on to pursue long and distinguished careers, making major contributions to our knowledge of Scottish geology.
Extensional tectonics in the North Atlantic Caledonides: a regional view
Authors: Fossen Haakon 
Published: June 2010

Abstract
Extensional structures characterize significant parts of the North Atlantic Caledonides. Silurian extensional deformation took place, particularly in the heated crust in the southern Greenland Caledonides, but the majority of the mapped extensional structures are Devonian (403–380 Ma). They formed by reactivation of low-angle Caledonian thrusts and by the formation of hinterland-dipping shear zones, of which the largest system is located in SW Norway and related to exhumation of the subducted margin of Baltica. The Devonian extension was concentrated to the central and southern part of the Caledonides, with maximum extension occurring in the area between the Western Gneiss Region of SW Norway and the Fjord Region of East Greenland. Kinematic data indicate that the main tectonic transport direction was toward the hinterland, and this pattern suggests that the main Devonian extension/transtension in the southern part of the North Atlantic region was postcontractional while strike-slip motions and possibly transpression occurred farther north. Late Devonian to enigmatic Early Carboniferous ages from UHP metamorphic assemblages in NE Greenland suggest that intracontinental subduction was going on in NE Greenland at a time when extensional deformation governed the rest of the orogenic belt.