bluuebunny/crossref_metadata_2025_split huggingface dataset:
Involvement of CarA/LitR and CRP/FNR Family Transcriptional Regulators in Light-Induced Carotenoid Production in Thermus thermophilus
Authors: Takano Hideaki , Kondo Masato , Usui Noriyoshi , Usui Toshimitsu , Ohzeki Hiromichi , Yamazaki Ryuta , Washioka Misato , Nakamura Akira , Hoshino Takayuki , Hakamata Wataru , Beppu Teruhiko , Ueda Kenji 
Published: March 2011

ABSTRACT

Members of the CarA/LitR family are MerR-type transcriptional regulators that contain a C-terminal cobalamin-binding domain. They are thought to be involved in light-induced transcriptional regulation in a wide variety of nonphototrophic bacteria. Based on the distribution of this kind of regulator, the current study examined carotenoid production in
Thermus thermophilus
, and it was found to occur in a light-induced manner.
litR
and carotenoid and cobalamin biosynthesis genes were all located on the large plasmid of this organism.
litR
or cobalamin biosynthesis gene knockout mutants were unable to switch off carotenoid production under dark conditions, while a mutant with a mutation in the downstream gene adjacent to
litR
(TT_P0055), which encodes a CRP/FNR family transcriptional regulator, was unable to produce carotenoids, irrespective of light conditions. Overall, genetic and biochemical evidence indicates that LitR is bound by cobalamin and associates with the intergenic promoter region between
litR
and
crtB
(phytoene synthase gene), repressing the bidirectional transcription of
litR
and
crtB
. It is probable that derepression of LitR caused by some photodependent mechanism induces the expression of TT_P0055 protein, which serves as a transcriptional activator for the
crtB
operon and hence causes the expression of carotenoid biosynthesis and the DNA repair system under light condition.
Role of Maltose Enzymes in Glycogen Synthesis by Escherichia coli
Authors: Park Jong-Tae , Shim Jae-Hoon , Tran Phuong Lan , Hong In-Hee , Yong Hwan-Ung , Oktavina Ershita Fitria , Nguyen Hai Dang , Kim Jung-Wan , Lee Tae Soo , Park Sung-Hoon , Boos Winfried , Park Kwan-Hwa 
Published: March 2011

ABSTRACT

Mutants with deletion mutations in the
glg
and
mal
gene clusters of
Escherichia coli
MC4100 were used to gain insight into glycogen and maltodextrin metabolism. Glycogen content, molecular mass, and branch chain distribution were analyzed in the wild type and in Δ
malP
(encoding maltodextrin phosphorylase), Δ
malQ
(encoding amylomaltase), Δ
glgA
(encoding glycogen synthase), and Δ
glgA
Δ
malP
derivatives. The wild type showed increasing amounts of glycogen when grown on glucose, maltose, or maltodextrin. When strains were grown on maltose, the glycogen content was 20 times higher in the Δ
malP
strain (0.97 mg/mg protein) than in the wild type (0.05 mg/mg protein). When strains were grown on glucose, the Δ
malP
strain and the wild type had similar glycogen contents (0.04 mg/mg and 0.03 mg/mg protein, respectively). The Δ
malQ
mutant did not grow on maltose but showed wild-type amounts of glycogen when grown on glucose, demonstrating the exclusive function of GlgA for glycogen synthesis in the absence of maltose metabolism. No glycogen was found in the Δ
glgA
and Δ
glgA
Δ
malP
strains grown on glucose, but substantial amounts (0.18 and 1.0 mg/mg protein, respectively) were found when they were grown on maltodextrin. This demonstrates that the action of MalQ on maltose or maltodextrin can lead to the formation of glycogen and that MalP controls (inhibits) this pathway.
In vitro
, MalQ in the presence of GlgB (a branching enzyme) was able to form glycogen from maltose or linear maltodextrins. We propose a model of maltodextrin utilization for the formation of glycogen in the absence of glycogen synthase.
CRISPR Distribution within the Escherichia coli Species Is Not Suggestive of Immunity-Associated Diversifying Selection
Authors: Touchon Marie , Charpentier Sophie , Clermont Olivier , Rocha Eduardo P. C. , Denamur Erick , Branger Catherine 
Published: March 2011

ABSTRACTIn order to get further insights into the role of the clustered, regularly interspaced, short palindromic repeats (CRISPRs) inEscherichia coli, we analyzed the CRISPR diversity in a collection of 290 strains, in the phylogenetic framework of the strains represented by multilocus sequence typing (MLST). The set included 263 naturalE. coliisolates exposed to various environments and isolated over a 20-year period from humans and animals, as well as 27 fully sequenced strains. Our analyses confirm that there are two largely independent pairs of CRISPR loci (CRISPR1 and -2 and CRISPR3 and -4), each associated with a different type ofcasgenes (Ecoli and Ypest, respectively), but that each pair of CRISPRs has similar dynamics. Strikingly, the major phylogenetic group B2 is almost devoid of CRISPRs. The majority of genomes analyzed lack Ypestcasgenes and contain CRISPR3 with spacers matching Ypestcasgenes. The analysis of relatedness between strains in terms of spacer repertoire and the MLST tree shows a pattern where closely related strains (MLST phylogenetic distance of <0.005 corresponding to at least hundreds of thousands of years) often exhibit identical CRISPRs while more distantly related strains (MLST distance of >0.01) exhibit completely different CRISPRs. This suggests rare but radical turnover of spacers in CRISPRs rather than CRISPR gradual change. We found no link between the presence, size, or content of CRISPRs and the lifestyle of the strains. Our data suggest that, within theE. colispecies, CRISPRs do not have the expected characteristics of a classical immune system.
A MotN Mutant of Ralstonia solanacearum Is Hypermotile and Has Reduced Virulence
Authors: Meng Fanhong , Yao Jian , Allen Caitilyn 
Published: March 2011

ABSTRACT

Ralstonia solanacearum
is a soil-borne plant pathogen that causes bacterial wilt disease on many plant species. We previously showed that swimming motility contributes to virulence of this bacterium in the early stages of host invasion and colonization. In this study we identified a new negative regulator of motility, named
motN
, that is located in a cluster of motility-related genes. A
motN
mutant was hypermotile both on 0.3% agar motility plates and in rich and minimal medium broth. However, like its wild-type parent, it was largely nonmotile inside plants. The
motN
mutant cells appeared hyperflagellated, and sheared cell protein preparations from
motN
contained more flagellin than preparations from wild-type cells. The
motN
strain was significantly reduced in virulence in a naturalistic soil soak assay on tomato plants. However, the
motN
mutant had wild-type virulence when it was inoculated directly into the plant vascular system. This suggests that
motN
makes its contribution to virulence early in disease development. The
motN
mutant formed weaker biofilms than the wild type, but it attached normally to tomato roots and colonized tomato stems as well as its wild-type parent. Phenotypic analysis and gene expression studies indicated that MotN directly or indirectly represses transcription of the major motility regulator FlhDC. MotN was also connected with other known motility and virulence regulators, PehSR, VsrBC, and VsrAD, via uncertain mechanisms. Together, these results demonstrate the importance of precise regulation of flagellum-mediated motility in
R. solanacearum
.
Role of the Biofilm Master Regulator CsgD in Cross-Regulation between Biofilm Formation and Flagellar Synthesis
Authors: Ogasawara Hiroshi , Yamamoto Kaneyoshi , Ishihama Akira 
Published: March 2011

ABSTRACT

CsgD, the master regulator of biofilm formation, activates the synthesis of curli fimbriae and extracellular polysaccharides in
Escherichia coli
. To obtain insights into its regulatory role, we have identified a total of 20 novel regulation target genes on the
E. coli
genome by using chromatin immunoprecipitation (ChIP)-on-chip analysis with a high-density DNA microarray. By DNase I footprinting, the consensus CsgD-binding sequence predicted from a total of 18 target sites was found to include AAAAGNG(N
2
)AAAWW. After a promoter-
lacZ
fusion assay, the CsgD targets were classified into two groups: group I genes, such as
fliE
and
yhbT
, are repressed by CsgD, while group II genes, including
yccT
and
adrA
, are activated by CsgD. The
fliE
and
fliEFGH
operons for flagellum formation are directly repressed by CsgD, while CsgD activates the
adrA
gene, which encodes an enzyme for synthesis of cyclic di-GMP, a bacterial second messenger, which in turn inhibits flagellum production and rotation. Taking these findings together, we propose that the cell motility for planktonic growth is repressed by CsgD, thereby promoting the switch to biofilm formation.
Staphylococcus aureus CidA and LrgA Proteins Exhibit Holin-Like Properties
Authors: Ranjit Dev K. , Endres Jennifer L. , Bayles Kenneth W. 
Published: March 2011

ABSTRACT

The
Staphylococcus aureus
cid
and
lrg
operons are known to be involved in biofilm formation by controlling cell lysis and the release of genomic DNA, which ultimately becomes a structural component of the biofilm matrix. Although the molecular mechanisms controlling cell death and lysis are unknown, it has been hypothesized that the
cidA
and
lrgA
genes encode holin- and antiholin-like proteins and function to regulate these processes similarly to bacteriophage-induced death and lysis. In this study, we focused on the biochemical and molecular characterization of CidA and LrgA with the goal of testing the holin model. First, membrane fractionation and fluorescent protein fusion studies revealed that CidA and LrgA are membrane-associated proteins. Furthermore, similarly to holins, CidA and LrgA were found to oligomerize into high-molecular-mass complexes whose formation was dependent on disulfide bonds formed between cysteine residues. To determine the function of disulfide bond-dependent oligomerization of CidA, an
S. aureus
mutant in which the wild-type copy of the
cidA
gene was replaced with the cysteine mutant allele was generated. As determined by β-galactosidase release assays, this mutant exhibited increased cell lysis during stationary phase, suggesting that oligomerization has a negative impact on this process. When analyzed for biofilm development and maturation, this mutant displayed increased biofilm adhesion in a static assay and a greater amount of dead-cell accumulation during biofilm maturation. These studies support the model that CidA and LrgA proteins are bacterial holin-/antiholin-like proteins that function to control cell death and lysis during biofilm development.
Patient-reported fasting status for glucose-tolerance testing compared with fasting status identified by total bile-acid concentrations
Authors: Sargazi Mansour , Neithercut William D 
Published: March 2011

AimTo investigate whether patients follow advice regarding the duration of a fast, prior to blood tests which require an overnight fast for their correct interpretation.MethodPatients referred for a glucose-tolerance test gave informed consent. They were asked to complete a questionnaire regarding the duration of their fast, and an additional blood sample was collected for fasting total bile-acid measurement.Results184 patients were recruited. The median duration of fast self reported by patients was 14 h (range 12–26 h). Total bile-acid concentrations were within the fasting reference range except for six individuals. The median total bile-acid concentration found was 2.1 μmol/l (range 0.1–19.5 μmol/l).ConclusionAll patients who self-reported a duration of fast reported a fast recognised as being adequate for fasting blood tests. This was confirmed in almost all by low normal total bile-acid measurements, which were well within the fasting range.
Low-temperature aqueous mobility of the rare-earth elements during sandstone diagenesis
Authors: Bouch Jon E. , Hole Malcolm J. , Trewin Nigel H. , Morton Andrew C. 
Published: March 2011

Abstract

Diagenetic francolite (carbonate fluor-apatite) occurs as overgrowths on detrital apatite grains in sandstones from the Lower Jurassic Statfjord Formation of the North Sea. The francolite overgrowths are considerably more enriched in the rare-earth elements (up to 1 wt % Ce
2
O
3
), Sr and F than the detrital cores. These elements were carried in aqueous solution, probably in the form of complex ligands involving organically sourced carbon and halogens. It is possible that reported aberrant neodymium isotope model ages within the Statfjord Formation are the result of mobilization and relative fractionation of Sm and Nd during diagenesis, rather than a result of changes in provenance.
Late Ordovician extinctions and sea-level change
Authors: Wyatt A. R. 
Published: March 2011

Abstract
If Ordovician continental blocks had similar hypsometries to modern continental blocks, glacially-induced regressions would have increased shallow water areas. Thus species/area effects cannot be invoked to explain extinctions during these regressions. Because late Ordovician sea level was so high, glacially-induced regressions of similar magnitudes to Quaternary regressions would have dramatically increased the input of dissolved load into the shallow sea. This ‘pollution’ effect may have been one cause of the extinctions.
Dyke domains in the Mitsero graben, Troodos ophiolite, Cyprus: an off-axis model for graben formation at a spreading centre
Authors: van Everdingen D. A. , Cawood P. A. , van Everdingen D. A. , Cawood P. A. 
Published: March 2011

Abstract
Graben at oceanic spreading centres may form at on-axis or off-axis positions. Their formation is dependent on the tectonic processes active in the oceanic crust. Evidence for the position of formation of graben in oceanic analogues (ophiolites) can be obtained from the orientation of dykes within sheeted dyke complexes. Dyke orientation data and dyke relations from the Mitsero graben and environs, Troodos ophiolite, Cyprus, have been used to determine the tectonic setting of graben formation. Five major dyke domains were delineated on the basis of orientation of dykes in the Sheeted Dyke Complex in the Mitsero graben. Between domains, the mean strike rotates counter-clockwise by 25°. In the easternmost domain, dyke strikes are roughly 070°, and progressively westward, the mean strikes of dykes within domains are roughly 045°, 026°, 000°, and 324°. Within domains the dyke trends show no systematic changes in strike toward the domain edges. Dyke cross-cutting relations, the degree of their rotation, and relations to other features such as hydrothermal alteration leads to the suggestion that the Mitsero graben formed late in the history of the area, possibly in an off-axis position.
Lithostratigraphy of the volcanic sequences at Hole 917A, Leg 152, SE Greenland margin
Authors: Demant A. , Cambray H. , Vandamme D. ,   The ODP Leg 152 Scientific Party
Published: March 2011

Abstract
An overall high recovery rate (up to 52%) and 450 m of continuous logging data of good quality at ODP hole 917A, Leg 152, SE Greenland margin, allow us to refine the petrological descriptions made onboard and to establish a precise lithostratigraphy of the Palaeocene volcanic succession. Changes in the dips of the flow banding between the Upper Series and the Middle and Lower Series coincide with the transition from continental magmatism to post-breakup volcanism established by the geochemistry.
The Edoras Bank margin; continental break-up in the presence of a mantle plume
Authors: Barton A. J. , White R. S. 
Published: March 2011

Abstract

Edoras Bank lies on the eastern continental margin of the North Atlantic about 900 km south of the present-day Iceland plume. We studied the continent-ocean transition of the rifted margin using normal-incidence and wide-angle seismic reflection data. Seaward dipping reflectors are well-developed over much of the margin and are underlain by a high velocity (7.3–7.5 km s
−1
) lower crust. This is interpreted as either igneous underplating or as existing crust heavily intruded at the time of break-up by melts with high MgO contents and suggests that the thermal anomaly associated with the Iceland plume was well-developed in this area at the time of break-up.
The melting processes and composition of the North Atlantic (Iceland) plume: geochemical evidence from the Early Tertiary basalts
Authors: Kerr Andrew C. 
Published: March 2011

Abstract
Three successive geochemical magma types, which result from the decompression melting of the Iceland plume, can be identified throughout the North Atlantic Tertiary Igneous Province. Compared with Type 1, the geochemical signature of Type 2 can be interpreted in terms of shallower, more extensive melting, in response to lithospheric thinning. The chemistry of the youngest lavas and dykes (Type 3) suggests small degree melting at greater mantle depths than Type 2, perhaps below a lithospheric lid which had been re-thickened by underplating. The depleted (relative to Bulk Earth) geochemical signatures of Types 1 and 2 appear not to be derived from entrained upper MORB-source mantle, nor an immature HIMU plume. Rather, it is proposed that they are the melting products of an intrinsically depleted plume.
Magnesian basalts from the Hebrides, Scotland: chemical composition and relationship to the Iceland plume
Authors: Kent Ray W. 
Published: March 2011

Abstract

The Hebridean Tertiary igneous province lay 700–900 km south of a presumed plume centre, and >500 km landward of a rifted continental margin prior to opening of the northeast Atlantic. The Province includes a small number of magnesian basalts containing olivine phenocrysts with core compositions equal to, or in excess of, Fo
89
. Olivine-liquid equilibrium calculations suggest that these phenocrysts formed from liquids with MgO contents of 14–15 wt%, and in rare instances, 18–20 wt%. The liquidus temperatures of these magmas imply mantle potential temperatures of 1350–1460°C at distances up to 900 km from the axis of the Iceland plume. Their emplacement at
c.
60 Ma implies either a long-established hotspot, or active channeling of plume material along the base of the plate towards a region undergoing considerable lower crustal extension.
Sea-floor spreading in the presence of the Iceland plume: the structure of the Reykjanes Ridge at 61°40′N
Authors: Smallwood J. R. , White R. S. , Minshull T. A. 
Published: March 2011

Abstract
We present results from a combined normal incidence and wide-angle seismic survey of the Reykjanes Ridge at 61°40′N in the North Atlantic. The seismic data show that the crust is 8.4–10.0 km thick on the ridge axis. We attribute this thicker than normal oceanic crust to a high degree of melting caused by hot mantle from the Iceland plume beneath the speading centre. Layer 2A of the oceanic crust is significantly thicker at 0 Ma than in crust of age 4 Ma. Our results, combined with other seismic data from the North Atlantic, show that the crustal thickness decreases away from the plume centre to normal oceanic crustal thickness at a distance of approximately 1000 km.
Petrographic and geochemical variation along the Reykjanes Ridge, 57°N–59°N
Authors: Taylor Rex N. , Murton B. J. , Thirwall M. F. 
Published: March 2011

Abstract
High-density sampling of the neo-volcanic zone along the Reykjanes Ridge has been used to test the relationship between bathymetric features and geochemistry. The axial region has short wavelength features which correspond to elongate, en-echelon volcanic ridges. These ridges sit atop intermediate wavelength features, termed swells and troughs. A broad correspondence is found between the sections containing more fractionated samples and the intermediate wavelength swells. Conversely, the troughs are dominated by more primitive lavas. This suggests that swells represent areas of greater melt flux, resulting in thicker crust and hence generally more fractionation. Progressively higher concentrations of incompatible elements are found northwards along the ridge, with increases occurring as a series of steps that do not correlate with short or intermediate wavelength bathymetric features. The northward increase in ratios such as Nb/Zr suggests that sections of the ridge are fed by similar aggregate melt fractions, and that melt fractions become slightly smaller northwards. Changes or consistency in ratio, particularly Rb/Nb, cannot be explained by progressively greater northward incorporation of a component from the Icelandic plume mantle.
The temperature of the Iceland plume and origin of outward-propagating V-shaped ridges
Authors: White R. S. , Bown J. W. , Smallwood J. R. 
Published: March 2011

Abstract

Decompression melting of hot mantle rising in the convectively driven core of the Iceland plume generates igneous crust beneath Iceland that is
c.
25 km thick. Passive decompression of mantle beneath the adjacent Reykjanes Ridge spreading centre produces crust 7–10 km thick. The decrease between Iceland and the adjacent oceanic spreading centre in crustal thickness, in basement elevation and in melting column thickness deduced from rare earth element inversions of basaltic igneous rocks, suggests that the mantle beneath the spreading centre is markedly cooler (potential temperature less than 1400°C) than in the core of the plume under Iceland (potential temperature
c.
1500 °C). We suggest that the spreading centre is fed by mantle from a cooler sheath surrounding the narrow central core of the plume under Iceland, and that the mantle cools to the south until it reaches a normal potential temperature of 1300°C about 1350 km away from the centre of the plume. Prominent V-shaped topography and gravity anomalies on the Reykjanes Ridge record variations of up to 30°C in the temperature of the underlying asthenospheric mantle supplied by the plume, over timescales of 5–10 Ma.
A redescription of
Plesiosaurus propinquus
Tate & Blake, 1876 (Reptilia, Plesiosauria), from the Lower Jurassic (Toarcian) of Yorkshire, England
Authors: Vincent P. , Smith A. S. 
Published: March 2011

SUMMARY

The type specimen (WM 851.S, skull and post-cranial skeleton) of
Plesiosaurus propinquus
Tate & Blake, 1876, from the Toarcian (Upper Lias, Lower Jurassic) of Yorkshire, is re-examined. New observations permit a detailed understanding of the cranial anatomy of this specimen and hence its taxonomic affinity. The few differences between
Plesiosaurus propinquus
and
Rhomaleosaurus zetlandicus
cannot be considered diagnostic. Consequently,
Plesiosaurus propinquus
is here assigned to and considered a junior synonym of
Rhomaleosaurus zetlandicus
. Currently only three valid species of the genus
Rhomaleosaurus
are known; a complete revision of the specimens formerly attributed to
Rhomaleosaurus
must now be carried out.