bluuebunny/crossref_metadata_2025 huggingface dataset:
Bacterial community succession during in situ uranium bioremediation: spatial similarities along controlled flow paths
Authors: Hwang Chiachi , Wu Weimin , Gentry Terry J , Carley Jack , Corbin Gail A , Carroll Sue L , Watson David B , Jardine Phil M , Zhou Jizhong , Criddle Craig S , Fields Matthew W
Published: December 2008

Correction to: The ISME Journal (2009) 3, 47–64; doi:10.1038/ismej.2008.77 The authors of the above noted an error in publication of this paper (AOP and in this issue) in the labeling of the dots in Figure 8. The corrected Figure 8 is shown below.
Evolution of Thriftiness: An analytical viewpoint
Authors: Belsare Prajakta , Watve Milind
Published: December 2008

We examine here, using a simple mathematical model, the conditions under which thrifty genes or fetal programming could evolve. Obesity and related disorders are thought to have their roots in metabolic thirftiness that evolved to combat periodic starvation. The failure to detect any thrifty genes and the association of low birth weight with type 2 diabetes, caused a shift in the concept from thrifty gene to thrifty phenotype and fetal programming. This hypothesis assumes that intra-uterine undernutrition programs the body to be thrifty, predicting and preparing for starvation in later life. However, there are reproductive costs associated with thriftiness. Results of the model suggest that under no condition thrifty and non-thrifty genes would co-exist stably in a population. The conditions for evolution of fetal programming are also very restricted. For species with longer life spans, programming for thriftiness is unlikely to evolve if starvation is decided by seasonality or stochastic annual climatic variations since the correlation between intra-uterine and life-time conditions is poor. On the other hand, if starvation is governed by longer periodicity factors such as population oscillations or social hierarchies, there can be better correlation between intra-uterine and life time conditions. Therefore social and population processes are more likely to have selected for fetal programming rather than seasonal and climatic “feast and famine” conditions. Since social and population processes can have cues other than diet, these cues may also influence the incidence of obesity related disorders as some recent evidence suggest.
Lysine-specific gingipain promotes lipopolysaccharide- and active-vitamin D3-induced osteoclast differentiation by degrading osteoprotegerin
Authors: Yasuhara Rika , Miyamoto Yoichi , Takami Masamichi , Imamura Takahisa , Potempa Jan , Yoshimura Kentaro , Kamijo Ryutaro
Published: December 2008

Porphyromonas gingivalis is one of the major pathogens of periodontitis, a condition characterized by excessive alveolar bone resorption by osteoclasts. The bacterium produces cysteine proteases called gingipains, which are classified according to their cleavage-site specificity into Kgps (lysine-specific gingipains) and Rgps (arginine-specific gingipains). In the present study we examined the effects of gingipains on osteoclast differentiation. In co-cultures of mouse bone-marrow cells and osteoblasts, formation of multinucleated osteoclasts induced by 1α,25(OH)2D3 (1α,25-dihydroxyvitamin D3) was augmented by Kgp but not by RgpB. A physiological concentration (0.1 nM) of 1α,25(OH)2D3 induced the osteoclast formation in the presence of 100 nM Kgp to an extent comparable with that induced by 10 nM 1α,25(OH)2D3. Kgp also enhanced osteoclastogenesis induced by various microbial components, including lipopolysaccharide. Combined use of Kgp and 1α,25(OH)2D3 or lipopolysaccharide also increased the number of resorption pits developed on dentin slices, indicating that the osteoclasts formed in the presence of Kgp possess bone-resorbing activity. The enhanced osteoclastogenesis by Kgp was correlated with a depletion of osteoprotegerin in co-culture medium and was proteolytic-activity-dependent, since benzyloxycarbonyl-L-phenylalanyl-L-lysylacycloxyketone, an inhibitor of Kgp, completely abolished osteoclastogenesis induced by Kgp. Kgp digested osteoprotegerin, since its recombinant protein was susceptible to degradation by Kgp in the presence of serum. As a result, Kgp did not augment osteoclastogenesis in co-cultures of osteoprotegerin-deficient osteoblasts and bone-marrow cells. In addition, enhanced osteoclastogenesis by Kgp was abolished by an excess amount of recombinant osteoprotegerin. These findings suggest that degradation of osteoprotegerin is one of the mechanisms underlying promotion of osteoclastogenesis by Kgp.
Mapping of a copper-binding site on the small CP12 chloroplastic protein of Chlamydomonas reinhardtii using top-down mass spectrometry and site-directed mutagenesis
Authors: Erales Jenny , Gontero Brigitte , Whitelegge Julian , Halgand Frédéric
Published: December 2008

CP12 is a small chloroplastic protein involved in the Calvin cycle that was shown to bind copper, a metal ion that is involved in the transition of CP12 from a reduced to an oxidized state. In order to describe CP12's copper-binding properties, copper-IMAC experiments and site-directed mutagenesis based on computational modelling, were coupled with top-down MS [electrospray-ionization MS and MS/MS (tandem MS)]. Immobilized-copper-ion-affinity-chromatographic experiments allowed the primary characterization of the effects of mutation on copper binding. Top-down MS/MS experiments carried out under non-denaturing conditions on wild-type and mutant CP12–Cu2+ complexes then allowed fragment ions specifically binding the copper ion to be determined. Comparison of MS/MS datasets defined three regions involved in metal ion binding: residues Asp16–Asp23, Asp38–Lys50 and Asp70–Glu76, with the two first regions containing selected residues for mutation. These data confirmed that copper ligands involved glutamic acid and aspartic residues, a situation that contrasts with that obtaining for typical protein copper chelators. We propose that copper might play a role in the regulation of the biological activity of CP12.
Near-linear cost increase to reduce climate-change risk
Authors: Schaeffer Michiel , Kram Tom , Meinshausen Malte , van Vuuren Detlef P. , Hare William L.
Published: December 2008

One approach in climate-change policy is to set normative long-term targets first and then infer the implied emissions pathways. An important example of a normative target is to limit the global-mean temperature change to a certain maximum. In general, reported cost estimates for limiting global warming often rise rapidly, even exponentially, as the scale of emission reductions from a reference level increases. This rapid rise may suggest that more ambitious policies may be prohibitively expensive. Here, we propose a probabilistic perspective, focused on the relationship between mitigation costs and the likelihood of achieving a climate target. We investigate the qualitative, functional relationship between the likelihood of achieving a normative target and the costs of climate-change mitigation. In contrast to the example of exponentially rising costs for lowering concentration levels, we show that the mitigation costs rise proportionally to the likelihood of meeting a temperature target, across a range of concentration levels. In economic terms investing in climate mitigation to increase the probability of achieving climate targets yields “constant returns to scale,” because of a counterbalancing rapid rise in the probabilities of meeting a temperature target as concentration is lowered.
MIG-17/ADAMTS controls cell migration by recruiting nidogen to the basement membrane in
C. elegans
Authors: Kubota Yukihiko , Ohkura Kiyotaka , Tamai Katsuyuki K. , Nagata Kayo , Nishiwaki Kiyoji
Published: December 2008

Mutations in the
a d
isintegrin
a
nd
m
etalloprotease with
t
hrombo
s
pondin motifs (ADAMTS) family of secreted proteases cause diseases linked to ECM abnormalities. However, the mechanisms by which these enzymes modulate the ECM during development are mostly unexplored. The
Caenorhabditis elegans
MIG-17/ADAMTS protein is secreted from body wall muscle cells and localizes to the basement membrane (BM) of the developing gonad where it controls directional migration of gonadal leader cells. Here we show that specific amino acid changes in the ECM proteins fibulin-1C (FBL-1C) and type IV collagen (LET-2) result in bypass of the requirement for MIG-17 activity in gonadal leader cell migration in a nidogen (NID-1)-dependent and -independent manner, respectively. The MIG-17, FBL-1C and LET-2 activities are required for proper accumulation of NID-1 at the gonadal BM. However, mutant FBL-1C or LET-2 in the absence of MIG-17 promotes NID-1 localization. Furthermore, overexpression of NID-1 in
mig-17
mutants substantially rescues leader cell migration defects. These results suggest that functional interactions among BM molecules are important for MIG-17 control of gonadal leader cell migration. We propose that FBL-1C and LET-2 act downstream of MIG-17-dependent proteolysis to recruit NID-1 and that LET-2 also activates a NID-1-independent pathway, thereby inducing the remodeling of the BM required for directional control of leader cell migration.
Redundant mechanisms mediate bristle patterning on the
Drosophila
thorax
Authors: Usui Kazuya , Goldstone Claire , Gibert Jean-Michel , Simpson Pat
Published: December 2008

The thoracic bristle pattern of
Drosophila
results from the spatially restricted expression of the
achaete-scute
(
ac-sc
) genes in clusters of cells, mediated by the activity of many discrete
cis
-regulatory sequences. However, ubiquitous expression of
sc
or
asense
(
ase
) achieved with a heterologous promoter, in the absence of endogenous
ac-sc
expression, and the activity of the
cis
-regulatory elements, allows the development of bristles positioned at wild-type locations. We demonstrate that the products of the genes
stripe
,
hairy
, and
extramacrochaetae
contribute to rescue by antagonizing the activity of Sc and Ase. The three genes are expressed in specific but overlapping spatial domains of expression that form a prepattern that allows precise positioning of bristles. The redundant mechanisms might contribute to the robustness of the pattern. We discuss the possibility that patterning in
trans
by antagonism is ancestral and that the positional
cis
-regulatory sequences might be of recent origin.
Properties of developmental gene regulatory networks
Authors: Davidson Eric H. , Levine Michael S.
Published: December 2008

The modular components, or subcircuits, of developmental gene regulatory networks (GRNs) execute specific developmental functions, such as the specification of cell identity. We survey examples of such subcircuits and relate their structures to corresponding developmental functions. These relations transcend organisms and genes, as illustrated by the similar structures of the subcircuits controlling the specification of the mesectoderm in the
Drosophila
embryo and the endomesoderm in the sea urchin, even though the respective subcircuits are composed of nonorthologous regulatory genes.
Dissecting early regulatory relationships in the lamprey neural crest gene network
Authors: Nikitina Natalya , Sauka-Spengler Tatjana , Bronner-Fraser Marianne
Published: December 2008

The neural crest, a multipotent embryonic cell type, originates at the border between neural and nonneural ectoderm. After neural tube closure, these cells undergo an epithelial–mesenchymal transition, migrate to precise, often distant locations, and differentiate into diverse derivatives. Analyses of expression and function of signaling and transcription factors in higher vertebrates has led to the proposal that a neural crest gene regulatory network (NC-GRN) orchestrates neural crest formation. Here, we interrogate the NC-GRN in the lamprey, taking advantage of its slow development and basal phylogenetic position to resolve early inductive events, 1 regulatory step at the time. To establish regulatory relationships at the neural plate border, we assess relative expression of 6 neural crest network genes and effects of individually perturbing each on the remaining 5. The results refine an upstream portion of the NC-GRN and reveal unexpected order and linkages therein; e.g., lamprey AP-2 appears to function early as a neural plate border rather than a neural crest specifier and in a pathway linked to MsxA but independent of ZicA. These findings provide an ancestral framework for performing comparative tests in higher vertebrates in which network linkages may be more difficult to resolve because of their rapid development.
Imaging quantum confinement with optical and POWER (perturbations observed with enhanced resolution) NMR
Authors: Kempf James G. , Miller Michael A. , Weitekamp Daniel P.
Published: December 2008

The nanoscale distributions of electron density and electric fields in GaAs semiconductor devices are displayed with NMR experiments. The spectra are sensitive to the changes to the nuclear-spin Hamiltonian that are induced by perturbations delivered in synchrony with a line-narrowing pulse sequence. This POWER (perturbations observed with enhanced resolution) method enhanced resolution up to 10
3
-fold, revealing the distribution of perturbations over nuclear sites. Combining this method with optical NMR, we imaged quantum-confined electron density in an individual AlGaAs/GaAs heterojunction via hyperfine shifts. Fits to the coherent evolution and relaxation of nuclei within a hydrogenic state established one-to-one correspondence of radial position to frequency. Further experiments displayed the distribution of photo-induced electric field within the same states via a quadrupolar Stark effect. These unprecedented high-resolution distributions discriminate between competing models for the luminescence and support an excitonic state, perturbed by the interface, as the dominant source of the magnetically modulated luminescence.
Transgenic rice plants that overexpress transcription factors RF2a and RF2b are tolerant to rice tungro virus replication and disease
Authors: Dai Shunhong , Wei Xiaoping , Alfonso Antonio A. , Pei Liping , Duque Ulysses G. , Zhang Zhihong , Babb Gina M. , Beachy Roger N.
Published: December 2008

Rice tungro disease (RTD) is a significant yield constraint in rice-growing areas of South and Southeast Asia. Disease symptoms are caused largely by infection by the rice tungro bacilliform virus (RTBV). Two host transcription factors, RF2a and RF2b, regulate expression of the RTBV promoter and are important for plant development. Expression of a dominant negative mutant of these factors in transgenic rice resulted in phenotypes that mimic the symptoms of RTD, whereas overexpression of RF2a and RF2b had essentially no impact on plant development. Conversely, lines with elevated expression of RF2a or RF2b showed weak or no symptoms of infection after
Agrobacterium
inoculation of RTBV, whereas control plants showed severe stunting and leaf discoloration. Furthermore, transgenic plants exhibited reduced accumulation of RTBV RNA and viral DNA compared with nontransgenic plants. Similar results were obtained in studies after virus inoculation by green leafhoppers. Gaining disease resistance by elevating the expression of host regulators provides another strategy against RTD and may have implications for other pararetrovirus infections.
A prototype approach to sentences and sentence types
Authors: Panther Klaus-Uwe , Köpcke Klaus-Michael
Published: December 2008

This paper proposes a new solution to the age-old problem of defining the sentence and sentence types. Arguing against traditional definitions, we propose that the category SENTENCE exhibits a complex prototypical structure on the levels of morphosyntactic form, conceptual content, and pragmatic function. By positing that the central member of the category SENTENCE is the declarative sentence type, we can show how imperative sentences are related to the prototypical declarative sentence type and that imperatives exhibit an internal prototypical structure of their own. Finally, using a scenario approach, we show how the conceptual and pragmatic functions of declarative and imperative sentences may overlap.
Animaux, méprises et tromperies: Réflexions sur l'image littéraire de certains oiseaux dans la nouvelle italienne
Authors: Marruncheddu Sara
Published: December 2008

Dans la littérature médiévale les espèces animales agissent sur la base des stéréotypes que la société leur attribue. La présente contribution examine le cas des oiseaux, avec une réflexion spécifique sur les rapaces. La recherche se concentre sur un genre littéraire, la nouvelle d’aire italienne, et sur les situations où l’oiseau est le protagoniste d’une tromperie, par son geste ou par sa parole. Dans le cas des rapaces, on observe que les espèces employées dans la chasse jouissent d’une très bonne réputation et les écrivains adoptent des artifices afin de la garder, surtout dans les contextes qui pourraient laisser place à l’ambiguïté. On peut remarquer, en général, que la considération envers une espèce d’oiseaux a son influence sur le milieu de l’action (noble ou populaire), l’évolution du récit et l’opportunité de vendre ou de donner l’animal.
Murena id est Lampreda: Quelques observations lexicologiques et culinaires
Authors: Wille Clara
Published: December 2008

Le nom latin murena, un poisson fort apprécié à la table médiévale, est unanimement rendu par les gloses, les glossaires et les encyclopédies médiévaux par le terme anglo-normand et ancien français lamproie et vice-versa. Or, selon les histoires naturelles modernes, la murena est un poisson rapace qui vit dans les mers tropicales et sous-tropicales et elle appartient à l’ordre des anguilliformes et à la famille des muraenidae. La lampreda, par contre, fait partie de la famille des petromyzonidae et vit alternativement dans les eaux douces et les eaux salées des régions du nord. La superposition des deux termes désignant les deux poissons à l’époque médiévale s’explique par leur ressemblance: la murène et la lamproie ont une allure serpentine assez caractéristique. Mais il y a un second point qui a dû faciliter la confusion: tout comme la murène était un mets recherché par les riches Romains, la lamproie faisait les délices des rois anglo-normands et français. La lamproie ne manque en effet jamais dans les recueils de recettes de l’époque.

Cet essai se propose, à l’aide de textes historiques et culinaires et de documents iconographiques, d’éclaircir les rapports entre ces deux noms et les poissons qu’ils désignent.
Functional anergy in a subpopulation of naive B cells from healthy humans that express autoreactive immunoglobulin receptors
Authors: Duty J. Andrew , Szodoray Peter , Zheng Nai-Ying , Koelsch Kristi A. , Zhang Qingzhao , Swiatkowski Mike , Mathias Melissa , Garman Lori , Helms Christina , Nakken Britt , Smith Kenneth , Farris A. Darise , Wilson Patrick C.
Published: December 2008

Self-reactive B cells not controlled by receptor editing or clonal deletion may become anergic. We report that fully mature human B cells negative for surface IgM and retaining only IgD are autoreactive and functionally attenuated (referred to as naive IgD+IgM− B cells [BND]). These BND cells typically make up 2.5% of B cells in the peripheral blood, have antibody variable region genes in germline (unmutated) configuration, and, by all current measures, are fully mature. Analysis of 95 recombinant antibodies expressed from the variable genes of single BND cells demonstrated that they are predominantly autoreactive, binding to HEp-2 cell antigens and DNA. Upon B cell receptor cross-linkage, BND cells have a reduced capacity to mobilize intracellular calcium or phosphorylate tyrosines, demonstrating that they are anergic. However, intense stimulation causes BND cells to fully respond, suggesting that these cells could be the precursors of autoantibody secreting plasma cells in autoimmune diseases such as systemic lupus erythematosus or rheumatoid arthritis. This is the first identification of a distinct mature human B cell subset that is naturally autoreactive and controlled by the tolerizing mechanism of functional anergy.
TESTING GRAVITY WITH MOTION OF SATELLITES AROUND GALAXIES: NEWTONIAN GRAVITY AGAINST MODIFIED NEWTONIAN DYNAMICS
Authors: Klypin Anatoly , Prada Francisco
Published: December 2008

The motion of satellite galaxies around normal galaxies at distances 50–500 kpc provides a sensitive test for theories. We study the surface density and velocities of satellites around isolated red galaxies in the Sloan Digital Sky Survey. We find that the surface number density of satellites declines with the projected distance as a power law with the slope −1.5 to 2. The rms velocities gradually decline: observations exclude constant velocities at a ∼10σ level. We show that observational data strongly favor the standard model; all three major statistics of satellites—the number-density profile, the line-of-sight velocity dispersion, and the distribution function of the velocities—agree remarkably well with the predictions of the standard cosmological model. Thus, the success of the standard model extends to scales (50–500) kpc, much lower than what was previously considered. Modified Newtonian dynamics (MOND) fails on these scales for models which assume any single power-law number-density profile of satellites and any constant velocity anisotropy by predicting nearly constant rms velocities of satellites. Satellite data can be fit by fine-tuned models, which require (1) specific non-power-law density profile, (2) very radial orbits at large distances (velocity anisotropy β = 0.60.7 at
R
= 200–300 kpc), and (3) 2–2.5 times more stellar mass than what is found in the galaxies. The external gravity force—a necessary component for MOND—makes the situation even worse. We argue that a combination of satellite data and observational constraints on stellar masses make these models very problematic.
FRAME DRAGGING AND THE KINEMATICS OF GALACTIC-CENTER STARS
Authors: Kannan Rahul , Saha Prasenjit
Published: December 2008

We calculate the effects of frame dragging on the Galactic-Center stars. Assuming the stars are only slightly relativistic, we derive an approximation to the Kerr metric, which turns out to be a weak-field Schwarzschild metric plus a frame-dragging term. By numerically integrating the resulting geodesic equations, we compute the effect on Keplerian elements and the kinematics. We find that the kinematic effect at pericenter passage is proportional to (a(1 − e
2))−2. For known Galactic-center stars it is of order 10 m s−1. If observed, this would provide a measurement of the spin of the black hole.
Spin polarized d surface resonance state of fcc Co/Cu(001)
Authors: Miyamoto K , Iori K , Sakamoto K , Narita H , Kimura A , Taniguchi M , Qiao S , Hasegawa K , Shimada K , Namatame H , Blügel S
Published: December 2008

Spin- and angle-resolved photoemission spectroscopy has been applied to the study of the surface and bulk electronic structures of a face-centered cubic (fcc) Co thin film. We have experimentally resolved a negatively spin-polarized surface resonance state of fcc Co/Cu(001) at 0.4 eV below the Fermi energy. Moreover, we have found that the surface resonance state exhibits a strong spin–orbit interaction through an investigation of magnetic dichroism in the angular distribution spectrum of Co/Cu(001).
Estimating Gliadin and Albumin Variation at Intra‐ and Interaccession Level in USDA Oriental Wheat (Triticum turgidum L. subsp. turanicum (Jakubz.) (A. Lőve & D. Lőve) Collection Using Capillary Zone Electrophoresis
Authors: Piergiovanni Angela R.
Published: December 2008

Interest in so‐called ancient wheats (einkorn, emmer, oriental wheat, and spelt) has increased steadily in the last few decades. Oriental wheat (Triticum turgidum L. subsp. turanicum (Jakubz.) (A. Lőve & D. Lőve) is a neglected and underutilized tetraploid species that has survived over the centuries in some areas of the Near East and central Asia. Very little attention has been devoted by researchers to the evaluation and characterization of the oriental wheat germplasm. Knowledge of the variation of seed storage proteins within a germplasm collection is very useful for breeders interested in increasing the genetic bases of modern wheat cultivars. In this study, capillary zone electrophoresis (CZE) was used to analyze the gliadin and albumin extracts relative to 74 accessions belonging to the oriental wheat collection maintained at the USDA gene bank. Fourteen gliadin patterns were observed. Among the six most frequent patterns, one was widely predominant, being observed in 29 accessions, whereas eight were single types. Two profiles showing similar frequencies within the collection together with six single types were recognized for the albumins. The combination of the observed gliadin and albumin profiles gave rise to 25 combinations. In general, accessions collected in the same country shared the same combinations. This suggests that some accessions could be duplicates of the same genetic stock. Accessions collected in Iran and Turkey, which are indicated as the countries in which oriental wheat originated, were characterized by a higher degree of polymorphism.
Concentrations of Some Metabolites Produced by Fungi of the Genus Fusarium and Selected Elements in Spring Spelt Grain
Authors: Wiwart Marian , Kandler Wolfgang , Perkowski Juliusz , Berthiller Franz , Preinerstorfer Beatrix , Suchowilska Elżbieta , Buśko Maciej , Laskowska Magdalena , Krska Rudolf
Published: December 2008

The aim of this study was to determine the content of selected elements and metabolites produced by fungi of the genus Fusarium in spelt (Triticum spelta L.) grain and husks and common wheat (T. aestivum L.) grain. Concentrations of trichothecenes, a volatile metabolite trichodiene (TRICH), as well as ergosterol (ERG) and adenosine 5′‐triphosphate (ATP) (a total microbial biomass indicator), were assessed. Toxin concentrations in spelt grain and husks harvested in 2003 and 2004 were comparable. Average deoxynivalenol concentrations reached 450 and 523 μg/kg in grain and 2,162 and 855 μg/kg in husks, respectively. Spelt grain, in comparison with common wheat grain, contained significantly higher concentrations of P, S, Mg, Zn, and Cu and a lower concentration of Al, whereas the concentrations of Ca, Fe, and Pb were significantly higher in the husks than in the grain of this cereal. A comparison of concentrations of Fusarium spp. metabolites in the grain of spelt and common wheat showed that the total concentration of mycotoxins and TRICH was slightly lower in T. spelta, whereas common wheat grain contained lower concentrations of ERG and ATP. The obtained results indicate that spelt husks contain considerable concentrations of trichothecenes.
MEN ε/β nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles
Authors: Sunwoo Hongjae , Dinger Marcel E. , Wilusz Jeremy E. , Amaral Paulo P. , Mattick John S. , Spector David L.
Published: December 2008

Studies of the transcriptional output of the human and mouse genomes have revealed that there are many more transcripts produced than can be accounted for by predicted protein-coding genes. Using a custom microarray, we have identified 184 non-coding RNAs that exhibit more than twofold up- or down-regulation upon differentiation of C2C12 myoblasts into myotubes. Here, we focus on the Men ε/β locus, which is up-regulated 3.3-fold during differentiation. Two non-coding RNA isoforms are produced from a single RNA polymerase II promoter, differing in the location of their 3′ ends. Men ε is a 3.2-kb polyadenylated RNA, whereas Men β is an ∼20-kb transcript containing a genomically encoded poly(A)-rich tract at its 3′-end. The 3′-end of Men β is generated by RNase P cleavage. The Men ε/β transcripts are localized to nuclear paraspeckles and directly interact with NONO. Knockdown of MEN ε/β expression results in the disruption of nuclear paraspeckles. Furthermore, the formation of paraspeckles, after release from transcriptional inhibition by DRB treatment, was suppressed in MEN ε/β-depleted cells. Our findings indicate that the MEN ε/β non-coding RNAs are essential structural/organizational components of paraspeckles.
Alcohol research and the alcoholic beverage industry: issues, concerns and conflicts of interest
Authors: Babor Thomas F.
Published: December 2008

Aims Using terms of justification such as ‘corporate social responsibility’ and ‘partnerships with the public health community’, the alcoholic beverage industry (mainly large producers, trade associations and ‘social aspects’ organizations) funds a variety of scientific activities that involve or overlap with the work of independent scientists. The aim of this paper is to evaluate the ethical, professional and scientific challenges that have emerged from industry involvement in alcohol science.

Method Source material came from an extensive review of organizational websites, newspaper articles, journal papers, letters to the editor, editorials, books, book chapters and unpublished documents.

Results Industry involvement in alcohol science was identified in seven areas: (i) sponsorship of research funding organizations; (ii) direct financing of university‐based scientists and centers; (iii) studies conducted through contract research organizations; (iv) research conducted by trade organizations and social aspects/public relations organizations; (v) efforts to influence public perceptions of research, research findings and alcohol policies; (vi) publication of scientific documents and support of scientific journals; and (vii) sponsorship of scientific conferences and presentations at conferences.

Conclusion While industry involvement in research activities is increasing, it constitutes currently a rather small direct investment in scientific research, one that is unlikely to contribute to alcohol science, lead to scientific breakthroughs or reduce the burden of alcohol‐related illness. At best, the scientific activities funded by the alcoholic beverage industry provide financial support and small consulting fees for basic and behavioral scientists engaged in alcohol research; at worst, the industry's scientific activities confuse public discussion of health issues and policy options, raise questions about the objectivity of industry‐supported alcohol scientists and provide industry with a convenient way to demonstrate ‘corporate responsibility’ in its attempts to avoid taxation and regulation.
Postoperative PTH measurement facilitates day 1 discharge after total thyroidectomy
Authors: Grodski Simon , Lundgren Catharina Ihre , Sidhu Stan , Sywak Mark , Delbridge Leigh
Published: December 2008

Objective  A new protocol for postoperative calcium management was developed with the aim of achieving an increase in the proportion of patients being safely discharged on the first postoperative day. We present our experience with the first 50 patients treated under this new protocol.

Patients and design  A cohort study was performed involving the first 50 patients admitted for total or completion thyroidectomy, those data were then compared with a control group. Intact PTH (iPTH) was measured at 4‐h postoperatively and patients with iPTH in the normal range were discharged on the first postoperative day.

Results  Mean age and sex distribution were similar in both groups. Mean lowest postoperative corrected calcium levels in the study group were 2·19 mmol/l and 2·15 mmol/l in the control group (P = 0·24). Parathyroid auto‐transplantaion was associated with low PTH levels (risk ratio = 0·49). Over 50% of patients (n = 27) were successfully discharged on the first postoperative day in the study group and no patient required readmission. Length of stay was significantly shorter in the study group, mean 1·64 vs. 2·20 days (P < 0·05).

Conclusion  The use of iPTH accurately predicts hypocalcaemia after total thyroidectomy and can be used to facilitate safe early discharge for patients.
Haemophilia care then, now and in the future
Authors: OLDENBURG J. , DOLAN G. , LEMM G.
Published: December 2008

Summary.  Epidemiological data show the benefits of dramatically improved haemophilia care in all life‐stages. There are improved administration techniques and dosing regimens, a shift from on‐demand treatment to prophylaxis, successful treatment protocols for immune tolerance induction in patients with inhibitors and enhanced approaches to overall patient management. Improvements also include the introduction of virus inactivation methods for plasma derived clotting factor concentrates and the development of recombinant factor VIII therapy, which practically eliminated the risk of infectious disease transmission. Recombinant factor concentrates are recommended as treatment of choice by several guidelines today. All these developments have resulted in increased health‐related quality of life and life expectancy in haemophilia patients, who are transitioning from childhood to adulthood with healthy joints and an overall healthy status today. Because of increased life expectancy, these patients are expected to experience age‐related clinical problems that were not previously observed in this population. With respect to this, the spectrum of haemophilia care will be extended to diseases of older ages with the need of including further disciplines in comprehensive haemophilia care programmes. Despite these advances, the short half‐life of factor VIII, requiring re‐administration every 2 or 3 days and the development of inhibitors remains a challenge. Bayer’s research and development currently focuses on the optimization of recombinant coagulation factors to address these challenges. Haemophilia care has experienced significant improvements within the past decades. Novel technologies and continued clinical research have facilitated the development of treatment regimen that resulted in dramatic increases in the life expectancy and quality of life of haemophilia patients. To set the scene for the following papers dealing with haemophilia care from paediatrics to geriatrics, developments behind these improvements and some aspects of future research will be presented in this paper.
IUCN classification zones concord with, but underestimate, the population genetic structure of the zebra shark Stegostoma fasciatum in the Indo‐West Pacific
Authors: DUDGEON C. L. , BRODERICK D. , OVENDEN J. R.
Published: December 2008

The Indo‐West Pacific (IWP), from South Africa in the western Indian Ocean to the western Pacific Ocean, contains some of the most biologically diverse marine habitats on earth, including the greatest biodiversity of chondrichthyan fishes. The region encompasses various densities of human habitation leading to contrasts in the levels of exploitation experienced by chondrichthyans, which are targeted for local consumption and export. The demersal chondrichthyan, the zebra shark, Stegostoma fasciatum, is endemic to the IWP and has two current regional International Union for the Conservation of Nature (IUCN) Red List classifications that reflect differing levels of exploitation: ‘Least Concern’ and ‘Vulnerable’. In this study, we employed mitochondrial ND4 sequence data and 13 microsatellite loci to investigate the population genetic structure of 180 zebra sharks from 13 locations throughout the IWP to test the concordance of IUCN zones with demographic units that have conservation value. Mitochondrial and microsatellite data sets from samples collected throughout northern Australia and Southeast Asia concord with the regional IUCN classifications. However, we found evidence of genetic subdivision within these regions, including subdivision between locations connected by habitat suitable for migration. Furthermore, parametric FST analyses and Bayesian clustering analyses indicated that the primary genetic break within the IWP is not represented by the IUCN classifications but rather is congruent with the Indonesian throughflow current. Our findings indicate that recruitment to areas of high exploitation from nearby healthy populations in zebra sharks is likely to be minimal, and that severe localized depletions are predicted to occur in zebra shark populations throughout the IWP region.
Cospeciation of termite gut flagellates and their bacterial endosymbionts: Trichonympha species and ‘Candidatus Endomicrobium trichonymphae’
Authors: IKEDA‐OHTSUBO WAKAKO , BRUNE ANDREAS
Published: December 2008

Symbiotic flagellates play a major role in the digestion of lignocellulose in the hindgut of lower termites. Many termite gut flagellates harbour a distinct lineage of bacterial endosymbionts, so‐called Endomicrobia, which belong to the candidate phylum Termite Group 1. Using an rRNA‐based approach, we investigated the phylogeny of Trichonympha, the predominant flagellates in a wide range of termite species, and of their Endomicrobia symbionts. We found that Trichonympha species constitute three well‐supported clusters in the Parabasalia tree. Endomicrobia were detected only in the apical lineage (Cluster I), which comprises flagellates present in the termite families Termopsidae and Rhinotermitidae, but apparently absent in the basal lineages (Clusters II and III) consisting of flagellates from other termite families and from the wood‐feeding cockroach, Cryptocercus punctulatus. The endosymbionts of Cluster I form a monophyletic group distinct from many other lineages of Endomicrobia and seem to have cospeciated with their flagellate host. The distribution pattern of the symbiotic pairs among different termite species indicates that cospeciation of flagellates and endosymbionts is not simply the result of a spatial separation of the flagellate lineages in different termite species, but that Endomicrobia are inherited among Trichonympha species by vertical transmission. We suggest extending the previously proposed candidatus name ‘Endomicrobium trichonymphae’ to all Endomicrobia symbionts of Trichonympha species, and estimate that the acquisition by an ancestor of Trichonympha Cluster I must have occurred about 40–70 million years ago, long after the flagellates entered the termites.
Physical‐chemical plant‐derived signals induce differentiation in Ustilago maydis
Authors: Mendoza‐Mendoza Artemio , Berndt Patrick , Djamei Armin , Weise Carolin , Linne Uwe , Marahiel Mohamed , Vraneš Miroslav , Kämper Jörg , Kahmann Regine
Published: December 2008

Ustilago maydis is able to initiate pathogenic development after fusion of two haploid cells with different mating type. On the maize leaf surface, the resulting dikaryon switches to filamentous growth, differentiates appressoria and penetrates the host. Here, we report on the plant signals required for filament formation and appressorium development in U. maydis. In vitro, hydroxy‐fatty acids stimulate filament formation via the induction of pheromone genes and this signal can be bypassed by genetically activating the downstream MAP kinase module. Hydrophobicity also induces filaments and these resemble the dikaryotic filaments formed on the plant surface. With the help of a marker gene that is specifically expressed in the tip cell of those hyphae that have formed an appressorium, hydrophobicity is shown to be essential for appressorium development in vitro. Hydroxy‐fatty acids or a cutin monomer mixture isolated from maize leaves have a stimulatory role when a hydrophobic surface is provided. Our results suggest that the early phase of communication between U. maydis and its host plant is governed by two different stimuli.
Genome‐wide responses to carbonyl electrophiles in Bacillus subtilis: control of the thiol‐dependent formaldehyde dehydrogenase AdhA and cysteine proteinase YraA by the MerR‐family regulator YraB (AdhR)
Authors: Huyen Nguyen Thi Thu , Eiamphungporn Warawan , Mäder Ulrike , Liebeke Manuel , Lalk Michael , Hecker Michael , Helmann John D. , Antelmann Haike
Published: December 2008

Quinones and α,β‐unsaturated carbonyls are naturally occurring electrophiles that target cysteine residues via thiol‐(S)‐alkylation. We analysed the global expression profile of Bacillus subtilis to the toxic carbonyls methylglyoxal (MG) and formaldehyde (FA). Both carbonyl compounds cause a stress response characteristic for thiol‐reactive electrophiles as revealed by the induction of the Spx, CtsR, CymR, PerR, ArsR, CzrA, CsoR and SigmaD regulons. MG and FA triggered also a SOS response which indicates DNA damage. Protection against FA is mediated by both the hxlAB operon, encoding the ribulose monophosphate pathway for FA fixation, and a thiol‐dependent formaldehyde dehydrogenase (AdhA) and DJ‐1/PfpI‐family cysteine proteinase (YraA). The adhA–yraA operon and the yraC gene, encoding a γ‐carboxymuconolactone decarboxylase, are positively regulated by the MerR‐family regulator, YraB(AdhR). AdhR binds specifically to its target promoters which contain a 7‐4‐7 inverted repeat (CTTAAAG‐N4‐CTTTAAG) between the −35 and −10 elements. Activation of adhA–yraA transcription by AdhR requires the conserved Cys52 residue in vivo. We speculate that AdhR is redox‐regulated via thiol‐(S)‐alkylation by aldehydes and that AdhA and YraA are specifically involved in reduction of aldehydes and degradation or repair of damaged thiol‐containing proteins respectively.
Mediterranean contributions to cyclostratigraphy and astrochronology
Authors: FISCHER ALFRED G. , HILGEN FREDERIK J. , GARRISON ROBERT E.
Published: December 2008

In 1895, G.K. Gilbert suggested that rhythmical repetition of patterns in the sequences of strata correspond to orbital variations and could provide a chronology for Earth history. This suggestion remained a heuristic hypothesis in need of testing; in this, the Mediterranean region latterly played a crucial role. Its extended sequences of pelagic and lacustrine–paludal strata provide long time series of hierarchical rhythmic variations tied directly to biostratigraphy and to magnetic reversals. The latter provide historical control and links to astronomically calculated curves that have been extended progressively into the past. These comparisons verify the orbital origins of the major sedimentary rhythms and are serving to reduce the age uncertainties of the significant time stratigraphic levels (biostratigraphic and magnetostratigraphic zones) from an order ofca500 kyr toward the precessional (20 kyr) level. This refinement has essentially been reached for the last 14 Myr of Earth history in the Mediterranean, and beyond in the Pacific Ocean. The cyclic structure of shallow‐water platform carbonates is also hierarchical but here the identification with specific orbital cycles has been equivocal and complicated by conflicts with radiometric data. In the gap‐riddled shallow‐water successions showing hierarchical ‘sequences’, the identification of some third‐order, fourth‐order and fifth‐order ‘sequences’ or ‘parasequences’ with orbital forcing is being explored but remains inferential. Beyond chronology, the orbital variations constitute an endless series of experiments: similar variations in insolation, which resulted in sedimentary patterns formed by a chain of responses extending through atmospheric and hydrospheric dynamics to geological processes and the dynamics of the biotic systems. The emerging patterns offer glimpses into the past, to reveal previously unexpected phenomena such as systematic oscillations in deep‐water aeration and unexpected oscillations in composition of upper‐water plankton: patterns that pose new challenges to the understanding of Earth history.
Mud volcanoes, olistostromes and Argille scagliose in the Mediterranean region
Authors: CAMERLENGHI ANGELO , PINI GIAN ANDREA
Published: December 2008

Tectonic and sedimentary mélanges, rocks with block‐in‐matrix fabric often referred to as ‘chaotic’, are widespread in the circum‐Mediterranean collisional orogenic belts as well as in submerged Mediterranean Arcs. These rock types have been defined originally as ‘Argille scagliose’ (Bianconi, 1840) and ‘olistostromes’ (Flores, 1955, 1959) in the outcrops of the Apennine chain (Italy). Both terminology and concepts have undergone a rather complex evolution through time owing to the gradual recognition of similar chaotic bodies in all the circum‐Mediterranean orogenic belts. Submarine mud volcanoes of the Mediterranean region, also composed by block‐in‐matrix, more commonly referred to as mud breccias, have a much younger history. These mud breccias were discovered in 1981 and, since then, a growing number of sea‐going geophysical and geological expeditions have allowed the recognition of a major mud volcano belt in the Eastern Mediterranean and of a number of mud diapirs and mud volcano fields from the Black Sea to the Gulf of Cadiz. Structural, textural and genetic similarities between the mud breccias of the Mediterranean mud volcanoes and the olistostromes and Argille scagliose of the Apennines were noted from the very beginning, but the matter has not been the focus of any detailed study. In this paper, the use of the terms in the geological literature is analysed, the distribution of these rock units in the Mediterranean region explored and the assumed genetic processes are identified in order to formulate a common genetic model that can be applied to the evolution of the circum‐Mediterranean sedimentary basins.
Carbonate platforms in the Dolomites area of the Southern Alps – historic perspectives on progress in sedimentology
Authors: SCHLAGER WOLFGANG , KEIM LORENZ
Published: December 2008

The area of the Dolomites in the Southern Alps exhibits some of the best outcrops of carbonate platforms and platform‐to‐basin transitions in the world. The region has attracted geologists since the early 19th Century and has been a centre of stratigraphic and sedimentological research ever since. The interpretation of the platforms in the Dolomites as coral reefs dates back to the 1850s and was inspired by the work on modern reefs in the Pacific and Indian Oceans at that time. Very soon, however, studies in the Dolomites triggered developments of their own. Fieldwork on these Triassic atolls led to a first understanding of the dramatic facies changes at the periphery of reefs and atolls, including the recognition of slope facies and basinward transport of platform material by gravity. In addition, the platforms were used to prove long‐term syndepositional subsidence on the scale of kilometres as early as 1860. After World War II, the study of modern reefs and platforms led to process‐based facies models and this, in turn, guided the sedimentological analysis of the Alpine–Mediterranean belt. Repeatedly, however, the roles became reversed and the Alpine–Mediterranean platforms contributed to the fundamental underpinnings of sedimentology. In the 1980s, mountain‐size outcrops in the Alps and the Apennines were recognized as models for the interpretation of shoal‐water carbonates in seismic data. Seismic models of outcrops in the Dolomites, for instance, gave rise to the concept of pseudo‐unconformities, i.e. rapid lateral facies changes that appear as unconformities in seismic images. In the 1990s, the Alpine–Mediterranean Mesozoic along with the North American and European Palaeozoic revealed the significance of microbially induced carbonate precipitation in constructing large limestone bodies. Studies of ancient rocks led this development because this particular carbonate factory is far less prominent now than it was at certain times in the past.