bluuebunny/crossref_metadata_2025 huggingface dataset:
The alcohol industry and trade agreements: a preliminary assessment
Authors: Zeigler Donald W.
Published: December 2008

Aims To review trade agreements, their relation to alcohol control policy and examine the role of the alcohol industry in supporting and attempting to influence trade policy.

Methods Review of peer review, public health advocacy literature (both pro and con on free trade), business, press and government documents on trade agreements, assess current and potential challenges by trade agreements to alcohol control policy and investigate the means and extent of industry influence in trade agreements.

Findings ‘Free’ trade agreements reduce trade barriers, increase competition, lower prices and promote alcohol consumption. However, international treaties, negotiated by free trade experts in close consultation with corporate lobbyists and without significant, if any, public health input, governments and corporations contain significant provisions that will result in increased alcohol consumption and may challenge public health measures of other nations as constraints on trade. Conversely, alcohol control measures seek to reduce access and consumption, raise prices and restrict advertising and product promotion. The prospect is for increased alcohol consumption and concomitant problems throughout the world.

Conclusions Trade agreements challenge effective alcohol control policies. The alcohol industry seeks to influence agreements and can be expected to work through trade agreements to reduce tariffs, increase market access and seek to restrict effective domestic regulations. Further research is needed on the impact of trade agreements and the ongoing role of the industry. Advocates must recognize the inherent conflicts between unbridled free trade and public health, work to exclude alcohol from trade agreements, counter industry influence and protect alcohol control policies.
Litigation and alcohol policy: lessons from the US Tobacco Wars
Authors: Mosher James F.
Published: December 2008

Aims  This paper explores the role of litigation in preventing alcohol‐related harms, identifying lessons from the use of litigation in tobacco control policy in the United States. It analyzes the key components of litigation in an international context, provides a case study of its potential use in addressing the marketing of alcopops to youth and offers recommendations for pursuing litigation strategies in future alcohol policy efforts.

Methods  The paper's analyses are based on both original and secondary legal research. State and federal case law and secondary sources are reviewed in assessing lessons learned from tobacco litigation in the United States and the potential role of litigation in alcohol policy, both in the United States and internationally. Assessment of alcohol litigation cases and state and federal laws and regulations provides the foundation for the alcopops case study.

Findings  The tobacco litigation experience demonstrates that litigation is a powerful tool in addressing aggressive marketing by purveyors of addictive products such as alcohol.

Conclusions  To be effective at both national and international levels, litigation should encompass a broad array of legal tactics designed to identify and restrict unfair, deceptive and misleading alcohol marketing tactics and should be utilized in conjunction with complementary prevention strategies. Research conducted on the impact of alcohol marketing on youth alcohol consumption and problems is needed to support potential litigation claims. Developing litigation expertise within the alcohol policy field and building collaboration with litigation specialists in tobacco control should also be considered a high priority.
Interleukin‐6 (IL‐6) –572C→G promoter polymorphism is associated with type 2 diabetes risk in Koreans
Authors: Koh Soo Jeong , Jang Yangsoo , Hyun Yae Jung , Park Ju Yeon , Song Young Duk , Shin Kyung‐Kyun , Chae Jey Sook , Kim Byung‐Keuk , Ordovas Jose M. , Lee Jong Ho
Published: December 2008

Objective  Increased levels of inflammatory markers, such as interleukin‐6 (IL‐6), are associated with type 2 diabetes (T2DM). We investigated the association of IL‐6 gene polymorphisms with T2DM and circulating levels of IL‐6 in Koreans.

Subjects  A total of 1477 subjects with normal glucose tolerance and 476 T2DM patients were included.

Measurements  We examined IL‐6 –174G→C, –572C→G, –597G→A and –1363G→T promoter region polymorphisms. The main outcome measures were the odds ratio (OR) on T2DM risk and serum concentrations of IL‐6 and high‐sensitivity C‐reactive protein (hs‐CRP).

Results  Homozygosity for the rare G allele IL‐6 –572C→G was associated with a higher risk of T2DM [OR 1·69 (95%CI 1·11–2·58), P = 0·015]. Serum IL‐6 concentrations were associated with the IL‐6 –572C→G genotype in control subjects (G/G: 2·33 ± 0·41: C/G: 1·53 ± 0·09: C/C: 1·72 ± 0·08 ng/l, P = 0·023). Also in the control group, subjects homozygous for the rare G allele showed significantly higher concentrations of hs‐CRP than C/C and C/G carriers (G/G: 13·6 ± 2·9: C/G: 9·2 ± 0·6: C/C: 7·8 ± 0·4 mg/l, P = 0·003). The C‐allele at the IL‐6 –174 SNP was very rare (< 0·01) and –597G→A and –1363G→T were monomorphic in this population.

Conclusions  Our data demonstrate that the IL‐6 –572G/G genotype is associated with higher serum IL‐6 and hs‐CRP concentrations and with increased risk for T2DM.
Vitamin D, PTH and calcium levels in pregnant women and their neonates
Authors: Bowyer Lucy , Catling‐Paull Christine , Diamond Terrence , Homer Caroline , Davis Gregory , Craig Maria E.
Published: December 2008

Objectives  To determine the prevalence of vitamin D deficiency in pregnant women and their neonates and to examine factors associated with vitamin D deficiency.

Design and patients  Population‐based study of pregnant women and their neonates from South‐eastern Sydney, Australia.

Measurements  Serum 25 hydroxy‐vitamin D (25‐OHD), PTH, calcium, albumin, phosphate and alkaline phosphatase were measured in women at 23–32 weeks gestation and on cord blood at delivery. Maternal skin phototype was recorded using the Fitzpatrick scale.

Results  Vitamin D deficiency (defined as 25‐OHD ≤ 25 nmol/l) was found in 144 of 971 (15%) women and 98 of 901 (11%) neonates. Median 25‐OHD was 52 nmol/l (range 17–174) in mothers and 60 nmol/l (17–245) in neonates. Maternal 25‐OHD levels varied by season, with lowest levels in late winter/early spring (P < 0·001). Factors associated with maternal vitamin D deficiency in multiple logistic regression were (OR, 95% CI): maternal birthplace outside Australia: 2·2 (1·4–3·5, P = 0·001), dark skin phototype: 2·7 (1·6–4·5, P < 0·001), wearing a veil: 21·7 (11·7–40·3, P < 0·001) and younger maternal age: 0·93 (0·89–0·97, P = 0·001). Maternal vitamin D deficiency increased the risk of neonatal vitamin D deficiency (OR 17·2, 95% CI 8·8–34·3) and birth weight was lower among infants of deficient vs. sufficient mothers: mean (SD) 3245 g (545) vs. 3453 g (555), P < 0·001.

Conclusions  Vitamin D deficiency is common among pregnant women; immigrant, veiled and dark skinned women are at greatest risk. Maternal vitamin D deficiency increases the risk of neonatal vitamin D deficiency and lower birth weight.
Interleukin‐4 suppresses the cytotoxic potential of in vitro generated, adaptive regulatory CD4+ T cells by down‐regulation of granzyme B
Authors: Bratke Kai , Goettsching Hilke , Kuepper Michael , Geyer Simone , Luttmann Werner , Virchow J. Christian
Published: December 2008

Regulatory CD4+ T cells (Tregs) control immune responses using secretion of anti‐inflammatory cytokines and/or cytotoxic mechanisms and play a central role in the outcomes of several immune pathologies. Previous studies suggest an impaired function of Tregs in allergy, especially during allergen seasons, but the underlying mechanism is not known. Therefore, we analysed the impact of the T helper type 2 cytokine interleukin (IL)‐4 on in vitro generated adaptive Tregs (aTregs), which have been reported to use the granzyme B (GrB)/perforin pathway to kill autologous immune cells. aTregs were generated by co‐ligation of CD3 and CD46 on CD4+ T lymphocytes and granzyme expression was analysed using flow cytometry. To quantify GrB and perforin expression as well as IL‐10 secretion in response to IL‐4, specific enzyme‐linked immunosorbent assays were performed in cell lysates and/or culture supernatants. Using a flow cytometry‐based cytotoxicity assay the impact of IL‐4 on the cytotoxic potential of aTregs was investigated. While IL‐4 did not affect IL‐10 secretion and perforin expression in aTregs, a significant suppression of GrB synthesis was detected in the presence of IL‐4. In addition, IL‐4‐mediated suppression of GrB led to impaired cytotoxicity of aTregs against K562 target cells. In conclusion, our data suggest that IL‐4 might play a role in impaired aTreg function in allergy.
Evolution of the opossum major histocompatibility complex: evidence for diverse alternative splice patterns and low polymorphism among class I genes
Authors: Baker Michelle L. , Melman Sandra D. , Huntley James , Miller Robert D.
Published: December 2008

The opossum major histocompatibility complex (MHC) shares a similar organization with that of non‐mammals while containing a diverse set of class I genes more like that of eutherian (placental) mammals. There are 11 class I loci in the opossum MHC region, seven of which are known to be transcribed. The previously described Monodelphis domestica (Modo)‐UA1 and Modo‐UG display characteristics consistent with their being classical and non‐classical class I genes, respectively. Here we describe the characteristics of the remaining five transcribed class I loci (Modo‐UE, ‐UK, ‐UI, ‐UJ and ‐UM). All five genes have peptide‐binding grooves with low or no polymorphism, contain unpaired cysteines with the potential to produce homodimer formation and display genomic organizational features that would be unusual for classical class I loci. In addition, Modo‐UJ and ‐UM were expressed in alternatively spliced mRNA forms, including a potentially soluble isoform of Modo‐UJ. Thus, the MHC region of the opossum contains a single class I gene that is clearly classical and six other class I genes each with its own unique characteristics that probably perform roles other than or in addition to antigen presentation.
Effect of bone morphogenetic protein‐6 on macrophages
Authors: Hong Jun Hyuk , Lee Geun Taek , Lee Jae Ho , Kwon Seok Joo , Park Seok Hee , Kim Seong Jin , Kim Isaac Yi
Published: December 2008

Bone morphogenetic proteins (BMPs) are members of the transforming growth factor (TGF)‐β superfamily which regulates bone formation, haematopoiesis and development. While TGF‐β is known to be a negative regulator of the immune system, the effect of BMPs on the immune system is largely unknown. Herein, the effect of BMP‐6 on the innate immune system was investigated using the murine macrophage cell line RAW 264·7. BMP‐6 altered cellular morphology, inhibited cellular proliferation, increased the fraction of subG1 phase cells, and decreased the fraction of cells in the S and G2M phases, without changing the percentage of apoptotic cells. In addition, BMP‐6 induced expression of pro‐inflammatory inducible nitric oxide synthase (iNOS) and the cytokine tumour necrosis factor (TNF)‐α. Reverse transcription–polymerase chain reaction (RT‐PCR) analysis demonstrated the expression of all three known type II BMP receptors [BMP‐RII, activin (Act)‐RIIA and Act‐RIIB] and two of the three known type I receptors [activin receptor‐like kinase 2 (ALK2) and ALK3]. Over‐expression as well as knock‐down studies using short hairpin RNA (shRNA) demonstrated that BMP‐RII, ALK2 and ALK3 are the functional BMP‐6 receptors in macrophages. Finally, the effect of BMP‐6 was confirmed in murine peritoneal macrophages and the THP‐1 human monocyte cell line. Taken together, these results demonstrate that BMP‐6 regulates the proliferation and gene expression profile of macrophages.
Role of high‐affinity HLA‐DP specific CLIP‐derived peptides in beryllium binding to the HLA‐DPGlu69 berylliosis‐associated molecules and presentation to beryllium‐sensitized T cells
Authors: Amicosante Massimo , Berretta Floriana , Dweik Raed , Saltini Cesare
Published: December 2008

Berylliosis is driven by the accumulation in the lung of beryllium‐specific T helper type 1 (Th1) cells recognizing beryllium as antigen when presented principally by human leucocyte antigen DP molecules carrying a glutamate at position β69 (HLA‐DPGlu69). This study was designed to clarify the precise role of peptides in beryllium binding to the HLA‐DP groove’s pocket 4 and to identify peptides with higher affinity for pocket 4 that might prevent beryllium presentation and T‐cell stimulation. Beryllium/HLA‐DP interactions were analysed by the ability of beryllium to compete with CLIP and CLIP‐derived peptides to HLA‐DPGlu69 soluble molecule. The CLIP‐derived low‐affinity peptide CLIP‐AA, could not outcompete beryllium; while the CLIP‐derived high‐affinity peptides CLIP‐YY, CLIP‐QY and CLIP‐RF were only marginally influenced by the presence of beryllium in the competition assay. The effect of these CLIP‐derived high‐affinity peptides on beryllium presentation was determined by measuring interferon‐γ (IFN‐γ) release upon beryllium stimulation of peripheral blood mononuclear cells obtained from beryllium‐hypersensitive subjects. CLIP‐YY did inhibit beryllium presentation and T‐cell activation, while CLIP‐QY and CLIP‐RF markedly enhanced the IFN‐γ response to beryllium. Anti‐HLA‐DP monoclonal antibody blocked the beryllium‐induced IFN‐γ release in the presence of CLIP‐QY (88%) and CLIP‐RF (76%). A similar effect was observed for CLIP‐YY capability to block IFN‐γ release by beryllium stimulation in the presence of CLIP‐QY (79%) and CLIP‐RF (76%). Overall, these data support the proposal that HLA‐DP high‐affinity peptides might be used as a model for specific berylliosis therapy.
Calpain inhibition induces activation of the distinct signalling pathways and cell migration in human monocytes
Authors: Noma Haruyoshi , Kato Takayuki , Fujita Hisakazu , Kitagawa Maki , Yamano Tsunekazu , Kitagawa Seiichi
Published: December 2008

We have recently reported that constitutively active calpain negatively regulates activation of the distinct signalling pathways and cell migration in human neutrophils. Here, we report that a similar regulatory system is also functioning in human monocytes, but not lymphocytes. Calpain was constitutively active in resting human monocytes, but not lymphocytes. Mitogen‐activated protein kinases, including extracellular signal‐regulated kinase (ERK), p38 and c‐Jun N‐terminal kinase (JNK), phosphatidylinositol 3‐kinase (PI3K)/Akt and p21‐activated kinase (PAK, an effector molecule of Rac) were rapidly (within 1 min) activated in monocytes, but not lymphocytes, upon exposure to calpain inhibitors (PD150606 and N‐acetyl‐Leu‐Leu‐Nle‐CHO), but not PD145305 (the inactive analogue of PD150606). Following activation of these signalling pathways, monocytes displayed active migration within 5 min after exposure to calpain inhibitors, and active migration was sustained for more than 45 min. The micropipette method revealed that calpain inhibition‐mediated monocyte migration was chemotaxis, not random migration. The studies with pharmacological inhibitors suggest that calpain inhibition‐mediated monocyte migration is mediated by activation of ERK, p38, JNK, PI3K/Akt and Rac. NSC23766 (Rac inhibitor) and pertussis toxin (PTX) suppressed calpain inhibitor‐induced phosphorylation of distinct signalling molecules (PAK, ERK, p38, JNK and Akt) as well as cell migration, suggesting that the PTX‐sensitive G protein and Rac axis may be a possible key target of calpain inhibitors. These findings suggest that constitutively active calpain negatively regulates activation of the distinct signalling pathways and cell migration in resting monocytes, but not lymphocytes.
Accurate delineation of biogeographical regions depends on the use of an appropriate distance measure
Authors: Gagné Sara A. , Proulx Raphaël
Published: December 2008

The use of analytical techniques to delineate biogeographical regions is becoming increasingly popular. One recent example, Heikinheimo et al. (Journal of Biogeography, 2007, 34, 1053–1064), applied the k‐means clustering algorithm to define the biogeography of the European land mammal fauna. However, they used the Euclidean distance measure to cluster grid cells described by species‐occurrence data, which is inappropriate. The Euclidian distance yields misleading results when applied to species‐occurrence data because of the double‐zero problem and the species‐abundance paradox. We repeat their analysis using the Hellinger distance, a measure appropriate for species‐occurrence data and which has been shown to outperform other such measures. Our results differ substantially from those presented by Heikinheimo et al. We argue that the rigorous application of appropriate statistical techniques is of crucial concern within conservation biogeography.
Improved outcome in Wegener’s granulomatosis and microscopic polyangiitis? A retrospective analysis of 95 cases in two cohorts
Authors: Eriksson P. , Jacobsson L. , Lindell Å. , Nilsson J.‐Å. , Skogh T.
Published: December 2008

Objectives.  Mortality rates for Wegener’s granulomatosis (WG) and microscopic polyangiitis (MPA) have decreased after the introduction of cyclophosphamide. Standardized mortality ratio (SMR) expresses the overall mortality of patients compared with the general population. The aims of this study were to compare survival in an old and a recent cohort of patients with WG and MPA using SMR and to determine predictors for death in both groups combined.

Design.  Survival analyses were performed by Kaplan–Meier survival curves, SMR and proportional hazards regression models.

Setting.  The nephrology and rheumatology clinics at Linköping University Hospital, Sweden.

Subjects.  All patients diagnosed with WG or MPA in the catchment area during 1978–2005 were divided into two cohorts; patients diagnosed before (n = 32, old cohort) and after (n = 63, recent cohort) December 31, 1996.

Results.  The two cohorts differed regarding the proportion of WG (75% vs. 56%, P = 0.03) and a tendency for more pronounced kidney involvement in the old cohort: 266 μmol L−1 (16% dialysis‐dependent) vs. 192 μmol L−1 (5% dialysis‐dependent), but were comparable regarding disease severity. SMR at 1 and 5 years were 2.1 (95% CI: 0.43–6.09) and 1.6 (95% CI: 0.6–3.2) in the recent cohort and 5.2 (95% CI: 1.07–15.14) and 2.5 (95% CI: 0.93–5.52) in the old cohort. Five‐year survival was 87% and 81%. Serum creatinine, age, end‐stage renal disease, diagnosis before 1997 and first relapse were independent predictors for death.

Conclusion.  Patient survival in WG and MPA analysed with SMR may be better than previously believed. Severe renal disease and disease relapse were the major predictors of reduced survival.
Genetics, behaviour and chemical recognition of the invading ant Pheidole megacephala
Authors: FOURNIER DENIS , DE BISEAU JEAN‐CHRISTOPHE , ARON SERGE
Published: December 2008

Introduced species often become ecologically dominant, displacing native species and posing a serious threat to ecosystem function and global biodiversity. Ants are among the most widespread and damaging alien species; introductions are often accompanied by population‐level behavioural and genetic changes contributing to their success. We investigated the genetic structure, chemical profile and nestmate recognition in introduced populations of the invasive big‐headed ant, Pheidole megacephala, in Australia. Behavioural analyses show that workers are not aggressive towards conspecifics from different nests, even at large geographical scales (up to 3000 km) and between populations encompassing a wide range of environmental conditions. By contrast, interactions with workers of other species invariably result in agonistic behaviours. Genetic analyses reveal that populations have low genetic diversity. No genetic differentiation occurs among nests of the same population; differentiation between populations, though significant, remains weak. Chemical analyses indicate that cuticular lipids are similar between colonies of a population, and that differentiation between populations is low. Altogether, these results indicate that the big‐headed ant P. megacephala forms a large unicolonial population across northern/eastern Australia.
High genetic diversity and connectivity in the polyploid invasive seaweedAsparagopsis taxiformis(Bonnemaisoniales) in the Mediterranean, explored with microsatellite alleles and multilocus genotypes
Authors: ANDREAKIS NIKOS , KOOISTRA WIEBE H. C. F. , PROCACCINI GABRIELE
Published: December 2008

The red alga,Asparagopsis taxiformis, has recently expanded its distribution range into the Western Mediterranean Sea, and populations have now even been found on the Portuguese South coast. All Western Mediterranean populations belong to a single mitochondrial cryptic lineage (referred to as lineage 2 in earlier studies) and probably result from a recent invasion of Indo‐Pacific origin. Here we investigate fine‐scale population genetic diversity and structure within and among Mediterranean populations of lineage 2 using eight microsatellite loci and compare the obtained patterns with those observed in a Californian population of the same lineage. To generate an appropriate analytical method suitable to the polyploid status of this species, we score microsatellite loci as in a dominant marker system. Thereafter, we produce robust descriptors inferred from frequencies of both microsatellite alleles and multilocus genotypes. Populations from California and the Mediterranean Sea differ considerably in their levels of genetic diversity. In the Mediterranean, populations reproduce predominantly sexually and exhibit high levels of genotypic variation, suggestive either of multiple introductions or of a single introduction by a genetically diverse and large group of individuals. Bayesian clustering revealed one or possibly two weakly supported panmictic subpopulations, indicative of extensive admixture. The expansion of this lineage is rapid, possibly due to the absence of eco–physiological barriers to gene flow throughout its invasive trajectory.
Molecular genetic data provide support for a model of transmission dynamics in an Australian reptile tick, Bothriocroton hydrosauri
Authors: GUZINSKI JARO , BULL C. MICHAEL , DONNELLAN STEPHEN C. , GARDNER MICHAEL G.
Published: December 2008

Bothriocroton hydrosauri is a three‐host ixodid tick that infests large reptiles in southeastern Australia, where its most common host is a large scincid lizard Tiliqua rugosa. Based on previous ecological and behavioural studies of this system, we propose a ‘ripple’ model of tick population dynamics, where only a few female ticks succeed in producing surviving offspring. These females then are the centres of ripples of their progeny spreading into the broader landscape. The model predicts higher relatedness among larvae than among nymphs or adults on a host, and significant spatial autocorrelation in larvae extending further than for the later life stages. The model also predicts that adult ticks are likely to encounter related partners and that this will generate inbreeding within the population. We tested those predictions using nine polymorphic microsatellite loci on a sample of 848 ticks (464 larvae, 140 nymphs and 244 adults) collected from 98 lizard hosts from near Bundey Bore Station in South Australia. Our data support the predictions and indicate that the dynamics of transmission among hosts play an important role in parasite population structure.
Statistical hypothesis testing in intraspecific phylogeography: nested clade phylogeographical analysis vs. approximate Bayesian computation
Authors: TEMPLETON ALAN R.
Published: December 2008

Nested clade phylogeographical analysis (NCPA) and approximate Bayesian computation (ABC) have been used to test phylogeographical hypotheses. Multilocus NCPA tests null hypotheses, whereas ABC discriminates among a finite set of alternatives. The interpretive criteria of NCPA are explicit and allow complex models to be built from simple components. The interpretive criteria of ABC are ad hoc and require the specification of a complete phylogeographical model. The conclusions from ABC are often influenced by implicit assumptions arising from the many parameters needed to specify a complex model. These complex models confound many assumptions so that biological interpretations are difficult. Sampling error is accounted for in NCPA, but ABC ignores important sources of sampling error that creates pseudo‐statistical power. NCPA generates the full sampling distribution of its statistics, but ABC only yields local probabilities, which in turn make it impossible to distinguish between a good fitting model, a non‐informative model, and an over‐determined model. Both NCPA and ABC use approximations, but convergences of the approximations used in NCPA are well defined whereas those in ABC are not. NCPA can analyse a large number of locations, but ABC cannot. Finally, the dimensionality of tested hypothesis is known in NCPA, but not for ABC. As a consequence, the ‘probabilities’ generated by ABC are not true probabilities and are statistically non‐interpretable. Accordingly, ABC should not be used for hypothesis testing, but simulation approaches are valuable when used in conjunction with NCPA or other methods that do not rely on highly parameterized models.
Amino acid 310 determines the donor substrate specificity of serogroup W‐135 and Y capsule polymerases of Neisseria meningitidis
Authors: Claus Heike , Stummeyer Katharina , Batzilla Julia , Mühlenhoff Martina , Vogel Ulrich
Published: December 2008

The capsular polysaccharides of serogroup W‐135 and Y meningococci are sialic acid‐containing heteropolymers, with either galactose or glucose as the second sugar residue. As shown previously, sequences of the predicted enzymes that catalyse capsule polymerization, i.e. SiaDW‐135 and SiaDY, differ in only a few amino acids. By in vitro assays with purified recombinant proteins, SiaDW‐135 and SiaDY were now confirmed to be the capsule polymerases harbouring both hexosyltransferase and sialyltransferase activity. In order to identify amino acids crucial for substrate specificity of the capsule polymerases, polymorphic sites were narrowed down by DNA sequence comparisons and subsequent site‐directed mutagenesis. Serogroup‐specific amino acids were restricted to the N‐terminal part of the proteins. Exclusively amino acid 310, located within the nucleotide recognition domain of the enzymes' predicted hexosyltransferase moiety, accounted for substrate specificity as shown by immunochemistry and in vitro activity assay. Pro‐310 determined galactosyltransferase activity that resulted in a serogroup W‐135 capsule and Gly‐310 determined glucosyltransferase activity that resulted in a serogroup Y capsule. In silico analysis revealed a similar amino acid‐based association in other members of the same glycosyltransferase family irrespective of the bacterial species.
Genome‐wide regulon and crystal structure of BlaI (Rv1846c) from Mycobacterium tuberculosis
Authors: Sala Claudia , Haouz Ahmed , Saul Frederick A. , Miras Isabelle , Rosenkrands Ida , Alzari Pedro M. , Cole Stewart T.
Published: December 2008

Comparative genomics with Staphylococcus aureus suggested the existence of a regulatory system governing beta‐lactamase (BlaC) production in Mycobacterium tuberculosis. The crystal structure of Rv1846c, a winged helix regulator of previously unknown function, was solved thus revealing strong similarity to the BlaI and MecI repressors of S. aureus, which both respond to beta‐lactam treatment. Using chromatin immunoprecipitation and hybridization to microarrays (ChIP‐on‐chip), the Rv1846c regulon was shown to comprise five separate genomic loci. Two of these mediate responses and resistance to beta‐lactam antibiotics (rv1845c, rv1846c–rv1847; blaC–sigC); two encode membrane proteins of unknown function (rv1456c, rv3921c) while the last codes for ATP synthase (rv1303–atpBEFHAGDC–rv1312). The ChIP‐on‐chip findings were confirmed independently using electrophoretic mobility shift assays, DNAse footprinting and transcript analysis leading to Rv1846c being renamed BlaI. When cells were treated with beta‐lactams, BlaI was released from its operator sites causing derepression of the regulon and upregulation of ATP synthase transcription. The existence of a potential regulatory loop between cell wall integrity and ATP production was previously unknown.
DnaA protein interacts with RNA polymerase and partially protects it from the effect of rifampicin
Authors: Flåtten Ingvild , Morigen  , Skarstad Kirsten
Published: December 2008

The Escherichia coli DnaA protein forms an oligomer at the origin and initiates chromosome replication with the aid of architectural elements and transcription by RNA polymerase. Rifampicin inhibits initiation of transcription by RNA polymerase and thus also initiation of replication. Here, we report that wild‐type cells undergo rifampicin‐resistant initiation of replication during slow growth in acetate medium. The rifampicin‐resistant initiation was prevented by reducing the availability of DnaA. In vitro experiments showed that the DnaA protein interacted with RNA polymerase and that it afforded a partial protection from the negative effect of rifampicin. It is possible that rifampicin‐resistant rounds of replication occur when a surplus of DnaA is available at the origin. In rich medium wild‐type cells do not exhibit rifampicin‐resistant rounds of replication, possibly indicating that there is no surplus DnaA, and that DnaA activity is the factor limiting the process of initiation. During growth in acetate medium, on the contrary, DnaA activity is not limiting in the same way because an initiation potential is present and can be turned into extra rounds of replication when rifampicin is added. The result suggests that regulation of replication initiation may differ at different growth rates.
The role of the Mediterranean region in the development of sedimentary geology: a historical overview
Authors: FISCHER ALFRED G. , GARRISON ROBERT E.
Published: December 2008

The Mediterranean region, source of so much knowledge in the world, is the site of major advances in sedimentary geology. In addition to its economic and cultural richness, the geological and geographic diversity of the region, plus its active geological processes, have long stimulated indigenous scholars, along with attracting talented outsiders such as Steno, Lyell, Walther, Kuenen and Bagnold. Since classical Hellenic times, debates about the origin of fossils and the changing positions of sea‐level served as catalysts for studies of sediments, sedimentary rocks and ancient life. The presence of geologically young and easily interpreted marine shell beds in many Mediterranean coastal areas adjacent to their modern analogues was a particular stimulus for progress in sedimentary geology, for example, the very advanced stratigraphic ideas of Leonardo da Vinci, expressed solely in his unpublished notebooks. Impeding progress was the geological complexity of facies, faunas and structure in the circum‐Mediterranean Alpine belts. Once the secrets of these were unlocked, however, the Mediterranean region became the source of major discoveries about syn‐sedimentary tectonics, carbonate platforms, pelagic and anoxic sediments, turbidites, evaporites, aeolian processes, cyclostratigraphy, magnetic stratigraphy and impact events. In many of these Mediterranean discoveries, the critical element is the occurrence of extensive Mesozoic‐Cenozoic pelagic successions whose precise age dating was made possible by pioneering biostratgraphic studies using microfossils.
Controls on clastic sequence geometries in a shallow‐marine, transtensional basin: the Bohemian Cretaceous Basin, Czech Republic
Authors: ULIČNÝ DAVID , LAURIN JIŘÍ , ČECH STANISLAV
Published: December 2008

The Bohemian Cretaceous Basin combines features of a shallow‐water (mostly < 100 m) epicontinental seaway formed during a global transgression with those of a tectonically active, transtensional setting. The basin formed under a greenhouse climate and was affected by strong axial currents. Dense well‐log coverage, combined with locally high‐quality exposures and biostratigraphic control, make it possible to examine in three dimensions the geometries of genetic sequences and interpret their controlling variables. Sand‐dominated deltas formed sequences at several spatial scales that reflect nested transgressive–regressive cycles with durations ranging from tens of thousands of years to millions of years. Progradation directions and distances, thicknesses and internal geometry of the individual sequences were controlled primarily by intrabasinal faulting, basin‐scale changes in subsidence rate, eustatic fluctuations and localized bathymetric changes due to successive filling of the basin. Along‐strike change in sediment input from different parts of the source area and a short‐lived uplift of a secondary clastic source provided additional controls on the sequence geometry. Efficient hypopycnal transport combined with redeposition of fine clastics in shallow water promoted development of steep slopes of sand‐dominated deltas while preventing downlap of muddy clinoforms; most of the suspended load became deposited downcurrent in subhorizontal or gently dipping bottomsets. Long‐term accommodation rates were low during the Early to Middle Turonian, with minor intrabasinal faulting, but became accelerated in the Late Turonian and Early Coniacian. This acceleration was caused at least partly by increased subsidence rate accompanied by structural partitioning of the depocentre and partly compensated by increased sediment input indicating increased uplift rates in the Western Sudetic Island source area. This event probably reflected an increase in the regional strain rate in Central Europe. The succession of two major flooding events in the Early Turonian and late Early Coniacian, separated by a low‐accommodation interval in the Middle Turonian, shows a close similarity to published estimates of long‐term eustatic curves. However, the eustatic component of accommodation rate in the Bohemian Late Turonian and Coniacian is difficult to separate from accelerated subsidence. In several cases, evidence for short‐term (100 kyr scale) forced regressions, independent of basinal structural activity, suggests small‐scale eustatic falls at rates which, as presently understood, cannot be explained other than by a glacio‐eustatic mechanism.
Mediterranean Neogene stratigraphy: development and evolution through the centuries
Authors: CITA MARIA BIANCA
Published: December 2008

The Mediterranean area, in general, and Italy, in particular, played an important role in developing the principles of stratigraphy since the early days of geological thinking. In the middle of the 19th Century there was a rush to name all the intervals of the stratigraphic column. At that time, when invertebrate palaeontology was the principal source of information on the relative age of the rock units, dozens of stage names were created for the Neogene. Only a few of these stage names survive and are accepted worldwide as Langhian, Serravallian, Tortonian, Messinian, Zanclean and Piacenzian. In the later part of the 19th Century and in the first decades of the 20th Century, a wealth of new data was made available by extensive palaeontological studies but the correlation potential of the fossil faunas was constrained poorly, and understood less, leading to the development of a ‘floating’ stratigraphy. The situation improved after World War II, when micropalaeontology underwent a fast development. The creation of common stratigraphic guidelines, the introduction of the ‘stratotype’ concept followed by the ‘Golden Spike’ concept (global stratotype section and point), combined with the application of multiple stratigraphic methodologies (especially palaeomagnetic stratigraphy or magnetic polarity time scale, astrocyclostratigraphy or astronomical time scale) resulted in new scenarios. A turning point may be located around 1970, soon after the beginning of the Deep Sea Drilling Project, which greatly contributed to the development of a new approach to Neogene Stratigraphy. Now all the global stratotype sections and points for the Neogene stages are being defined by multiple criteria, with precise definitions in terms of magnetic polarity time scale and astronomical time scale. The Rossello composite section in Southern Sicily is the template for the Late Neogene stratigraphy, with the best time resolution provided by astronomical forcing. To complete the planned study, the same criteria have to be applied downwards and upwards.
Tethyan–Mediterranean organic carbon‐rich sediments from Mesozoic black shales to sapropels
Authors: EMEIS KAY‐CHRISTIAN , WEISSERT HELMUT
Published: December 2008

The Jurassic to Holocene record of black shale deposition in the Tethys‐Mediterranean region is unrivalled by that of any other ocean basin, either in land sections or drill cores. The term ‘black shale’ is used here broadly for sediments with elevated organic carbon concentrations (> 1%), including the Pliocene to Recent sapropels. Most of the black shales are devoid of benthonic organisms, are laminated, and were deposited in distinct rhythms during periods when the deep waters of the ocean basins were anoxic or dysoxic. The Tethyan black shale records have become essential in studies of the transfer of organic carbon into the sediment record and for astronomical tuning and geological time scales. These records have been central in understanding climate control on ocean dynamics and biogeochemical cycles. The Mesozoic black shales were deposited within well‐defined time envelopes of around 0·5 to 1 Myr. These black shales, which were confined to certain chronostratigraphic intervals in the Jurassic and Cretaceous, were recognized as expressions of global Oceanic Anoxic Events in the mid‐1970s and subsequently named after prominent researchers (Bonarelli, Selli, Goguel). The black shale episodes were dated by biostratigraphic methods and by high‐resolution chemostratigraphy and cyclostratigraphy. Mesozoic black shales are now interpreted as the oceanographic expression of major perturbations of the global carbon cycle and climate. Research into younger (Pliocene to Pleistocene) sedimentary cycles (including black shales, termed sapropels) exposed in land sections, or found in pelagic and hemipelagic marine sediment cores of Late Quaternary age, started in the 1950s. Main threads pursued from this end of the record were the climatic control of oceanic processes that permitted the development of highly detailed and precise time scales tuned to the astronomical clock of insolation changes, palaeoclimate evolution of the circum‐Mediterranean area and biogeochemical dynamics in anoxic basins. After 50 years of intensive research, the Tethyan and Mediterranean black shales remain subjects of fascination in Earth Science. Tracing the origins and building upon recent progress, the current hypotheses on their formation are reviewed here. It is a panorama of complex interplays between global and regional tectonics, climate dynamics during both Ice House and Greenhouse states of global and regional climate, oceanographic responses to these climate changes, and biogeochemical adaptations that were all needed to shape an extraordinary archive of global change in the absence of human activity.
Dolomite Mountains and the origin of the dolomite rock of which they mainly consist: historical developments and new perspectives
Authors: MCKENZIE JUDITH A. , VASCONCELOS CRISOGONO
Published: December 2008

Beginning in the late 18th Century, the Dolomite Mountains in Northern Italy have been the location for major sedimentological developments, from the discovery of the mineral dolomite to the formulation of the coral‐reef hypothesis to explain the origin of the massive dolomite structures that define the splendid scenery of the region. Further, the Dolomite Mountains have inspired voluminous research into the origin of dolomite, questioning whether dolomite is a primary precipitate or a secondary replacement product. Recently, with the recognition that microbes can mediate dolomite precipitation, a new geomicrobiological approach, combining the study of modern natural environments with bacterial culture experiments, is now being used to calibrate or interpret microbial evidence derived from the dolomite rock record. This three‐pronged methodology applied to the study of dolomite formation holds great promise for future research into the ‘Dolomite Problem’ and provides a new impetus to revisit the Dolomite Mountains in the 21st Century.
Decoding the Mediterranean salinity crisis
Authors: RYAN WILLIAM B. F.
Published: December 2008

This historical narrative traces the steps to unravel, over a span of 40 years, an extraordinary event in which 5% of the dissolved salt of the oceans of the world was extracted in a fraction of a million years to form a deposit more than 1 million km3in volume. A buried abyssal salt layer was identified with reflection profiling and sampled during the Deep Sea Drilling Project, Leg 13. The dolomite, gypsum, anhydrite and halite in the drill cores paint a surprising picture of a Mediterranean desert lying more than 3 km below the Atlantic Ocean with brine pools that shrank and expanded by the evaporative power of the sun. The desert drowned suddenly when the Gibraltar barrier gave way. The explanation of ‘deep‐basin, shallow‐water’ desiccation and the notion of a catastrophic Zanclean flood had a mixed reception. However, the hypothesis became broadly accepted following subsequent drilling expeditions. Nevertheless, as experts examined the evaporate facies and sequences of equivalent age in the terrestrial outcrops, weaknesses appeared in the concept of repeated flooding and drying to account for the magnitude of the deposits. The ‘Rosetta Stone’, used to decipher conflicting interpretations, turns out not to be the deposits but the erosion surfaces that enclose them. These surfaces and their detritus – formed in response to the drop in base level during evaporative drawdown – extend to the basin floor. Evaporative drawdown began halfway through the salinity crisis when influx from the Atlantic no longer kept up with evaporation. Prior to that time, a million years passed as a sea of brine concentrated towards halite precipitation. During the later part of this interval, more than 14 cyclic beds of gypsum accumulated along shallow margins, modulated by orbital forcing. The thick salt on the deep seabed precipitated in just the next few cycles when drawdown commenced and the brine volume shrank. Upon closure of the Atlantic spillway, the remnants of the briny sea transformed into salt pans and endorheic lakes fed from watersheds of Eurasia and Africa. The revised model of evaporative concentration now has shallow‐margin, shallow‐water and deep‐basin, deep‐water precursors to desiccation.
Persistence of costly novel genes in the absence of positive selection
Authors: ESCOBAR‐PÁRAMO P. , FAIVRE N. , BUCKLING A. , GOUGAT‐BARBERA C. , HOCHBERG M. E.
Published: December 2008

Many genetic changes that ultimately lead to adaptive evolution come with a short‐term cost expressed in terms of reduced survival and reproduction. In the absence of genetic drift, it is unclear how such costly mutations may persist. Here we experimentally demonstrate that parasites can promote the persistence of costly genetic variants. We employed a genetically engineered strain (GMMO) of the bacterium Pseudomonas fluorescens as a model of the acquisition of a new gene either through a major mutation or through horizontal transfer, and examined its persistence in different evolving communities comprising an ancestral strain and a lytic bacteriophage. Whereas competition resulted in the elimination of the GMMO, inclusion of the phage promoted GMMO persistence. We provide evidence for why this effect is due to the differential susceptibility of GMMO and ancestral bacteria to phage.
Phosphite impact on the in vitro production and viability of selfed oospores by Phytophthora cinnamomi
Authors: McCarren K. L. , McComb J. A. , Shearer B. L. , Hardy G. E. St J.
Published: December 2008

Four isolates of Phytophthora cinnamomi were able to produce selfed oospores when cultured in vitro on modified Ribeiro’s minimal medium. Phosphite inhibited the production of selfed oospores at 100 μg phosphite/ml, lower concentrations had no effect. Selfed oospores were considered dormant as 16–47% of selfed oospores were found viable using viability staining techniques such as thiazolyl blue tetrazolium bromide and 4′,6‐diamidino‐2‐phenylindole·2HCl yet they did not germinate on a range of media. Phosphite up to 100 μg/ml did not change the proportion of viable selfed oospores. This study shows that phosphite does not affect the production of selfed oospores.
In vitro influence of phosphite on chlamydospore production and viability of Phytophthora cinnamomi
Authors: McCarren K. L. , McComb J. A. , Shearer B. L. , Hardy G. E. St J.
Published: December 2008

Chlamydospores of four isolates of Phytophthora cinnamomi were produced on mycelium grown on medium with or without 100 μg phosphite/ml, then tested for germination on medium containing no phosphite or 100 or 160 μg phosphite/ml. For each isolate when spores were produced on medium without phosphite, there was no effect of phosphite on germination. However, chlamydospores produced in the presence of 100 μg phosphite/ml showed significantly lower germination on media with no phosphite, 100 or 160 μg phosphite/ml than those produced in the absence of phosphite. For isolates known to be phosphite sensitive, the level of viable non‐germinated chlamydospores was higher amongst those produced on medium containing phosphite than amongst the controls, suggesting phosphite induces chlamydospore dormancy in some isolates of P. cinnamomi. Chlamydospores were produced uniformly across the radius of colonies on solid or liquid control media, but on media containing 100 μg phosphite/ml, chlamydospore production was lower in the centre of the colony and peaked at a point where mycelial morphology changed from tightly packed to sparse. This change in mycelial morphology and the peak in chlamydospore numbers did not occur when the pathogen was grown on liquid medium renewed every few days. In renewed medium, chlamydospores were evenly distributed across the radius of the colony.