Molecular and biochemical analysis of the {\it Drosophila\/} segmentation gene {\it runt\/}

Genetic evidence has indicated that the segmentation gene runt plays a key role in regulating gene expression of the pair-rule genes hairy, even-skipped, and fushi tarazu. In contrast to other pair-rule genes, sequence data of the runt open reading frame did not reveal homologies to DNA-binding motifs of known transcriptional regulatory proteins. This thesis project examined several properties of the runt gene based on the sequence of the transcription unit, including the subcellular localization of the protein in vivo, its ability to bind DNA, and the functionality of a putative nucleotide binding domain.^ A runt-specific antibody was generated and used to demonstrate that runt is localized in the nucleus. Since the precise overlap of the pair-rule stripes is thought to be critical for the determination of cellular identity along the anterior-posterior axis, phasing of early runt expression in the blastoderm was examined with regard to the segmentation genes hairy, even-skipped, and fushi tarazu. runt was also expressed at later stages of embryogenesis, including expression in neuroblasts, and ganglion mother cells of the developing nervous system. Expression at this stage was required for the subsequent formation of specific neurons and runt was extensively expressed in the central and peripheral nervous systems.^ Several experiments were done to address the biochemical function of the runt protein. A direct interaction of runt with DNA was first examined. Although bacterial expressed runt was found to bind dsDNA-cellulose, subsequent experiments failed to detect sequence-specific interactions with DNA. Inter-species conservation of the putative nucleotide binding domain suggested that this region was functionally important, and runt protein bound a labeled ATP analog with high affinity in vitro. Finally, the effect of substitution of a critical residue of the nucleotide binding domain on runt activity was examined in vivo. Ectopic expression of the mutant protein indicated that this conserved substitution altered, but did not eliminate, runt activity as evaluated by segmentation phenotype and viability. ^

Habitat-dependent geographical variation in ontogenetic allometry of the shiner perch Cymatogaster aggregata Gibbons (Teleostei: Embiotocidae)

Studies of intraspecific morphological variation in fishes have traditionally focused on freshwater rather than marine species. In addition, such studies typically focus on adults, although causes and intensities of selective pressures most likely vary through an individual’s lifetime. In this study, body and head shape of a marine species, shiner perch Cymatogaster aggregata Gibbons were compared among localities along the Pacific Northwest coast of North America. Evidence was found for intraspecific variation in ontogenetic allometry, and for a closer correlation of body shape with environment rather than geographical proximity. This correlation with environment was more evident in younger fish, thereby demonstrating the importance of analysing multiple life stages. A common garden experiment suggests both environmental and genetic bases for the observed differences. Recognizing intraspecific ecomorphological complexity and its specificity to habitat and/or life stage can have important consequences for understanding the role of local adaptation and population dynamics in macroecology.

Optimizing Models of the North Atlantic Spring Bloom Using Physical, Chemical and Bio-Optical Observations from a Lagrangian Float

The North Atlantic spring bloom is one of the main events that lead to carbon export to the deep ocean and drive oceanic uptake of CO(2) from the atmosphere. Here we use a suite of physical, bio-optical and chemical measurements made during the 2008 spring bloom to optimize and compare three different models of biological carbon export. The observations are from a Lagrangian float that operated south of Iceland from early April to late June, and were calibrated with ship-based measurements. The simplest model is representative of typical NPZD models used for the North Atlantic, while the most complex model explicitly includes diatoms and the formation of fast sinking diatom aggregates and cysts under silicate limitation. We carried out a variational optimization and error analysis for the biological parameters of all three models, and compared their ability to replicate the observations. The observations were sufficient to constrain most phytoplankton-related model parameters to accuracies of better than 15 %. However, the lack of zooplankton observations leads to large uncertainties in model parameters for grazing. The simulated vertical carbon flux at 100 m depth is similar between models and agrees well with available observations, but at 600 m the simulated flux is larger by a factor of 2.5 to 4.5 for the model with diatom aggregation. While none of the models can be formally rejected based on their misfit with the available observations, the model that includes export by diatom aggregation has a statistically significant better fit to the observations and more accurately represents the mechanisms and timing of carbon export based on observations not included in the optimization. Thus models that accurately simulate the upper 100 m do not necessarily accurately simulate export to deeper depths.

A Model Study of the Seasonal Circulation in the Gulf of Maine

The Princeton Ocean Model is used to study the circulation in the Gulf of Maine and its seasonal transition in response to wind, surface heat flux, river discharge, and the M-2 tide. The model has an orthogonal-curvature linear grid in the horizontal with variable spacing from 3 km nearshore to 7 km offshore and 19 levels in the vertical. It is initialized and forced at the open boundary with model results from the East Coast Forecast System. The first experiment is forced by monthly climatological wind and heat flux from the Comprehensive Ocean Atmosphere Data Set; discharges from the Saint John, Penobscot, Kennebec, and Merrimack Rivers are added in the second experiment; the semidiurnal lunar tide (M-2) is included as part of the open boundary forcing in the third experiment. It is found that the surface heat flux plays an important role in regulating the annual cycle of the circulation in the Gulf of Maine. The spinup of the cyclonic circulation between April and June is likely caused by the differential heating between the interior gulf and the exterior shelf/slope region. From June to December the cyclonic circulation continues to strengthen, but gradually shrinks in size. When winter cooling erodes the stratification, the cyclonic circulation penetrates deeper into the water column. The circulation quickly spins down from December to February as most of the energy is consumed by bottom friction. While inclusion of river discharge changes details of the circulation pattern, the annual evolution of the circulation is largely unaffected. On the other hand, inclusion of the tide results in not only the anticyclonic circulation on Georges Bank but also modifications to the seasonal circulation.

Incomplete Distal Renal Tubular Acidosis from a Heterozygous Mutation of the V-ATPase B1 Subunit

Congenital distal renal tubular acidosis (dRTA) from mutations of the B1 subunit of the V-ATPase is considered an autosomal recessive disease. We analyzed a dRTA kindred with a truncation-mutation of B1 (p.Phe468fsX487) previously shown to have failure of assembly into the V1 domain of the V-ATPase. All heterozygous carriers in this kindred have normal plasma bicarbonate concentrations, thus evaded the diagnosis of RTA. However, inappropriately high urine pH, hypocitraturia, and hypercalciuria are present either individually or in combination in the heterozygotes at baseline. Two of the heterozygotes studied also have inappropriate urinary acidification with acute ammonium chloride loading and impaired urine-blood pCO2 gradient during bicarbonaturia indicating presence of H+ gradient and flux defects. In normal human renal papillae, wild type B1 is located primarily on the plasma membrane but papilla from one of the heterozygote who had kidney stones had renal tissue secured from surgery showed B1 in both plasma membrane as well as a diffuse intracellular staining. Titrating increasing amounts of the mutant B1 subunit did not exhibit negative dominance over the expression, cellular distribution, or H+-pump activity of the wild type B1 in mammalian HEK293 cells and in V-ATPase-deficient S. cerevisiae. This is the first demonstration of renal acidification defects and nephrolithiasis in heterozygous carriers of mutant B1 subunit; which cannot be attributable to negative dominance. We propose that heterozygosity may lead to mild real acidification defects due to haploinsufficiency. B1 heterozygosity should be considered in patients with calcium nephrolithiasis and urinary abnormalities such as alkalinuria or hypocitraturia.

CD41 T cell recovery during suppression of HIV replication: an international comparison of the immunological efficacy of antiretroviral therapy in North America, Asia and Africa.

BACKGROUND Even among HIV-infected patients who fully suppress plasma HIV RNA replication on antiretroviral therapy, genetic (e.g. CCL3L1 copy number), viral (e.g. tropism) and environmental (e.g. chronic exposure to microbial antigens) factors influence CD4 recovery. These factors differ markedly around the world and therefore the expected CD4 recovery during HIV RNA suppression may differ globally. METHODS We evaluated HIV-infected adults from North America, West Africa, East Africa, Southern Africa and Asia starting non-nucleoside reverse transcriptase inhibitorbased regimens containing efavirenz or nevirapine, who achieved at least one HIV RNA level <500/ml in the first year of therapy and observed CD4 changes during HIV RNA suppression. We used a piecewise linear regression to estimate the influence of region of residence on CD4 recovery, adjusting for socio-demographic and clinical characteristics. We observed 28 217 patients from 105 cohorts over 37 825 person-years. RESULTS After adjustment, patients from East Africa showed diminished CD4 recovery as compared with other regions. Three years after antiretroviral therapy initiation, the mean CD4 count for a prototypical patient with a pre-therapy CD4 count of 150/ml was 529/ml [95% confidence interval (CI): 517–541] in North America, 494/ml (95% CI: 429–559) in West Africa, 515/ml (95% CI: 508–522) in Southern Africa, 503/ml (95% CI: 478–528) in Asia and 437/ml (95% CI: 425–449) in East Africa. CONCLUSIONS CD4 recovery during HIV RNA suppression is diminished in East Africa as compared with other regions of the world, and observed differences are large enough to potentially influence clinical outcomes. Epidemiological analyses on a global scale can identify macroscopic effects unobservable at the clinical, national or individual regional level.

Molecular Consequences of the SERPINH1/HSP47 Mutation in the Dachshund Natural Model of Osteogenesis Imperfecta.

Osteogenesis imperfecta (OI) is a heritable connective tissue disease characterized by bone fragility and increased risk of fractures. Up to now, mutations in at least 18 genes have been associated with dominant and recessive forms of OI that affect the production or post-translational processing of procollagen or alter bone homeostasis. Among those, SERPINH1 encoding heat shock protein 47 (HSP47), a chaperone exclusive for collagen folding in the ER, was identified to cause a severe form of OI in dachshunds (L326P) as well as in humans (one single case with a L78P mutation). To elucidate the disease mechanism underlying OI in the dog model, we applied a range of biochemical assays to mutant and control skin fibroblasts as well as on bone samples. These experiments revealed that type I collagen synthesized by mutant cells had decreased electrophoretic mobility. Procollagen was retained intracellularly with concomitant dilation of ER cisternae and activation of the ER stress response markers GRP78 and phospho-eIF2α, thus suggesting a defect in procollagen processing. In line with the migration shift detected on SDS-PAGE of cell culture collagen, extracts of bone collagen from the OI dog showed a similar mobility shift, and on tandem mass spectrometry, the chains were post-translationally overmodified. The bone collagen had a higher content of pyridinoline than control dog bone. We conclude that the SERPINH1 mutation in this naturally occurring model of OI impairs how HSP47 acts as a chaperone in the ER. This results in abnormal post-translational modification and cross-linking of the bone collagen.

Geometry and kinematics of the Roisan-Cignana Shear Zone, and the orogenic evolution of the Dent Blanche Tectonic System (Western Alps)

The Dent Blanche Tectonic System (DBTS) is a composite thrust sheet derived from the previously thinned passive Adriatic continental margin. A kilometric high-strain zone, the Roisan-Cignana Shear Zone (RCSZ) defines the major tectonic boundary within the DBTS and separates it into two subunits, the Dent Blanche s.s. nappe to the northwest and the Mont Mary nappe to the southeast. Within this shear zone, tectonic slices of Mesozoic and pre-Alpine meta-sediments became amalgamated with continental basement rocks of the Adriatic margin. The occurrence of high pressure assemblages along the contact between these tectonic slices indicates that the amalgamation occurred prior to or during the subduction process, at an early stage of the Alpine orogenic cycle. Detailed mapping, petrographic and structural analysis show that the Roisan-Cignana Shear Zone results from several superimposed Alpine structural and metamorphic stages. Subduction of the continental fragments is recorded by blueschist-facies deformation, whereas the Alpine collision is reflected by a greenschist facies overprint associated with the development of large-scale open folds. The postnappe evolution comprises the development of low-angle brittle faults, followed by large-scale folding (Vanzone phase) and finally brittle extensional faults. The RCSZ shows that fragments of continental crust had been torn off the passive continental margin prior to continental collision, thus recording the entire history of the orogenic cycle. The role of preceding Permo-Triassic lithospheric thinning, Jurassic rifting, and ablative subduction processes in controlling the removal of crustal fragments from the reactivated passive continental margin is discussed. Results of this study constrain the temporal sequence of the tectono-metamorphic processes involved in the assembly of the DBTS, but they also show limits on the interpretation. In particular it remains difficult to judge to what extent precollisional rifting at the Adriatic continental margin preconditioned the efficiency of convergent processes, i.e. accretion, subduction, and orogenic exhumation.

The Dark Side of the Moon: Meta-analytical Impact of Recruitment Strategies on Risk Enrichment in the Clinical High Risk State for Psychosis

Background: The individual risk of developing psychosis after being tested for clinical high-risk (CHR) criteria (posttest risk of psychosis) depends on the underlying risk of the disease of the population from which the person is selected (pretest risk of psychosis), and thus on recruitment strategies. Yet, the impact of recruitment strategies on pretest risk of psychosis is unknown. Methods: Meta-analysis of the pretest risk of psychosis in help-seeking patients selected to undergo CHR assessment: total transitions to psychosis over the pool of patients assessed for potential risk and deemed at risk (CHR+) or not at risk (CHR−). Recruitment strategies (number of outreach activities per study, main target of outreach campaign, and proportion of self-referrals) were the moderators examined in meta-regressions. Results: 11 independent studies met the inclusion criteria, for a total of 2519 (CHR+: n = 1359; CHR−: n = 1160) help-seeking patients undergoing CHR assessment (mean follow-up: 38 months). The overall meta-analytical pretest risk for psychosis in help-seeking patients was 15%, with high heterogeneity (95% CI: 9%–24%, I 2 = 96, P < .001). Recruitment strategies were heterogeneous and opportunistic. Heterogeneity was largely explained by intensive (n = 11, β = −.166, Q = 9.441, P = .002) outreach campaigns primarily targeting the general public (n = 11, β = −1.15, Q = 21.35, P < .001) along with higher proportions of self-referrals (n = 10, β = −.029, Q = 4.262, P = .039), which diluted pretest risk for psychosis in patients undergoing CHR assessment. Conclusions: There is meta-analytical evidence for overall risk enrichment (pretest risk for psychosis at 38monhts = 15%) in help-seeking samples selected for CHR assessment as compared to the general population (pretest risk of psychosis at 38monhts=0.1%). Intensive outreach campaigns predominantly targeting the general population and a higher proportion of self-referrals diluted the pretest risk for psychosis.

At risk or not at risk? A meta-analysis of the prognostic accuracy of psychometric interviews for psychosis prediction

An accurate detection of individuals at clinical high risk (CHR) for psychosis is a prerequisite for effective preventive interventions. Several psychometric interviews are available, but their prognostic accuracy is unknown. We conducted a prognostic accuracy meta-analysis of psychometric interviews used to examine referrals to high risk services. The index test was an established CHR psychometric instrument used to identify subjects with and without CHR (CHR+ and CHR-). The reference index was psychosis onset over time in both CHR+ and CHR- subjects. Data were analyzed with MIDAS (STATA13). Area under the curve (AUC), summary receiver operating characteristic curves, quality assessment, likelihood ratios, Fagan's nomogram and probability modified plots were computed. Eleven independent studies were included, with a total of 2,519 help-seeking, predominately adult subjects (CHR+: N=1,359; CHR-: N=1,160) referred to high risk services. The mean follow-up duration was 38 months. The AUC was excellent (0.90; 95% CI: 0.87-0.93), and comparable to other tests in preventive medicine, suggesting clinical utility in subjects referred to high risk services. Meta-regression analyses revealed an effect for exposure to antipsychotics and no effects for type of instrument, age, gender, follow-up time, sample size, quality assessment, proportion of CHR+ subjects in the total sample. Fagan's nomogram indicated a low positive predictive value (5.74%) in the general non-help-seeking population. Albeit the clear need to further improve prediction of psychosis, these findings support the use of psychometric prognostic interviews for CHR as clinical tools for an indicated prevention in subjects seeking help at high risk services worldwide.

Evaluation of the Morphological Characteristics of Laser-Irradiated Dentin

OBJECTIVE The aim of this study was to investigate the effect of different energy settings of Er:YAG laser irradiation on dentin surface morphology with respect to the number of opened dentinal tubules. BACKGROUND DATA An ideally prepared dentin surface with opened dentinal tubules is a prerequisite for adhesive fixation. No study, however, has yet compared the numbers of opened dentinal tubules with regard to statistical differences. METHODS Conventional preparations using a bur with or without additional acid etching acted as control groups. Dentin specimens were prepared from human third molars and randomly divided into eight groups according to the energy settings of the laser (1, 1.5, 4, 6, 7.5, and 8 W) and two controls (bur and bur plus acid etching). After surface preparation, dentin surfaces were analyzed with a scanning electron microscope, and the number of opened dentinal tubules in a defined area was counted. RESULTS The control groups showed smooth surfaces with (bur plus acid etching) and without opened dentinal tubules (bur), whereas all laser-irradiated surfaces showed rough surfaces. Using the energy setting of 4 W resulted in significantly more opened dentinal tubules than the conventional preparation technique using the bur with additional acid etching. In contrast, the energy setting of 8 W showed significantly fewer opened dentinal tubules, and also exhibited signs of thermal damage. CONCLUSIONS The Er:YAG laser with an energy setting of 4 W generates a dentin surface with opened dentinal tubules, a prerequisite for adhesive fixation.

Effect of the REG1 anticoagulation system versus bivalirudin on outcomes after percutaneous coronary intervention (REGULATE-PCI): a randomised clinical trial.

BACKGROUND REG1 is a novel anticoagulation system consisting of pegnivacogin, an RNA aptamer inhibitor of coagulation factor IXa, and anivamersen, a complementary sequence reversal oligonucleotide. We tested the hypothesis that near complete inhibition of factor IXa with pegnivacogin during percutaneous coronary intervention, followed by partial reversal with anivamersen, would reduce ischaemic events compared with bivalirudin, without increasing bleeding. METHODS We did a randomised, open-label, active-controlled, multicentre, superiority trial to compare REG1 with bivalirudin at 225 hospitals in North America and Europe. We planned to randomly allocate 13,200 patients undergoing percutaneous coronary intervention in a 1:1 ratio to either REG1 (pegnivacogin 1 mg/kg bolus [>99% factor IXa inhibition] followed by 80% reversal with anivamersen after percutaneous coronary intervention) or bivalirudin. Exclusion criteria included ST segment elevation myocardial infarction within 48 h. The primary efficacy endpoint was the composite of all-cause death, myocardial infarction, stroke, and unplanned target lesion revascularisation by day 3 after randomisation. The principal safety endpoint was major bleeding. Analysis was by intention to treat. This trial is registered at ClinicalTrials.gov, identifier NCT01848106. The trial was terminated early after enrolment of 3232 patients due to severe allergic reactions. FINDINGS 1616 patients were allocated REG1 and 1616 were assigned bivalirudin, of whom 1605 and 1601 patients, respectively, received the assigned treatment. Severe allergic reactions were reported in ten (1%) of 1605 patients receiving REG1 versus one (<1%) of 1601 patients treated with bivalirudin. The composite primary endpoint did not differ between groups, with 108 (7%) of 1616 patients assigned REG1 and 103 (6%) of 1616 allocated bivalirudin reporting a primary endpoint event (odds ratio [OR] 1·05, 95% CI 0·80-1·39; p=0·72). Major bleeding was similar between treatment groups (seven [<1%] of 1605 receiving REG1 vs two [<1%] of 1601 treated with bivalirudin; OR 3·49, 95% CI 0·73-16·82; p=0·10), but major or minor bleeding was increased with REG1 (104 [6%] vs 65 [4%]; 1·64, 1·19-2·25; p=0·002). INTERPRETATION The reversible factor IXa inhibitor REG1, as currently formulated, is associated with severe allergic reactions. Although statistical power was limited because of early termination, there was no evidence that REG1 reduced ischaemic events or bleeding compared with bivalirudin. FUNDING Regado Biosciences Inc.

Report of the Second European Zebrafish Principal Investigator Meeting in Karlsruhe, Germany, March 21-24, 2012.

The second European Zebrafish Principal Investigator (PI) Meeting was held in March, 2012, in Karlsruhe, Germany. It brought together PIs from all over Europe who work with fish models such as zebrafish and medaka to discuss their latest results, as well as to resolve strategic issues faced by this research community. Scientific discussion ranged from the development of new technologies for working with fish models to progress in various fields of research such as injury and repair, disease models, and cell polarity and dynamics. This meeting also marked the establishment of the European Zebrafish Resource Centre (EZRC) at Karlsruhe that in the future will serve as an important focus and community resource for zebrafish- and medaka-based research.

THE NATURAL BACKGROUND GAMMA RADIATION EXPOSURE IN THE METROPOLITAN AREA OF THE VALLEY OF MEXICO

Measurements of the natural background radiation have been made at numerous places throughout the world. Very little work in this field has been done in developing countries. In Mexico the natural radiation to which the population is exposed has not been assessed. This dissertation represents a pioneer study in this environmental area. The radiation exposure which occupants within buildings receive as a result of naturally occurring radionuclides present in construction materials is the principal focus.^ Data were collected between August 1979 and November 1980. Continuous monitoring was done with TLDs placed on site for periods of 3 to 6 months. The instrumentation used for "real-time" measurements was a portable NaI (Tl) scintillation detector. In addition, radiometric measurements were performed on construction materials commonly used in Mexican homes.^ Based on TLD readings taken within 75 dwellings, the typical indoor exposure for a resident of the study area is 9.2 (mu)Rh('-1). The average reading of the 152 indoor scintillometer surveys was 9.5 (mu)Rh('-1), the outdoor reading 7.5 (mu)Rh('-1). Results of one-way and multi-way analyses of the exposure data to determine the effect due to building materials type, geologic subsoil, age of dwelling, and elevation are also presented. The results of 152 indoor scintillometer surveys are described. ^