Design and anticipated outcomes of the eMERGE-PGx project: a multicenter pilot for preemptive pharmacogenomics in electronic health record systems

We describe here the design and initial implementation of the eMERGE-PGx project. eMERGE-PGx, a partnership of the eMERGE and PGRN consortia, has three objectives : 1) Deploy PGRNseq, a next-generation sequencing platform assessing sequence variation in 84 proposed pharmacogenes, in nearly 9,000 patients likely to be prescribed drugs of interest in a 1–3 year timeframe across several clinical sites; 2) Integrate well-established clinically-validated pharmacogenetic genotypes into the electronic health record with associated clinical decision support and assess process and clinical outcomes of implementation; and 3) Develop a repository of pharmacogenetic variants of unknown significance linked to a repository of EHR-based clinical phenotype data for ongoing pharmacogenomics discovery. We describe site-specific project implementation and anticipated products, including genetic variant and phenotype data repositories, novel variant association studies, clinical decision support modules, clinical and process outcomes, approaches to manage incidental findings, and patient and clinician education methods.

Delta(13)C and tree-ring width reflect different drought responses in Quercus ilex and Pinus halepensis

Holm oak (Quercus ilexL.) and Aleppo pine (Pinus halepensisMill) are representative of two different functional types of trees extensively found in the Mediterranean: evergreen sclerophyllous and drought-adapted conifers. The former is considered a partially drought-tolerant species, whereas the latter is a typically drought-avoiding, water-saving species. We postulated that contrasting strategies in response to water deficits in Q. ilex and P. halepensis would lead to a differential sensitivity to changes in water availability. To test this hypothesis, we compared the response of both species in growth rate (measured as radial increments) and intrinsic water use efficiency WUE(i), as inferred from carbon isotope discrimination (Delta(13)C) in wood samples] among sites from different provenance regions in NE Spain. We found significant differences in Delta(13)C and growth among provenance regions, partly explained by contrasting water availability. Wood Delta(13)C was positively related with precipitation and the ratio between precipitation and potential evapotranspiration (P/ E). However, these relationships were stronger in P. halepensis (for P / E, r(2)=0.67, P <0.001) than in Q. ilex ( r(2)=0.42, P <0.01). In addition, radial growth was positively related with precipitation and Delta(13)C in P. halepensis ( r(2)=0.32 and r(2)=0.35, respectively, P <0.01), but not in Q. ilex. We concluded that P. halepensis was more sensitive than Q. ilex to water availability, showing faster increase in WUE(i) in response to water stress. We also found that the effect of north/south aspect on Delta(13)C and growth was site-specific, and unrelated to climatic variables.

Transmembrane Pickets Connect Cyto- and Pericellular Skeletons Forming Barriers to Receptor Engagement

Phagocytic receptors must diffuse laterally to become activated upon clustering by multivalent targets. Receptor diffusion, however, can be obstructed by transmembrane proteins ("pickets") that are immobilized by interacting with the cortical cytoskeleton. The molecular identity of these pickets and their role in phagocytosis have not been defined. We used single-molecule tracking to study the interaction between Fcγ receptors and CD44, an abundant transmembrane protein capable of indirect association with F-actin, hence likely to serve as a picket. CD44 tethers reversibly to formin-induced actin filaments, curtailing receptor diffusion. Such linear filaments predominate in the trailing end of polarized macrophages, where receptor mobility was minimal. Conversely, receptors were most mobile at the leading edge, where Arp2/3-driven actin branching predominates. CD44 binds hyaluronan, anchoring a pericellular coat that also limits receptor displacement and obstructs access to phagocytic targets. Force must be applied to traverse the pericellular barrier, enabling receptors to engage their targets.

Hepatitis B virus (HBV)/hepatitis D virus (HDV) coinfection in outbreaks of acute hepatitis in the Peruvian Amazon basin: the roles of HDV genotype III and HBV genotype F

Recurring outbreaks of acute hepatitis have been a significant cause of morbidity and mortality among Peruvian military personnel stationed in the Amazon Basin region of Peru. The role of hepatitis B virus (HBV) and hepatitis D virus (HDV) infection was investigated as the possible cause of acute hepatitis among 88 military patients stationed at four different jungle outposts during 1992-1993. Analysis of serum markers indicated that 95% (84/88) had evidence of acute HBV infection; 64% (54/84) were also infected with HDV. Genetic analysis of PCR-amplified HDV and HBV fragments showed exclusively HDV genotype III and HBV genotype F. Furthermore, HDV RNA sequences were similar among patients from the same outpost but different from those at other jungle locations. The data suggested focal sources of HDV infection in the jungle environment of the outposts and, further, confirmed the unique association of HDV genotype III with severe cases of human disease in northern South America.

Basichondrocranium anomalies in adult Chiari type I malformation: a morphometric study

The purpose of this study was to determine the frequency of anomalies of the basichondrocranium in a series of 42 patients with Chiari type I malformation compared with a control group of 46 subjects. Sixteen patients also had syringomyelia. Linear, angular and posterior fossa surface area measurements were taken on conventional lateral skull x-rays. Posterior fossa volume was estimated by CT scanning. In patients there was shortening of clivus length, Twining-opisthion distance and Chamberlain's line. Basal and Boogard angles were enlarged. The size of the posterior fossa was smaller in patients than in controls. Only 10 (23.8%) patients had no evidence of occipital dysplasia. When discriminant analysis was applied to the data, the most discriminative variables were posterior fossa area and clivus length which allowed accurate identification of 76% of patients as belonging to the patient group and 79% of controls as belonging to the control group. These findings prove that under-development of the basichondrocranium with a small size of the posterior fossa is an outstanding feature in adult Chiari type I malformation, and support the hypothesis that tonsillar ectopia is secondary to the disproportion between the posterior fossa and the cerebellum, which is forced to grow into the cervical spinal canal.

A composition-dependent molecular clutch between T cell signaling condensates and actin

During T cell activation, biomolecular condensates form at the immunological synapse (IS) through multivalency-driven phase separation of LAT, Grb2, Sos1, SLP-76, Nck, and WASP. These condensates move radially at the IS, traversing successive radially-oriented and concentric actin networks. To understand this movement, we biochemically reconstituted LAT condensates with actomyosin filaments. We found that basic regions of Nck and N-WASP/WASP promote association and co-movement of LAT condensates with actin, indicating conversion of weak individual affinities to high collective affinity upon phase separation. Condensates lacking these components were propelled differently, without strong actin adhesion. In cells, LAT condensates lost Nck as radial actin transitioned to the concentric network, and engineered condensates constitutively binding actin moved aberrantly. Our data show that Nck and WASP form a clutch between LAT condensates and actin in vitro and suggest that compositional changes may enable condensate movement by distinct actin networks in different regions of the IS.

The R71G BRCA1 is a founder Spanish mutation and leads to aberrant splicing of the transcript

In a BRCA1 screening in familial breast cancer carried out in different centres in Spain, France, and United Kingdom, a missense mutation 330A>G which results in a Arg to Gly change at codon 71 (R71G) was independently identified in 6 families, all of them with Spanish ancestors. This residue coincides with the -2 position of the exon 5 donor splice site. We further investigated the effect of this base substitution on the splicing of BRCA1 mRNA. The sequence analysis of the cDNA indicated that 22 bp of exon 5 were deleted, creating with the first bases of exon 6 a termination codon at position 64, which results in a truncated protein. The BRCA1 haplotype of the R71G carrier patients and Spanish controls was analysed by use of six microsatellites located within or near BRCA1. Our results are consistent with the possibility that these families shared a common ancestry with BRCA1 R71G being a founder mutation of Spanish origin.

Transcriptional analysis of the 5'-noncoding region of the human involucrin gene

Human involucrin whose gene transcription is directed by a 2456-nucleotide (nt) 5'-noncoding region is a structural component of the epithelial cornified layer. Transient transfection assays demonstrated that this region is transcriptionally active in multiplying keratinocytes and is enhanced by 2 mM CaCl2 treatment. Calcium-independent transcriptional activity and the interaction with the AP-1 transcriptional factor was located on the proximal part (nt -159 to -1) of the 5'-noncoding region. However, CaCl2 responsiveness was mapped to a distal 1185-nt fragment (nt -2456 to -1272). Moreover, this fragment potentiated the Herpes simplex thymidine kinase promoter in normal keratinocytes and is responsive to calcium treatment in a cell type-specific manner. Interestingly, the absence of a 491-nt fragment located between the two enhancer domains (nt -651 to -160) resulted in transcriptional activation in multiplying keratinocytes. This fragment interacts with AP-1 and the YY1 transcriptional silencer. It is concluded that human involucrin 5'-noncoding region contains at least three regulatory domains, a distal CaCl2-responsive enhancer, a putative transcriptional silencer (that interacts with AP-1 and YY1), and a proximal enhancer/promoter (that interacts with AP-1). Thus, this study demonstrates the presence of particular transcriptional factors can potentially regulate the human involucrin expression.

Gene expression associated with compatible viral diseases in grapevine cultivars

Viral diseases affect grapevine cultures without inducing any resistance response. Thus, these plants develop systemic diseases and are chronically infected. Molecular events associated with viral compatible infections responsible for disease establishment and symptoms development are poorly understood. In this study, we surveyed viral infection in grapevines at a transcriptional level. Gene expression in the Vitis vinifera red wine cultivars Carménère and Cabernet-Sauvignon naturally infected with GLRaV-3 were evaluated using a genome-wide expression profiling with the Vitis vinifera GeneChip from Affymetrix. We describe numerous genes that are induced or repressed in viral infected grapevines leaves. Changes in gene expression involved a wide spectrum of biological functions, including processes of translation and protein targeting, metabolism, transport, and cell defense. Considering cellular localization, the membrane and endomembrane systems appeared with the highest number of induced genes, while chloroplastic genes were mostly repressed. As most induced genes associated with the membranous system are involved in transport, the possible effect of virus in this process is discussed. Responses of both cultivars are analyzed and the results are compared with published data from other species. This is the first study of global gene profiling in grapevine in response to viral infections using DNA microarray.

Multistep Track Segmentation and Motion Classification for Transient Mobility Analysis

Molecular interactions are often transient and might change within the window of observation, leading to changes in molecule movement. Therefore, accurate motion analysis often requires transient motion classification. Here we present an accurate and computationally efficient transient mobility analysis framework, termed "divide-and-conquer moment scaling spectrum" (DC-MSS). DC-MSS works in a multistep fashion: 1) it utilizes a local movement descriptor throughout a track to divide it into initial segments of putatively different motion classes; 2) it classifies these segments via moment scaling spectrum (MSS) analysis of molecule displacements; and 3) it uses the MSS analysis results to refine the track segmentation. This strategy uncouples the initial identification of motion switches from motion classification, allowing DC-MSS to circumvent the sensitivity-accuracy tradeoff of classic rolling window approaches for transient motion analysis, while at the same time harnessing the classification power of MSS analysis. Testing of DC-MSS demonstrates that it detects switches among free diffusion, confined diffusion, directed diffusion, and immobility with great sensitivity. To illustrate the utility of DC-MSS, we have applied it to single-particle tracks of the transmembrane protein CD44 on the surface of macrophages, revealing actin cortex-dependent transient mobility changes.

Effects of task complexity and practice on performance during acute alcohol intoxication

A battery of psychological tests was administered to 26 medical students in a counterbalanced cross-over design to determine the effects of an acute dose of alcohol on perceptual, perceptual-motor and cognitive capacities. The tests included: temporal acuity (critical flicker fusion threshold), perceptual speed and attention (Stroop), perceptual-motor coordination (Purdue Pegboard), perceptual-motor speed (simple and choice reaction time), immediate memory (WAIS Digit Span), short-term memory (dichotic stimulation), and intellectual and conceptual capacity (Shipley Institute of Living Scale). Three general conclusions were drawn: (1) alcohol exerted a deteriorating effect on performance on all tasks except the Stroop, (2) retesting 48 hr. later showed that practice or familiarity with the task mitigated the effects of the alcohol, and (3) contrary to the hypothesis advanced by Jellineck and McFarland (1940), no systematic relationship was observed between task complexity and degree of impairment from the alcohol.

Nanoplastics are bioaccumulated in fish liver and muscle and cause DNA damage after a chronic exposure

The extent of the widespread, planetary contamination by plastic waste is difficult to fully capture. Nanoplastics (NPs) are currently in the center of research concerning plastic litter, both for the analytical challenges they pose and for their potential to provoke hazardous effects in organisms. However, there are still many unanswered questions in this multidisciplinary field, with a crucial missing piece being the quantification of NPs in fish tissues after in vivo exposures. Another relevant question that is still greatly unexplored is how a chronic exposure to NPs will affect fish health. This study aims to provide answers to both of these relevant knowledge gaps. To this end, goldfish (Carassius auratus) were exposed to 44 nm polystyrene (PS)-NPs via water for 30 days. Following the exposure, gastrointestinal tract, liver and muscle were sampled for PS-NPs analysis by means of size exclusion chromatography coupled to high resolution mass spectrometry. PS-NPs were detected in all liver and muscle samples of exposed fish, with higher concentrations in liver than in muscle, whereas no PS-NPs were detected in the gastrointestinal tract. Nevertheless, exposure to PS-NPs did not induce changes in hematology parameters nor in cortisol and glucose levels in plasma. On the other hand, even a relatively low concentration of PS-NPs was able to cause DNA damage, measured by an increase in erythrocyte nuclear abnormalities, suggesting that PS-NPs can reach the cell nucleus and cause genotoxicity. These results show for the first time that PS-NPs find their way to fish muscle after chronic exposure, where they bioaccumulate, but do not alter fish survival nor hematological or physiological stress indicators. The accumulation of PS-NPs in fish muscle can represent a threat to human health as a possible route of exposure to small-sized plastics. The present results in a model fish species open windows for future studies in edible fish species.

Synthesis and pharmacological properties of a series of antidopaminergic piperidyl benzamides

The synthesis and pharmacological screening for anti-apomorphine, stomach emptying and local anaesthetic activities of some new piperidylbenzamides is described. One of these, N-(1'-benzyl-4'-piperidyl)-2-methoxy-4-amino-5-chlorobenzamide (clebopride) is more potent than metoclopramide in tests related to blockade of cerebral dopamine receptors.

A conformation change in the carboxyl terminus of Alzheimer's Abeta (1-40) accompanies the transition from dimer to fibril as revealed by fluorescence quenching analysis

Alzheimer's disease is characterized by the presence of insoluble, fibrous deposits composed principally of amyloid beta (Abeta) peptide. A number of studies have provided information on the fibril structure and on the factors affecting fiber formation, but the details of the fibril structure are not known. We used fluorescence quenching to investigate the solvent accessibility and surface charge of the soluble Abeta(1-40) dimer and amyloid fibrils. Analogs of Abeta(1-40) containing a single tryptophan were synthesized by substituting residues at positions 4, 10, 34, and 40 with tryptophan. Quenching measurements in the dimeric state indicate that the amino-terminal analogs (AbetaF4W and AbetaY10W) are accessible to polar quenchers, and the more carboxyl-terminal analog AbetaV34W is less accessible. AbetaV40W, on the other hand, exhibits a low degree of quenching, indicating that this residue is highly shielded from the solvent in the dimeric state. Correcting for the effect of reduced translational and rotational diffusion, fibril formation was associated with a selective increase in solvent exposure of residues 34 and 40, suggesting that a conformation change may take place in the carboxyl-terminal region coincident with the dimer to fibril transition.

Design, synthesis, and biological activities of new thieno[3,2-d] pyrimidines as selective type 4 phosphodiesterase inhibitors

A common pharmacophore for compounds structurally related to nitraquazone has been derived. Using this pharmacophore, new structures have been designed, synthesized, and evaluated for their inhibitory potencies against cyclic adenosine 5'-monophosphate (cAMP) specific phosphodiesterase (PDE 4). From these compounds, 4-benzylamino-2-butylthieno[3,2-d]pyrimidine (4) was selected for optimization. The effects of changes to the lipophilic groups and the amino linkage on the PDE 4 activity have been investigated. As a result, some potent PDE 4 inhibitors, selective with respect to PDE 3, have been identified. A selected group of compounds have been further evaluated for their ability to displace [3H]rolipram from its binding site and also to potentiate isoprenaline-induced cAMP accumulation in isolated guinea pig eosinophils. Of these, 2-butyl-4-cyclohexylaminothieno[3,2-d]pyrimidine (33) has an interesting profile, with an important improvement in PDE 4/[3H]rolipram ratio with respect to reference drugs, and good activity in cAMP potentiation, consistent with efficient cell penetration.

Classification of missense variants of unknown significance inBRCA1based on clinical and tumor information

Classification of rare missense variants in disease susceptibility genes as neutral or disease-causing is important for genetic counseling. Different criteria are used to help classify such variants in BRCA1 and BRCA2; however, the strongest evidence tends to come from segregation analysis and observed cooccurrence with known pathogenic mutations, which both require information that is not readily available in most circumstances. A likelihood-based model has been developed, integrating most of the data currently used to classify these variants. We have adapted the original model, including only that information that could be more easily obtained from a cancer genetics laboratory, such as loss of heterozygosity (LOH), grade, and immunohistochemical analysis to assess estrogen receptor (ER) status for the tumors of carriers of these variants. We also considered summary family history (personal or first-degree family history of bilateral breast or ovarian cancer), which was not incorporated into the original model. To test the ability of the modified model to classify missense variants in BRCA1, we analyzed 17 variants, of which 10 have previously been classified as pathogenic mutations or neutral polymorphisms. We also included a prior step consisting of the screening of the variants among 1,000 controls, with which we were able to classify five as neutral, based solely on their observed frequency. We found that combining this relatively easily collected information can be sufficient to classify variants as pathogenic or neutral if tumors from at least three carriers of the same variant can be collected and analyzed.

Effects of staphylococcal enterotoxin B on rodent mast cells

Staphylococcal enterotoxin B (SEB) was tested in rodent mast cell cultures for the release of serotonin. Both rat RBL-2H3 mast cells and murine peritoneal cells released serotonin after SEB stimulation in culture. Release of serotonin in RBL-2H3 cells depended on the concentration of SEB; an appreciable release was seen at 50 micrograms/ml. The release of serotonin was not due to cell death. Serotonin release could be enhanced by bradykinin but not by vasoactive intestinal peptide, substance P, lipopolysaccharide from Salmonella typhimurium, the calcium ionophore A23187, acetylcholine, adenosine, 5-hydroxyeicosatetraenoic acid, indomethacin, or phorbol myristate acetate. SEB bound directly to the membrane of RBL-2H3 mast cells, and the SEB-binding site, the presumptive receptor, appeared to be a protein. The SEB receptor could not be capped under membrane-capping conditions, and serotonin release could not be enhanced by attempts to cross-link the receptor. These results suggest that mast cells may be an important cell type involved in SEB toxicosis and that release of serotonin may be enhanced by activation of the kinin-kallikrein system.