A new Miconia (Melastomatacaeae) from Bolivia, with remarks on angular-branched species in the Andes

A new species of Melastomataceae frorm Bolivia is described, illustrated and placed in a phenetic context within Miconia, a genus of 1000 species and about 2000 published names. Miconia quadrialata is readily distinguished from its Congeners by two-colored leaves and sharply four-angular and winged branchlets. A search for quadrangular-branched miconias revealed that 12 of 15 such species (in four sections), including the new species, occur in cloud forest in the Andes, raising the question of the adaptive significance of quadrangular branchlets

A common variant associated with dyslexia reduces expression of the KIAA0319 gene

This work was supported by the Wellcome Trust (MYD, SP, TSS, JCK, RWM, PC, SB, and APM), the Intramural Research Programs of the National Human Genome Research Institute (MYD and EDG) and National Cancer Institute (MPO), and the NIH/Ox-Cam Graduate Partnership Program (MYD).Numerous genetic association studies have implicated the KIAA0319 gene on human chromosome 6p22 in dyslexia susceptibility. The causative variant(s) remains unknown but may modulate gene expression, given that (1) a dyslexia-associated haplotype has been implicated in the reduced expression of KIAA0319, and (2) the strongest association has been found for the region spanning exon 1 of KIAA0319. Here, we test the hypothesis that variant(s) responsible for reduced KIAA0319 expression resides on the risk haplotype close to the gene's transcription start site. We identified seven single-nucleotide polymorphisms on the risk haplotype immediately upstream of KIAA0319 and determined that three of these are strongly associated with multiple reading-related traits. Using luciferase-expressing constructs containing the KIAA0319 upstream region, we characterized the minimal promoter and additional putative transcriptional regulator regions. This revealed that the minor allele of rs9461045, which shows the strongest association with dyslexia in our sample (max p-value = 0.0001), confers reduced luciferase expression in both neuronal and non-neuronal cell lines. Additionally, we found that the presence of this rs9461045 dyslexia-associated allele creates a nuclear protein-binding site, likely for the transcriptional silencer OCT-1. Knocking down OCT-1 expression in the neuronal cell line SHSY5Y using an siRNA restores KIAA0319 expression from the risk haplotype to nearly that seen from the non-risk haplotype. Our study thus pinpoints a common variant as altering the function of a dyslexia candidate gene and provides an illustrative example of the strategic approach needed to dissect the molecular basis of complex genetic traits.PostprintPeer reviewe

Human-specific CpG 'beacons' identify human-specific prefrontal cortex H3K4me3 chromatin peaks

Therefore, CpG-focused comparative sequence analysis can precisely pinpoint chromatin structures that contribute to the human-specific phenotype and further supports an integrated approach in genomic and epigenomic studie

Accurate measurement of 5-methylcytosine and 5-hydroxymethylcytosine in human cerebellum DNA by oxidative bisulfite on an array (OxBS-array).

The Infinium 450K Methylation array is an established tool for measuring methylation. However, the bisulfite (BS) reaction commonly used with the 450K array cannot distinguish between 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). The oxidative-bisulfite assay disambiguates 5mC and 5hmC. We describe the use of oxBS in conjunction with the 450K array (oxBS-array) to analyse 5hmC/5mC in cerebellum DNA. The "methylation" level derived by the BS reaction is the combined level of 5mC and 5hmC at a given base, while the oxBS reaction gives the level of 5mC alone. The level of 5hmC is derived by subtracting the oxBS level from the BS level. Here we present an analysis method that distinguishes genuine positive levels of 5hmC at levels as low as 3%. We performed four replicates of the same sample of cerebellum and found a high level of reproducibility (average r for BS = 98.3, and average r for oxBS = 96.8). In total, 114,734 probes showed a significant positive measurement for 5hmC. The range at which we were able to distinguish 5hmC occupancy was between 3% and 42%. In order to investigate the effects of multiple replicates on 5hmC detection we also simulated fewer replicates and found that decreasing the number of replicates to two reduced the number of positive probes identified by > 50%. We validated our results using qPCR in conjunction with glucosylation of 5hmC sites followed by MspI digestion and we found good concordance with the array estimates (r = 0.94). This experiment provides a map of 5hmC in the cerebellum and a robust dataset for use as a standard in future 5hmC analyses. We also provide a novel method for validating the presence of 5hmC at low levels, and highlight some of the pitfalls associated with measuring 5hmC and 5mC.S. Balasubramanian is a Senior Investigator of The Wellcome Trust and the Balasubramanian group is core-funded by Cancer Research UK. We would like to thank Tobias Ost and Christine Clark of Cambridge Epigenetix Ltd. for valuable discussions and development of the method.This article was originally published in PLOS ONE (Field SF, Beraldi D, Bachman M, Stewart SK, Beck S, Balasubramanian S, PLoS ONE 2015, 10(2): e0118202. doi:10.1371/journal.pone.0118202

The association between celiac disease and eosinophilic esophagitis in children and adults

BACKGROUND: An association between eosinophilic esophagitis (EoE) and celiac disease (CD) has been suggested in the literature. Our aim was to confirm and quantify the association between these two diseases. METHODS: All patients in a large Canadian city diagnosed with EoE or CD over a five-year period were identified. Standardized incidence ratios (SIRs) with 95% confidence intervals (CIs) were calculated. RESULTS: Over the five-year study EoE was diagnosed in 421 patients and CD was diagnosed in 763 patients. The incidence of EoE ranged from 2.1 to 10.7 cases per 100,000 population. The incidence of CD ranged from 10.4 to 15.7 cases per 100,000 population. Among the EoE cohort, 83 (20%) cases of EoE and 245 (32%) cases of CD were diagnosed in pediatric patients. The incidence of EoE in the pediatric subpopulation ranged from 3.7 to 6.9 cases per 100,000 population. The incidence of CD in the pediatric subpopulation ranged from 9.5 to 22.7 cases per 100,000 population. The concomitant diagnosis of both EoE and CD was made in three patients, all of whom were pediatric males. The SIR for EoE in the CD cohort was 48.4 (95% CI = 9.73, 141.41) with a SIR for CD within the paediatric EoE cohort of 75.05 (95% CI = 15.08, 219.28). CONCLUSIONS: This study confirms the association between EoE and CD. However, this association may be limited to pediatrics where the risk of each condition is increased 50 to 75-fold in patients diagnosed with the alternative condition. The concomitant diagnosis of these conditions should be considered in pediatric patients with upper gastrointestinal symptoms

Plant species selection by free-ranging cattle in southern Bolivian tropical montane forests

The frequency of selection of functional groups and plant species by free-ranging cattle foraging in a diverse environment and its changes during the dry and the following prehumid seasons were investigated using direct observations and bite counting. The study was conducted at two sites in the Bolivian-Tucuman montane forests in southern Bolivia, by including datasets of a total of 16 animals. Across both study sites and the entire observation period (May to October/November), the cattle were found to select a broad spectrum of plant species from different functional groups. However, just a limited number of species made up a considerable contribution to overall plant selection. The functional group of the graminoids was selected most frequently, but their contribution to plant selection decreased significantly from 63.5% of total bites in May to 15.9% in September/October, in accordance with a decrease in availability. Selection of woody plants (shrubs and tree parts, the latter mainly in the form of leaf litter and fruits) increased with time, reaching its peak at the beginning of the prehumid season, while the herbs showed a curvilinear pattern of selection which was highest in August. Plant species belonging to the functional groups of ferns, climbers and epiphytes were also selected by the cattle, but generally at low relative proportions. Plant selection might be influenced by temporal differences in nutritional quality and availability of the preferred plant species and functional groups. Sampling behaviour seems to be the most likely reason for the inclusion of a broad range of plant species with overall low contribution to plant selectio

Splanchnic Vasoregulation After Major Abdominal Surgery in Pigs

Background: Unrecognized reduction of blood supply to intestinal organs is associated with significant postoperative morbidity in abdominal surgery. The aim of this study was to determine whether—in the absence of hypovolemia—intestinal hypoperfusion as a result of blood flow redistribution occurs after abdominal surgery. Methods: Standardized operative trauma was induced in 14 healthy pigs. Systemic, regional, and local blood flow, intestinal and gastric intraluminal-to-end-tidal pCO2 gradients representing mucosal perfusion, and oxygen transport variables were measured for 10 postoperative hours. Normovolemia was maintained using continuous infusion of Ringer's lactate and additional boluses of colloids in response to blood pressure, pulmonary wedge pressure, and urinary output. Results: Postoperative blood flow was significantly increased in the celiac trunk (76% increase [percentage of baseline flow], p=0.003) and the hepatic (136% increase, p=0.002) and splenic (36% increase, p=0.025) arteries. Blood flow was significantly decreased in the mesenteric artery (25% decrease, p=0.007) and portal vein (13% decrease, p=0.028). Carotid and renal artery blood flow remained unchanged. Conclusions: Maintenance of normovolemia is insufficient to protect from intestinal hypoperfusion after abdominal surgery. Postoperative redistribution of cardiac output results in decreased intestinal and increased hepatic and splenic arterial blood flo

a follow-up on bone graft stability and implant success

Background Until now, sinus floor elevation represents the gold standard procedure in the atrophic maxilla in order to facilitate dental implant insertion. Although the procedure remains highly predictive, the perforation of the Schneiderian membrane might compromise the stability of the augmented bone and implant success due to chronic sinus infection. The aim of this retrospective cohort study was to show that a membrane tear, if detected and surgically properly addressed, has no influence on the survival of dental implants and bone resorption in the augmented area. Methods Thirty-one patients with 39 perforations could be included in this evaluation, and a control group of 32 patients with 40 sinus lift procedures without complications were compared regarding the radiographically determined development of bone level, peri-implant infection, and implant loss. Results Implant survival was 98.9% in the perforation group over an observation period of 2.7 (± 2.03) years compared to 100% in the control group after 1.8 (± 1.57) years. The residual bone level was significantly lower in the perforation group (p = 0.05) but showed no difference direct postoperatively (p = 0.7851) or in the follow-up assessment (p = 0.2338). Bone resorption remained not different between both groups (p = 0.945). A two-stage procedure was more frequent in the perforation group (p = 0.0003) as well as peri-implantitis (p = 0.0004). Conclusions Within the limits of our study, the perforation of the Schneiderian membrane did not have a negative impact on long-term graft stability or the overall implant survival