Pilot RCT Testing A Mailing About Sleeping Pills and Cognitive Behavioral Therapy for Insomnia: Impact on Benzodiazepines and Z-Drugs

OBJECTIVES

The aim is to pilot a low-touch program for reducing benzodiazepine receptor agonist (BZRA; benzodiazepines, z-drugs) prescriptions among older veterans.

METHODS

Pilot randomized controlled trial consists of 2,009 veterans aged ≥ 65 years who received BZRA prescriptions from a Veterans Health Administration pharmacy (Colorado or Montana) during the prior 18 months. Active: Arm 1 was a mailed brochure about BZRA risks that also included information about a free, online cognitive behavioral therapy for the insomnia (CBTI) program. Arm 2 was a mailed brochure (same as arm 1) and telephone reinforcement call. Control: Arm 3 was a mailed brochure without insomnia treatment information. Active BZRA prescriptions at follow-up (6 and 12 months) were measured.

RESULTS

In logistic regression analyses, the odds of BZRA prescription at 6- and 12-month follow-ups were not significantly different for arm 1 or 2 (active) versus arm 3 (control), including models adjusted for demographics and prescription characteristics (p-values >0.36).

CONCLUSIONS

Although we observed no differences in active BZRA prescriptions, this pilot study provides guidance for conducting a future study, indicating a need for a more potent intervention. A full-scale trial testing an optimized program would provide conclusive results.

CLINICAL IMPLICATIONS

Mailing information about BZRA risks and CBTI did not affect BZRA prescriptions.

Burnout assessment among pharmacist-academic detailers at the US Veterans Health Administration

BACKGROUND

Burnout among clinical pharmacist practitioners has been well established, but not among those who perform academic detailing.

OBJECTIVES

To measure burnout among clinical pharmacist practitioners who perform academic detailing (pharmacist-academic detailers) at the United States Veterans Health Administration and compare the findings using 2 validated burnout instruments for healthcare professionals.

METHODS

A cross-sectional study design was performed to measure burnout in VHA pharmacist-academic detailers across all VA regions between April 2023 and May 2023. Burnout was measured using the Oldenburg Burnout Inventory (OLBI) and a validated single-item burnout measure (SIMB). OLBI has 2 domains (exhaustion and disengagement) and categorizes burnout into Low, Moderate, and High based on scores above or below 1 standard deviation (SD) of the mean. The validated SIMB categorized burnout as having a score of 3 or greater (range: 1-5). Interrater reliability testing between the OLBI and the SIMB at detecting burnout among pharmacist-academic detailers was performed using the kappa test. Correlation between the 2 burnout instruments was assessed using the Spearman rho test.

RESULTS

A total of 50 pharmacist-academic detailers completed the burnout survey. A large proportion of respondents had Moderate levels of burnout for the total (72%) burnout score, disengagement (64%) domain, and exhaustion (74%) domain. In total, 86% of pharmacist-academic detailers reported having Moderate to High levels of burnout on the total OLBI score. On the SIMB, a total of 14 (28%) pharmacist-academic detailers reported having one or more symptoms of burnout. Interrater reliability was considered poor/slight agreement between the OLBI and SIMB. Correlation between the 2 burnout instruments was considered moderately correlated (rho = 0.67, P < 0.001).

CONCLUSION

This study provides an empirical analysis of burnout among pharmacist-academic detailers; however, the ability to detect burnout among pharmacist-academic detailers may be impacted by the selection of burnout instrument used.

Determinants of renin cell differentiation: a single cell epi-transcriptomics approach

Rationale

Renin cells are essential for survival. They control the morphogenesis of the kidney arterioles, and the composition and volume of our extracellular fluid, arterial blood pressure, tissue perfusion, and oxygen delivery. It is known that renin cells and associated arteriolar cells descend from FoxD1 + progenitor cells, yet renin cells remain challenging to study due in no small part to their rarity within the kidney. As such, the molecular mechanisms underlying the differentiation and maintenance of these cells remain insufficiently understood.

Objective

We sought to comprehensively evaluate the chromatin states and transcription factors (TFs) that drive the differentiation of FoxD1 + progenitor cells into those that compose the kidney vasculature with a focus on renin cells.

Methods and Results

We isolated single nuclei of FoxD1 + progenitor cells and their descendants from FoxD1 ^cre/+ ; R26R-mTmG mice at embryonic day 12 (E12) (n _cells =1234), embryonic day 18 (E18) (n _cells =3696), postnatal day 5 (P5) (n _cells =1986), and postnatal day 30 (P30) (n _cells =1196). Using integrated scRNA-seq and scATAC-seq we established the developmental trajectory that leads to the mosaic of cells that compose the kidney arterioles, and specifically identified the factors that determine the elusive, myo-endocrine adult renin-secreting juxtaglomerular (JG) cell. We confirm the role of Nfix in JG cell development and renin expression, and identified the myocyte enhancer factor-2 (MEF2) family of TFs as putative drivers of JG cell differentiation.

Conclusions

We provide the first developmental trajectory of renin cell differentiation as they become JG cells in a single-cell atlas of kidney vascular open chromatin and highlighted novel factors important for their stage-specific differentiation. This improved understanding of the regulatory landscape of renin expressing JG cells is necessary to better learn the control and function of this rare cell population as overactivation or aberrant activity of the RAS is a key factor in cardiovascular and kidney pathologies.

Replicative Instability Drives Cancer Progression

In the past decade, defective DNA repair has been increasingly linked with cancer progression. Human tumors with markers of defective DNA repair and increased replication stress exhibit genomic instability and poor survival rates across tumor types. Seminal studies have demonstrated that genomic instability develops following inactivation of BRCA1, BRCA2, or BRCA-related genes. However, it is recognized that many tumors exhibit genomic instability but lack BRCA inactivation. We sought to identify a pan-cancer mechanism that underpins genomic instability and cancer progression in BRCA-wildtype tumors. Methods: Using multi-omics data from two independent consortia, we analyzed data from dozens of tumor types to identify patient cohorts characterized by poor outcomes, genomic instability, and wildtype BRCA genes. We developed several novel metrics to identify the genetic underpinnings of genomic instability in tumors with wildtype BRCA. Associated clinical data was mined to analyze patient responses to standard of care therapies and potential differences in metastatic dissemination. Results: Systematic analysis of the DNA repair landscape revealed that defective single-strand break repair, translesion synthesis, and non-homologous end-joining effectors drive genomic instability in tumors with wildtype BRCA and BRCA-related genes. Importantly, we find that loss of these effectors promotes replication stress, therapy resistance, and increased primary carcinoma to brain metastasis. Conclusions: Our results have defined a new pan-cancer class of tumors characterized by replicative instability (RIN). RIN is defined by the accumulation of intra-chromosomal, gene-level gain and loss events at replication stress sensitive (RSS) genome sites. We find that RIN accelerates cancer progression by driving copy number alterations and transcriptional program rewiring that promote tumor evolution. Clinically, we find that RIN drives therapy resistance and distant metastases across multiple tumor types.

Abstract 011: Epigenetic Determinants Of Renin Cell Identity

Renin secreting cells are restricted in adult mammals within the walls of renal arterioles near the entrance to the glomeruli and are therefore known as juxtaglomerular (JG) cells. These JG cells are critical for survival through the maintenance of homeostasis via the release of the peptide hormone renin in response to changes in blood pressure. By performing independently paired scATAC-seq and scRNA-seq during mouse kidney development, we sought to identify epigenetic markers of renin cell identity. While we lack spatial information, we identified putative JG cells through the identification of cells enriched in canonical markers (Ren1 and Akr1b7) of JG cell identity using both expression and accessibility derived measures of gene activity. We constructed a pseudotime trajectory of cells that lead to the mature JG population and performed pairwise comparisons of cell populations to identify the genomic regions and transcription factors (TFs) contributing to JG cell identity. As JG cells form along this trajectory, significantly different (Log2FC>0.5 and FDR<0.1) regions of accessible chromatin define the JG cell population. Within these open regions, the MEF2 family of TF motifs are significantly enriched (log10Padj > 20). We further identify a specific region of accessible chromatin (chr1:133345385-133345885) unique to the initial population of JG cells located within a Ren1 super enhancer previously identified by our group. This region is co-accessible with several regions of open chromatin within the greater Ren1 gene region (correlation > 0.75) where we identify putative binding sites for Mef2b, 2c, and 2d at these co-accessible regions. As the mature renin-expressing cells further differentiate into terminally differentiated cell populations including pericytes and mesangial cells, we continue to see significant enrichment of the MEF2 TF family within the JG cell population compared to downstream populations (log10Padj > 646.6891). Overall, we have presented the first investigation and finding using single-cell -omics of the JG cell population and uncover the importance of the MEF2 family of TFs as significant drivers of JG cell formation and identity.

Single-cell transcriptome and accessible chromatin dynamics during endocrine pancreas development

Delineating gene regulatory networks that orchestrate cell-type specification is a continuing challenge for developmental biologists. Single-cell analyses offer opportunities to address these challenges and accelerate discovery of rare cell lineage relationships and mechanisms underlying hierarchical lineage decisions. Here, we describe the molecular analysis of mouse pancreatic endocrine cell differentiation using single-cell transcriptomics, chromatin accessibility assays coupled to genetic labeling, and cytometry-based cell purification. We uncover transcription factor networks that delineate β-, α-, and δ-cell lineages. Through genomic footprint analysis, we identify transcription factor-regulatory DNA interactions governing pancreatic cell development at unprecedented resolution. Our analysis suggests that the transcription factor Neurog3 may act as a pioneer transcription factor to specify the pancreatic endocrine lineage. These findings could improve protocols to generate replacement endocrine cells from renewable sources, like stem cells, for diabetes therapy.

GenomicDistributions: fast analysis of genomic intervals with Bioconductor

Background

Epigenome analysis relies on defined sets of genomic regions output by widely used assays such as ChIP-seq and ATAC-seq. Statistical analysis and visualization of genomic region sets is essential to answer biological questions in gene regulation. As the epigenomics community continues generating data, there will be an increasing need for software tools that can efficiently deal with more abundant and larger genomic region sets. Here, we introduce GenomicDistributions, an R package for fast and easy summarization and visualization of genomic region data.

Results

GenomicDistributions offers a broad selection of functions to calculate properties of genomic region sets, such as feature distances, genomic partition overlaps, and more. GenomicDistributions functions are meticulously optimized for best-in-class speed and generally outperform comparable functions in existing R packages. GenomicDistributions also offers plotting functions that produce editable ggplot objects. All GenomicDistributions functions follow a uniform naming scheme and can handle either single or multiple region set inputs.

Conclusions

GenomicDistributions offers a fast and scalable tool for exploratory genomic region set analysis and visualization. GenomicDistributions excels in user-friendliness, flexibility of outputs, breadth of functions, and computational performance. GenomicDistributions is available from Bioconductor (https://bioconductor.org/packages/release/bioc/html/GenomicDistributions.html).

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08467-y.

Implementation of a pharmacy-led virtual academic detailing program at the US Veterans Health Administration

DISCLAIMER

In an effort to expedite the publication of articles related to the COVID-19 pandemic, AJHP is posting these manuscripts online as soon as possible after acceptance. Accepted manuscripts have been peer-reviewed and copyedited, but are posted online before technical formatting and author proofing. These manuscripts are not the final version of record and will be replaced with the final article (formatted per AJHP style and proofed by the authors) at a later time.

PURPOSE

To provide a summary of the implementation of a virtual academic detailing pilot program at the US Department of Veterans Affairs (VA).

SUMMARY

In September 2018, VA Pharmacy Benefits Management implemented a virtual academic detailing ("e-Detailing") pilot program across three regional networks. Academic detailing involves multifaceted collaborative outreach delivered by trained healthcare clinicians to other clinicians using targeted educational interventions that improve clinical decision-making. Across VA, academic detailing programs are primarily staffed by specially trained clinical pharmacist specialists. Implementation began with an in-person meeting to train academic detailers on using the virtual academic detailing platform (VA Video Connect) and virtual soft skills, which was followed by regular facilitation meetings to address issues and share experiences. During e-Detailing program implementation, the coronavirus disease 2019 (COVID-19) emerged, prompting the US Department of Health and Human Services to declare a public health emergency. VA followed with restrictions on nonessential travel for all employees, thus hampering in-person academic detailing activities. Fortunately, e-Detailing provided an alternative channel for academic detailers across VA to continue delivering critical outreach to providers during the pandemic. Qualitative assessment of academic detailers' and providers' perceptions on e-Detailing highlighted the need for local leadership support for e-Detailing and telehealth, the efficiency of virtual compared to in-person visits, and potential time savings resulting from avoidance of long commutes.

CONCLUSION

The timing of e-Detailing implementation during the COVID-19 pandemic illustrates the need and potential for a virtual platform to deliver timely provider outreach.

Topology of synaptic connectivity constrains neuronal stimulus representation, predicting two complementary coding strategies

In motor-related brain regions, movement intention has been successfully decoded from in-vivo spike train by isolating a lower-dimension manifold that the high-dimensional spiking activity is constrained to. The mechanism enforcing this constraint remains unclear, although it has been hypothesized to be implemented by the connectivity of the sampled neurons. We test this idea and explore the interactions between local synaptic connectivity and its ability to encode information in a lower dimensional manifold through simulations of a detailed microcircuit model with realistic sources of noise. We confirm that even in isolation such a model can encode the identity of different stimuli in a lower-dimensional space. We then demonstrate that the reliability of the encoding depends on the connectivity between the sampled neurons by specifically sampling populations whose connectivity maximizes certain topological metrics. Finally, we developed an alternative method for determining stimulus identity from the activity of neurons by combining their spike trains with their recurrent connectivity. We found that this method performs better for sampled groups of neurons that perform worse under the classical approach, predicting the possibility of two separate encoding strategies in a single microcircuit.

An application of neighbourhoods in digraphs to the classification of binary dynamics

A binary state on a graph means an assignment of binary values to its vertices. A time dependent sequence of binary states is referred to as binary dynamics. We describe a method for the classification of binary dynamics of digraphs, using particular choices of closed neighbourhoods. Our motivation and application comes from neuroscience, where a directed graph is an abstraction of neurons and their connections, and where the simplification of large amounts of data is key to any computation. We present a topological/graph theoretic method for extracting information out of binary dynamics on a graph, based on a selection of a relatively small number of vertices and their neighbourhoods. We consider existing and introduce new real-valued functions on closed neighbourhoods, comparing them by their ability to accurately classify different binary dynamics. We describe a classification algorithm that uses two parameters and sets up a machine learning pipeline. We demonstrate the effectiveness of the method on simulated activity on a digital reconstruction of cortical tissue of a rat, and on a non-biological random graph with similar density.

PEPATAC: an optimized pipeline for ATAC-seq data analysis with serial alignments

As chromatin accessibility data from ATAC-seq experiments continues to expand, there is continuing need for standardized analysis pipelines. Here, we present PEPATAC, an ATAC-seq pipeline that is easily applied to ATAC-seq projects of any size, from one-off experiments to large-scale sequencing projects. PEPATAC leverages unique features of ATAC-seq data to optimize for speed and accuracy, and it provides several unique analytical approaches. Output includes convenient quality control plots, summary statistics, and a variety of generally useful data formats to set the groundwork for subsequent project-specific data analysis. Downstream analysis is simplified by a standard definition format, modularity of components, and metadata APIs in R and Python. It is restartable, fault-tolerant, and can be run on local hardware, using any cluster resource manager, or in provided Linux containers. We also demonstrate the advantage of aligning to the mitochondrial genome serially, which improves the accuracy of alignment statistics and quality control metrics. PEPATAC is a robust and portable first step for any ATAC-seq project. BSD2-licensed code and documentation are available at https://pepatac.databio.org.

Embeddings of genomic region sets capture rich biological associations in lower dimensions

MOTIVATION

Genomic region sets summarize functional genomics data and define locations of interest in the genome such as regulatory regions or transcription factor binding sites. The number of publicly available region sets has increased dramatically, leading to challenges in data analysis.

RESULTS

We propose a new method to represent genomic region sets as vectors, or embeddings, using an adapted word2vec approach. We compared our approach to two simpler methods based on interval unions or term frequency-inverse document frequency and evaluated the methods in three ways: First, by classifying the cell line, antibody, or tissue type of the region set; second, by assessing whether similarity among embeddings can reflect simulated random perturbations of genomic regions; and third, by testing robustness of the proposed representations to different signal thresholds for calling peaks. Our word2vec-based region set embeddings reduce dimensionality from more than a hundred thousand to 100 without significant loss in classification performance. The vector representation could identify cell line, antibody, and tissue type with over 90% accuracy. We also found that the vectors could quantitatively summarize simulated random perturbations to region sets and are more robust to subsampling the data derived from different peak calling thresholds. Our evaluations demonstrate that the vectors retain useful biological information in relatively lower-dimensional spaces. We propose that vector representation of region sets is a promising approach for efficient analysis of genomic region data.

AVAILABILITY

https://github.com/databio/regionset-embedding.

PEPPRO: quality control and processing of nascent RNA profiling data

Nascent RNA profiling is growing in popularity; however, there is no standard analysis pipeline to uniformly process the data and assess quality. Here, we introduce PEPPRO, a comprehensive, scalable workflow for GRO-seq, PRO-seq, and ChRO-seq data. PEPPRO produces uniformly processed output files for downstream analysis and assesses adapter abundance, RNA integrity, library complexity, nascent RNA purity, and run-on efficiency. PEPPRO is restartable and fault-tolerant, records copious logs, and provides a web-based project report. PEPPRO can be run locally or using a cluster, providing a portable first step for genomic nascent RNA analysis.

Virtual academic detailing (e-Detailing): A vital tool during the COVID-19 pandemic

As the coronavirus disease (COVID-19) pandemic continues its course in 2020, telehealth technology provides opportunities to connect patients and providers. Health policies have been amended to allow easy access to virtual health care, highlighting the field's dynamic ability to adapt to a public health crisis. Academic detailing, a peer-to-peer collaborative outreach designed to improve clinical decision-making, has traditionally relied on in-person encounters for effectiveness. A growth in the adoption of telehealth technology translates to increases in academic detailing reach for providers unable to meet with academic detailers in person. The U.S. Department of Veterans Affairs (VA) has used academic detailing to promote and reinforce evidence-based practices and has encouraged more virtual academic detailing (e-Detailing). Moreover, VA academic detailers are primarily clinical pharmacy specialists who provide clinical services and education and have made meaningful contributions to improving health care at VA. Amid the COVID-19 pandemic and physical isolation orders, VA academic detailers have continued to meet with providers to disseminate critical health care information in a timely fashion by using video-based telehealth. When working through the adoption of virtual technology for the delivery of medical care, providers may need time and nontraditional delivery of "evidence" before eliciting signals for change. Academic detailers are well suited for this role and can develop plans to help address provider discomfort surrounding the use of telehealth technology. By using e-Detailing as a method for both familiarizing and normalizing health professionals with video-based telehealth technology, pharmacists are uniquely poised to deliver consultation and direct-care services. Moreover, academic detailing pharmacists are ambassadors of change, serving an important role navigating the evolution of health care in response to emergent public health crises and helping define the norms of care delivery to follow.

Nervonic acid limits weight gain in a mouse model of diet-induced obesity

Lipid perturbations contribute to detrimental outcomes in obesity. We previously demonstrated that nervonic acid, a C24:1 ω-9 fatty acid, predominantly acylated to sphingolipids, including ceramides, are selectively reduced in a mouse model of obesity. It is currently unknown if deficiency of nervonic acid-sphingolipid metabolites contribute to complications of obesity. Mice were fed a standard diet, a high fat diet, or these diets supplemented isocalorically with nervonic acid. The primary objective was to determine if dietary nervonic acid content alters the metabolic phenotype in mice fed a high fat diet. Furthermore, we investigated if nervonic acid alters markers of impaired fatty acid oxidation in the liver. We observed that a nervonic acid-enriched isocaloric diet reduced weight gain and adiposity in mice fed a high fat diet. The nervonic acid enrichment led to increased C24:1-ceramides and improved several metabolic parameters including blood glucose levels, and insulin and glucose tolerance. Mechanistically, nervonic acid supplementation increased PPARα and PGC1α expression and improved the acylcarnitine profile in liver. These alterations indicate improved energy metabolism through increased β-oxidation of fatty acids. Taken together, increasing dietary nervonic acid improves metabolic parameters in mice fed a high fat diet. Strategies that prevent deficiency of, or restore, nervonic acid may represent an effective strategy to treat obesity and obesity-related complications.

Analytical Approaches for ATAC-seq Data Analysis

ATAC-seq, the assay for transposase-accessible chromatin using sequencing, is a quick and efficient approach to investigating the chromatin accessibility landscape. Investigating chromatin accessibility has broad utility for answering many biological questions, such as mapping nucleosomes, identifying transcription factor binding sites, and measuring differential activity of DNA regulatory elements. Because the ATAC-seq protocol is both simple and relatively inexpensive, there has been a rapid increase in the availability of chromatin accessibility data. Furthermore, advances in ATAC-seq protocols are rapidly extending its breadth to additional experimental conditions, cell types, and species. Accompanying the increase in data, there has also been an explosion of new tools and analytical approaches for analyzing it. Here, we explain the fundamentals of ATAC-seq data processing, summarize common analysis approaches, and review computational tools to provide recommendations for different research questions. This primer provides a starting point and a reference for analysis of ATAC-seq data. © 2020 Wiley Periodicals LLC.

1110 Characteristics Of Untreated Sleep Disturbance During Intensive Outpatient Treatment For Substance Use Disorders: Preliminary Results From A Longitudinal Study

Introduction

Previous studies have shown that sleep problems are commonly reported during treatment for substance use disorders (SUDs) and sleep complaints have been linked to subsequent relapse. However, most of these findings were in well-controlled clinical trials and may not generalize to the public. Little is known about the natural progression of sleep complaints during treatment in community clinics, the most common treatment approach for SUDs. The aim of this study is to longitudinally assess prevalence of clinically significant sleep disturbance at baseline and post-treatment in a community-based intensive outpatient (IOP) SUD treatment program using a multi-method approach with well-validated measures of sleep.

Methods

Adults beginning IOP SUD treatment completed the Pittsburgh Sleep Quality Index (PSQI), Insomnia Severity Index (ISI), Nightmare Disorder index (NDI), and one week of actigraphy and sleep diaries. Measures were repeated following treatment (approximately 5 weeks later).

Results

Preliminary analyses on 21 adults who have been enrolled thus far revealed 85.6% of participants experienced sleep disturbance (PSQI &gt; 5) at baseline. 28.5% of participants reached cutoff for moderate-to-severe insomnia symptoms (ISI &gt; 15) and 42.9% reported nightmares more than once per week. Sleep parameters taken from actigraphy and sleep diaries revealed mean sleep efficiency was 77.5% (TST M = 6.2 hours; TIB M = 7.9 hours). These variables did not improve from baseline to post-treatment. Further, most measures indicated a worsening of sleep, though this did not reach significance (all ps &gt; .05).

Conclusion

This preliminary data show a high prevalence of self-reported sleep complaints and objectively measured poor sleep efficiency that do not improve over the course of treatment. Data collection is ongoing and expected to at least double. More robust analyses, including differences between SUD type (e.g., cannabis vs. opioid) and relationship to relapse at post-treatment, will then be completed.

Support

K12DA031794

Refgenie: a reference genome resource manager

BACKGROUND

Reference genome assemblies are essential for high-throughput sequencing analysis projects. Typically, genome assemblies are stored on disk alongside related resources; e.g., many sequence aligners require the assembly to be indexed. The resulting indexes are broadly applicable for downstream analysis, so it makes sense to share them. However, there is no simple tool to do this.

RESULTS

Here, we introduce refgenie, a reference genome assembly asset manager. Refgenie makes it easier to organize, retrieve, and share genome analysis resources. In addition to genome indexes, refgenie can manage any files related to reference genomes, including sequences and annotation files. Refgenie includes a command line interface and a server application that provides a RESTful API, so it is useful for both tool development and analysis.

CONCLUSIONS

Refgenie streamlines sharing genome analysis resources among groups and across computing environments. Refgenie is available at https://refgenie.databio.org.

A whole canopy gas exchange system for the targeted manipulation of grapevine source-sink relations using sub-ambient CO2

BACKGROUND

Elucidating the effect of source-sink relations on berry composition is of interest for wine grape production as it represents a mechanistic link between yield, photosynthetic capacity and wine quality. However, the specific effects of carbohydrate supply on berry composition are difficult to study in isolation as leaf area or crop adjustments can also change fruit exposure, or lead to compensatory growth or photosynthetic responses. A new experimental system was therefore devised to slow berry sugar accumulation without changing canopy structure or yield. This consisted of six transparent 1.2 m3 chambers to enclose large pot-grown grapevines, and large soda-lime filled scrubbers that reduced carbon dioxide (CO2) concentration of day-time supply air by approximately 200 ppm below ambient.

RESULTS

In the first full scale test of the system, the chambers were installed on mature Shiraz grapevines for 14 days from the onset of berry sugar accumulation. Three chambers were run at sub-ambient CO2 for 10 days before returning to ambient. Canopy gas exchange, and juice hexose concentrations were determined. Net CO2 exchange was reduced from 65.2 to 30 g vine- 1 day- 1, or 54%, by the sub-ambient treatment. At the end of the 10 day period, total sugar concentration was reduced from 95 to 77 g L- 1 from an average starting value of 23 g L- 1, representing a 25% reduction. Scaling to a per vine basis, it was estimated that 223 g of berry sugars accumulated under ambient supply compared to 166 g under sub-ambient, an amount equivalent to 50 and 72% of total C assimilated.

CONCLUSIONS

Through supply of sub-ambient CO2 using whole canopy gas exchange chambers system, an effective method was developed for reducing photosynthesis and slowing the rate of berry sugar accumulation without modifying yield or leaf area. While in this case developed for further investigations of grape and wine composition, the system has broader applications for the manipulation and of study of grapevine source-sink relations.

Grape Berry Flavonoid Responses to High Bunch Temperatures Post Véraison: Effect of Intensity and Duration of Exposure

Climate models predict an increase in the frequency and duration of heatwaves with an increase in intensity already strongly evident worldwide. The aim of this work was to evaluate the effect of two heatwave-related parameters (intensity and duration) during berry ripening and identify a threshold for berry survival and flavonoid accumulation. A Doehlert experimental design was used to test three temperature intensities (maxima of 35, 46, and 54 °C) and five durations (3 to 39 h), with treatments applied at the bunch level shortly after véraison. Berry skin and seeds were analysed by liquid chromatography-triple quadrupole-mass spectrometry (LC-QqQ-MS) for flavonoids (flavonols, anthocyanins, free flavan-3-ols, and tannins). Berries exposed to 46 °C showed little difference compared to 35 °C. However, berries reaching temperatures around 54 °C were completely desiccated, and all flavonoids were significantly decreased except for skin flavonols on a per berry basis and seed tannins in most cases. Some compounds, such as dihydroxylated flavonoids and galloylated flavan-3-ols (free and polymerised), were in higher proportion in damaged berries suggesting they were less degraded or more synthesised upon heating. Overall, irreversible berry damages and substantial compositional changes were observed and the berry survival threshold was estimated at around 50-53 °C for mid-ripe Shiraz berries, regardless of the duration of exposure.

Grape berry flavonoids: a review of their biochemical responses to high and extreme high temperatures

Climate change scenarios predict an increase in average temperatures and in the frequency, intensity, and length of extreme temperature events in many wine regions around the world. In already warm and hot regions, such changes may compromise grape growing and the production of high quality wine as high temperature has been found to affect berry composition critically. Most recent studies focusing on the sole effect of temperature, separated from light and water, on grape berry composition found that high temperature affects a wide range of metabolites, and in particular flavonoids-key compounds for berry and wine quality. A decrease in total anthocyanins is reported in most cases, and appears to be directly associated with high temperature. Changes in anthocyanin composition, and flavonol and proanthocyanidin responses are however less consistent, and reflect the complexity of the underlying biosynthetic pathways and diversity of experimental treatments that have been used in these studies. This review examines the impact of high temperature on the biosynthesis, accumulation, and degradation of flavonoids, and attempts to reconcile the diversity of responses in relation to the latest understanding of flavonoid chemistry and molecular regulation.

Vitis vinifera berry metabolic composition during maturation: Implications of defoliation

Leaves are an important contributor toward berry sugar and nitrogen (N) accumulation, and leaf area, therefore, affects fruit composition during grapevine (Vitis vinifera) berry ripening. The aim of this study was to investigate the impact of leaf presence on key berry quality attributes in conjunction with the accumulation of primary berry metabolites. Shortly after the start of véraison (berry ripening), potted grapevines were defoliated (total defoliation and 25% of the control), and the accumulation of berry soluble solids, N and anthocyanins were compared to that of a full leaf area control. An untargeted approach was undertaken to measure the content in primary metabolites by gas chromatography/mass spectrometry. Partial and full defoliation resulted in reduced berry sugar and anthocyanin accumulation, while total berry N content was unaffected. The juice yeast assimilable N (YAN), however, increased upon partial and full defoliation. Remobilized carbohydrate reserves allowed accumulation of the major berry sugars during the absence of leaf photoassimilation. Berry anthocyanin biosynthesis was strongly inhibited by defoliation, which could relate to the carbon (C) source limitation and/or increased bunch exposure. Arginine accumulation, likely resulting from reserve translocation, contributed to increased YAN upon defoliation. Furthermore, assessing the implications on various products of the shikimate pathway suggests the C flux through this pathway to be largely affected by leaf source limitation during fruit maturation. This study provides a novel investigation of impacts of leaf C and N source presence during berry maturation, on the development of key berry quality parameters as underlined by alterations in primary metabolism.

Reducing Benzodiazepine Prescribing in Older Veterans: A Direct-to-Consumer Educational Brochure

This quality improvement project used an educational brochure to help older veterans reduce their benzodiazepine use.

Circadian regulation of grapevine root and shoot growth and their modulation by photoperiod and temperature

Some plant species demonstrate a pronounced 24 h rhythm in fine root growth but the endogenous and exogenous factors that regulate these diel cycles are unclear. Photoperiod and temperature are known to interact with diel patterns in shoot growth but it is uncertain how these environmental factors are interrelated with below-ground growth. In this particular study, the fine root system of two grapevine species was monitored over a period of ten days with a high resolution scanner, under constant soil moisture and three different photoperiod regimes. Pronounced diel rhythms in shoot and root growth rates were apparent under a fixed 14 h photoperiod. Maximal root growth rate occurred 1-2 h prior to- and until 2 h after the onset of darkness. Subsequently, during the latter part of the dark period, root growth rate decreased and reached minimal values at the onset of the light period. Relative to 22 °C, exposure to a 30 °C air and soil temperature halved root growth but stimulated shoot growth. Notably, the shoot extension rate peak shifted from late afternoon to midnight at this higher temperature zone. When plants were exposed to a delayed photoperiod or progressively shortening photoperiod, the diel changes in root growth rate followed the same pattern as in the fixed photoperiod, regardless of whether the plant was in light or dark. This suggests that light was not the predominant trigger for stimulating root elongation. Conversely, shoot growth rates were not fixed to a clock, with minimum growth consistently at the completion of the dark period regardless of the time of day. In summary, fine root growth of grapevines was found to have a pronounced diel pattern and an endogenous circadian clock appears to orchestrate this rhythm. Soil temperature modified the amplitude of this pattern, but we argue here that, as evidenced from exhausted starch reserves within root tips by early morning, carbon supply from photosynthesis is also required to maintain maximum root growth.

Learning and memory is modulated by cannabidiol when administered during trace fear-conditioning

Cannabidiol (CBD) is thought to have therapeutic potential for treating psychiatric conditions that affect cognitive aspects of learning and memory, including anxiety and post-traumatic stress disorder (PTSD). Studies have shown that CBD enhances extinction of fear memory when given after conditioning. This led us to hypothesize that CBD, if administered prior to fear conditioning, might modulate cognitive learning and memory processes in additional ways that would further guide its potential use for treating PTSD. Therefore, we designed a study to investigate effects of CBD on fear learning and memory when administered to mice prior to administering a trace fear conditioning protocol which imposes cognitive demands on the learning and memory process. We show that CBD-treated animals had increased levels of freezing during conditioning, enhanced generalized fear, inhibited cue-dependent memory extinction, slightly increased levels of freezing during an auditory-cued memory test, and increased contextual fear memory. Because synaptic plasticity is the fundamental mechanism of learning and memory, we also evaluated the impact of CBD on trace conditioning-dependent dendritic spine plasticity which occurred in the dorsal lateral amygdala and CA1 region of the ventral hippocampus. We showed that CBD mildly enhanced spine densities independent of conditioning, and inhibited conditioning-dependent spine increases in the hippocampi, but not the amygdala of fear conditioned animals. Overall, the memory-modulating effects of a single pre-conditioning dose of CBD, which we show here, demonstrate the need to more fully characterize its basic effects on memory, suggest caution when using it clinically as an anxiolytic, and point to a need for more research into its potential as a therapeutic for treating memory-loss disorders.

Vitis vinifera root and leaf metabolic composition during fruit maturation: implications of defoliation

Grapevine (Vitis vinifera) roots and leaves represent major carbohydrate and nitrogen (N) sources, either as recent assimilates, or mobilized from labile or storage pools. This study examined the response of root and leaf primary metabolism following defoliation treatments applied to fruiting vines during ripening. The objective was to link alterations in root and leaf metabolism to carbohydrate and N source functioning under conditions of increased fruit sink demand. Potted grapevine leaf area was adjusted near the start of véraison to 25 primary leaves per vine compared to 100 leaves for the control. An additional group of vines were completely defoliated. Fruit sugar and N content development was assessed, and root and leaf starch and N concentrations determined. An untargeted GC/MS approach was undertaken to evaluate root and leaf primary metabolite concentrations. Partial and full defoliation increased root carbohydrate source contribution towards berry sugar accumulation, evident through starch remobilization. Furthermore, root myo-inositol metabolism played a distinct role during carbohydrate remobilization. Full defoliation induced shikimate pathway derived aromatic amino acid accumulation in roots, while arginine accumulated after full and partial defoliation. Likewise, various leaf amino acids accumulated after partial defoliation. These results suggest elevated root and leaf amino N source activity when leaf N availability is restricted during fruit ripening. Overall, this study provides novel information regarding the impact of leaf source restriction, on metabolic compositions of major carbohydrate and N sources during berry maturation. These results enhance the understanding of source organ carbon and N metabolism during fruit maturation.

Use of Allogeneic Bone Marrow Labeled with Neomycin Resistance Gene to Examine Bone Marrow-Derived Chimerism in Experimental Organ Transplantation

Posttransplant infusion of viable donor bone marrow cells (DBMC) has been shown in our previous studies to promote acceptance of incompatible kidney allografts in rhesus monkeys after treatment with polyclonal antithymocyte globulin to deplete peripheral T-lymphocytes. In this nonhuman primate model, the infusion of the DBMC is requisite for the induction of functional graft tolerance and specific MLR and CTLp unresponsiveness, although the relevant role and fate of bone marrow-derived chimeric cells is uncertain. Standard immunological and molecular techniques applied to this monkey model are unable to differentiate between chimeric cells derived from the infused DBMC and those derived from allograft-borne passenger leukocyte emigrants. To distinguish chimerism due to infused DBMC, we transduced DBMC with a functional neomycin resistance gene (Neor) using the retroviral vector pHSG-Neo. Neor-Mransduced BMC were infused into recipients approximately 2 wk after kidney transplantation and treatment with rabbit antithymocyte globulin. No maintenance immunosuppressive drugs were given. Genomic DNA isolated from peripheral blood leukocytes was used to monitor the presence of Neor-positive cells. Tissue samples obtained at necropsy also were assessed for Neor-positive chimeric cells. The presence of DBMC-derived chimerism was assessed by polymerase chain reaction using Neor sequence-specific primers (PCR-SSP). Chimerism was detectable in recipient tissues at various times for up to 6 mo after DBMC infusion. These studies using gene transduction methodology indicate that a stable genetic marker can provide capability to examine DBMC-derived chimerism for prolonged periods in a nonhuman primate model. This approach should facilitate future studies in preclinical models to study the role and type of chimeric cell lineages in relation to functional allograft tolerance.

Socio-Political Bases of Senior Citizen Mobilization

The analyses deal with four areas of issue salience that were designated by the elderly. Health issues and in-home services spell this out. Beliefs regarding the areas of salience appeared to be constrained rather than fragmented. And social characteristics of the respondents did not engender cleavages in the four areas of issue salience. Implications of this research are briefly noted.

New Treatments for Hepatitis C

Currently available direct-acting antiviral therapies have improved sustained virologic response, and more new treatment options are in the pipeline.

First Report of Bacterial Leaf Blight on Mustard Greens (Brassica juncea) Caused by Pseudomonas cannabina pv. alisalensis in Mississippi

In 2010, a brassica leafy greens grower in Sunflower County, MS, observed scattered outbreaks of a leaf blight on mustard greens (Brassica juncea) in a 180-ha field. A severe outbreak of leaf blight occurred on mustard greens and turnip greens (B. rapa) in the same field in 2011 with more than 80 ha affected. The affected field, established in 2010, had no prior history of being cropped to brassica leafy greens. Symptoms appeared on the 6-week-old transplants as brown to tan necrotic spots with faint chlorotic borders and associated water-soaking. Lesions varied from 4 mm to 3 cm in diameter and often coalesced to cover >90% of older leaves. Whole plants of the mustard greens cv. Florida Broadleaf were collected in 2011 from the symptomatic field. Leaves were surface-disinfested with 0.5% NaOCl for 5 min, rinsed twice in sterilized distilled water [(sd)H₂O], macerated in sdH₂O, then streaked onto nutrient agar (NA), pseudomonas agar F (PAF), and potato dextrose agar (PDA). Little or no bacterial growth was observed on PDA, while on NA and PAF the majority of bacterial growth appeared to be a single colony type. All strains collected (25 total, one per plant) were gram-negative and fluoresced blue-green under UV light after 48 h at 28°C on PAF. All 25 strains were identified as belonging to Pseudomonas group 1a using Lelliot's determinative assay (2). Ten of the 25 strains were tested for pathogenicity on Florida Broadleaf, and turnip greens cv. Alamo. Bacteria were grown on PAF for 48 h, and a bacterial suspension was prepared and adjusted to an optical density of 0.1 at 600 nm. Three-week-old plants (three plants per cultivar) were sprayed with the appropriate bacterial suspension to runoff, placed at 100% relative humidity for 48 h, and then put in a growth chamber at 28°C with a 16-h diurnal light cycle for 14 days. Additionally, three plants each of Florida Broadleaf and Alamo were either sprayed with H₂O or inoculated with Pseudomonas cannabina pv. alisalensis (Pca) pathotype strain BS91 (1). All 10 strains, as well as the Pca pathotype strain, were pathogenic on both cultivars and caused symptoms similar to those observed in the field. Symptoms were not observed on H₂O-sprayed plants. Comparative rep-PCR analysis using the BOXA1R primer showed the 10 strains had identical DNA-banding profiles and were identical to that of Pca BS91 (5). Five strains tested using a Pca-specific, 'light-tagged' reporter bacteriophage gave a strong positive reaction, while a negative control strain, P. syringae pv. maculicola, gave no signal (3). From these tests, the isolated bacteria were determined to be Pca. Bacteria re-isolated on PAF from the inoculated Florida Broadleaf plants had identical rep-PCR profiles with those of the strains used for inoculations. Over the past 10 years, Pca has been found in numerous states in the United States, as well as in Europe, Australia, and Japan (4). As brassica leafy greens production expands to new fields and new states, leaf blight caused by Pca appears to become a problem rapidly. Since resistant cultivars and highly effective bactericides are lacking, growers are extremely concerned about the rapid spread of this disease into existing and new brassica leafy greens regions. References: (1) N. A. Cintas et al. Plant Dis. 86:992, 2002. (2) R. Lelliott. J. Appl. Bacteriol. 29:470, 1066. (3) D. Schofield et al. Appl. Environ. Microbiol. 78:3592, 2012. (4) F. Takahashi et al. J. Gen. Plant Pathol. 79:260, 2013. (5) J. Versalovic et al. Methods Mol. Cell Biol 5:25, 1994.

A pharmacist-managed telemedicine clinic for hepatitis C care: a descriptive analysis

Summary

We established a pharmacist-led telemedicine clinic to manage patients with chronic hepatitis C infection. The clinic used individual pharmacist-to-patient consultations. There was also a group hepatitis C patient education class. The hepatitis C telemedicine service began in February 2011 and was available at three remote sites (Santa Maria, Bakersfield and East Los Angeles) from the main site in West Los Angeles. A total of 96 patients were seen through telemedicine in the first nine months. A patient satisfaction survey was conducted at the end of 2011 and 18 questionnaires were returned. In comparison with visits to the clinic in West Los Angeles, all patients were at least equally satisfied with telemedicine and there were no patients who were less satisfied with telemedicine. Telemedicine reduced the travelling distance and time it took for patients to attend their clinic appointment. 82% of patients preferred their future hepatitis C clinic visits to be conducted via telemedicine and 78% would prefer any future clinic visit for any disease state management to be conducted via telemedicine. The use of telemedicine increased the opportunities for patients living in remote areas to receive care for hepatitis C management.

Who pays for the health benefits of exclusive breastfeeding? An analysis of maternal time costs

BACKGROUND

The benefits of exclusive breastfeeding, including public health cost savings, are widely recognized, but breastfeeding requires maternal time investments.

OBJECTIVE

This study investigates the time taken to exclusively breastfeed at 6 months compared with not exclusively breastfeeding.

METHODS

Time use data were examined from an Australian survey of new mothers conducted during 2005-2006. Data from 139 mothers with infants age 6 months were analyzed using chi-square tests of independence to examine socioeconomic and demographic characteristics and 2-sided t tests to compare average weekly hours spent on milk feeding, feeding solids, preparing feeds, and the total of these. The comparison was of exclusively breastfeeding mothers with other mothers. We also compared exclusively breastfeeding with partially breastfeeding and formula feeding mothers using a 1-way between-groups analysis of variance (ANOVA).

RESULTS

The exclusively breastfeeding (vs other) mothers spent 7 hours extra weekly on milk feeding their infants but 2 hours less feeding solids. These differences were statistically significant. ANOVA revealed significant differences between exclusively breastfeeding mothers, breastfeeding mothers who had introduced solids, and mothers who fed any formula, in time spent feeding milk, and solids, and preparing feeds.

CONCLUSION

Exclusive breastfeeding is time intensive, which is economically costly to women. This may contribute to premature weaning for women who are time-stressed, lack household help from family, or cannot afford paid help. Gaining public health benefits of exclusive breastfeeding requires strategies to share maternal lactation costs more widely, such as additional help with housework or caring for children, enhanced leave, and workplace lactation breaks and suitable child care.

"Lost milk?": Counting the economic value of breast milk in gross domestic product

BACKGROUND

The contribution of breastfeeding and mothers milk to the economy is invisible in economic statistics.

OBJECTIVE

This article demonstrates how the economic value of human milk production can be included in economic statistics such as gross domestic product (GDP) and provides estimates for Australia, the United States, and Norway.

METHODS

The contribution of human milk and lactation to GDP in these countries is estimated using United Nations (System of National Accounting) guidelines and conventional economic valuation approaches to measuring production in GDP.

RESULTS

In Australia, current human milk production levels exceed $3 billion annually. The United States has the potential to produce human milk worth more than US$110 billion a year, but currently nearly two thirds of this value is lost due to premature weaning. In Norway, production valued at US$907 million annually is 60% of its potential value.

CONCLUSIONS

The potential loss of economic value from not protecting women's lactation and milk production from competing market pressures is large. Failure to account for mothers' milk production in GDP and other economic data has important consequences for public policy. The invisibility of human milk reduces the perceived importance of programs and regulations that protect and support women to breastfeed. The value of human milk can be measured using accepted international guidelines for calculating national income and production. It is quantitatively nontrivial and should be counted in GDP.

Expression of Bacterial Blight Resistance in Brassica Leafy Greens Under Field Conditions and Inheritance of Resistance in a Brassica juncea Source

Brassica leafy greens are one of the most economically important vegetable commodity groups grown in the southeastern United States, and more than 28,000 metric tons of these crops are harvested in the United States annually. Collard and kale (Brassica oleracea Acephala group), mustard green (B. juncea), and turnip green (B. rapa) are the most commonly planted members of the brassica leafy greens group. In the last 10 years, numerous occurrences of bacterial blight on these leafy vegetables have been reported in several states. One of the pathogens responsible for this blight is designated Pseudomonas cannabina pv. alisalensis. Two B. rapa (G30710 and G30499) and two B. juncea (PI418956 and G30988) plant introductions (PIs) that exhibited moderate to high levels of resistance to this pathogen in greenhouse studies were tested for field resistance in comparison with eight commercial cultivar representatives of turnip green, mustard green, collard, and kale. The two B. juncea PIs and one of the B. rapa PIs (G30499) were found to have significantly less disease than all tested cultivars except 'Southern Curled Giant' mustard green (B. juncea) and 'Blue Knight' kale (B. oleracea). Inheritance of resistance studies performed with populations derived from the resistant G30988 and two susceptible PIs provided some evidence that resistance may be controlled by a single recessive gene.

Lack of association between asymmetric dimethylarginine and in vivo microvascular and macrovascular endothelial function in patients with rheumatoid arthritis

OBJECTIVES

The aim of the present study was to investigate if assymetric dimethylarginine (ADMA) is increased in patients with rheumatoid arthritis (RA) compared to healthy controls and to examine associations between ADMA, RA disease activity and in vivo assessments of microvascular and macrovascular endothelial function.

METHODS

Sixty-seven RA patients (age [mean ± standard deviation]: 56 ± 12 years, disease duration median [25th-75th percentile]: 8 [3-15] years, 48 women) and 29 healthy controls (age [mean ± standard deviation]: 42 ± 12, 21 women) underwent assessments of microvascular endothelial function (Laser Doppler imaging with iontophoresis of acetylcholine and sodium-nitroprusside), and macrovascular endothelial function (flow-mediated dilatation and glyceryl-trinitrate-mediated dilatation) as well as arterial stiffness. ADMA levels were measured in contemporary specimens using an immunoassay ELISA kit.

RESULTS

ADMA levels were significantly higher (p=0.004) in RA patients compared with healthy controls after adjustment for age (difference=0.088, 95% confidence interval 0.029-0.147). ADMA levels did not correlate with demographic or disease characteristics. No correlation was found between ADMA and microvascular and macrovascular endothelial function or with arterial stiffness.

CONCLUSIONS

ADMA levels are increased in patients with RA but there was no significant correlation with in vivo assessments of endothelial function. Further studies are needed to unfold the pathophysiological role of nitric oxide/ADMA pathway derangement in endothelial dysfunction and cardiovascular risk in RA.

Evaluation of human immunodeficiency virus and hepatitis C telemedicine clinics

BACKGROUND

Geographical barriers to subspecialty care may prevent optimal care of patients living in rural areas. We assess the impact of human immunodeficiency virus (HIV) and hepatitis C telemedicine consultation on patient-oriented outcomes in a rural Veterans Affairs population.

METHODS

This was a pre- and post-intervention study comparing telemedicine with in-person subspecialty clinic visits for HIV and hepatitis C. Eligible patients resided in 2 rural catchment areas. The primary binary outcome was clinic completion. We estimated a logistic regression model with patient-level fixed effects. This approach controls for the clustering of visits by patient, uses each patient's in-person clinic experience as an internal control group, and eliminates confounding by person-level factors. We also surveyed patients to assess satisfaction and patient-perceived reductions in health visit-related time.

RESULTS

There were 43 patients who accounted for 94 telemedicine visits and 128 in-person visits. Clinic completion rates were higher for telemedicine (76%) than for in-person visits (61%). In regression analyses, telemedicine was strongly predictive of clinic completion (OR 2.2; 95% confidence interval [CI]: 1.0-4.7). The adjusted effect of telemedicine on clinic completion rate was 13% (95% CI: 12-13). Of the 30 patients (70%) who completed the survey, more than 95% rated telemedicine at the highest level of satisfaction and preferred telemedicine to in-person clinic visits. Patients reported a significant reduction in health visit-related time (median 340 minutes, interquartile range 250-440), mostly due to decreased travel time.

CONCLUSIONS

HIV and hepatitis C telemedicine clinics are associated with improved access, high patient satisfaction, and reduction in health visit-related time.

Soil temperature moderates grapevine carbohydrate reserves after bud break and conditions fruit set responses to photoassimilatory stress

In cultivated grapevines (Vitis vinifera L.), suboptimal photoassimilatory conditions during flowering can lead to inflorescence necrosis and shedding of flowers and young ovaries and, consequently, poor fruit set. However, before this study it was not known whether carbohydrate reserves augment fruit set when concurrent photoassimilation is limited. Carbohydrate reserves are most abundant in grapevine roots and soil temperature moderates their mobilisation. Accordingly, we grew potted Chardonnay grapevines in soil at 15°C (cool) or 26°C (warm) from bud break to the onset of flowering to manipulate root carbohydrate reserve status. Then to induce photoassimilatory responses we subjected the plants to low (94µmolmol-1) CO2 or ambient (336µmolmol-1) CO2 atmospheres during fruit setting. Analyses of photoassimilation and biomass and carbohydrate reserve distribution confirmed that fruit set was limited by concurrent photoassimilation. Furthermore, the availability of current photoassimilates for inflorescence development and fruit set was conditioned by the simultaneous demands for shoot and root growth, as well as the restoration of root carbohydrate reserves. Results indicate that great seasonal variability in grapevine fruit set is a likely response of cultivated grapevines to photoassimilatory stresses, such as shading, defoliation and air temperature and to variations in carbohydrate reserve status before flowering.

The characterization of twenty sequenced human genomes

We present the analysis of twenty human genomes to evaluate the prospects for identifying rare functional variants that contribute to a phenotype of interest. We sequenced at high coverage ten “case” genomes from individuals with severe hemophilia A and ten “control” genomes. We summarize the number of genetic variants emerging from a study of this magnitude, and provide a proof of concept for the identification of rare and highly-penetrant functional variants by confirming that the cause of hemophilia A is easily recognizable in this data set. We also show that the number of novel single nucleotide variants (SNVs) discovered per genome seems to stabilize at about 144,000 new variants per genome, after the first 15 individuals have been sequenced. Finally, we find that, on average, each genome carries 165 homozygous protein-truncating or stop loss variants in genes representing a diverse set of pathways.

We report here the nearly complete genomic sequence of 20 different individuals, determined using “next-generation” sequencing technologies. We use these data to characterize the type of genetic variation carried by humans in a sample of this size, which is to our knowledge the largest set of unrelated genomic sequences that have been reported. We summarize different categories of variation in each genome, and in total across all 20 of the genomes, finding a surprising number of variants predicted to reduce or remove the proteins encoded by many different genes. This work provides important fundamental information about the scope of human genetic variation, and suggests ways to further explore the relationship between these genetic variants and human disease.

Whole-genome sequencing of a single proband together with linkage analysis identifies a Mendelian disease gene

Although more than 2,400 genes have been shown to contain variants that cause Mendelian disease, there are still several thousand such diseases yet to be molecularly defined. The ability of new whole-genome sequencing technologies to rapidly indentify most of the genetic variants in any given genome opens an exciting opportunity to identify these disease genes. Here we sequenced the whole genome of a single patient with the dominant Mendelian disease, metachondromatosis (OMIM 156250), and used partial linkage data from her small family to focus our search for the responsible variant. In the proband, we identified an 11 bp deletion in exon four of PTPN11, which alters frame, results in premature translation termination, and co-segregates with the phenotype. In a second metachondromatosis family, we confirmed our result by identifying a nonsense mutation in exon 4 of PTPN11 that also co-segregates with the phenotype. Sequencing PTPN11 exon 4 in 469 controls showed no such protein truncating variants, supporting the pathogenicity of these two mutations. This combination of a new technology and a classical genetic approach provides a powerful strategy to discover the genes responsible for unexplained Mendelian disorders.

Screening the human exome: a comparison of whole genome and whole transcriptome sequencing

Background

There is considerable interest in the development of methods to efficiently identify all coding variants present in large sample sets of humans. There are three approaches possible: whole-genome sequencing, whole-exome sequencing using exon capture methods, and RNA-Seq. While whole-genome sequencing is the most complete, it remains sufficiently expensive that cost effective alternatives are important.

Results

Here we provide a systematic exploration of how well RNA-Seq can identify human coding variants by comparing variants identified through high coverage whole-genome sequencing to those identified by high coverage RNA-Seq in the same individual. This comparison allowed us to directly evaluate the sensitivity and specificity of RNA-Seq in identifying coding variants, and to evaluate how key parameters such as the degree of coverage and the expression levels of genes interact to influence performance. We find that although only 40% of exonic variants identified by whole genome sequencing were captured using RNA-Seq; this number rose to 81% when concentrating on genes known to be well-expressed in the source tissue. We also find that a high false positive rate can be problematic when working with RNA-Seq data, especially at higher levels of coverage.

Conclusions

We conclude that as long as a tissue relevant to the trait under study is available and suitable quality control screens are implemented, RNA-Seq is a fast and inexpensive alternative approach for finding coding variants in genes with sufficiently high expression levels.

First Report of Bacterial Leaf Blight on Broccoli and Cabbage Caused by Pseudomonas syringae pv. alisalensis in South Carolina

In May of 2009, leaf spot and leaf blight symptoms were observed on broccoli (Brassica oleracea var. italica) and cabbage (B. oleracea var. capitata) on several farms in Lexington County, the major brassica-growing region of South Carolina. Affected areas ranged from scattered disease foci within fields to entire fields. Initial infection symptoms on leaves of both crops included circular and irregular-shaped necrotic lesions that were 3 to 10 mm in diameter, often with yellow halos and water soaking. As the disease progressed, the lesions tended to coalesce into a general blight of the entire leaf. Diseased leaves from both broccoli and cabbage were collected from each of four fields at different locations in the county. Leaves were surface disinfested, macerated in sterile distilled water, then aliquots of the suspension were spread on King's medium B (KB) agar. All samples produced large numbers of bacterial colonies that fluoresced blue under UV light after 24 h of growth. In total, 23 isolates (13 from broccoli and 10 from cabbage) were collected. These isolates were gram negative, levan production positive, oxidase negative, pectolytic activity negative, arginine dihydrolase negative, and produced a hypersensitive response on tobacco, thus placing them in the Pseudomonas syringae LOPAT group (2). Two broccoli and two cabbage isolates were selected at random and tested for pathogenicity to cabbage cv. Early Jersey Wakefield, broccoli cv. Decicco, turnip cv. Topper, broccoli raab cv. Spring, collard cv. Hi-Crop, and oat cv. Montezuma in greenhouse tests. Bacteria were grown on KB agar for 24 h and a bacterial suspension was prepared and adjusted to an optical density of 0.1 at 600 nm. Three-week-old plants were spray inoculated to runoff and held at 100% relative humidity for 12 h after inoculation, prior to return to the greenhouse bench (4). P. syringae pv. maculicola strain F18 (4) and the pathotype strain of P. syringae pv. alisalensis BS91 were included as controls, along with a water-inoculated negative control. Plants were evaluated at 14 days postinoculation. The four unknown bacterial isolates and BS91 were pathogenic on all brassica plants tested, as well as on oat. In contrast, the P. syringae pv. maculicola strain F18 was not pathogenic on broccoli raab or oat. Symptoms produced by all isolates and strains tested were similar to those observed in the field. No symptoms were observed on water-inoculated plants. Comparative repetitive sequence-based (rep)-PCR DNA analysis using the BOXA1R primer (3) resulted in a DNA banding pattern of each of the isolates from the South Carolina fields (23 isolates), as well as those reisolated from inoculated plants, that was identical to P. syringae pv. alisalensis BS91 and differed from the P. syringae pv. maculicola F18 strain. On the basis of the rep-PCR assays and the differential host range (1), the current disease outbreak on broccoli and cabbage in South Carolina is caused by the bacterium P. syringae pv. alisalensis. Broccoli is a relatively new, albeit rapidly expanding, production vegetable in South Carolina; this disease may represent a limiting factor to future production. References: (1) N. A. Cintas et al. Plant Dis. 86:992, 2002. (2) R. A. Lelliott et al. J. Appl. Bacteriol. 29:470, 1966. (3) J. Versalovic et al. Methods Mol. Cell. Biol. 5:25, 1994. (4) Y. F. Zhao et al. Plant Dis. 84:1015, 2000.

Common genetic variation and the control of HIV-1 in humans

To extend the understanding of host genetic determinants of HIV-1 control, we performed a genome-wide association study in a cohort of 2,554 infected Caucasian subjects. The study was powered to detect common genetic variants explaining down to 1.3% of the variability in viral load at set point. We provide overwhelming confirmation of three associations previously reported in a genome-wide study and show further independent effects of both common and rare variants in the Major Histocompatibility Complex region (MHC). We also examined the polymorphisms reported in previous candidate gene studies and fail to support a role for any variant outside of the MHC or the chemokine receptor cluster on chromosome 3. In addition, we evaluated functional variants, copy-number polymorphisms, epistatic interactions, and biological pathways. This study thus represents a comprehensive assessment of common human genetic variation in HIV-1 control in Caucasians.

What predicts obesity in patients with rheumatoid arthritis? An investigation of the interactions between lifestyle and inflammation

OBJECTIVE

To assess whether physical activity, diet or inflammation is a more important determinant of body mass index (BMI) and body fat (BF) in patients with rheumatoid arthritis (RA).

METHODS

A total of 150 RA patients (102 female) were assessed for BMI and BF. Their habitual physical activity was assessed with the international physical activity questionnaire (IPAQ) and their energy intake with a 3-day food diary. Pro-inflammatory cytokines (interleukins, IL-1 and IL-6, and tumor necrosis factor-alpha), erythrocyte sedimentation rate, C-reactive protein, disease activity score-28 and physical function (Health Assessment Questionnaire-HAQ) were also measured.

RESULTS

BMI correlated inversely with IPAQ (r=-0.511, P=0.000) and positively with energy intake (r=0.331, P=0.016) and HAQ (r=0.133, P=0.042). BF correlated inversely with IPAQ (r=-0.575, P=0.000) and positively with HAQ (r=0.201, P=0.037). Normal weight patients were more physically active compared with those who were either overweight (P=0.006) or obese (P=0.000). Underweight patients consumed significantly fewer calories compared with other patients (P<0.05 in all cases). Cytokines or HAQ did not differ between weight groups. IPAQ was the sole predictor of obesity, whereas energy intake was the sole predictor of underweight.

CONCLUSIONS

Inflammation does not seem to influence BMI and BF in RA. As in the general population, high levels of habitual physical activity associate with low BMI and BF in RA. Energy intake is a major determinant of being underweight in those who consume fewer calories. Further research is needed to investigate the suitability of exercise and diet modalities, and their effects on the body composition of RA patients.