Using single‐plant‐omics in the field to link maize genes to functions and phenotypes

Most of our current knowledge on plant molecular biology is based on experiments in controlled laboratory environments. However, translating this knowledge from the laboratory to the field is often not straightforward, in part because field growth conditions are very different from laboratory conditions. Here, we test a new experimental design to unravel the molecular wiring of plants and study gene-phenotype relationships directly in the field. We molecularly profiled a set of individual maize plants of the same inbred background grown in the same field and used the resulting data to predict the phenotypes of individual plants and the function of maize genes. We show that the field transcriptomes of individual plants contain as much information on maize gene function as traditional laboratory-generated transcriptomes of pooled plant samples subject to controlled perturbations. Moreover, we show that field-generated transcriptome and metabolome data can be used to quantitatively predict individual plant phenotypes. Our results show that profiling individual plants in the field is a promising experimental design that could help narrow the lab-field gap

Rhodococcus equi Infection after Alemtuzumab Therapy for T-cell Prolymphocytic Leukemia

Rhodococcus equi, mainly known from veterinary medicine as a pathogen in domestic animals, can also cause infections in immunocompromised humans, especially in those with defects in cellular immunity. Alemtuzumab, an anti-CD52 monoclonal antibody, causes lymphocytopenia by eliminating CD52-positive cells. We report a patient in whom Rhodococcus equi infection developed after alemtuzumab therapy

Comparison of Changes in Bone Density and Turnover with Abacavir-Lamivudine versus Tenofovir-Emtricitabine in HIV-Infected Adults: 48-Week Results from the ASSERT Study

Background. Abacavir-lamivudine and tenofovir DF-emtricitabine fixed-dose combinations are commonly used as first-line antiretroviral therapies. However, few studies have comprehensively compared their relative safety profiles. Methods. In this European, multicenter, open-label, 96-week study, antiretroviral-naive adult subjects with human immunodeficiency virus (HIV) infection were randomized to receive either abacavir-lamivudine or tenofovir- emtricitabine with efavirenz. Primary analyses were conducted after 48 weeks of treatment. Bone mineral density (BMD), a powered secondary end point, was assessed by dual energy x-ray absorptiometry. Bone turnover markers (osteocalcin, procollagen 1 N-terminal propeptide, bone specific alkaline phosphatase, and type 1 collagen cross-linked C telopeptide [CTx]) were assessed in an exploratory analysis. Results. A total of 385 subjects were enrolled in the study. BMD loss was observed in both treatment groups, with a significant difference in the change from baseline in both total hip (abacavir-lamivudine group, -1.9%; tenofovir-emtricitabine group, -3.6%; P= 6% was more common in the tenofovir-emtricitabine group (13% of the tenofovir-emtricitabine group vs 3% of the abacavir-lamivudine group had a loss of >= 6% in the hip; 15% vs 5% had a loss of >= 6% in the spine). Bone turnover markers increased in both treatment groups over the first 24 weeks, stabilizing or decreasing thereafter. Increases in all markers were significantly greater in the tenofovir-emtricitabine treatment group than in the abacavir-lamivudine group at week 24. All but CTx remained significantly different at week 48 (eg, osteocalcin: abacavir-lamivudine group, +8.07 mg/L; tenofovir-emtricitabine group, +11.92 mg/L; P Conclusions. This study demonstrated the impact of first-line treatment regimens on bone. Greater increases in bone turnover and decreases in BMD were observed in subjects treated with tenofovir-emtricitabine than were observed in subjects treated with abacavir-lamivudine

Yield of yearly routine physical examination in HIV-1 infected patients is limited:A retrospective cohort study in the Netherlands

Background Routine physical examinations might be of value in HIV-infected patients, but the yield is unknown. We determined the diagnoses that would have been missed without performing annual routine physical examinations in HIV-infected patients with stable disease. Methods Data were collected from the medical records of 299 HIV-1-infected patients with CD4 count >350 cells/mm(3) if not using combination antiretroviral therapy (cART), or CD4 count >100 cells/mm3 and undetectable viral load if using cART. We defined the diagnoses that would have been missed without performing routine physical examinations on annual check-ups in 2010. Exclusion criteria were hepatitis B/C co-infection, start/switch of cART Results 215 patients (72%) had positive findings: lipodystrophy (30%), lymphadenopathy (16%) and hypertension (8.4%) were the most common. Two-thirds of all findings were not new or were based on complaints indicating a physical examination even if not routinely scheduled. For 24 patients (8.0%) the routine physical examination led to the finding of a new diagnosis: six-all men who have sex with men (MSM)-had a concurrent sexually transmitted infection, eight had hypertension, and ten others had a large variety of diagnoses. A total atrioventricular block with bradycardia was the most clinically relevant finding. Conclusions Annual physical examinations of HIV-infected patients with stable disease brought few new diagnoses that would have been missed without performing a routine examination. Our results suggest that standard assessments could be restricted to six-monthly measuring blood pressure in all patients and annually performing anogenital and digital rectal examination on MSM

Definitions and sharpness of the extratropical tropopause : a trace gas perspective

Author Posting. © American Geophysical Union, 2004. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 109 (2004): D23103, doi:10.1029/2004JD004982.Definitions of the extratropical tropopause are examined from the perspective of chemical composition. Fine-scale measurements of temperature, ozone, carbon monoxide, and water vapor from approximately 70 aircraft flights, with ascending and descending tropopause crossings near 40°N and 65°N, are used in this analysis. Using the relationship of the stratospheric tracer O3 and the tropospheric tracer CO, we address the issues of tropopause sharpness and where the transitions from troposphere to stratosphere occur in terms of the chemical composition. Tracer relationships indicate that mixing of stratospheric and tropospheric air masses occurs in the vicinity of the tropopause to form a transition layer. Statistically, this transition layer is centered on the thermal tropopause. Furthermore, we show that the transition is much sharper near 65°N (a region away from the subtropical jet) but spans a larger altitude range near 40°N (in the vicinity of the subtropical jet). This latter feature is consistent with enhanced stratosphere-troposphere exchange and mixing activity near the tropopause break.This work is supported in part by the National Science Foundation through its support to the University Corporation for Atmospheric Research, by the NASA Upper Atmosphere Research Satellite guest investigator program, and by the NASA Atmospheric Chemistry Modeling and Analysis Program. Work performed at the Jet Propulsion Laboratory, California Institute of Technology, was carried out under a contract with the National Aeronautics and Space Administration

Functional analysis of genes involved in the biosynthesis of isoprene in Bacillus subtilis

In comparison to other bacteria Bacillus subtilis emits the volatile compound isoprene in high concentrations. Isoprene is the smallest representative of the natural product group of terpenoids. A search in the genome of B. subtilis resulted in a set of genes with yet unknown function, but putatively involved in the methylerythritol phosphate (MEP) pathway to isoprene. Further identification of these genes would give the possibility to engineer B. subtilis as a host cell for the production of terpenoids like the valuable plant-produced drugs artemisinin and paclitaxel. Conditional knock-out strains of putative genes were analyzed for the amount of isoprene emitted. Differences in isoprene emission were used to identify the function of the enzymes and of the corresponding selected genes in the MEP pathway. We give proof on a biochemical level that several of these selected genes from this species are involved in isoprene biosynthesis. This opens the possibilities to investigate the physiological function of isoprene emission and to increase the endogenous flux to the terpenoid precursors, isopentenyl diphosphate and dimethylallyl diphosphate, for the heterologous production of more complex terpenoids in B. subtilis

The extratropical upper troposphere and lower stratosphere

The extratropical upper troposphere and lower stratosphere (Ex-UTLS) is a transition region between the stratosphere and the troposphere. The Ex-UTLS includes the tropopause, a strong static stability gradient and dynamic barrier to transport. The barrier is reflected in tracer profiles. This region exhibits complex dynamical, radiative, and chemical characteristics that place stringent spatial and temporal requirements on observing and modeling systems. The Ex-UTLS couples the stratosphere to the troposphere through chemical constituent transport (of, e.g., ozone), by dynamically linking the stratospheric circulation with tropospheric wave patterns, and via radiative processes tied to optically thick clouds and clear-sky gradients of radiatively active gases. A comprehensive picture of the Ex-UTLS is presented that brings together different definitions of the tropopause, focusing on observed dynamical and chemical structure and their coupling. This integral view recognizes that thermal gradients and dynamic barriers are necessarily linked, that these barriers inhibit mixing and give rise to specific trace gas distributions, and that there are radiative feedbacks that help maintain this structure. The impacts of 21st century anthropogenic changes to the atmosphere due to ozone recovery and climate change will be felt in the Ex-UTLS, and recent simulations of these effects are summarized and placed in context