Changes in gene expression in space and time orchestrate environmentally mediated shaping of root architecture

Shaping of root architecture is a quintessential developmental response that involves the concerted action of many different cell types, is highly dynamic and underpins root plasticity. To determine to what extent the environmental regulation of lateral root development is a product of cell type preferential activities, we tracked transcriptomic responses to two different treatments that both change root development in Arabidopsis thaliana, at an unprecedented level of temporal detail. We found that individual transcripts are expressed with a very high degree of temporal and spatial specificity, yet biological processes are commonly regulated, in a mechanism we term response nonredundancy. Using causative gene network inference to compare the genes regulated in different cell types and during responses to nitrogen and a biotic interaction we found that common transcriptional modules often regulate the same gene families, but control different individual members of these families, specific to response and cell type. This reinforces that the activity of a gene cannot be defined simply as molecular function; rather, it is a consequence of spatial location, expression timing and environmental responsiveness

Global Conservation Significance of Ecuador's Yasuní National Park

Margot S. Bass is with Finding Species, Matt Finer is with Save America's Forests, Clinton N. Jenkins is with Duke University and University of Maryland, Holger Kreft is with University of California San Diego, Diego F. Cisneros-Heredia is with King's College London and Universidad San Francisco de Quito, Shawn F. McCracken is with Texas State University and the TADPOLE Organization, Nigel C. A. Pitman is with Duke University, Peter H. English is with UT Austin, Kelly Swing is with Universidad San Francisco de Quito, Gorky Villa is with Finding Species, Anthony Di Fiore is with New York University, Christian C. Voigt is with Leibniz Institute for Zoo and Wildlife Research, Thomas H. Kunz is with Boston University.Background -- The threats facing Ecuador's Yasuní National Park are emblematic of those confronting the greater western Amazon, one of the world's last high-biodiversity wilderness areas. Notably, the country's second largest untapped oil reserves—called “ITT”—lie beneath an intact, remote section of the park. The conservation significance of Yasuní may weigh heavily in upcoming state-level and international decisions, including whether to develop the oil or invest in alternatives. Methodology/Principal Findings -- We conducted the first comprehensive synthesis of biodiversity data for Yasuní. Mapping amphibian, bird, mammal, and plant distributions, we found eastern Ecuador and northern Peru to be the only regions in South America where species richness centers for all four taxonomic groups overlap. This quadruple richness center has only one viable strict protected area (IUCN levels I–IV): Yasuní. The park covers just 14% of the quadruple richness center's area, whereas active or proposed oil concessions cover 79%. Using field inventory data, we compared Yasuní's local (alpha) and landscape (gamma) diversity to other sites, in the western Amazon and globally. These analyses further suggest that Yasuní is among the most biodiverse places on Earth, with apparent world richness records for amphibians, reptiles, bats, and trees. Yasuní also protects a considerable number of threatened species and regional endemics. Conclusions/Significance -- Yasuní has outstanding global conservation significance due to its extraordinary biodiversity and potential to sustain this biodiversity in the long term because of its 1) large size and wilderness character, 2) intact large-vertebrate assemblage, 3) IUCN level-II protection status in a region lacking other strict protected areas, and 4) likelihood of maintaining wet, rainforest conditions while anticipated climate change-induced drought intensifies in the eastern Amazon. However, further oil development in Yasuní jeopardizes its conservation values. These findings form the scientific basis for policy recommendations, including stopping any new oil activities and road construction in Yasuní and creating areas off-limits to large-scale development in adjacent northern Peru.The Blue Moon Fund, the Conservation, Food & Health Foundation, and the Forrest and Frances Lattner Foundation funded MF. The US National Science Foundation (Graduate Research Fellowship Program), Texas State University-Department of Biology, and TADPOLE funded SM. The US National Science Foundation, the L.S.B. Leakey Foundation, the Wenner-Gren Foundation for Anthropological Research, and Primate Conservation, Inc. funded AD. Establishment of the Tiputini Biodiversity Station supported by the US National Science Foundation–DBI-0434875 (Thomas H. Kunz, PI, with Laura M. MacLatchy, Christopher J. Schneider, and C. Kelly Swing, Co-PIs). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Biological Sciences, School o

In vivo assessment of human brainstem cerebrovascular function: a multi-inversion time pulsed arterial spin labelling study

The brainstem (BS) is involved in critical physiologic processes, including control of cardiovascular and respiratory functions. This study implements a multi-inversion time pulsed arterial spin labelling (MTI PASL) imaging sequence that addresses the challenges of BS imaging and aims to measure normal and elevated BS perfusion in healthy volunteers. An initial experiment was performed to obtain the kinetic curve of the label in the BS and consequently to estimate the label arrival times and tissue perfusion in seven participants. A second experiment estimated the BS cerebral vascular reactivity (CVR) to hypercapnia in 10 participants. Images were acquired with a gradient-echo sequence with two spiral interleaves and short echo time (TE=2.7 ms). Data were analyzed with a two-compartment model, including a tissue and arterial component. In both experiments, perfusion in the BS was significantly lower than in cortical gray matter (repeated measures analysis of variance (RM-ANOVA), P<0.05), which is as expected since the BS consists of gray and white matter, the latter typically showing lower perfusion. The BS CVR found here is comparable to previous reports obtained with positron emission tomography (PET) imaging. Multi-inversion time pulsed ASL in combination with a two-compartment signal model can be used to assess BS perfusion and CVR

Barriers and opportunities for evidence-based health service planning: the example of developing a Decision Analytic Model to plan services for sexually transmitted infections in the UK

Decision Analytic Models (DAMs) are established means of evidence-synthesis to differentiate between health interventions. They have mainly been used to inform clinical decisions and health technology assessment at the national level, yet could also inform local health service planning. For this, a DAM must take into account the needs of the local population, but also the needs of those planning its services. Drawing on our experiences from stakeholder consultations, where we presented the potential utility of a DAM for planning local health services for sexually transmitted infections (STIs) in the UK, and the evidence it could use to inform decisions regarding different combinations of service provision, in terms of their costs, cost-effectiveness, and public health outcomes, we discuss the barriers perceived by stakeholders to the use of DAMs to inform service planning for local populations, including (1) a tension between individual and population perspectives; (2) reductionism; and (3) a lack of transparency regarding models, their assumptions, and the motivations of those generating models

Delineation of the movement disorders associated with FOXG1 mutations

Objective: The primary objective of this research was to characterize the movement disorders associated with FOXG1 mutations. Methods: We identified patients with FOXG1 mutations who were referred to either a tertiary movement disorder clinic or tertiary epilepsy service and retrospectively reviewed medical records, clinical investigations, neuroimaging, and available video footage. We administered a telephone-based questionnaire regarding the functional impact of the movement disorders and perceived efficacy of treatment to the caregivers of one cohort of participants. Results: We identified 28 patients with FOXG1 mutations, of whom 6 had previously unreported mutations. A wide variety of movement disorders were identified, with dystonia, choreoathetosis, and orolingual/facial dyskinesias most commonly present. Ninety-three percent of patients had a mixed movement disorder phenotype. In contrast to the phenotype classically described with FOXG1 mutations, 4 patients with missense mutations had a milder phenotype, with independent ambulation, spoken language, and normocephaly. Hyperkinetic involuntary movements were a major clinical feature in these patients. Of the symptomatic treatments targeted to control abnormal involuntary movements, most did not emerge as clearly beneficial, although 4 patients had a caregiver-reported response to levodopa. Conclusions: Abnormal involuntary movements are a major feature of FOXG1 mutations. Our study delineates the spectrum of movement disorders and confirms an expanding clinical phenotype. Symptomatic treatment may be considered for severe or disabling cases, although further research regarding potential treatment strategies is necessary

Medication review plus person-centred care:a feasibility study of a pharmacy-health psychology dual intervention to improve care for people living with dementia

BACKGROUND: "Behaviour that Challenges" is common in people living with dementia, resident in care homes and historically has been treated with anti-psychotics. However, such usage is associated with 1800 potentially avoidable deaths annually in the UK. This study investigated the feasibility of a full clinical trial of a specialist dementia care pharmacist medication review combined with a health psychology intervention for care staff to limit the use of psychotropics. This paper focuses on feasibility; including recruitment and retention, implementation of medication change recommendations and the experiences and expectations of care staff. METHODS: West Midlands care homes and individuals meeting the inclusion criteria (dementia diagnosis; medication for behaviour that challenges), or their personal consultee, were approached for consent. A specialist pharmacist reviewed medication. Care home staff received an educational behaviour change intervention in a three-hour session promoting person-centred care. Primary healthcare staff received a modified version of the training. The primary outcome measure was the Neuropsychiatric Inventory-Nursing Home version at 3 months. Other outcomes included quality of life, cognition, health economics and prescribed medication. A qualitative evaluation explored expectations and experiences of care staff. RESULTS: Five care homes and 34 of 108 eligible residents (31.5%) were recruited, against an original target of 45 residents across 6 care homes. Medication reviews were conducted for 29 study participants (85.3%) and the pharmacist recommended stopping or reviewing medication in 21 cases (72.4%). Of the recommendations made, 57.1% (12 of 21) were implemented, and implementation (discontinuation) took a mean of 98.4 days. In total, 164 care staff received training and 21 were interviewed. Care staff reported a positive experience of the intervention and post intervention adopting a more holistic patient-centred approach. CONCLUSIONS: The intervention contained two elements; staff training and medication review. It was feasible to implement the staff training, and the training appeared to increase the ability and confidence of care staff to manage behaviour that challenges without the need for medication. The medication review would require significant modification for full trial partly related to the relatively limited uptake of the recommendations made, and delay in implementation. TRIAL REGISTRATION: ISRCTN58330068 . Registered 15 October 2017. Retrospectively registered

Clinical impact of a targeted next-generation sequencing gene panel for autoinflammation and vasculitis.

BACKGROUND: Monogenic autoinflammatory diseases (AID) are a rapidly expanding group of genetically diverse but phenotypically overlapping systemic inflammatory disorders associated with dysregulated innate immunity. They cause significant morbidity, mortality and economic burden. Here, we aimed to develop and evaluate the clinical impact of a NGS targeted gene panel, the "Vasculitis and Inflammation Panel" (VIP) for AID and vasculitis. METHODS: The Agilent SureDesign tool was used to design 2 versions of VIP; VIP1 targeting 113 genes, and a later version, VIP2, targeting 166 genes. Captured and indexed libraries (QXT Target Enrichment System) prepared for 72 patients were sequenced as a multiplex of 16 samples on an Illumina MiSeq sequencer in 150bp paired-end mode. The cohort comprised 22 positive control DNA samples from patients with previously validated mutations in a variety of the genes; and 50 prospective samples from patients with suspected AID in whom previous Sanger based genetic screening had been non-diagnostic. RESULTS: VIP was sensitive and specific at detecting all the different types of known mutations in 22 positive controls, including gene deletion, small INDELS, and somatic mosaicism with allele fraction as low as 3%. Six/50 patients (12%) with unclassified AID had at least one class 5 (clearly pathogenic) variant; and 11/50 (22%) had at least one likely pathogenic variant (class 4). Overall, testing with VIP resulted in a firm or strongly suspected molecular diagnosis in 16/50 patients (32%). CONCLUSIONS: The high diagnostic yield and accuracy of this comprehensive targeted gene panel validate the use of broad NGS-based testing for patients with suspected AID

Evidence-informed recommendations on managing breast screening atypia : perspectives from an expert panel consensus meeting reviewing results from the sloane atypia project

Evidence-based clinical guidelines are essential to maximise patient benefit and to reduce clinical uncertainty and inconsistency in clinical practice. Gaps in the evidence base can be addressed by data acquired in routine practice. At present, there is no international consensus on management of women diagnosed with atypical lesions in breast screening programmes. Here we describe how routine NHS breast screening data collected by the Sloane atypia project was used to inform a management pathway that maximises early detection of cancer and minimises over investigation of lesions with uncertain malignant potential. A half-day consensus meeting with 11 clinical experts, 1 representative from Independent Cancer Patients’ Voice, 6 representatives from NHS England (NHSE) including from Commissioning, and 2 researchers was held to facilitate discussions of findings from an analysis of the Sloane atypia project. Key considerations of the expert group in terms of the management of women with screen detected atypia were: a) frequency and purpose of follow-up; b) communication to patients; c) generalisability of study results; d) workforce challenges. The group concurred that the new evidence does not support annual surveillance mammography for women with atypia, irrespective of type of lesion, or woman’s age. Continued data collection is paramount to monitor and audit the change in recommendations

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy

The role of dendritic cells in driving genital tract inflammation and HIV transmission risk: are there opportunities to intervene?

CAPRISA, 2015.Abstract available in pdf