Analise in silico e in vivo da diversidade nucleotidica em Coffea ssp.

Polimorfismos de modificações nucleotídicas (SNPs ? Single Nucleotide Polymorphisms, INDELs ? Insertion / Deletions) têm uma alta freqüência nos genomas da maioria dos organismos, incluindo plantas. Eles vêm se tornando a escolha principal de marcador para trabalhos de melhoramento, genotipagem e diagnóstico. A identificação destes polimorfismos irá fornecer marcadores que poderão ser utilizados para o mapeamento genético, estudos de genética de população e de associação. Portanto, os objetivos deste trabalho foram: 1) identificar in silico SNPs e INDELS existentes em seqüências de ESTs disponíveis; e 2) analisar a diversidade nucleotídica em Coffea spp. Um pipeline para identificação de SNPs e INDELs foi desenvolvido utilizando seqüências de ESTs disponíveis de Coffea spp. Foi utilizado uma estratégia para detecção de SNPs em dentro de 23.019 contigs. Um total 23.062 SNPs e 2.165 INDELS foram encontrados em 5184 contigs que continham pelo menos quatro ESTs. Analises in silico permitiram a identificação de diferentes alelos de C. canephora e C. eugenioides que estão presentes em C. arabica. A maioria dos ESTs de C. arabica vieram de apenas dois alelos, uma evidência molecular sobre a especiação de C. arabica. De acordo com essas análises cerca de 55% das seqüências de C. arabica são derivadas do genoma de C. eugenioides e 45% de C. canephora. Além disso, foi possível observar que o genoma de C. eugenioides contribui principalmente para genes relacionados a metabolismo basal, enquanto que os genes de C. canephora estão envolvidos com sinais de tradução e regulação da expressão gênica. Análises in vivo estão sendo realizadas através do sequenciamento de diversos genes em 24 genótipos de Coffea sendo 12 de C. arabica, 9 de C. canephora e três de outras espécies de Coffea, para uma analise maior da diversidade nucleotídica do gênero. Resultados referentes ao sequenciamento do gene de sacarose fosfato sintase (SPS) apresentaram 21 polimorfismos, sendo a maioria interespecíficos (C. arabica, C. canephora, C. eugenioides e C. racemosa). Para os genótipos de C. canephora foram observados nove polimorfismos intraespecíficos. Já os polimorfismos encontrados entre os genótipos de C. arabica forma os mesmos detectados entre C. canephora e C. eugenioides

Probiotics, prebiotics, and the host microbiome: the science of translation

Recent advances in our understanding of the community structure and function of the human microbiome have implications for the potential role of probiotics and prebiotics in promoting human health. A group of experts recently met to review the latest advances in microbiota/microbiome research and discuss the implications for development of probiotics and prebiotics, primarily as they relate to effects mediated via the intestine. The goals of the meeting were to share recent advances in research on the microbiota, microbiome, probiotics, and prebiotics, and to discuss these findings in the contexts of regulatory barriers, evolving healthcare environments, and potential effects on a variety of health topics, including the development of obesity and diabetes; the long-term consequences of exposure to antibiotics early in life to the gastrointestinal (GI) microbiota; lactose intolerance; and the relationship between the GI microbiota and the central nervous system, with implications for depression, cognition, satiety, and mental health for people living in developed and developing countries. This report provides an overview of these discussions

Imaging the distribution of an antibody-drug conjugate constituent targeting mesothelin with Zr-89 and IRDye 800CW in mice bearing human pancreatic tumor xenografts

Mesothelin is a tumor differentiation antigen expressed by epithelial tumors, including pancreatic cancer. Currently, mesothelin is being targeted with an antibodydrug conjugate (ADC) consisting of a mesothelin-specific antibody coupled to a highly potent chemotherapeutic drug. Considering the toxicity of the ADC and reduced accessibility of pancreatic tumors, non-invasive imaging could provide necessary information. We therefore developed a zirconium-89 (Zr-89) labeled anti-mesothelin antibody (Zr-89-AMA) to study its biodistribution in human pancreatic tumor bearing mice. Biodistribution and dose-finding of Zr-89-AMA were studied 144 h after tracer injection in mice with subcutaneously xenografted HPAC. MicroPET imaging was performed 24, 72 and 144 h after tracer injection in mice bearing HPAC or Capan-2. Tumor uptake and organ distribution of Zr-89-AMA were compared with nonspecific 111In-IgG. Biodistribution analyses revealed a dose-dependent Zr-89-AMA tumor uptake. Tumor uptake of Zr-89-AMA was higher than 111In-IgG using the lowest tracer dose. MicroPET showed increased tumor uptake over 6 days, whereas activity in blood pool and other tissues decreased. Immunohistochemistry showed that mesothelin was expressed by the HPAC and CAPAN-2 tumors and fluorescence microscopy revealed that AMA-800CW was present in tumor cell cytoplasm. Zr-89-AMA tumor uptake is antigen-specific in mesothelin-expressing tumors. Zr-89-AMA PET provides non-invasive, real-time information about AMA distribution and tumor targeting

Effectiveness and cost-effectiveness of an internet intervention for family caregivers of people with dementia: design of a randomized controlled trial

<p>Abstract</p> <p>Background</p> <p>The number of people with dementia is rising rapidly as a consequence of the greying of the world population. There is an urgent need to develop cost effective approaches that meet the needs of people with dementia and their family caregivers. Depression, feelings of burden and caregiver stress are common and serious health problems in these family caregivers. Different kinds of interventions are developed to prevent or reduce the negative psychological consequences of caregiving. The use of internet interventions is still very limited, although they may be a cost effective way to support family caregivers in an earlier stage and diminish their psychological distress in the short and longer run.</p> <p>Methods/design</p> <p>A pragmatic randomized controlled trial is designed to evaluate the effectiveness and cost-effectiveness of ‘Mastery over Dementia’, an internet intervention for caregivers of people with dementia. The intervention aims at prevention and decrease of psychological distress, in particular depressive symptoms. The experimental condition consists of an internet course with 8 sessions and a booster session over a maximum period of 6 months guided by a psychologist. Caregivers in the comparison condition receive a minimal intervention. In addition to a pre and post measurement, an intermediate measurement will be conducted. In addition, there will be two follow-up measurements 3 and 6 months after post-treatment in the experimental group only. To study the effectiveness of the intervention, depressive symptoms are used as the primary outcome, whereas symptoms of anxiety, role overload and caregiver perceived stress are used as secondary outcomes. To study which caregivers profit most of the internet intervention, several variables that may modify the impact of the intervention are taken into account. Regarding the cost-effectiveness, an economic evaluation will be conducted from a societal perspective.</p> <p>Discussion</p> <p>This study will provide evidence about the effectiveness and cost-effectiveness of an internet intervention for caregivers. If both can be shown, this might set the stage for the development of a range of internet interventions in the field of caregiving for people with dementia. This is even more important because future generations of caregivers will be more familiar with the use of internet.</p> <p>Trial registration</p> <p>NTR-2051/RCT-DDB</p

Identification of candidate genes for drought tolerance in coffee by high-throughput sequencing in the shoot apex of different Coffea arabica cultivars.

BACKGROUND: Drought is a widespread limiting factor in coffee plants. It affects plant development, fruit production, bean development and consequently beverage quality. Genetic diversity for drought tolerance exists within the coffee genus. However, the molecular mechanisms underlying the adaptation of coffee plants to drought are largely unknown. In this study, we compared the molecular responses to drought in two commercial cultivars (IAPAR59, drought-tolerant and Rubi, drought-susceptible) of Coffea arabica grown in the field under control (irrigation) and drought conditions using the pyrosequencing of RNA extracted from shoot apices and analysing the expression of 38 candidate genes. RESULTS: Pyrosequencing from shoot apices generated a total of 34.7 Mbp and 535,544 reads enabling the identification of 43,087 clusters (41,512 contigs and 1,575 singletons). These data included 17,719 clusters (16,238 contigs and 1,575 singletons) exclusively from 454 sequencing reads, along with 25,368 hybrid clusters assembled with 454 sequences. The comparison of DNA libraries identified new candidate genes (n = 20) presenting differential expression between IAPAR59 and Rubi and/or drought conditions. Their expression was monitored in plagiotropic buds, together with those of other (n = 18) candidates genes. Under drought conditions, up-regulated expression was observed in IAPAR59 but not in Rubi for CaSTK1 (protein kinase), CaSAMT1 (SAM-dependent methyltransferase), CaSLP1 (plant development) and CaMAS1 (ABA biosynthesis). Interestingly, the expression of lipid-transfer protein (nsLTP) genes was also highly up-regulated under drought conditions in IAPAR59. This may have been related to the thicker cuticle observed on the abaxial leaf surface in IAPAR59 compared to Rubi. CONCLUSIONS: The full transcriptome assembly of C. arabica, followed by functional annotation, enabled us to identify differentially expressed genes related to drought conditions. Using these data, candidate genes were selected and their differential expression profiles were confirmed by qPCR experiments in plagiotropic buds of IAPAR59 and Rubi under drought conditions. As regards the genes up-regulated under drought conditions, specifically in the drought-tolerant IAPAR59, several corresponded to orphan genes but also to genes coding proteins involved in signal transduction pathways, as well as ABA and lipid metabolism, for example. The identification of these genes should help advance our understanding of the genetic determinism of drought tolerance in coffee

SEIS: Insight's Seismic Experiment for Internal Structure of Mars.

By the end of 2018, 42 years after the landing of the two Viking seismometers on Mars, InSight will deploy onto Mars' surface the SEIS (Seismic Experiment for Internal Structure) instrument; a six-axes seismometer equipped with both a long-period three-axes Very Broad Band (VBB) instrument and a three-axes short-period (SP) instrument. These six sensors will cover a broad range of the seismic bandwidth, from 0.01&nbsp;Hz to 50&nbsp;Hz, with possible extension to longer periods. Data will be transmitted in the form of three continuous VBB components at 2 sample per second (sps), an estimation of the short period energy content from the SP at 1&nbsp;sps and a continuous compound VBB/SP vertical axis at 10&nbsp;sps. The continuous streams will be augmented by requested event data with sample rates from 20 to 100 sps. SEIS will improve upon the existing resolution of Viking's Mars seismic monitoring by a factor of ∼ 2500 at 1&nbsp;Hz and ∼ 200 000 at 0.1&nbsp;Hz. An additional major improvement is that, contrary to Viking, the seismometers will be deployed via a robotic arm directly onto Mars' surface and will be protected against temperature and wind by highly efficient thermal and wind shielding. Based on existing knowledge of Mars, it is reasonable to infer a moment magnitude detection threshold of M w ∼ 3 at 40 ∘ epicentral distance and a potential to detect several tens of quakes and about five impacts per year. In this paper, we first describe the science goals of the experiment and the rationale used to define its requirements. We then provide a detailed description of the hardware, from the sensors to the deployment system and associated performance, including transfer functions of the seismic sensors and temperature sensors. We conclude by describing the experiment ground segment, including data processing services, outreach and education networks and provide a description of the format to be used for future data distribution.Electronic supplementary materialThe online version of this article (10.1007/s11214-018-0574-6) contains supplementary material, which is available to authorized users

The Swiss Multiple Sclerosis Cohort-Study (SMSC): A Prospective Swiss Wide Investigation of Key Phases in Disease Evolution and New Treatment Options.

The mechanisms leading to disability and the long-term efficacy and safety of disease modifying drugs (DMDs) in multiple sclerosis (MS) are unclear. We aimed at building a prospective cohort of MS patients with standardized collection of demographic, clinical, MRI data and body fluids that can be used to develop prognostic indicators and biomarkers of disease evolution and therapeutic response. The Swiss MS Cohort (SMSC) is a prospective observational study performed across seven Swiss MS centers including patients with MS, clinically isolated syndrome (CIS), radiologically isolated syndrome or neuromyelitis optica. Neurological and radiological assessments and biological samples are collected every 6-12 months. We recruited 872 patients (clinically isolated syndrome [CIS] 5.5%, relapsing-remitting MS [RRMS] 85.8%, primary progressive MS [PPMS] 3.5%, secondary progressive MS [SPMS] 5.2%) between June 2012 and July 2015. We performed 2,286 visits (median follow-up 398 days) and collected 2,274 serum, plasma and blood samples, 152 cerebrospinal fluid samples and 1,276 brain MRI scans. 158 relapses occurred and expanded disability status scale (EDSS) scores increased in PPMS, SPMS and RRMS patients experiencing relapses. Most RRMS patients were treated with fingolimod (33.4%), natalizumab (24.5%) or injectable DMDs (13.6%). The SMSC will provide relevant information regarding DMDs efficacy and safety and will serve as a comprehensive infrastructure available for nested research projects

Evaluation of Commercial Probiotic Products

Although there is a vast number of probiotic products commercially available due to their acceptability and increasing usage, their quality control has continuously been a major concern. This study aimed to assess some commercially available probiotics on the UK market for content in relation to their label claim. Seven products were used for the study. The bacteria content were isolated, identified and enumerated on selective media. The results revealed that all products evaluated contained viable probiotic bacteria but only three out of the seven products (43%) contained the claimed culture concentration or more. None of the multispecies product contained all the labelled probiotic bacteria. Misidentification of some species occurred. The results concurred with previous studies and showed that quality issues with commercial probiotics remain. Since probiotic activity is linked with probiotic concentration and is strain specific, the need exist for a global comprehensive legislation to control the quality of probiotics whose market is gaining huge momentum

Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria

ERIC, the Enteropathogen Resource Integration Center (www.ericbrc.org), is a new web portal serving as a rich source of information about enterobacteria on the NIAID established list of Select Agents related to biodefense—diarrheagenic Escherichia coli, Shigella spp., Salmonella spp., Yersinia enterocolitica and Yersinia pestis. More than 30 genomes have been completely sequenced, many more exist in draft form and additional projects are underway. These organisms are increasingly the focus of studies using high-throughput experimental technologies and computational approaches. This wealth of data provides unprecedented opportunities for understanding the workings of basic biological systems and discovery of novel targets for development of vaccines, diagnostics and therapeutics. ERIC brings information together from disparate sources and supports data comparison across different organisms, analysis of varying data types and visualization of analyses in human and computer-readable formats