Chemical outbreak for tobacco mosaic virus control

Tobacco mosaic virus (TMV) represents a paradigm in virology, and its control may open the way to effective treatment against phytoviruses. However, the use of chemicals to eliminate the virus from infected plants is very difficult. In this state of the art survey we include trials on a) natural compounds derived from organisms, b) synthetic compounds and c) plant or microorganism extracts, from 2006 to 2015. Plants have been the main source of natural products for anti-TMV tests in the last ten years, and Nicotiana tabacum was the main focus of research, particularly between 2014-2015. Since 2012, there has been a great increase in publications (+45%) and identified compounds (+241%). Between 2012-2015, an average of 31 papers were published and 140 compounds were tested each year, compared to 9 papers and 26 compounds in 2006-2011. Unfortunately, there is little information on the action mechanisms of newly discovered or modified compounds. Cross references to the basic structure of compounds is provided in this review. This chemical outbreak this massive interest in chemical solutions to TMV could be due to the increasing availability of instruments for the analysis of organic compounds. Alternatively Another explanation could be that the chemistry advances in synthesis, which have provided countless drugs with potential benefits for TMV control, have overwhelmed overloaded the plant pathology screening needed to discriminate between compounds and to provide useful agrochemicals for farmers

Effect of intranasal NGF administration in injured spinal cord and leptin levels in adult rats

Spinal cord injury alters a number of endogenous biological signals known to be involved in the modulation of neurotrophic and neuroprotective events. Nerve growth factor (NGF) is a neurotrophic factor expressed in neuronal and non-neuronal tissues including spinal cord, and increases after spinal cord injury. Recent findings revealed that leptin, an adipocyte-derived cytokine (adipokine), enhance neuronal survival and exert neuroprotective action, and played an important role in nociceptive behavior induced by nerve injury. Whether NGF affects the expression of leptin in injured spinal cord has not been investigated. The present study was designed to evaluate: (i) whether intranasal NGF administration reached the spinal cord of the rat, (ii) if NGF affects the expression of leptin in the spinal cord and adipose tissue, and (iii) whether intranasal NGF affects the behavioral and spinal cord neuronal deficits induced by spinal cord injury. The result showed that intranasal NGF enhances the expression of (i) NGF and NGF-receptors (TrkA and p75NTR) in injured spinal cord exerting behavioral and neuroprotective action, and (ii) leptin in injured spinal cord and in subcutaneous (white) and interscapular (brown) adipose tissue. Altogether, the present data demonstrate the efficacy of intranasal administration of NGF, and suggest a link between the neurotrophin NGF and the adipokine leptin that may be therapeutically explored in injured spinal cord.Adipobiology 2012; 4: 67-75

Detection of grapevine yellows symptoms in Vitis vinifera L. with artificial intelligence

Abstract Grapevine yellows (GY) are a significant threat to grapes due to the severe symptoms and lack of treatments. Conventional diagnosis of the phytoplasmas associated to GYs relies on symptom identification, due to sensitivity limits of diagnostic tools (e.g. real time PCR) in asymptomatic vines, where the low concentration of the pathogen or its erratic distribution can lead to a high rate of false-negatives. GY's primary symptoms are leaf discoloration and irregular wood ripening, which can be easily confused for symptoms of other diseases making recognition a difficult task. Herein, we present a novel system, utilizing convolutional neural networks, for end-to-end detection of GY in red grape vine (cv. Sangiovese), using color images of leaf clippings. The diagnostic test detailed in this work does not require the user to be an expert at identifying GY. Data augmentation strategies make the system robust to alignment errors during data capture. When applied to the task of recognizing GY from digital images of leaf clippings—amongst many other diseases and a healthy control—the system has a sensitivity of 98.96% and a specificity of 99.40%. Deep learning has 35.97% and 9.88% better predictive value (PPV) when recognizing GY from sight, than a baseline system without deep learning and trained humans respectively. We evaluate six neural network architectures: AlexNet, GoogLeNet, Inception v3, ResNet-50, ResNet-101 and SqueezeNet. We find ResNet-50 to be the best compromise of accuracy and training cost. The trained neural networks, code to reproduce the experiments, and data of leaf clipping images are available on the internet. This work will advance the frontier of GY detection by improving detection speed, enabling a more effective response to the disease

Complete gene expression profiling of Saccharopolyspora erythraea using GeneChip DNA microarrays

The Saccharopolyspora erythraea genome sequence, recently published, presents considerable divergence from those of streptomycetes in gene organization and function, confirming the remarkable potential of S. erythraea for producing many other secondary metabolites in addition to erythromycin. In order to investigate, at whole transcriptome level, how S. erythraea genes are modulated, a DNA microarray was specifically designed and constructed on the S. erythraea strain NRRL 2338 genome sequence, and the expression profiles of 6494 ORFs were monitored during growth in complex liquid medium

MicroRNA expression in HTLV-1 infection and pathogenesis

Our laboratory is examining the profiles of microRNA expression in ATLL cells and infected T-cell lines using microarrays and small RNA libraries. Microarray analysis of ATLL samples revealed 6 upregulated and 21 downregulated microRNAs in ATLL cells compared to CD4+ T-cell controls. Potential targets for deregulated microRNAs were identified by integrating microRNA and mRNA expression profiles. Current experiments are aimed at verifying these predicted microRNA-target interactions

Evaluation of human gene variant detection in amplicon pools by the GS-FLX parallel Pyrosequencer

<p>Abstract</p> <p>Background</p> <p>A new priority in genome research is large-scale resequencing of genes to understand the molecular basis of hereditary disease and cancer. We assessed the ability of massively parallel pyrosequencing to identify sequence variants in pools. From a large collection of human PCR samples we selected 343 PCR products belonging to 16 disease genes and including a large spectrum of sequence variations previously identified by Sanger sequencing. The sequence variants included SNPs and small deletions and insertions (up to 44 bp), in homozygous or heterozygous state.</p> <p>Results</p> <p>The DNA was combined in 4 pools containing from 27 to 164 amplicons and from 8,9 to 50,8 Kb to sequence for a total of 110 Kb. Pyrosequencing generated over 80 million base pairs of data. Blind searching for sequence variations with a specifically designed bioinformatics procedure identified 465 putative sequence variants, including 412 true variants, 53 false positives (in or adjacent to homopolymeric tracts), no false negatives. All known variants in positions covered with at least 30× depth were correctly recognized.</p> <p>Conclusion</p> <p>Massively parallel pyrosequencing may be used to simplify and speed the search for DNA variations in PCR products. Our results encourage further studies to evaluate molecular diagnostics applications.</p

The monitoring program of grapevine phytoplasmas in Tuscany (Italy): results of a four year survey

Quantitative PCR protocols for phytoplasma detection were used tomonitor grapevine yellows (GY) in 373 vineyards located in nine Tuscan districts. Among more than 70,000 plants visually monitored, 1.867 plants were sampled and “flavescence dorée” phytoplasmas (FD) were detected in 122 plants and mainly identified as trains belonging to 16SrV-C subgroup. The “bois noir” (BN) phytoplasma was found in 734 samples, with prevalence of tufB type-b strains. The 2013–2015 monitoring program was strongly influenced by the first survey (2012) in which FD was found consistently in the North West (15 samples), whereas only a few cases were observed in the East territory (2 samples). Both areas were thoroughly monitored in the following years: few foci were found in the East (2 in 2014, 1 in 2015), while several infected areas were found in the North West (6, 10 and 22 foci in 2013, 2014 and 2015, respectively). Definitely, the novel FD foci detected in the survey (17, 6, 12 and 23 in each year of survey) and the widespread of BN, suggest a dangerous distribution of GY in Tuscany