West Nile Virus Encephalitis in Haematological Setting: Report of Two Cases and a Brief Review of the Literature

West Nile virus is a zoonotic agent causing life-threatening encephalitis in a proportion of infected patients. Older age, immunosuppression, and mutations in specific host genes (e.g., CCR5 delta-32 mutation) predispose to neuroinvasive infection. We report on two cases of severe West Nile encephalitis in recently-treated, different-aged, chronic lymphocytic leukemia patients. Both patients developed high-grade fever associated with severe neurological impairment. The younger one harboured germ-line CCR5 delta-32 mutation, which might have played a role in the pathogenesis of its neuroinvasive manifestations

High prevalence of patent foramen ovale in migraine with aura

In this study we evaluated the presence of patent foramen ovale (PFO) in a cohort of 25 consecutive patients suffering from migraine with aura (MA) during an attack presenting to the emergency ward of an Italian hospital. Patients underwent brain magnetic resonance imaging (MRI) with contrast medium, routine coagulation tests, contrast transcranial echocolour–coded sonography (c–TCCS) and transoesophageal echocardiography (TEE). Of the enrolled patients, 88.7% showed a PFO according to the c–TCCS test, whereas only in 72% TEE confirmed the presence of PFO. This discordance could be due to the fact that c–TCCS is more sensitive even with shunts with minimal capacity also located in the pulmonary vasculature. After surgical treatment of the PFO, MA disappeared within two months. Also, the treatment with warfarin as well as with acetylsalicylic acid and flunarizine was able to dramatically reduce the frequency of migraine attacks. These data indicate a higher prevalence of PFO in MA vs. normal population (OR=2.92) and could suggest that the presence of arteriovenous (AV) shunts could represent a trigger for MA attacks as well as for stroke, but more studies are needed to confirm this preliminary hypothesis

Combining next-generation pyrosequencing with microarray for large scale expression analysis in non-model species

<p>Abstract</p> <p>Background</p> <p>The next generation sequencing technologies provide new options to characterize the transcriptome and to develop affordable tools for functional genomics. We describe here an innovative approach for this purpose and demonstrate its potential also for non-model species.</p> <p>Results</p> <p>The method we developed is based on 454 sequencing of 3' cDNA fragments from a normalized library constructed from pooled RNAs to generate, through <it>de novo </it>reads assembly, a large catalog of unique transcripts in organisms for which a comprehensive collection of transcripts or the complete genome sequence, is not available. This "virtual transcriptome" provides extensive coverage depth, and can be used for the setting up of a comprehensive microarray based expression analysis. We evaluated the potential of this approach by monitoring gene expression during berry maturation in <it>Vitis vinifera </it>as if no other sequence information was available for this species. The microarray designed on the berries' transcriptome derived from half of a 454 run detected the expression of 19,609 genes, and proved to be more informative than one of the most comprehensive grape microarrays available to date, the GrapeArray 1.2 developed by the Italian-French Public Consortium for Grapevine Genome Characterization, which could detect the expression of 15,556 genes in the same samples.</p> <p>Conclusion</p> <p>This approach provides a powerful method to rapidly build up an extensive catalog of unique transcripts that can be successfully used to develop a microarray for large scale analysis of gene expression in any species, without the need for prior sequence knowledge.</p

cDNA-AFLP analysis of plant and pathogen genes expressed in grapevine infected with Plasmopara viticola

<p>Abstract</p> <p>Background</p> <p>The oomycete <it>Plasmopara viticola </it>(Berk. and Curt.) Berl. and de Toni causes downy mildew in grapevine (<it>Vitis vinifera </it>L.). This pathogen is strictly biotrophic, thus completely dependent on living host cells for its survival. The molecular basis of compatibility and disease development in this system is poorly understood. We have carried out a large-scale cDNA-AFLP analysis to identify grapevine and <it>P. viticola </it>genes associated with the infection process.</p> <p>Results</p> <p>We carried out cDNA-AFLP analysis on artificially infected leaves of the susceptible cultivar Riesling at the oil spot stage, on water-treated leaves and on a sample of pure sporangia as controls. Selective amplifications with 128 primer combinations allowed the visualization of about 7000 transcript-derived fragments (TDFs) in infected leaves, 1196 of which (17%) were differentially expressed. We sequenced 984 fragments, 804 of which were identified as grapevine transcripts after homology searching, while 96 were homologous to sequences in <it>Phytophthora </it>spp. databases and were attributed to <it>P. viticola</it>. There were 82 orphan TDFs. Many grapevine genes spanning almost all functional categories were downregulated during infection, especially genes involved in photosynthesis. Grapevine genes homologous to known resistance genes also tended to be repressed, as were several resistance gene analogs and carbonic anhydrase (recently implicated in pathogen resistance). In contrast, genes encoding cytoskeletal components, enzymes of the phenylpropanoid and beta-oxidation pathways, and pathogenesis related proteins were primarily upregulated during infection. The majority of <it>P. viticola </it>transcripts expressed <it>in planta </it>showed homology to genes of unknown function or to genomic <it>Phytophthora </it>sequences, but genes related to metabolism, energy production, transport and signal transduction were also identified.</p> <p>Conclusion</p> <p>This study provides the first global catalogue of grapevine and <it>P. viticola </it>genes expressed during infection, together with their functional annotations. This will help to elucidate the molecular basis of the infection process and identify genes and chemicals that could help to inhibit the pathogen.</p

Planning for assisted colonization of plants in a warming world

Assisted colonization is one way of facilitating range shifts for species that are restricted in their ability to move in response to climate change. Here we conceptualize and apply a new decision framework for modelling assisted colonization of plant species prior to in situ realization. Three questions were examined: a) Is species translocation useful in a certain area? b) where, and c) how long will it be successful in the future? Applying our framework to Carex foetida in Italy at the core of its distribution and its southern edge revealed that assisted colonization could be successful in short-term (2010–2039) climate conditions, partially in medium (2040–2069) but not in long-term (2070–2099) scenarios. We show that, for some species, it is likely that assisted colonization would be successful in some portions of the recipient site under current and short-term climate conditions, but over the mid- and long-term, climate changes will make species translocation unsuccessful. The proposed decision framework can help identify species that will need different conservation actions (seed banks and/or botanical gardens) when assisted colonization is unlikely to be successful. Furthermore it has broad applicability, as it can support planning of assisted migration in mountainous areas in the face of climate change.University of Pavia

Effects of a dietary crude fibre concentrate on growth in weaned piglets

Many fibre sources can help the adaptation of piglets at weaning, improving the growth. In this study, the effects of a dietary crude fibre concentrate (CFC) on piglet’s growth was investigated. From 31 to 51 days of age, 108 weaned piglets (D×(Lw×L)), had access to two isofibrous, isoenergetic and isonitrogenous diets, supplemented with 1% of CFC (CFC group) or not (control (CON) group). From days 52 to 64 all piglets received the same starter diet. During the dietary treatment period the CFC group showed higher average daily gain, average daily feed intake and feed efficiency (P&lt;0.001) than CON group. At 64 days of age, BW was higher in CFC group compared with CON group (P&lt;0.001). Blood samples were collected at days 31, 38, 45 and 52 of age. From days 31 to 52 significant differences in the somatotropic axis between groups were observed. In particular, growth hormone levels were higher only at the end of the 1st week of dietary treatment (P&lt;0.05) in CFC group animals compared with CON group animals. The IGF-I trend was similar between groups even if the IGF-I levels were higher in the CFC group than CON group 1 week after starting treatment (P&lt;0.01). The IGF-binding protein 3 (IGFBP-3) levels were higher in the first 2 weeks of dietary treatment and lower in the 3rd week in CON group compared with CFC group (P&lt;0.01). Specifically, the IGFBP-3 profile was consistent with that of IGF-I in CFC group but not in CON group. At the same time, an increase of leptin in CFC compared with CON group was observed (P&lt;0.05). Piglets fed the CFC diet showed a lower diarrhoea incidence (P&lt;0.05) and a lower number of antibiotic interventions (P&lt;0.05) than CON diet from 31 to 51 days of age. Pig-major acute-phase protein plasma level (P&lt;0.01) and interleukin-6 gene expression (P&lt;0.05) were higher in CON group than CFC group at the end of 1st week of dietary treatment. In conclusion, this study showed that CFC diet influences the hormones related to energy balance enhancing the welfare and growth of piglets. Furthermore, the increase in feed intake during 3 weeks of dietary treatment improved the feed efficiency over the entire post-weaning period

The ascorbic acid content of tomato fruits is associated with the expression of genes involved in pectin degradation

<p>Abstract</p> <p>Background</p> <p>High levels of ascorbic acid (AsA) in tomato fruits provide health benefits for humans and also play an important role in several aspects of plant life. Although AsA metabolism has been characterized in detail, the genetic mechanisms controlling AsA accumulation in tomatoes are poorly understood. The transcriptional control of AsA levels in fruits can be investigated by combining the advanced genetic and genomic resources currently available for tomato. A comparative transcriptomic analysis of fruit tissues was carried out on an introgression line containing a QTL promoting AsA accumulation in the fruit, using a parental cultivar with lower AsA levels as a reference.</p> <p>Results</p> <p>Introgression line IL 12-4 (<it>S. pennellii </it>in a <it>S. lycopersicum </it>background) was selected for transcriptomic analysis because it maintained differences in AsA levels compared to the parental genotypes M82 and <it>S. pennellii </it>over three consecutive trials. Comparative microarray analysis of IL 12-4 and M82 fruits over a 2-year period allowed 253 differentially-expressed genes to be identified, suggesting that AsA accumulation in IL 12-4 may be caused by a combination of increased metabolic flux and reduced utilization of AsA. In particular, the upregulation of a pectinesterase and two polygalacturonases suggests that AsA accumulation in IL12-4 fruit is mainly achieved by increasing flux through the L-galactonic acid pathway, which is driven by pectin degradation and may be triggered by ethylene.</p> <p>Conclusions</p> <p>Based on functional annotation, gene ontology classification and hierarchical clustering, a subset of the 253 differentially-expressed transcripts was used to develop a model to explain the higher AsA content in IL 12-4 fruits in terms of metabolic flux, precursor availability, demand for antioxidants, abundance of reactive oxygen species and ethylene signaling.</p

General and species-specific transcriptional responses to downy mildew infection in a susceptible (Vitis vinifera) and a resistant (V. riparia) grapevine species

<p>Abstract</p> <p>Background</p> <p>Downy mildew is a destructive grapevine disease caused by <it>Plasmopara viticola </it>(Berk. and Curt.) Berl. and de Toni, which can only be controlled by intensive fungicide treatments. Natural sources of resistance from wild grapevine (<it>Vitis</it>) species are used in conventional breeding approaches, but the signals and effectors involved in resistance in this important crop species are not well understood.</p> <p>Results</p> <p>Early transcriptional changes associated with <it>P. viticola </it>infection in susceptible <it>V. vinifera </it>and resistant <it>V. riparia </it>plants were analyzed using the Combimatrix microarray platform. Transcript levels were measured 12 and 24 h post-inoculation, reflecting the time points immediately preceding the onset of resistance in <it>V. riparia</it>, as determined by microscopic analysis. Our data indicate that resistance in <it>V. riparia </it>is induced after infection, and is not based on differences in basal gene expression between the two species. The strong and rapid transcriptional reprogramming involves the induction of pathogenesis-related proteins and enzymes required for the synthesis of phenylpropanoid-derived compounds, many of which are also induced, albeit to a lesser extent, in <it>V. vinifera</it>. More interestingly, resistance in <it>V. riparia </it>also involves the specific modulation of numerous transcripts encoding components of signal transduction cascades, hypersensitive reaction markers and genes involved in jasmonate biosynthesis. The limited transcriptional modulation in <it>V. vinifera </it>represents a weak attempted defense response rather than the activation of compatibility-specific pathways.</p> <p>Conclusions</p> <p>Several candidate resistance genes were identified that could be exploited in future biotechnological approaches to increase disease resistance in susceptible grapevine species. Measurements of jasmonic acid and methyl jasmonate in infected leaves suggest that this hormone may also be involved in <it>V. riparia </it>resistance to <it>P. viticola</it>.</p

Correction: High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera

The version of this article published in BMC Genomics 2009, 10:558, contains data in Table 1 which are now known to be unreliable, and an illustration, in Figure 1, of unusual miRNA processing events predicted by these unreliable data. In this full-length correction, new data replace those found to be unreliable, leading to a more straightforward interpretation without altering the principle conclusions of the study. Table 1 and associated methods have been corrected, Figure 1 deleted, supplementary file 1 added, and modifications made to the sections "Deep sequencing of small RNAs from grapevine leaf tissue" and "Microarray analysis of miRNA expression". The editors and authors regret the inconvenience caused to readers by premature publication of the original paper

High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera

<p>Abstract</p> <p>Background</p> <p>MicroRNAs are short (~21 base) single stranded RNAs that, in plants, are generally coded by specific genes and cleaved specifically from hairpin precursors. MicroRNAs are critical for the regulation of multiple developmental, stress related and other physiological processes in plants. The recent annotation of the genome of the grapevine (<it>Vitis vinifera </it>L.) allowed the identification of many putative conserved microRNA precursors, grouped into multiple gene families.</p> <p>Results</p> <p>Here we use oligonucleotide arrays to provide the first indication that many of these microRNAs show differential expression patterns between tissues and during the maturation of fruit in the grapevine. Furthermore we demonstrate that whole transcriptome sequencing and deep-sequencing of small RNA fractions can be used both to identify which microRNA precursors are expressed in different tissues and to estimate genomic coordinates and patterns of splicing and alternative splicing for many primary miRNA transcripts.</p> <p>Conclusion</p> <p>Our results show that many microRNAs are differentially expressed in different tissues and during fruit maturation in the grapevine. Furthermore, the demonstration that whole transcriptome sequencing can be used to identify candidate splicing events and approximate primary microRNA transcript coordinates represents a significant step towards the large-scale elucidation of mechanisms regulating the expression of microRNAs at the transcriptional and post-transcriptional levels.</p