Stress-related transcriptomic changes associated with GFP transgene expression and active transgene silencing in plants.

Plants respond to biotic and abiotic stress by activating and interacting with multiple defense pathways, allowing for an efficient global defense response. RNA silencing is a conserved mechanism of regulation of gene expression directed by small RNAs important in acquired plant immunity and especially virus and transgene repression. Several RNA silencing pathways in plants are crucial to control developmental processes and provide protection against abiotic and biotic stresses as well as invasive nucleic acids such as viruses and transposable elements.

PSTVd infection in plants has a minor yet detectable effect on CG methylation.

Viroids are small circular RNAs infecting a wide range of plants. They do not code for any protein or peptide and therefore rely on their structure for their biological cycle. Observed phenotypes of viroid infected plants are thought to occur through changes at the transcriptional/translational level of the host.

Complete genome sequence of a carlavirus identified in grapevine (Vitis sp) in Greece.

Using high-throughput sequencing, we identified a novel carlavirus sequence in a 28-year-old 'Kotsifali' grapevine sample collected in Heraklion (Crete, Greece). Using RT-PCR and 5'/3' RACE together with Sanger sequencing, the complete genome sequence of 8299 nt was confirmed and found to contain five open reading frames (ORFs) but to lack an ORF6, which is present in some members of the genus Carlavirus. The novel sequence is most similar to those of two carlaviruses infecting caper, and taking into account the ICTV nomenclature, we propose the name "grapevine carlavirus 1" for this new virus.

Molecular basis of mood and cognitive adverse events elucidated via a combination of pharmacovigilance data mining and functional enrichment analysis.

Drug-induced Mood- and Cognition-related adverse events (MCAEs) are often only detected during the clinical trial phases of drug development, or even after marketing, thus posing a major safety concern and a challenge for both pharmaceutical companies and clinicians. To fill some gaps in the understanding and elucidate potential biological mechanisms of action frequently associated with MCAEs, we present a unique workflow linking observational population data with the available knowledge at molecular, cellular, and psychopharmacology levels. It is based on statistical analysis of pharmacovigilance reports and subsequent signaling pathway analyses, followed by evidence-based expert manual curation of the outcomes.

From depression to neurodegeneration and heart failure: re-examining the potential of MAO inhibitors.

Initially introduced in the 1950s for treating depression, monoamine oxidase (MAO) inhibitors were gradually abandoned, mainly owing to their potential for drug-drug and drug-food interactions, the most widely known being with tyramine-containing food (the 'cheese' effect). Since then, more selective MAO-A or MAO-B inhibitors have been developed with substantially reduced risks, and have been approved for the treatment of depression and Parkinson's disease, respectively. Recent research suggests that some of these drugs also have neuroprotective properties, while preclinical evidence expands the spectrum of potential indications to heart failure, renal diseases and multiple sclerosis.

Literature mining, ontologies and information visualization for drug repurposing.

The immense growth of MEDLINE coupled with the realization that a vast amount of biomedical knowledge is recorded in free-text format, has led to the appearance of a large number of literature mining techniques aiming to extract biomedical terms and their inter-relations from the scientific literature. Ontologies have been extensively utilized in the biomedical domain either as controlled vocabularies or to provide the framework for mapping relations between concepts in biology and medicine. Literature-based approaches and ontologies have been used in the past for the purpose of hypothesis generation in connection with drug discovery.

Drug repurposing and adverse event prediction using high-throughput literature analysis.

Drug repurposing is the process of using existing drugs in indications other than the ones they were originally designed for. It is an area of significant recent activity due to the mounting costs of traditional drug development and scarcity of new chemical entities brought to the market by bio-pharmaceutical companies. By selecting drugs that already satisfy basic toxicity, ADME and related criteria, drug repurposing promises to deliver significant value at reduced cost and in dramatically shorter time frames than is normally the case for the drug development process.

CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL function synergistically in the circadian clock of Arabidopsis.

The circadian clock is an endogenous mechanism that coordinates biological processes with daily and seasonal changes in the environment. Heterodimerization of central clock components is an important way of controlling clock function in several different circadian systems. CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY) are Myb-related proteins that function in or close to the central oscillator in Arabidopsis (Arabidopsis thaliana).

The clock protein CCA1 and the bZIP transcription factor HY5 physically interact to regulate gene expression in Arabidopsis.

The circadian clock regulates the expression of an array of Arabidopsis genes such as those encoding the LIGHT-HARVESTING CHLOROPHYLL A/B (Lhcb) proteins. We have previously studied the promoters of two of these Arabidopsis genes--Lhcb1*1 and Lhcb1*3--and identified a sequence that binds the clock protein CIRCADIAN CLOCK ASSOCIATED 1 (CCA1). This sequence, designated CCA1-binding site (CBS), is necessary for phytochrome and circadian responsiveness of these genes.

Mining of relations between proteins over biomedical scientific literature using a deep-linguistic approach.

Objective: The amount of new discoveries (as published in the scientific literature) in the biomedical area is growing at an exponential rate. This growth makes it very difficult to filter the most relevant results, and thus the extraction of the core information becomes very expensive. Therefore, there is a growing interest in text processing approaches that can deliver selected information from scientific publications, which can limit the amount of human intervention normally needed to gather those results.

Identification of echocardiographic indices for the early detection of left-ventricular systolic dysfunction in beta-thalassaemia via Self-Organizing Maps: a data-exploration study.

Congestive heart failure (CHF) remains the primary cause of death in patients suffering from beta-thalassaemia major. Its early detection allows the prompt initiation of aggressive chelation therapy, when the condition can still be reversed. We aimed at identifying echocardiographic indices for the early detection of left ventricular (LV) systolic dysfunction, the physiological abnormality underlying CHF, in these patients.

Novel biological networks modulated by complement.

The almost complete deciphering of the human genome has paved the way for the application of new technology platforms in understanding the contribution of complex biological pathways to human pathophysiology and disease. In the post-genomic era, the concept of systems biology has gained significant momentum and biomedical research is now being conducted on an integrated and cross-disciplinary platform that pulls together its resources from diverse fields such as computational biology, bioinformatics, functional genomics, structural biology, and proteomics. In this perspective, the identity of established biologic systems is being re-examined in the light of novel findings that suggest novel associations between otherwise unrelated pathways and individual proteins.