Origin, evolution and stability of overlapping genes in viruses: A systematic review

During their long evolutionary history viruses generated many proteins de novo by a mechanism called “overprinting”. Overprinting is a process in which critical nucleotide substitutions in a pre-existing gene can induce the expression of a novel protein by translation of an alternative open reading frame (ORF). Overlapping genes represent an intriguing example of adaptive conflict, because they simultaneously encode two proteins whose freedom to change is constrained by each other. However, overlapping genes are also a source of genetic novelties, as the constraints under which alternative ORFs evolve can give rise to proteins with unusual sequence properties, most importantly the potential for novel functions. Starting with the discovery of overlapping genes in phages infecting Escherichia coli, this review covers a range of studies dealing with detection of overlapping genes in small eukaryotic viruses (genomic length below 30 kb) and recognition of their critical role in the evolution of pathogenicity. Origin of overlapping genes, what factors favor their birth and retention, and how they manage their inherent adaptive conflict are extensively reviewed. Special attention is paid to the assembly of overlapping genes into ad hoc databases, suitable for future studies, and to the development of statistical methods for exploring viral genome sequences in search of undiscovered overlaps

Tailoring the photonic bandgap of porous silicon dielectric mirror

A systematic method to fabricate porous silicon one dimensional photonic crystals has been engineered to have a photonic bandwidth up to 2000nm. The observation of the tailorability of the photonic bandgap (PBG) underscores the requirement of the large refractive index contrast for making broad PBG structures. In this letter, we present the fabrication and characteristics of such structures that may be promising structures for a large variety of applications.Comment: Published in Appl. Phys. Let

Computational methods for inferring location and genealogy of overlapping genes in virus genomes: approaches and applications

Viruses may evolve to increase the amount of encoded genetic information by means of overlapping genes, which utilize several reading frames. Such overlapping genes may be especially impactful for genomes of small size, often serving a source of novel accessory proteins, some of which play a crucial role in viral pathogenicity or in promoting the systemic spread of virus. Diverse genome-based metrics were proposed to facilitate recognition of overlapping genes that otherwise may be overlooked during genome annotation. They can detect the atypical codon bias associated with the overlap (e.g. a statistically significant reduction in variability at synonymous sites) or other sequence-composition features peculiar to overlapping genes. In this review, I compare nine computational methods, discuss their strengths and limitations, and survey how they were applied to detect candidate overlapping genes in the genome of SARS-CoV-2, the etiological agent of COVID-19 pandemic

Endoscopic-assisted removal of ventricular catheter in high-risk patients

Introduction. Ventriculoperitoneal shunt carries a non-negligible failure rate often requiring multiple surgical procedures during patient’s lifetime. The most common cause is obstruction of the ventricular catheter that can be embedded in adhesions with choroid plexus, ependymal tissue, and fibrous material. In such cases, or when an intraventricular tumor is present, particular attention must be paid when removal of the ventricular catheter is required. The potential adhesions with the tip of the ventricular catheter results in an increased risk of life-threatening hemorrhage. Materials and methods. We present the case of a ventriculoperitoneal shunt proximal revision in a von Hippel–Lindau affected patient. The neuroendoscopic exploration to restore the patency of the ventricular system made it possible to notice a fibrous adhesion between the tip of the catheter and a pituitary hemangioblastoma abutting into the third ventricle. Discussion. Pituitary stalk hemangioblastoma is an infrequent localization, although it represents the most common supratentorial site of hemangioblastoma in patients affected by von Hippel–Lindau syndrome. In this and in similar cases, endoscopic-assisted shunt revision allows visualizing the tip of the ventricular catheter and eventual adhesions that can be coagulated and cut by simple maneuvers, without any morbidity for patients. Conclusion. In a ventriculoperitoneal shunt revision with the concomitant presence of an intraventricular tumor or lesion at risk of bleeding, the surgical procedure should be performed under neuroendoscopic observation to reduce the risk of intraventricular hemorrhage

Cavernous Angioma of the Corpus Callosum Presenting with Acute Psychosis

Psychiatric symptoms may occasionally be related to anatomic alterations of brain structures. Particularly, corpus callosum lesions seem to play a role in the change of patients’ behavior. We present a case of a sudden psychotic attack presumably due to a hemorrhagic cavernous angioma of the corpus callosum, which was surgically removed with complete resolution of symptoms. Although a developmental defect like agenesis or lipoma is present in the majority of these cases, a growing lesion of the corpus callosum can rarely be the primary cause. Since it is potentially possible to cure these patients, clinicians should be aware of this association

Antifungal and antibacterial activities of eugenol and non-polar extract of Syzygium aromaticum L.

The antimicrobial activity of eugenol and the non-polar extract from cloves (Syzygium aromaticum), was tested against the Staphylococcus aureus strain resistant to cefotaxime, Escherichia coli and Candida albicans using the disc diffusion antibiotic sensitivity technique. Soxhlet extraction was performed to separate the essential oil and GCMS method was used to identify the eugenol which is the main component of the clove essential oil. The measured growth inhibition zones showed significant activity against the 3 microbes. To conclude, eugenol is the major active ingredient of the clove essential oil extract

Power efficiency estimation of silicon nanocrystals based light emitting devices in alternating current regime

n/