An enhanced workflow for variant interpretation in UniProtKB/Swiss-Prot improves consistency and reuse in ClinVar.

Personalized genomic medicine depends on integrated analyses that combine genetic and phenotypic data from individual patients with reference knowledge of the functional and clinical significance of sequence variants. Sources of this reference knowledge include the ClinVar repository of human genetic variants, a community resource that accepts submissions from external groups, and UniProtKB/Swiss-Prot, an expert-curated resource of protein sequences and functional annotation. UniProtKB/Swiss-Prot provides knowledge on the functional impact and clinical significance of over 30 000 human protein-coding sequence variants, curated from peer-reviewed literature reports. Here we present a pilot study that lays the groundwork for the integration of curated knowledge of protein sequence variation from UniProtKB/Swiss-Prot with ClinVar. We show that existing interpretations of variant pathogenicity in UniProtKB/Swiss-Prot and ClinVar are highly concordant, with 88% of variants that are common to the two resources having interpretations of clinical significance that agree. Re-curation of a subset of UniProtKB/Swiss-Prot variants according to American College of Medical Genetics and Genomics (ACMG) guidelines using ClinGen tools further increases this level of agreement, mainly due to the reclassification of supposedly pathogenic variants as benign, based on newly available population frequency data. We have now incorporated ACMG guidelines and ClinGen tools into the UniProt Knowledgebase (UniProtKB) curation workflow and routinely submit variant data from UniProtKB/Swiss-Prot to ClinVar. These efforts will increase the usability and utilization of UniProtKB variant data and will facilitate the continuing (re-)evaluation of clinical variant interpretations as data sets and knowledge evolve.

Upper eyelid necrosis and reconstruction after spider byte: case report and review of the literature.

Spider bites are not very common, especially in the Mediterranean area, and those affecting the ocular-palpebral region involving reconstructive surgery are particularly rare. In May 2010, the case of a Caucasian 24-year-old female patient was brought to the attention of the Dermatology Department, University of Cagliari, Italy. The patient reported she woke up feeling an intense pain with itching and that also she had noticed a spider of an unknown species on her bed. The dermatosis had affected the right orbital region, where there was a considerable red and violet erythema and a hard edema, not foldable. When the necrosis appeared the patient was treated at the Plastic Surgery Unit where she underwent a reconstruction of the eyelid with a full thickness skin graft from the retroauricular area. The post-operative course was regular with a perfect in-take of the skin graft. When the patient was discharged she was sent to an Entomological University Centre to identify the spider species and the possible venom which caused the skin lesion. The spider which caused the injury has been a Loxosceles rufescens (Dufour, 1820). Loxoscelism is a necrotic arachnoidism caused by the poisonous bite of spiders belonging to the Loxosceles species. It is very important to identify what sort of lesion it is and to treat it in a combined way in order to choose the proper timing for surgery to avoid damages to the eyelid functioning.

Surfactant-Induced hydrogen production in cyanobacteria.

Addition of Tween 85 to aqueous suspensions of Anabaena variabilis induced photosynthetic evolution of hydrogen over a time span of several weeks: As much as 148 nmol H(2)/h . mg dry weight was produced in the first week by a suspension containing 4.2 mg dry weight of cells and 77 mM Tween 85. The chemical structure of Tween 85 was a necessary prerequisite for inducing hydrogen production, as compounds such as Tween 20, 60, and 80 had a quite different effect. There was a coupling between photosynthetic oxygen evolution and hydrogen evolution: Hydrogen evolution started to be effective only when oxygen evolution subdued. The presence of heterocysts in A. variabilis was also required for the Tween-induced hydrogen production. Based on these observations, possible mechanisms for the photosynthetic effect of Tween 85 are advanced and discussed.

Photosynthetic activity of cyanobacteria in water-in-oil microemulsions.

The solubilization and the photosynthetic activity of cyanobacteria (Anabaena variabilis) in water-in-oil microemulsions consisting of (Tween85/Span80)/hexadecane/water is investigated. Transparent and stable solutions containing up to 10(8) cells/mL could be obtained. The physical state and stability of the cells in the microemulsion, as evidenced from optical and electron microscopy, is dependent upon the physical parameters of the system, and in particular on the hydrophilic-lypophilic balance (HLB) of the surfactant system. Conditions could be found, under which the cells in the microemulsion system display photosynthetic activity This was judged by measuring polarographically the oxygen evolution and by studying the photosynthetic activity in the presence of specific inhibitors.

Gene block encoding production of cytotoxic necrotizing factor 1 and hemolysin in Escherichia coli isolates from extraintestinal infections.

Cytotoxic necrotizing factors (CNFs) are Escherichia coli protein toxins causing cell multinucleation and enlargement in tissue cultures and necrosis in rabbit skin. In E. coli isolates causing urinary tract infections in humans, the production of CNF1 is closely associated with hemolysin production. In this study, we obtained data suggesting that this phenotypic association is due to the genetic linkage of the determinants of the two toxins on the chromosome of uropathogenic E. coli. The genes encoding hemolysin and CNF1 were shown to be closely linked in a 37-kb cloned DNA fragment from an E. coli urinary tract isolate of serotype O4:K12:H5 (E-B35). A DNA region encoding CNF1 production but not hemolysin production was further subcloned as a 12-kb SalI-EcoRI fragment and used as a CNF1-specific gene probe. DNA hybridization experiments indicated that the CNF1 and hemolysin determinants were closely linked on the chromosomes of isolate E-B35 and six additional extraintestinal isolates belonging to serogroups O2, O4, O6, O22, O75, and O85.

Efectividad y tolerancia de dosis única de Rifampicina en la Uretritis Gonocócica / Tolerance and effectiveness single doses of Rifampicina in the gonococcal urethritis

Se estudiaron 100 pacientes de sexo masculino con diagnóstico de uretritis gonocócica aguda no complicada, confirmado por examen bacteriológico directo y cultivo. Se realizó tratamiento con 1.200 mg de Rifampicina en una sola dosis (4 cápsulas de 300 mg) y 48-72 hrs. después se constató curación clínica y bacteriológica en 93 pacientes. En un segundo control, 7-10 días después del tratamiento, se observaron 10 reinfecciones. Se constataron además 12 uretritis postgonocócicas. La C.I.M. de Rifampicina para el 60% de las cepas fue entre 0,063 y 0,125 mcg/ml y para el 90% de las cepas fue de 0,5 mcg/ml. Estos valores se compararon con los correspondientes a tetraciclina y espectinomicina. No se observaron reacciones adversas