Phyletic Profiling with Cliques of Orthologs Is Enhanced by Signatures of Paralogy Relationships

New microbial genomes are sequenced at a high pace, allowing insight into the genetics of not only cultured microbes, but a wide range of metagenomic collections such as the human microbiome. To understand the deluge of genomic data we face, computational approaches for gene functional annotation are invaluable. We introduce a novel model for computational annotation that refines two established concepts: annotation based on homology and annotation based on phyletic profiling. The phyletic profiling-based model that includes both inferred orthologs and paralogs—homologs separated by a speciation and a duplication event, respectively—provides more annotations at the same average Precision than the model that includes only inferred orthologs. For experimental validation, we selected 38 poorly annotated Escherichia coli genes for which the model assigned one of three GO terms with high confidence: involvement in DNA repair, protein translation, or cell wall synthesis. Results of antibiotic stress survival assays on E. coli knockout mutants showed high agreement with our model''s estimates of accuracy: out of 38 predictions obtained at the reported Precision of 60%, we confirmed 25 predictions, indicating that our confidence estimates can be used to make informed decisions on experimental validation. Our work will contribute to making experimental validation of computational predictions more approachable, both in cost and time. Our predictions for 998 prokaryotic genomes include ∼400000 specific annotations with the estimated Precision of 90%, ∼19000 of which are highly specific—e.g. “penicillin binding,” “tRNA aminoacylation for protein translation,” or “pathogenesis”—and are freely available at http://gorbi.irb.hr/.     

Ground beetle assemblages and distribution of functional traits in olive orchards and vineyards depend on the agricultural management practice

BioControl - Biodiversity in the Mediterranean is undergoing a decline resulting in reduced ecosystem service provisions. Here we analysed the functional diversity of ground beetles in...     

ApoE genotyping and response to galanthamine in Alzheimer's disease--a real life retrospective study

This study was undertaken to evaluate the effect of galanthamine, a new cholinesterase inhibitor on cognitive performances in 84 patients with various apoE genotype and Alzheimer's disease (AD) during the six-month treatment. The diagnosis of AD was made on the basis of NINCDS/ADRDN criteria. ApoE4 genotype was determined by PCR procedure. The cognitive performance was assessed MMSE at baseline and six months later. The difference among the groups was statistically analyzed by ANOVA model and Pearson's chi2-test. The MMSE at baseline in all completes was 18.0 +/- 3.73, whereas the mean value of MMSE after 6 months was 16.4 +/- 5.61 indicating significant deterioration (p < 0.01). Of the 84 patients, 14 (169%) were apoE4 homozygous, 41 (49%) were heterozygous, whereas 29 (35%) were apoE4 negative. The significant number of responders was observed among apoE4 homozygous patients (71%; chi2 = 6.89; p = 0.032). The subgroup of apoE4 homozygous patients with AD in its mild to moderate stage may be considered as responders to galanthamine.     

Bilateral amaurosis caused by Salmonella enteritidis infection

The aim of this paper was to show the potential of Salmonella enteritidis infection to eventually result in visual impairment. A case of salmonellosis in a 6-year-old boy, caused by intake of a cake made from eggs infected with Salmonella enteritidis, is presented. Prolonged duration of the disease was followed by complete remission of neurologic complications and persistent amaurosis with bilateral optic nerve atrophy. A severe form of Salmonella enterocolitis with neurologic involvement can lead to optic nerve lesion with consequential loss of vision.     

Comparative morphology of incisor enamel and dentin in humans and fat dormice (Glis glis)

The structure of teeth in all living beings is genetically predetermined, although it can change under external physiological and pathological factors. The author's hypothesis was to indicate evolutional shifts resulting from genetic, functional and other differences. A comparative study about certain characteristics of incisors in humans and myomorpha, the fat dormouse (Glis glis) being their representative as well, comprised measurements of enamel and dentin thickness in individual incisor segments, evaluation of external enamel index, and also assessment of histological structure of enamel and dentin. The study results involving dormice showed the enamel to be thicker in lower than in the upper teeth, quite contrary to enamel thickness in humans. In the upper incisors in dormice the enamel is the thickest in the medial layer of the crown, and in the cervical portion of the crown in the lower incisors. The thickness of dentin in dormice is greater in the oral than in the vestibular side. These findings significantly differ from those reported in reference literature, but they are based on the function of teeth in dormice. Histological characteristics of hard dental tissues in dormice are similar to those in humans, with exception of uniserial structure of enamel and appearance of dentinoenamel junction.     

Holistic approach to functional anatomy of the injured ankle joint

Talocrural joint injuries are among the most common injuries of the joints and therefore there is a need for a holistic approach to analysis of morphology, biomechanics and visualization of the talocrural joint ligamentary apparatus in different positions. The research was carried out on 20 fresh and conserved anatomical specimens of the lower leg on which X-ray, computed tomography, ultrasonography and stress analysis were performed before and after the lesion of ligaments. Also the gait of 130 adults without (100) and with ligament and joint capsule lesion (30) was analyzed by infrared telemetry. After complete discission of the lateral ligaments, arthrography and CT could register the lesion, while X-ray and ultrasonography could not detect it. Gait analysis of healthy and injured leg showed that the injured leg was significantly less loaded.     

(+)-(S)-alapyridaine--a general taste enhancer?

N-(1-Carboxyethyl)-6-hydroxymethyl-pyridinium-3-ol inner salt (alapyridaine), recently identified in heated sugar/amino acid mixtures as well as in beef bouillon, has been shown to exhibit general taste-enhancing activities, although tasteless on its own. Differing from other taste enhancers reported so far, racemic (R/S)-alapyridaine and, to an even greater extent (+)-(S)-alapyridaine, the physiologically active enantiomer, are able to enhance more than one basic taste quality. The threshold concentrations for the sweet taste of glucose and sucrose, for the umami taste of monosodium L-glutamate (MSG) and guanosine-5'-monophosphate (GMP), as well as the salty taste of NaCl, were significantly decreased when alapyridaine was present. In contrast, perception of the bitter tastes of caffeine and L-phenylalanine, as well as of sour-tasting citric acid, was unaffected. Furthermore, alapyridaine was shown to intensify known taste synergies such as, for example, the enhancing effect of L-arginine on the salty taste of NaCl, as well as that of GMP on the umami taste of MSG. The activity of (+)-(S)-alapyridaine could be observed not only in solutions of single taste compounds, but also in more complex tastant mixtures; for example, the umami, sweet and salty taste of a solution containing MSG, sucrose, NaCl and caffeine was significantly modulated, thus indicating that alapyridaine is a general taste enhancer.