Predicting deleterious nsSNPs: an analysis of sequence and structural attributes

Background  

There has been an explosion in the number of single nucleotide polymorphisms (SNPs) within public databases. In this study we focused on non-synonymous protein coding single nucleotide polymorphisms (nsSNPs), some associated with disease and others which are thought to be neutral. We describe the distribution of both types of nsSNPs using structural and sequence based features and assess the relative value of these attributes as predictors of function using machine learning methods. We also address the common problem of balance within machine learning methods and show the effect of imbalance on nsSNP function prediction. We show that nsSNP function prediction can be significantly improved by 100% undersampling of the majority class. The learnt rules were then applied to make predictions of function on all nsSNPs within Ensembl.     

Size, shape and structural versatility of the skull of the subterranean rodent Ctenomys (Rodentia, Caviomorpha): functional and morphological analysis

Morphological analysis of the skull of the subterranean rodent Ctenomys , a highly speciose genus which uses both claws and teeth when digging, shows that for a broad range of species size, scaling was associated with both variation and maintenance of shape. Our results show that the angle of incisor procumbency (AIP), a character largely viewed as an adaptation to digging with teeth, is highly variable. We found a non-significant relationship between AIP and basicranial axis (basioccipital + basisphenoid) length, a measure of overall skull size. Accordingly, both small and large Ctenomys species possess either high or low AIP. A significant relationship between AIP and diastema length, given the rostral allometry seen in Ctenomys , suggests that hypermorphosis to a certain extent influences AIP. However, the roots of the incisor are lateral to those of the cheek teeth and their position may thus shift freely. This observation supports the notion that skull structural design, and to a certain extent rostral allometry, underlies variation in AIP. On the other hand, the positive allometry of incisor width and thickness indicates that, in larger species, proportionately powerful incisors are able to resist greater bending forces. We found that the out-lever arm of the jaw adductor muscles scales with positive allometry against basicranial axis length. However, we found an isometric relationship between in- and out-lever arms. In this case, conservation of skull proportions, regardless of variation in size, is a feature possibly related to the maintenance of an effective tooth digging capability. Functional and ecological data are discussed when assessing the implications of size and shape variation in the skull of Ctenomys .  © 2003 The Linnean Society of London. Biological Journal of the Linnean Society , 2003, 78 , 85−96.     

Stable expression of Phytase (phyA) in canola (Brassica napus) seeds: towards a commercial product

TheAspergillus niger gene encoding phytase(phyA) was expressed in canola (Brassicanapus). Phytase expression is controlled by the seed-specificcruciferin (CruA) promoter. Secretion of the enzyme was aimed for byincorporating the cruciferin signal peptide in the expression construct.Transgenic canola lines were generated by Agrobacteriummediated transformation using nptII as the selectable marker. Ninety-fiveindependent transgenic events were generated. Phytase expression in the T1seedsranged from 0 to 600 U/g seed. Single-copy lines were selected(based on segregation for kanamycin resistance, phytase expression and Southernanalyses) from originally multi-copy transgenic lines. Phytase was expressed inthese sub-lines up to 103 U/g. Expression levels were monitoredthrough an additional 3–4 generations (in the greenhouse and in thefield)and the accumulation of phytase appeared to be fairly stable. In the expressionrange studied, phytase expression was gene-dosage dependent.     

Chemical biology: Paper alert

A selection of interesting papers that were published in the two months before our press date in major journals most likely to report significant results in chemical biology.     

Acclimation or stress symptom? An integrated study of intraspecific variation in the clonal plant Aechmea bromeliifolia,a widespread CAM tank‐bromeliad

The clonal tank-bromeliad Aechmea bromeliifolia (Rudge) Baker was found in four different habitats in a restinga (vegetation mosaic on sandy coastal plains), of south-eastern Brazil. These habitats (swamp forest, dry forest, dry shrubland and herbaceous marsh) lie within a few hundred metres of each other along a gradient extending inland from the coast, and differ markedly in terms of light and flood regime. We compared ramet morphology, leaf anatomy and physiology, and population parameters to examine the amplitude of trait variation of this widespread species in the studied restinga. This integrated approach allowed us to examine which variation conferred acclimation and which was merely a stress symptom. A . bromeliifolia showed site-specific differences in abundance, distribution, rosette size and shape, leaf anatomical arrangement and photochemical efficiency (potential quantum yield; F _v/ F _m) during the day. Most of the variation found seemed to be related to the interaction of light and flooding. The lowest number and size of ramets at the exposed, dry shrubland was matched by a marked leaf photoinhibition, which suggested poor acclimation to local levels of light intensity and limited water supply. In the other habitats, the morpho-physiological parameters measured suggested adequate foraging behaviour and site acclimation.  © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society, 2002, 140 , 391-401.