Proteogenomics to discover the full coding content of genomes: A computational perspective

Proteogenomics has emerged as a field at the junction of genomics and proteomics. It is a loose collection of technologies that allow the search of tandem mass spectra against genomic databases to identify and characterize protein-coding genes. Proteogenomic peptides provide invaluable information for gene annotation, which is difficult or impossible to ascertain using standard annotation methods. Examples include confirmation of translation, reading-frame determination, identification of gene and exon boundaries, evidence for post-translational processing, identification of splice-forms including alternative splicing, and also, prediction of completely novel genes. For proteogenomics to deliver on its promise, however, it must overcome a number of technological hurdles, including speed and accuracy of peptide identification, construction and search of specialized databases, correction of sampling bias, and others. This article reviews the state of the art of the field, focusing on the current successes, and the role of computation in overcoming these challenges. We describe how technological and algorithmic advances have already enabled large-scale proteogenomic studies in many model organisms, including arabidopsis, yeast, fly, and human. We also provide a preview of the field going forward, describing early efforts in tackling the problems of complex gene structures, searching against genomes of related species, and immunoglobulin gene reconstruction.     

Utilization of milk energy by suckling mink kits

A total of 36 mink dams and their litters of 3, 6 or 9 kits were used for determination of milk intake of the suckling young by means of deuterium dilution technique, and chemical composition of milk and of kit bodies. Measurements were performed during lactation weeks 1?–?4, each week with 3 dams with each litter size. Milk intake was determined over a 48?h measurement period, and by the end of this milk samples were collected and 2 kits (litters of 6 and 9) or 1 kit per litter (litters of 3) were killed for body chemical composition. Based on the results, different models were applied for calculation of the energetic efficiency of milk. Dam milk yield increased steadily from week 1 until week 3 but only slightly from week 3 to 4. The increase declined with increasing litter size, and for dams suckling 9 kits the increment from week 3 to week 4 was only 2?g. The dry matter content of milk increased significantly as lactation progressed, being reflected in crude protein increasing from 6.9% in lactation week 1 to 8.1% in week 4. Milk fat increased concomitantly from 5.6% to 8.0%. In kit bodies, crude protein content increased from 9.4% in week 1 to about 12% in weeks 3 and 4. Body fat content increased from week 1 (4.1%) to week 3 (8.4%) and then declined in week 4 (7.1%). Animals suckled in litters of 3 kits had the highest milk intake and live weight and kits suckled in litters of 9 had the lowest milk intake, live weight and daily gain. In terms of milk intake per g gain kits in litters of 6 were the most efficient, with 4.1?g milk per g body gain. The metabolizable energy requirement for maintenance (MEm) was estimated to 448 kJ/kg^0.75 and the efficiency of utilization of ME for body gain (k_g) to 0.67, the estimates being higher (MEm) or in good agreement with previous findings (k_g) in suckling mink kits.     

Fluctuating asymmetry in bank vole populations (Rodentia, Arvicolinae) reflects stress caused by landscape fragmentation in the Mont-Saint-Michel Bay

In intensively farmed, reclaimed areas (polders) of Mont-St-Michel Bay, France, bank voles ( Clethrionomys glareolus ) live in fragmented hedgerows, where populations are small and dispersal rates and genetic diversity are low. These small populations are likely to have been exposed to potential environmental and/or genetic stress. The sensitivity of development to stress can be measured by fluctuating asymmetry (FA). FA was calculated for three samples from a disturbed area and one sample from an adjacent, more connected and undisturbed landscape. Size FA was estimated from 16 measurements of the skull and teeth whilst shape asymmetry was estimated from the skull alone. Bank voles in fragmented hedgerows of the disturbed area had a higher degree of FA than bank voles from the more extensive and more connected hedges of the undisturbed area. These results were confirmed by the study of shape asymmetry, body mass and centroid size of the skull. There were no differences in FA between the three disturbed area samples. We conclude that FA does not reveal differences in the development of bank voles living in isolation under different local conditions in the various parts of the disturbed area. However, FA may allow differentiation between populations from greatly contrasting landscapes.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 80, 37–44.     

Morphology of the facets of the proximal Tarsi bones from an ancient population

The analysis of morphological variation of tali and calcanei articular surfaces from “S'Illot des Porros” (Majorca, 2430±200 BP) has been made. It indicates the high frequency of extensions of the talocrural and subtalar surfaces, which are shown to be produced not only by a high level of stress on the bones. The presence of the sulcus tali facet in most cases could indicate, however, a greater degree of lateral movement of the foot.     

Plant palatability and disturbance level in aquatic habitats: an experimental approach using the snail Lymnaea stagnalis (L.)

1. The palatability of aquatic macrophytes to the snail Lymnaea stagnalis was investigated in the laboratory. Eight species of macrophyte were selected from habitats that differed in either flood disturbance regime or nutrient status.
2. In a non-choice test, single macrophyte species were offered to individual snails. The average amount of plant dry mass consumed per Lymnaea dry mass ranged from 3.6 ± 1.4 (±SE) to 63.6 ± 13.9 mg g^–1 day^–1 across plant species. In a choice test, all eight plant species were presented simultaneously to sets of five snails. The average total consumption was 66.1 ± 3.8 mg g^–1 day^–1 and the maximum average consumption for a single plant was 26.2 ± 3.6 mg g^–1 day^–1.
3. In both tests, the amount consumed by snails differed significantly between the plant species. The species growing in undisturbed habitats were the least consumed. Habitat nutrient status was unrelated to plant palatability.
4. These results suggest that macrophyte species growing in habitats that are rarely disturbed by floods allocate a greater proportion of their resources to resisting herbivory.     

Exceptional carbon uptake in European forests during the warm spring of 2007: a data–model analysis

Temperate and boreal forests undergo drastic functional changes in the springtime, shifting within a few weeks from net carbon (C) sources to net C sinks. Most of these changes are mediated by temperature. The autumn 2006–winter 2007 record warm period was followed by an exceptionally warm spring in Europe, making spring 2007 a good candidate for advances in the onset of the photosynthetically active period. An analysis of a decade of eddy covariance data from six European forests stands, which encompass a wide range of functional types (broadleaf evergreen, broadleaf deciduous, needleleaf evergreen) and a wide latitudinal band (from 44° to 62°N), revealed exceptional fluxes during spring 2007. Gross primary productivity (GPP) of spring 2007 was the maximum recorded in the decade examined for all sites but a Mediterranean evergreen forest (with a +40 to +130 gC m^?2 anomaly compared with the decadal mean over the January–May period). Total ecosystem respiration (TER) was also promoted during spring 2007, though less anomalous than GPP (with a +17 to +93 gC m^?2 anomaly over 5 months), leading to higher net uptake than the long‐term mean at all sites (+12 to +79 gC m^?2 anomaly over 5 months). A correlative analysis relating springtime C fluxes to simple phenological indices suggested spring C uptake and temperatures to be related. The CASTANEA process‐based model was used to disentangle the seasonality of climatic drivers (incoming radiation, air and soil temperatures) and biological drivers (canopy dynamics, thermal acclimation of photosynthesis to low temperatures) on spring C fluxes along the latitudinal gradient. A sensitivity analysis of model simulations evidenced the roles of (i) an exceptional early budburst combined with elevated air temperature in deciduous sites, and (ii) an early relief of winter thermal acclimation in coniferous sites for the promotion of 2007 spring assimilation.