VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL

SUMMARY: The program varsplic.pl uses information present in the SWISS-PROT and TrEMBL databases to create new records for alternatively spliced isoforms. These new records can be used in similarity searches. AVAILABILITY: The program is available at ftp://ftp.ebi.ac.uk/pub/software/swissprot/, together with regularly updated output files. CONTACT: pkersey@ebi.ac.uk     

Time course of the effects of static stretching on cycling economy

Stretching has been implemented as part of the warm-up before physical events and widely thought to promote increased sport performance and decreased injury risk. However, recent research has concluded that static stretching before many exercises inhibits acute power, strength, and sprinting performance. There is little research examining the time course of these effects on moderate intensity cycling. The purpose of this study was to examine the time course of static stretching on cycling economy. The subjects consisted of 5 men and 5 women highly trained endurance cyclists. The first of 3 visits was baseline testing of their cycling VO2max. The second and third visits were either stretching or no stretching before a 30-minute stationary ride at 65% of their VO2max. The stretching condition consisted of four 30-second repetitions of 5 stretches with an average total stretching time of 16 minutes. VO2 demonstrated a significant condition by time interaction with the 5-minute time point being significantly less in the nonstretching condition (32.66 ± 5.35 ml·kg(-1)·min(-1)) than stretching (34.39 ± 5.39 ml·kg(-1)·min(-1)). No other time points were different. Our results demonstrate that static stretching yielded an acute increase in submaximal VO2; therefore, coaches and highly trained endurance cyclists should exclude static stretching immediately before moderate intensity cycling because it reduces acute cycling economy.     

Linking publication, gene and protein data

The computational reconstruction of biological systems, 'systems biology', is necessarily dependent on the existence of well-annotated data sets defining and describing the components of these systems, especially genes and the proteins they encode. Information about these components can be accessed either through structured bioinformatics databases, which store basic chemical and functional information abstracted from (or supplementing) the scientific literature, or through the literature itself, which is richer in content but essentially unstructured.     

Large Hawk‐Cuckoo Hierococcyx sparverioides parasitism on the Chinese Babax Babax lanceolatus may be an evolutionarily recent host–parasite system

We documented brood parasitism by the poorly studied Large Hawk‐Cuckoo on a previously unknown host species, the Chinese Babax. Furthermore, we describe a new egg colour for the Large Hawk‐Cuckoo. The parasitism rate of Chinese Babax nests over 4 years was 6.9% (11 of 159 nests), with significant temporal variation. The Large Hawk‐Cuckoo laid immaculate white eggs that appeared non‐mimetic to the blue Babax eggs, an impression that was confirmed by avian visual modelling. Nevertheless, most Cuckoo eggs were accepted by the host, suggesting that this host–parasite system may be evolutionarily recent.     

Bioturbation in a declining oxygen environment, in situ observations from Wormcam

Bioturbation, the displacement and mixing of sediment particles by fauna or flora, facilitates life supporting processes by increasing the quality of marine sediments. In the marine environment bioturbation is primarily mediated by infaunal organisms, which are susceptible to perturbations in their surrounding environment due to their sedentary life history traits. Of particular concern is hypoxia, dissolved oxygen (DO) concentrations ≤2.8 mg l(-1), a prevalent and persistent problem that affects both pelagic and benthic fauna. A benthic observing system (Wormcam) consisting of a buoy, telemetering electronics, sediment profile camera, and water quality datasonde was developed and deployed in the Rappahannock River, VA, USA, in an area known to experience seasonal hypoxia from early spring to late fall. Wormcam transmitted a time series of in situ images and water quality data, to a website via wireless internet modem, for 5 months spanning normoxic and hypoxic periods. Hypoxia was found to significantly reduce bioturbation through reductions in burrow lengths, burrow production, and burrowing depth. Although infaunal activity was greatly reduced during hypoxic and near anoxic conditions, some individuals remained active. Low concentrations of DO in the water column limited bioturbation by infaunal burrowers and likely reduced redox cycling between aerobic and anaerobic states. This study emphasizes the importance of in situ observations for understanding how components of an ecosystem respond to hypoxia.     

Parnassia palustris: a genetically diverse species in Scandinavia

Patterns of variation at nine enzyme loci were examined in 528 plants representing diploid and tetraploid populations of Parnassia palustris s. l. in Europe to assess genetic variation patterns and migration history. Half of the plants showed a unique multilocus phenotype and 75% of all phenotypes occurred only in Scandinavia. Diploid populations showed similar levels of genetic diversity as other widespread outbreeding species with animal-mediated pollination and F -statistics indicated excessive heterozygosity and low rates of gene flow among them. In spite of dramatic population histories caused by the ice ages, diploid populations have maintained the same genetic diversity in Scandinavia as in central and southern Europe. Northern populations have apparently been established through the gradual advance of genetically variable populations and patterns of variation at individual loci indicate different migration routes, from the south-south-west and the east-north-east, respectively. The data strongly support a repeated autoploid origin of the tetraploid cytotype which has been much more successful than the diploid progenitors in colonizing new land since the last ice age. High genetic diversity in Scandinavia has apparently been obtained by a combination of immigration of plants from different source areas and recurrent formation of autotetraploids from diploid progenitors.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 142 , 347−372.     

Modeling the Effect of Hypoxia on Macrobenthos Production in the Lower Rappahannock River,Chesapeake Bay,USA

Hypoxia in Chesapeake Bay has substantially increased in recent decades, with detrimental effects on macrobenthic production; the production of these fauna link energy transfer from primary consumers to epibenthic and demersal predators. As such, the development of accurate predictive models that determine the impact of hypoxia on macrobenthic production is important. A continuous-time, biomass-based model was developed for the lower Rappahannock River, a Bay tributary prone to seasonal hypoxia. Phytoplankton, zooplankton, and macrobenthic state variables were modeled, with a focus on quantitatively constraining the effect of hypoxia on macrobenthic biomass. This was accomplished through regression with Z'': a sigmoidal function between macrobenthic biomass and dissolved oxygen concentration, derived using macrobenthic data collected from the Rappahannock River during the summers of 2007 and 2008, and applied to compute hypoxia-induced mortality as a rate process. The model was verified using independent monitoring data collected by the Chesapeake Bay Program. Simulations showed that macrobenthic biomass was strongly linked to dissolved oxygen concentrations, with fluctuations in biomass related to the duration and severity of hypoxia. Our model demonstrated that hypoxia negatively affected macrobenthic biomass, as longer durations of hypoxia and greater hypoxic severity resulted in an increasing loss in biomass. This exercise represents an important contribution to modeling anthropogenically impacted coastal ecosystems, by providing an empirically constrained relationship between hypoxia and macrobenthic biomass, and applying that empirical relationship in a mechanistic model to quantify the effect of the severity, duration, and frequency of hypoxia on benthic biomass dynamics.