Translational Bioinformatics:Past,Present, and Future

Though a relatively young discipline, translational bioinformatics (TBI) has become a key component of biomedical research in the era of precision medicine. Development of high-throughput technologies and electronic health records has caused a paradigm shift in both healthcare and biomedical research. Novel tools and methods are required to convert increasingly voluminous datasets into information and actionable knowledge. This review provides a definition and contex-tualization of the term TBI, describes the discipline’s brief history and past accomplishments, as well as current foci, and concludes with predictions of future directions in the field.     

Resource partitioning between ungulate populations in arid environments

Herbivores are major drivers of ecosystem structure, diversity, and function. Resilient ecosystems therefore require viable herbivore populations in a sustainable balance with environmental resource availability. This balance is becoming harder to achieve, with increasingly threatened species reliant on small protected areas in increasingly harsh and unpredictable environments. Arid environments in North Africa exemplify this situation, featuring a biologically distinct species assemblage exposed to extreme and volatile conditions, including habitat loss and climate change‐associated threats. Here, we implement an integrated likelihood approach to relate scimitar‐horned oryx (Oryx dammah) and dorcas gazelle (Gazella dorcas) density, via dung distance sampling, to habitat, predator, and geographic correlates in Dghoumes National Park, Tunisia. We show how two threatened sympatric ungulates partition resources on the habitat axis, exhibiting nonuniform responses to the same vegetation gradient. Scimitar‐horned oryx were positively associated with plant species richness, selecting for vegetated ephemeral watercourses (wadis) dominated by herbaceous cover. Conversely, dorcas gazelle were negatively associated with vegetation density (herbaceous height, litter cover, and herbaceous cover), selecting instead for rocky plains with sparse vegetation. We suggest that adequate plant species richness should be a prerequisite for areas proposed for future ungulate reintroductions in arid and semi‐arid environments. This evidence will inform adaptive management of reintroduced ungulates in protected environments, helping managers and planners design sustainable ecosystems and effective conservation programs.     

Levan production byBacillus polymyxa

Summary A levan-producing bacterium was isolated from soils and its characteristics for polysaccharide synthesis were studied. A series of enrichment and plating techniques enabled the isolation of a levan-producing bacterium from closely related contaminants. Cultural and physiological characteristics of the isolate identified the organism an a strain ofBacillus polymyxa. The organism produced about 40 g extracellular polysaccharide per liter of sucrose medium, which was about three times more yield than levan obtained from known levan producers. The highest amount of polysaccharide was on a 8% sucrose medium. Hydrolysis of the product showed that the polysaccharide consisted entirely ofd-fructose, and¹³C.n.m.r. spectra confirmed that the product was levan, a fructose polymer linked by B-(26) fructofuranosyl linkage.     

Resource manipulations in natural vegetation: a review

This paper reviews the effects that resource manipulations, especially nutrient additions, have on productivity, diversity, species interactions and succession in natural and semi-natural low-growth-form terrestrial restrial vegetation. In most studies, fertilization has resulted in an increase in productivity with a concomitant decrease in species diversity. Plant community productivity in nutrient-poor habitats (e.g. arctic tundra) however, has been relatively little affected by nutrient additions. Results from several fertilization experiments in nutrient-poor habitats indicate that competition may be an important component of community dynamics. Resource additions generally do not affect co-occurring species equally. In many cases, this results from an alteration of the relative competitive abilities of species. Several short-term fertilization studies have suggested that the rate of succession is increased by the addition of nutrients. Opposite trends however, have been reported in long-term studies. Contradictory results among some resource manipulation studies appear to stem largely from design limitations (e.g. only one resource was manipulated). Variability in habitat fertility, the type of resource added and the duration of enrichment also contribute to the difficulties involved in interpreting and comparing field experiments. A pluralistic approach combining glasshouse studies with both neighbour and resource manipulations in the field can be expected to lead to a greater depth of understanding of current controversies over the effects of habitat fertility on the intensity of competition and the relationship between competitive ability and tolerance of resource impoverishment.     

Interplant variation in creosotebush foliage characteristics and canopy arthropods

Summary We conducted a field study to test the hypothesis that creosotebush (Larrea tridentata) shrubs growing in naturally nutrient-rich sites had better quality foliage and supported greater populations of foliage arthropods than shrubs growing in nutrient-poor sites. Nutrient-rich sites had significantly higher concentrations of soil nitrogen than nutrient-poor sites. Multivariate analysis of variance revealed significant differences between high nutrient and low nutrient shrubs based on a number of structural and chemical characteristics measured. High nutrient shrubs were larger, had denser foliage, greater foliage production, higher concentrations of foliar nitrogen and water, and lower concentrations of foliar resin than low nutrient shurbs. Numbers of foliage arthropods, particularly herbivores and predators, were significantly higher on high nutrient shrubs. Shrub characteristics and foliage arthropod abundances varied considerably from shrub to shrub. Shrub characteristics representing shrub size, foliage density, foliage growth, and foliar nitrogen and water concentrations were positively correlated with arthropod abundances. Foliar resin concentrations were negatively correlated with foliage arthropod abundances. The positive relationship between creosotebush productivity and foliage arthropods is contradictory to the tenet that physiologically stressed plants provide better quality foliage to insect herbivores.     

The form of the talus in some higher primates: a multivariate study

Sixteen measurements of the talus have been taken on 334 tali of a total of eleven primate groups and several additional single individual specimens. Multivariate morphometric (canonical and generalized distance) analyses of these data in extant higher primates are presented and used to define the relative morphological positions of fossils of the genera Proconsul and Limnopithecus, of individual specimens from Kromdraai, Olduvai and Kiik-Koba (Homo neanderthalensis), and a group of specimens of Bronze Age man from Jericho. Following preliminary studies the ultimate analysis suggests that the various extant arboreal primates examined fall within an envelope that is defined by Macaca together with various other Old World monkeys and extending in different directions to the extreme genera (a) Pongo, (b) Hylobates and (c) Ateles. This separation is thus one which defines generally quadrupedal monkeys and separates the various extreme arboreal locomotor modes of (a) acrobatic climbing and hanging, (b) richochetal brachiation and (c) prehensile-tailed arm-swinging and hanging, respectively. Man and the African apes are well separated both from each other and from this spectrum of arboreally adapted genera. Bronze Age man from Jericho and Neandertal man from Kiik-Koba lie relatively close to the position for modern man although significantly separated from him. Limnopithecus, Proconsul, and the specimens from Kromdraai and Olduvai all lie within the envelope of arboreal species and specifically rather close to, although significantly different from, the orang-utan; they differ markedly from both man and the African apes. The possibility exists that the resemblances of Proconsul and Limnopithecus relate to arboreal habitus in these species. The findings for the specimens from Kromdraai and Olduvai suggest either that the morphological resemblances to arboreal forms relate to a previous arboreal history for these species, or that bipedality is much less advanced or uniquely different from that displayed by Homo. It is not inconceivable that both conditions might apply.     

Some African fossil foot bones: a note on the interpolation of fossils into a matrix of extant species

Certain fossil foot bones (a terminal toe phalanx from Olduvai, specimens of tali from Spy, Skhūl, Olduvai, Kromdraai, Songhor and Rusinga) have been investigated by other workers using the multivariate statistical approach. The conclusions of their studies have, in the main, been based upon examination of early canonical variates alone. It is demonstrated here that if the full analyses (generalized distances) are taken into account, then almost exactly opposite conclusions obtain. The terminal toe phalanx from Olduvai is widely different from those of modern men; the Neandertal tali differ more from modern human bones than previously realized; the specimens from Olduvai, Kromdraai, Songhor and Rusinga are all completely dissimilar from both African ape and modern human tali.     

Effects of density and predation on Scaphiopus couchi tadpoles in desert ponds

Summary The effects of density on growth and development of Scaphiopus couchi tadpoles in desert ponds were investigated, and sources of mortality over a three-year period were documented. In 16 of the 82 ponds monitored, predation was the principal cause of death, demonstrating that tadpoles in desert ponds may be exposed to high levels of predation, although the overall importance of predation is less here than in more mesic areas. Desiccation was the primary cause of mortality in 49 ponds. Growth and development were extremely slow in most high density ponds and as a result most tadpoles were unable to metamorphose before ponds dried. Only 8 ponds produced metamorphs, and mortality was high even in these. Food-supplementation resulted in some metamorphosis in high density ponds, although the effect was diminished by the extreme crowding in most ponds. In low density ponds, S. couchi tadpoles can develop very quickly and metamorphose. High mortality due to desiccation is largely a consequence of high density: tadpoles rarely completed development in high density ponds, regardless of pond duration.     

Effect of pH on microbial degradation of leaf litter in seven streams of the English Lake District

Summary Rates of degradation of alder, oak and grass leaf packs with associated microbial populations were measured in seven streams pH 6.8–4.9. Streams were chosen from upland and lowland sites of the same river for contrasts in pH, water chemistry and riparian vegetation. The most important factor governing rates of degradation is the physical and chemical nature of the leaf material. At pH 6.8 rates of degradation, k, and microbial colonization were higher than at pH 5.5: k on alder x6; on oak x2; on grass x2. At lowland sites, pH 6.8, higher decay rates were associated with high levels of microbial colonization including c.14 spp of aquatic hyphomycete fungi—regardless of riparian vegetation. Decay rates were similar at upland sites, pH 6.8 and 6.6, involving high levels of colonization by fewer fungal species and fewer bacteria—regardless of riparian vegetation-though grass was barely degraded at upland sites of any pH. At pH 5.5, slow decay rates were associated with low levels of microbial colonization and few fungal species. Largest microbial populations at low pH associated with riparian trees did not lead to markedly increased decay rates. Factors of water chemistry at low pH appear to inhibit microbial metabolism. The implications of these findings for stream invertebrates active in the winter is discussed.     

Soil moisture influence on micronutrient cation availability under aerobic conditions

Summary The three major soil series comprising the Gezira scheme (Sudan) are Hosh, Suleimi, and Laota. Surface soil samples from each soil series were employed to study the effect of soil moisture on the DTPA-extractable micronutrient cation under aerobic conditions. The study continued for 8 weeks using an incubation technique at two levels of soil moisture (continuously moist and moist/dry cycles). The DTPA-extractable Cu, Fe, Mn and Zn from air-dry soil samples were much higher compared to values from their incubated counterparts. For the three soils the CO₂ production (microbial activity) reached the maximum in 5 weeks and then levelled off while the lowest values of micronutrient cation from the incubated soils were obtained between 2 to 8 weeks.Generally, the study suggests that the hot dry months preceding crop growth should increase clay surface acidity and hence availability of mironutrient cations.Contribution from the Texas Agricultural Experiment Station, Texas A&M University, College Station. TX 77843, U.S.A.