Can sugarcoated fingerprints be used to identify lurking viruses?

Comparative proteomics is increasingly used to detect biomarkers and therapeutic targets that differ between healthy and diseased populations; however, differences in posttranslational modifications have received less attention. In this issue, Yang et al. (Proteomics 2016, 16, 1872–1880) present data indicating that a glycoproteomics approach can detect N‐glycosylated membrane protein differences between non‐HIV‐infected and latently infected human CD4⁺ T‐cell lines, identifying 172 proteins differentially expressed by these cells. Latently infected CD4⁺ T cells are thought to represent the major barrier to eventual HIV cure, but do not express detectable levels of viral protein and have not been shown to express biomarkers that can distinguish them from the vastly more abundant uninfected CD4⁺ T‐cell population. The findings of Yang et al. suggest that glycoproteomic analyses may have untapped potential to identify novel biomarkers and therapeutic targets in cell populations not readily distinguishable be standard proteomic analyses.     

Stomatal sensitivity to abscisic acid: can it be defined?

Abstract. Evidence is presented that the sensitivity of stomata to abscisic acid is greatly influenced by two factors which are known to vary in leaves, namely concentrations of potassium and of indol-3-ylacetic acid. It is suggested that the notion of 'quantitative tissue sensitivity', by which Trewavas explains the action of growth substances in developmental phenomena, may be applicable to stomatal responses to abscisic acid.     

Can species data only be appropriately used to conserve biodiversity?

Despite widely acknowledged handicaps of the species approach to identifying priority conservation areas, many workers continue to use these flawed techniques as the backbone of their analyses. Species-based approaches address only a small part of biological diversity by ignoring different levels of organisation as well as the functional linkages among these levels. These data are often biased and incomplete and are often used in preference to data dealing with higher biological levels of organisation though the latter may be readily available. Within the framework of Noss's [(1990) Conservation Biology 4: 355–364] hierarchical definition of biodiversity (and Scott etal. [(1993) Wildlife Monographs 123: 1–31] gap analysis), we propose a top-down model dealing with broad organisational levels first, and finer-scale species distributions last. Note that we do not discard the latter approach, but merely argue for its use at a stage when, in our opinion, it adds most to the value of the prioritisation exercise. The model is flexible so that additional information, particularly those related to threats to biological diversity, can be added when they are available.     

Can species traits be used to predict marine macroalgal introductions?

Species traits which facilitate introduction and predominance have been quantitatively ranked using interval arithmetic to search for common patterns among 113 marine macroalgae introduced in Europe. Three main categories were used: dispersal, establishment and ecological impact. These were further subdivided into more specific categories, a total of 13. Introduced species were compared with the same number of native species randomized from the same families as the introduced. Invasive species (i.e. species having a negative ecological or economical impact) were also compared with non-invasive introductions, separately for the three algal groups. In many categories, as well as when adding all species, the introduced species ranked more hazardous than the native species and the invasive species ranked higher than the non-invasive ones. The ranking within the three main categories differed, reflecting different strategies between the species within the three algal groups. When all categories (excluding salinity and temperature) were summed, the top five risk species, all invasive, were, in descending order, Codium fragile spp.tomentosoides, Caulerpa taxifolia, Undaria pinnatifida, Asparagopsis armata and Grateloupia doryphora, while Sargassum muticum ranked eight and Caulerpa racemosa ten. Fifteen of the twenty-six species listed as invasive were among the twenty highest ranked.     

Can health care databases be used to identify incident cases of osteonecrosis?

Introduction  

Osteonecrosis (ON) is a rare disease associated with alcohol and glucocorticoid use. Identifying additional risk factors is difficult as the number of cases at any single center is small. We investigated whether data available in large health care databases can be used to identify incident ON cases.     

Human cloning: can it be made safe?

There are continued claims of attempts to clone humans using nuclear transfer, despite the serious problems that have been encountered in cloning other mammals. It is known that epigenetic and genetic mechanisms are involved in clone failure, but we still do not know exactly how. Human reproductive cloning is unethical, but the production of cells from cloned embryos could offer many potential benefits. So, can human cloning be made safe?     

Can species distribution models be used to describe plant abundance patterns?

In recent years, there has been increasing interest in modelling of species abundance data in addition to presence data. In this study, we assessed the similarities and differences between presence‐absence distributions and abundance distributions along similar environmental gradients, derived, respectively, from presence‐absence and abundance data. Moreover, we examined the possibility of using presence‐absence distribution models to derive abundance distributions. For this purpose, we used Braun‐Blanquet abundance scores for 243 vascular species at 10 996 French forest sites. Species distribution models were used to analyse the link between the patterns of occurrence, low abundance and high abundance for each species with regard to mean annual temperature, June water balance, and soil pH. For each species, differences in the modelled distributions were characterised by the ecological optimum and ecological amplitude. A comparison of the presence‐absence and abundance distributions for all species revealed similar optima and different amplitudes along the three ecological factors. An abundant‐centre distribution was observed in environmental space, with species abundance being greatest at the optimal conditions and lower at less favourable conditions of the species occurrence response. Geographical habitat mapping also shows centred, high‐abundance suitability within the presence habitat of each species. We conclude that species distribution models derived from presence‐absence data provide useful information about the ecological optima of abundance distributions but overestimate the range of habitats suitable for high species abundance. This study demonstrates the utility of presence‐absence data for ecologist and conservation biologist when they are interested in the optimal conditions of high species abundance.     

Marine microbial diversity: can it be determined?

Estimates of the order of magnitude for the total number of microbial species on Earth range from 10(3) to 10(9). Despite global dispersal of microorganisms, this number is probably rather large. The total biodiversity of an ecosystem is composed of two elements: first, a set of abundant taxa that carry out most ecosystem functions, grow actively and suffer intense losses through predation and viral lysis. These taxa are retrievable with molecular techniques but are difficult to grow in culture. Second, there is a seed bank of many rare taxa that are not growing or grow extremely slowly, do not experience viral lysis and predation is reduced. Such taxa are seldom retrieved by molecular techniques but many can be grown in culture, which explains the dictum 'everything is everywhere'.     

CBO guidelines to prevent accidental falls in the elderly: how can it be used in the institutionalized elderly?

Fall incidents occur frequently in the community dwelling elderly and even more in the institutionalised elderly. Fall-related research data indicate positive effects of a multifactorial intervention targeted on prevention of falls and fall-related injuries. In November 2004 the guideline "Prevention of fall incidents in the elderly" developed by The Dutch Institute for Healthcare Improvement (CBO) was published. This guideline pays attention to the risk factors for falling and the prevention of fall incidents in all settings. The highlights for nursing homes are: all nursing home patients are at risk; perform a fall risk assessment to direct fall preventive activities; together with specific fall prevention for the patient general fall prevention for the institute has to be undertaken; a multifactorial approach is indicated. In nursing homes it is possible to perform such approach multidisciplinary.     

2D protein electrophoresis: can it be perfected?

23 years after O'Farrel developed two-dimensional gel electrophoresis we still debate if the technique can be improved, or if there are other alternative separation technologies that can challenge its central position in proteomic projects. These questions are relevant as the pharmaceutical industry expects proteomic studies to provide novel protein targets for drug discovery and diagnostics. In our opinion, there are various aspects of the technology that can be improved, including resolution, sample preparation and detection, but so far there is no alternative technique(s) available, or any under development, that can replace it.     

Can model species be used to advance the field of invasion ecology?

Hypotheses for explaining plant invasions have focused on a variety of factors that may influence invasion success, including propagule pressure, interactions of the introduced species with the biotic, abiotic, or disturbance properties of the new ecosystem, or the genetic characteristics of the invader itself. Evaluating the relative importance of these factors has been difficult because for most invaders key information about the introduced population or the introduction event is not available. We propose that natural experiments using model species is an important tool to test multiple invasion hypotheses at the same time, providing a complementary approach to meta-analysis and literature review. By focusing on a single candidate species, Pinus contorta, we explore several attributes that we propose constitute a good model, including: (a) intentional and relatively well documented introduction into a wide range of environments and countries across the world during the past century, where invasion success or failure has already occurred, (b) conspicuous growth form that simplifies assessment of growth rates, and comparisons across native and introduced ecosystems around the world, and, (c) documented and replicated variability of introduction intensity, genetic characteristics of the introduced populations, contrasting biotic communities present at sites of introduction, and abiotic conditions within and across introduced ecosystems. We propose that identifying model species with these characteristics will provide opportunities to disentangle the relative importance of different mechanisms hypothesized to influence invasion success, and thereby advance the field of invasion ecology.     

Can pre-collected register data be used to identify dairy herds with good cattle welfare?

Background

Pre-recorded register data from dairy herds are available in almost all Nordic countries. These databases can be used for research purposes, and one of the research areas is animal welfare. The aim of this study was to investigate if pre-recorded register data could be used to identify herds with good welfare, and to investigate if a combination of register data sets could be used to be able to more correctly distinguish between herds with good welfare and herds with welfare deficiencies.

Methods

As a first step, nine animal-based measurements on calves, young stock and cows in 55 randomly selected herds were performed on-farm as the basis for a classification of welfare at the herd level. The definition for being a case herd with “good welfare” was no score lying among the 10% worst in any of the nine welfare measurements. Twenty-eight of the 55 herds were cases according to this definition. As a second step, 65 potential welfare indicators, based on register data in a national dairy database, were identified by expert opinion. In the final step, the extent to which the suggested welfare indicators predicted farms’ as having good welfare according to the stated definition was assessed. Moreover, the effect of combining in sequence a previously developed model that identified herds with poor welfare with the present model identifying herds with good welfare was investigated.

Results

The final set of welfare indicators used to identify herds with good animal welfare included two fertility measures, cow mortality, stillbirth rate, mastitis incidence and incidence of feed-related diseases (including gastrointestinal disturbances but excluding paralyses and cramps). This set had a test sensitivity of correctly classifying herds with no score lying among the 10% worst of the nine welfare measurements of 96 %. However, the specificity of the test was only 56% indicating difficulties for the test to correctly classifying herds with one or more scores lying among the 10% worst. Combining the previously developed model with the present model, improved the welfare classification.

Conclusions

This study shows that pre-collected register data may be used to give approval to dairy farms with “good welfare” and that combining different sets of register data can improve the classification of herd welfare.

     

Attraction of a predator to chemical information related to nonprey: when can it be adaptive?

Information specificity can be important to animals in makingoptimal decisions. However, it is not always necessary to useevery level of specificity. We analyzed the response of thepredatory mite Phytoseiulus persimilis to plant-produced informationrelated to a nonprey herbivore. This predator is a specialistfeeding on spider mites in the genus Tetranychus. Caterpillarsof Spodoptera exigua cannot serve as prey. Plants respond toan infestation by herbivores with the emission of volatilesthat attract carnivorous enemies of the herbivores. Conspecific plants infested with different herbivore species can emit blendsthat are qualitatively identical, while differing in the ratiosof blend components. However, different plant species emitvolatile blends that differ qualitatively. We demonstratedthat the predator P. persimilis is attracted to volatiles frombean plants infested with S. exigua caterpillars, but thatthis attraction is affected by predator starvation and host-plantexperience. One-hour and 24-h starved predators were made to represent predators that just lost a prey patch versus predatorsthat have totally lost a prey patch. Predators reared on spidermites on bean were attracted to bean plants infested with caterpillarswhen starved for 1 h but not when starved for 24 h. Both predatorgroups were attracted to bean plants infested with prey (i.e.,spider mites). One-hour starved predators can use the odorto relocate the rewarding prey patch they just lost contactwith, and using a general olfactory representation of the blendis sufficient for relocation. In contrast, for 24-h starvedpredators, the perception of a plant's odor blend is unlikelyto represent the prey patch lost, and discriminating betweenan odor blend representing prey or nonprey will avoid investingtime in finding a nonprey herbivore. In contrast, predatorsthat had been reared on spider mites on cucumber and thus hadexperienced a qualitatively different odor blend were not attractedto volatiles from caterpillar-infested bean plants. They wereattracted to spider mite-infested bean plants, irrespectiveof starvation level. To cucumber-experienced predators, theperception of bean plant odor cannot represent the prey patch lost, but only a new prey patch. Being discriminative and onlyresponding to prey-infested plants is adaptive in this situation.Our results are discussed in the context of optimal informationprocessing.     

Can microsatellites be used to infer phylogenies? Evidence from population affinities of the Western Canary Island lizard (Gallotia galloti)

Population phylogeographic studies are generally based solely on mtDNA without corroboration, from an independent segregating unit (i.e., nuclear genes), that the mtDNA gene tree represents the organismal phylogeny. This paper attempts to evaluate the utility of microsatellites for this process by use of the Western Canary Island lacertid (Gallotia galloti) as a model. The geological times of island eruptions are known, and well-supported mtDNA phylogenies exist (corroborated as the organismal phylogeny rather than just a gene tree by nuclear random amplified polymorphic DNAs (RAPDs)). The allelic variation in 12 populations from four islands (representing five haplotype lineages) was investigated in five unlinked microsatellite loci. Analysis of molecular variance showed this data to be highly structured. A series of genetic distances among populations was computed based on both the variance in allele frequency (i.e., F(st) related) and the variance in repeat numbers (i.e., R(st) related). The genetic distances based on the former were more highly correlated with the mtDNA genetic distances than those based on the latter. All trees based on both models supported the primary division shown by mtDNA and RAPDs, which is dated at ca. 2.8 to 5.6 mybp (depending on calibration of the mtDNA clock) and which could, under the evolutionary species concept, be regarded separate species. This was achieved despite theoretical problems posed by the use of few loci, suspected bottlenecks, and large population sizes. The finer details were less consistently represented. Nevertheless, this study demonstrates that even a small number of microsatellites can be useful in corroborating the deeper divisions of a population phylogeny.