Genetic research and consent: On the crossroads of human and data research

This paper explores the legal and ethical concept of human subject research in order to determine whether genetic research with already available biosamples and data falls within this concept. Although the ethical concept seems to have evolved to recognize research based on data as human research, from a supranational legal perspective this form of research is not considered human subject research. Thus human subject research regulations do not apply and therefore do not invoke the requirement of obtaining consent prior to using an individual’s biosample or genetic data in research. Furthermore, it remains ambiguous in both the legal and ethical realm whether the use of biosamples or genetic data without additional links to the individual would invoke the same safeguards as research involving additional or specific identifiers. Seeing that research based on already available biosamples and genetic data is not governed by rules concerning human subject research, the second part of the paper analyses whether any consent requirements apply for the further use of already available bio‐samples or genetic data in research. Whereas further use of biosamples is subject to considerably lax consent requirements under Article 22 of the Oviedo Convention, under the General Data Protection Regulation further use of genetic data might not be subject to a prior consent requirement at all, unless it is stipulated in national laws. When it comes to clinical trials, however, sponsors will have the possibility under Article 28(2) of Regulation 536/2014 to obtain open consent for further use of data in any kind of future research.     

Origins and selection of epidermal progenitors and stem cells: a challenge for tissue engineering

The use of epidermal stem cells and their progeny for tissue engineering and cell therapy represents a source of hope and major interest in view of applications such as replacing the loss of functionality in failing tissues or obtaining physiologic skin equivalents for skin grafting. The use of such cells necessitates the isolation and purification of rare populations of keratinocytes and then increasing their numbers by mass culture. This is not currently possible since part of the specific phenotype of these cells is lost once the cells are placed in culture. Furthermore, few techniques are available to unequivocally detect the presence of skin stem cells and/or their progeny in culture and thus quantify them. Two different sources of stem cells are currently being studied for skin research and clinical applications: skin progenitors either obtained from embryonic stem cells (ESC) or from selection from adult skin tissue. It has been shown that "keratinocyte-like" cells can be derived from ESC; however, the culturing processes must still be optimized to allow for the mass culture of homogeneous populations at a controlled stage of differentiation. The functional characterization of such populations must also be more thoroughly achieved. In order to use stem cells from adult tissues, improvements must be made in order to obtain a satisfactory degree of purification and characterization of this rare population. Distinguishing stem cells from progenitor cells at the molecular level also remains a challenge. Furthermore, stem cell research inevitably requires cultivating these cells outside their physiological environment or niche. It will thus be necessary to better understand the impact of this specific environmental niche on the preservation of the cellular phenotypes of interest.     

Using Inverse Probability Bootstrap Sampling to Eliminate Sample Induced Bias in Model Based Analysis of Unequal Probability Samples

In ecology, as in other research fields, efficient sampling for population estimation often drives sample designs toward unequal probability sampling, such as in stratified sampling. Design based statistical analysis tools are appropriate for seamless integration of sample design into the statistical analysis. However, it is also common and necessary, after a sampling design has been implemented, to use datasets to address questions that, in many cases, were not considered during the sampling design phase. Questions may arise requiring the use of model based statistical tools such as multiple regression, quantile regression, or regression tree analysis. However, such model based tools may require, for ensuring unbiased estimation, data from simple random samples, which can be problematic when analyzing data from unequal probability designs. Despite numerous method specific tools available to properly account for sampling design, too often in the analysis of ecological data, sample design is ignored and consequences are not properly considered. We demonstrate here that violation of this assumption can lead to biased parameter estimates in ecological research. In addition, to the set of tools available for researchers to properly account for sampling design in model based analysis, we introduce inverse probability bootstrapping (IPB). Inverse probability bootstrapping is an easily implemented method for obtaining equal probability re-samples from a probability sample, from which unbiased model based estimates can be made. We demonstrate the potential for bias in model-based analyses that ignore sample inclusion probabilities, and the effectiveness of IPB sampling in eliminating this bias, using both simulated and actual ecological data. For illustration, we considered three model based analysis tools—linear regression, quantile regression, and boosted regression tree analysis. In all models, using both simulated and actual ecological data, we found inferences to be biased, sometimes severely, when sample inclusion probabilities were ignored, while IPB sampling effectively produced unbiased parameter estimates.     

An investigation of the sources of nonuniqueness in deterministic identifiability

While a choice of techniques exists for checking the deterministic (structural) identifiability of a specific linear, time-invariant model from a specific experiment, and some progress has been made towards topological criteria for identifiability, no method at present available allows quick and reliable checking of a range of models for globally unique identifiability from a range of experiments. Even individual cases are sometimes difficult and tedious to check. The reasons are examined by exhaustive case-by-case analysis of single-input experiments on all possible three-compartment models. All patterns of loss to the environment are covered, and all combinations of observed compartments. Catalogues of minimal observation sets for globally unique identifiability, and of nonuniquely identifiable cases, are presented. The structural causes of nonuniqueness are discussed by reference to examples from the latter catalogue. Methods are given for shortening the derivation of the structural equations giving rise to nonunique parameters. From the diversity of behavior found, it is concluded that the prospects of obtaining a comprehensive set of necessary and sufficient structural conditions for globally unique identifiability are poor.     

Perspective: Time scales in scientific research with an emphasis on microbial cellular and molecular research

Scientists use time to describe and research the universe in which humans live. Geologists and evolutionary biologists often use time scales in the millions to billions of years while biochemists and molecular biologists use time scales in the milliseconds or less. The atom smashers use time scales that are almost the speed of light. However, in some areas of research such as molecular-based activities in cells, it is very challenging to obtain data sets in molecular time scales. This has been a challenge to obtaining accurate and precise measurements at the cell and molecular levels of organization in living organisms. Measurements of specific cellular and molecular activities are often made over time scales longer than the actual molecular events. The data sets obtained become estimates over seconds, minutes and hours and not measurements over milli- and nanoseconds. The question can then be posed — how representative and accurate are our data sets when the time scales are not synchronized with the actual living events? In this article, the role of time scales in scientific research and our understanding of living microorganisms are examined with an emphasis on cell and molecular time scales.     

BmuG@Sbase--a microarray database and analysis tool

The manufacture and use of a whole-genome microarray is a complex process and it is essential that all data surrounding the process is stored, is accessible and can be easily associated with the data generated following hybridization and scanning. As part of a program funded by the Wellcome Trust, the Bacterial Microarray Group at St. George's Hospital Medical School (BmuG@S) will generate whole-genome microarrays for 12 bacterial pathogens for use in collaboration with specialist research groups. BmuG@S will collaborate with these groups at all levels, including the experimental design, methodology and analysis. In addition, we will provide informatic support in the form of a database system (BmuG@Sbase). BmuG@Sbase will provide access through a web interface to the microarray design data and will allow individual users to store their data in a searchable, secure manner. Tools developed by BmuG@S in collaboration with specific research groups investigating analysis methodology will also be made available to those groups using the arrays and submitting data to BmuG@Sbase.     

Three-dimensional video analysis of facial movements: a new method to assess the quantity and quality of the smile

The results of neuromuscular reconstructions of the paralyzed face are difficult to assess. Very sophisticated methods are necessary to measure the motor deficits of facial paralysis or the functional recovery in the face. The aim of this development was a relatively simple system for data acquisition, which is easy to handle and which makes it relatively cheap to delegate data acquisition to centers all over the world, which will not be able to derive a data analysis on their own, but will send their data to a center with specialized equipment. A complex mirror system was developed to get three different views of the face at the same time on the video screen. At each investigation, a digital video is taken from a calibration grid and from standardized facial movements of the patient. Secondary analysis of the digital videofilm is made possible at any time later on by the support of a computer program, which calculates distances and movements three-dimensionally from the frontal image and the right and left mirror images. Pathologies of the mimic movements can be identified as well as improvements after surgical procedures by this system. The significant advantage is the possibility to watch the same movement on the video which is under study and to apply any kind of study later on. Taking the video needs only a few minutes, and fatigue of the patient's mimic system is prevented. Measurements usually at the endpoints of the movements give excellent information on the quantity of the movement or the degree of the facial palsy, whereas the video itself is very informative regarding the quality of the smile. Specific computer software was developed for standardized three-dimensional analysis of the video-documented facial movements and for data presentation. There are options like two-dimensional graphs of single moving points in the face or three-dimensional graphs of the movements of all measured points at the same time during a standardized facial movement. By a comparison of the right- and left-sided alterations of specific distances between two points during the facial movements, the degree of normal symmetry or pathologic asymmetry is quantified. This system is more suitable for detailed scientific multicenter studies than any other system previously established. A very sensitive instrument for exact evaluation of mimic function is now available.     

Is the Wild Coast in eastern South Africa a distinct marine bioregion?

The South African coastline can be divided into at least four temperature-defined marine bioregions, including the tropical north-east coast, the subtropical east coast, the warm-temperate south coast, and the cool-temperate west coast. There are also two biogeographical transition zones, the south-west coast and the south-east coast (or Wild Coast). The former is sometimes considered a distinct marine bioregion, but no such status has yet been suggested for the Wild Coast. Previous data on the distribution of a recently described but very common coastal crab, Hymenosoma longicrure, indicated that this species could be a Wild Coast endemic. If confirmed, this would be a first indication that this region harbours unique fauna, and that additional research is required to determine whether the Wild Coast constitutes a distinct bioregion that needs to be managed separately from other coastal regions. In the present study, we generated novel genetic data for H. longicrure and compared the species’ range with that of its southern African congeners. We found that H. longicrure occurs north of the Wild Coast, where its range overlaps with that of H. projectum. This finding rejects the idea that the Wild Coast harbours endemic fauna and suggests that the ranges of the two species may be linked to the subtropical and tropical bioregions, respectively, with some southward dispersal facilitated by the southward-flowing Agulhas Current. We conclude that there is as yet no compelling evidence that the Wild Coast is a distinct marine bioregion, and concur with previous biogeographical studies which have suggested that the Wild Coast is an area in which species from the subtropical and warm-temperate bioregions have overlapping ranges. Nonetheless, that fact that no biological information is available for the majority of the region’s estuaries highlights the necessity of comprehensively documenting the biodiversity of this understudied region to fully resolve this issue.     

Extracting haplotypes from diploid organisms

Each diploid organism has two alleles at every gene locus. In sexual organisms such as most plants, animals and fungi, the two alleles in an individual may be genetically very different from each other. DNA sequence data from individual alleles (called a haplotype) can provide powerful information to address a variety of biological questions and guide many practical applications. The advancement in molecular technology and computational tools in the last decade has made obtaining large-scale haplotypes feasible. This review summarizes the two basic approaches for obtaining haplotypes and discusses the associated techniques and methods. The first approach is to experimentally obtain diploid sequence information and then use computer algorithms to infer haplotypes. The second approach is to obtain haplotype sequences directly through experimentation. The advantages and disadvantages of each approach are discussed. I then discussed a specific example on how the direct approach was used to obtain haplotype information to address several fundamental biological questions of a pathogenic yeast. With increasing sophistication in both bioinformatics tools and high-throughput molecular techniques, haplotype analysis is becoming an integrated component in biomedical research.     

Will genomics revolutionise pharmaceutical R&D?

The successful identification of drug targets requires an understanding of the high-level functional interactions between the key components of cells, organs and systems, and how these interactions change in disease states. This information does not reside in the genome, or in the individual proteins that genes code for, it is to be found at a higher level. Genomics will succeed in revolutionising pharmaceutical research and development only if these interactions are also understood by determining the logic of healthy and diseased states. The rapid growth in biological databases, models of cells, tissues and organs, and in computing power has made it possible to explore functionality all the way from the level of genes to whole organs and systems. Combined with genomic and proteomic data, in silico simulation technology is set to transform all stages of drug discovery and development. The major obstacle to achieving this will be obtaining the relevant experimental data at levels higher than genomics and proteomics.     

Physiological properties of a drought-resistant wild soybean genotype: Transpiration control with soil drying and expression of root morphology

Aims

Wild soybean accession PI 468917 [Glycine soja (Sieb. and Zucc.)] was examined for traits that could potentially be beneficial for development of drought resistant soybean cultivars.

Methods

Water use was examined in controlled environment chambers at three temperatures (25, 30, and 35 °C). Root morphology of plants grown in hydroponics was analyzed using digital imaging software.

Results

Wild soybean had lower transpiration efficiency in producing mass than the domesticated soybean cultivar Hutcheson at all temperatures. As soil dried, wild soybean decreased transpiration earlier (at a higher soil water content) than domesticated soybean, but only at 25 °C. Wild soybean had much greater root length than the modern soybean when grown at 25 or 30 °C in hydroponics, with the increase observed in the 0.25 to 0.50 mm diameter class. Wild soybean’s advantages dissipated at higher growth temperatures.

Conclusions

Wild soybean populations, potentially, can offer useful traits for improving drought resistance of modern soybean. Sensitive transpiration control in response to soil drying would contribute to ‘slow-wilting’ strategies known to be advantageous for drought resistance, and greater root length would enhance water acquisition from the soil profile. Use of the traits in breeding programs will require extending the temperature range for trait expression.     

Evaluation of molecular biology reagents used in plcR-tergeted RSI-PCR assay for B. anthracis identification and their influence on time necessary for obtaining results

Fast and reliable identification of B. anthracis is crucial for a successful therapy of persons exposed to anthrax spores. Use of molecular biology techniques significantly reduces time necessary for obtaining results. However, the molecular identification is hampered by the high genetic similarity of the B. cereus group bacteria. A lot of published B. antharcis identification approaches turned out to be non-specific. Nevertheless, theplcR-targeted RSI-PCR assay described in 2007 is still regarded as highly specific for anthrax identification. In this paper possibility of significant reduction of time necessary for obtaining results by the use of modern, "fast" polymerases and restriction enzymes will be presented. The use of a such reagents enable to reduce time of the plcR-targeted RSI-PCR assay to about two hours.     

A comparison of abundance estimates from extended batch‐marking and Jolly–Seber‐type experiments

Little attention has been paid to the use of multi‐sample batch‐marking studies, as it is generally assumed that an individual's capture history is necessary for fully efficient estimates. However, recently, Huggins et al. ( 2010 ) present a pseudo‐likelihood for a multi‐sample batch‐marking study where they used estimating equations to solve for survival and capture probabilities and then derived abundance estimates using a Horvitz–Thompson‐type estimator. We have developed and maximized the likelihood for batch‐marking studies. We use data simulated from a Jolly–Seber‐type study and convert this to what would have been obtained from an extended batch‐marking study. We compare our abundance estimates obtained from the Crosbie–Manly–Arnason–Schwarz (CMAS) model with those of the extended batch‐marking model to determine the efficiency of collecting and analyzing batch‐marking data. We found that estimates of abundance were similar for all three estimators: CMAS, Huggins, and our likelihood. Gains are made when using unique identifiers and employing the CMAS model in terms of precision; however, the likelihood typically had lower mean square error than the pseudo‐likelihood method of Huggins et al. ( 2010 ). When faced with designing a batch‐marking study, researchers can be confident in obtaining unbiased abundance estimators. Furthermore, they can design studies in order to reduce mean square error by manipulating capture probabilities and sample size.     

The CR digital radiography system in traditional X-ray studies (according to the materials of the Moscow Regional Clinical Research Institute)

The basic idea of the author's paper is to attempt to estimate and prove whether it is advisable to use the CR digital radiography system in a multidisciplinary therapeutic institution mainly at the municipal level. The pre-requisites for this were the results of diagnostic studies of different diseases of organs and systems. Emphasis is laid on the specific features of use of this digital system; namely, it can convert several analogue X-ray apparatuses to digital ones and it is more profitable than indirect image numeralization apparatuses and produces lower radiation loads. This all makes the use of these digital systems tempting in traditional X-ray study. A comparatively large material (4237 cases) was used to show the efficiency of the CR digital radiography system in the diagnosis of ENT diseases, osteology, interventional radiology, gastroenterology, pediatrics and to demonstrate a modernized approach to having a solid copy of a digital image, the possibilities of postprocessing that may enhance the validity of existing X-ray symptoms. This all allows the author to recommend that the CR digital radiography systems be used in traditional X-ray study for the diagnosis of various diseases occurring in a multidisciplinary health care facility mainly at municipal and regional levels.     

Exploring local consequences of two land-use alternatives for the supply of urban ecosystem services in Stockholm year 2050

Ecosystem services (ESs) are gaining ground in urban policy as a key to attaining sustainable cities. However, strategic and land-use planners need operational and accessible tools to better understand the consequences of policy and planning measures. Based on a study of the City of Stockholm and its surrounding region, we argue that spatially explicit land-use mapping is a good base for modeling and visualizing the supply of urban ESs provided by different patterns of Service Providing Units. By adding more detailed characteristics of land use through the concept of Service Providing Elements (SPEs), and by assessing synergies and trade-offs between these attributes, implications for the supply of ESs at different scale levels could be identified and discussed. Detailed land-use mapping and ES modeling were applied to two future land-use alternatives. The supply of eight urban ESs was found to vary significantly between the two alternatives depending on the ratios of different SPEs, even within identical land-use classes. One of the land-use alternatives had significantly higher potential for food and energy provision, much higher air cooling and air quality regulation capacity especially in densely built areas, showed less surface sealing, and provided better conditions for mental recreation. The exception was supply of physical recreation opportunities, where the other land-use option had an advantage. These differences became more accentuated when we zoomed in on two local urban areas. Based on these findings, our main conclusion is that, in order to provide planning and policy-making with an adequate knowledge base, it is necessary to move beyond land-use classes, as defined by European data sets like Urban Atlas, and toward tools capable of capturing more detailed aspects of land use and its relations to the supply of urban ESs. This should be made a priority, especially in early stages of planning and policy formation, and also used to support development of urban by-laws, procurement arrangements, neighborhood and building certification, etc. The approaches used in the study can serve as a valid starting point for further development of such tools and methods compatible with planners’ ordinary working modes. However, to make such progress possible, the ecosystem service research community needs to step up to the challenge of delivering locally specific and useful data on how urban land-use links to ES supply, including synergies and trade-offs between different ESs.     

Chlorine in the Netherlands, Part II: Risk Management in Uncertainty for Chlorine

The debate over chlorine in industrialized economies has become extremely polarized in the last decade. Environmental pressure groups are striving for a virtual phaseout of chlorine and chlorinated hydrocarbons (CHCs), because they are convinced that the risks cannot be managed. Industry argues this is not necessary because environmental risks can be controlled, nor is it feasible, because at least 60% of all firms use CHCs, produds made with CHCs, or elemental chlorine. In an attempt to give this discussion a more factual basis, the Dutch minister of environment launched a strategic study on chlorine (see Kleijn et al. I997;Tukker et al. 1995). Using all available knowledge about emissions and contemporary evaluation methods, the study found only a limited number of environmental issues outstanding related to the chlorine chain: however, it also found important uncertainties. This article describes the outstanding uncertainties in more detail. It defines which uncertainties have to be regarded as chlorine-specific and the extent to which additional research can resolve them. For the remaining uncertainties the potential benefts of uncertainty reduction strategies are evaluted, relying mainly on the precautionary principle     

Bioinformatics tools and database resources for systems genetics analysis in mice--a short review and an evaluation of future needs

During a meeting of the SYSGENET working group 'Bioinformatics', currently available software tools and databases for systems genetics in mice were reviewed and the needs for future developments discussed. The group evaluated interoperability and performed initial feasibility studies. To aid future compatibility of software and exchange of already developed software modules, a strong recommendation was made by the group to integrate HAPPY and R/qtl analysis toolboxes, GeneNetwork and XGAP database platforms, and TIQS and xQTL processing platforms. R should be used as the principal computer language for QTL data analysis in all platforms and a 'cloud' should be used for software dissemination to the community. Furthermore, the working group recommended that all data models and software source code should be made visible in public repositories to allow a coordinated effort on the use of common data structures and file formats.     

国家重点保护野生植物的保护现状及潜在分布区预测分析

野生植物是自然生态系统的重要组成部分,中国是野生植物种类最丰富的国家之一。研究国家重点保护野生植物的分布特征、保护现状以及潜在分布区,对于制定与支持生物多样性保护策略具有重要意义。该研究基于1 032种(隶属于129科315属)国家重点保护野生植物,利用前5%丰富度算法识别其热点地区,并与自然保护区叠加评估其保护成效、确定保护空缺,进而运用MaxEnt模型预测了国家重点保护野生植物的潜在分布区分布与变化趋势。结果表明:(1)中国南部和西南部是国家重点保护野生植物物种丰富度最高的地区,尤其是四川中部、云南南部和东南部、广西北部、广东北部与海南。(2)热点网格的保护成效分析表明,171个(85.50%)热点网格得到了有效保护(含80.50%的物种),29个(14.50%)热点网格未得到自然保护区的保护(含51.20%物种)。(3)通过比较当前与未来气候变化下国家重点保护野生植物的潜在分布区分布,发现未来潜在分布区将向西藏东南部、广西西南部、广东南部以及福建南部等地扩张,而向环四川盆地、云南南部和贵州南部等地缩减。因此,需要加强这些区域生物多样性的动态监测,持续关注气候变化对该区域国家重点保护野生植物的影响。基于该研究所确定的热点网格、保护成效以及潜在分布区的分析结果,可为国家重点保护野生植物多样性优先保护区的确定和保护政策的制定提供有力的数据支持与参考。     

Performance Comparison of Digital microRNA Profiling Technologies Applied on Human Breast Cancer Cell Lines

MicroRNA profiling represents an important first-step in deducting individual RNA-based regulatory function in a cell, tissue, or at a specific developmental stage. Currently there are several different platforms to choose from in order to make the initial miRNA profiles. In this study we investigate recently developed digital microRNA high-throughput technologies. Four different platforms were compared including next generation SOLiD ligation sequencing and Illumina HiSeq sequencing, hybridization-based NanoString nCounter, and miRCURY locked nucleic acid RT-qPCR. For all four technologies, full microRNA profiles were generated from human cell lines that represent noninvasive and invasive tumorigenic breast cancer. This study reports the correlation between platforms, as well as a more extensive analysis of the accuracy and sensitivity of data generated when using different platforms and important consideration when verifying results by the use of additional technologies. We found all the platforms to be highly capable for microRNA analysis. Furthermore, the two NGS platforms and RT-qPCR all have equally high sensitivity, and the fold change accuracy is independent of individual miRNA concentration for NGS and RT-qPCR. Based on these findings we propose new guidelines and considerations when performing microRNA profiling.     

Perspectives on the development of biological control agents in Africa

Concern over the impact of chemical pesticides on human health and the environment continues to stimulate the study of alternative, biological pest control agents (BCA). In Africa, use of BCA products is just emerging, primarily in the export sector where growers are using a mixture of products from new African companies and products imported from outside Africa. In contrast, although interest in BCA for use in domestic markets has been widely supported by development funding partners for many years, few products have become available to these growers. The limited uptake of BCA in Africa suggests there may be constraints and issues working against their wider implementation. Here, we focus on non-technical constraints and issues facing microbial BCA applied inundatively, but arguments extend to a greater or lesser degree to all BCA. The challenges to wider BCA availability could be overcome by: a more coherent approach to their regulation across the continent; support for BCA development that is based on evidence of need and applicability; and political advocacy to lobby for necessary resources being made available to all stakeholders.