A novel approach to segregate and identify functional loop regions in protein structures using their Ramachandran maps

The loops which connect or flank helices/sheets in protein structures are known to be functionally important. However, ironically they also belong to the part of protein whose structure is least accurately predicted. Here, a new method to isolate and analyze loop regions in protein structure is proposed using the spatial coordinates of the solved three‐dimensional structure. The extent of dispersion among points of successive amino acid residues in the Ramachandran map of protein region is utilized to calculate the Mean Separation between these points in the Ramachandran Plot (MSRP). Based on analysis of 2935 protein secondary structure regions obtained using DSSP software, spanning a range from 2 to 64 residues, taken from a set of 170 proteins, it is shown that helices (MSRP < 17) and strands (MSRP < 64) stand effectively demarcated from the loop regions (MSRP > 130). Analysis of 43 DNA binding and 98 ligand binding proteins revealed several loop regions with clear change in MSRP subsequent to binding. The population of such loops correlated with the magnitude of backbone displacement in the protein subsequent to binding. Can changes in MSRP quantify the temporal oscillations in dihedral angles among structured/unstructured regions in proteins? Molecular dynamics simulations (10 ns) revealed that deviations in MSRP among different snapshots in the trajectory were at least twofold higher for unstructured proteins in comparison with ordered proteins. The above results validate the use of MSRP parameter as a tool to identify and investigate functionally active loops and unstructured regions in protein structures. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Evaluation of the impact of a Herd Health and Production Management programme in organic dairy cattle farms: a process evaluation approach

Animal health planning activities are not always providing a satisfactory positive impact on herd health and welfare. Moreover, evaluating the impact of advisory programmes is complex due to multiple interacting elements that influence its outcome. Therefore, measuring solely health outcomes is not sufficient: the whole process of the implementation and use of such programmes should be evaluated. In order to evaluate the impact of an intervention with a Herd Health and Production Management (HHPM) programme a process evaluation framework was designed and used. The intervention involved 20 organic dairy cattle farmers and their advisors, in both France and Sweden. In both countries 20 organic dairy farms were selected as control herds. The evaluation of the HHPM programme was based on: (a) the compliance to the programme; (b) the programme’s functions influencing herd health management practices and stimulating dialogue between farmers and advisors; (c) its effectiveness in terms of improving herd health compared with control farms. Complete compliance to the programme was fulfilled by 21 out of 40 farmers–advisors. Results from a questionnaire showed that the programme functioned as intended (e.g. by allowing early identification of herd health problems), stimulated change in farmers’ herd health management practices and farmer–advisor dialogue. Even though the majority of the users perceived that the programme contributed to herd health improvements, no significant differences in health outcomes were found when compared with control farms 12 months after the start of the intervention. The programme allowed creating an environment promoting the exchange of information between farmers and advisors, necessary to define pertinent advice in a farm-specific situation. Future research should aim at improving methods for the evaluation of the effect of advisory programmes, by identifying early indicators for effective advice and developing methods to evaluate the quality of advisory situations without interfering with them.     

COMPARISON OF PREFERENCE MAPPING TECHNIQUES FOR THE OPTIMIZATION OF STRAWBERRY YOGURT

Many product optimization methods, known in general terms as preference mapping, have been described in the literature. However, a direct comparison of some of the different approaches (e.g., internal versus external mapping) has not been undertaken. This was attempted here by formulating strawberry yogurt prototypes according to an experimental design including three factors, investigating four approaches of optimization, comparing the sensory profiles of the ideal solutions and formulating the ideal solutions for validation with consumers. Results of this study show that the optimization methods did not yield identical ideal solutions but tended to agree on the ideal level for two of the three sensory dimensions investigated. These results warrant further investigation and comparison of the preference mapping methods available today.

PRACTICAL APPLICATIONS

The research conducted in this study may be useful to consumer scientists and product developers as it provides a direct comparison of preference mapping methodology performance for the optimization of product formulations. Although the work is not intended to establish superiority of one method over another, it provides a template for others who may wish to compare these methodologies.     

Annual Review

In recent years, the science teaching community and curriculum developers have emphasised the importance of teaching inquiry and teaching science as inquiry. One way of developing learners' skills for planning and carrying out scientific research is by allowing them to perform independent research, guided by a teacher. It was recently discovered that there are considerable differences between experiments conducted by scientists and those conducted by students, with regard to the cognitive processes that the experimenters go through. Developing inquiry study activities that emphasise authentic inquiry was suggested in order to introduce students to cognitive activity that more closely resembles that of scientific professionals. This article describes the Biomind programme, intended for students of Grades 11 and 12 (ages 16 to 18 years) majoring in biology. The curriculum, developed by biology teachers, enables students to conduct independent research under teacher guidance. The curriculum emphasises the learning process, not just the outcome, and so students must reflect upon the work in progress. Moreover, the Biomind curriculum follows the principles of authentic inquiry. Biomind may improve students' scientific thinking abilities, expand the guidance aspect of teachers' work, and inspire curriculum developers to further emphasise inquiry.     

A retrospective appraisal of the importance of high-resolution sampling for harmful algal blooms: Lessons from long-term phytoplankton monitoring at Sherkin Island,S.W. Ireland

The ongoing Sherkin Island Marine Station phytoplankton monitoring programme began in 1978. The present stations were established in 1980. Surveying has been carried out continuously since then, employing a more comprehensive sampling strategy than the few other published long-term records. Examples are presented here of cell concentrations for several HAB species and other bloom species from the Sherkin Island record. These show far more short-term and long-term natural variation in time and space than might be expected from the other records in the literature used to investigate HAB, suggesting that ecological complexity may be critically misrepresented in such investigations. This has serious implications for scientists evaluating reports of past HAB (what cell densities were responsible?) and predicting future HAB. Evidence presented here also suggests limitations that should be recognized in using cell concentrations from plankton in models for predictions of HAB.     

Introduction. Oxidative stress in mitochondria disorders of aging

These special issues of Biological Signals and Receptors are intended to describe mitochondrial DNA damage, oxidative stress and human diseases, including neurodegenerative and neuromuscular diseases, disorders associated with aging, and ischemia-perfusion injury. Traditionally, mitochondria have been viewed as the 'powerhouse' of the cell, i.e., the site of the oxidative phosphorylation machinery involved in adenosine triphosphate (ATP) production. Consequently, much of the research conducted on mitochondria over the past 4 decades has focused on elucidating both those molecular events involved in ATP synthesis by oxidative phosphorylation and those involved in the biogenesis of the oxidative phosphorylation machinery. While monumental achievements have been made, and continue to be made, in the study of these remarkable but extremely complex processes essential for the life of most animal cells, it has been only in recent years that a large body of biological and biomedical scientists have come to recognize that mitochondria participate in other important processes. Two of these are cell death and aging which, not surprisingly, are related processes both involving, in part, the oxidative phosphorylation machinery. This new awareness has sparked a new and growing area of mitochondrial research that has become of great interest to a wide variety of scientists ranging from those involved in elucidating the role of mitochondria in cell death and aging to those interested in either suppressing or facilitating these processes as it relates to identifying new therapies or drugs for human disease.     

Between (Racial) Groups and a Hard Place: An Exploration of Social Science Approaches to Race and Genetics, 2000–2014

As the social sciences expand their involvement in genetic and genomic research, more information is needed to understand how theoretical concepts are applied to genetic data found in social surveys. Given the layers of complexity of studying race in relation to genetics and genomics, it is important to identify the varying approaches used to discuss and operationalize race and identity by social scientists. The present study explores how social scientists have used race, ethnicity, and ancestry in studies published in four social science journals from 2000 to 2014. We identify not only how race, ethnicity, and ancestry are classified and conceptualized in this growing area of research, but also how these concepts are incorporated into the methodology and presentation of results, all of which structure the discussion of race, identity, and inequality. This research indicates the slippage between concepts, classifications, and their use by social scientists in their genetics-related research. The current study can assist social scientists with clarifying their use and interpretations of race and ethnicity with the incorporation of genetic data, while limiting possible misinterpretations of the complexities of the connection between genetics and the social world.     

Slugging it out for science: volunteers provide valuable data on the diversity and distribution of heterobranch sea slugs

ABSTRACT

There is increasing interest in participation by volunteers in data collection for marine ecosystems. Here we evaluate the contribution that citizen scientists can make to documenting marine biodiversity through underwater photography of targeted taxa. In a series of 13, 24-hr censuses of sea slugs, at intervals of three months from December 2013 to December 2016, volunteers recorded similar species richness (89%) to scientists at Port Stephens, NSW, Australia. Volunteer numbers only partially (24.9% of variation) explained the relative performance of volunteers against scientists, or the number of species found by volunteers (20.5%). Species richness in censuses was similar (97%) to estimates obtained during four-week lead-up periods. The programme provided novel information on diversity and seasonality of sea slugs, revealing strong seasonal patterns for chromodorid nudibranchs, and cyclical temporal change at the assemblage level. The programme inspired many of the participants to take part in multiple events, generated educational material, and led to the extension of the programme to other locations. The potential benefits of programmes such as this go beyond the generation of data to address specific research questions and, combined with extension activities, can help to deliver and reinforce messages about the importance of marine ecosystem health.     

The urgency of building global capacity for biodiversity science

The biodiversity sciences represent the disciplines of whole-organism biology, including systematics, ecology, population biology, behaviour and the fields of comparative biology. The biodiversity sciences are critically important to society because it is knowledge of whole-organisms that is essential for managing and conserving the world's species. Because of an acceleration in environmental degradation and global biodiversity loss in recent decades, the need for the biodiversity sciences has never been more urgent. Yet, biodiversity science is not well supported relative to other fields of science, and thus the need for knowledge about organisms and their environment is far outstripping biologists' ability to provide it. National and international capacity for biodiversity science must therefore be increased substantially. Each nation should establish a national biodiversity research programme coordinated across all government agencies. An international biodiversity research programme should also be established, perhaps with an organizational structure that parallels the International Geosphere-Biosphere Programme. Biodiversity scientists must assume a leadership role in educating the public and bringing about policy changes that will enhance our understanding of the world's species and their ecosystems.     

EMF and current cancer concepts

Exposure to power frequency electric and magnetic fields (EMF) is ubiquitous, and a body of epidemiologic studies has produced evidence suggestive of a possible link between EMF exposure and cancer of several types. This paper provides a perspective that holds key findings in the EMF literature against the background of important models and established principles in cancer biology. It is intended primarily for scientists whose expertise lies outside of cancer biology and animal bioassays. Current thinking holds that carcinogenesis is a multistep process that requires at least two genotoxic events in its critical path but that is facilitated by nongenotoxic proliferative effects on target cells. EMF, which itself is not believed to be genotoxic, could influence carcinogenesis if it exerted either direct or indirect effects on target cell turnover. Such effects could operate through receptor-mediated or nonreceptor-mediated pathways. However, effects relevant to carcinogenesis have not been confirmed, and a mode of action for EMF has not been determined. Chronic bioassays in rodents are in progress to examine the potential carcinogenicity of EMFs. EMF research has the opportunity to capitalize on the recent major advances in our understanding of carcinogenic processes. © 1996 Wiley-Liss, Inc.     

The International Proteomics Tutorial Programme (IPTP): a teaching tool box for the proteomics community

The most critical functions of the various proteomics organisations are the training of young scientists and the dissemination of information to the general scientific community. The education committees of the Human Proteome Organisation (HUPO) and the European Proteomics Association (EuPA) together with their national counterparts are therefore launching the International Proteomics Tutorial Programme to meet these needs. The programme is being led by Peter James (Sweden), Thierry Rabilloud (France) and Kazuyuki Nakamura (Japan). It involves collaboration between the leading proteomics journals: Journal of Proteome Research, Journal of Proteomics, Molecular and Cellular Proteomics, and Proteomics. The overall level is aimed at Masters/PhD level students who are starting out their research and who would benefit from a solid grounding in the techniques used in modern protein-based research. The tutorial program will cover core techniques and basics as an introduction to scientists new to the field. At a later stage the programme may be expanded with a series of more advanced topics focussing on the application of proteomics techniques to biological problem solving. The entire series of articles and slides will be made freely available for teaching use at the Journals and Organisations homepages and at a special website, www.proteomicstutorials.org.     

Does the Committee Peer Review Select the Best Applicants for Funding? An Investigation of the Selection Process for Two European Molecular Biology Organization Programmes

Does peer review fulfill its declared objective of identifying the best science and the best scientists? In order to answer this question we analyzed the Long-Term Fellowship and the Young Investigator programmes of the European Molecular Biology Organization. Both programmes aim to identify and support the best post doctoral fellows and young group leaders in the life sciences. We checked the association between the selection decisions and the scientific performance of the applicants. Our study involved publication and citation data for 668 applicants to the Long-Term Fellowship programme from the year 1998 (130 approved, 538 rejected) and 297 applicants to the Young Investigator programme (39 approved and 258 rejected applicants) from the years 2001 and 2002. If quantity and impact of research publications are used as a criterion for scientific achievement, the results of (zero-truncated) negative binomial models show that the peer review process indeed selects scientists who perform on a higher level than the rejected ones subsequent to application. We determined the extent of errors due to over-estimation (type I errors) and under-estimation (type 2 errors) of future scientific performance. Our statistical analyses point out that between 26% and 48% of the decisions made to award or reject an application show one of both error types. Even though for a part of the applicants, the selection committee did not correctly estimate the applicant''s future performance, the results show a statistically significant association between selection decisions and the applicants'' scientific achievements, if quantity and impact of research publications are used as a criterion for scientific achievement.     

H3Africa: An Africa exemplar? Exploring its framework on protecting human research participants

The Human Heredity and Health in Africa (H3Africa) Consortium is a conglomeration of research and infrastructure projects spread throughout Africa whose aim is to apply genomic methodology to diseases affecting the people in the region. Its operation is innovative in the sense that it is doing something new; that is, filling a hitherto existing void in genomic research capability of African scientists and infusing resources and manpower to institutions and investigators across Africa. But aside from developing and sustaining capacity in genomic research and biorepositories, H3Africa is also invested in developing appropriate ethical regulatory regime to govern research in these areas. This latter concern –research ethics governance – is the major subject of this paper. Specifically, the paper discusses protection of research participants as envisaged by H3Africa in the area of consent, safeguarding privacy, maintaining confidentiality of health information and sharing of data/biospecimens. The ultimate goal is to determine whether H3Africa initiatives and processes are consistent or at odds with international guidelines and best practices.     

The method of synthesis in ecology

Synthesis of results from different investigations is an important activity for ecologists but when compared with analysis the method of synthesis has received little attention. Ecologists usually proceed intuitively and this can lead to a problem in defining differences between the syntheses made by different scientists. It also leads to criticism from scientists favoring analytical approaches that the construction of general theory is an activity that does not follow the scientific method. We outline a methodology for scientific inference about integrative concepts and the syntheses made in constructing them and illustrate how this can be applied in the development of general theory from investigations into particular ecological systems. The objective is to construct a causal scientific explanation. This has four characteristics. (1) It defines causal and/or organizational processes that describe how systems function. (2) These processes are consistent – under the same conditions they will produce the same effect. (3) A causal scientific explanation provides general information about events of a similar kind. (4) When experiments are possible then a designed manipulation will produce a predictable response. The essential characteristic of making synthesis to construct a causal scientific explanation is that it is progressive and we judge progress made by assessing the coherence of the explanation using six criteria: acceptability of individual propositions including that they have been tested with data, consistency of concept definitions, consistency in the type of concepts used in making the explanation, that ad hoc propositions are not used, that there is economy in the number of propositions used, that the explanation applies to broad questions. We illustrate development of a causal scientific explanation for the concept of long-lived pioneer tree species, show how the coherence of this explanation can be assessed, and how it could be improved.     

A guideline for analyzing circadian wheel-running behavior in rodents under different lighting conditions

Most behavioral experiments within circadian research are based on the analysis of locomotor activity. This paper introduces scientists to chronobiology by explaining the basic terminology used within the field. Furthermore, it aims to assist in designing, carrying out, and evaluating wheel-running experiments with rodents, particularly mice. Since light is an easily applicable stimulus that provokes strong effects on clock phase, the paper focuses on the application of different lighting conditions.     

Guidelines: From artificial evolution to computational evolution: a research agenda

Computational scientists have developed algorithms inspired by natural evolution for at least 50 years. These algorithms solve optimization and design problems by building solutions that are 'more fit' relative to desired properties. However, the basic assumptions of this approach are outdated. We propose a research programme to develop a new field: computational evolution. This approach will produce algorithms that are based on current understanding of molecular and evolutionary biology and could solve previously unimaginable or intractable computational and biological problems.     

Senescence and programmed cell death: substance or semantics?

The terms senescence and programmed cell death (PCD) have led to some confusion. Senescence as visibly observed in, for example, leaf yellowing and petal wilting, has often been taken to be synonymous with the programmed death of the constituent cells. PCD also obviously refers to cells, which show a programme leading to their death. Some scientists noted that leaf yellowing, if it has not gone too far, can be reversed. They suggested calling leaf yellowing, before the point of no return, 'senescence' and the process after it 'PCD'. However, this runs into several problems. It is counter to the historical definitions of senescence, both in animal and plant science, which stipulate that senescence is programmed and directly ends in death. It would also mean that only leaves and shoots show senescence, whereas several other plant parts, where reversal has not (yet) been shown, have no senescence, but only PCD. This conflicts with ordinary usage (as in root and flower senescence). Moreover, a programme can be reversible and therefore it is not counter to logic to regard the cell death programme as potentially reversible. In green leaf cells a decision to die, in a programmed way, has been taken, in principle, before the cells start to remobilize their contents (that is, before visible yellowing) and only rarely is this decision reversed. According to the arguments developed here there are no good reasons to separate a senescence phase and a subsequent PCD phase. Rather, it is asserted, senescence in cells is the same as PCD and the two are fully synchronous.     

From bark to weed: the history of artemisinin

In the 1970's, in China, some brilliant and courageous scientists carried out a research programme, which lead to the discovery of artemisinin derivatives and new quinoleines that are used today, in combination, as first line treatment of malaria.