Assessing the variation and genetic architecture of asparagine content in wheat: What can plant breeding contribute to a reduction in the acrylamide precursor?

Key message

A large genetic variation, moderately high heritability, and promising prediction ability for genomic selection show that wheat breeding can substantially reduce the acrylamide forming potential in bread wheat by a reduction in its precursor asparagine.

Abstract

Acrylamide is a potentially carcinogenic substance that is formed in baked products of wheat via the Maillard reaction from carbonyl sources and asparagine. In bread, the acrylamide content increases almost linearly with the asparagine content of the wheat grains. Our objective was, therefore, to investigate the potential of wheat breeding to contribute to a reduction in acrylamide by decreasing the asparagine content in wheat grains. To this end, we evaluated 149 wheat varieties from Central Europe at three locations for asparagine content, as well as for sulfur content, and five important quality traits regularly assessed in bread wheat breeding. The mean asparagine content ranged from 143.25 to 392.75 mg/kg for the different wheat varieties, thus underlining the possibility to reduce the acrylamide content of baked wheat products considerably by selecting appropriate varieties. Furthermore, a moderately high heritability of 0.65 and no negative correlations with quality traits like protein content, sedimentation volume and falling number show that breeding of quality wheat with low asparagine content is feasible. Genome-wide association mapping identified few QTL for asparagine content, the largest explaining 18% of the genotypic variance. Combining these QTL with a genome-wide prediction approach yielded a mean cross-validated prediction ability of 0.62. As we observed a high genotype-by-environment interaction for asparagine content, we recommend the costly and slow laboratory analysis only for late breeding generations, while selection in early generations could be based on marker-assisted or genomic selection.

     

Mapping spatial pattern in biodiversity for regional conservation planning: where to from here?

Vast gaps in available information on the spatial distribution of biodiversity pose a major challenge for regional conservation planning in many parts of the world. This problem is often addressed by basing such planning on various biodiversity surrogates. In some situations, distributional data for selected taxa may be used as surrogates for biodiversity as a whole. However, this approach is less effective in data-poor regions, where there may be little choice but to base conservation planning on some form of remote environmental mapping, derived, for example, from interpretation of satellite imagery or from numerical classification of abiotic environmental layers. Although this alternative approach confers obvious benefits in terms of cost-effectiveness and rapidity of application, problems may arise if congruence is poor between mapped land-classes and actual biological distributions. I propose three strategies for making more effective use of available biological data and knowledge to alleviate such problems by (1) more closely integrating biological and environmental data through predictive modeling, with increased emphasis on modeling collective properties of biodiversity rather than individual entities; (2) making more rigorous use of remotely mapped surrogates in conservation planning by incorporating knowledge of heterogeneity within land-classes, and of varying levels of distinctiveness between classes, into measures of conservation priority and achievement; and (3) using relatively data-rich regions as test-beds for evaluating the performance of surrogates that can be readily applied across data-poor regions.     

Does the seed bank contribute to the restoration of species‐rich vegetation in wet dune slacks?

Questions: What is the contribution of the seed bank to restoration of species‐rich vegetation in oligotrophic wet dune slacks? Does the restoration management affect the seed bank? Location: Calcareous coastal dune slacks at the west coast of The Netherlands. Methods: Species composition of the seed bank and the above‐ground vegetation was sampled in dune slacks that had a variable extent of groundwater level rise in combination with either topsoil removal or mowing. Results: The seed bank had a high potential for restoration of species‐rich vegetation: 60 species were found in the seed bank of which 14 were characteristic of oligotrophic, wet dune vegetation. While topsoil removal almost completely removed the seed bank, groundwater level rise did not permanently submerge the seed bank of species of oligotrophic, wet conditions. Changes in abundance in the established vegetation were unrelated to species abundance in the seed bank. Of all new species establishments in the vegetation relevés, 76% occurred where the species was not found in the seed bank. The chance that presence of a species in the seed bank led to establishment the following year was only 11%. Conclusion: The seed bank was not the dominant source for newly establishing species following the large disturbance that was induced by restoration management. Changes in species abundance after the restoration impact were not related to species abundance in the seed bank, but to ongoing succession and current year dispersal. To attain a high number of new establishments, restoration projects should preferably be planned in the proximity of refuge populations, rather than relying on the seed bank alone.     

What can sown wildflower strips contribute to butterfly conservation?: an example from a Swiss lowland agricultural landscape

The objective of this study was to compare butterfly abundances and diversity between wildflower strips and extensively used meadows to identify which butterfly species can be supported by establishing wildflower strips. Butterflies were recorded along transects during one season in twenty-five sown wildflower strips and eleven extensively used meadows in a Swiss lowland agricultural landscape (600 ha). In total 1,669 butterflies of 25 species were observed (25 in the strips, 18 in meadows). This can be related to 38 species recorded in the region (lowland part of Kanton Fribourg) within the Swiss Biodiversity Monitoring Programme. In wildflower strips the number of butterflies per transect meter was significantly higher than in the meadows, but there was no significant difference in species richness. Butterfly communities, though, were quite different between the two habitat types. Habitat type, abundances of flowering plants and presence of forest within 50 m were identified as factors influencing butterfly species richness. Butterfly abundances were affected by habitat type and abundance of flowering plants. In wildflower strips, 65% of all flower visits by butterflies were observed on Origanum. It can be concluded that sown wildflower strips can support a substantial part of a regions species pool. This is mostly true for common species, but can apply to rare species when, for example, larval food plant requirements are met.     

HLA-DQ system and insulin-dependent diabetes mellitus in Japanese: does it contribute to the development of IDDM as it does in Caucasians?

Fifty-six unrelated Japanese patients with insulin-dependent diabetes mellitus (IDDM) were HLA-typed, and restriction fragment length polymorphism (RFLP) analysis was performed after enzyme digestion with Bam HI and Taq I by using both DR and DQ probes. As previously reported, increased frequencies of Bw54, Cw1, DR4, and DRw53, which are in strong linkage disequilibrium in the Japanese population and make the characteristic Japanese haplotype, were confirmed. DQw4, a new allele of the DQ system recognized by the monoclonal antibody HU-46 and in linkage disequilibrium with this haplotype, presented the highest IDDM association. The RFLP analysis also showed the strongest correlation to IDDM when the DQ probe was applied. These results indicate that HLA-DQ might play the most important role in the development of IDDM in Japanese as well as in Caucasians. The correlation of DQ amino acid sequences strongly associated with IDDM in Japanese are discussed in this study, and contrasting results were found when such sequences were compared with those of Caucasians.Abbreviations used in this paper IDDM insulin-dependent diabetes mellitus - RFLP restriction fragment length polymorphism - Asp aspartic acid - Asp-57 aspartic acid at the 57th residue of the DQ chain - non-Asp-57 nonaspartic acid at the 57th residue of the DQ chain - R.R. relative risk of Woolf and Haldane     

Bioengineering nitrogen acquisition in rice: can novel initiatives in rice genomics and physiology contribute to global food security?

Rice is the most important crop species on earth, providing staple food for 70% of the world's human population. Over the past four decades, successes in classical breeding, fertilization, pest control, irrigation and expansion of arable land have massively increased global rice production, enabling crop scientists and farmers to stave off anticipated famines. If current projections for human population growth are correct, however, present rice yields will be insufficient within a few years. Rice yields will have to increase by an estimated 60% in the next 30 years, or global food security will be in danger. The classical methods of previous green revolutions alone will probably not be able to meet this challenge, without being coupled to recombinant DNA technology. Here, we focus on the promise of these modern technologies in the area of nitrogen acquisition in rice, recognizing that nitrogen deficiency compromises the realization of rice yield potential in the field more than any other single factor. We summarize rice-specific advances in four key areas of research: (1). nitrogen fixation, (2). primary nitrogen acquisition, (3). manipulations of internal nitrogen metabolism, and (4). interactions between nitrogen and photosynthesis. We develop a model for future plant breeding possibilities, pointing out the importance of coming to terms with the complex interactions among the physiological components under manipulation, in the context of ensuring proper targeting of intellectual and financial resources in this crucial area of research.     

Actin in the nucleus: what form and what for?

Actin is an abundant protein in most nonmuscle cells. It has often been observed in isolated nuclei, yet cytoplasmic contamination was of course initially regarded as the most plausible origin. Numerous studies on nuclear actin appeared in the 1970s and 1980s, but the picture remained rather muddy. The viewpoint at that time was that actin-shown to move freely between cytoplasm and nucleus-was a mere "thermodynamic wanderer," transiently occupying the nucleus. More recently, evidence has been mounting that actin's presence in the nucleus is not simply governed by the laws of diffusion. The same holds true for the finding of various actin-related proteins in the nucleus, and the case for nuclear myosin, specifically myosin I, is now quite convincing. Moreover, the first intimations of functional roles of nuclear actin are now emerging. Here we examine the overall subject from cell biological and chemical perspectives. The major issue is no longer the presence of actin in the nucleus but rather its supramolecular organization, intranuclear locations, and, of course, functions. These issues interface with recent findings that reveal a surprisingly diverse repertoire of actin conformations and oligomer and polymer forms beyond monomeric G-actin and polymeric F-actin. We present ideas for advancing the nuclear actin field and call for a renewed attack on this major problem in cell biology.     

The critical cue in pattern discrimination for the honey bee: Color or form?

When honey bees approach blossoms, they are attracted by the color and form of the goal in their visual field, and they use these cues for a successful revisit. Their visual system receives cues by two main types of parallel channels behind the retina; one channel for colors, and a monochrome channel for the orientation and edge of the item in their visual field. In the integration process of these 2 channels, the priority and interaction between them are significant due to the fact that these chromatic and achromatic signals coexist naturally. To investigate this issue, we trained bees to detect form and color and then tested them with combinations of opposite patterns. We observed that the bees chose the correct color but the wrong form pattern in the above experiment as well as for other manipulations as follows. The effect of the color training for the blue reward pattern differed from that of the green reward pattern. The color pattern choices tended to be more correct if blue was the target during the training process, indicating that the chromatic signal was the main cue in pattern discrimination. In other words, color tended to be the decisive factor in a conflicting situation. In addition, the color blue was preferred over the color green, indicating that color preference was involved in visual recognition.     

From A to Z and back? Multicompartment proteins in the sarcomere

Sarcomeres, the smallest contractile units of striated muscle, are conventionally perceived as the most regular macromolecular assemblies in biology, with precisely assigned localizations for their constituent proteins. However, recent studies have revealed complex multiple locations for several sarcomere proteins within the sarcomere and other cellular compartments such as the nucleus. Several of these proteins appear to relocalize in response to mechanical stimuli. Here, we review the emerging role of these protein networks as dynamic information switchboards that communicate between the contractile machinery and the nucleus to central pathways controlling cell survival, protein breakdown, gene expression and extracellular signaling.     

Summer kill rates and predation pattern in a wolf–moose system: can we rely on winter estimates?

So far the vast majority of studies on large carnivore predation, including kill rates and consumption, have been based on winter studies. Because large carnivores relying on ungulates as prey often show a preference for juveniles, kill rates may be both higher and more variable during the summer season than during the rest of the year leading to serious underestimates of the total annual predation rate. This study is the first to present detailed empirical data on kill rates and prey selection in a wolf–moose system during summer (June–September) as obtained by applying modern Global Positioning System-collar techniques on individual wolves (Canis lupus) in Scandinavia. Moose (Alces alces) was the dominant prey species both by number (74.4%) and biomass (95.6%); 89.9% of all moose killed were juveniles, representing 76.0% of the biomass consumed by wolves. Kill rate in terms of the kilogram biomass/kilogram wolf per day averaged 0.20 (range: 0.07–0.32) among wolf territories and was above, or well above, the daily minimum food requirements in most territories. The average number of days between moose kills across wolf territories and study periods was 1.71 days, but increased with time and size of growing moose calves during summer. Over the entire summer (June–September, 122 days), a group (from two to nine) of wolves killed a total of 66 (confidence interval 95%; 56–81) moose. Incorporation of body growth functions of moose calves and yearlings and wolf pups over the summer period showed that wolves adjusted their kill rate on moose, so the amount of biomass/kilogram wolf was relatively constant or increased. The kill rate was much higher (94–116%) than estimated from the winter period. As a consequence, projecting winter kill rates to obtain annual estimates of predation in similar predator–prey systems may result in a significant underestimation of the total number of prey killed. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

From the gene to the clinic: prostate cancer death can now be an exception?

The most significant discovery of the second half of the XXth century in the field of prostate cancer therapy is probably the observation that the human prostate, as well as many other peripheral human tissues, synthesize locally an important amount of androgens from the inactive steroid precursors dehydroepiandrosterone (DHEA) and its sulfate DHEA-S. In parallel with these observations, two important discoveries also made by our group are applied in the clinic worldwide, namely the use of LHRH (luteininizing hormone-releasing hormone) agonists to completely block testicular androgens, while, simultaneously, the androgens made locally in the prostate from DHEA are blocked in their access to the androgen receptor by a pure antiandrogen of the class of flutamide. This treatment, called combined androgen blockade, has been the first treatment demonstrated to prolong life in prostate cancer. While the first studies were performed in patients with advanced and metastatic disease, our recent data indicate a remarkable level of efficacy of the same treatment applied to localized prostate cancer, namely a 90% possibility of cure. However, in order to be able to treat localized prostate cancer, early diagnosis must be achieved. In the first large-scale randomized study of prostate cancer screening, we have demonstrated that 99% of prostate cancers can be diagnosed at the localized or potentially curable stage, using simple annual measurement of PSA (prostatic specific antigen). Today's data show that with the simple application of the available diagnostic and therapeutic tools, death from prostate cancer should be an exception.     

Stress and the epigenetic landscape: a link to the pathobiology of human diseases?

Accumulating evidence points to a major role for chronic stress of cell renewal systems in the pathogenesis of important human diseases, including cancer, atherosclerosis and diabetes. Here we discuss emerging evidence that epigenetic abnormalities may make substantial contributions to these stress-induced pathologies. Although the mechanisms remain to be fully elucidated, we suggest that chronic stress can elicit heritable changes in the chromatin landscape that 'lock' cells in abnormal states, which then lead to disease. We emphasize the need to investigate epigenetic states in disease and links to stress and to consider how the knowledge gained through these studies may foster new means of disease prevention and management.     

Wading through the swamp: what does tropical peatland restoration mean to national‐level stakeholders in Indonesia?

Ecological restoration is considered to play an important role in mitigating climate change, protecting biodiversity, and preventing environmental degradation. Yet, there are often multiple perspectives on what outcomes restoration should be aiming to achieve, and how we should get to that point. In this study we interview a range of policymakers, academics, and non‐governmental organization (NGO) representatives to explore the range of perspectives on the restoration of Indonesia's tropical peatlands—key global ecosystems that have undergone large‐scale degradation. Thematic analysis suggests that participants agreed about the importance of restoration, but had differing opinions on how effective restoration activities to date have been and what a restored peatland landscape should look like. These results exemplify how ecological restoration can mean different things to different people, but also highlight important areas of consensus for moving forward with peatland restoration strategies.     

How do glutamatergic and GABAergic cells contribute to synchronization in the medial septum?

The medial septum-diagonal band (MSDB) complex is considered as a pacemaker for the hippocampal theta rhythm. Identification of the different cell types, their electro-physiological properties and their possible function in the generation of a synchronized activity in the MSDB is a hot topic. A recent electro-physiological study showed the presence of two antiphasically firing populations of parvalbumin containing GABAergic neurons in the MSDB. Other papers described a network of cluster-firing glutamatergic neurons, which is able to generate synchronized activity in the MSDB. We propose two different computer models for the generation of synchronized population theta oscillation in the MSDB and compare their properties. In the first model GABAergic neurons are intrinsically theta periodic cluster-firing cells; while in the second model GABAergic cells are fast-firing cells and receive periodic input from local glutamatergic neurons simulated as cluster-firing cells. Using computer simulations we show that the GABAergic neurons in both models are capable of generating antiphasic theta periodic population oscillation relying on local, septal mechanisms. In the first model antiphasic theta synchrony could emerge if GABAergic neurons form two populations preferentially innervate each other. In the second model in-phase synchronization of glutamatergic neurons does not require specific network structure, and the network of these cells are able to act as a theta pacemaker for the local fast-firing GABAergic circuit. Our simulations also suggest that neurons being non-cluster-firing in vitro might exhibit clustering properties when connected into a network in vivo. Action Editor: David Golomb     

Human dignity: a guide to policy making in the biotechnology era?

This article explores the ways in which human dignity is used in debates about controversial biotechnologies, including biobanks, human gene patents, stem cell research and human cloning. Increasingly, human dignity is used as a form of general condemnation and as blanket justification for regulatory restraint. However, this use of human dignity marks a significant departure from the traditional, human-rights informed view of human dignity that has dominated bioethics debates for decades. In addition, on its own, it stands as dubious justification for policies that are aimed at constraining controversial biotechnologies.     

On governance in the long-term vegetation process: How to discover the rules?

Ecological practice is telling us that to identify Nature’s rules, we should look for regularities in the resulting effects. Hidden rules are involved and the effects are manifested by compositional, functional, and structural transitions. This paper’s focus is on two conjectures regarding the governance of specific transition components, the first supposedly under global co-ordination, and the second under superimposed site specific instability oscillations. The reality of any apparent regularity in these is the sole condition for the regularity’s acceptance as a rule. Reality is testable but in retrospect only, based on time series analyses. Since long pollen spectra supply the evidence, the time period involved is measured in thousands of years. For maximal usefulness, a spectrum should have a long period length, dated horizons intensely sampled at short time steps, and precisely identified taxa. Period length and time step width matter because both may have a masking effect on the regularities. There is, of course, a natural limit for period length, which is set by the age of the pollen bearing sediments. We completed the analysis of 23 spectra using techniques deemed suitable for testing the conjectures. The spectra originated from sites in the Americas where we found suitable spectra in sufficient numbers and in geographic contiguity from the Arctic region to the Antarctic. The presented results have clear indications that the two conjectures identify real rules. The main body of the paper narrates the analyses and provides explanations. Informative materials, too voluminous for inclusion in the paper, are made available on the Internet at URL: www.vegetationdynamics.com linking to “Appendices Ta”.     

What can proteomic analyses contribute to understanding the molecular biology and clinical behavior of prostate cancer?

Identifying the proteins and their complex interactions that promote and/or sustain the aggressive malignant phenotype is essential for understanding key effectors of the molecular biology of prostate cancer. This is also essential for development of new clinical applications. A variety of proteomic techniques, ranging from mass spectrometry to new methods of multiplexing protein identification, have great potential for rapidly achieving these goals. However, in order to obtain meaningful results, these techniques must be applied within the context of our knowledge of the heterogeneity of prostate tissues and tumors, the impact of specimen processing on both the quality and quantity of proteins detected and a thorough understanding of prostate cell biology. Collaboration between the protein chemist and the prostate cell biologist will expedite progress in this important field.     

Do changes in gene expression contribute to sexual isolation and reinforcement in the house mouse?

Expression divergence, rather than sequence divergence, has been shown to be important in speciation, particularly in the early stages of divergence of traits involved in reproductive isolation. In the two European subspecies of house mice, Mus musculus musculus and Mus musculus domesticus, earlier studies have demonstrated olfactory‐based assortative mate preference in populations close to their hybrid zone. It has been suggested that this behaviour evolved following the recent secondary contact between the two taxa (~3,000 years ago) in response to selection against hybridization. To test for a role of changes in gene expression in the observed behavioural shift, we conducted a RNA sequencing experiment on mouse vomeronasal organs. Key candidate genes for pheromone‐based subspecies recognition, the vomeronasal receptors, are expressed in these organs. Overall patterns of gene expression varied significantly between samples from the two subspecies, with a large number of differentially expressed genes between the two taxa. In contrast, only ~200 genes were found repeatedly differentially expressed between populations within M. m. musculus that did or did not display assortative mate preferences (close to or more distant from the hybrid zone, respectively), with an overrepresentation of genes belonging to vomeronasal receptor family 2. These receptors are known to play a key role in recognition of chemical cues that handle information about genetic identity. Interestingly, four of five of these differentially expressed receptors belong to the same phylogenetic cluster, suggesting specialization of a group of closely related receptors in the recognition of odorant signals that may allow subspecies recognition and assortative mating.