The horse genome project - sequence based insights into male reproductive mechanisms

The growing knowledge on physiology, cell biology and biochemistry of the reproductive organs has provided many insights into molecular mechanisms that are required for successful reproduction. Research directed at the investigation of reproduction physiology in domestic animals was hampered in the past by a lack of species-specific genomic information. The genome sequences of dog, cattle and horse have become publicly available in 2005, 2006 and 2007 respectively. Although the gene content of mammalian genomes is generally very similar, genes involved in reproduction tend to be less conserved than the average mammalian gene. The availability of genome sequences provides a valuable resource to check whether any protein that may be known from human or mouse research is present in cattle and/or horse as well. Currently there are more than 200 genes known that are involved in the production of fertile sperm cells. Great progress has been made in the understanding of genetic aberrations that lead to male infertility. Additionally, the first genetic mechanisms are being discovered that contribute to the quantitative variation of fertility traits in fertile male animals. Here, I will review some selected aspects of genetic research in male fertility and offer some perspectives for the use of genomic sequence information.

Impact factor statistics and publication practice: What can we learn? (Editorial)

Peer review procedures and citation statistics are important yet often neglected components of the scientific publication process. Here I discuss fundamental consequences of such quality measures for the scientific community and propose three remedial actions: (1) use of a ''Combined Impact Estimate'' as a measure of citation statistics, (2) adoption of an open reviewing policy and (3) acceleration of the publication process in order to raise the reputation of the entire discipline (in our case: behavioural science). Authors, reviewers and editors are invited to contribute to the improvement of publication practice.

Resolving the tragedy of the commons: the feedback between intraspecific conflict and population density

Competition and conflict among individuals can favour exploitative strategies that undermine the common good. Theory suggests that this can lead to a tragedy of the commons and ultimately population extinction, a phenomenon known as evolutionary suicide. Here, I present a model of the evolutionary tragedy of the commons that explicitly considers the population dynamics where individuals invest in individually costly competitive traits. In the simplest form, this supports the notion that selection for high levels of conflict can cause evolutionary suicide. However, as competition comes with survival and fecundity costs, a feedback between the investment in competition and population density can act to reduce the level of conflict and prevent the population from going extinct. This suggests that the interaction between population ecology and the evolution of competition and conflict among individuals may be an important mechanism in resolving the level of competition and conflict among individuals.

Golden-winged Warbler habitat model validation for northern Wisconsin and central Minnesota

Between 1966 and 2003, the Golden-winged Warbler (Vermivora chrysoptera) experienced declines of 3.4% per year in large parts of the breeding range and has been identified by Partners in Flight as one of 28 land birds requiring expedient action to prevent its continued decline. It is currently being considered for listing under the Endangered Species Act. A major step in advancing our understanding of the status and habitat preferences of Golden-winged Warbler populations in the Upper Midwest was initiated by the publication of new predictive spatially explicit Golden-winged Warbler habitat models for the northern Midwest. Here, I use original data on observed Golden-winged Warbler abundances in Wisconsin and Minnesota to compare two population models: the hierarchical spatial count (HSC) model with the Habitat Suitability Index (HSI) model. I assessed how well the field data compared to the model predictions and found that within Wisconsin, the HSC model performed slightly better than the HSI model whereas both models performed relatively equally in Minnesota. For the HSC model, I found a 10% error of commission in Wisconsin and a 24.2% error of commission for Minnesota. Similarly, the HSI model has a 23% error of commission in Minnesota; in Wisconsin due to limited areas where the HSI model predicted absences, there was incomplete data and I was unable to determine the error of commission for the HSI model. These are sites where the model predicted presences and the Golden-winged Warbler did not occur. To compare predicted abundance from the two models, a 3x3 contingency table was used. I found that when overlapped, the models do not complement one another in identifying Golden-winged Warbler presences. To calculate discrepancy between the models, the error of commission shows that the HSI model has only a 6.8% chance of correctly classifying absences in the HSC model. The HSC model has only 3.3% chance of correctly classifying absences in the HSI model. These findings highlight the importance of grasses for nesting, shrubs used for cover and foraging, and trees for song perches and foraging as key habitat characteristics for breeding territory occupancy by singing males.

Compensatory growth in moose and its relationship to sex, longevity, intraspecific competition, and senescence

Individual life history theory is largely focused on understanding the extent to which various phenotypes of an organism are adaptive and whether they represent life history trade-offs. Compensatory growth (CG) is increasingly appreciated as a phenotype of interest to evolutionary ecologists. CG or catch-up growth involves the ability of an organism to grow at a faster-than-normal rate following periods of under-nutrition once conditions subsequently improve. Here, I examine CG in a population of moose (Alces alces) living on Isle Royale, a remote island in Lake Superior, North America. I gained insights about CG from measurements of skeletal remains of 841 moose born throughout a 52-year period. In particular, I compared the length of the metatarsal bone (ML) with several skull measurements. While ML is an index of growth while the moose is in utero and during the first year or two of life, a moose skull continues to grow until a moose is approximately 5 years of age. Because of these differences, the strength of correlation between ML and skull measurements, for a group of moose (say female moose) is an indication of that group’s capacity for CG. Using this logic, I conducted analyses whose results suggest that the capacity for CG did not differ between sexes, between individuals born during periods of high and low population densities, or between individuals exhibiting signs of senescence and those that do not. The analysis did however suggest that long-lived individuals had a greater capacity for CG than short-lived individuals. These results suggest that CG in moose is an adaptive trait and might not be associated with life history trade-offs.

International social work education at the crossroads

Social work has been a player in the international arena since 1928 when the International Association of Schools of Social Work (IASSW) was founded alongside its sister organisations, the International Federation of Social Workers (IFSW) and the International Council for Social Welfare (ICSW). These divided their remit into education, practice and policy respectively. Their development has been an interesting one, but the details of it need not detain us here. I only want to lay aside the argument that having an interest in the international domain is a new phenomenon in social work. At the same time, I want to emphasise how impressive it is that a profession that has been so tied into modernity, linked to the modern nation-state (Lorenz, 1994) and rooted in local legislation and traditions has such a long-standing history of involvements that have crossed borders to promote understanding and knowledge-building. In these encounters, social work educators and practitioners have engaged with others who were different from them while struggling to make their interactions egalitarian and respectful ones.

Social Work Education and Training in Europe and the Bologna Process

A short review of the last three decades shows that social work programmes have developed similarly in (almost) all European countries, both in terms of structural and content-related characteristics. Here I would like to focus on the following aspects: Increased academic focus of training, Generalist programme, International/European orientation. Increased academic focus means that social work programmes have been established at uni-versities or comparable higher education institutions, such as universities of applied sciences. The only exception is France where the approximately 150, generally fairly small colleges and the 14 larger instituts regionaux have a hybrid position between vocational colleges and universities and are roughly comparable to academies.

The “Out of Africa Tribe” (II): Paleolithic warriors with big canoes and protective weapons

It is generally difficult to establish a timeline for the appearance of different technologies and tools during human cultural evolution. Here I use stochastic character mapping of discrete traits using human mtDNA phylogenies rooted to the Reconstructed Sapiens Reference Sequence (RSRS) as a model to address this question. The analysis reveals that the ancestral state of Homo sapiens was hunting, using material innovations that included bows and arrows, stone axes and spears. However, around 80,000 y before present, a transition occurred, from this ancestral hunting tradition, toward the invention of protective weapons such as shields, the appearance of ritual fighting as a socially accepted behavior and the construction of war canoes for the fast transport of large numbers of warriors. This model suggests a major cultural change, during the Palaeolithic, from hunters to warriors. Moreover, in the light of the recent Out of Africa Theory, it suggests that the “Out of Africa Tribe” was a tribe of warriors that had developed protective weapons such as shields and used big war canoes to travel the sea coast and big rivers in raiding expeditions.

Semantic Representation of Synaesthesia

Synaesthesia has multifaceted consequences for both subjective experience and cognitive performance. Here, I broach the issue of how synaesthesia is represented in semantic memory. I hypothesize that, for example, in grapheme colour synaesthesia, colour is represented as an additional feature in the semantic network that enables the formation of associations that are not present in non-synaesthetes. Thus, synaesthesia provokes richer memory representations which enable learning opportunities that are not present in non-synaesthetes, provides additional memory cues, and may trigger creative ideas.

Implicit task sequence learning

Implicit task sequence learning (TSL) can be considered as an extension of implicit sequence learning which is typically tested with the classical serial reaction time task (SRTT). By design, in the SRTT there is a correlation between the sequence of stimuli to which participants must attend and the sequence of motor movements/key presses with which participants must respond. The TSL paradigm allows to disentangle this correlation and to separately manipulate the presences/absence of a sequence of tasks, a sequence of responses, and even other streams of information such as stimulus locations or stimulus-response mappings. Here I review the state of TSL research which seems to point at the critical role of the presence of correlated streams of information in implicit sequence learning. On a more general level, I propose that beyond correlated streams of information, a simple statistical learning mechanism may also be involved in implicit sequence learning, and that the relative contribution of these two explanations differ according to task requirements. With this differentiation, conflicting results can be integrated into a coherent framework.

The closing door of climate targets

Robust evidence from a range of climate–carbon cycle models shows that the maximum warming relative to pre-industrial times caused by the emissions of carbon dioxide is nearly proportional to the total amount of emitted anthropogenic carbon (1, 2). This proportionality is a reasonable approximation for simulations covering many emissions scenarios for the time frame 1750 to 2500 (1). This linear relationship is remarkable given the different complexities of the models and the wide range of emissions scenarios considered. It has direct implications for the possibility of achieving internationally agreed climate targets such as those mentioned in the Copenhagen Accord and the Cancun Agreements (3, 4). Here I explain some of the implications of the linear relationship between peak warming and total cumulative carbon emissions.

The Immune Inhibitor A1 Protease of Bacillus anthracis

Bacillus anthracis, an organism ubiquitous in the soil and the causative agent of anthrax, utilizes multiple mechanisms to regulate secreted factors; one example is the activity of secreted proteases. One of the most abundant proteins in the culture supernates of B. anthracis is the Immune Inhibitor A1 (InhA1) protease. Here, I demonstrate that InhA1 modulates the abundance of approximately half of the proteins secreted into the culture supernates, including substrates that are known to contribute to the ability of the organism to cause virulence. For example, InhA1 cleaves the anthrax toxin proteins, PA, LF, and EF. InhA1 also targets a number of additional proteases, including Npr599, contributing to a complex proteolytic regulatory cascade with far-reaching affects on the secretome. Using an intra-tracheal mouse model of infection, I found that an inhA-null strain is attenuated in relation to the parent strain. The data indicate that reduced virulence of the inhA mutant strain may be the result of toxin protein deregulation, decreased association with macrophages, and/or the inability to degrade host antimicrobial peptides. Given the significant modulation of the secretome by InhA1, it is likely that expression of the protease is tightly regulated. To test this I examined inhA1 transcript and protein levels in the parent and various isogenic mutant strains and found that InhA1 expression is regulated by several mechanisms. First, the steady state levels of inhA1 transcript are controlled by the regulatory protein SinR, which inhibits inhA1 expression. Second, InhA1 abundance is inversely proportional to the SinR-regulated protease camelysin, indicating the post-transcriptional regulation of InhA1 by camelysin. Third, InhA1 activity is dependent on a conserved zinc binding motif, suggesting that zinc availability regulates InhA1 activity. The convergence of these regulatory mechanisms signifies the importance of tight regulation of InhA1 activity, activity that substantially affects how B. anthracis interacts with its environment.

Regulation of Set1-mediated methylation of Dam1

Eukaryotic genomes exist within a dynamic structure named chromatin in which DNA is wrapped around an octamer of histones forming the nucleosome. Histones are modified by a range of posttranslational modifications including methylation, phosphorylation, and ubiquitination, which are integral to a range of DNA-templated processes including transcriptional regulation. A hallmark for transcriptional activity is methylation of histone H3 on lysine (K) 4 within active gene promoters. In S. cerevisiae, H3K4 methylation is mediated by Set1 within the COMPASS complex. Methylation requires prior ubiquitination of histone H2BK123 by the E2-E3 ligases Rad6 and Bre1, as well as the Paf1 transcriptional elongation complex. This regulatory pathway exemplifies cross-talk in trans between posttranslational modifications on distinct histone molecules. Set1 has an additional substrate in the kinetochore protein Dam1, which is methylated on K233. This methylation antagonizes phosphorylation of adjacent serines by the Ipl1 Aurora kinase. The discovery of a second Set1 substrate raised the question of how Set1 function is regulated at the kinetochore. I hypothesized that transcriptional regulatory factors essential for H3K4 methylation at gene promoters might also regulate Set1-mediated methylation of Dam1K233. Here I show that the regulatory factors essential for COMPASS activity at gene promoters is also indispensable for the methylation of Dam1K233. Deletion of members of the COMPASS complex leads to loss of Dam1K233 methylation. In addition, deletion of Rad6, Bre1, or members of the Paf1 complex abolishes Dam1 methylation. The role of Rad6 and Bre1 in Dam1 methylation is dependent on H2BK123 ubiquitination, as mutation of K123 within H2B results in complete loss of Dam1 methylation. Importantly, methylation of Dam1K233 is independent of transcription and occurs at the kinetochore. My results demonstrate that Set1-mediated methylation is regulated by a general pathway regardless of substrate that is composed of transcriptional regulatory factors functioning independently of transcription at the kinetochore. My data provide the first example of cross-talk in trans between modifications on a histone and a non-histone protein. Additionally, my results indicate that several factors previously thought to be required for Set1 function at gene promoters are more generally required for the catalytic activity of the COMPASS complex regardless of substrate or cellular process.

ROLE OF THE GCN5 HISTONE ACETYLTRANSFERASE IN SPINOCEREBELLAR ATAXIA TYPE 7 AND IN IMMATURE NEURONS

Spinocerebellar Ataxia type 7 (SCA7) is a neurodegenerative disease caused by expansion of a CAG repeat encoding a polyglutamine tract in ATXN7, a component of the SAGA histone acetyltransferase (HAT) complex. Previous studies provided conflicting evidence regarding the effects of polyQ-ATXN7 on the activity of Gcn5, the HAT catalytic subunit of SAGA. Here I showed that reducing Gcn5 expression accelerates both cerebellar and retinal degeneration in a mouse model of SCA7. Deletion of Gcn5 in Purkinje cells in mice expressing wild type Atxn7, however, causes only mild ataxia and does not lead to the early lethality observed in SCA7 mice. Reduced Gcn5 expression strongly enhances retinopathy in SCA7 mice, but does not affect the transcriptional targets of Atxn7, as expression of these genes is not further altered by Gcn5 depletion. These findings demonstrate that loss of Gcn5 functions can contribute to the time of onset and severity of SCA7 phenotypes, but suggest that non-transcriptional functions of SAGA may play a role in neurodegeneration in this disease.

THE ROLE OF E2F1 IN THE RESPONSE TO DNA DOUBLE STRAND BREAKS

The importance of E2F transcription factors in the processes of proliferation and apoptosis are well established. E2F1, but not other E2F family members, is also phosphorylated and stabilized in response to various forms of DNA damage to regulate the expression of cell cycle and pro-apoptotic genes. E2F1 also relocalizes and forms foci at sites of DNA double-strand breaks but the function of E2F1 at sites of damage is still unknown. Here I reveal that E2F1 deficiency leads to increased spontaneous DNA break and impaired recovery following exposure to ionizing radiation. In response to DNA double-strand breaks, NBS1 phosphorylation and foci formation are defective in cells lacking E2F1, but NBS1 expression levels are unaffected. Moreover, it was observed that an association between NBS1 and E2F1 is increased in response to DNA damage, suggesting that E2F1 may promote NBS1 foci formation through a direct or indirect interaction at sites of DNA breaks. E2F1 deficient cells also display impaired foci formation of RPA and Rad51, which suggests a defect in DNA end resection and formation of single-stranded DNA at DNA double-strand breaks. I also found E2F1 status affects foci formation of the histone acetyltransferase GCN5 in response to DNA double-strand breaks. E2F1 is phosphorylated at serine 31 (serine 29 in mouse) by the ATM kinase as part of the DNA damage response. To investigate the importance of this event, our lab developed an E2F1 serine 29 mutant mouse model. I find that E2F1 serine 29 mutant cells show loss of E2F1 foci formation in response to DNA double-strand breaks. Furthermore, DNA repair and NBS1 foci formation are impaired in E2f1S29A/S29A cells. Taken together, my results indicate novel roles for E2F1 in the DNA damage response, which may directly promote DNA repair and genome maintenance.