With the loss of global biodiversity, signals of the speciation process are progressively being erased as populations dwindle and species disappear. We propose to develop and implement an integrative approach that will draw from new advances in computational biology, field ecology, and population genomics. We anticipate that our approach will be broadly applicable to other non-model biological systems, especially those that diverged recently and rapidly and for which species boundaries are cryptic. Our findings, as well as in-country collaboration, will have immediate relevance to conservation policy in the ecologically complex and poorly studied regions of Southeastern Madagascar.

Most organisms that reproduce sexually use a special type of cell division, called meiosis, that is important for the creation of genetic variation and halving the chromosome numbers in gametes. During meiosis, numerous programmed DNA double strand-breaks (DSBs) are formed and processed by the meiotic recombination pathway to form crossovers, which are the points of reciprocal exchange of genetic information between chromosomes. Crossovers are essential to create novel genetic variation in each generation. There is a major interest to understand meiosis in plants because domestication and intense selective breeding have led to a substantial loss of genetic variation in crops. Continued genetic improvement of elite cultivars to mitigate the challenge of climate change will require the introgression of beneficial alleles from wild varieties through the formation of crossovers. Unfortunately, crossovers are mainly formed at the end of the chromosomes, representing less than 15% of the genome, whereas more centric regions, which contain certain genes of agricultural relevance, like defence response genes, rarely recombine in most major crops. Therefore, it is both timely and imperative to understand the factors influencing crossover patterning and to create strategies to reposition crossovers in crops. Substantial cellular variation in DSB and crossover numbers is observed between species and within individuals. Arabidopsis and wheat anthers contain a mixture of hypo- and hyper-recombinant meiotic cells varying in DSB and crossover numbers by up to 70%. Our previous studies revealed that the frequency and position of the crossovers are influenced by the transcript levels of ASY1 and HEI10 in Arabidopsis. Therefore, we propose that the recombination outcome of a meiocyte is influenced by a fine balance of expression of several genes. Hence, heterogeneity in the transcriptome could be responsible for the hypo- and hyper-recombination meiocytes observed in anthers. However, all genomic studies carried out on plant meiosis have so far included pools of cells, thus preventing the identification of heterogeneous factors responsible for such variation. In this project, we propose to generate a single cell transcriptomic atlas of Arabidopsis meiocytes at two key time points of meiotic recombination (T1 during DSB formation, T2 during crossover formation) to understand the transcriptome dynamics from the formation of DSBs to their conversion into crossovers. In addition, we will group cells that are transcriptionally highly correlated and infer the cluster of cells that contains the hyper-recombinant meiocytes using information from known genes (e.g. higher HEI10 transcript level corresponds to higher crossover rate). We will then use this data to identify genes with a putative role in recombination heterogeneity. We will complement this study with the characterisation of a set of Arabidopsis over-expressing lines to find genes influencing recombination based on their transcript level. Lastly, we will perform a proof-of-principle experiment, using the dosage-sensitive gene ASY1 as a reference, to test if increasing meiotic gene expression in wheat could reposition crossovers to favour recombination in regions which are not easily accessible in conventional breeding. These new data will provide impact through the use of innovative approaches to understand the inter-relationship between transcriptome and recombination heterogeneity, decipher the transcriptome dynamics during meiosis and discover genes involved in meiosis. This project also aims to explore a novel route for impact in wheat using gene over-expression to influence the recombination landscape, which could confer lasting benefits for the breading sector. This proposed work supports BBSRC strategic priorities "Frontier bioscience: understanding the rules of life" and "Bioscience for sustainable agriculture and food".

All cells have intrinsic immune defences against viruses: to survive in a given species, viruses must evolve matched counter-measures. To block DNA viruses that reproduce in the nucleus, cells require: A sensing strategy that can differentiate between invading viral genomic DNA, and cell DNA. An output of this sensing that can prevent the viral DNA from executing its functions. Our understanding of how cells distinguish host and viral DNA in the nucleus is sketchy: we know some proteins that help repress viral gene expression, and some that induce production of antiviral signalling molecules (particularly interferon). However, none of these proteins have a defined mechanism for distinguishing between foreign and cellular DNA. The "Speckled protein" Sp100 is part of a nuclear protein complex (ND10) known to repress DNA viruses. Sp100 has a short isoform (Sp100A) and several longer isoforms. The longer isoforms have a DNA-binding SAND domain, and can inhibit diverse DNA viruses. The Sp100 SAND domain binds unmethylated DNA, but not the methylated DNA that makes up most of the cell's genome. Sp100 also accumulates at sites of DNA damage, but is not required for DNA repair. Most or all herpesviruses have protein(s) that act against Sp100: Herpes simplex virus (HSV1) protein ICP0 degrades Sp100 alongside the other ND10 components; herpesvirus saimiri (HVS - a squirrel monkey virus) uses ORF3 to degrade Sp100 but not ND10; Epstein-Barr virus (EBV) uses EBNA-LP to bind Sp100 and disrupt its function. Corresponding mutant viruses lacking these countermeasures exhibit reduced viral gene expression upon infection. By knocking out cell genes in combination, we have discovered that: Another speckled protein - Sp140L, found only in primates - also represses these viruses; Repression by Sp100 does not need functions downstream of the SAND domain; Sp100A expression can rescue mutant viruses; EBNA-LP inhibiting long speckled protein isoforms prolongs survival of proliferating naïve B cells. demonstrating both overlapping and opposed functions of different Sp100 isoforms and homologues. We propose to determine fundamental properties of speckled proteins, using EBV, HVS and HSV1 infection to define their roles during DNA virus infection, with the following aims: Identify which parts of which speckled proteins help inhibit virus genes or interferon production, and identify which other antiviral proteins work with Sp100/140L functions. Determine the binding specificity of the SAND domains of the four speckled protein isoforms, to see which might distinguish viral DNA from cellular DNA in the nucleus. Establish whether Sp100 long isoforms and Sp140L associate with infecting herpesvirus genomes. We will produce antibodies against Sp140L and Sp100 long isoforms to help us (and others) study these proteins. Use the sequence variation primate EBNA-LPs and corresponding speckled proteins to provide insights into how speckled proteins function. This study will be the first to assess speckled proteins as a family. Understanding whether and how speckled proteins sense and respond to viral (and other abnormal) DNA has broad implications for DNA virus biology, immunology and gene therapy, as well as repair of damaged DNA - relevant for cancer development particularly in high radiation environments from the beach to outer space. Additionally, a novel potential role in limiting naïve B cell lifespans has implications for EBV-associated lymphomas, vaccinology and autoimmunity, including primary biliary cholangitis (which often exhibits auto-antibodies against speckled proteins) and the involvement of EBV in multiple sclerosis and other autoimmune diseases.

The general problem approached by the SNAP project is exemplified by the inconsistency of and irregular overlap between the many huge databases of persons, names, and other personal data on the Internet. (These databases are familiar and ubiquitous, from lists of actors and creators in the Internet Movie Database or historical figures in Wikipedia, to private individuals via all sorts of social networking sites.) How does a researcher or analyst determine whether two records refer to the same person or are related in some other way, and whether other related information refers to both people equally? For this project we shall directly address these issues on a much smaller scale: there are very many historical prosopographies and onomastica (databases of persons and names), even within the relatively tight domain of Greco-Roman antiquity, and many of the same questions of identity and provenance apply. These databases can be worked on without the concerns raised by modern social network accounts: there are not the ethical and privacy concerns of working with living people; the scale, while still massive, is more tractable; there is much more academic coherence within the data, which, diverse as it is, is produced by a discipline with well-established working practices. The SNAP project will pilot a new approach to working with diverse person data, using as a starting point three large datasets from the classical world: the Lexicon of Greek Personal Names, an Oxford-based corpus of persons mentioned in ancient Greek texts; Trismegistos, a Leuven-run database of names and persons from Egyptian papyri; Prosopographia Imperii Romani, a series of printed books listing senators and other elites from the first three centuries of the Roman Empire. We shall model a simple structure using Web and Linked data technologies to represent relationships between databases and to link from references in primary texts to authoritative lists of persons and names. We shall invite new projects and datasets in the domain to participate in the SNAP network, to help us test the structures and contribute material on ancient people to the collection, and will help these projects to transform their data into a form that can be linked and annotated. We also plan to produce tools for illustration of the value of this data, and demonstrate research methods for working with the new material and information produced. The project will also show how to enhance and produce new data, generating new person references and links from classical texts that have not yet been looked at in this way (Greek and Latin inscriptions). We shall share our recommendations and our results through workshops, public conference papers, and a range of technical, academic and popular publications.

Research on bullying started in earnest in 1982 when three young boys killed themselves in short succession in Norway, all leaving notes that they had been bullied by their peers. Many more suicides in children attributed to bullying have occurred since then. Killing oneself is the most extreme form of escaping the bullies. If not self-harm, being a victim of bullying can lead to a range of mental health and physical health problems in childhood. The increasing evidence of harm by bullying led to a conference on the prevention of bullying organised by President Obama and the First Lady in March 2011. In the President's words "If there's one goal of this conference, it's to dispel the myth that bullying is just a harmless rite of passage or an inevitable part of growing up. It's not." (1) However, whether children can put their experiences aside once they graduate from school, or whether involvement in bullying throws a long shadow over the lives of affected children is unknown. The first objective of this study is to find out about the long term effects of being bullied on health, work life and success, crime involvement and social adaptation in young adulthood. This will be accomplished by studying the effect of bullying in childhood on young adult outcome in two long term studies, the Avon Longitudinal Study in the UK (ALSPAC) and the Great Smoky Mountain Study in the USA (GSMS) that investigated children up to 18 and 26 years, respectively. Most approaches to beat bullying to date have focussed on schools. School interventions have been shown to have some but limited effects on reducing rates of bullying. To develop new innovative prevention or intervention strategies beyond the school setting, it is important to understand what makes children likely targets of bullies even before they enter school. Families are the primary place where children learn rules of how to behave, negotiate with their parents and siblings, or where they observe how parents and siblings treat each other and deal with conflicts. Thus when parents are harsh or hostile in their parenting or often fight with each other, does it affect how children deal with bullying by peers? Furthermore, even before the child is born, stress in pregnancy can affect the development of organs such as the brain and how children later deal with stress. Unknown is whether stress in pregnancy may make some children more likely to become targets of bullying because they show easily a reaction such as getting upset or start crying. Bullies home in on children who show strong emotional reactions. Finally, being a member of an ethnic minority group may result in more bullying. The second objective is to find out whether stress in pregnancy (family adversity, maternal anxiety and depression), family relations in the preschool years (i.e. problematic partner relationships, parenting) and individual characteristics (how emotional the child is, ethnicity) predicts who becomes a victim or bully at school age. The findings will help to develop new strategies to strengthen families and children and prevent children from becoming the target of bullying or use bullying to torment other children. Sources: 1 http://www.whitehouse.gov/blog/2011/03/10/president-obama-first-lady-white-house-conference-bullying-prevention