The most serious issue facing the global human population is the 10 billion person question. Can the world support production of enough high-quality, nutritious food to feed a projected 10 billion people by 2050, against a backdrop of climate change that will make fertile land more scarce and weather more unpredictable (droughts, floods, temperature spikes). It is certain that rice will play a central role in feeding much of the globe. At present, rice provides the major daily caloric need for 50% of the human population. The genus as a whole, including the two main branches of domesticated rice (Oryza sativa Japonica and Indica), and a huge variety of wild relatives, has the capacity to grow under an exceptionally wide range of environments. Research teams around the world have been working closely with breeders to help identify desirable traits present in local landraces (i.e. locally adapted varieties) and their wild relatives, such as resistance to periodic droughts, flooding or high temperatures, and perform crosses to transfer such genes/traits into high yielding, and widely distributed varieties. Genomic science is now central to research and development efforts. The genome of one reference variety of Japonica and one of Indica were sequenced around 15 years ago. However, the genome sequence is just the starting point. For the data to be useful for research, requires a process called genome annotation. Annotation involves finding and defining the genes within the genome, and working out what functional roles those genes code for. Annotation usually involves several different software packages, which high error rates, followed by manual work to fix errors and improve genes over many years. Rice gene annotation efforts have unfortunately suffered from a lack of international coordination, leading to several different independent efforts to annotate rice genes using different methods, which persist in different databases today. New genomes for varieties representing a wider pool of landraces and wild rice species are just coming online, and thus without a major effort in international coordination, this problem will get rapidly worse. Plant scientists and breeders will find it very challenging to interpret and compare information collected from different rice varieties. This project aims to solve this issue, bringing together six international partners with a shared goal of creating consistency in the rice gene set across all varieties. We will build new software and protocols for sharing data, which will enable us to define what genes are present (and the proteins they encode) in the genomes of all rice types, called a pan-genome or pan gene set. The outcomes of our project will "future-proof" rice genomic resources, so that researchers can focus their efforts on understanding the biology of rice, and searching for desirable traits that span the genetic diversity of cultivated Asian rice.
Motives are objects encoding arithmetic and geometry at the same time. This project is about derived symmetric powers in the Morel-Voevodsky motivic stable category over a field.In mathematics it is important to relate additive and multiplicative operations in an algebraic structure, or in a category of geometrical or arithmetical nature. For example, the Kuenneth rule expresses the multiplicative n-th power of a sum A + B in terms of the sum of products of multiplicative i-th and (n-i)-th powers of A and B respectively. A categorified lambda-structure in a symmetric monoidal triangulated category T is a set of endofunctors of T, indexed by non-negative integers, which behave similarly to a usual algebraic lambda-structure in a commutative ring. In particular, the values of the n-th endofunctor on the vertices in a distinguished triangle are related by means of a tower (called Kuenneth tower) of morphisms in T whose cones can be computed by the Kuenneth rule. Our first aim is to show that if T is an abstract stable homotopy category, i.e. the homotopy category of symmetric spectra over a nice simplicial symmetric monoidal model category C, then left derived symmetric powers do exist in T, and they give a lambda-structure in the above sense, provided some natural symmetrizability assumption on cofibrations in C. Left derived symmetric powers will be homotopical symmetric powers, i.e. homotopy colimits of the action of symmetric groups on monoidal powers. Lambda-structures of left derived symmetric powers bring a powerful computational tool to compute homotopical symmetric powers in many stable homotopy categories. For example, this works well in topology, when T is the homotopy category of the category of topological symmetric spectra.Being applied in the Morel-Voevodsky motivic stable category, such lambda-structures encode deep geometrical and arithmetical properties of algebraic varieties over the ground field, which do not appear in the topological setting. In particular, the relation symmetric powers with the contraction of the affine line to a point, and with operations arising from symmetric powers of algebraic varieties over a field, attract our special attention in this project. Thus, we aim to construct and to study a lambda-structure of left derived symmetric powers in the Morel-Voevodsky motivic stable category, and to use it in order to discover completely new phenomena in arithmetic algebraic geometry and motivic theory.
Refer to ATLAS-UK upgrade proposal to PPRP: "UPGRADING THE ATLAS EXPERIMENT FOR THE LUMINOSITY FRONTIER AT THE LARGE HADRON COLLIDER" PPRP meeting, September 2012
In 1998, Niklasson and others reported that the incidence of three human diseases in Sweden, human myocarditis, diabetes and Guillain-Barre syndrome, varied with the 3-4 year abundance cycles of the bank vole. Subsequently, a new virus, Ljungan virus (LV) was isolated from Swedish diabetic bank voles. LV is also present in wild voles in Denmark and the USA and has recently been isolated, and myocarditis and clinical diabetes reported, in several other species of wild voles and lemmings in northern Sweden. An on-going study at Liverpool has been looking at a range of infections (but not LV) in wild rodents, focusing especially on populations living in Kielder Forest, on the English-Scottish border. Niklasson has visited Liverpool and examined voles removed from the Kielder populations. Preliminary analyses have provided a strong prima facie case for the presence of LV in these populations. The distribution of type 1 diabetes amongst children and young adults is not well understood, although both genetic and environmental factors are likely to be involved. A number of studies suggest a possible role for infections and/or immunological responses. Space-time clustering (excess numbers of cases observed within small geographical locations for limited periods of time) is especially suggestive of an infection. Several studies have identified space-time clustering in childhood diabetes. This proposed project would: 1) survey the Kielder populations and those of other rodent species nearby (including peri-domestic rats and mice) in order to initiate a mapping of LV (and possible human risk) in UK rodents; and 2) analyse human epidemiological data bases in the region of the rodent populations to seek correlations either spatially (regionally) or temporally between incidences of type 1 diabetes and measures of rodent abundance or activity; If these pilot studies provide negative results in either or especially both respects (no confirmation of Ljungan virus and/or no overt patterns in the public health records), then it will be unlikely that patterns observed in Sweden also apply in the UK, and research on this topic can be considered of low priority. But if either or especially both studies provide positive results, then Ljungan virus has the potential to become the most important wildlife zoonosis in the UK and further work will be essential.
Some females mate once in their lifetime while others mate with many different males. This results in enormous differences between species in everything from their physiology and behaviour, to how their social systems are arranged and their population dynamics. Many animals are highly adapted to a system where females mate frequently. A male will generally have fewer offspring if a female he mates with remates to another male, as generally the last male to mate sires the subsequent offspring. This pressure on males to prevent female remating has caused the evolution of traits that reduce female remating such as mate guarding and the transfer of molecules in the ejaculate that suppress female receptivity. Females in turn have evolved traits that allow them to avoid control by males, and remate with males of their choosing. However, despite decades of research and plentiful between-species variation, we know little about why females have evolved to mate as often as they do. This lack of knowledge derives from lack of an 'easy' lab species in which variation in female remating rate is present in nature. We have recently found that females of the North American fruit fly D. pseudoobscura flies mate more frequently in Northern populations that Southern, and that this is determined by genetic differences between the populations. We will observe and collect flies in nature to find out how they live, and replicate these conditions in the laboratory to work out the circumstances under which females benefit from mating with many males. This species is also a 'genetic model, and gives us an opportunity to find the genes underlying female remating, which would be a big step towards understanding this variation. We can crossbreed flies from Montana (Northern USA, high remating) and Arizona (Southern USA, low remating) over several generations. This will result in lines of flies that contain a random mix of Northern and Southern genes. We can then test these flies for willingness to remate. Some will be willing to remate despite inheriting only a few genes from the Northern (willing to remate) population, indicating genes for high willingness to remate must be found in that section of the genome. By looking at tiny differences in the genome of flies from the two populations at regular intervals along each chromosome, we will be able to determine how many areas of the genome are important for remating. We will compare this to genes examined in closely related fly species suggested to be important in controlling female remating. Our previous work has shown that female remating rate is very important for controlling the frequency of selfish genes that distort sex ratios. In Southern populations, the selfish X-chromosome SR is common. Normal X-chromosomes are passed on to half a male's offspring, while the other half inherits his Y chromosome. But when males carry the SR chromosome all their Y bearing sperm die during production and all their offspring inherit the SR X chromosome. This allows the SR chromosome to spread as it is passed on to more offspring that the normal X chromosome and can cause populations to consist mainly of females, and if SR spread to a high enough frequency can wipe out entire populations due to not producing any males. However, female remating reduces the transmission of the driving chromosome. We will create mathematical models to work out whether the fitness benefits we find for polyandry in different environments are sufficient to control the abundance of SR, and hence population sex ratio. We will work out whether SR is ever likely to escape this regulation by females, and spread to such high levels that it causes populations to go extinct.