Search results for "26"
showing 10 items of 3194 documents
Engineering CRISPR guide RNA riboswitches for in vivo applications
2019
CRISPR-based genome editing provides a simple and scalable toolbox for a variety of therapeutic and biotechnology applications. Whilst the fundamental properties of CRISPR proved easily transferable from the native prokaryotic hosts to eukaryotic and multicellular organisms, the tight control of the CRISPR-editing activity remains a major challenge. Here we summarise recent developments of CRISPR and riboswitch technologies and recommend novel functionalised synthetic-gRNA (sgRNA) designs to achieve inducible and spatiotemporal regulation of CRISPR-based genetic editors in response to cellular or extracellular stimuli. We believe that future advances of these tools will have major implicati…
Experimental Introgression To Evaluate the Impact of Sex Specific Traits on Drosophila melanogaster Incipient Speciation
2019
AbstractSex specific traits are involved in speciation but it is difficult to determine whether their variation initiates or reinforces sexual isolation. In some insects, speciation depends of the rapid change of expression in desaturase genes coding for sex pheromones. Two closely related desaturase genes are involved in Drosophila melanogaster pheromonal communication: desat1 affects both the production and the reception of sex pheromones while desat2 is involved in their production in flies of Zimbabwe populations. There is a strong asymmetric sexual isolation between Zimbabwe populations and all other “Cosmopolitan” populations: Zimbabwe females rarely copulate with Cosmopolitan males w…
Determining stingray movement patterns in a wave-swept coastal zone using a blimp for continuous aerial video surveillance
2020
Stingrays play a key role in the regulation of nearshore ecosystems. However, their movement ecology in high-energy surf areas remains largely unknown due to the notorious difficulties in conducting research in these environments. Using a blimp as an aerial platform for video surveillance, we overcame some of the limitations of other tracking methods, such as the use of tags and drones. This novel technology offered near-continuous coverage to characterise the fine-scale movements of stingrays in a surf area in Kiama, Australia, without any invasive procedures. A total of 98 stingray tracks were recorded, providing 6 h 27 min of movement paths. The tracking data suggest that stingrays may u…
Drosophila Evolution over Space and Time (DEST) : A New Population Genomics Resource
2021
Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate datasets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a…
Fishery-dependent and -independent data lead to consistent estimations of essential habitats
2016
AbstractSpecies mapping is an essential tool for conservation programmes as it provides clear pictures of the distribution of marine resources. However, in fishery ecology, the amount of objective scientific information is limited and data may not always be directly comparable. Information about the distribution of marine species can be derived from two main sources: fishery-independent data (scientific surveys at sea) and fishery-dependent data (collection and sampling by observers in commercial vessels). The aim of this paper is to compare whether these two different sources produce similar, complementary, or different results. We compare them in the specific context of identifying the Es…
OMICfpp: a fuzzy approach for paired RNA-Seq counts
2019
© The Author(s) 2019.
Novel subpopulations in date palm (Phoenix dactylifera) identified by population-wide organellar genome sequencing
2019
Background The date palm is one of the oldest cultivated fruit trees. The tree can withstand high temperatures and low water and the fruit can be stored dry offering nutrition across the year. The first region of cultivation is believed to be near modern day Iraq, however, where and if the date palm was domesticated is still a topic of debate. Recent studies of chloroplast and genomic DNA revealed two major subpopulations of cultivars centered in both the Eastern range of date palm cultivation including Arabian Peninsula, Iraq and parts of South Asia, and the Western range, including North Africa. Results To better understand the origins of date palm cultivation we sequenced and analyzed ov…
A high-quality genome assembly from short and long reads for the non-biting midge Chironomus riparius (Diptera)
2020
AbstractBackgroundChironomus riparius is of great importance as a study species in various fields like ecotoxicology, molecular genetics, developmental biology and ecology. However, only a fragmented draft genome exists to date, hindering the recent rush of population genomic studies in this species.FindingsMaking use of 50 NGS datasets, we present a hybrid genome assembly from short and long sequence reads that make C. riparius’ genome one of the most contiguous Dipteran genomes published, the first complete mitochondrial genome of the species and the respective recombination rate as one of the first insect recombination rates at all.ConclusionsThe genome and associated resources will be h…
Neighbor-list-free molecular dynamics on sunway TaihuLight supercomputer
2020
Molecular dynamics (MD) simulations are playing an increasingly important role in many research areas. Pair-wise potentials are widely used in MD simulations of bio-molecules, polymers, and nano-scale materials. Due to a low compute-to-memory-access ratio, their calculation is often bounded by memory transfer speeds. Sunway TaihuLight is one of the fastest supercomputers featuring a custom SW26010 many-core processor. Since the SW26010 has some critical limitations regarding main memory bandwidth and scratchpad memory size, it is considered as a good platform to investigate the optimization of pair-wise potentials especially in terms of data reusage. MD algorithms often use a neighbor-list …