Pulling the wool over their eyes?:Object permanence, numerical competence and categorisation in alternative livestock species

The adaptive abilities of grazing livestock species are not well understood, despite the potential link between behaviour driven decision making and the overall productive efficiency of the animal through foraging strategy. This study aimed to assess and compare these adaptive behaviours, relating to i) object permanence, ii) numerical competence, and iii) categorisation capabilities of domesticated species that possess distinctly different digestive physiologies and backgrounds. Seven animals from each species, including sheep (Ovis aries) (avg. 5 years of age, 60 kg initial weight), goats (Capra hircus) (avg. 3 years, 45 kg initial weight), and alpacas (Lama pacos (Linnaeus, 1758)) (avg. 3 years, 70 kg initial weight), were presented with a total of nine choice tasks, grouped relative to the three abilities being tested (object permanence, numerical competence, and categorisation). Specifically, the stage of object permanence for each subject was tested based on their ability to solve simple visible displacement, to overcome perseveration error, and double invisible displacement tasks. Subjects were also presented with a two-choice task of different open-centre and filled shapes to assess the capacity for simple discrimination and open-ended categorisation. Lastly, numerical competence was compared across five trials consisting of different ratios and volumes of food reward. A basic awareness of object permanence was found in all subjects. Overall, the goats demonstrated the greatest capacity for object permanence across the three species, particularly when presented with more complex three-cup A-not-B tasks. This increase in complexity had no significant effect on goat performance as a group (p = 0.13), whereas alpaca (p = 0.0005) and sheep performance significantly declined (p = 0.04). We also found no evidence to demonstrate contrasting cognitive capabilities between these species in relation to spontaneous numerical cognition (p &gt; 0.05), or in the use of perceptual cues in open-ended categorisation (p = 0.246). This study is the first instance of multiple direct comparisons of cognitive capability across domesticated livestock species. Furthermore, this work is the first account of object permanence, numerical competence and categorisation in alpacas, as well as object permanence in sheep and numerical competence in sheep and goats. This information could prove useful to predict the outcome of interaction between these species in a grazing context and for inferences relating to behaviour driven decision making, such as foraging strategy, and the overall productive efficiency of the animal. Here, we conclude that the three species tested possess comparable capacity for physical cognition in the tasks discussed.</p

Attenuated Codon Optimality Contributes to Neural-Specific mRNA Decay in Drosophila.

Tissue-specific mRNA stability is important for cell fate and physiology, but the mechanisms involved are not fully understood. We found that zygotic mRNA stability in Drosophila correlates with codon content: optimal codons are enriched in stable transcripts associated with metabolic functions like translation, while non-optimal codons are enriched in unstable transcripts, including those associated with neural development. Bioinformatic analyses and reporter assays revealed that similar codons stabilize or destabilize mRNAs in the nervous system and other tissues, but the link between codon content and stability is attenuated in the nervous system. We confirmed that optimal codons are decoded by abundant tRNAs while non-optimal codons are decoded by less abundant tRNAs in embryos and in the nervous system. We conclude that codon optimality is a general determinant of zygotic mRNA stability, and attenuation of codon optimality allows trans-acting factors to exert greater influence over mRNA decay in the nervous system

Chromophore-bearing NH_2-terminal domains of phytochromes A and B determine their photosensory specificity and differential light lability

In early seedling development, far-red-light-induced deetiolation is mediated primarily by phytochrome A (phyA), whereas red-light-induced deetiolation is mediated primarily by phytochrome B (phyB). To map the molecular determinants responsible for this photosensory specificity, we tested the activities of two reciprocal phyA/phyB chimeras in diagnostic light regimes using overexpression in transgenic Arabidopsis. Although previous data have shown that the NH_2-terminal halves of phyA and phyB each separately lack normal activity, fusion of the NH_2-terminal half of phyA to the COOH-terminal half of phyB (phyAB) and the reciprocal fusion (phyBA) resulted in biologically active phytochromes. The behavior of these two chimeras in red and far-red light indicates: (i) that the NH2-terminal halves of phyA and phyB determine their respective photosensory specificities; (ii) that the COOH-terminal halves of the two photoreceptors are necessary for regulatory activity but are reciprocally inter-changeable and thus carry functionally equivalent determinants; and (iii) that the NH_2-terminal halves of phyA and phyB carry determinants that direct the differential light lability of the two molecules. The present findings suggest that the contrasting photosensory information gathered by phyA and phyB through their NH_2-terminal halves may be transduced to downstream signaling components through a common biochemical mechanism involving the regulatory activity of the COOH-terminal domains of the photoreceptors

Quantitative insertion-site sequencing (QIseq) for high throughput phenotyping of transposon mutants

Genetic screening using random transposon insertions has been a powerful tool for uncovering biology in prokaryotes, where whole-genome saturating screens have been performed in multiple organisms. In eukaryotes, such screens have proven more problematic, in part because of the lack of a sensitive and robust system for identifying transposon insertion sites. We here describe quantitative insertion-site sequencing, or QIseq, which uses custom library preparation and Illumina sequencing technology and is able to identify insertion sites from both the 5' and 3' ends of the transposon, providing an inbuilt level of validation. The approach was developed using piggyBac mutants in the human malaria parasite Plasmodium falciparum but should be applicable to many other eukaryotic genomes. QIseq proved accurate, confirming known sites in &gt;100 mutants, and sensitive, identifying and monitoring sites over a &gt;10,000-fold dynamic range of sequence counts. Applying QIseq to uncloned parasites shortly after transfections revealed multiple insertions in mixed populations and suggests that &gt;4000 independent mutants could be generated from relatively modest scales of transfection, providing a clear pathway to genome-scale screens in P. falciparum QIseq was also used to monitor the growth of pools of previously cloned mutants and reproducibly differentiated between deleterious and neutral mutations in competitive growth. Among the mutants with fitness defects was a mutant with a piggyBac insertion immediately upstream of the kelch protein K13 gene associated with artemisinin resistance, implying mutants in this gene may have competitive fitness costs. QIseq has the potential to enable the scale-up of piggyBac-mediated genetics across multiple eukaryotic systems

Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes.

BAckground: Massively parallel sequencing technology is revolutionizing approaches to genomic and genetic research. Since its advent, the scale and efficiency of Next-Generation Sequencing (NGS) has rapidly improved. In spite of this success, sequencing genomes or genomic regions with extremely biased base composition is still a great challenge to the currently available NGS platforms. The genomes of some important pathogenic organisms like Plasmodium falciparum (high AT content) and Mycobacterium tuberculosis (high GC content) display extremes of base composition. The standard library preparation procedures that employ PCR amplification have been shown to cause uneven read coverage particularly across AT and GC rich regions, leading to problems in genome assembly and variation analyses. Alternative library-preparation approaches that omit PCR amplification require large quantities of starting material and hence are not suitable for small amounts of DNA/RNA such as those from clinical isolates. We have developed and optimized library-preparation procedures suitable for low quantity starting material and tolerant to extremely high AT content sequences. Results: We have used our optimized conditions in parallel with standard methods to prepare Illumina sequencing libraries from a non-clinical and a clinical isolate (containing ~53% host contamination). By analyzing and comparing the quality of sequence data generated, we show that our optimized conditions that involve a PCR additive (TMAC), produces amplified libraries with improved coverage of extremely AT-rich regions and reduced bias toward GC neutral templates. Conclusion: We have developed a robust and optimized Next-Generation Sequencing library amplification method suitable for extremely AT-rich genomes. The new amplification conditions significantly reduce bias and retain the complexity of either extremes of base composition. This development will greatly benefit sequencing clinical samples that often require amplification due to low mass of DNA starting material

Efficient depletion of host DNA contamination in malaria clinical sequencing.

The cost of whole-genome sequencing (WGS) is decreasing rapidly as next-generation sequencing technology continues to advance, and the prospect of making WGS available for public health applications is becoming a reality. So far, a number of studies have demonstrated the use of WGS as an epidemiological tool for typing and controlling outbreaks of microbial pathogens. Success of these applications is hugely dependent on efficient generation of clean genetic material that is free from host DNA contamination for rapid preparation of sequencing libraries. The presence of large amounts of host DNA severely affects the efficiency of characterizing pathogens using WGS and is therefore a serious impediment to clinical and epidemiological sequencing for health care and public health applications. We have developed a simple enzymatic treatment method that takes advantage of the methylation of human DNA to selectively deplete host contamination from clinical samples prior to sequencing. Using malaria clinical samples with over 80% human host DNA contamination, we show that the enzymatic treatment enriches Plasmodium falciparum DNA up to ∼9-fold and generates high-quality, nonbiased sequence reads covering >98% of 86,158 catalogued typeable single-nucleotide polymorphism loci

Intelligent integrated maintenance for wind power generation

A novel architecture and system for the provision of Reliability Centred Maintenance (RCM) for offshore wind power generation is presented. The architecture was developed by conducting a bottom-up analysis of the data required to support RCM within this specific industry, combined with a top-down analysis of the required maintenance functionality. The architecture and system consists of three integrated modules for Intelligent Condition Monitoring, Reliability and Maintenance Modelling, and Maintenance Scheduling that provide a scalable solution for performing dynamic, efficient and cost effective preventative maintenance management within this extremely demanding renewable energy generation sector. The system demonstrates for the first time, the integration of state-of-the-art advanced mathematical techniques: Random Forests, Dynamic Bayesian Networks, and Memetic Algorithms in the development of an intelligent autonomous solution. The results from the application of the intelligent integrated system illustrated the automated detection of faults within a wind farm consisting of over 100 turbines, the modelling and updating of the turbines’ survivability and creation of a hierarchy of maintenance actions, and the optimising of the maintenance schedule with a view to maximising the availability and revenue generation of the turbines