An assessment of the ability of the stay-green phenotype in Lolium species to provide an improved protein supply for ruminants

Kingston-Smith, A. H., Bollard, A. L., Humphreys, M. O,, Theodorou, M. K. (2002). An assessment of the ability of the stay-green phenotype in Lolium species to provide an improved protein supply for ruminants. Annals of Botany, 89(6), 731-740. Sponsorship: BBSRC/MAFF/Milk Development Council/Meat and Livestock Commission/Industry. RAE2008

Beyond signaling and human capital: Education and the revelation of ability

We provide evidence that college graduation plays a direct role in revealing ability to the labor market. Using the NLSY79, our results suggest that ability is observed nearly perfectly for college graduates, but is revealed to the labor market more gradually for high school graduates. Consequently, from the beginning of their careers, college graduates are paid in accordance with their own ability, while the wages of high school graduates are initially unrelated to their own ability. This view of ability revelation in the labor market has considerable power in explaining racial differences in wages, education, and returns to ability.

High-coverage sequencing and annotated assemblies of the budgerigar genome.

BACKGROUND: Parrots belong to a group of behaviorally advanced vertebrates and have an advanced ability of vocal learning relative to other vocal-learning birds. They can imitate human speech, synchronize their body movements to a rhythmic beat, and understand complex concepts of referential meaning to sounds. However, little is known about the genetics of these traits. Elucidating the genetic bases would require whole genome sequencing and a robust assembly of a parrot genome. FINDINGS: We present a genomic resource for the budgerigar, an Australian Parakeet (Melopsittacus undulatus) -- the most widely studied parrot species in neuroscience and behavior. We present genomic sequence data that includes over 300× raw read coverage from multiple sequencing technologies and chromosome optical maps from a single male animal. The reads and optical maps were used to create three hybrid assemblies representing some of the largest genomic scaffolds to date for a bird; two of which were annotated based on similarities to reference sets of non-redundant human, zebra finch and chicken proteins, and budgerigar transcriptome sequence assemblies. The sequence reads for this project were in part generated and used for both the Assemblathon 2 competition and the first de novo assembly of a giga-scale vertebrate genome utilizing PacBio single-molecule sequencing. CONCLUSIONS: Across several quality metrics, these budgerigar assemblies are comparable to or better than the chicken and zebra finch genome assemblies built from traditional Sanger sequencing reads, and are sufficient to analyze regions that are difficult to sequence and assemble, including those not yet assembled in prior bird genomes, and promoter regions of genes differentially regulated in vocal learning brain regions. This work provides valuable data and material for genome technology development and for investigating the genomics of complex behavioral traits.

Computational Inference of Genome-Wide Protein-DNA Interactions Using High-Throughput Genomic Data

Transcriptional regulation has been studied intensively in recent decades. One important aspect of this regulation is the interaction between regulatory proteins, such as transcription factors (TF) and nucleosomes, and the genome. Different high-throughput techniques have been invented to map these interactions genome-wide, including ChIP-based methods (ChIP-chip, ChIP-seq, etc.), nuclease digestion methods (DNase-seq, MNase-seq, etc.), and others. However, a single experimental technique often only provides partial and noisy information about the whole picture of protein-DNA interactions. Therefore, the overarching goal of this dissertation is to provide computational developments for jointly modeling different experimental datasets to achieve a holistic inference on the protein-DNA interaction landscape.

We first present a computational framework that can incorporate the protein binding information in MNase-seq data into a thermodynamic model of protein-DNA interaction. We use a correlation-based objective function to model the MNase-seq data and a Markov chain Monte Carlo method to maximize the function. Our results show that the inferred protein-DNA interaction landscape is concordant with the MNase-seq data and provides a mechanistic explanation for the experimentally collected MNase-seq fragments. Our framework is flexible and can easily incorporate other data sources. To demonstrate this flexibility, we use prior distributions to integrate experimentally measured protein concentrations.

We also study the ability of DNase-seq data to position nucleosomes. Traditionally, DNase-seq has only been widely used to identify DNase hypersensitive sites, which tend to be open chromatin regulatory regions devoid of nucleosomes. We reveal for the first time that DNase-seq datasets also contain substantial information about nucleosome translational positioning, and that existing DNase-seq data can be used to infer nucleosome positions with high accuracy. We develop a Bayes-factor-based nucleosome scoring method to position nucleosomes using DNase-seq data. Our approach utilizes several effective strategies to extract nucleosome positioning signals from the noisy DNase-seq data, including jointly modeling data points across the nucleosome body and explicitly modeling the quadratic and oscillatory DNase I digestion pattern on nucleosomes. We show that our DNase-seq-based nucleosome map is highly consistent with previous high-resolution maps. We also show that the oscillatory DNase I digestion pattern is useful in revealing the nucleosome rotational context around TF binding sites.

Finally, we present a state-space model (SSM) for jointly modeling different kinds of genomic data to provide an accurate view of the protein-DNA interaction landscape. We also provide an efficient expectation-maximization algorithm to learn model parameters from data. We first show in simulation studies that the SSM can effectively recover underlying true protein binding configurations. We then apply the SSM to model real genomic data (both DNase-seq and MNase-seq data). Through incrementally increasing the types of genomic data in the SSM, we show that different data types can contribute complementary information for the inference of protein binding landscape and that the most accurate inference comes from modeling all available datasets.

This dissertation provides a foundation for future research by taking a step toward the genome-wide inference of protein-DNA interaction landscape through data integration.

Improving Photovoltaics with High Luminescence Efficiency Quantum Dot Layers

A solar cell relies on its ability to turn photons into current. Because short wavelength photons are typically absorbed near the top surface of a cell, the generated charge carriers recombine before being collected. But when a layer of quantum dots (nanoscale semiconductor particles) is placed on top of the cell, it absorbs short wavelength photons and emits them into the cell at longer wavelengths, which enables more efficient carrier collection. However, the resulting power conversion efficiency of the system depends critically on the quantum dot luminescence efficiency – the nature of this relationship was previously unknown. Our calculations suggest that a quantum dot layer must have high luminescence efficiency (at least 80%) to improve the current output of existing photovoltaic (PV) cells; otherwise, it may worsen the cell’s efficiency. Our quantum dot layer (using quantum dots with over 85% quantum yield) slightly reduced the efficiency of our PV cells. We observed a decrease in short circuit current of a commercial-grade cell from 0.1977 A to 0.1826 A, a 7.6% drop, suggesting that improved optical coupling from the quantum dot emission into the solar cell is needed. With better optical coupling, we predict current enhancements between ~6% and ~8% for a solar cell that already has an antireflection coating. Such improvements could have important commercial impacts if the coating could be deployed in a scalable fashion.

Psychology and interventions for pupils at risk of underachievement and school exclusion: the year 10 effect

Findings are presented from a longitudinal study of over 1,500 adolescents. Some were engaged in interventions aimed at reducing social disaffection. Participants completed measures of social-identification, academic self-concept and motivation, and social, emotional and behavioural difficulties. Consistent with our previous research, developmental trends in identity and self-concept were found - adolescents became more negative about some school-based factors and more positive about aspects of identity. Trends were less clear in the 120 adolescents receiving interventions. Findings demonstrate the importance of psychology in work with young people. [Source: (2008) 'Invited Address, IUPsyS Invited Symposium, Invited Symposium, Symposium, Paper Session, Poster Session', International Journal of Psychology, 43:3, 348 - 527]

High dispersal potential has maintained long-term population stability in the North Atlantic copepod Calanus finmarchicus

The cool-water copepod Calanus finmarchicus is a key species in North Atlantic marine ecosystems since it represents an important food resource for the developmental stages of several fish of major economic value. Over the last 40 years, however, data from the Continuous Plankton Recorder survey have highlighted a 70 per cent reduction in C. finmarchicus biomass, coupled with a gradual northward shift in the species's distribution, which have both been linked with climate change. To determine the potential for C. finmarchicus to track changes in habitat availability and maintain stable effective population sizes, we have assessed levels of gene flow and dispersal in current populations, as well as using a coalescent approach together with palaeodistribution modelling to elucidate the historical population demography of the species over previous changes in Earth's climate. Our findings indicate high levels of dispersal and a constant effective population size over the period 359 000–566 000 BP and suggest that C. finmarchicus possesses the capacity to track changes in available habitat, a feature that may be of crucial importance to the species's ability to cope with the current period of global climate change.

Maintenance of abyssal benthic foraminifera under high pressure and low temperature: some preliminary results

Abyssal benthic foraminifera have been maintained alive for periods of several weeks under laboratory simulated deep-sea conditions of high pressure and low temperature. In separate experiments, bacterial-sized fluorescent microspheres and three species of microalgae were supplied as food particles. Subsequent light and electron microscopy showed that the algae had been ingested by several foraminiferal species. Furthermore, the fine structure of the foraminiferal cytoplasm was well-preserved which indicates, along with the ingestion of algal food, that they had remained in a viable condition during the incubation. Other observations indicate that abyssal benthic foraminifera ingest naturally occurring photosynthetic cells carried to the deep-sea bed by rapidly sedimenting aggregates. The ability to keep foraminifera originating from depths exceeding 4000 m alive in the laboratory paves the way for the experimental investigation of some important issues in deep-sea biology and palaeoceanography.

High-resolution view of the spring bloom initiation and net community production in the Subantarctic Southern Ocean using glider data

In the Southern Ocean, there is increasing evidence that seasonal to subseasonal temporal scales, and meso- to submesoscales play an important role in understanding the sensitivity of ocean primary productivity to climate change. This drives the need for a high-resolution approach to re- solving biogeochemical processes. In this study, 5.5 months of continuous, high-resolution (3 h, 2 km horizontal resolution) glider data from spring to summer in the Atlantic Subantarctic Zone is used to investigate: (i) the mechanisms that drive bloom initiation and high growth rates in the region and (ii) the seasonal evolution of water column production and respiration. Bloom initiation dates were analysed in the context of upper ocean boundary layer physics highlighting sensitivities of different bloom detection methods to different environmental processes. Model results show that in early spring (September to mid-November) increased rates of net community production (NCP) are strongly affected by meso- to submesoscale features. In late spring/early summer (late-November to mid-December) seasonal shoaling of the mixed layer drives a more spatially homogenous bloom with maximum rates of NCP and chlorophyll biomass. A comparison of biomass accumulation rates with a study in the North Atlantic highlights the sensitivity of phytoplankton growth to fine-scale dynamics and emphasizes the need to sample the ocean at high resolution to accurately resolve phytoplankton phenology and improve our ability to estimate the sensitivity of the biological carbon pump to climate change.

Differences in mitochondrial and nuclear DNA status of high-density and low-density sperm fractions after density centrifugation preparation

Background: In order to isolate the â??bestâ?? sperm for assisted conception a discontinuous two-step density gradient centrifugation is usually employed. This technique is known to isolate a subpopulation with good motility, morphology and nuclear DNA (nDNA) integrity. As yet its ability to isolate sperm with unfragmented mitochondrial DNA (mtDNA) is unknown. Methods: Semen was obtained from men (n=28) attending our Regional Fertility Centre for infertility investigations. We employed a modified long polymerase chain reaction to study mtDNA and a modified alkaline Comet assay to determine nDNA fragmentation. Results: The high- density fraction displayed significantly more wild type mtDNA (75% of samples) than that of the low- density fraction (25% of samples). In the high-density fraction, there was a higher incidence of single, rather than double or multiple deletions and the deletions were predominantly small scale (0.1-4.0kb). There was a strong correlation between nDNA fragmentation, the number of mtDNA deletions (r=0.7, p

Reduced vision in older adults with age related macular degeneration interferes with ability to care for self and impairs role as carer

Aim: To study the relation between visual impairment and ability to care for oneself or a dependant in older people with age related macular degeneration (AMD). Method: Cross sectional study of older people with visual impairment due to AMD in a specialised retinal service clinic. 199 subjects who underwent visual function assessment (fully corrected distance and near acuity and contrast sensitivity in both eyes), followed by completion of a package of questionnaires dealing with general health status (SF36), visual functioning (Daily Living Tasks Dependent on Vision, DLTV) and ability to care for self or provide care to others. The outcome measure was self reported ability to care for self and others. Three levels of self reported ability to care were identified—inability to care for self (level 1), ability to care for self but not others (level 2), and ability to care for self and others (level 3). Results: People who reported good general health status and visual functioning (that is, had high scores on SF36 and DLTV) were more likely to state that they were able to care for self and others. Similarly people with good vision in the better seeing eye were more likely to report ability to care for self and others. People with a distance visual acuity (DVA) worse than 0.4 logMAR (Snellen 6/15) had less than 50% probability of assigning themselves to care level 3 and those with DVA worse than 1.0 logMAR (Snellen 6/60) had a probability of greater than 50% or for assigning themselves to care level 1. Regression analyses with level of care as the dependent variable and demographic factors, DLTV subscales, and SF36 dimensions as the explanatory variables confirmed that the DLTV subscale 1 was the most important variable in the transition from care level 3 to care level 2. The regression analyses also confirmed that the DLTV subscale 2 was the most important in the transition from care level 3 to care level 1. Conclusions: Ability to care for self and dependants has a strong relation with self reported visual functioning and quality of life and is adversely influenced by visual impairment. The acuity at which the balance of probability shifts in the direction of diminished ability to care for self or others is lower than the level set by social care agencies for provision of support. These findings have implications for those involved with visual rehabilitation and for studies of the cost effectiveness of interventions in AMD.

Filling Ability and Passing Ability of Self-Consolidating Concrete

This paper reviews statistical models obtained from a composite factorial design study, which was carried out to determine the influence of three key parameters of mixture composition on filling ability and passing ability of self-consolidating concrete (SCC). This study was a part of the European project “Testing SCC”- GRD2-2000-30024. The parameters considered in this study were the dosages of water and high-range water-reducing admixture (HRWRA), and the volume of coarse aggregates. The responses of the derived statistical models were slump flow, T50 , T60, V-funnel flow time, Orimet flow time, and blocking ratio (L-box). The retention of these tests was also measured at 30 and 60 minutes after adding the first water. The models are valid for mixtures made with 188 to 208 L/m3 (317 to 350 lb/yd3) of water, 3.8 to 5.8 kg/m3 (570 to 970 mL/100 kg of binder) of HRWRA, and 220 to 360 L/m3 (5.97 to 9.76 ft3/yd3) of coarse aggregates. The utility of such models to optimize concrete mixtures and to achieve a good balance between filling ability and passing ability is discussed. Examples highlighting the usefulness of the models are presented using isoresponse surfaces to demonstrate single and coupled effects of mixture parameters on slump flow, T50 , T60 , V-funnel flow time, Orimet flow time, and blocking ratio. The paper also illustrates the various trade-offs between the mixture parameters on the derived responses that affected the filling and the passing ability.

Analysis of the reading and comprehension control in scientific texts in high school students

Students' learning process can be negatively affected when their reading and comprehension control is not appropriated. This research focuses on the analysis of how a group of students from high school evaluate their reading comprehension in manipulated scientific texts. An analysis tool was designed to determine the students' degree of comprehension control when reading a scientific short text with an added contradiction. The results have revealed that the students from 1st and 3rd ESO do not properly self-evaluated their reading comprehension. A different behavior has been observed in 1st Bachillerato, where appropriate evaluation and regulation seem to be more frequent. Moreover, no significant differences have been found regarding the type of text, year or gender. Finally, as identified by previous research, the correlations between the students' comprehension control and their school marks have shown to have a weak relationship and inversely proportional to the students' age.

High-solid-content hydroxyapatite slurry for the production of bone substitute scaffolds

Key to various bone substitute scaffold production techniques is the development of free-flowing ceramic slurry with optimum theological properties. The aim is to achieve a colloidal suspension with as high a solid content as possible while maintaining a low viscosity which easily penetrates the pores of relevant sacrificial templates. The following investigation describes the optimization of a hydroxyapatite slip and demonstrates its potential application in scaffold production. Using predominantly spherical particles of hydroxyapatite of between 0.82 mu m and 16.2 mu m, coupled with a 2 wt % addition of the anionic polyelectrolyte, ammonium polyacrylate, an 80 wt % (55.9 vol %) hydroxyapatite solid loaded slip with a viscosity of approximately 126 mPa s has been developed. Its ability to infiltrate and replicate porous preforms has been shown using polyurethane foam. The enhanced particle packing achieved has allowed for the production of scaffolds with highly dense and uniform grain structures. The results represent a significant improvement in current slurry production techniques and can be utilized to develop high-density ceramic bone substitute scaffolds.

High dispersal potential has maintained long-term population stability in the North Atlantic copepod Calanus finmarchicus

The cool-water copepod Calanus finmarchicus is a key species in North Atlantic marine ecosystems since it represents an important food resource for the developmental stages of several fish of major economic value. Over the last 40 years, however, data from the Continuous Plankton Recorder survey have highlighted a 70 per cent reduction in C. finmarchicus biomass, coupled with a gradual northward shift in the species's distribution, which have both been linked with climate change. To determine the potential for C. finmarchicus to track changes in habitat availability and maintain stable effective population sizes, we have assessed levels of gene flow and dispersal in current populations, as well as using a coalescent approach together with palaeodistribution modelling to elucidate the historical population demography of the species over previous changes in Earth's climate. Our findings indicate high levels of dispersal and a constant effective population size over the period 359 000-566 000 BP and suggest that C. finmarchicus possesses the capacity to track changes in available habitat, a feature that may be of crucial importance to the species's ability to cope with the current period of global climate change.