Alignment of the genomes of brachypodium distachyon and temperate cereals and grasses using bacterial artificial chromosome landing with fluorescence in situ hybridization

Robert Hasterok, Agnieszka Marasek, Iain S. Donnison, Ian Armstead, Ann Thomas, Ian P. King, Elzbieta Wolny, Dominika Idziak, John Draper and Glyn Jenkins (2006). Alignment of the genomes of brachypodium distachyon and temperate cereals and grasses using bacterial artificial chromosome landing with fluorescence in situ hybridization.Genetics, 73 (1), 349-362. Sponsorship: Royal Society / BBSRC;BBSRC RAE2008

An association mapping approach to identify flowering time genes in natural populations of Lolium perenne (L.)

Sk?t, L., Humphreys, M. O., Armstead, I. P., Heywood, S., Sk?t, K. P., Sanderson, R., Thomas, I. D., Chorlton, K. H., & Sackville Hamilton, N. R. (2005). An association mapping approach to identify flowering time genes in natural populations of Lolium perenne (L.). Molecular Breeding, 15(3), 233-245. Sponsorship: BBSRC RAE2008

Investigation of numerical atomic orbitals for first-principles calculations of the electronic and transport properties of silicon nanowire structures

This thesis is focused on the application of numerical atomic basis sets in studies of the structural, electronic and transport properties of silicon nanowire structures from first-principles within the framework of Density Functional Theory. First we critically examine the applied methodology and then offer predictions regarding the transport properties and realisation of silicon nanowire devices. The performance of numerical atomic orbitals is benchmarked against calculations performed with plane waves basis sets. After establishing the convergence of total energy and electronic structure calculations with increasing basis size we have shown that their quality greatly improves with the optimisation of the contraction for a fixed basis size. The double zeta polarised basis offers a reasonable approximation to study structural and electronic properties and transferability exists between various nanowire structures. This is most important to reduce the computational cost. The impact of basis sets on transport properties in silicon nanowires with oxygen and dopant impurities have also been studied. It is found that whilst transmission features quantitatively converge with increasing contraction there is a weaker dependence on basis set for the mean free path; the double zeta polarised basis offers a good compromise whereas the single zeta basis set yields qualitatively reasonable results. Studying the transport properties of nanowire-based transistor setups with p+-n-p+ and p+-i-p+ doping profiles it is shown that charge self-consistency affects the I-V characteristics more significantly than the basis set choice. It is predicted that such ultrascaled (3 nm length) transistors would show degraded performance due to relatively high source-drain tunnelling currents. Finally, it is shown the hole mobility of Si nanowires nominally doped with boron decreases monotonically with decreasing width at fixed doping density and increasing dopant concentration. Significant mobility variations are identified which can explain experimental observations.

Molecular composition of biogenic secondary organic aerosols using ultrahigh resolution mass spectrometry: comparing laboratory and field studies

Numerous laboratory experiments have been performed in an attempt to mimic atmospheric secondary organic aerosol (SOA) formation. However, it is still unclear how close the aerosol particles generated in laboratory experiments resemble atmospheric SOA with respect to their detailed chemical composition. In this study, we generated SOA in a simulation chamber from the ozonolysis of α-pinene and a biogenic volatile organic compound (BVOC) mixture containing α- and β-pinene, Δ3-carene, and isoprene. The detailed molecular composition of laboratory-generated SOA was compared with that of background ambient aerosol collected at a boreal forest site (Hyytiälä, Finland) and an urban location (Cork, Ireland) using direct infusion nanoelectrospray ultrahigh resolution mass spectrometry. Kendrick Mass Defect and Van Krevelen approaches were used to identify and compare compound classes and distributions of the detected species. The laboratory-generated SOA contained a distinguishable group of dimers that was not observed in the ambient samples. The presence of dimers was found to be less pronounced in the SOA from the VOC mixtures when compared to the one component precursor system. The elemental composition of the compounds identified in the monomeric region from the ozonolysis of both α-pinene and VOC mixtures represented the ambient organic composition of particles collected at the boreal forest site reasonably well, with about 70% of common molecular formulae. In contrast, large differences were found between the laboratory-generated BVOC samples and the ambient urban sample. To our knowledge this is the first direct comparison of molecular composition of laboratory-generated SOA from BVOC mixtures and ambient samples.

High-efficiency photovoltaics through mechanically stacked integration of solar cells based on the InP lattice constant

Solar Energy is a clean and abundant energy source that can help reduce reliance on fossil fuels around which questions still persist about their contribution to climate and long-term availability. Monolithic triple-junction solar cells are currently the state of the art photovoltaic devices with champion cell efficiencies exceeding 40%, but their ultimate efficiency is restricted by the current-matching constraint of series-connected cells. The objective of this thesis was to investigate the use of solar cells with lattice constants equal to InP in order to reduce the constraint of current matching in multi-junction solar cells. This was addressed by two approaches: Firstly, the formation of mechanically stacked solar cells (MSSC) was investigated through the addition of separate connections to individual cells that make up a multi-junction device. An electrical and optical modelling approach identified separately connected InGaAs bottom cells stacked under dual-junction GaAs based top cells as a route to high efficiency. An InGaAs solar cell was fabricated on an InP substrate with a measured 1-Sun conversion efficiency of 9.3%. A comparative study of adhesives found benzocyclobutene to be the most suitable for bonding component cells in a mechanically stacked configuration owing to its higher thermal conductivity and refractive index when compared to other candidate adhesives. A flip-chip process was developed to bond single-junction GaAs and InGaAs cells with a measured 4-terminal MSSC efficiency of 25.2% under 1-Sun conditions. Additionally, a novel InAlAs solar cell was identified, which can be used to provide an alternative to the well established GaAs solar cell. As wide bandgap InAlAs solar cells have not been extensively investigated for use in photovoltaics, single-junction cells were fabricated and their properties relevant to PV operation analysed. Minority carrier diffusion lengths in the micrometre range were extracted, confirming InAlAs as a suitable material for use in III-V solar cells, and a 1-Sun conversion efficiency of 6.6% measured for cells with 800 nm thick absorber layers. Given the cost and small diameter of commercially available InP wafers, InGaAs and InAlAs solar cells were fabricated on alternative substrates, namely GaAs. As a first demonstration the lattice constant of a GaAs substrate was graded to InP using an InxGa1-xAs metamorphic buffer layer onto which cells were grown. This was the first demonstration of an InAlAs solar cell on an alternative substrate and an initial step towards fabricating these cells on Si. The results presented offer a route to developing multi-junction solar cell devices based on the InP lattice parameter, thus extending the range of available bandgaps for high efficiency cells.

A genetically engineered thermally responsive sustained release curcumin depot to treat neuroinflammation.

Radiculopathy, a painful neuroinflammation that can accompany intervertebral disc herniation, is associated with locally increased levels of the pro-inflammatory cytokine tumor necrosis factor alpha (TNFα). Systemic administration of TNF antagonists for radiculopathy in the clinic has shown mixed results, and there is growing interest in the local delivery of anti-inflammatory drugs to treat this pathology as well as similar inflammatory events of peripheral nerve injury. Curcumin, a known antagonist of TNFα in multiple cell types and tissues, was chemically modified and conjugated to a thermally responsive elastin-like polypeptide (ELP) to create an injectable depot for sustained, local delivery of curcumin to treat neuroinflammation. ELPs are biopolymers capable of thermally-triggered in situ depot formation that have been successfully employed as drug carriers and biomaterials in several applications. ELP-curcumin conjugates were shown to display high drug loading, rapidly release curcumin in vitro via degradable carbamate bonds, and retain in vitro bioactivity against TNFα-induced cytotoxicity and monocyte activation with IC50 only two-fold higher than curcumin. When injected proximal to the sciatic nerve in mice via intramuscular (i.m.) injection, ELP-curcumin conjugates underwent a thermally triggered soluble-insoluble phase transition, leading to in situ formation of a depot that released curcumin over 4days post-injection and decreased plasma AUC 7-fold.

Revising Justice: Punitory Thought and Action in the Work of Atwood, Jordan, and Oates

*Designated as an exemplary master's project for 2015-16*

Tolerancia a la inundación de especies gramíneas forrajeras megatérmicas : bases ecofisiológicas relacionadas con su instalación y producción

La inundación es un factor importante que afecta la implantación y producción de especies forrajeras en ecosistemas de pastizales anegables. Chloris gayana K. y Panicum coloratum L. son dos gramíneas tropicales cuyo uso como forrajera en ambientes templados se ha incrementado recientemente. En esta tesis se realizaron dos experimentos para evaluar la tolerancia de estas especies a eventos de inundación en los estadíos de plántula (implantación, Exp. 1) y de planta adulta (producción, Exp. 2). En el primer experimento plántulas de dos semanas de ambas especies fueron sometidas a tratamientos i) control, ii) sumersión parcial (SP) y iii) sumersión completa (SC) por 14 días, seguidos de un período de recuperación de 12 días. Ambas especies presentaron aerénquima constitutivo en sus raíces, que aumentó considerablemente bajo tratamientos de sumersión. La altura de plántulas sólo difirió de los controles en SC: C. gayana aumentó su altura rápidamente emergiendo del agua mientras P. coloratum no creció, manteniéndose siempre bajo el agua. La respuesta de "escape. exhibida por C. gayana se asoció a una asignación preferencial de biomasa hacia la parte aérea y un marcado alargamiento de las láminas foliares. P. coloratum no mostró cambios en la asignación de biomasa y sus hojas fueron más pequeñas. La biomasa final de C. gayana fue similar bajo SP y SC; mientras que P. coloratum redujo notablemente la biomasa bajo SC incluso al final del experimento, indicando que los daños provocados fueron persistentes. Así, C. gayana parece ser más prometedora para su implantación en pastizales propensos a inundaciones de mayor intensidad. En el segundo experimento se evaluó tolerancia a inundación de plantas adultas en diferentes momentos del ciclo de crecimiento (inundación invernal durante el reposo vegetativo vs. inundación primaveral durante el rebrote). Plantas de 10 meses (mayor a 30 cm altura) fueron sujetas a tratamientos (i) control (ii) inundación invernal por 50 días durante el reposo vegetativo (I), (iii) inundación primaveral por 20 días durante el rebrote (P) y (iv) inundación continua por 70 días (I+P). Luego, se dejaron crecer las plantas por 30 días para evaluar su recuperación. La inundación durante el invierno provocó una reducción del 43-57 por ciento en la biomasa aérea y radical de C. gayana; mientras que P. coloratum no fue afectado. C. gayana mostró una leve mejor tolerancia a la inundación primaveral en comparación a P. coloratum mientras que cuando fue inundada en ambos períodos se detectaron efectos aditivos depresores sobre su biomasa, efecto que en P. coloratum no fue registrado. Al final del período de recuperación las plantas de ambas especies lograron recuperarse completamente, alcanzando una biomasa equivalente a los controles independientemente del tratamiento previo de inundación. Estos resultados sugieren que ambas especies son tolerantes a la inundación en fase adulta, con un compromiso en la reducción de biomasa que no supera el 30 por ciento. Se concluye que ambas especies resultan promisorias para su introducción en los pastizales anegables de la Pampa Deprimida, destacándose C. gayana para sitios donde la intensidad de inundación puede comprometer la sumersión completa en las primeras fases del establecimiento de las plantas.

Tolerancia a la inundación de especies gramíneas forrajeras megatérmicas : bases ecofisiológicas relacionadas con su instalación y producción

La inundación es un factor importante que afecta la implantación y producción de especies forrajeras en ecosistemas de pastizales anegables. Chloris gayana K. y Panicum coloratum L. son dos gramíneas tropicales cuyo uso como forrajera en ambientes templados se ha incrementado recientemente. En esta tesis se realizaron dos experimentos para evaluar la tolerancia de estas especies a eventos de inundación en los estadíos de plántula (implantación, Exp. 1)y de planta adulta (producción, Exp. 2). En el primer experimento plántulas de dos semanas de ambas especies fueron sometidas a tratamientos i)control, ii)sumersión parcial (SP)y iii)sumersión completa (SC)por 14 días, seguidos de un período de recuperación de 12 días. Ambas especies presentaron aerénquima constitutivo en sus raíces, que aumentó considerablemente bajo tratamientos de sumersión. La altura de plántulas sólo difirió de los controles en SC: C. gayana aumentó su altura rápidamente emergiendo del agua mientras P. coloratum no creció, manteniéndose siempre bajo el agua. La respuesta de "escape. exhibida por C. gayana se asoció a una asignación preferencial de biomasa hacia la parte aérea y un marcado alargamiento de las láminas foliares. P. coloratum no mostró cambios en la asignación de biomasa y sus hojas fueron más pequeñas. La biomasa final de C. gayana fue similar bajo SP y SC; mientras que P. coloratum redujo notablemente la biomasa bajo SC incluso al final del experimento, indicando que los daños provocados fueron persistentes. Así, C. gayana parece ser más prometedora para su implantación en pastizales propensos a inundaciones de mayor intensidad. En el segundo experimento se evaluó tolerancia a inundación de plantas adultas en diferentes momentos del ciclo de crecimiento (inundación invernal durante el reposo vegetativo vs. inundación primaveral durante el rebrote). Plantas de 10 meses (mayor a 30 cm altura)fueron sujetas a tratamientos (i)control (ii)inundación invernal por 50 días durante el reposo vegetativo (I), (iii)inundación primaveral por 20 días durante el rebrote (P)y (iv)inundación continua por 70 días (I+P). Luego, se dejaron crecer las plantas por 30 días para evaluar su recuperación. La inundación durante el invierno provocó una reducción del 43-57 por ciento en la biomasa aérea y radical de C. gayana; mientras que P. coloratum no fue afectado. C. gayana mostró una leve mejor tolerancia a la inundación primaveral en comparación a P. coloratum mientras que cuando fue inundada en ambos períodos se detectaron efectos aditivos depresores sobre su biomasa, efecto que en P. coloratum no fue registrado. Al final del período de recuperación las plantas de ambas especies lograron recuperarse completamente, alcanzando una biomasa equivalente a los controles independientemente del tratamiento previo de inundación. Estos resultados sugieren que ambas especies son tolerantes a la inundación en fase adulta, con un compromiso en la reducción de biomasa que no supera el 30 por ciento. Se concluye que ambas especies resultan promisorias para su introducción en los pastizales anegables de la Pampa Deprimida, destacándose C. gayana para sitios donde la intensidad de inundación puede comprometer la sumersión completa en las primeras fases del establecimiento de las plantas.

Quantification of urinary excretion of ethosuximide enantiomers and their major metabolites in the rat.

A chiral gas chromatographic assay has been developed for quantitative analysis of ethosuximide and its major metabolites in rat urine. The extraction procedure was found to be precise and reproducible. Recovery was in the range of 94-98%, intraday CV(%) was 0.92% for (S)-ethosuximide (50 mug/ml) and 0.51% for (R)-ethosuximide (50 mug/ml). Interday CV(%) was 1.12% for (S)-ethosuximide and 0.72% for (R)-ethosuximide. The limit of detection was determined to be around 0.01 mug/ml for each enantiomer. Following administration of rac-ethosuximide by i.v., i.p. and oral routes, unchanged ethosuximide was detected in urine up to 72h after drug administration. The appearance of all detected metabolites occurred Within 24h of drug administration. Significantly more (S)-ethosuximide was excreted unchanged than (R)-ethosuximide with all three routes studied. A substantial amount of the drug was eliminated as the 2-(1-hydroxyethyl)-2-methylsuccinimide (2 pairs of diastereoisomers). Much less drug was eliminated as the 2-ethyl-3-hydroxy-2-methylsuccinimide with only one diastereoisomer observed. Examination of the one pair of diastereoisomers of 2-(1-hydroxyethyl)-2-methylsuccinimide that was resolved showed preferential excretion of one isomer. Comparison of both pairs of diastereoisomers showed that one pair was formed in preference to the other with a ratio of approximately 0.8:1. It is concluded that stereoselective metabolism of ethosuximide occurs. Copyright (C) 2001 John Wiley & Sons, Ltd. Author Keywords: chiral pharmacokinetics; ethosuximide enantiomers; metabolism; rat; urinary excretion; gas chromatography

Myocardial expression of the endothelin system in endotoxin-treated rats.

Although circulating plasma levels of endothelin (ET)-1 are elevated in endotoxemia, little is known about the myocardial expression of the ET system in endotoxic shock. We assessed the temporal mRNA expression pattern of key components of the ET system (pre-pro ET (ppET) -1, -2, ET-converting enzyme-1, ETA and ETB receptors) by reverse transcription polymerase chain reaction in a rat model of early endotoxic shock. Lipopolysaccharide (5 mg/kg, i.p.) caused a transient increase (p 12-fold increase; p

Microbial analysis of soil and groundwater from a gasworks site and comparison to a sequenced biological reactive barrier remediation process (SEREBAR)

Aims: To investigate the distribution of a polymicrobial community of biodegradative bacteria in (i) soil and groundwater at a former manufactured gas plant (FMGP) site and (ii) in a novel SEquential REactive BARrier (SEREBAR) bioremediation process designed to bioremediate the contaminated groundwater. Methods and Results: Culture-dependent and culture-independent analyses using denaturing gradient gel electrophoresis (DGGE) and polymerase chain reaction (PCR) for the detection of 16S ribosomal RNA gene and naphthalene dioxygenase (NDO) genes of free-living (planktonic groundwater) and attached (soil biofilm) samples from across the site and from the SEREBAR process was applied. Naphthalene arising from groundwater was effectively degraded early in the process and the microbiological analysis indicated a dominant role for Pseudomonas and Comamonas in its degradation. The microbial communities appeared highly complex and diverse across both the sites and in the SEREBAR process. An increased population of naphthalene degraders was associated with naphthalene removal. Conclusion: The distribution of micro-organisms in general and naphthalene degraders across the site was highly heterogeneous. Comparisons made between areas contaminated with polycyclic aromatic hydrocarbons (PAH) and those not contaminated, revealed differences in the microbial community profile. The likelihood of noncultured bacteria being dominant in mediating naphthalene removal was evident. Significance and Impact of the Study: This work further emphasizes the importance of both traditional and molecular-based tools in determining the microbial ecology of contaminated sites and highlights the role of noncultured bacteria in the process.

Improved stability, insulin-releasing activity and antidiabetic potential of two novel N-terminal analogues of gastric inhibitory polypeptide: N-acetyl-GIP and pGlu-GIP

Aims/hypothesis: This study examined the plasma stability, biological activity and antidiabetic potential of two novel N-terminally modified analogues of gastric inhibitory polypeptide (GIP).

Methods: Degradation studies were carried out on GIP, N-acetyl-GIP (Ac-GIP) and N-pyroglutamyl-GIP (pGlu-GIP) in vitro following incubation with either dipeptidylpeptidase IV or human plasma. Cyclic adenosine 3'5' monophosphate (cAMP) production was assessed in Chinese hamster lung fibroblast cells transfected with the human GIP receptor. Insulin-releasing ability was assessed in vitro in BRIN-BD11 cells and in obese diabetic (ob/ob) mice.

Results: GIP was rapidly degraded by dipeptidylpeptidase IV and plasma (t1/2 2.3 and 6.2 h, respectively) whereas Ac-GIP and pGlu-GIP remained intact even after 24 h. Both Ac-GIP and pGlu-GIP were extremely potent (p<0.001) at stimulating cAMP production (EC50 values 1.9 and 2.7 nmol/l, respectively), almost a tenfold increase compared to native GIP (18.2 nmol/l). Both Ac-GIP and pGlu-GIP (10–13–10–8 mmol/l) were more potent at stimulating insulin release compared to the native GIP (p<0.001), with 1.3-fold and 1.2-fold increases observed at 10–8 mol/l, respectively. Administration of GIP analogues (25 nmol/kg body weight, i.p.) together with glucose (18 mmol/kg) in (ob/ob) mice lowered (p<0.001) individual glucose values at 60 min together with the areas under the curve for glucose compared to native GIP. This antihyperglycaemic effect was coupled to a raised (p<0.001) and more prolonged insulin response after administration of Ac-GIP and pGlu-GIP (AUC, 644±54 and 576±51 ng·ml–1·min, respectively) compared with native GIP (AUC, 257±29 ng·ml–1·min).

Conclusion/interpretation: Ac-GIP and pGlu-GIP, show resistance to plasma dipeptidylpeptidase IV degradation, resulting in enhanced biological activity and improved antidiabetic potential in vivo, raising the possibility of their use in therapy of Type II (non-insulin-dependent) diabetes mellitus.