Allostery and Applications of the Lac Repressor

The lac repressor has been extensively studied for nearly half a century; this long and complicated experimental history leaves many subtle connections unexplored. This thesis sought to forge those connections from isolated and purified components up to functioning lac genetic switches in cells and even organisms. We first connected the genetics and structure of the lac repressor to in vivo gene regulation in Escherichia coli. We found that point mutations of amino acids that structurally make specific contacts with DNA can alter repressor-operator DNA affinity and even the conformational equilibrium of the repressor. We then found that point mutations of amino acids that structurally make specific contacts with effector molecules can alter repressor-effector affinity and the conformational equilibrium. All results are well explained by a Monod, Wyman, and Changeux model of allostery. We next connected purified in vitro components with in vivo gene regulation in E. coli. We used an in vitro transcription assay to measure repressor-operator DNA binding affinity, repressor-effector binding affinity, and conformational equilibrium. Only the repressor-operator DNA binding affinity disagreed with literature values from other in vitro experiments, however it did agree with a published value which should hold under in vivo conditions. We were able to use our in vitro thermodynamic parameters to accurately predict the in vivo gene regulation when cell crowding was considered. Finally we developed an autogenously regulated lac repressor for AAV-mediated gene therapy. We were able to improve the gene regulation of the autogenous switch by using multiple operator DNA sites, a tetrameric lac repressor, and point mutations to the lac repressor. The autogenous switch was shown to function in various cell types and was capable of reversible regulation of luciferase in living mice

The microstratigraphy of middens: capturing daily routine in rubbish at Neolithic Çatalhöyük, Turkey

Microstratigraphy — the sequencing of detailed biological signals on site — is an important new approach being developed in the Çatalhöyük project. Here the authors show how microscopic recording of the strata and content of widespread middens on the tell are revealing daily activities and the selective employment of plants in houses and as fuel. Here we continue to witness a major advance in the practice of archaeological investigation.</jats:p

Enhancement of latent fingerprints on fabric using the cyanoacrylate fuming method followed by infrared spectral mapping

A method has been developed for the visualization of latent fingerprints on fabrics, which is based upon cyanoacrylate (superglue) fuming followed by imaging using an infrared microscope. Results show that imaging on smooth, shiny fabrics such as polyester, silk, nylon and acetate of different colors and patterns can give an improvement over existing enhancement methods. Results for cotton and polycotton were less successful and it is thought this may be due a combination of the presence of the carbonyl functional group in these fabrics as well as their absorbency to fingerprint sweat. The carbonyl peak (1700 cm-1) provided the optimum spectroscopic feature to map and image a fingerprint. Comparisons between infrared mapping at a specific frequency range and principal component analysis showed that improved imaging was obtained with principal component analysis

Enhancement of aged and denatured fingerprints using the cyanoacrylate fuming technique following dusting with amino acid-containing powders

We have carried out experiments to investigate the ageing of latent fingerprints deposited on black PVC over a period of 4-15 weeks. A thumbprint was used in each case and before deposition of the print the donor rubbed their thumb around their nose to add sebaceous deposits. We have studied the effect of heat, light and moisture and we find that moisture is the most significant factor in the degradation of the latent print. We have attempted to enhance these latent prints by dusting with valine powder or powders composed of valine mixed with gold or red fluorescent commercial fingerprint powders. In order to make a direct comparison between “treated” and “untreated” prints, the prints were cut in half with one half being “treated” and one not. Our studies show the best results being obtained when powders of valine and red fluorescent powders are applied prior to cyanoacrylate fuming

A virtual clinic to improve long-term outcomes in chronic kidney disease

Chronic kidney disease (CKD) is common. A small proportion of patients with CKD progress to require interventions, which may include dialysis. Monitoring patients with CKD is supported by national guidelines. Monitoring systems to plan management of CKD vary in form. A novel monitoring system, the virtual CKD clinic (VC) was introduced at our hospital. The VC is a non-face-to-face results review of patients with CKD. We found that the VC was an effective monitoring system. None of the patients from the VC required emergency dialysis, suggesting robust surveillance. Survival was similar to patients with CKD discharged to primary care

The use of diffuse reflectance infrared spectroscopy to monitor the oxidation of UV irradiated and naturally aged bitumen and asphalt

Between 2013 and 2014 it cost £4.2 billion to repair roads in England [Department for Transport, Statistical Release. (2014). Road conditions in England 2014. Retrieved from https://www.gov.uk/government/uploads/system/uploads/attachment]. Currently, road surface quality is monitored visually and repairs effected when visible damage arises. At this point, repair is unfeasible and costly and time-consuming resurfacing is required. Hence the ability to perform non-invasive monitoring and prediction of road surface degradation could provide a significant advance in highway maintenance. The oxidation of bitumen in road surfaces is known to promote failure of road surfaces as it reduces the cohesion between bitumen and aggregate. This paper reports the use of non-contact, diffuse reflectance infrared Fourier transfer (DRIFT) spectroscopy to monitor the oxidation process in bitumen and asphalt. We outline the comparison between natural and enhanced, artificially promoted ageing of bitumen and asphalt samples using UV light. The IR spectroscopic results show the evolution of oxidation product functional groups and allow the ageing of the samples to be monitored. After 4 weeks of UV ageing and a total exposure of 350 kW/m2 the area of the carbonyl feature had increased from 0.17 to 3.25 and the combined carboxylic & sulphoxide feature had increased from 0.93 to 8.97, while the C–H feature had decreased from 8.16 to 1.18, indicating an increase in the oxidation of the bitumen

Developing cellulosic waste products as platform chemicals: protecting group chemistry of α-glucoisosaccharinic acid

Alpha and beta-glucoisosaccharinic acids ((2S,4S)-2,4,5-trihydroxy-2-(hydroxymethyl)pentanoic acid and (2R,4S)-2,4,5-trihydroxy-2-(hydroxymethyl)pentanoic acid) which are produced when cellulosic materials are treated with aqueous alkali are potentially valuable platform chemicals. Their highly functionalised carbon skeleton, with fixed chirality at C-2 and C-4, makes them ideal starting materials for use in synthesis. In order to assess the potential of these saccharinic acids as platform chemicals we have explored the protecting group chemistry of the lactone form of alpha-glucoisosaccharinic acid (α-GISAL). We report here the use of single and multiple step reaction pathways leading to the regioselective protection of the three different hydroxyl groups of α-GISAL. We report strategies for protecting the three different hydroxyl groups individually or in pairs. We also report the synthesis of a range of tri-O-protected α-GISAL derivatives where a number of the products contain orthogonal protecting groups