Miracle-dz/UniFAR-FTUs huggingface dataset:
Discovery and development of imaging-capable bacterial nitroreductases and their cytotoxic prodrugs for Clostridium sporogenes based gene therapy

i Acknowledgements . ii Table of contents . iii List of figures . vii List of tables . xi Glossary . xii Chapter 1. Literature review . 1 1.1. Chemotherapy . 1 1.2. Cancer gene therapy . 2 1.2.1. Enzyme/prodrug combinations . 3 1.2. 2. Gene therapy delivery systems . 8 1.3. Clostridia . 11 1.3. 1. Necrosis as a prognostic indicator in human tumours . 12 1.3. 2. Discovery and development of Clostridia as an anticancer agent . 12 1.3. 3. Utility of Clostridia as a vector for cancer gene therapy . 14 1.4. Nitrogen mustard prodrugs . 16 1.4. 1. The bystander effect . 16 1.4. 2. Dinitrobenzamide mustard prodrugs . 16 1.4. 3. PR-104 . 18 1.5. Positron emission tomography (PET) imaging. 20 1.5. 1. Gene therapy imaging modalities . 22 1.5. 2. 2-Nitroimidazoles . 24 1.6. Identification of E. coli NfsA for dual prodrug and PET agent activation . 25 1.7. Objectives and organisation of this thesis . 27 Chapter 2. Materials and methods . 29 2.1. Materials . 29
Influence of Nutrients and Grazing on the Response of Stream Periphyton Communities to a Scour Disturbance

We examined the effect of nutrient input and grazing intensity on resistance and resilience of periphyton communities in laboratory streams to a scour disturbance. Previous theoretical studies using stream models indicated that resilience of nutrient-limited streams, as defined by the return time to the initial state, is strongly related to the residence time of nutrients in the system and to the presence of herbivores. To experimentally test this prediction we established two levels of nutrient input by altering the flow regime (once-through flow and 98% recirculated flow) and two levels of grazing intensity by the presence or absence of the snail Elimia clavaeformis, resulting in a 2 × 2 factorial design with two replicate streams per treatment. After the streams reached an approximately stable level of periphyton biomass, a scour disturbance was imposed on all streams. Measures of the resistance and resilience of the periphyton to this disturbance were made. The resistance of most structural characteristics of the periphyton was significantly higher in streams with snails than in streams without snails. Nutrient input had little effect on resistance of all periphyton characteristics. Resilience was measured by two parameters: rate of increase of a particular characteristic over time following the disturbance (r), and time to return to the pre-disturbance state (Ts). The experimental results on resilience were complex. In general, high grazing intensity resulted in low values of r for most periphyton characteristics, but also shorter Ts for some characteristics. The shorter Ts values were attributed to lower pre-disturbance biomass and metabolism in the streams with snails compensating for lower r for these characteristics following the disturbance. Contrary to model predictions, low nutrient input generally did not result in low resilience for most characteristics in the streams without snails, probably because increased nutrient recycling compensated for low inputs. However, for the streams with snails, resilience of most periphyton characteristics was lower in streams with low nutrient input compared with streams with higher nutrient input. This contrast in resilience suggests a positive feedback between biomass accrual and nutrient recycling that helps maintain high productivity despite low nutrient inputs during recovery of stream periphyton communities from disturbance.
Covalent immobilization of KR-12 peptide onto a titanium surface for decreasing infection and promoting osteogenic differentiation

Infection and poor bone-implant integration are the two main reasons for titanium (Ti) implant failure. Here, we investigated the feasibility of functionalizing Ti with the antimicrobial peptide, KR-12, derived from the human cationic antimicrobial peptide. The minimal inhibitory concentration and cell viability effects of KR-12 were investigated prior to immobilization on the Ti surface. The results showed that KR-12 possessed a wide anti-bacterial spectrum with no cytotoxicity to human bone marrow mesenchymal stem cells (hBMSCs). Successful covalent immobilization of KR-12 onto an amine-functionalized Ti (Ti-KR-12) surface was characterized by X-ray photoelectron spectroscopy. Gram-positive bacteria, Staphylococcus epidermidis and methicillin resistant Staphylococcus epidermidis were employed for antibacterial characterization. Ti-KR-12 substrates could significantly inhibit adhesion and colonization of common pathogenic bacteria and the drug resistance of pathogenic bacteria. The results of the CCK-8 assay, confocal laser scanning microscopy, and scanning electron microscopy showed that KR-12 covalently immobilized on Ti improved adhesion and proliferation of hBMSCs. The osteogenic differentiation of hBMSCs on samples was investigated by alkaline phosphatase staining, sirius red staining, alizarin red staining, and real-time PCR. The staining and real-time PCR results demonstrated that hBMSCs grown on Ti-KR-12 surfaces for 10 and 14 days under conditions inducing osteogenic differentiation displayed significantly higher alkaline phosphatase activity, larger extracellular matrix calcium deposition area, and higher expression of alkaline phosphatase, osteocalcin, osteopontin, and collagen type-1 mRNA than bare Ti. Our results demonstrated the KR-12 peptide was suitable for improving the biological properties of bioinert titanium. KR-12 showed antibacterial activity and the capability to promote cell proliferation and Ti-KR-12 surfaces significantly decreased bacteria adhesion, whilst promoting the osteogenic differentiation of hBMSCs.
Rôle de la lysyl oxidase-like-2 endothéliale et tumorale au cours de l’angiogenèse dans le carcinome du rein à cellules claires

L’angiogenese est un processus majeur intervenant au cours du remodelage du microenvironnement tumoral, induit par l’hypoxie et le VEGF. La lysyl oxydase like-2 (LOXL2) appartient a la famille des lysyl oxydases, impliquee dans le pontage de constituants matriciels. Notre equipe a montre que l’induction de LOXL2 par l’hypoxie conduit a sa secretion par les cellules endotheliales et son accumulation dans la matrice extracellulaire endotheliale. Nous avons montre que LOXL2 joue un role dans l’angiogenese au cours du developpement. Des etudes ont montre que LOXL2 est surexprimee dans de nombreux cancers et que l’inhibition de LOXL2 extracellulaire empeche la formation d’un microenvironnement tumoral. Mon travail de these a porte sur l’etude du role de LOXL2, exprimee par les cellules endotheliales et tumorales, au cours de l’angiogenese dans le carcinome du rein a cellules claires (ccRCC) humain. Nous avons montre que LOXL2 est exprimee a la fois par les cellules stromales et tumorales dans le ccRCC humain, mais aussi que LOXL2 pourrait jouer un role specifique en fonction de son origine cellulaire dans ces tumeurs. L’etude de la contribution de LOXL2 endotheliale nous a permis de demontrer que LOXL2 promeut l’angiogenese in vitro et in vivo dans le ccRCC, avec une implication partielle de son activite catalytique dans ce processus. Nous avons montre que LOXL2 secretee par les cellules tumorales stimule l’angiogenese in vitro et in vivo, avec la participation de son activite catalytique, notamment en modulant la proliferation des cellules endotheliales. LOXL2 endotheliale et tumorale promeuvent l’angiogenese dans le ccRCC, dependamment ou non de son activite catalytique.
Establishment of co-existing Mediterranean tree species under a varying soil moisture regime

Abstract We investigated the responses of two co-existing Mediterranean trees with different regeneration strategies (Phillyrea latifolia seedlings and Quercus ilex sprouts) to experimental drought below the forest canopy. We considered different recruitment stages and used leaf isotopic discrimination to estimate water use efficiency (WUE) and nitrogen availability and use. Drought decreased the emergence and survival of seedlings and sprouts. Survival and growth of older saplings were not influenced by drought. Seedling emergence of P. latifolia was higher than Q. ilex sprout production, but Q. ilex sprouts had higher survival and growth rates. These differences disappeared in the sapling stage. Carbon isotopic discrimination suggested that Q. ilex sprouts had higher WUE than P. latifolia seedlings. Drought increased WUE of recruits, particularly in Q. ilex. Water use regulation increased with ageing, particularly in P. latifolia. Q. ilex had higher δ15N values than P. latifolia; these were also higher under drier soil conditions. Current year seedlings had higher δ15N than saplings, particularly in P. latifolia, suggesting they exploit superficial soil layers. These results suggest that sprouts obtain benefit from resources stored in parent plants. At earlier stages, they perform better than seedlings. This response is not coupled to adult vulnerability to drought for these species, revealing the difficulty of predicting species dynamics during climate change. Abbreviations: TDR = Time domain reflectometry; WUE = Water use efficiency. Nomenclature: Bolòs et al. (1990).
Current awareness on yeast

In order to keep subscribers up‐to‐date with the latest developments in their field, this current awareness service is provided by John Wiley & Sons and contains newly‐published material on yeasts. Each bibliography is divided into 10 sections. 1 Reviews; 2 General; 3 Biochemistry; 4 Biotechnology; 5 Cell Biology; 6 Gene Expression; 7 Genetics; 8 Physiology; 9 Medical Mycology; 10 Recombinant DNA Technology. Within each section, articles are listed in alphabetical order with respect to author. If, in the preceding period, no publications are located relevant to any one of these headings, that section will be omitted. (4 weeks journals ‐ search completed 5th. Mar. 2008)
Phosphoproteomics

Current analytical protein methods show phosphorylation to be the most ubiquitous, evolutionary conserved post‐translational modification Post‐Translational Modification (PTM). The reversible and transient nature of protein phosphorylation allows signal transduction pathways to carry out diverse cellular functions. From bacteria to humans, phosphorylation serves to modify protein function by altering protein stability, cellular location, substrate affinity, complex formation, and activity; thus allowing essential events such as cell cycle and growth to occur at precise times and locations. Phosphorylation controls a variety of events at many biological levels including: housekeeping activities controlled by single cells such as DNA transcription, cell‐cycle regulation, and energy metabolism; and cellular processes that involve signaling between cells or the environment including such as neuronal migration and immune system recognition. This review summarizes state‐of‐the‐art proteomics technologies available to study phosphorylation in biological systems. We highlight the tremendous steps the field has made in the last 5 years which allow quantitative global analyses while pointing out caveats in experimentation. Copyright © 2009 John Wiley & Sons, Inc.
Sequence Analysis of Mutants from Rhodopseudomonas viridis Resistant to the Herbicide Terbutryn

Several mutants resistant to terbutryn (2-thiom ethyl-4-ethylamino-6-t-butylamino-s-triazine) from the purple bacterium Rhodopseudom onas viridis have been isolated. The sequence analysis of that part of the DNA coding for the herbicide binding site in the photosynthetic reaction centre showed that only two genetically different mutant strains were obtained. The sequence data are discussed with respect to recent crystallographic results.
ENERGY REQUIREMENTS OF SEABIRD COMMUNITIES: A BIOENERGETICS MODEL

SUMMARY (1) Methods used to estimate energy requirements of avian communities are listed, and their inadequacies discussed. In particular, the published estimates lack confidence intervals. (2) A simulation model is described which estimates daily energy requirements of seabird populations. Biomasses of breeders, non-breeders and chicks present in the vicinity of the colony, are coupled with an ambient temperature function, the bioenergetic equations of Kendeigh, and calculations of the energy costs of digestion, activity, egg production and growth. (3) The model is tested using input data sets for great skua Catharacta skua Brinnich and Arctic tern Sterna paradisaea Pontopp. Sensitivity of the model to errors in input parameters, and the output errors resulting from known imprecisions in the forty-four input parameters are examined. Output precision is largely determined by a few parameters, which depend partly on the life-style energy allocation of the species. (4) A Monte Carlo simulation is used to determine the precision of the estimated energy requirements of the two species' populations. This suggests that, using currently available input data, the population energy requirement estimate has a 95% confidence interval of + 50o of the mean. (5) Energy requirements could be considerably more precisely determined if only a small number of input parameters were more precisely known. These limiting parameters are listed. (6) The model is applied to one particular seabird community, on Foula, Shetland, for which detailed data have been collected. The mean estimate of the total energy requirement of this community (1 2 x 101 0 kcal yr - 1) represents 29% of the mean estimate of the total annual fish production within a 45 km radius of the colony. This implies that seabirds, predatory demersal fish and industrial fisheries are in direct competition for the energy flow from pelagic fish, such that any increase in the energy flow to one of these would result in a reduced energy availability to the others.
DNA fingerprint construction and genetic relationship analysis of dragon fruit germplasm in guizhou by ISSR markers

【Objective】The objective of the stuety is to estimate the genetic relationships among the germplasms as well as to construct DNA fingerprints of dragon fruit. 【Method】A total of 19 excellent lines of dragon fruit with white flesh and red flesh had been selected in Guizhou province during the past years.Currently,ISSR markers and NTSYS 2.01 were employed to unravel their genetic relationship. 【Result】 The results showed that a total of 364 bands were yielded from the 52 selected primers,among which 215(60%) were polymorphic.The specific markers generated from primer M08,845 and 881 might effectively distinguish the tested accessions,therefore,ISSR marker is accessible for fingerprinting in this crop.Computed by NTSYS 2.01,the similarity coefficients among the tested accessions were in the range of 0.70 to 0.96,and the average was 0.81. The mean similarity coefficients among the red-flesh lines and white-flesh lines were 0.82 and 0.89,respectively.The UPGMA dendrogram demonstrated that 22 germplasm could be divided into two groups(white-flesh and red-flesh types) at a cutpoint of 0.77. 【Conclusion】These data reflected that somatic variation occurrence of dragon fruit is fairly high,and variation in red-flesh line is higher than that of white-flesh line,thereby bud sport selection may be the chief way for genetic improvement in this crop.
A comparative study on four survey methods used in ungulate population size estimation in winter in North China

Research on reliable ungulate population size estimation has always been a core and confusing problem in north China. Currently,four methods are widely used in ungulate population size survey in north China,i. e. ,transect method,belt transect method,sample plot and non-invasive CMR method. However,these four methods are based on different assumptions and calculating methods,which may lead to significant differences in results generated by different methods. It is an urgent need to make a validity evaluation for the effectiveness of the four methods. We used the four methods mentioned above to assess the population size of moose( Alces alces cameloides) in an area of about 120km2 in Hanma National Nature Reserve in two time frame,Feb. to Mar. 2012 and Dec. 2012. Theresults showed that population size estimated by these methods were 168( 109—227) individuals,237( 165—309) individuals,37( 23—50) individuals,55( 43—68) individuals,correspondingly. It is obvious that results from the two methods( transect method and belt transect method) traditionally used in north China are significantly higher than those of the two methods( sample plot and non-invasive CMR method) newly introduced to China. We further discuss the reliability,limitation and applicability of different methods to provide scientific reference to selection and application of suitable ungulate population survey methodsduring winter in north China.
Importance of kelp detritus as a component of suspended particulate organic matter in giant kelp Macrocystis pyrifera forests

To determine the potential of giant kelp Macrocystis pyrifera detritus as a food resource for coastal suspension feeders, we quantified the production and size distribution of small particulate (<1 cm) kelp detritus in relation to water motion, state of kelp blade erosion, and percent cover of the bryozoan Membranipora serrilamella on blades. We enclosed kelp blades in the laboratory and in the field to collect detritus particles, which we then fractionated by size. Carbon and nitrogen content were quantified for each size fraction. Suspension feeders typically consume particles up to 250 μm in size, and most kelp detritus particles that we collected were within this size range. Blade degradation state and blade mass were found to be weak but significant predictors of detrital generation. We used the data from our laboratory and field experiments combined with 5 yr of monthly biomass measurements of giant kelp and suspended particulate organic matter (POM) to estimate the contribution of kelp detritus to suspended particulate organic carbon (POC) and nitrogen (PON) in the kelp forest at Mohawk Reef off Santa Barbara. Results showed that detrital kelp carbon contributed <0.2% of total suspended reef POC and PON. Therefore, despite the high production rate of kelp and the importance of exported kelp detritus to intertidal and deep-water ecosystems, our results suggest that small kelp detrital par ticles do not represent a significant food source to kelp forest suspension feeders.
Errata

The authors of Rivera et al. (2005) would like to publish the following clarification: in our review, we emphasized the fact that using Cs+ as an internal cation in whole-cell recordings results in a profound dysfunction of the neuronal K+–Cl− cotransporter, KCC2. This is because Cs+ is a very poor substrate of this ion transporter, with a maximum transport rate (Vmax) for Cs+ that is < 20% of the value for K+ (Williams & Payne, 2004). On page 29, we stated that ‘Unfortunately, the kinetic data in the only published model of neuronal K+–Cl− cotransport in neurones (Staley & Proctor, 1999) were obtained using Cs+ in whole-cell experiments – and hence, in the absence of functional KCC2! ’ Since the publication of our review, it has been brought to our attention that both K+ and Cs+ were used by the authors, with essentially similar results. This is true and, if anything, it strengthens our concerns about the validity of the above modelling study which yielded a value of Vmax for Cs+ that is higher than for K+ (about 7 mmol l−1 s−1 for Cs+ and about 5–6 mmol l−1 s −1 for K+).
Preparation and Food Product Development From Macrotyloma Uniflorum (Horse Gram) Bovine Milk Blends

Horse gram (Macrotyloma uniflorum) is one of the inexpensive sources of protein, calcium and iron. The present study, aimed at developing horse gram extract-bovine milk blends (HEBMB), encompassed three phases. The first phase involved preparation of horse gram extract (HGE) using household processing steps, the second phase comprised analysis of proximate, minerals (calcium and iron) and antinutrients (tannins and total phenol) of HGE. The final phase involved blending of HGE with bovine milk (BM) in different ratios (40:60, 50:50 and 60:40) and developing milk based products (kulfi, papaya shake and kadhi) from them. Results of the study revealed that HGE contained 91.99 g moisture, 3.64 g protein, 0.25 g fat, 0.80 g crude fibre, 0.13 g ash and 3.19 g carbohydrates per 100 ml. Sensory evaluation of products, on the basis of 9-point hedonic scale, revealed that all the variants of the various products prepared were acceptable.
Evaluation of protective effect of rutin on lead acetate-induced testicular toxicity in Wistar rats

Abstract In this study, the effect of rutin (RT) was investigated on lead-induced testis tissue damage in rats. Oral administration of rutin (50 mg/kg) effectively inhibited the levels of marker enzymes and antioxidant enzymes as compared with lead acetate-treated group. Antioxidant enzyme activities of superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx), glutathione-S-transferase (GST), and histopathological changes of testes were investigated. Lead acetate decreased the levels of SOD, CAT, GPx, and GST compared with the control group. Light microscopic analyses revealed that lead acetate induced several histopathological changes in testis tissue. In the RT-treated group, there were statistically significantly decreases in antioxidant enzyme activities and pathological changes in the tissue. The results suggest that RT possesses significant potential in reduced lead acetate-induced testicular toxicity.
Effects of pre-harvest irrigation regime and crop level on yield, fruit size distribution and fruit quality of field-grown ‘Black Amber’ Japanese plum

Summary The effect of pre-harvest irrigation level and crop level on yield, fruit size distribution, fruit growth and fruit quality was studied on field-grown ‘Black Amber’ Japanese plum in a commercial orchard in a semi-arid zone. Differential irrigation treatments were applied at stage III of fruit growth, from mid-May until harvest. Crop coefficients during the month prior to harvest ranged from 0.24 to 1.17 and from 0.13 to 1.33 of potential evapotranspiration in 2001 and 2002, respectively. Fruit growth and midday stem water potential were measured throughout the season. The yield from each experimental tree was harvested on 19 and 24 June, 2001 and on 19 June, 2002. The yield was weighed and fruit size distribution was determined with a commercial grading machine. The optimum crop coefficient appears to lie between 0.6 and 0.8 of the potential evapotranspiration. Fruit yield and size increased with increasing irrigation rate. Limitation of availability of assimilates was apparent in the low irrigation treatments at high crop levels. Relative fruit growth rates in all treatments decreased dramatically during an extremely warm, dry week, when temperature and vapour pressure deficit exceeded 40°C and 8 kPa, respectively. The decrease in relative fruit growth rate during this week was inversely proportionate to the irrigation level.The soluble solids content in the fruit juice decreased with the increase in the irrigation level.
In-situ focused ion beam implantation for the fabrication of a hot electron transistor oscillator structure

Recent advances using in situ focused ion beam implantation during an MBE growth interruption have been exploited to fabricate planar GaAs hot electron structures without the need for shallow ohmic contacts. This novel fabrication route shows a very high yield and has been used to demonstrate a prototype high-frequency oscillator structure based on electron multiplication in the base layer. Existing devices show transfer factors in excess of unity as well as reversal of the base current at high injection levels, which are the prerequisites for oscillator action. Future improvements in device design are discussed.