Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of EGF receptor dynamics by protein tyrosine phosphatases

The phosphorylated epidermal growth factor receptor (EGFR) initiates intracellular signaling processes that regulate cell growth, survival, and migration, and disregulated EGFR-mediated signaling occurs in many cancers. While the processes that lead to EGFR activation and phosphorylation have been studied in detail, quantitative aspects of the spatiotemporal regulation of EGFR by protein tyrosines phosphatases (PTPs) are not well understood. To begin to address this, we developed a new compartmentalized mechanistic model of EGFR phosphorylation dynamics and used it to interpret quantitative biochemical measurements to show that EGFR is dephosphorylated at the plasma membrane and in the cell interior with a time scale that is small compared to the time scales for EGFR internalization. By expanding our computational model and experimental data set, we went on to demonstrate that EGFR dephosphorylation at the plasma membrane surprisingly does not affect phosphorylation-dependent EGFR internalization because a separation of phospho-dependent time scales enables EGFR to enter clathrin-coated pits prior to being acted upon by PTPs. This same separation of time scales does, however, allow PTPs to control EGFR association with adapter proteins that regulate downstream signaling. Thus, our model provides new quantitative understanding of how EGFR participates in a number of simultaneous processes that compete for EGFR Cterminal phosphotyrosines. We went on to apply this new quantitative understanding of EGFR regulation by PTPs by developing predictive models to understand how such regulation might differentially impact the efficacy of antibodies and kinase inhibitors targeting EGFR. We also developed new computational models to quantitatively predict how receptor dephosphorylation kinetics as rapid as we found for EGFR might differentially control signaling initiated by receptor tyrosine kinases that dimerize in structurally distinct ways observed naturally among the family of receptor tyrosine kinases (RTKs). Ultimately, the new quantitative understanding of EGFR regulation by PTPs developed in this thesis significantly refines our understanding of the dynamics of EGFR-mediated signaling, provides a number of additional testable predictions related to fundamental aspects of EGFR signaling complex nucleation and efficacy of EGFR-targeted therapeutics, and offers a basic quantitative framework for exploring the regulation of other receptor tyrosine kinases by PTPs. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Chemical and Biomolecular Engineering First Advisor Matthew J. Lazzara
Responses of Ectomycorrhizal Fungi to Mineral Substrates

Boreal forest soils are complex, heterogeneous growth substrates where organic and mineral components provide nutrient resources for soil organisms and plants. Mineral nutrients are cycled between living and dead organic components of the forest soil and weathering of soil minerals provides an important input of new resources, compensating for losses from the ecosystem. Predicting soil responses to changing climate and management practices is important to determine their effect on forest production. Models for this purpose are largely based on the concept of the soil solution as the interface controlling soil processes such as weathering and nutrient uptake by plants, whereas soil microbiology recognises microbial processes as the driving force in soil nutrient cycling. In boreal forests most tree root tips are colonised by ectomycorrhizal fungi. The mycelia of these symbiotic fungi mediate nutrient uptake by their tree hosts. These fungi are abundant in the organic layer of forest soils and ectomycorrhizal research has therefore largely focused on nutrient uptake from this horizon. Minerals in the soil may, however, also serve as nutrient resources for ectomycorrhizal fungi. Through combined chemical and physical processes fungi can affect nutrient availability by weathering minerals. This thesis describes a field experiment investigating the distribution of different ectomycorrhizal fungi in organic and mineral forest soil horizons, in vitro studies of fungal acidification of artificial substrates with different mineral element composition, microcosm studies of growth and carbon allocation in intact ectomycorrhizal systems colonising heterogeneous mineral substrates and a preliminary investigation of changes in surface micro-topography of minerals colonised by ectomycorrhizal hyphae. Half of the fungal species identified in the forest soil occurred exclusively in the mineral horizons. Mycelial growth, carbon allocation and substrate acidification by fungi colonising different mineral substrates in vitro and in microcosms appeared to be influenced by mineral element composition. Interpretation of possible modification of mineral surface micro-topography is more difficult but together the results obtained suggest that ectomycorrhizal fungi may contribute to the development of microenvironments on colonised mineral surfaces, where increased weathering can take place. Processes regulating nutrient availability in such microenvironments are different from those estimated from the bulk soil solution.
Trapper profiles and strategies: insights into sustainability from hunter behaviour

Hunters are the critical link between demand and supply of bushmeat. An understanding of the incentives that drive hunter behaviour might thus help to predict the impacts of hunting and inform management of bushmeat hunting systems. However, hunter behaviour has been generally under‐represented in studies of exploitation, in particular trapper behaviour, despite the fact that trapping is the most common form of hunting in central Africa. We collected data on hunter profiles and measures of catch and effort over 15 months in the Monte Mitra area of continental Equatorial Guinea, through interviews, hunter follows and an offtake survey. Younger trappers, and those not born in the village, were found to expend the greatest trapping effort. Trappers operated under three distinct strategies, reflecting different levels of effort and impact: low‐impact village trappers, medium‐impact forest trappers and high‐impact forest trappers. Among different measures of effort, time expended and distance travelled were found to be less important in predicting trapping success than the number of effective traps, a measure that incorporates trap age. Regular checking of traps was found to be important in reducing wastage and therefore increases trapping success. Trapping is currently the main hunting method in Monte Mitra, due to lower barriers to entry and higher profits compared with gun hunting, but increasing affordability and availability of guns and cartridges warns of a possible future switch to gun hunting in the area, which is likely to have adverse impacts on vulnerable species, particularly arboreal primates. An understanding of the influence of a hunter's profile on hunting effort and success enables a prediction of the impacts of socioeconomic changes on wildlife populations and management actions to improve hunting sustainability.
Biosynthesis of polyhydroxyalkanoates for cardiac tissue engineering applications

As a result of the enormous clinical need, cardiac tissue engineering has become a prime focus of research within the field of tissue engineering. In this project, Poly(3- hydroxyoctanoate), P(3HO), a medium chain length (mcl-PHAs) biodegradable, biocompatible and elastomeric polyhydroxyalkanoate, was studied as a potential material for cardiac tissue engineering. Mcl-PHAs are an alternative source of polymers produced by Pseudomonas sp. As Gram-negative bacteria, Pseudomonas sp. contains lipopolysaccharides in the membrane, which are co-purified with PHAs and may cause immunogenic reactions. This limits the biomedical applications of the mcl-PHAs in several cases. In this work, the Pseudomonas mendocina PHA synthase gene (phaC1) was expressed in the LPS free, GRAS, Gram-positive microorganism, Bacillus subtilis so as to produce LPS-free mcl-PHAs. Our results showed that the recombinant Bacillus subtilis containing the phaC1 gene produced poly(3-hydroxybutirate), P(3HB), with a maximum yield of 32.3 % DCW, an unexpected result. This result thus revealed the unusually broad substrate specificity of the PHA synthase from P. mendocina, which is able to catalyse both medium and short chain length PHAs biosynthesis depending on the metabolic pool available in the host organism. Sequence comparison of this PHA synthase with stringent mcl-PHA synthases revealed possible residues influencing the substrate specificity of PHA synthases. As studies on mcl-PHAs remain limited mainly because of the lack of availability of mcl- PHAs in large quantities, the capacity to scale-up P(3HO) production from 2 L to 20 L and 72 L pilot plant bioreactors, based on constant oxygen transference, was studied. The interaction of freshly isolated rat cardiomyocytes with the P(3HO) polymer, during contraction, was studied when cells were stimulated at a range of frequencies of electrical pulses or calcium concentrations. These results showed that P(3HO) did not have any deleterious effects on the contraction of adult cardiomyocytes. P(3HO) cardiac patches nonporous, porous or with P(3HO) electrospun fibres deposited on their surface were developed. Our results showed that the mechanical properties of the final constructs were close to that of the cardiac structures, with a Young’s modulus value of 0.41±0.03 MPa. Myoblast (C2Cl2) cell proliferation was studied on the different constructs showing an enhanced cell adhesion and proliferation when both porous and fibrous structures were incorporated together. Finally, for further enhancement of the cardiac patch function, VEGF and RGD peptide were incorporated. Results obtained in this project showed that the P(3HO) multifunctional cardiac patches were potentially promising constructs for efficient cardiac tissue engineering.
BEYOND PEROXISOME: ABCD2 MODIFIES PPARα SIGNALING AND IDENTIFIES A SUBCLASS OF PEROXISOMES IN MOUSE ADIPOSE TISSUE

OF DISSERTATION BEYOND PEROXISOME: ABCD2 MODIFIES PPAR SIGNALING AND IDENTIFIES A SUBCLASS OF PEROXISOMES IN MOUSE ADIPOSE TISSUE ABCD2 (D2) has been proposed as a peroxisomal long-chain acyl-CoA transporter that is essential for very long chain fatty acid metabolism. In the livers of mice, D2 is highly induced by fenofibrate, a PPARligand that has been widely used as a lipid lowering agent in the treatment of hypertriglyceridemia. To determine if D2 is a modifier of fibrate responses, wild-type and D2 deficient mice were treated with fenofibrate for 14 days. The absence of D2 altered expression of gene clusters associated with lipid metabolism, including PPARsignaling. Using 3T3-L1 adipocytes, which express high levels of D2, we confirmed that knock-down of D2 modified genomic responses to fibrate treatment. We next evaluated the impact of D2 on effects of fibrates in a mouse model of dietinduced obesity. Fenofibrate treatment opposed the development of obesity, hypertriglyceridemia, and insulin resistance. However, these effects were unaffected by D2 genotype. We concluded that D2 can modulate genomic responses to fibrates, but that these effects are not sufficiently robust to alter the effects of fibrates on diet-induced obesity phenotypes. Although proposed as a peroxisomal transporter, the intracellular localization of D2, especially in adipose tissue, has not been validated with direct experimental evidence. Sequential centrifugation of mouse adipose homogenates generated a fraction enriched with D2, but lacked well-known peroxisome markers including catalase, PEX19, and ABCD3 (D3). Electron microscopic imaging of this fraction confirmed the presence of D2 protein on an organelle with evidence of a dense matrix and a diameter of ~200 nm, the typical structure and size of a microperoxisome. D2 and PEX19 antibodies recognized distinct structures in mouse adipose. Immunoisolation of the D2-containing compartment from adipose tissue confirmed the scarcity of PEX19. Proteomic profiling of the D2 compartment revealed the presence of proteins associated peroxisome, endoplasmic reticulum (ER), and mitochondria. We conclude that D2 is localized to a distinct subclass of peroxisomes that lack many peroxisome proteins and may physically associate with mitochondria and the ER.
An evaluation of three quick methods commonly used to assess sward height in ecology

Summary 1 Many ecological studies and applications involve measuring the height of grassland swards. An evaluation was made of the practicality, accuracy and comparability of using the sward stick, drop disc and direct methods of measurement. Each method proved to be appropriate for measuring swards that contain a wide range of heights, each was quick to perform, and recorder effects were negligible. Yet each had strengths and weaknesses. 2 The sward stick gave the most variable results: it was considered the best method for recording the architecture of the sward surface, and hence invertebrate niches, but was poor for measuring short turf. The drop disc was the worst method for recording microheterogeneity in sward architecture and was completely unsuitable for measuring variation in short turf. But in medium-tall swards, it was considered to be the best method for measuring productivity, vertebrate herbivory and for large-scale monitoring of land managed for conservation and under agri-environment schemes. The direct method gave the most consistent and accurate results compared with an independent parameter, soil temperature. It was the only method suitable for measuring variation in short turf. 3 A serious problem exists when research results, recommendations and assays involve measurements made by more than one method. The sward stick consistently gave higher absolute values than either of the other methods and, apart from in short turf (for which it is unsuitable), the drop disc gave values that were 73% and up to 40% lower, respectively, than those obtained using the sward stick and direct methods. This can lead to major misapplications of ecological results and recommendations in conservation and agri-environmental projects.
A systematic review of Planaltina (Teleostei: Characiformes: Characidae: Glandulocaudinae: Diapomini) with a description of two new species from the upper rio Paraná, Brazil

Two new species, Planaltina glandipedis and Planaltina britskii, glandulocaudine fishes of the family Characidae, tribe Diapomini, are described herein. They were collected from tributaries of the rio Grande and or the rio Tiete, both tributaries of the upper rio Parana in the State of Sao Paulo, Brazil. The previously described species, Planaltina myersi, until now known almost exclusively from the holotype, is here redescribed from 47 specimens taken from tributaries of the rio Corumba, a tributary of the upper rio Parana. The two new species differ most prominently from the previously known species by possession of three somewhat elongate scales along the dorsal border of the male's caudal pouch opening. There is only one elongate scale in P. myersi. Planaltina glandipedis differs from P. britskii in having six or seven horizontal scale rows between the dorsal-fin origin and the lateral line versus five in the later species. The possible phylogenetic relationships among the three inseminating species within the tribe Diapomini, subfamily Glandulocaudinae, are discussed along with the putative phylogenetic relationships of the Diapomini to the newly recognized glandulocaudine outgroup containing the characid genera Knodus and a new genus related to Attonitus. Brief comments are presented concerning the geographical distribution and ecology of the species of Planaltina.
Stochasticity in biological networks : two sides of a golden coin

Cells live with fluctuations arising from various sources and occurring at a broad spectrum of scales. Stochasticity plays an amazing role in cellular functions and physiological behaviors through biological networks that compose a living cell. Like two faces of a coin, noise may be destructive in many biological systems but can also be constructive on the other hand. In this work, I combined computational, theoretical and experimental approaches to explore stochasticity in biological networks. The origins, consequences and significance of stochasticity were investigated through the developments of methodological techniques as well as studies of specific yet important networks. Effective temperature was proposed as a measurement of noise in gene networks. It serves as an alternative to noise classification by intrinsic'' and extrinsic'' contributions and is in some sense a more fundamental approach. A generalized Gillespie algorithm was derived for stochastic simulation of biochemical reactions that allows one to simulate biological systems with time-dependent reaction rates and system volumes. In addition to these developments, an important network topology abstracted from the multi-site phosphorylation networks of nuclear factors of activated T-cells was studied. Signal transduction of the network was mapped onto a random walker problem in nonequilibrium statistical mechanics and an optimal enzyme concentration was found that favors fast transduction. Noise at the cellular population level was also studied. A generalized variation index was proposed to measure variability and diversity of cellular populations. We found that cellular population variability may depend on its initial conditions and environments. Finally we turned to stochastic recombinant events in a gene circuit. A synthetic switch with both phenotypic and genotypic transitions was studied using combined experimental and theoretical approaches. This led to the result that there is always a bias of cellular population to one specific fate. These studies show the two sides of stochasticity and help us to better understand noise in biological systems and to aid in better design strategy of genetic circuits
Combined crossbred and purebred selection in animal breeding

The aim of this thesis is to study the selection methods to optimize genetic response in crossbreds by combining both crossbred and purebred information in selection. (1) The locus model study clarified theoretically the meaning and use of genetic parameters related to crossbreds, which are generally not a function of parameters in parental lines. (2) Additive and dominance variances were estimated for egg production traits using linear mixed models and a restricted maximum likelihood. Sire-dam model, additive animal model and dominance animal model were compared in estimating heritability. (3) A combined crossbred and purebred selection method (CCPS) was developed to optimize crossbred response. The method was compared with the pure line selection and crossbred selection methods. Robustness of the method against inappropriate values of genetic parameters was studied. A linear mixed model was presented to apply CCPS. (4) The application of CCPS in animal breeding was extensively discussed.
Determination of primary combustion source organic carbon-to-elemental carbon (OC / EC) ratio using ambient OC and EC measurements: secondary OC-EC correlation minimization method

Abstract. Elemental carbon (EC) has been widely used as a tracer to track the portion of co-emitted primary organic carbon (OC) and, by extension, to estimate secondary OC (SOC) from ambient observations of EC and OC. Key to this EC tracer method is to determine an appropriate OC / EC ratio that represents primary combustion emission sources (i.e., (OC / EC)pri) at the observation site. The conventional approaches include regressing OC against EC within a fixed percentile of the lowest (OC / EC) ratio data (usually 5–20 %) or relying on a subset of sampling days with low photochemical activity and dominated by local emissions. The drawback of these approaches is rooted in its empirical nature, i.e., a lack of clear quantitative criteria in the selection of data subsets for the (OC / EC)pri determination. We examine here a method that derives (OC / EC)pri through calculating a hypothetical set of (OC / EC)pri and SOC followed by seeking the minimum of the coefficient of correlation (R2) between SOC and EC. The hypothetical (OC / EC)pri that generates the minimum R2(SOC,EC) then represents the actual (OC / EC)pri ratio if variations of EC and SOC are independent and (OC / EC)pri is relatively constant in the study period. This Minimum R Squared (MRS) method has a clear quantitative criterion for the (OC / EC)pri calculation. This work uses numerically simulated data to evaluate the accuracy of SOC estimation by the MRS method and to compare with two commonly used methods: minimum OC / EC (OC / ECmin) and OC / EC percentile (OC / EC10 %). Log-normally distributed EC and OC concentrations with known proportion of SOC are numerically produced through a pseudorandom number generator. Three scenarios are considered, including a single primary source, two independent primary sources, and two correlated primary sources. The MRS method consistently yields the most accurate SOC estimation. Unbiased SOC estimation by OC / EC min and OC / EC10 % only occurs when the left tail of OC / EC distribution is aligned with the peak of the (OC / EC)pri distribution, which is fortuitous rather than norm. In contrast, MRS provides an unbiased SOC estimation when measurement uncertainty is small. MRS results are sensitive to the magnitude of measurement uncertainty but the bias would not exceed 23 % if the uncertainty is within 20 %.
BLOOD POLYMORPHISM AND ITS RELATION WITH SHEEP PRODUCTION AND REPRODUCTION .

Group of animal consist of 300 Awassi ewes, 32 rams and 322 offspring were typed for blood potassium and hemoglobin, HK gene frequencies for ewes, rams, and lambs were of the order of 0.89, 0.93 and 0.88, respectively; for the HbB gene the corresponding frequencies were related 0.98, 1.00 and 0.99, respectively. B HK (High potassium, Hb type B) ewes showed a significantly higher lambing percentage, fleece weight, fiber diameter, fleece wax percentage and alkali solubility percentage, 98.5%, 20kg, 29. 6µ, 2.2% and 7.6% corresponding with related 95.5%, 1.8kg, 28. 6µ, 1.8% and 7.1% of B LK type respectively. B LK (Low potassium, Hb type B) ewes produced significantly more female lambs while B LK lambs, compared with B HK ones, had significantly higher birth and weaning weights. The association between B HK types and fitness was proposed as the explanation of the high gene frequency of this type.