There are many tools available for the study of post-translational modifications. The majority of these tools is specific towards the individual modification and involves separation of modified proteins from non-modified ones. The drawback of using a modification specific method is that there is a lack of flexibility in its usage for other modifications. The goal of these studies was to investigate the possibility of obtaining a similar separation effect by fractionating post-translationally modified proteins based on the physical properties of proteins. The post-translational modification chosen to be the basis of this study was the O-GlcNAc modification. Using the C2C12 mouse myoblast cell line, it was determined that the optimal conditions for producing lysates containing increased yields of O-GlcNAc modified proteins was to treat differentiated C2C12 cells with 10nM insulin, 12g/L glucose and 2mM of the O-GlcNAcase inhibitor Streptozotocin for 24 hours. Using the optimized lysis buffer, it was shown that protein separation by surface charge using standard anion exchange separation did not provide enough resolution or material to obtain any identifications of modified proteins. However, when a chromatofocusing method which separates proteins on the basis of their isoelectric points was used, a separation scheme with larger capacity and higher resolution was possible. Using this separation method followed by gel electrophoresis of individual fractions, proteins which are potentially O-GlcNAc modified were identified by mass spectrometry. It was evident from the number of protein bands observed per fraction on the Coomassie stained gels and the number of proteins identified per protein band by mass spectrometry that further reduction in sample complexity was required to assist in the positive identification of O-GlcNAc modified proteins. Among the identified proteins, 32 percent were metabolic proteins, 21 percent were protein processing proteins, 16 percent were structural proteins and the remainder a mix of other proteins. Unfortunately, it was not possible to validate the presence or absence of the O-GlcNAc modification on these proteins using available methodologies such as immunoprecipitation. As such, further work is required to optimize the separation strategy and to verify the usefulness of this separation strategy in identifying O-GlcNAc/post-translationally modified proteins.

The major antinutritive factor in Leucaena for ruminants is condensed tannin (CT). CT bind proteins, incurring a negative effect on protein utilisation. The two major factors affecting the ability of CT to bind protein have been purported to be CT size and the pH of the reaction environment. To test these hypotheses the protein precipitating capacities of CT extracted from four promising Leucaena genotypes, L. leucocephala (K636), L. pallida (CQ3439), L. trichandra (CPI46568), and L. collinsii (OFI52/88) were assessed. L. leucocephala had approximately half the ability to precipitate protein on a g/g basis than L. pallida or L. trichandra while L. collinsii gave no measurable ability to precipitate protein (reaction environment=pH 5.0). Increasing or decreasing the pH of the reaction solution away from pH 5.0 (the isoelectric point of the protein) reduced the ability of CT from all the species to precipitate protein; the decrease being higher a pH 2.5 than at pH 7.5. At pH 2.5 L. leucocephala CT completely lost its capacity to precipitate protein. The relatively poor ability of L. leucocephala CT to bind protein at pH’s approximating those at the abomasum suggests L. leucocephala may have the greatest potential of the four Leucaena’s tested for increasing the extent of feed protein escaping ruminant degradation for later release and digestion in the small intestine, hence increasing the total amount of protein absorbed by ruminants. CT fractions from each Leucaena were also separated into individual CT’s, by size-exclusion chromatography and examined for protein precipitating capacity. In general it was found that the larger sized CT of the accessions L. pallida and L. trichandra could precipitate more protein than the smaller sized CT. This pattern was not found for L. leucocephala.

Thesis (PhD)--Macquarie University, Division of Environmental & Life Sciences, Dept. of Chemistry & Biomolecular Sciences, 2009. / Bibliography: p. 200-212.

The work in the dissertation expands the applications of DIEF and describes the development of incorporating DIEF in a microfluidic chip to create a comprehensive proteomics tool. Proof-of-concept DIEF experiments have been done previously, so the focus of this work is to explore the capabilities of DIEF. Dynamic isoelectric focusing (DIEF) is a separation technique invented by Dr. Luke Tolley. It is similar to capillary isoelectric focusing except it uses four high voltage electrodes to form a pH gradient instead of only two. The additional two electrodes are able to manipulate the pH gradient resulting in selection of the region and of the range of pH within a pre-defined sampling or extraction point. One of the first applications described for DIEF was to isolate a single protein from a complex mixture. The protein isolated was a cellulase enzyme capable of degrading multiple cellulose materials over a wide range of environmental conditions. DIEF did isolate the protein in a pH span of 0.005 which is equivalent to 0.075% of the total pH range. Fractions were collected for sequencing analysis, but the fractions were contaminated with keratin both times. DIEF was also successfully performed in an open air channel. Though other electromigration techniques have been successfully done in open air channels, these techniques were severely time and pH limited. In contrast, DIEF in an open air channel is capable of using the entire 3-10 pH range and can perform isolations until the proteins are completely separated. The device developed was also an improvement on increasing sample capacity. The channel was significantly bigger than the traditional glass capillaries used. Since the channel was open, fraction collection was made simpler by collecting using a pipette. This work also demonstrated that DIEF can be made through the use of silicone molding compounds and polyurethane. The amount of milling needed is reduced, the pieces are produced quickly, and a single mold can produce several pieces. Machining pieces with fragile bits is not needed to be done as much since only one acrylic piece is required produce a mold. The mold can produce several polyurethane pieces. This fabrication method has proven useful for making DIEF holders. The next step was to make DIEF a truly comprehensive proteomic tool by incorporating it into a microfluidic chip. Multiple sample fractions are rapidly generated on chip through the use of multiple bubbles simultaneously injected into the separation channel. This stops the separation and, since each droplet is isolated from others by a bubble on each side, the protein peaks are not able to broaden. This novel use of digital microfluidics is still a work in progress, but the fundamentals have been demonstrated. The fabrication protocol for making molds and PDMS casts was developed using materials and procedures that can be done in a common laboratory environment. DIEF is a separation technique still in its infancy, with a wide variety of available applications. DIEF will continue to be tested in other areas and developed into a comprehensive proteomic tool.

Le cerveau génère spontanément des activités électriques enregistrables à toutes les échelles spatiales, de l'électroencéphalogramme (EEG) jusqu'à la membrane neuronale. La fréquence et l'amplitude de ces activités varient en fonction des états de vigilance. Afin de comprendre comment cette activité synaptique endogène sculpte à chaque instant l'intégration des événements exogènes, j'ai mis au point une nouvelle stratégie expérimentale in vivo visant à comparer les réponses neuronales à divers stimuli, en présence et en absence d'activité endogène. J'ai généré, chez le rat, une activité de type éveil ou sommeil puis, j'ai induit un état isoélectrique durant lequel toute activité spontanée était supprimée. J'ai montré que la suppression de l'activité synaptique dans les neurones du cortex somatosensoriel induisait une diminution de sensibilité neuronale et un accroissement de la régularité des réponses. La persistance d'une excitabilité neuronale dans cet état de coma profond m'a conduit à poursuivre mes recherches avec le service de réanimation neurologique afin d'explorer, chez des patients placés dans un tel coma, la réactivité corticale à des stimulations sensorielles. J'ai démontré chez l'homme et l'animal la persistance de potentiels évoqués sensoriels dans l'EEG et les neurones corticaux. Ces réponses apparaissaient plus tardivement, avec une amplitude plus importante et une plus grande fiabilité d'un essai à l'autre. Ainsi, il apparaît que l'activité synaptique spontanée, qui caractérise le fonctionnement " normal " du cerveau, a essentiellement comme effet d'augmenter la sensibilité des neurones ainsi que la variabilité statistique des réponses à l'environnement. / The brain spontaneously generates electrical activities, which can be recorded at all the spatial level, from the electroencephalogram (EEG) to the neuronal membrane. The frequency and the amplitude of these activities vary with the states of vigilance. To understand how this endogenous synaptic activity sculpts the integration of exogenous events, I developed a new in vivo experimental strategy to compare the cortical neuronal responses to various stimuli in the presence and absence of endogenous activity. I generated a waking-like or sleep-like synaptic activity in the rat. Then, I induced an isoelectric state in which spontaneous activity was completely suppressed. I showed that the suppression of synaptic activity in somatosensory cortex neurons resulted in a decrease in neuronal sensitivity and an increase in the regularity of responses to repeated identical stimuli. The persistence of neuronal excitability while the animal was immersed in a deep comatose led me to continue my research in collaboration with the neurological intensive care unit to explore the sensory-evoked cortical responses in patients exhibiting an isoelectric EEG. I demonstrated in humans and animals the persistence of sensory-evoked potentials in the EEG and individual cortical neurons. These cortical responses occurring in the absence of spontaneous brain activity had an augmented latency, a larger amplitude and a higher trial-to-trial reliability. It thus seems that the primary effect of the sustained background synaptic activity, the hallmark of a "normal" functioning of the brain, is to increase the sensitivity of neurons and the statistical variability of responses to the environment.

There are many tools available for the study of post-translational modifications. The majority of these tools is specific towards the individual modification and involves separation of modified proteins from non-modified ones. The drawback of using a modification specific method is that there is a lack of flexibility in its usage for other modifications. The goal of these studies was to investigate the possibility of obtaining a similar separation effect by fractionating post-translationally modified proteins based on the physical properties of proteins. The post-translational modification chosen to be the basis of this study was the O-GlcNAc modification. Using the C2C12 mouse myoblast cell line, it was determined that the optimal conditions for producing lysates containing increased yields of O-GlcNAc modified proteins was to treat differentiated C2C12 cells with 10nM insulin, 12g/L glucose and 2mM of the O-GlcNAcase inhibitor Streptozotocin for 24 hours. Using the optimized lysis buffer, it was shown that protein separation by surface charge using standard anion exchange separation did not provide enough resolution or material to obtain any identifications of modified proteins. However, when a chromatofocusing method which separates proteins on the basis of their isoelectric points was used, a separation scheme with larger capacity and higher resolution was possible. Using this separation method followed by gel electrophoresis of individual fractions, proteins which are potentially O-GlcNAc modified were identified by mass spectrometry. It was evident from the number of protein bands observed per fraction on the Coomassie stained gels and the number of proteins identified per protein band by mass spectrometry that further reduction in sample complexity was required to assist in the positive identification of O-GlcNAc modified proteins. Among the identified proteins, 32 percent were metabolic proteins, 21 percent were protein processing proteins, 16 percent were structural proteins and the remainder a mix of other proteins. Unfortunately, it was not possible to validate the presence or absence of the O-GlcNAc modification on these proteins using available methodologies such as immunoprecipitation. As such, further work is required to optimize the separation strategy and to verify the usefulness of this separation strategy in identifying O-GlcNAc/post-translationally modified proteins. / Medicine, Faculty of / Medicine, Department of / Experimental Medicine, Division of / Graduate

Content: Many areas of leather production rely heavily on the manipulation of acidic and basic residues within the primary collagen structure to vary the overall charge of the substrate. For example, it is the basis which enables swelling during liming, deswelling during deliming, penetration of chromium after addition of chrome tanning salts and the fixing of chrome to carboxylate residues during basification. Manipulation of the charge on collagen is readily achieved through the addition of acids or bases into the float which may react with these residues to alter the charge. Often, the increase in anionic charge and reduction in cationic charge with increasing pH are shown to happen concurrently and linearly with the iso-electric point (IEP) given as the point at which the positive and negative charges present on the collagen are equal. However, the pH at which carboxylate/acid groups undergo protonation/deprotonation is significantly lower than that at which an amine/ammonium is protonated/deprotonated, meaning the linear model described above is not a true representation of charge of collagen at varying pH. Here we model the charge of a collagen substrate based off the amino acid profile of bovine skin, considering their relative levels within the collagen and concentrations within a water/collagen matrix, representative for collagen saturated with water. Models are presented for raw and limed bovine hides. This broader approach enables greater understanding of the influence of charge on the collagen substrate compared to IEP on its own, revealing contrasting charge profiles in acidic and alkaline regions of raw collagen, providing greater understanding of their differing behaviour during alkali swelling.

The aim of this Master Thesis is the optimization and verification of conditions of separation of proteins from biological materials. For the separation a developed technique called micropreparative isoelectric focusing is being used. The theoretical part describes analytical methods of biological materials with a focus on proteins which were used for the optimization of the developing system in general. This part of the Master Thesis also presents this method itself. Furthermore, basic characteristics of other techniques used to control the efficiency of the micropreparative isoelectric focusing are introduced. The experimental part depicts the individual steps of optimization of the micropreparative isoelectric focusing. The ideal separation procedure was firstly found out on the individual standard proteins, secondly on their mixture and lastly the optimised procedure was applied to a real biological sample. The efficiency of the micropreparative isoelectric focusing was verified by SDS-PAGE and MALDI-TOF mass spectrometry.

Allozyme frequencies and general protein patterns were surveyed among selected Texas marine fishes and shellfishes to illustrate the application of biochemical genetic techniques to stock and species identification in fisheries management.

Congenital disorders of glycosylation (CDG) represent a heterogeneous group of mul- tisystemic metabolic disorders which are caused by defects in biosynthetic pathways of glycoproteins. The screening test for N-glycosylation disorders is the analyses of sialylated isoforms of serum transferrin (Tf) by means of isoelectric focusing (IEF). Two distinct pathological IEF patterns of Tf are observed. A type I pattern is cha- racterized by a decrease of tetra- and an increase of di- and asialotransferrin, whereas a type II pattern shows in addition an increase of tri- and monosialotransferrin. The aims of diploma thesis were: 1) to evaluate reference range for spectrum of sialylated forms of Tf separated by IEF and 2) to perform biochemical and molecular analyses in three patients (P1-P3) with clinical suspicion for CDG. Serum and genomic DNA from three patients with clinical suspicion for CDG and family members of P1 were analysed. Sera from 99 healthy volunteers within the age range of 2-42 years served as a control group. Tf was analysed by IEF with direct immunofixation, SDS-PAGE and Western blot using specific antibody against human Tf (Dako). Profiles of Tf were quantified by AlphaEaseFC software (Alpha Innotech). Data were analysed by software STATISTICA 9.0 (StatSoft). TF a PMM2 genes were analysed...