No description available.

No description available.

This study was conducted to compare the availability of Zn from two Zn sources, an amino acid chelate and ZnSO₄. In three experiments, 78 Zn depleted and 24 Zn adequate pigs were used. Pigs were depleted of Zn by feeding an isolated soy protein, semi purified diet containing 17 ppm Zn. Of the 78 depleted pigs, 60 pigs were Zn repleted. During Zn repletion in Exp. 1, depleted pigs were fed the low Zn diet supplemented with 5, 15, or 45 ppm Zn either as ZnSO₄ or as Zn amino acid chelate (ZnAAC). In Exp. 2 and 3, low Zn diets were only supplemented with 45 ppm Zn. Zinc adequate pigs, used in Exp. 1 and 2, were fed the 45 ppm supplemental Zn diets. To evaluate differences in site and rate of apparent Zn absorption, chromic oxide was added to the diets of depleted pigs in Exp. 1 and 3. In all experiments, a 24-d period was sufficient to severely deplete the porcine body Zn stores, and to cause parakeratosis and growth retardation. Serum Zn concentrations and serum ALP-activities of depleted pigs dramatically decreased (P < .01) during the first 14 d of Zn depletion. At the end of Zn depletion, Zn contents in liver, kidney, pancreas, brain, and small intestine tissues of pigs fed the low Zn diet were reduced (P < .01) by 10 to 40 % compared with the adequate pigs fed the ZnSO₄ and ZnAAC diets. In Exp. 2, the growth retardation was associated with a low (P < .05) serum mitogenic activity and pituitary RNA content of depleted pigs compared with pair-fed adequate pigs. Moreover, the growth hormone mRNA fraction tended to be reduced (P < .10) for the Zn depleted pigs. In Exp. 1, the apparent absorption of Zn was higher (P < .01) for pigs fed ZnAAC compared with the ZnSO₄ group; however, this was not confirmed in Exp. 3 unless coefficients were corrected for Cr recovery. Furthermore, absorption of Zn occurred primarily within jejunal and distal segments of the small intestine. In the balance of Exp. 3, disappearance rates of Zn, Cu, Fe and DM were higher (P < .01) in depleted pigs fed ZnAAC compared with ZnSO₄. The recovery of Cr also was different (P < .01) between pigs fed the ZnSO₄ (87 %) and ZnAAC (70 %) diets. Moreover, the moisture content of the fecal matter was 11 % higher (P < .01) for the ZnAAC group compared with pigs fed ZnSO₄. In Exp. 1, depleted pigs fed the 15 ppm ZnSO₄ and ZnAAC diets regained their ability to grow, however, replenishment of body fluid and tissue Zn pools did not occur within the 24-d Zn repletion period. Both the 5 ppm ZnSO₄ and ZnAAC groups did not respond to Zn repletion within a 12-d period. In all experiments, the rate and degree of repletion of body fluid and tissue Zn stores was not different between pigs fed the 45 ppm ZnSOq and ZnAAC diets, although a higher (P < .05) serum mitogenic activity was observed for the adequate pigs fed ZnAAC compared with ZnSO4. In conclusion, an amino acid chelate did not improve growth, or rate and degree of replenishment of body fluid and tissue levels of Zn compared with pigs fed ZnSO₄. However, ZnAAC may have influenced intestinal luminal conditions since a higher rate of disappearance of Zn, Cu, Fe, Cr, and DM was measured. / Ph. D.

No / The L-glutamate transporter GLT-1 is an abundant central nervous system (CNS) membrane protein of the excitatory amino acid transporter (EAAT) family that controls extracellular L-glutamate levels and is important in limiting excitotoxic neuronal death. Using reverse transcription-polymerase chain reaction, we have determined that four mRNAs encoding GLT-1 exist in mouse brain, with the potential to encode four GLT-1 isoforms that differ in their N and C termini. We expressed all four isoforms (termed MAST-KREK, MPK-KREK, MAST-DIETCI, and MPK-DIETCI according to amino acid sequence) in a range of cell lines and primary astrocytes and show that each isoform can reach the cell surface. In transfected human embryonic kidney (HEK) 293 or COS-7 cells, all four isoforms support high-affinity sodium-dependent L-glutamate uptake with identical pharmacological and kinetic properties. Inserting a viral epitope (tagged with V5, hemagglutinin, or FLAG) into the second extracellular domain of each isoform allowed coimmunoprecipitation and time-resolved Forster resonance energy transfer (tr-FRET) studies using transfected HEK-293 cells. Here we show for the first time that each of the four isoforms is able to combine to form homomeric and heteromeric assemblies, each of which is expressed at the cell surface of primary astrocytes. After activation of protein kinase C by phorbol ester, V5-tagged GLT-1 is rapidly removed from the cell surface of HEK-293 cells and degraded. This study provides direct biochemical evidence for oligomeric assembly of GLT-1 and reports the development of novel tools to provide insight into the trafficking of GLT-1.

Obwohl die methodische Entwicklung der Peptidsynthese gewöhnlich eine automatisierte Herstellung erlaubt, sind für die Herstellung einer Reihe von Peptiden auch gegenwärtig Grenzen gesetzt. Einerseits kann eine im Verlauf der Kettenverlängerung auftretende Bildung intra- und /oder intermolekularer Wasserstoffbrücken zu einer begrenzten Solvatation und damit Zugänglichkeit der zu acylierenden Aminokomponente am Syntheseharz führen, andererseits kommt es beim Einbau sterisch anspruchsvoller Aminosäuren zu ungenügenden Acylierungsausbeuten. Urethangeschützte Aminosäurefluoride haben sich für den Einbau von alpha, alpha-Dialkylaminosäuren als geeignet erwiesen. Die reaktiveren urethangeschützten Aminosäurechloride sind zwar herstellbar, besitzen aber in Gegenwart einer Hilfsbase, die zum Abfangen der während ihrer Reaktion gebildeten HCl notwendig ist, eine zu geringe Stabilität (Oxazolonbildung, Abspaltung der Schutzgruppen). Erst die Verwendung von N(alpha)-Schutzgruppen, die keinen reaktionsfähigen Carbonylkohlenstoff enthalten, wie Arensulfonyl- Schutzgruppen, ermöglichen die volle Ausschöpfung der hohen Reaktivität der Aminosäurechloride. Mit Hilfe dieser Schutzgruppen gelang ein erster Vergleich der Reaktivität der Aminosäurechloride und -fluoride. Bei den durchgeführten Reaktionen wurde keine Stereomutation beobachtet. Unter Verwendung von Arensulfonylschutzgruppen war es erstmals möglich, zwei aufeinanderfolgende N-Alkyl-alpha, alpha-dialkylaminosäuren in Peptide einzubauen. Weiterhin konnten wir zeigen, daß derart geschützte Aminosäuren sich für in situ Aktivierungen mit Thionylchlorid eignen. Als Fänger für überschüssiges Aktivierungsreagenz wurden tertiäre Alkohole bzw. Amine eingesetzt. Arensulfonyl-geschützte Aminosäurechloride haben wir darüber hinaus erfolgreich in der Festphasenpeptidsynthese verwendet. In Kombination von Arensylfonyl-Schutz mit der Standard-Fmoc-Strategie gelang die Synthese eines biologisch aktiven Analogen des CRF, eines 41-mer Peptides mit einer eingefügten Tetrapeptidsequenz -Ala-MeAib-MeAib-Aib-. / Despite its wide field of application automatic peptide synthesis is still limited in certain cases. One of the limiting factors is the possibility of intra- or intermolecular hydrogen bond formation during the elongation of the peptide chain. This causes decreased solvation and thus reduced accessibility to the resin-bound amino component. Another limitation is the incorporation of sterically hindered amino acids that usually give rise to insufficient yields of acylation. Urethane protected amino acid fluorides have been shown suitable for the incorporation of alpha,alpha-dialkyl amino acids. Though the more reactive urethane protected amino acid chlorides can be readily synthesized, they do not possess the necessary stability in the presence of an auxiliary base that must be used for trapping of the hydrochloric acid formed during the reaction. Formation of oxazolons and deprotection of formerly protected functional groups would occur. Only the advent of protecting groups for the amino acid N-alpha that do not have a reactive carbonyl function - like arene sulfonyl groups - allowed to take full advantage of the high reactivity of the amino acid chlorides. These protecting groups enabled us to compare the reactivities of amino acid chlorides and fluorides for the first time. We didn't observe any stereo mutation in our experiments. The use of arene sulfonyl protecting groups permitted the consecutive incorporation of two N-alkyl-alpha,alpha-dialkyl amino acids into a peptide for the first time. Furthermore we could show, that amino acids protected in this way, are suitable for in situ activation with thionyl chloride. Tertiary alcohols and amines were used as scavenger for excessive activating reagent. Arene sulfonyl protected amino acids were also successfully used in solid phase peptide synthesis. By combining this protecting concept with the standard Fmoc approach we were able to synthesize a biologically active analogue of CRF, a peptide containing 41 residues into which we inserted the tetrapeptide Ala-MeAib-MeAib-Aib.

No description available.

No description available.

Protein sequencing has produced overwhelming amount of protein sequences, especially in the last decade. Nevertheless, the majority of the proteins' functional and structural classes are still unknown, and experimental methods currently used to determine these properties are very expensive, laborious and time consuming. Therefore, automated computational methods are urgently required to accurately and reliably predict functional and structural classes of the proteins. Several bioinformatics methods have been developed to determine such properties of the proteins directly from their sequence information. Such methods that involve signal processing methods have recently become popular in the bioinformatics area and been investigated for the analysis of DNA and protein sequences and shown to be useful and generally help better characterise the sequences. However, there are various technical issues that need to be addressed in order to overcome problems associated with the signal processing methods for the analysis of the proteins sequences. Amino acid indices that are used to transform the protein sequences into signals have various applications and can represent diverse features of the protein sequences and amino acids. As the majority of indices have similar features, this project proposes a new set of computationally derived indices that better represent the original group of indices. A study is also carried out that resulted in finding a unique and universal set of best discriminating amino acid indices for the characterisation of allergenic proteins. This analysis extracts features directly from the protein sequences by using Discrete Fourier Transform (DFT) to build a classification model based on Support Vector Machines (SVM) for the allergenic proteins. The proposed predictive model yields a higher and more reliable accuracy than those of the existing methods. A new method is proposed for performing a multiple sequence alignment. For this method, DFT-based method is used to construct a new distance matrix in combination with multiple amino acid indices that were used to encode protein sequences into numerical sequences. Additionally, a new type of substitution matrix is proposed where the physicochemical similarities between any given amino acids is calculated. These similarities were calculated based on the 25 amino acids indices selected, where each one represents a unique biological protein feature. The proposed multiple sequence alignment method yields a better and more reliable alignment than the existing methods. In order to evaluate complex information that is generated as a result of DFT, Complex Informational Spectrum Analysis (CISA) is developed and presented. As the results show, when protein classes present similarities or differences according to the Common Frequency Peak (CFP) in specific amino acid indices, then it is probable that these classes are related to the protein feature that the specific amino acid represents. By using only the absolute spectrum in the analysis of protein sequences using the informational spectrum analysis is proven to be insufficient, as biologically related features can appear individually either in the real or the imaginary spectrum. This is successfully demonstrated over the analysis of influenza neuraminidase protein sequences. Upon identification of a new protein, it is important to single out amino acid responsible for the structural and functional classification of the protein, as well as the amino acids contributing to the protein's specific biological characterisation. In this work, a novel approach is presented to identify and quantify the relationship between individual amino acids and the protein. This is successfully demonstrated over the analysis of influenza neuraminidase protein sequences. Characterisation and identification problem of the Influenza A virus protein sequences is tackled through a Subgroup Discovery (SD) algorithm, which can provide ancillary knowledge to the experts. The main objective of the case study was to derive interpretable knowledge for the influenza A virus problem and to consequently better describe the relationships between subtypes of this virus. Finally, by using DFT-based sequence-driven features a Support Vector Machine (SVM)-based classification model was built and tested, that yields higher predictive accuracy than that of SD. The methods developed and presented in this study yield promising results and can be easily applied to proteomic fields.

The production of Nitric Oxide (NO) under physiological conditions has beneficial roles in acting as a key signaling component of many biological processes as well as having an anti-microbial effect. However its effects following excess production by the inducible NO pathway is potentially detrimental in the pathogenesis of chronic inflammation including sepsis and several other inflammatory diseases. Understanding the mechanisms that regulate the expression of the inducible nitric oxide synthase (iNOS) responsible for producing the excessive amounts of NO in disease states is therefore critical. In this regards, experiments were carried out to identify the signaling pathways that may mediate this process, focusing specifically on the JAK/STAT cascade. The reason for selecting the latter is because our research group, amongst others, has carried out extensive work investigating other signaling pathways, including the mitogen activated kinases (MAPK). Moreover, studies have also been carried out in an attempt to identify the critical role of JAK/STAT signaling for iNOS induction. These studies however failed to conclusively demonstrate whether, as with the MAPKs, the JAK/STATs may also play an essential role. Furthermore there is indeed controversy in the literature with researchers unable to agree whether expression of iNOS does require JAK/STAT activation. Thus, the aim of the project described in this thesis was to establish unequivocally whether activation of the JAK/STATs preceeds induction of iNOS. The studies were extended to L-arginine transport as well because the latter is widely reported to be induced in parallel with iNOS and substrate supply to iNOS may be critical for sustained NO production. Changes in transporter activity as well as their expression profiles were assessed. All experiments were carried out in either rat aortic smooth muscle cells (RASMCs) or in the J774 macrophage cell line. These cell types were selected because RASMCs are one of the prime targets for induced NO production in vascular inflammation and the macrophages are involved in host defence, acting in part through NO production. To establish the role of JAK/STATs, pharmacological and molecular approaches were used. Pharmacologically, two inhibitors were used and these were AG490 and JAK inhibitor I. The former is reported to be a selective JAK2 inhibitor and the other blocks all known JAK proteins. The potential of the GTPases to regulate the induction of iNOS was also examined using selective inhibitor known to regulate these proteins. In addition to these drugs, siRNA targeting JAK2 was also exploited and western blotting was extensively used to detect expression of various proteins including iNOS, native and phosphorylated JAK2 and TYK2. Changes in iNOS activity was monitored by determining nitrite production using the Griess assay and L-arginine transport was monitored using tritiated arginine (L-[3H]arginine). RASMCs were treated with a combination of LPS (100 µg/ml) and IFN- (100 U/ml) and the macrophages with LPS (1 µg/ml) to induce iNOS and transporter activity. Consistent with previous reports, the above treatment of both cell types resulted in the expression of iNOS, production of NO and enhanced transport of L-arginine. These effects were not affected by AG490 but blocked by JAK inhibitor I. Furthermore, although both cell types expressed the key JAKs (JAK2 and TYK2), neither of these proteins were phosphorylated under conditions of induced NO production. Moreover, siRNA experiments showed that JAK2 expression could be abolished without any significant change in NO production, confirming that at least JAK2 may not be required for this process. Whether TYK2 is involved still remains to be resolved as the phosphor-protein could not be detected. However the conclusive siRNA knockdown studies could not be carried out due to time and cost constraints. Apart from iNOS and NO production, changes in induced L-arginine transport were also not significantly affected under the experimental conditions described above suggesting that like with iNOS, induction of L-arginine transport is independent of at least JAK2. Interestingly however, STAT-1 was phosphorylated and this was blocked by JAK inhibitor I but not AG490. Thus, STAT-1 activation may be essential but its activation may be independent of the JAKs. One possible alternate upstream activator of STAT-1 may be the GTPases. Indeed these proteins have been indicated to phosphorylate STAT-1 independent of the JAKs. However, in this project, inhibition of the GTPase pathway enhanced NO production and L-arginine transport suggesting that the GTPases downregulate these processes. In conclusion, the studies carried out in this thesis have shown that induction of iNOS, NO production and L-arginine transport in both RASMCs and J774 macrophages are independent of JAK2 but require STAT-1 activation which may be phosphorylated independently of the JAKs. The role of other JAKs such as TYK2 although unlikely, will need to be resolved using a more specific approach such as siRNA.

This thesis examines the dynamic mechanical properties of natural silk fibres, mainly from silkworm species Bombyx mori (B. mori) and spider species Nephila edulis, using dynamic mechanical thermal analysis, DMTA. The aim is not only to provide novel data on mechanical properties of silk, but also to relate these properties to the structure and morphology of silk. A systematic approach is adopted to evaluate the effect of the three principal factors of stress, temperature and hydration on the properties and structure of silk. The methods developed in this work are then used to examine commercially important aspects of the ‘quality’ of silk. I show that the dynamic storage modulus of silks increases with loading stress in the deformation through yield to failure, whereas the conventional engineering tensile modulus decreases significantly post-yield. Analyses of the effects of temperature and thermal history show a number of important effects: (1) the loss peak at -60 °C is found to be associated the protein-water glass transition; (2) the increase in the dynamic storage modulus of native silks between temperature +25 and 100 °C is due simply to water loss; (3) a number of discrete loss peaks from +150 to +220°C are observed and attributed to the glass transition of different states of disordered structure with different intermolecular hydrogen bonding. Excess environmental humidity results in a lower effective glass transition temperature (Tg) for disordered silk fractions. Also, humidity-dynamic mechanical analysis on Nephila edulis spider dragline silks has shown that the glass transition induces a partial supercontraction, called Tg contraction. This new finding leads to the conclusion of two independent mechanisms for supercontraction in spider dragline silks. Study of three commercial B. mori cocoon silk grades and a variety of processed silks or artificial silks shows that lower grade and poorly processed silks display lower Tg values, and often have a greater loss tangent at Tg due to increased disorder. This suggests that processing contributes significantly to the differences in the structural order among natural or unnatural silks. More importantly, dynamic mechanical thermal analysis is proposed to be a potential tool for quality evaluation and control in silk production and processing. In summary, I demonstrate that DMTA is a valuable analytical tool for understanding the structure and properties of silk, and use a systematic approach to understand quantitatively the important mechanical properties of silk in terms of a generic structural framework in silk proteins.