Structural identifiability analysis of some highly structured families of statespace models using differential algebra

In this paper we identify biologically relevant families of models whose structural identifiability analysis could not be performed with available techniques directly. The models considered come from both the immunological and epidemiological literature.     

Effect of temperature and guanidine hydrochloride on ferrocytochrome<Emphasis Type="Italic"> c</Emphasis> at neutral pH

Thermally denatured horse heart ferrocytochrome c (ferrocyt c) has been characterized using absorption spectroscopy, differential scanning calorimetry (DSC) and viscometry at pH 7.0. DSC experiments have yielded the transition temperature of denaturant-free ferrocyt c unfolding as 100.6±0.3 °C, indicating an extremely high stability of the protein. The presence of guanidine hydrochloride (GdnHCl) facilitated estimation of the structural features of thermally unfolded ferrocyt c. The stability of the protein, expressed by G _D at 25 °C, is 59±5 kJ mol^–1 (DSC) and 65±6 kJ mol^–1 (absorption spectroscopy). An absorption spectrum of ferrocyt c demonstrates that the heme occurs in the high-spin state at extreme denaturing conditions (94 °C, 6.6 M GdnHCl). Absorption spectroscopy, using heme as a probe, shows that thermal denaturation of ferrocyt c occurs as a transition from a native low-spin (Met80/His18) to a high-spin disordered state with involvement of non-native, low-spin (bis-His) species.Abbreviations CD circular dichroism - cyt c cytochrome c - DSC differential scanning calorimetry - ferricyt c ferricytochrome c - ferrocyt c ferrocytochrome c - GdnHCl guanidine hydrochloride - NHE normal hydrogen electrode     

Molecular cloning of protamine-2 and expression with aging in Japanese monkey (<Emphasis Type="Italic">Macaca fuscata</Emphasis>)

In order to isolate genes relating spermatogenesis with postnatal development and aging, we have attempted to obtain genes showing differences in expression in testis of Japanese monkeys (Macaca fuscata) by means of differential display PCR, and we have cloned, sequenced and characterized protamine-2 (PRM2) of Japanese monkey. The predicted open reading frame encoded a protein of 103 amino acid residues, most of which are common to those of other mammals. Northern analysis revealed that the PRM2 gene is expressed at adult and aged stages, but not at the juvenile stage. In situ hybridization revealed that the PRM2 gene is expressed mainly in late spermatids and its expressional potential is decreased from adult to aged stages. It suggests that PRM2 in spermiogenesis is mediated by the age of the animal.     

Differential RNA interference: replacement of endogenous with recombinant low density lipoprotein receptor-related protein (LRP)

The interpretation of experiments involving the overexpression of a recombinant cDNA is often hampered by the interference of mRNA expression from the endogenous gene locus. Unless cell lines from naturally occurring mutations or knockout mice are available, difficult and time-consuming gene targeting techniques are required to inhibit endogenous gene expression. Using a method we refer to as "differential RNA interference" we demonstrate that RNA interference can be used to selectively suppress endogenous gene expression without affecting the expression of a co-transfected recombinant version of the same protein. Functional analyses of recombinant low density lipoprotein receptor-related protein (LRP) to study its involvement in lipid metabolism have been shown to be extremely difficult due to its large cDNA and the unavailability of suitable LRP-deficient cell lines. We constructed an expression vector containing the full-length coding sequence of human LRP fused to EGFP and a vector expressing small hairpin RNA directed against the 3'-untranslated region of the wild-type human LRP mRNA (LRP-shRNA). When overexpressed, EGFP-tagged LRP colocalizes with endogenous LRP and stimulates the uptake of LRP ligands. Overexpression of LRP-shRNA vectors significantly inhibits LRP expression, as judged by quantitative RT-PCR, Western blot and immunofluorescence analysis, and it dramatically decreases receptor-associated protein (RAP) uptake. Finally, co-transfection of EGFP-LRP and LRP-shRNA vectors demonstrates selective inhibition of endogenous LRP expression without affecting simultaneous expression of recombinant LRP protein. Thus, utilization of "differential RNA interference" provides a new experimental approach to selectively study the function of any recombinant protein in any given cell line without interference of endogenous protein expression.     

Mechanisms of hydrazine toxicity in rat liver investigated by proteomics and multivariate data analysis

A proteomics approach combined with multivariate data analysis was used to examine the hepatotoxic effect of hydrazine in 30 male Sprague Dawley rats, assigned to four treatment groups and two control groups. Liver samples from the individual animals were resolved by two-dimensional differential gel electrophoresis (2-D DIGE) and protein patterns from the 2-D gels were analyzed by principal component analysis (PCA) and partial least squares regression (PLSR). The PCA plot was able to describe the variation in the protein expression related to dose and time, by separation or clustering of different animal groups. PLSR followed by variable selection (Jack-knifing) was used to select proteins that varied significantly in relation to the dose related response of the hydrazine treatment. The 10 up-regulated and 10 down-regulated proteins with highest rank in the PLSR model were identified by mass spectrometry. Hydrazine treatment induced altered expression of proteins related to lipid metabolism, Ca(2+) homeostasis, thyroid hormone pathways and stress response. Several of the identified proteins have not previously been implicated in hydrazine toxicity and may thus be regarded as new potential biomarkers of induced liver toxicity.     

A review of bioinformatics degrees in Australia

Bioinformatics has been a hot topic in Australia's biotechnology circles for the past five years. As with biotechnology in the 1990s, there has been a sudden increase in the number of Bioinformatics undergraduate degrees. For students in the 2005 intake there are six undergraduate Bioinformatics degrees to choose from and another five Bioinformatics streams within a Bachelor of Science degree. The courses vary from three to four years of full-time study. This report aims at dissecting each of these degrees to determine where the differences lie, to give the prospective students an idea as to which degree suits their career goals and to give an overview of the pedagogy of Australian bioinformatics education.     

Decreased expression of the pancreatic secretory trypsin inhibitor II gene during aging of the rat liver

The genetic constitution and differential gene expression of an organism play important roles in controlling the species-specific rate of aging and the maximum life span potential. We utilized a differential-display polymerase chain reaction technique to identify the age-dependent expression of genes in the rat liver. We demonstrate in this report, for the first time, that expression of the pancreatic secretory trypsin inhibitor II (PSTI-II) gene declines drastically during aging. We confirmed this decrease by Northern blot analysis. Low PSTI-II levels in aged animals might result in a lack of protection from prematurely activated trypsin-like proteases, which would thus enhance inflammation.Supported by funds from the Department of Biotechnology and by Research Fellowships (to H.P. and G.Z.) from the Council of Scientific and Industrial Research (Government of India).     

Differential pulse anodic voltammetric determination of pantoprazole in pharmaceutical dosage forms and human plasma using glassy carbon electrode

Pantoprazole is used as an anti-ulcer drug through inhibition of H(+), K(+)-adenosine 5(')-triphosphatase in gastric parietal cells. It reduces the gastric acid secretion regardless of the nature of stimulation. The use of differential pulse voltammetry for the determination of pantoprazole in pharmaceutical dosage forms and human plasma using a glassy carbon electrode has been examined. The best voltammetric response was reached for a glassy carbon electrode in Britton-Robinson buffer solution of pH 5.0 submitted to a scan rate of 20.0 mVs(-1) and a pulse amplitude of 50.0 mV. This electroanalytical procedure was able to determine pantoprazole in the concentration range 6.0 x 10(-6)-8.0 x 10(-4)M. Precision and accuracy of the developed method was checked with recovery studies. The limit of detection and limit of quantitation were found to be 4.0 x 10(-7) and 9.0 x 10(-7)M, respectively. Rapidity, precision, and good selectivity were also found for the determination of pantoprazole in pharmaceutical dosage forms and human plasma. For comparative purposes high-performance liquid chromatography with a diode array and UV/VIS detection at 290.0 nm determination also was developed.     

Physicochemical characterization of silicon-containing glycolipids by DSC,FT-Raman spectroscopy and X-ray diffraction

Derivatives of dimethylalkylchlorosilanes are novel substances which may be used in formulations for drug targeting. In order to design their properties it is essential to perform physicochemical characterization. For this purpose, a combination of differential scanning calorimetry (DSC), FT-Raman spectroscopy and X-ray diffraction is well suited. For the starting material dimethyloctadecylchlorosilane (DMOC), the assignment of Raman bands is discussed. The influence of sugar-containing head groups on the structures of the hydrocarbon chains of 1-O-(dimethyldodecylsilyl)-[2,3,4,6-tetra-O-acetyl-beta-D-glucopyranoside] and 1-O-(dimethyloctadecylsilyl)-[2,3,4,6-tetra-O-acetyl-beta-D-glucopyranoside] was investigated using the band position of the symmetric methylene mode. The temperature dependence of conformationally sensitive bands in the CH(2)-stretching region (2800-2900 cm(-1)), C-C-stretching region (1000-1150 cm(-1)) and CH(3)-rocking region (830-900 cm(-1)) was studied to characterize the state of order of the alkyl chains. Using X-ray diffraction, the repeating distances of layered structures was determined. The phase transitions occurring were found to be completely reversible. The subcell of DMOC shows an orthorhombic perpendicular packing structure in the crystalline state.