Binding free energy calculations of galectin-3-ligand interactions

Galectins show remarkable binding specificity towards ß-galactosides.A recently developed method for calculating binding free energiesbetween a protein and its substrates has been used to evaluatethe binding specificity of galectin-3. Five disaccharides anda tetrasaccharide were used as the substrates. The calculatedbinding free energies agree quite well with the experimentaldata and the ranking of binding affinities is well reproduced.For all the six protein–ligand complexes it was observedthat electrostatic interactions oppose binding whereas the non-polarcontributions drive complex formation. The observed bindingspecificity of galectin-3 for galactosides rather than glucosidesis discussed in light of our results.     

Coeliac activity of the gliadin peptides CT-1 and CT-2

Summary The coeliac active peptide B 3142, which has been isolated from a peptic-tryptic digest of gliadin [1] and which consists of 53 amino-acid sequences [2], was partially hydrolyzed with -chymotrypsin. The two fragment peptides CT-1 (positions 1–22 of B 3142) and CT-2 (positions 23–53) were separated by high-performance liquid chromatography on octadecyl silica gel and purified by gel filtration on Biogel P2. The examination in the organ-culture test including 18 coeliac patients on normal diet and 7 control persons have shown that the toxicity is preserved after the chymotryptic treatment and that the peptides B 3142, CT-1 and CT-2 do not significantly differ from one another according to their coeliac-specific effect.

---

Coeliakieaktivitat der Gliadinpeptide CT-1 und CT-2

Zusammenfassung Das coeliakieaktive Peptid B 3142, das aus einem peptisch-tryptischen Partialhydrolysat von Gliadin gewonnen wurde [1] und aus einer Sequenz von 53 Aminosäureresten besteht [2], wurde mit -Chymotrypsin partiell hydrolysiert. Die beiden Fragment-peptide CT-1 (Positionen 1–22 von B 3142) und CT-2 (Positionen 23–53) wurden durch Hochdruckflüssig-keitschromatographie an Octadecyl-Kieselgel aufgetrennt und an Biogel P2 gereinigt. Die Prüfung im Organkultur-Test unter Einbeziehung von 18 Coeliakie-patienten unter Normalkost und von 7 Kontrollpersonen zeigte, daß die Toxizität nach chymotryptischer Spaltung erhalten bleibt, und daß sich die Peptide B 3142, CT-1 und CT-2 in ihrer coeliakiespezifischen Wirkung nicht wesentlich unterscheiden.

---

---

Supported by a grant from Deutsche Forschungsgemeinschaft. We gratefully acknowledge the excellent assistance given by Mrs. U. Schützler and Ms. B. Mosler     

Printing cotton fabrics with reactive dyes of high reactivity from an acidic printing paste

The behaviour of reactive dyes of high reactivity during the printing process of 100% cotton fabrics from an alkaline and acidic printing paste was studied in detail. The printing pastes were stored for different periods of time and then the fabrics were printed. The samples were subjected to two methods of fixation, the first by steaming and the second by thermofixation. The effects of different factors such as alkali and acid concentration, storage time of the printing pastes and method of fixation on the K/S values of the prints were investigated. The fastness properties of the printed areas were also measured to determine the improvement obtained by acidic printing with high-reactivity reactive dyes on cotton fabrics.     

Realization of a quantum gate using gravitational search algorithm by perturbing three-dimensional harmonic oscillator with an electromagnetic field

The aim of this paper is to design a current source obtained as a representation of p information symbols \(\{I_k\}\) so that the electromagnetic (EM) field generated interacts with a quantum atomic system producing after a fixed duration T a unitary gate U(T) that is as close as possible to a given unitary gate \(U_g\). The design procedure involves calculating the EM field produced by \(\{I_k\}\) and hence the perturbing Hamiltonian produced by \(\{I_k\}\) finally resulting in the evolution operator produced by \(\{I_k\}\) up to cubic order based on the Dyson series expansion. The gate error energy is thus obtained as a cubic polynomial in \(\{I_k\}\) which is minimized using gravitational search algorithm. The signal to noise ratio (SNR) in the designed gate is higher as compared to that using quadratic Dyson series expansion. The SNR is calculated as the ratio of the Frobenius norm square of the desired gate to that of the desired gate error.     

A user-friendly PC-based data acquisition and analysis system for respirometric investigations

We have developed an easy-to-use computer-based system for recording, displaying, storing and analyzing signals generated by Clark-type oxygen electrodes. A user-friendly interface of Windows-based program BioMed significantly increases the productivity of investigations. It allows to process, control, present and archive the experimental data in real time. A 12-bit analog-to-digital-converter, analog and digital filters, a possibility to zoom the obtained respiratory curves and calculation of the respiration rates by a linear regression method increase the resolution of the estimated oxygen consumption rates. The new system enables to register even small changes, such as 3-5 ngatoms O/min, in respiration rates of biological objects -- enzymes, mitochondria and permeabilized muscle fibers. The system has been developed and is regularly used for the respirometric investigations at the Laboratory of Biochemistry, Institute for Biomedical Research, Kaunas University of Medicine.     

Toxicity of different wheat gliadins in coeliac disease

Summary To determine the toxic effect of different gliadins on coeliac patients, which has been variably assessed in the literature, wheat prolamines (gliadin) were separated into the main fractions-, -, -, and-gliadins by chromatography on Sulfopropyl Sephadex C-50. The chemical compositions of the gliands were characterized by polyacrylamide gel electrophoresis, amino-acid analysis, determination of amide nitrogen and peptide maps.The peptide fractions B2 and B3 were isolated from the gliadins by a peptic tryptic digestion, ultrafiltration and gel filtration on Sephadex G-50.The gliadins and the peptide fractions were examined for coeliac activity by immunological tests (LIF tests) and by organ-culture tests.The results show that the peptide fractions are generally more active than their respective gliadins. The peptide fractions of all gliadins have a coeliac-specific toxic effect; their activities correlate with the chemical composition of the gliadins.

---

Untersuchungen von Gliadinfraktionen des Weizens auf Cöliakieaktivität

Zusammenfassung Zur Überprufung der teilweise widersprüchlichen Angaben in der Literatur über die cöliakieauslösende Wirkung einzelner Gliadinfraktionen wird Weizenprolamin (Gliadin) durch Ionenaustauschchromatographie an Sulfopropyl-Sephadex C-50 in die Hauptfraktionen-, -, - und-Gliadin aufgetrennt. Die Gliadine werden durch PAG-Elektrophorese, Aminosäureanalyse, Amid-N-Bestimmung und über die nach partieller enzymatischer Hydrolyse erhaltenen Peptidmuster in ihrer chemischen Zusammensetzung charakterisiert. Durch peptisch-tryptische Partialhydrolyse, Ultrafiltration und Gelchromatographie an Sephadex G-50 werden aus den einzelnen Gliadinen die Peptidfraktionen 132 und 133 gewonnen. Die Protein- und Peptidfraktionen werden in einem immunologischen Test (LIF-Test) bzw. in einem Organkultur-Test auf Cöliakieaktivität untersucht.Die Ergebnisse zeigen, daß die Peptidfraktionen durchweg größere Aktivität haben als die entsprechenden Proteine, und daß von den Peptidfraktionen aller Gliadine eine cöliakiespezifische Wirkung ausgeht, wobei die Aktivität mit der chemischen Zusammensetzung der Gliadine korreliert ist.

---

---

Supported by a grant from Stiftung Volkswagenwerk     

Generation and Selection of Specific Aptamers Targeting Brucella Species through an Enhanced Cell-SELEX Methodology

Brucellae are Gram-negative, aerobic, non-motile coccobacilli causing brucellosis in man and animals. The disease is one of the most significant yet neglected global zoonoses. Especially in developing countries, brucellosis is causing public health problems and economic losses to private animal owners and national revenues. Composed of oligonucleotides, aptamers are chemical analogues of antibodies that are promising components for developing aptamer-based rapid, sensitive, and specific tests to identify the Brucella group of bacteria. For this purpose, aptamers were generated and selected by an enhanced protocol of cell systematic evolution of ligands by exponential enrichment (cell-SELEX). This enhanced cell-SELEX procedure involved the combination of both conventional and toggle cell-SELEX to boost the specificity and binding affinity to whole Brucella cells. This procedure, combined with high-throughput sequencing of the resulting aptamer pools, comprehensive bioinformatics analysis, and wet lab validation assays, led to the selection of a highly sensitive and specific aptamer for those Brucella species known to circulate in Egypt. The isolated candidate aptamer showed dissociation constant (K_D) values of 43.5 ± 11, 61.5 ± 8, and 56 ± 10.8 nM for B. melitensis, B. abortus, and B. suis, respectively. This is the first development of a Brucella-specific aptamer using an enhanced combination of conventional and toggle cell-SELEX to the authors’ best knowledge.     

Morphology,Mineralogy and Mixing of Individual Atmospheric Particles Over Kanpur (IGP): Relevance of Homogeneous Equivalent Sphere Approximation in Radiative Models

Estimation of the direct radiative forcing (DRF) by atmospheric particles is uncertain to a large extent owing to uncertainties in their morphology (shape and size), mixing states, and chemical composition. A region-specific database of the aforementioned physico-chemical properties (at individual particle level) is necessary to improve numerically-estimated optical and radiative properties. Till date, there is no detailed observation of the above mentioned properties over Kanpur in the Indo-Gangetic Plain (IGP). To fill this gap, an experiment was carried out at Kanpur (IITK; 26.52°N, 80.23°E, 142 m msl), India from April to July, 2011. Particle types broadly classified as (a) Cu-rich particles mixed with carbon and sulphur (b) dust and clays mixed with carbonaceous species (c) Fe-rich particles mixed with carbon and sulfur and (d) calcite (CaCO₃) particles aged with nitrate, were observed. The frequency distributions of aspect ratio (AR; indicator of extent of particle non-sphericity) of total 708 particles from April to June reveal that particles with aspect ratio range >1.2 to ≤1.4 were abundant throughout the experiment except during June when it was found to shift to high AR range, >1.4 to ≤1.6 (followed with another peak of AR i.e. >2 to ≤2.4) due to dust storm conditions enhancing the occurrence of more non-spherical particles over the sampling site. The spherical particles (and close to spherical shape; AR range, 1.0 to ≤1.2) were found to be <20% throughout the experiment with a minimum (11.5%) during June. Consideration of Homogeneous Equivalent Sphere Approximation (HESA) in the optical/radiative model over the study region is found to be irrelevant during the campaign.