Periodic patterns in distributions of peptide masses

We are investigating the distribution of the number of peptides for given masses, and especially the observation that peptide density reaches a local maximum approximately every 14Da. This wave pattern exists across species (e.g. human or yeast) and enzyme digestion techniques. To analyze this phenomenon we have developed a mathematical method for computing the mass distributions of peptides, and we present both theoretical and empirical evidence that this 14-Da periodicity does not arise from species selection of peptides but from the number- theoretic properties of the masses of amino acid residues. We also describe other, more subtle periodic patterns in the distribution of peptide masses. We also show that these periodic patterns are robust under a variety of conditions, including the addition of amino acid modifications and selection of mass accuracy scale. The method used here is also applicable to any family of sequential molecules, such as linear hydrocarbons, RNA, single- and double-stranded DNA.     

Are heat waves susceptible to mitigate the expansion of a species progressing with global warming?

A number of organisms, especially insects, are extending their range in response of the increasing trend of warmer temperatures. However, the effects of more frequent climatic anomalies on these species are not clearly known. The pine processionary moth, Thaumetopoea pityocampa, is a forest pest that is currently extending its geographical distribution in Europe in response to climate warming. However, its population density largely decreased in its northern expansion range (near Paris, France) the year following the 2003 heat wave. In this study, we tested whether the 2003 heat wave could have killed a large part of egg masses. First, the local heat wave intensity was determined. Then, an outdoor experiment was conducted to measure the deviation between the temperatures recorded by weather stations and those observed within sun‐exposed egg masses. A second experiment was conducted under laboratory conditions to simulate heat wave conditions (with night/day temperatures of 20/32°C and 20/40°C compared to the control treatment 13/20°C) and measure the potential effects of this heat wave on egg masses. No effects were noticed on egg development. Then, larvae hatched from these egg masses were reared under mild conditions until the third instar and no delayed effects on the development of larvae were found. Instead of eggs, the 2003 heat wave had probably affected directly or indirectly the young larvae that were already hatched when it occurred. Our results suggest that the effects of extreme climatic anomalies occurring over narrow time windows are difficult to determine because they strongly depend on the life stage of the species exposed to these anomalies. However, these effects could potentially reduce or enhance the average warming effects. As extreme weather conditions are predicted to become more frequent in the future, it is necessary to disentangle the effects of the warming trend from the effects of climatic anomalies when predicting the response of a species to climate change.     

First results on label-free detection of DNA and protein molecules using a novel integrated sensor technology based on gravimetric detection principles

A novel integrated bio-sensor technology based on thin-film bulk acoustic wave resonators on silicon is presented and the feasibility of detecting DNA and protein molecules proofed. The detection principle of these sensors is label-free and relies on a resonance frequency shift caused by mass loading of an acoustic resonator, a principle very well known from quartz crystal micro balances. Integrated ZnO bulk acoustic wave resonators with resonance frequencies around 2 GHz have been fabricated, employing an acoustic mirror for isolation from the silicon substrate. DNA oligos have been thiol-coupled to the gold electrode by on-wafer dispensing. In a further step, samples have either been hybridised or alternatively a protein has been coupled to the receptor. The measurement results show the new bio-sensor being capable of both, detecting proteins as well as the DNA hybridisation without using a label. Due to the substantially higher oscillation frequency, these sensors already show much higher sensitivity and resolution comparable to quartz crystal micro balances. The potential for these sensors and sensors arrays as well as technological challenges will be discussed in detail.     

Automated multiple structure alignment and detection of a common substructural motif

While a number of approaches have been geared toward multiple sequence alignments, to date there have been very few approaches to multiple structure alignment and detection of a recurring substructural motif. Among these, none performs both multiple structure comparison and motif detection simultaneously. Further, none considers all structures at the same time, rather than initiating from pairwise molecular comparisons. We present such a multiple structural alignment algorithm. Given an ensemble of protein structures, the algorithm automatically finds the largest common substructure (core) of C(alpha) atoms that appears in all the molecules in the ensemble. The detection of the core and the structural alignment are done simultaneously. Additional structural alignments also are obtained and are ranked by the sizes of the substructural motifs, which are present in the entire ensemble. The method is based on the geometric hashing paradigm. As in our previous structural comparison algorithms, it compares the structures in an amino acid sequence order-independent way, and hence the resulting alignment is unaffected by insertions, deletions and protein chain directionality. As such, it can be applied to protein surfaces, protein-protein interfaces and protein cores to find the optimally, and suboptimally spatially recurring substructural motifs. There is no predefinition of the motif. We describe the algorithm, demonstrating its efficiency. In particular, we present a range of results for several protein ensembles, with different folds and belonging to the same, or to different, families. Since the algorithm treats molecules as collections of points in three-dimensional space, it can also be applied to other molecules, such as RNA, or drugs.     

The fine structure of the adipose cell of the leech Glossiphonia complanata

The two distinct types of cytoplasm seen with the light microscope in the adipose cell of the leech Glossiphonia complanata have been identified in the electron microscope image of this cell. One of these, the basophil cytoplasm, contains many well oriented, paired membranes which are much more clearly evident when calcium ions are added to the fixative. The membranes sometimes appear as concentric arrays of lamellae and are thought to represent sections through a phospholipide-containing body. The paired membranes and the concentric lamellae have granules attached to them and resemble in size and structure the membranes of the endoplasmic reticulum encountered in many mammalian cells. Small dense cytoplasmic particles are present throughout the cell; they may be ferritin molecules, derived from the breakdown of haemoglobin taken in as food. On the basis of a previous histochemical study and the present electron microscope investigation, it is suggested that these paired membranes are similar to the organized type of mammalian ER and the results seem to confirm the belief that these membranes are composed of layers of phospholipoprotein together with attached particles of ribonucleoprotein.     

A 14-3-3γ dimer-based scaffold bridges CtBP1-S/BARS to PI(4)KIIIβ to regulate post-Golgi carrier formation

Large pleiomorphic carriers leave the Golgi complex for the plasma membrane by en bloc extrusion of specialized tubular domains, which then undergo fission. Several components of the underlying molecular machinery have been identified, including those involved in the budding/initiation of tubular carrier precursors (for example, the phosphoinositide kinase PI(4)KIIIβ, the GTPase ARF, and FAPP2), and in the fission of these precursors (for example, PKD, CtBP1-S/BARS). However, how these proteins interact to bring about carrier formation is poorly understood. Here, we describe a protein complex that mediates carrier formation and contains budding and fission molecules, as well as other molecules, such as the adaptor protein 14-3-3γ. Specifically, we show that 14-3-3γ dimers bridge CtBP1-S/BARS with PI(4)KIIIβ, and that the resulting complex is stabilized by phosphorylation by PKD and PAK. Disrupting the association of these proteins inhibits the fission of elongating carrier precursors, indicating that this complex couples the carrier budding and fission processes.     

An automated algorithm for sequence confirmation of chemically modified oligonucleotides by tandem mass spectrometry

We have developed a tandem mass spectrometry (MS/MS) data analysis program for confirmation of sequence of chemically modified oligonucleotides. The method is based on the analysis of deconvoluted MS/MS data for fragment ions from three charge states and comparison of these data against a set of computer-generated masses from expected fragmentation patterns. The algorithm compares the experimental masses not only against the fragment set predicted for the expected sequence but also against a wider test set covering all next-neighbor position switches of the original sequence and all pairwise swaps of nucleosides, which in synthesis would result in molecules with masses within a preset mass tolerance. The algorithm is capable of identifying incorrect sequences that would not be distinguished by identity testing with electrospray ionization mass spectrometry. The method has been tested with permutations of the two 21-mer single strands of a chemically modified short interfering RNA containing 2′-O-methyl and phosphorothioate linkages. For both strands, challenge sequences were synthesized and tested with the premise that they were the original sequences. The algorithm correctly reported the locations of next-neighbor position switches and nucleoside swaps. The results confirm the approach as useful for MS/MS-based identity test methods for synthetic oligonucleotides.     

Preparation and characterization of immunoconjugates for antibody-targeted photolysis.

Monoclonal antibody (MAb)-dextran-tin(IV) chlorin e6 (SnCe6) immunoconjugates were prepared by a new technique involving the use of reducing, terminal-modified dextran carriers and site-specific modification of the Fc oligosaccharide moiety on the antibodies. Dextran carriers were synthesized to increase the number of SnCe6 molecules attached to a MAb. The dextran carriers were coupled to the MAb via a single, chain-terminal hydrazide group to prevent aggregation of MAbs. Conjugates were prepared with antimelanoma MAb 2.1 containing up to 18.9 SnCe6 molecules per MAb. Under neutral conditions, no hydrolysis of the hydrazone bond between the MAb and the dextran carrier could be detected, and the hydrazone was not stabilized by reduction with NaCNBH3 or NaBH4. Analysis of the purified immunoconjugates showed that approximately two dextran carrier chains were attached to a MAb regardless of the number of SnCe6 molecules linked to a dextran carrier. Site-specific covalent attachment of the SnCe6-dextran chains to the MAb was confirmed by SDS-PAGE. HPLC analysis of the conjugates gave a single species eluting in the range of 200-240 kDa. As determined by a competitive inhibition radioimmunoassay using viable SK-MEL-2 human malignant melanoma cells, the conjugates showed excellent retention of antigen-binding activity relative to unconjugated MAb.     

The Fine Structure of the Adipose Cell of the Leech Glossiphonia complanata

The two distinct types of cytoplasm seen with the light microscope in the adipose cell of the leech Glossiphonia complanata have been identified in the electron microscope image of this cell. One of these, the basophil cytoplasm, contains many well oriented, paired membranes which are much more clearly evident when calcium ions are added to the fixative. The membranes sometimes appear as concentric arrays of lamellae and are thought to represent sections through a phospholipide-containing body. The paired membranes and the concentric lamellae have granules attached to them and resemble in size and structure the membranes of the endoplasmic reticulum encountered in many mammalian cells. Small dense cytoplasmic particles are present throughout the cell; they may be ferritin molecules, derived from the breakdown of haemoglobin taken in as food. On the basis of a previous histochemical study and the present electron microscope investigation, it is suggested that these paired membranes are similar to the organized type of mammalian ER and the results seem to confirm the belief that these membranes are composed of layers of phospholipoprotein together with attached particles of ribonucleoprotein.     

Uptake and metabolism of exogenous glycosphingolipids by cultured cells

Exogenous glycosphingolipids, especially gangliosides, are used to study transport and metabolism of their endogenous counterparts as well as their role in cell adhesion, cell recognition and signal transduction. Unlike monodispersed solutes, in aqueous media ganglioside molecules aggregate into micelles (or bilayer structures) with a very low critical micellar concentration. Upon addition to cells in culture, exogenous gangliosides bind to the cell surface in three operationally defined modes: loosely associated micelles removable by serum; tightly attached micelles removable by proteases such as trypsin; and ganglioside molecules inserted into the outer leaflet of the plasma membrane. As shown by a biotin-labeled derivative of the ganglioside GM1 these inserted molecules are endocytosed and transported to intralysosomal membranes for catabolism. The benefit from using (partially) nondegradable as well as semi-truncated glycosphingolipids in transport studies is discussed.     

Synthesis and comparison of antibody recognition of conjugates containing herpes simplex virus type 1 glycoprotein D epitope VII

Synthetic oligopeptides comprising linear or continuous topographic B-cell epitope sequences of proteins might be considered as specific and small size antigens. It has been demonstrated that the strength and specificity of antibody binding could be altered by conjugation to macromolecules or by modification in the flanking regions. However, no systematic studies have been reported to describe the effect of different carrier macromolecules in epitope conjugates. To this end, the influence of carrier structure and topology on antibody recognition of attached epitope has been studied by comparing the antibody binding properties of a new set of conjugates with tetratuftsin analogue (H-[Thr-Lys-Pro-Lys-Gly](4)-NH(2), T20) sequential oligopeptide carrier (SOC(n)), branched chain polypeptide, poly[Lys(Ser(i)-DL-Ala(m))] (SAK), multiple antigenic peptide (MAP), and keyhole limpet hemocyanine (KLH). In these novel constructs, peptide (9)LKNleADPNRFRGKDL(22) ([Nle(11)]-9-22) representing an immunodominant B cell epitope of herpes simplex virus type 1 glycoprotein D (HSV-1 gD) was conjugated to polypeptides through a thioether or amide bond. Here we report on the preparation of sequential and polymeric polypeptides possessing chloroacetyl groups in multiple copies at the alpha- and/or epsilon-amino group of the polypeptides and its use for the conjugation of epitope peptides possessing Cys at C-terminal position. We have performed binding studies (direct and competitive ELISA) with monoclonal antibody (Mab) A16, recognizing the HSV gD-related epitope, [Nle(11)]-9-22, and conjugates containing identical and uniformly oriented epitope peptide in multiple copies attached to five different macromolecules as carrier. Data suggest that the chemical nature of the carrier and the degree of substitution have marked influence on the strength of antibody binding.     

Investigating the most appropriate methods for attached solids determination in moving-bed biofilm reactors

Moving-bed biofilm reactors (MBBR) have been employed worldwide as an efficient technology for the treatment of a diverse set of wastewaters. Although the attached biomass represents the major fraction of solids in MBBR systems, there is still no standard for its reliable quantification. An extensive literature review indicated that several methods for attached biomass assessment are applied, hindering the comparability of results issued from different studies. Therefore, the most reported methods for biofilm quantification in the MBBR literature were compared using three different carriers. The results revealed that the performance of each method was biased depending on the carrier type and shape. Moreover, differences in total attached solids (TAS) concentrations varied from 13% up to more than 90%, depending on the employed method for a given carrier. Overall, direct weighing of the carrier containing the biofilm, accounting for the clean carrier weight, and manual extraction of the biofilm, preceded or not by sonication for at least 15 min, were the most suitable techniques for assessing TAS and the volatile/total solids ratio in non-porous medias, respectively. The results here presented may be used as a frame of reference for standardization of the methods for assessing the biofilm mass in MBBR carriers.

     

Molecular genetics of biotin metabolism: old vitamin, new science

Biotin is a water-soluble vitamin that participates as a cofactor in gluconeogenesis, fatty acid synthesis and branched chain amino acid catabolism. It functions as the carboxyl carrier for biotin-dependent carboxylases. Its covalent attachment to carboxylases is catalyzed by holocarboxylase synthetase. Our interest in biotin has been through the genetic disease, "biotin-responsive multiple carboxylase deficiency," caused by deficient activity of holocarboxylase synthetase. As part of these studies, we made the unexpected findings that the enzyme also targets to the nucleus and that it catalyzes the attachment of biotin to histones. We found that patients with holocarboxylase synthetase deficiency have a much reduced level of biotinylated histones, yet the importance of this process is unknown. The dual nature of biotin, as the carboxyl-carrier cofactor of carboxylases and as a ligand of unknown function attached to histones, is an enigma that suggests a much more involved role for biotin than anticipated. It may change our outlook on the optimal nutritional intake of biotin and its importance in biological processes such as development, cellular homeostasis and regulation.     

Role of heparan sulfate proteoglycans in cell-cell signaling in Drosophila.

Heparan sulfate proteoglycans (HSPGs) are abundant molecules associated with the cell surface and extracellular matrix, and consist of a protein core to which heparan sulfate (HS) glycosaminoglycan (GAG) chains are attached. Although these molecules have been the focus of intense biochemical studies in vitro, their biological functions in vivo were unclear until recently. We have undertaken an in vivo functional study of HSPGs in Drosophila. Our studies, as well as others, demonstrate the critical roles of HSPGs in several major signaling pathways, including ibroblast growth factor (FGF), Wnt, Hedgehog (Hh) and TGF-beta. Our results also suggest that specific HS GAG chain modifications, as well as specific HSPG protein cores, are involved in specific signaling pathways.     

Quantification of bifunctional diethylenetriaminepentaacetic acid derivative conjugation to monoclonal antibodies by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

The results of the characterization of a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry-based method that was developed to establish the stoichiometry of CHX-A'-diethylenetriaminepentaacetic acid (DTPA) or benzyl-DTPA conjugated to a recombinant immunoglobulin G (IgG) are reported. This simple method does not require an accurate measurement of the sample protein concentration to accurately quantify the number of DTPA conjugated. It is also not necessary to thoroughly remove nonconjugated DTPA from the sample. The average number of moles of DTPA attached per mole of IgG was calculated from the difference in the observed masses of DTPA-IgG and nonconjugated IgG divided by the molecular weight of the DTPA derivative. As more DTPA is attached, the [M+H](+) peak of DTPA-IgG becomes broader and noisier. Also, the signal intensity in the mass spectrum decreases, apparently due to the increase in the heterogeneity in the number of DTPA attached to each molecule of IgG. The standard deviation of the measured mass and that of the stoichiometry of the DTPA attached per IgG increased as more DTPA was attached. The standard deviation, expressed as coefficient of variation for samples with 2 to 4 mol of DTPA attached per mole of IgG, was 8 to 9%.     

The pH and temperature dependence of the interaction of steroid hormones with the transport system of glucose in human erythrocytes.

The thermodynamic parameters deltaH degrees, deltaF degrees, deltaS degrees and the pH dependence of the interaction between steroids and the glucose carrier in human erythrocytes have been studied. The results indicate that, according to the structure of the steroids, hydrophilic as well as hydrophobic bonds can be involved in the association. For the binding of the C-21-steroids to the carrier the polarity rule has been observed to be valid. On the basis of the thermodynamic parameters it has been found that in the association process of the steroids with the carrier, simultaneous randomization of ordered water molecules is important.     

The Mutual Impact of Syndecan-1 and Its Glycosaminoglycan Chains—A Multivariable Puzzle

Proteoglycans, with their core proteins and attached glycosaminoglycan chains, are recognized as important partners in many biological processes, yet often experimental analysis of their molecular action is considered for only part of these molecules: either the protein or the carbohydrate unit. In this article, we have tried to summarize, with an example of the syndecan family in general and more specifically with syndecan-1, what is known considering the mutual influence of these different components, and we follow whether the nature of the glycosaminoglycan chains matters for these effects.     

Effects of positional and geometrical isomerism on the biological activity of some novel oxazolidinones

Some novel oxazolidinone derivatives with benzotriazole as pendant have been synthesized and tested for antibacterial activity. Linearly attached benzotriazole derivative showed more potency compared to angular one in vitro. Out of E/Z-isomers of angularly attached derivatives E-isomer was found to be more potent than Z-isomer. Either less active or inactive molecules were obtained, when benzotriazole was replaced with benzimidazole, benzthiazole, or benzoxazole. Finally, thioacetamide analogue of linear compound gave a lead having activity similar to linezolid in vitro.     

Real-time imaging of single DNA molecules with fluorescence microscopy.

A fluorescence microscopy technique was used to image the dynamics of individual DNA molecules. Lambda, calf thymus, cosmid (circular), and T4 DNA were studied with the fluorescent dye acridine orange. Experiments with DNAase I were conducted, and the results indicate that these observations correspond to DNA molecules. The results of experiments with circular DNA provide strong evidence that these were single DNA molecules. Molecules were observed free in solution or attached to a glass or copper surface at one or several points. The Brownian motion of these molecules was observed, indicating that DNA in solution exists in a partially supercoiled state. Some molecules appeared stretched and were attached to the surface by their termini; the lengths of these molecules were measured. Such molecules also exhibited elastic behavior upon breaking. The power of this technique is demonstrated in images of cosmid DNA molecules, catenanes, and DNA extending from T4 phage particles. These results suggest immediate applications to molecular biology, such as examining the dynamics of protein-DNA interactions. Areas of ongoing research are discussed.