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At least 145 records · Page 8Linked to original sources
PubMed2005

Botulinum toxins--cause of botulism and systemic diseases?

Toxins of Clostridium botulinum (types A-G) are known as 'neurotoxins', causing the clinically well-known picture of flaccid muscular paralysis. The molecular biological background is the blocking of acetylcholine secretion in neuromuscular junctions by enzymatic cleavage of molecules forming the machinery of exocytosis. Two 'non-neurotoxins' (types C2, C3) are produced by some strains of C. botulinum types C and D. These affect the cytoskeleton by ribosylating actin filaments. All these toxins are used as cell biological tools for the study of specific actions and effects in different eukaryotic cells. Pharmaceutical and molecular biological research has shown their influence on several crucial organs (or cell cultures thereof) of humans and animals (brain and spinal cord, cerebellum, hippocampus, hypophysis, pancreas, adrenal glands, salivary glands and others). Under natural conditions, botulinum toxins may pass the intestinal barrier and circulate in the bloodstream for a certain time. Carriers occurring naturally in food, such as wheat germ agglutinin, digitonin or saponin, and bacterial toxins such as streptolysin O, perfringolysins, C2 toxin or botulinolysin may also form pores in cell walls. They facilitate the entry of botulinum toxins into cells that may not have natural binding receptors. It is concluded that in vivo actions of different botulinum toxins after their entry into the organism may contribute to the onset of different diseases of hitherto cryptogenic origin. Some examples are given and future problems are discussed.

Animals↗
PubMed2005

Fluorescence microscopy today.

Fluorescence microscopy has undergone a renaissance in the last decade. The introduction of green fluorescent protein (GFP) and two-photon microscopy has allowed systematic imaging studies of protein localization in living cells and of the structure and function of living tissues. The impact of these and other new imaging methods in biophysics, neuroscience, and developmental and cell biology has been remarkable. Further advances in fluorophore design, molecular biological tools and nonlinear and hyper-resolution microscopies are poised to profoundly transform many fields of biological research.

Animals↗
PubMed2006

Taverna: a tool for building and running workflows of services.

Taverna is an application that eases the use and integration of the growing number of molecular biology tools and databases available on the web, especially web services. It allows bioinformaticians to construct workflows or pipelines of services to perform a range of different analyses, such as sequence analysis and genome annotation. These high-level workflows can integrate many different resources into a single analysis. Taverna is available freely under the terms of the GNU Lesser General Public License (LGPL) from http://taverna.sourceforge.net/.

Computational Biology↗
PubMed2006

[Pneumocystis jiroveci: a new name for an old pathogen].

Pneumonia due to Pneumocystis is an important cause of morbidity-mortality among immunodepressed patients, above all with human immunodeficiency virus infection and finally in patients with transplants, oncology patients and those subjected to drug immunodepression. Its lack of capacity to grow in the usual culture mediums has hindered knowledge on many aspects of this infection (transmission, acquisition mode, infection sources). However, the incorporation of molecular biology tools in recent years has made it possible to go deeper into the understanding of the epidemiology, biology and characteristics of the infection by this pathogen. These advances have led to the modification of the taxonomic classification of this atypical fungus and change in the name of the Pneumocystis responsible for the infection in humans, which is now called Pneumocystis jirovecii. During this article, we will show some of the most recent advances in the knowledge of the human pneumocystosis.

Humans↗
PubMed2005

The use of prokaryotic DNA methyltransferases as experimental and analytical tools in modern biology.

Prokaryotic DNA methyltransferases (MTases) are used as experimental and research tools in molecular biology and molecular genetics due to their ability to recognize and transfer methyl groups to target bases in specific DNA sequences. As a practical tool, prokaryotic DNA MTases can be used in recombinant DNA technology for in vitro alteration and enhancing of cleavage specificity of restriction endonucleases. The ability of prokaryotic DNA MTases to methylate cytosine residues in specific sequences, which are also methylated in eukaryotic DNA, makes it possible to use them as analytical reagent for determination of the site-specific level of methylation in eukaryotic DNA. In vivo DNA methylation by prokaryotic DNA MTases is used in different techniques for probing chromatin structure and protein-DNA interactions. Additional prospects are opened by development of the methods of DNA methylation targeted to predetermined DNA sequences by fusion of DNA MTases to DNA binding proteins. This review will discuss the application of prokaryotic DNA MTases of Type II in the methods and approaches mentioned above.

Animals↗
PubMed2000

Control and statistical analysis of in vitro reporter gene assays.

The use of in vitro gene reporter assays is becoming increasingly widespread in biology and particularly in drug metabolism, where the need for rapid screening of novel compounds is a driving factor. There is, however, little standardization of technique in the control of such assays, nor in the interpretation of results. This leads to confusion in the literature, with the possibility of a single piece of data being interpreted by several different methods, potentially giving vastly differing results. We have developed a reporter gene assay methodology that controls for many biological and experimental variables in the system and allows the application of a mathematical model to determine statistical significance between groups. Use of this methodology, we feel, allows an accurate and reproducible method of analyzing in vitro reporter gene assay data and increases its value as a biological tool.

Animals↗
PubMed2006

Protein modification in aging: an update.

Post-translational modifications of proteins are an important biologic tool for the production of various protein species from a single gene, which may vary in conformation, function, biologic half-life and complex formation with other proteins. The present minireview summarizes a few selected research observations important for the role of post-translational modifications in biologic aging and age-related diseases, including farnesylation, methylglyoxal-derivatization, transglutaminase pathways and the formation of 3-nitrotyrosine and 2-oxo-histidine in vivo.

Aging↗
PubMed2001

[New antithrombotic drugs (excluding plasminogen activators].

New platelet antagonists act on the activation by ADP (clopidogrel, ATP analogue) or on the mechanism of aggregation itself, by binding to the IIb/IIIa glycoprotein complex. The new anticoagulants are as follows: saccharide structures such as danaparoïd and the pentasaccharide of antithrombin binding, and direct thrombin inhibitors, such as recombinating hirudines (desirudine, lepirudine), bivalirudine, melagatran.... Other molecular targets are possible, both at platelet and blood clotting levels but, for the moment, the dilemma remains and reinforcement of antithrombotic activity goes hand in hand with a greater decrease in the defensive mechanisms against bleeding. In general, there is no antidote and the products are often associated, which increases the risk of haemorrhage. The research and development in this field are handicapped by the lack of biological tools for pertinent, homogenous, reproducible evaluation of the effects on haemostasis. The present tendency is to do without biological monitoring for adapting dosage in favour of optimisation of the impact in a given situation, perhaps, above all, with respect to the preceding problem.

Anticoagulants↗
PubMed2002

Molecular genetic approaches to investigate individual variations in behavioral and neuroendocrine stress responses.

A large response range can be observed in both behavioral and neuroendocrine responses to environmental challenges. This variation can arise from central mechanisms such as those involved in the shaping of general response tendencies (temperaments) or involves only one or the other output system (behavioral vs. endocrine response). The participation of genetic factors in this variability is demonstrated by family and twin studies in humans, the comparison of inbred strains and selection experiments in animals. Those inbred strains diverging for specific traits of stress reactivity are invaluable tools for the study of the molecular bases of this genetic variability. Until recently, it was only possible to study biological differences between contrasting strains, such as neurotransmitter pathways in the brain or hormone receptor properties, in order to suggest structural differences in candidate genes. The increase of the power of molecular biology tools allows the systematic screening of significant genes for the search of molecular variants. More recently, it was possible to search for genes without any preliminary functional hypothesis (mRNA differential expression, nucleic acid arrays, QTL search). The approach known as quantitative trait loci (QTL) analysis is based on the association between polymorphic anonymous markers and the phenotypical value of the trait under study in a segregating population (such as F2 or backcross). It allows the location of chromosomal regions involved in trait variability and ultimately the identification of the mutated gene(s). Therefore, in a first step, those studies skip the 'black box' of intermediate mechanisms, but the knowledge of the gene(s) responsible for trait variability will point out to the pathway responsible for the phenotypical differences. Since variations in stress-related responses may be related to numerous pathological conditions such as behavioral and mood disorders, drug abuse, cardiovascular diseases or obesity, and production traits in farm animals, these studies can be expected to bring significant knowledge for new therapeutic approaches in humans and improved efficiency of selection in farm animals.

Animals↗
PubMed2004

[Malaria research in the post-genomic era].

Genomic sequence determination of Plasmodium falciparum and other species of the genus, as well as that of Anopheles gambiae, and human, rat and mouse genome sequencing have completely changed the landscape of fundamental research about malaria. These data should urgently be exploited, in order to develop new tools to combat the disease: new drugs, fine dissection of the cascade of events following infection of the various vector species and vertebrate host, analysis of the complex interaction leading to the pathology or, inversely, contributing to sustained protection. Powerful population biology tools are now available, allowing to investigate genetic exchanges within natural population and to identify factors structuring parasitic and vector populations. Nevertheless, important impediments persist, including the complexity of experimental systems and the unclear relevance of animals models. Numerous challenges are to be faced; they call upon a more efficient organisation of research efforts in the systematic explorations using the powerful novel post-genomic technologies, as well as the development of new tools and experimental models required by functional genomics and integrative biology.

Animals↗
PubMed1997

Laminin and the mechanism of neuronal outgrowth.

This review summarizes the structure of the laminin molecule and the role it plays in development, pathfinding and regeneration in the vertebrate nervous system. Laminin has proven to be an influential glycoprotein of the extracellular matrix which guides and promotes the differentiation and growth of neurons. Its numerous domains, its association with carbohydrate moieties, and its many isoforms associated with specific sites and stages will be important in elucidating its function. How laminin's signals become translated into changes in the behavior of cells remains one of the thorniest issues facing scientists working at the interface between neuronal growth cone and extracellular matrix. New approaches using molecular biological tools and immunological tools for dissecting the laminin molecule have provided hints of intramolecular shifts in laminin's properties which influence cell behavior. These shifts occur in response to other molecules in the extracellular matrix such as carbohydrates, or in response to moieties on the cell surface itself. Thus, reduction of laminin's structure to fragments and ultimately polypeptide sequences is leading to renewed significance of laminin's tertiary and quaternary structure with respect to laminin's biological interactions. Such insights about laminin's structure are providing new tools for probing growth cone behavior, tools that need to be coupled with equally sophisticated analyses of growth cone behavior using biophysical and biochemical measures at a biological level suitable for analyzing responses induced by the probes.

Alzheimer Disease↗
PubMed2003

Metabolic engineering--a genetic toolbox for small molecule organic synthesis.

Metabolic engineering is an emerging field that exploits biosynthetic machinery as a means to genetically design small molecule production within heterologous host organisms. Molecular design and synthesis with biological tools has lagged behind total synthesis technology for about seventy-five years and owes its existence to relatively new molecular biology techniques. Here the field of metabolic engineering is explained as a comparison to total organic synthesis, including the sequence of scientific events leading up to successful implementation and future goals in the field. It is expected that metabolic engineering will take a place alongside traditional organic synthesis as a powerful means to design and create small organic molecules.

Journal Article↗
PubMed2000

Protein transduction: a new tool for the study of cellular ageing and senescence.

Protein transduction can be described as the direct uptake by the cell of exogenous proteins/peptides or protein/peptide:chemical complexes, as a result of a specific property of the protein/peptide component. In this review, the three most widely studied protein transducing activities are described, with particular emphasis on the TAT protein transduction domain. Current progress in protein transduction technology suggests the potential development of a variety of molecular and cell biology tools that will enable researchers to by-pass conventional genetic routes for modulating the cells' biological activity, thus negating many of the problems associated with genetic intervention. The potential application of this class of molecule in the development of tools for the study of senescent populations is discussed.

Animals↗
PubMed2003

The shielding effect of glycerol against protein ionization in electrospray mass spectrometry.

Most commercial recombinant proteins used as molecular biology tools, as well as many academically made preparations, are generally maintained in the presence of high glycerol concentrations after purification to maintain their biological activity. The present study shows that larger proteins containing high concentrations of glycerol are not amenable to analysis using conventional electrospray ionization mass spectrometry (ESI-MS) interfaces. In this investigation the presence of 25% (v/v) glycerol suppressed the signals of Taq DNA polymerase molecules, while 1% (v/v) glycerol suppressed the signal of horse heart myoglobin. The signal suppression was probably caused by the interaction of glycerol molecules with the proteins to create a shielding effect that prevents the ionization of the basic and/or acidic groups in the amino acid side chains. To overcome this difficulty the glycerol concentration was decreased to 5% (v/v) by dialyzing the Taq polymerase solution against water, and the cone voltage in the ESI triple-quadrupole mass spectrometer was set at 80-130 V. This permitted observation of a mass spectrum that contained ions corresponding to protonation of up to 50% of the ionizable basic groups. In the absence of glycerol up to 85% of the basic groups of Taq polymerase became ionized, as observed in the mass spectrum at relatively low cone voltages. An explanation of these and other observations is proposed, based on strong interactions between the protein molecules and glycerol. For purposes of comparison similar experiments were performed on myoglobin, a small protein with 21 basic groups, whose ionization was apparently suppressed in the presence of 1% (v/v) glycerol, since no mass spectrum could be obtained even at high cone voltages.

Animals↗
PubMed1998

Cytogenetics and the biological basis of sarcomas.

Recently, much research has been directed toward gaining a better understanding of sarcoma biology. To accomplish this goal, researchers have focused on characterizing the cytogenetic abnormalities that are detectable by routine karyotyping. With the use of widely-available molecular biologic tools, new information on the genetic abnormalities of sarcomas is rapidly emerging. In addition, physicians are beginning to successfully apply cytogenetic and molecular biologic findings to clinical settings in the form of molecular diagnostic and prognostic tests. Moreover, detailed study of these genetic abnormalities is leading to a better understanding of the molecular pathology of sarcomas, which may eventually lead to better therapy. In this paper, we will review the important new findings on genetic abnormalities in sarcomas, clinical applications of cytogenetic studies, and insight into the biology of sarcomas.

Chromosome Aberrations↗
PubMed2000

An experimental and theoretical study of the gas-phase decomposition of monoprotonated peptide nucleic acids.

Peptide nucleic acids (PNAs) are DNA/RNA mimics which have recently generated considerable interest due to their potential use as antisense and antigene therapeutics and as diagnostic and molecular biology tools. These synthetic biomolecules were designed with improved properties over corresponding oligonucleotides such as greater binding affinity to complementary nucleic acids, enhanced cellular uptake, and greater stability in biological systems. Because of the stability and unique structure of PNAs, traditional sequence confirmation methods are not effective. Alternatively, electrospray ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry shows great potential as a tool for the characterization and structural elucidation of these oligonucleotide analogs. Extensive gas-phase fragmentation studies of a mixed nucleobase 4-mer (AACT) and a mixed nucleobase 4-mer with an acetylated N-terminus (N-acetylated AACT) have been performed. Gas-phase collision-induced dissociation of PNAs resulted in water loss, cleavage of the methylene carbonyl linker containing a nucleobase, cleavage of the peptide bond, and the loss of nucleobases. These studies show that the fragmentation behavior of PNAs resembles that of both peptides and oligonucleotides. Molecular mechanics (MM+), semiempirical (AM1), and ab initio (STO-3G) calculations were used to investigate the site of protonation and determine potential low energy conformations. Computational methods were also employed to study prospective intramolecular interactions and provide insight into potential fragmentation mechanisms.

Acetylation↗
PubMed1996

A method for introducing site-specific mutations using oligonucleotide primers and its application to site-saturation mutagenesis.

Oligonucleotide primer-directed mutagenesis is a useful molecular biological tool, which is invaluable for the study of the structure/function relationships in proteins and for the creation of mutant proteins possessing modified or novel biological activities. Mutagenesis studies in which a site-saturation approach is employed require a high-efficiency mutagenesis procedure, which will generate a population of mutated molecules containing an even distribution of all possible amino acid changes, or a subset thereof. This article describes such a mutagenesis technique and discusses the adaptations that are necessary to perform site-saturation mutagenesis.

DNA Primers↗