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Biomedical subjects

J Colchero

Publications and source records attributed to J Colchero.

15 recordsLinked to original sources
PubMed2004

Atomic force microscopy contact, tapping, and jumping modes for imaging biological samples in liquids.

The capabilities of the atomic force microscope for imaging biomolecules under physiological conditions has been systematically investigated. Contact, dynamic, and jumping modes have been applied to four different biological systems: DNA, purple membrane, Alzheimer paired helical filaments, and the bacteriophage phi29. These samples have been selected to cover a wide variety of biological systems in terms of sizes and substrate contact area, which make them very appropriate for the type of comparative studies carried out in the present work. Although dynamic mode atomic force microscopy is clearly the best choice for imaging soft samples in air, in liquids there is not a leading technique. In liquids, the most appropriate imaging mode depends on the sample characteristics and preparation methods. Contact or dynamic modes are the best choices for imaging molecular assemblies arranged as crystals such as the purple membrane. In this case, the advantage of image acquisition speed predominates over the disadvantage of high lateral or normal force. For imaging individual macromolecules, which are weakly bonded to the substrate, lateral and normal forces are the relevant factors, and hence the jumping mode, an imaging mode which minimizes lateral and normal forces, is preferable to other imaging modes.

Bacillus Phages↗
PubMed2003

Interaction forces and conduction properties between multi wall carbon nanotube tips and Au(111).

We have studied the interaction forces and electrical conduction properties arising between multiwall carbon nanotube tips and the Au(111) surface in air, by means of amplitude modulation scanning force microscopy, also called intermittent contact. We have centered our work on tips with metallic electronic structure and for the specific parameters used we have found a preliminary interaction range where there is no contact between tip and surface. Stable imaging in this non-contact range is possible with multiwall carbon nanotube tips. These tips have also been used to obtain simultaneous topographic and current maps of the surface. They show excellent properties as tips due to their high aspect ratio and durability, as a result of their elastic and non-reactive properties. Correspondingly, multiwall carbon nanotube tips allow high resolution local analysis of electrical conductivity on a nanometer scale.

Elasticity↗
PubMed2003

DNA height in scanning force microscopy.

The measured height of DNA molecules adsorbed on a mica substrate by scanning probe microscopy is always less than the theoretical diameter. In this paper we show that, when imaged in ambient conditions, the molecules are usually immersed in the salt layer used to adsorb them to the substrate. This layer distorts the measurement of DNA height and is the main source of error but not the only one. We have performed different experiments to study this problem using two scanning force techniques: non-contact tapping mode in air and jumping mode in aqueous solution, where the dehydration phenomena is minimized. Height measurements of DNA in air using tapping mode reveal a height of 0.7+/-0.2nm. This value increases up to 1.5+/-0.2nm when the salt layer, in which the molecules are embedded, is removed. Jumping experiments in water give a value of 1.4+/-0.3nm when the maximum applied force is 300pN and 1.8+/-0.2nm at very low forces, which confirms the removal of the salt layer. Still, in all our experiments, the measured height of the DNA is less than the theoretical value. Our results show that although the salt layer present is important, some sample deformation due to either the loading force of the tip or the interaction with the substrate is also present.

Adsorption↗
PubMed2002

Contactless experiments on individual DNA molecules show no evidence for molecular wire behavior.

A fundamental requirement for a molecule to be considered a molecular wire (MW) is the ability to transport electrical charge with a reasonably low resistance. We have carried out two experiments that measure first, the charge transfer from an electrode to the molecule, and second, the dielectric response of the MW. The latter experiment requires no contacts to either end of the molecule. From our experiments we conclude that adsorbed individual DNA molecules have a resistivity similar to mica, glass, and silicon oxide substrates. Therefore adsorbed DNA is not a conductor, and it should not be considered as a viable candidate for MW applications. Parallel studies on other nanowires, including single-walled carbon nanotubes, showed conductivity as expected.

DNA↗
PubMed2002

Nonlinear resistance versus length in single-walled carbon nanotubes.

In this work fundamental properties of the electrical transport of single-walled carbon nanotubes as a function of their length are investigated. For this purpose, we have developed a new technique that allows us to characterize electronic transport properties of single-walled carbon nanotubes by probing them at different spots. This technique uses scanning force microscopy to make mechanical and electrical nanocontacts at any selected spot of a given image. We have applied this technique to molecules with high intrinsic resistance. The results show a nonlinear resistance vs distance behavior as the nanotube is probed along its length. This is an indication of elastic electronic transport in one-dimensional systems.

Journal Article↗
PubMed2001

Imaging and mapping protein-binding sites on DNA regulatory regions with atomic force microscopy.

Regulation of gene expression is fundamental in biological systems. A systematic search for protein binding sites in gene promoters has been done in recent years. Biochemical techniques are easy and reliable when analysing protein interactions with short pieces of DNA, but are difficult and tedious when long pieces of DNA have to be analysed. Here we propose AFM as a reliable and easy technique for identifying protein interaction sites in long DNA molecules like gene promoters. We support this idea using a well-known model: the interaction of the Pho4 protein with the PHO5 gene promoter. We have also applied the technique to demonstrate that Mig1 protein binds to two motifs in the promoter of HXK2 gene. Our results allow us to define Mig1p as a new factor probably contributing to the carbon source-dependent transcription regulation of HXK2 gene.

Amino Acid Sequence↗
PubMed2001

Macroscopic water deposits on polycrystalline gold measured by scanning force microscopy.

Data of water adsorption on polycrystalline gold show the formation of a multilayer film of several nanometers with the increase of relative humidity. We have measured this adsorption process by scanning force microscopy in both dynamic and jumping modes. We find interesting differences in the adsorption of water on the terraces and at grain boundaries. Measurements of adhesion force are also reported.

Journal Article↗
PubMed2000

Absence of dc-conductivity in lambda-DNA.

The electrical conductivity of biomaterials on a molecular scale is of fundamental interest in the life sciences. We perform first principles electronic structure calculations, which clearly indicate that lambda-DNA chains should present large resistance values. We also present two direct procedures to measure electrical currents through DNA molecules adsorbed on mica. The lower limit for the resistivity is 10(6) Omega . cm, in agreement with our calculations. We also show that low energy electron bombardment induces a rapid contamination and dramatically affects the measured conductivity, thus providing an explanation to recent reports of high DNA conductivity.

Animals↗
PubMed1999

Analysis by atomic force microscopy of Med8 binding to cis-acting regulatory elements of the SUC2 and HXK2 genes of saccharomyces cerevisiae.

Med8 protein is a regulator that specifically binds to upstream activating sequences (UASs) of SUC2 promoter, to downstream repressing sequences (DRSs) of the HXK2 gene and to the carboxy-terminal domain of the RNA polymerase II. Atomic force microscopy has allowed for direct visualization of Med8 interactions with a 305 bp fragment of SUC2 promoter and with a 676 bp fragment of HXK2 gene, containing respectively the UASs and DRSs regulatory regions. This approach has provided complementary information about the position and the structure of the DNA-protein complexes. Med8 binding to DNA results in total covering of one of the two existing 7 bp motives (consensus, (A/C)(A/G)GAAAT) in the studied DNA fragments. No preference for binding either of the two UASs of SUC2 promoter as well as for the two DRSs of HXK2 gene has been found. We also discuss whether this protein works as dimer or as a monomer.

Carrier Proteins↗
PubMed1995

[Severe gastrointestinal complication of Behcet's disease].

We describe a case of Behçet's syndrome with ileoceal affection of the gastrointestinal track, torpid course evolving to an intermittent febrile syndrome and associated to clinical signs of acute abdomen and latter septic complication due to a fecaloid fistula after surgery. We discuss the similarities with the inflammatory intestinal disease and the problem of the diagnosis and treatment of this particular implication of Behçet's syndrome.

Adult↗
PubMed1994

Haemophilus aphrophilus as a rare cause of arthritis.

A case of septic arthritis due to Haemophilus aphrophilus is presented. This organism has rarely been reported as a cause of bone or joint infections. We believe this is the third reported case of septic arthritis caused by this microorganism. We review the clinical and bacteriologic findings and the previously reported cases of infection caused by H. aphrophilus. Treatment with ceftriaxone was followed by full recovery without sequelae.

Arthritis, Infectious↗
PubMed1992

Na,K-ATPase in crystalline form investigated by scanning force microscopy.

Na,K-ATPase has been isolated in purified membrane fragments from kidney tissue and crystallized by phospholipase treatment to obtain two-dimensional, membrane-bound protein crystals. Scanning force microscopy has been used to identify and analyze the topography of the membrane fragments. Specific patterns in accordance with electron microscopic images have been found. In biological material under physiological conditions the scanning force is a crucial parameter for the resulting image at high resolution.

Animals↗
PubMed1990

[HTLV-I infection in a high-risk group].

The aim of this study is to detect the presence of HTLV-1 in a high-risk population in west Andalusia. We studied 267 samples of serum from 255 patients: 179 of these patients being intravenous drug-users, 14 had ADVP sexual partners, 16 were inhalation drug-users, 4 were hemophiliacs, 9 had other high-risk habits and 25 hematological patients afflicted with leukemia or lymphoma. All of them were tested for antibodies against HTLV-1 by means of an in vitro qualitative ELISA technique (ELISA Du Pont HTLV-1). The positive results were confirmed by the Western blot technique. Additionally, the p24 antigen and the antibodies against VIH-1 and VIH-2 (ENV/CORE) were analysed, except in the 25 hematological patients. We found 20 serum samples positive to HTLV-1 by ELISA (7.4%), but only 1 (0.3%) was confirmed by the Western blot technique. The prevalence of VIH-1 was 46%; 9% had p24 VIH antigen and 26% had false positive ELISA to VIH-2. We found a statistically significant relationship (p = 0.0005) between positive ELISA to HTLV-1 and antibodies against VIH. We conclude that HTLV-1 has penetrated into the high-risk population of west Andalusia , although not yet to a great degree, and point out the need for seric epidemiological surveillance to prevent the spread of the retrovirus in these groups.

False Positive Reactions↗