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At least 811 records · Page 45Linked to original sources
PubMed2005

The future of post-genomic biology at the proteomic level: an outlook.

Drug discovery and early-stage drugs and biomarkers development is a continuous adaptation and maturation process. The cycle of changes based on new findings is coupled with shifts in research priorities and make this part of pharmaceutical research a challenging endeavour. Over the last years, the emphasis on genomics has shifted to proteomics, the science of understanding how proteins translate gene information into function, and metabonomics, the science of small metabolites that are further apart from genomic projects. Proteomics describes the analysis of the protein complement of a biological sample with respect to temporal and spatial resolution. This technology is based on separation of complex protein mixtures by 2D gel-electrophoresis, in gel digest and mass spectrometric analysis of the protein fragments. Proteomics has been recently flanked by peptidomics, a new research direction aimed at the comprehensive analysis of small (1-20 kDa) polypeptides, thus covering the gap between proteomics and metabonomics. The refinement of peptidomics is based on an essential paradigm related to modularity and diversity. Peptides are a paramount example of how one single gene can release multiple functionalities. We can expect fast progress in understanding protein and peptide networks from a systems biology approach ending in the discovery of new peptide targets. However, the way from a complex sample to potential diagnostic and therapeutic targets will depend on technological developments and from the ability to discriminate true disease-related signals from false positive and negative signals, and the way from target discovery to target validation will not be short.

Aged↗
PubMed1998

X-ray imaging and microspectroscopy of plants and fungi.

X-ray fluorescence microscopy and microspectroscopy with micrometre spatial resolution and unprecedented capabilities for the study of biological and environmental samples are reported. These new capabilities are a result of both the combination of high-brilliance synchrotron radiation and high-performance X-ray microfocusing optics and the intrinsic advantages of X-rays for elemental mapping and chemical-state imaging. In this paper, these capabilities are illustrated by experimental results on hard X-ray phase-contrast imaging, X-ray fluorescence (XRF) imaging and microspectroscopy of mycorrhizal plant roots and fungi in their natural hydrated state. The XRF microprobe is demonstrated by the simultaneous mapping of the elemental distributions of P, S, K, Ca, Mn, Fe, Ni, Cu and Zn with a spatial resolution of approximately 1 x 3 micron and with an elemental sensitivity of approximately 500 p.p.b. Microspectroscopy with the same spatial resolution is demonstrated by recording near-edge X-ray absorption (XANES) spectra of Mn at a concentration of approximately 3 p.p.m.

Journal Article↗
PubMed1996

An in vitro study on the influence of limited frequency resolution on contrast agent-enhanced Doppler signals.

Ultrasound contrast agents for vascular use are gas-filled microspheres and will increase the backscatter from blood and therefore enhance the Doppler signal. Studies have shown that Doppler enhancement may result in an increased maximum velocity when observed as the envelope of the spectral Doppler screen. Change in observed velocity may be due to biological or instrumentational effects. The purpose of this study was to investigate the possible instrumentational effects on the Doppler signal after injection of the contrast agent (Infoson). By performing the measurements on a Doppler phantom, the biological effects was eliminated. Computer simulations of limited frequency resolution were compared to measurements. The conclusion was that the increase in detected maximum velocity after Infoson injection is due to the combined effect of signal enhancement and limited frequency resolution. It is shown that a large change in signal strength can change the estimated maximum frequency from the spectral Doppler whether this is due to a contrast agent or instrument settings. It is therefore important in a clinical situation to have an adequate, but not too strong or too weak signal in order to make the best velocity estimates.

Albumins↗
PubMed2003

Two-dimensional imaging biosensor for the monitoring of lactate released from brain slices.

Real-time monitoring of lactate release from brain slices has been studied with an optical two-dimensional (2D) imaging biosensor. The 2D biosensor is prepared by direct immobilization of lactate dehydrogenase (LDH) molecules onto a flat silica glass surface through a covalent binding mechanism. The biosensor is able to spatially differentiate lactate concentration variations with conventional optical microscopic spatial resolution. This biosensor has the capability to effectively detect lactate down to a concentration of 100 nM. The 2D biosensor responds uniformly with 2.5% RSD from pixel to pixel. With a 100 ms response time, this 2D biosensor has the capability of monitoring simultaneously many cells in one image. We have studied the impact of KCI on lactate release from brain slices. Clear differences have been observed in lactate release for different regions of the tissue. The real-time determination of the newly released lactate from the mouse brain slices clearly demonstrates the feasibility of monitoring lactate release from living specimens. The 2D biosensor will enable us to study cellular communications and possibly other biological processes that require simultaneous temporal and spatial resolution.

Animals↗
PubMed2006

Sexual conflict over mating and fertilization: an overview.

Sexual conflict is a conflict between the evolutionary interests of individuals of the two sexes. The sexes can have different trait optima but this need not imply conflict if their optima can be attained simultaneously. Conflict requires an interaction between males and females (e.g. mating or parental care), such that the optimal outcomes for each sex cannot be achieved simultaneously. It is important to distinguish between battleground models, which define the parameter space for conflict and resolution models, which seek solutions for how conflicts are resolved. Overt behavioural conflict may or may not be manifest at resolution. Following Fisherian principles, an immediate (i.e. direct) benefit to a male that has a direct cost to his female partner can have an indirect benefit to the female via her male progeny. Female resistance to mating has been claimed to represent concurrence rather than conflict, due to female benefits via sons (males with low mating advantage are screened out by resistance). However, the weight of current evidence (both theoretical and empirical) supports sexual conflict for many cases. I review (i) conflicts over mate quality, encounters between males and females of genetically diverged subpopulations, mating rate and inbreeding, (ii) the special features of postcopulatory sexual conflict and (iii) some general features of importance for conflict resolution.

Animals↗
PubMed2003

Visualizing signals moving in cells.

Cells display a highly complex spatiotemporal organization, required to exert a wide variety of different functions, for example, detection, processing, and propagation of nerve impulses by neurons; contraction and relaxation by muscle cells; movement by leukocytes; and adsorption and secretion of nutrients and metabolites by epithelial cells lining the gut. Successful execution of these complex processes requires highly dynamic information transfer between different regions and compartments within cells. Through the development of fluorescent sensors for intracellular signaling molecules coupled with improved microscopic imaging techniques, it has now become possible to investigate signal propagation in cells with high spatial and temporal resolution.

Animals↗
PubMed2024

The burgeoning spatial multi-omics in human gastrointestinal cancers.

The development and progression of diseases in multicellular organisms unfold within the intricate three-dimensional body environment. Thus, to comprehensively understand the molecular mechanisms governing individual development and disease progression, precise acquisition of biological data, including genome, transcriptome, proteome, metabolome, and epigenome, with single-cell resolution and spatial information within the body's three-dimensional context, is essential. This foundational information serves as the basis for deciphering cellular and molecular mechanisms. Although single-cell multi-omics technology can provide biological information such as genome, transcriptome, proteome, metabolome, and epigenome with single-cell resolution, the sample preparation process leads to the loss of spatial information. Spatial multi-omics technology, however, facilitates the characterization of biological data, such as genome, transcriptome, proteome, metabolome, and epigenome in tissue samples, while retaining their spatial context. Consequently, these techniques significantly enhance our understanding of individual development and disease pathology. Currently, spatial multi-omics technology has played a vital role in elucidating various processes in tumor biology, including tumor occurrence, development, and metastasis, particularly in the realms of tumor immunity and the heterogeneity of the tumor microenvironment. Therefore, this article provides a comprehensive overview of spatial transcriptomics, spatial proteomics, and spatial metabolomics-related technologies and their application in research concerning esophageal cancer, gastric cancer, and colorectal cancer. The objective is to foster the research and implementation of spatial multi-omics technology in digestive tumor diseases. This review will provide new technical insights for molecular biology researchers.

Humans↗
PubMed2003

Single-pollen analysis by laser-induced breakdown spectroscopy and Raman microscopy.

The application of laser-induced breakdown spectroscopy to the analysis of single biological microparticles (bioaerosols) is described, exemplified here for a range of pollens. Spectra were recorded by exposure of the pollen to a single laser pulse from a Nd:YAG laser (lambda = 1064 nm, Ep approximately 30 mJ). The intensities of the single-pulse laser-induced breakdown spectra fluctuated dramatically, but an internal signal calibration procedure was applied that referenced elemental line intensities to the carbon matrix of the sample (represented by molecular bands of CN and C2). This procedure allowed us to determine relative element concentration distributions for the different types of pollen. These pollens exhibited some distinct concentration variations, for both major and minor (trace) elements in the biomatrix, through which ultimately individual pollens might be identified and classified. The same pollen samples were also analyzed by Raman microscopy, which provided molecular compositional data (even with spatial resolution). These data allowed us to distinguish between biological and nonbiological specimens and to obtain additional classification information for the various pollen families, complementing the laser-induced breakdown spectroscopy measurement data.

Aerosols↗
PubMed2002

Proteomics in alcohol research.

The proteome is the complete set of proteins in an organism. It is considerably larger and more complex than the genome--the collection of genes that encodes these proteins. Proteomics deals with the qualitative and quantitative study of the proteome under physiological and pathological conditions (e.g., after exposure to alcohol, which causes major changes in numerous proteins of different cell types). To map large proteomes such as the human proteome, proteins from discrete tissues, cells, cell components, or biological fluids are first separated by high-resolution two-dimensional electrophoresis and multidimensional liquid chromatography. Then, individual proteins are identified by mass spectrometry. The huge amount of data acquired using these techniques is analyzed and assembled by fast computers and bioinformatics tools. Using these methods, as well as other technological advances, alcohol researchers can gain a better understanding of how alcohol globally influences protein structure and function, protein-protein interactions, and protein networks. This knowledge ultimately will assist in the early diagnosis and prognosis of alcoholism and the discovery of new drug targets and medications for treatment.

Alcoholism↗
PubMed1967

High-resolution nuclear magnetic resonance spectroscopy. Advances in instrumentation in this field are leading to new applications in chemistry and biology.

The rapid development of NMR spectroscopy has been characterized by a succession of discrete, significant advances in instrumentation, as well as by less dramatic but cumulatively important improvements in instrument performance, experimental techniques, spectral analysis, and theory. Most significant are the advances in magnet technology, which within 13 years increased the available field strengths from 7.04 to 51.7 kilogauss (with corresponding increase in the PMR frequency from 30 to 220 megahertz). Great improvements in spectrometer stability and in the coupling of spectrometers with on-line computers have so improved sensitivity that some nuclei possessing less favorable NMR characteristics can now be studied.

Alkenes↗
PubMed2000

Reproducibility and applicability of gallium replication as evaluated by biological specimen use.

Structures of biological surfaces pressed on to a pure liquid gallium surface were successfully traced on to the gallium surface by quick-freezing below the melting point (28.78 degrees C) in air or water for replication in scanning electron microscopy. Gallium's high surface tension (approximately 700 mN m(-1) at 30 degrees C) deteriorates the spatial resolution of replicas and destroys some types of specimens. Five different biological surfaces were replicated on to gallium surfaces to evaluate spatial resolution and specimen resistance, i.e. reproducibility and applicability. Gallium replication of jewel beetle wing and human hair demonstrated submicron spatial resolution in the horizontal direction at least. Trials of protozoa, bacteria, and culture cell replication showed that protozoa are suited to replication because the cell membrane has characteristic structures with sufficient resistance to the gallium surface.

Animals↗
PubMed1998

Cryo X-ray microscopy with high spatial resolution in amplitude and phase contrast.

The resolution of transmission X-ray microscopes (TXMs) using zone plate optics is presently about 30 nm. Theory and experiments presented here show that this resolution can be obtained in radiation sensitive hydrated biological material by using shock frozen samples. For this purpose the interaction of X-rays with matter and the image formation with zone plates is described. For the first time the influence of the limited apertures of the condenser and the zone plate objective are in included in calculations of the image contrast, the photon density and radiation dose required for the object illumination. Model considerations show that lowest radiation dose and high image contrast are obtained in optimized phase contrast which exploits absorption as well as phase shift. The damaging effect of the absorbed X-rays is quantitatively evaluated by radiation-induced kinetics showing that cryogenic samples are structurally stable. To verify these theoretical models the TXM was modified to allow imaging of frozen-hydrated samples at atmospheric pressure. Details inside cells and algae as small as 35 nm are visible at 2.4 nm wavelength in amplitude contrast mode. At this resolution the cryogenic samples show no structural changes. As predicted, optimized phase contrast shows structures inside the frozen-hydrated objects with high contrast. Stereo-pair images of algae reveal the 3D organization of the organelles. Element analysis and micro-tomography of whole cryogenic cells are possible.

Cryoelectron Microscopy↗
PubMed2003

Evidence for abrupt climate changes in annually laminated marine sediments.

Annually laminated sediments from marine or lacustrine settings represent valuable high-resolution archives of climate change that record variation due to changing precipitation and run-off from land or variation in biological productivity and flux in the water column. Because of their annual resolution such sediments may capture abrupt changes of interannual to decadal scales rivaling corals and ice cores in resolution. Laminated sediments often occur intermittently in the sediment column, and the onset and cessation of laminae commonly record the abrupt crossing of thresholds related to climate change, for example, in the degree of oxygenation of bottom waters. Such records from marginal basins and continental margins have been pivotal in demonstrating that abrupt changes hitherto documented only in high-latitude ice cores are synchronous with climatic change at low latitudes. These insights into global teleconnections have improved our understanding of the mechanisms of rapid climate change. In deep-sea settings, the discovery of the episodic occurrence of laminated diatom-rich sediments in the Equatorial Pacific and Southern Ocean provides evidence for massive climate-related biogeochemical excursions tied to abrupt changes in the input, distribution and availability of nutrients in the oceans.

Climate↗
PubMed2003

Feeling the forces: atomic force microscopy in cell biology.

Atomic force microscopy allows three-dimensional imaging and measurements of unstained and uncoated biological samples in air or fluid. Using this technology it offers resolution on the nanometer scale and detection of temporal changes in the mechanical properties, i.e. surface stiffness or elasticity in live cells and membranes. Various biological processes including ligand-receptor interactions, reorganization, and restructuring of the cytoskeleton associated with cell motility that are governed by intermolecular forces and their mode of detection will be discussed.

Animals↗
PubMed2001

Atomic structure holography using thermal neutrons.

The idea of atomic-resolution holography has its roots in the X-ray work of Bragg and in Gabor's electron interference microscope. Gabor's lensless microscope was not realized in his time, but over the past twelve years there has been a steady increase in the number of reports on atomic-resolution holography. All of this work involves the use of electrons or hard X-rays to produce the hologram. Neutrons are often unique among scattering probes in their interaction with materials: for example, the relative visibility of hydrogen and its isotopes is a great advantage in the study of polymers and biologically relevant materials. Recent work proposed that atomic-resolution holography could be achieved with thermal neutrons. Here we use monochromatic thermal neutrons, adopting the inside-source concept of Szöke, to image planes of oxygen atoms located above and below a single hydrogen atom in the oxide mineral simpsonite.

Journal Article↗
PubMed2001

Digital in-line holography for biological applications.

Digital in-line holography with numerical reconstruction has been developed into a new tool, specifically for biological applications, that routinely achieves both lateral and depth resolution, at least at the micron level, in three-dimensional imaging. The experimental and numerical procedures have been incorporated into a program package with a very fast reconstruction algorithm that is now capable of real-time reconstruction. This capability is demonstrated for diverse objects, such as suspension of microspheres and biological samples (diatom, the head of Drosophila melanogaster), and the advantages are discussed by comparing holographic reconstructions with images taken by using conventional compound light microscopy.

Algorithms↗
PubMed1988

Chromatography and electrophoresis of creatinine and other guanidino compounds.

Chromatographic methods, in general, are considered as the definitive and reference procedure. The HPLC procedures reviewed all seem to provide improved and adequate specificity and sensitivity for CRN assay. The HPLC methods are relatively easy to use, have nearly complete recoveries (greater than or equal to 95%) and have good precision. The within- and between-day variations are often less than 4% [85,87,90,94-97,99]. Most of the methods developed [84,85,90,91,94,97,99] were tested for potential interference and the specificity for CRN was demonstrated. One important advantage of the HPLC method [85] is that the presence of an interfering substance in the biological sample can most likely be detected by its influence on the sharpness and resolution of the CRN peak. It is understandable that there are possibilities that other constituents in the biological sample may also be co-eluting with CRN and the investigator should carefully examine the chromatogram obtained for any sign of interference. Ginman and Colliss [107] reported that azathioprine, cyclosporin A, cefotaxime and prednisolone used in patients after renal transplant interfered with the HPLC assay: the results are 40% higher than those by Jaffe method. These interferences, however, were corrected with a slight modification of the HPLC conditions [107]. Because of the non-specificity associated with the Jaffe reaction, the results obtained from Jaffe-based assays often exceed those from HPLC methods [95,108,109]. Such overestimation would be especially significant when the serum CRN is in the normal range where small changes may be indicative of a significant change in a patient's renal function [95,111]. It appears that HPLC methods are the methods of choice for simultaneous analysis of endogenous guanidino compounds. Depending on the purpose of analysis, one would choose a particular type of method, e.g., one among those representative methods listed in Table 1. If one is interested in measuring MG and GSA levels in serum or plasma, then depending on the sensitivity requirement and available instrumentations, one could choose many method listed in Table 1. However, if one needs to measure AARG, ARG and ARA, in addition to MG and GSA, then method 4 in Table 1 would be more appropriate. If TAU is the compound of interest, then one of the methods 2,3,4,5, and 7 with an appropriate deproteinization procedure would be desirable.

Animals↗
PubMed2006

Synthesis and evaluation of polymeric continuous bed (monolithic) reversed-phase gradient stationary phases for capillary liquid chromatography and capillary electrochromatography.

There is a demand of novel high resolution separation media for separation of complex mixtures, particularly biological samples. One of the most flexible techniques for development of new separation media currently is synthesis of the continuous bed (monolithic) stationary phases. In this study the capillary format gradient stationary phases were formed using continuous bed (monolith) polymerization in situ. Different reversed-phase stationary phase gradients were tailored and their resolution using capillary liquid chromatography and capillary electrochromatography at isocratic mobile phase conditions was evaluated. It is demonstrated, that efficiency and resolution of the gradient stationary phases can be substantially increased comparing to the common (isotropic) stationary phases. The proposed formation approach of the gradient stationary phase is reproducible and compatible with the capillary format or microchip format separations. It can be easily automated for the separation optimizations or mass production of the capillary columns or chips.

Benzene Derivatives↗