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At least 361 records · Page 20Linked to original sources

PubMed2003

Scanning eye movements in homonymous hemianopia documented by scanning laser ophthalmoscope retinal perimetry.

Sparing or partial recovery of visual fields in hemianopic patients is frequently difficult to document. This is because when testing large field losses, the standard automated or manual visual field testing systems have limited fixation controls. Measured visual field recovery in these cases may not be real but instead may be due to an artifact such as scanning eye movement. This article illustrates a way to separate the actual visual field sparing from scanning eye movement artifact by using perimetry testing with the scanning laser ophthalmoscope (SLO). During the SLO perimetry, the examiner has a direct and magnified view of the retinal fixation locus. This direct view allows for the added ability to monitor the fixation stability during target presentation. When eye movements larger than 1 degrees are noted, the examiner can repeat the trial. During static perimetry, our SLO records the retinal position of the fixation target at the end of the stimulus presentation and corrects scanning eye movements that occur during stimulus presentation. These special features enable us to identify when the apparent sparing of the visual field is due to the artifact of scanning. To demonstrate this, we selected the records of four hemianopic patients whose fields were examined by both standard perimetry and the SLO. We then compared the clinical visual fields with the SLO perimetry fields. One of the patients had a complete homonymous hemianopia on both the clinical perimetry and the SLO perimetry. A second patient was found by the SLO to have unstable fixation during testing. The SLO perimetry revealed that the apparent spared fields seen in standard perimetry were the result of eye scanning and not an actual enlargement of the visual field. Two other patients were confirmed by the SLO findings to have valid partial recovery of the visual field, one with and one without scanning eye movements. The advantages and limitations of SLO perimetry in analyzing hemianopic field sparing are discussed.

Adolescent↗

PubMedDate not supplied

[Conformational transitions of DNA in concentrated neutral salt solutions].

Salt anions can be arranged in lyotropic series of the action of conformational stability of DNA. This effect is universal for proteins and DNA. It is explained by the salt changes of transfer free energy of macromolecular inner groups to the solvent. Effect mechanism is the combination of anion direct interaction with the exposed inner groups and in indirect way through the changes of water structure. Individual features of the salt effect on DNA are the induced transitions in DNA duplex and the changes of differential stability of AT- and GC-base pairs. An important role in these phenomena plays the dehydration of DNA in the reduction of water activity in concentrated salt solutions. Local changes in medium polarity, hydration level of DNA molecule at different stages of their functioning can explain the regulatory role in intracellular processes, as well as selectivity and specificity of the action of individual ions in the cell.

Circular Dichroism↗

PubMed1996

Chaos and synchrony in a model of a hypercolumn in visual cortex.

Neurons in cortical slices emit spikes or bursts of spikes regularly in response to a suprathreshold current injection. This behavior is in marked contrast to the behavior of cortical neurons in vivo, whose response to electrical or sensory input displays a strong degree of irregularity. Correlation measurements show a significant degree of synchrony in the temporal fluctuations of neuronal activities in cortex. We explore the hypothesis that these phenomena are the result of the synchronized chaos generated by the deterministic dynamics of local cortical networks. A model of a "hypercolumn" in the visual cortex is studied. It consists of two populations of neurons, one inhibitory and one excitatory. The dynamics of the neurons is based on a Hodgkin-Huxley type model of excitable voltage-clamped cells with several cellular and synaptic conductances. A slow potassium current is included in the dynamics of the excitatory population to reproduce the observed adaptation of the spike trains emitted by these neurons. The pattern of connectivity has a spatial structure which is correlated with the internal organization of hypercolumns in orientation columns. Numerical simulations of the model show that in an appropriate parameter range, the network settles in a synchronous chaotic state, characterized by a strong temporal variability of the neural activity which is correlated across the hypercolumn. Strong inhibitory feedback is essential for the stabilization of this state. These results show that the cooperative dynamics of large neuronal networks are capable of generating variability and synchrony similar to those observed in cortex. Auto-correlation and cross-correlation functions of neuronal spike trains are computed, and their temporal and spatial features are analyzed. In other parameter regimes, the network exhibits two additional states: synchronized oscillations and an asynchronous state. We use our model to study cortical mechanisms for orientation selectivity. It is shown that in a suitable parameter regime, when the input is not oriented, the network has a continuum of states, each representing an inhomogeneous population activity which is peaked at one of the orientation columns. As a result, when a weakly oriented input stimulates the network, it yields a sharp orientation tuning. The properties of the network in this regime, including the appearance of virtual rotations and broad stimulus-dependent cross-correlations, are investigated. The results agree with the predictions of the mean field theory which was previously derived for a simplified model of stochastic, two-state neurons. The relation between the results of the model and experiments in visual cortex are discussed.

Models, Neurological↗

PubMed2005

Choosing the right chromatographic support in making a new acetylcholinesterase-micro-immobilised enzyme reactor for drug discovery.

The aim of the present study was to optimize the preparation of an immobilized acetylcholinesterase (AChE)-based micro-immobilized enzyme reactor (IMER) for inhibition studies. For this purpose two polymeric monolithic disks (CIM, 3 mm x 12 mm i.d.) with different reactive groups (epoxy and ethylendiamino) and a packed silica column (3 mm x 5 mm i.d.; Glutaraldehyde-P, 40 microm) were selected as solid chromatographic supports. All these reactors were characterized in terms of rate of immobilization, stability, conditioning time for HPLC analyses, optimum mobile phase and peak shape, aspecific interactions and costs. Advantages and disadvantages were defined for each system. Immobilization through Schiff base linkage gave more stable reactors without any significant change in the enzyme behaviour; monolithic matrices showed very short conditioning time and fast recovery of the enzymatic activity that could represent very important features in high throughput analysis and satisfactory reproducibility of immobilization yield. Unpacked silica material allowed off-line low costs studies for the optimization of the immobilization step.

Acetylcholinesterase↗

PubMed1986

Packings and stationary phases in preparative column liquid chromatography.

Although the theoretical treatment of chromatographic processes on a preparative scale provides guidelines to the extent to which packing and stationary phase properties affect the target quantities such as sample input, throughput and resolution times sample input, a series of additional criteria were established to judge the quality of a packing in preparative column liquid chromatography. These include bed stability and flow resistance, chemical resistance and purity, solute accessibility, mass and biological recovery, fouling, regeneration and cost. Applying these criteria, the relative importance of physical and chemical structure parameters of packings and stationary phases was assessed. Commercial packings with mean particle diameters dp greater than 20 micron were listed for adsorption, size exclusion, ion-exchange and affinity chromatography. An analysis of the characteristic features of phase systems showed that adsorption media offer a high selectivity combined with adequate loadability, whereas ion exchangers and affinity media were best suited for biospecific solutes, particularly biopolymers, which can be attributed to their high selectivity and loadability.

Chemical Phenomena↗

PubMed2005

A potent and selective tacrine analog--biomembrane permeation and physicochemical characterization.

Cholinesterase inhibitors have been used for years in treatment of Alzheimer's disease (AD). Tacrine is the first acetylcholinesterase inhibitor approved for treating AD by the regulatory agencies around the world. Unfortunately, a number of studies have shown tacrine to be associated with some severe side effects, including hepatotoxicity. These adverse effects may be attributed to its poor selectivity for acetylcholinesterase and have thus necessitated the research and development of more selective cholinesterase inhibitors with a greater specificity and higher potency. The heptylene-linked bis-tacrine analog (bis-THA) of Tacrine is a second-generation inhibitor of acetylcholinesterase, which has a potency that is 1000 times more potent than Tacrine in inhibition of the rat brain acetylcholinesterase and 10,000 times more selective for acetylcholinesterase over butyrylcholinesterase. A series of investigations have thus been initiated to characterize the physicochemical properties (e.g., pKa, partition coefficient, and stability) of this bis-THA analog as compared to its parent molecule (Tacrine). For AD treatment, the cholinesterase inhibitors need to be taken daily for long periods of time. Use of controlled-release dosage forms to deliver drugs for chronic administration, by taking advantage of their rate-controlling drug delivery features, has gained increasing popularity in recent years. On the other hand, the nasal route, which has been used to deliver drugs for achieving a direct delivery to the brain (via the olfactory pathway), could offer the benefits of brain targeting to the delivery of Tacrine and bis-THA. To investigate this feasibility, the permeation of Tacrine and bis-THA across the nasal mucosa was evaluated (in comparison with other absorptive mucosae). Studies of their permeation kinetics across the various absorptive mucosae, which were freshly excised from the domestic pig, indicated that the nasal mucosa could present a viable pathway for the systemic delivery of bis-THA. Delipidization studies suggested that the lipophilic components in the absorptive mucosae could play an important role in the permeation of bis-THA. The bis-THA has a pKa of approximately 8 and its partition coefficient showed a sigmoidal pattern with solution pHs. It was found to be relatively stable at acidic pHs but subjected to a base-catalyzed degradation at the alkaline pHs (> or = 8) and at higher temperatures (> or = 50 degrees C).

Animals↗

PubMed2004

DNA adducts with chlorophyll and chlorophyllin as antimutagenic agents: synthesis, stability, and structural features.

Porphyrins and their metal derivatives are strong DNA binders with association constants of 10(5) M(-1) to 10(7) M(-1). Some of these compounds have been used for radiation sensitization therapy of cancer and are targeted to interact with cellular DNA. Chlorophyll (CHL) and chlorophyllin (CHLN), a food-grade derivative of chlorophyll, the ubiquitous green plant pigment widely consumed by humans, are potent inhibitors of experimental carcinogenesis. The aim of this report was to examine the interaction of calf-thymus DNA with CHL and CHLN in aqueous solution at physiological pH, with pigment/DNA(phosphate) molar ratios (r) of 1/80 to 1/2. Fourier transform infrared (FTIR) difference spectroscopic method was used to determine the pigment binding mode, binding constant, sequence selectivity, DNA secondary structure and structural variations of the pigment-DNA complexes in aqueous solution.

Animals↗

PubMed1992

Cutaneous T-cell lymphoma. Evaluation of pretreatment skin biopsy specimens by a panel of pathologists.

BACKGROUND AND DESIGN: Cutaneous T-cell lymphoma (CTCL) frequently presents a difficult diagnostic challenge for the clinician and pathologist. To assess the diagnostic validity of conventional histopathologic findings in CTCL, pretreatment skin biopsy specimens were scored prospectively and independently by a panel of five to seven dermatopathologists and pathologists. Scores were compared with disease outcome. Repeatability of these scores was examined among observers and for the same observer. The study population consisted of 165 subjects, initially referred for suspected mycosis fungoides or Sézary syndrome. Ninety-two patients determined to have CTCL have been followed up for 6.3 +/- 3.5 years (mean +/- SD) and are categorized according to disease outcome: 22 are in complete remission, 35 are in partial remission, three have progressive lymphoma, 15 died of disease, 13 died of other causes, and four were unavailable for follow-up. Seventy-three patients determined not to have CTCL have been followed up for 5.3 +/- 3.2 years without subsequent clinicopathologic evidence of CTCL. These longitudinal data allowed comparisons of the clinical course with the original histologic interpretations. RESULTS: Data showed that the histologic scores rendered by the pathology panel did not correlate with stage of disease and were not an accurate predictor of clinical outcome, because the histologic ratings did not discriminate between patients who eventually had complete remission and those with either progressive lymphoma or who have died of disease. The results also substantiate the low inherent reliability of histopathologic findings in CTCL. Large differences existed among pathologists in scoring the study populations and repeated reading of selected cases by the same panel member resulted in a change of diagnosis 15% of the time. Among the histologic features evaluated, only the presence of mitoses in the infiltrating cells showed a trend toward an unfavorable outcome. CONCLUSION: Pathologic diagnosis in the CTCL disease spectrum should be interpreted with caution and then only in conjunction with the clinical evaluation. As expected, the use of an average value from a panel of readers added a component of stability to the histologic interpretation.

Biopsy↗

PubMed2003

Fast kinetic determination of 1-naphthylacetic acid in commercial formulations, soils, and fruit samples using stopped-flow phosphorimetry.

A kinetic method has been developed for the determination of 1-naphthylacetic acid by means of micellar-stabilized room temperature phosphorescence (MSRTP) using the stopped-flow mixing technique. The main feature of this system is that it diminishes the time required for the deoxygenation of the micellar medium and for the phosphorescence development. Phosphorescence enhancers such thallium(I) nitrate, sodium dodecyl sulfate (SDS), and sodium sulfite were optimized to obtain maximum sensitivity. The pH was also optimized as it strongly affects the luminescent properties of 1-naphthylacetic acid. A pH of 6.6 was selected as adequate for the phosphorescence development. The kinetic curve of 1-naphthylacetic acid phosphorescence was scanned at lambda(ex) = 278 nm and lambda(em) = 490 nm, and the maximum rate of phosphorescence was taken as the analytical signal. This was obtained by calculating the maximum slope of the curve in an interval of 3.6 s as it provided a good noise-to-signal ratio. This method permitted the determination of 1-naphthylacetic acid throughout a concentration range of 100-1800 ng mL(-1) with high precision (relative standard error = 0.91% and relative standard deviation = 2.30%; 1-naphthylacetic acid concentration = 800 ng mL(-1)). According to the Clayton criterion, the detection limit was 45 ng mL(-1). The same limit resulted in 39.3 ng mL(-1) when the error propagation theory was applied. The applicability of the method was successfully demonstrated by determining 1-naphthylacetic acid in different kind of samples, such as phytosanitary products, soils, pears, and apples. Recovery values not significantly different from the nominal content or the spiked amount were found for these determinations.

Agrochemicals↗

PubMed2004

Tetrapeptides induce selective recognition for G-quadruplexes when conjugated to a DNA-binding platform.

3,6-Bis-peptide acridine and acridone conjugates have been designed and synthesised to selectively interact with G-quadruplex DNA. The ligand properties are peptide sequence dependent, the highest discrimination being obtained with the FRHR tetrapeptide (up to >50-fold specificity). Molecular modeling studies have helped us rationalise the data and suggest that human telomeric quadruplex DNA can readily accommodate tetrapeptides, and furthermore that FRHR contributes to stabilization of the complex by non-bonded interactions within the TTA loop pockets of the quadruplex. These studies indicate that targeting distinct features of a G-quadruplex with hybrid molecules is a promising strategy for discriminating between quadruplex and duplex DNA.

Acridines↗

PubMed2003

Nonpeptidic chymase inhibitors: design and structure-activity relationships of pyrimidinone derivatives based on the predicted binding mode of a peptidic inhibitor.

While the biological reaction of chymase have been often studied for ten years, the pathophysiological role of chymase has not been fully elucidate due to a lack of effective inhibitors featuring potent inhibitory activity, specificity, and metabolic stability. Recently the discovery of a structurally varied range of novel nonpeptidic inhibitors presents new opportunities to explore the role of chymase under both physiological and pathophysiological conditions and to develop therapeutic agents for chymase-induced diseases. In this article the structure and the inhibitory mechanism of nonpeptidic chymase inhibitors are discussed, with special emphasis on design and structure-activity relationships of pyrimidinone derivative where inhibitory activity, protease selectivity, and pharmacokinetic profile are clarified.

Animals↗

PubMed1991

Kinetics of rapid RNA evolution in vitro.

A rapidly acquired partial resistance to the replicase antagonist, ethidium bromide (EB), seen by Spiegelman and coresearchers in Q beta RNA variants competitively replicating under defined conditions in vitro, reflected existence of a pool of mutant RNA molecules, preadapted to EB, and their cross-propagation from the pre-EB optimum species, MDV-1, and from other kindred variants, some of which remained undetected, according to this quantitative analysis of midivariant RNA replication kinetics. DNAlike features of their evolution, such as the cloning of variants from an MDV-1 subtype and a compliance with the fundamental theorem of natural selection, resulted from the suppression, both real and apparent, of intrinsic RNA heterogeneity through sampling and detection methods, and also by the ascendency of self-propagation over cross-propagation with advancement of a superior variant. The deficit in mean polymer fitness, compared with optimum levels, determines the lower limit of this heterogeneity. Stability conditions for frequency equilibrium and strategies for counteracting viral drug resistance have been considered.

Biological Evolution↗

PubMed2026

Yeast Rad55-Rad57-SHU paralog complex dynamically promotes Rad51 filament formation.

Homologous recombination (HR) is an important DNA repair pathway that safeguards genome integrity. During HR, the Rad51 nucleoprotein filaments catalyze strand invasion into a homologous duplex DNA. Filament formation requires a conserved family of Rad51 paralogs that act as tumor suppressors in humans. By capturing six distinct states using cryo-electron microscopy, we reveal that the Saccharomyces cerevisiae Rad51 paralog complex, composed of the Rad55-Rad57 heterodimer and the SHU (Psy3-Csm2-Shu1-Shu2) complex, selectively brings Rad51 to single-stranded DNA to seed filament formation. Rad51 itself is a transient yet integral component of this machinery which binds along the Rad57 subunit to complete a high-affinity DNA-binding site. We also uncover a dual-nucleotide regulatory mechanism: a structural ADP molecule stabilizes the complex, while a second, catalytic ATPase site at the Rad57-Rad51 interface promotes the release of the paralog complex. These structural and mechanistic features provide a blueprint for understanding the function of Rad51 paralogs across eukaryotes.

Saccharomyces cerevisiae Proteins↗

PubMed2000

Onconase: an unusually stable protein.

Several members of the RNase A superfamily are endowed with antitumor activity, showing selective cytotoxicity toward tumor cell lines. One of these is onconase, the smallest member of the superfamily, which at present is undergoing phase-III clinical trials as an antitumor drug. Our investigation focused on other interesting features of the enzyme, such as its unusually high denaturation temperature, its low catalytic activity, and its renal toxicity as a drug. We used differential scanning calorimetry, circular dichroism, fluorescence measurements, and limited proteolysis to investigate the molecular determinants of the stability of onconase and of a mutant, (M23L)-ONC, which is catalytically more active than the wild-type enzyme, and fully active as an antitumor agent. The determination of the main thermodynamic parameters of the protein led to the conclusion that onconase is an unusually stable protein. This was confirmed by its resistance to proteolysis. On the basis of this analysis and on a comparative analysis of the (M23L)-ONC variant of the protein, which is less stable and more sensitive to proteolysis, a model was constructed in line with available data. This model supports a satisfactory hypothesis of the molecular basis of onconase stability and low-catalytic activity.

Amino Acid Substitution↗

PubMed2006

Engineering and characterization of a stabilized alpha1/alpha2 module of the class I major histocompatibility complex product Ld.

The major histocompatibility complex (MHC) is the most polymorphic locus known, with thousands of allelic variants. There is considerable interest in understanding the diversity of structures and peptide-binding features represented by this class of proteins. Although many MHC proteins have been crystallized, others have not been amenable to structural or biochemical studies due to problems with expression or stability. In the present study, yeast display was used to engineer stabilizing mutations into the class I MHC molecule, Ld. The approach was based on previous studies that showed surface levels of yeast-displayed fusion proteins are directly correlated with protein stability. To engineer a more stable Ld, we selected Ld mutants with increased surface expression from randomly mutated yeast display libraries using anti-Ld antibodies or high affinity, soluble T-cell receptors (TCRs). The most stable Ld mutant, Ld-m31, consisted of a single-chain MHC module containing only the alpha1 and alpha2 domains. The enhanced stability was in part due to a single mutation (Trp-97 --> Arg), shown previously to be present in the allele Lq. Mutant Ld-m31 could bind to Ld peptides, and the specific peptide.Ld-m31 complex (QL9.Ld-m31) was recognized by alloreactive TCR 2C. A soluble form of the Ld-m31 protein was expressed in Escherichia coli and refolded from inclusion bodies at high yields. Surface plasmon resonance showed that TCRs bound to peptide.Ld-m31 complexes with affinities similar to those of native full-length Ld. The TCR and QL9.Ld-m31 formed complexes that could be resolved by native gel electrophoresis, suggesting that stabilized alpha1/alpha2 class I platforms may enable various structural studies.

Alleles↗

PubMed2026

NCBoost v2: a classifier for non-coding single-nucleotide variants in Mendelian diseases.

MOTIVATION: The current diagnostic rate of rare diseases through whole-genome sequencing has stabilized at around 30% on average, highlighting the need for improved computational scores to identify pathogenic variants. In 2019, we developed NCBoost, a supervised-learning approach that mined a comprehensive set of sequence constraint features and proved particularly well suited to identifying high-effect pathogenic non-coding variants in genetic diseases. Since its first release, the substantial increase in the number of variants available for training, as well as the enhanced capacity to detect purifying selection signals from large-scale genome sequencing projects, motivated an update of NCBoost. RESULTS: We implemented NCBoost v2, a pathogenicity score for non-coding single-nucleotide variants, trained on the largest set of curated pathogenic variants in monogenic Mendelian diseases available to date. It leverages conservation features computed from recent large-scale genomic consortia such as Zoonomia and gnomAD, and incorporates recent splice-altering predictive scores. NCBoost v2 outperformed alternative state-of-the-art methods in a variety of scenarii, providing more consistent scores across non-coding genomic regions and fine-tuning the scoring of pathogenic splice-altering variants in Mendelian disease genes. AVAILABILITY AND IMPLEMENTATION: NCBoost v2 software is implemented in Python 3.10 and is freely available under the GNU General Public License Version 3 at https://doi.org/10.5281/zenodo.16029049 and https://github.com/RausellLab/NCBoost-2, together with precomputed scores for the human genome assembly GRCh38.

Polymorphism, Single Nucleotide↗

PubMed2005

UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs.

The 5' and 3' untranslated regions of eukaryotic mRNAs play crucial roles in the post-transcriptional regulation of gene expression through the modulation of nucleo-cytoplasmic mRNA transport, translation efficiency, subcellular localization and message stability. UTRdb is a curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs, derived from several sources of primary data. Experimentally validated functional motifs are annotated (and also collated as the UTRsite database) and cross-links to genomic and protein data are provided. The integration of UTRdb with genomic and protein data has allowed the implementation of a powerful retrieval resource for the selection and extraction of UTR subsets based on their genomic coordinates and/or features of the protein encoded by the relevant mRNA (e.g. GO term, PFAM domain, etc.). All internet resources implemented for retrieval and functional analysis of 5' and 3' untranslated regions of eukaryotic mRNAs are accessible at http://www.ba.itb.cnr.it/UTR/.

3' Untranslated Regions↗

PubMed1993

Development of a MUMPS-based anticoagulant management system.

A computerised anticoagulant management system written in Digital Standard MUMPS, and incorporated into an ACT Medisys Computer Integrated Laboratory Management System (CILMS), has been developed. The system will automatically adjust and prescribe warfarin dosage for selected patients and set clinic appointments based upon defined criteria. Other significant features include printed patient dosage cards, cumulative worksheets for clinicians, clinic and transport lists, statistical searches, rapid enquiry facilities and operator alerts. After 20 months of successful running, a system has evolved which has greatly improved the efficiency of the anticoagulant clinic and the quality of anticoagulant control. Significant savings have been made in medical staff time, patient waiting times have been greatly reduced and the stability of warfarin control has increased. The service has more recently been extended to patients controlled by their general practitioners, with all the associated benefits.

Anticoagulants↗