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At least 757 records · Page 42Linked to original sources
PubMed1990

Calculation of binding energies using a robust molecular mechanics technique: application to an antibody-antigen complex.

A novel molecular mechanics technique, which is both computationally efficient and robust, for calculation of relative stability of macromolecules and binding energies is presented. The technique delivers exact results for a number of hypothetical systems; the technique can be used to energy minimize a number of similar macromolecules simultaneously; simultaneous minimization of many structures requires computer time only fractionally over that needed to energy minimize one such structure. The method has been used to successfully calculate the relative stability and binding of two avian lysozymes to the monoclonal antibody D1.3.

Antibody Specificity↗
PubMed1991

Robust electromagnetic probe for the monitoring of lithotriptor output.

The ability to measure the powers and pressures generated by extracorporeal lithotriptors is important for both patient safety and treatment planning. Regular measurements of output have been impossible in the past because there have been no instruments available that could withstand prolonged or repeated exposure to lithotriptor fields. The literature contains reports of various devices that have been used to make measurements of lithotriptor output, and these are briefly described here. The authors report the use of a new electromagnetic probe as a robust monitoring device. It has been tested by comparison with a PVdF coplanar membrane hydrophone, by comparison with the results of disintegrating a series of synthetic stones and by impact measurements. The electromagnetic probe has also been used to monitor the output of a piezoelectric extracorporeal lithotriptor over a 12-month period. Fluctuations in pulse energy of up to 350% were observed.

Electromagnetic Phenomena↗
PubMed1991

NMDA receptors participate differentially in two different synaptic inputs in neurons of the zebra finch robust nucleus of the archistriatum in vitro.

Intracellular recordings were made from neurons of the zebra finch song control nucleus, the robust nucleus of the archistriatum (RA), in slice preparations to examine synaptic responses. RA neurons receive two separate inputs from the lateral magnocellular nucleus of the anterior neostriatum (1MAN) and the caudal nucleus of the ventral hyperstriatum (HVc). Excitatory postsynaptic potentials (EPSPs) elicited by stimulation of the fibers of the 1MAN were greatly reduced by 2-amino-5-phosphonopentanoic acid in many cells, whereas EPSPs elicited by stimulation of the fibers of the HVc were greatly reduced by 6-cyano-7-nitroquinoxaline-2,3-dione in all cells. It is concluded that RA neurons receive inputs mediated mostly by N-methyl-D-aspartate (NMDA) receptors from the 1MAN, and inputs mediated mostly by non-NMDA receptors from the HVc.

2-Amino-5-phosphonovalerate↗
PubMed1993

Robust induction of AP-1 transcription factor DNA binding activity in the hippocampus of aged rats.

Activation of expression of genes encoding components of AP-1 transcription factor (c-fos, c-jun and their cognates) as well as AP-1 itself has been repeatedly shown to coincide with long-term cellular responses. For the proliferating cells where functional involvement of AP-1 in physiological activity has been proved, cellular senescence as well as aging at level of the organism results in an alteration of the AP-1. The aim of the present study was to analyze whether there is an aging-related defect in the formation of AP-1 transcription factor in the brain. AP-1 has been shown previously to be inducible by several stimuli in the cells of the central nervous system, including proconvulsant treatment of pentylenetetrazole (PTZ). The present studies found that PTZ robustly induced AP-1 DNA binding activity, evaluated by the electrophoretic mobility shift assay, in hippocampi of aged (2-year-old) rats, indicating no aging-related AP-1 defect in the rat brain.

Aging↗
PubMed1979

Homo sapiens ascorbicus, a biochemically corrected robust human mutant.

Homo sapiens' gene pool contains a defective gene for the synthesis of the active enzyme protein, L-gulonolactone oxidase(GLO). The absence of GLO in the human liver blocks the normal mammalian conversion of blood sugar into ascorbate, leading to the potentially-fatal "inborn error of carbohydrate metabolism", the genetic disease, Hypoascorbemia (in the older nomenclature- scurvy). To survive, humans need exogenous sources of daily ascorbate. Most mammals have the intact gene for GLO synthesis and produce generous daily amounts of the liver metabolite, ascorbate; for instance, an unstressed 70 Kg goat is capable of producing over 13 grams of ascorbate daily and much more under stress. The recommended dietary allowance of 45 milligrams of ascorbate a day for human adults, now proposed and used by nutritionists, is grossly inadequate to restore Homo sapiens to a normal mammalian ascorbate physiology. To correct fully this human genetic defect and banish epidemic chronic subclinical scurvy requires daily intakes of ascorbate equivalent to, at least, the amounts synthesized by the other mammals. Humans kept on a long term regime of full correction of this birth defect show great salutary benefits in health maintenance, disease therapy and slowing of the aging process. This can be regarded as the creation of a new and more robust, longer-living, tough human sub-species, Homo sapiens ascorbicus, by the biochemical reversal of a primate mutation occurring some 60 million years ago. Some of the practical benefits and pathways of future clinical research are discussed.

Aging↗
PubMed2025

General and robust sample preparation strategies for cryo-EM studies of CRISPR-Cas9 and Cas12 enzymes.

Cas9 and Cas12 are RNA-guided DNA endonucleases derived from prokaryotic CRISPR-Cas adaptive immune systems that have been repurposed as versatile genome-engineering tools. Computational mining of genomes and metagenomes has expanded the diversity of Cas9 and Cas12 enzymes that can be used to develop versatile, orthogonal molecular toolboxes. Structural information is pivotal to uncovering the precise molecular mechanisms of newly discovered Cas enzymes and providing a foundation for their application in genome editing. In this chapter, we describe detailed protocols for the preparation of Cas9 and Cas12 enzymes for cryo-electron microscopy. These methods will enable fast and robust structural determination of newly discovered Cas9 and Cas12 enzymes, which will enhance the understanding of diverse CRISPR-Cas effectors and provide a molecular framework for expanding CRISPR-based genome-editing technologies.

Cryoelectron Microscopy↗
PubMed2005

Touchdown thermocycling program enables a robust single nucleotide polymorphism typing method based on allele-specific real-time polymerase chain reaction.

Different methods have been developed for single nucleotide polymorphism (SNP) typing during recent years. Allele-specific polymerase chain reaction (ASPCR) is a cost-saving method that scores SNPs by difference of the PCR efficiency of allele-specific primers. However, ASPCR for SNP typing is notoriously confounded for its locus-specific unpredictability and the laborious gel electrophoresis. In the current study, we investigated the real-time kinetics of ASPCR and found that a simple touchdown thermocycling protocol improved its specificity significantly. Combined with real-time PCR, we developed a homogeneous genotyping method and scored more than 1000 genotypes, including all transition and transversion SNPs. A clear genotyping result was identified and validated the robustness of the method. Optimization of reactions and intrinsic modification of allele-specific primers, a laborious process but one that is repeatedly reported to be inevitable for successful ASPCR, was proved to be unnecessary with our method. Accuracy was confirmed with mass spectrometry. These characters enabled real-time ASPCR with the touchdown thermocycling protocol being very competitive among various SNP typing methods for large-scale genetic studies.

Alleles↗
PubMed2006

Jumbo squid beaks: inspiration for design of robust organic composites.

The hard tissues found in some invertebrate marine organisms represent intriguing paradigms for robust, lightweight materials. The present study focuses on one such tissue: that comprising the beak of the jumbo squid (Dosidicus gigas). Its main constituents are chitin fibers (15-20wt.%) and histidine- and glycine-rich proteins (40-45%). Notably absent are mineral phases, metals and halogens. Despite being fully organic, beak hardness and stiffness are at least twice those of the most competitive synthetic organic materials (notably engineering polymers) and comparable to those of Glycera and Nereis jaws. Furthermore, the combination of hardness and stiffness makes the beaks more resistant to plastic deformation when in contact with blunt abrasives than virtually all metals and polymers. The 3,4-dihydroxy-l-phenylalanine and abundant histidine content in the beak proteins as well as the pigmented hydrolysis-resistant residue are suggestive of aromatic cross-linking. A high cross-linking density between the proteins and chitin may be the single most important determinant of hardness and stiffness in the beak. Beak microstructure is characterized by a lamellar arrangement of the constituents, with a weak interface that promotes crack deflection and endows the structure with high fracture toughness. The susceptibility of this microstructure to cracking along these interfaces from contact stresses at the external surface is mitigated by the presence of a protective coating.

Animals↗
PubMed2007

Creating a robust public health infrastructure for physical activity promotion.

The essential role of physical activity both as an independent protective factor against numerous common chronic diseases and as a means to maintain a healthy weight is gaining increasing scientific recognition. Although the science of physical activity promotion is advancing rapidly, the practice of promoting physical activity at a population level is in its infancy. The virtual absence of a public health practice infrastructure for the promotion of physical activity at the local level presents a critical challenge to control policy for chronic disease, and particularly obesity. To translate the increasing evidence of the value of physical activity into practice will require systemic, multilevel, and multisectoral intervention approaches that build individual capability and organizational capacity for behavior change, create new social norms, and promote policy and environmental changes that support higher levels of energy expenditure across the population. This paper highlights societal changes contributing to inactivity; describes the evolution and current status of population-based public health physical activity promotion efforts in research and practice settings; suggests strategies for engaging decision makers, stakeholders, and the general public in building the necessary infrastructure to effectively promote physical activity; and identifies specific recommendations to spur the creation of a robust public health infrastructure for physical activity.

Exercise↗
PubMed2006

Robust preference for a flavor paired with intragastric glucose acquired in a single trial.

Rats learn to prefer flavors followed by postingestive action of nutrients. This experiment demonstrates that such preferences can be acquired with only a single, brief pairing of a novel flavor with intragastric (IG) glucose infusion. Male rats with IG catheters consumed unflavored saccharin in daily 10-min sessions, and then received in counterbalanced order on separate days a single pairing of coffee- or vinegar-flavored saccharin with IG glucose, and of the opposite flavor with IG water. Rats subsequently preferred the glucose-paired flavor in a choice test in the absence of glucose infusion. Preference was robust, persisting through repeated non-reinforced testing.

Animals↗
PubMed2006

Determination of 222Rn in fresh water: development of a robust method of analysis by alpha/beta separation liquid scintillation spectrometry.

Liquid scintillation spectrometry is used widely for determining (222)Rn in natural waters; however, the benefits of alpha/beta separation have not been fully explored. The extractants toluene and Ultima Gold F were compared, and both performed well for a range of extreme waters. A robust method for calibrating extraction and counting efficiencies has been developed. Detection limits are 20 mBql(-1) (toluene) and 16 mBql(-1) (UGF) for a 60 min count and 600-ml sample, halving the required sample volume.

Alpha Particles↗
PubMed2006

Spectral and kinetic resolution of the bc1 complex components in situ: a simple and robust alternative to the traditional difference wavelength approach.

The kinetics of the cytochrome (cyt) components of the bc(1) complex (ubiquinol: cytochrome c oxidoreductase, Complex III) are traditionally followed by using the difference of absorbance changes at two or more different wavelengths. However, this difference-wavelength (DW) approach is of limited accuracy in the separation of absorbance changes of components with overlapping spectral bands. To resolve the kinetics of individual components in Rhodobacter sphaeroides chromatophores, we have tested a simplified version of a least squares (LS) analysis, based on measurement at a minimal number of different wavelengths. The success of the simplified LS analysis depended significantly on the wavelengths used in the set. The "traditional" set of 6 wavelengths (542, 551, 561, 566, 569 and 575 nm), normally used in the DW approach to characterize kinetics of cyt c(tot) (cyt c(1)+cyt c(2)), cyt b(L), cyt b(H), and P870 in chromatophores, could also be used to determine these components via the simplified LS analysis, with improved resolution of the individual components. However, this set is not sufficient when information about cyts c(1) and c(2) is needed. We identified multiple alternative sets of 5 and 6 wavelengths that could be used to determine the kinetics of all 5 components (P870 and cyts c(1), c(2), b(L), and b(H)) simultaneously, with an accuracy comparable to that of the LS analysis based on a full set of wavelengths (1 nm intervals). We conclude that a simplified version of LS deconvolution based on a small number of carefully selected wavelengths provides a robust and significant improvement over the traditional DW approach, since it accounts for spectral interference of the different components, and uses fewer measurements when information about all five individual components is needed. Using the simplified and complete LS analyses, we measured the simultaneous kinetics of all cytochrome components of bc(1) complex in the absence and presence of specific inhibitors and found that they correspond well to those expected from the modified Q-cycle. This is the first study in which the kinetics of all cytochrome and reaction center components of the bc(1) complex functioning in situ have been measured simultaneously, with full deconvolution over an extended time range.

Electron Transport Complex III↗
PubMed2004

Highly robust lipid membranes on crystalline S-layer supports investigated by electrochemical impedance spectroscopy.

In the present work, S-layer supported lipid membranes formed by a modified Langmuir-Blodgett technique were investigated by electrochemical impedance spectroscopy (EIS). Basically two intermediate hydrophilic supports for phospholipid- (DPhyPC) and bipolar tetraetherlipid- (MPL from Thermoplasma acidophilum) membranes have been applied: first, the S-layer protein SbpA isolated from Bacillus sphaericus CCM 2177 recrystallized onto a gold electrode; and second, as a reference support, an S-layer ultrafiltration membrane (SUM), which consists of a microfiltration membrane (MFM) with deposited S-layer carrying cell wall fragments. The electrochemical properties and the stability of DPhyPC and MPL membranes were found to depend on the used support. The specific capacitances were 0.53 and 0.69 microF/cm(2) for DPhyPC bilayers and 0.75 and 0.77 microF/cm(2) for MPL monolayers resting on SbpA and SUM, respectively. Membrane resistances of up to 80 mega Ohm cm(2) were observed for DPhyPC bilayers on SbpA. In addition, membranes supported by SbpA exhibited a remarkable long-term robustness of up to 2 days. The membrane functionality could be demonstrated by reconstitution of membrane-active peptides such as valinomycin and alamethicin. The present results recommend S-layer-supported lipid membranes as promising structures for membrane protein-based biosensor technology.

Alamethicin↗
PubMed2004

MK-0767, a novel dual PPARalpha/gamma agonist, displays robust antihyperglycemic and hypolipidemic activities.

Here, we characterize the actions of MK-0767, a dual ligand of the nuclear receptors peroxisome proliferator-activated receptor (PPAR)alpha and PPARgamma. In cell-based assays, MK-0767 produced potent activation of human PPARgamma and PPARalpha with a gamma:alpha potency ratio of approximately 2. The dual agonist induced high affinity interactions of PPARalpha and PPARgamma with the transcriptional coactivator CBP in vitro. In ob/ob mice, MK-0767 normalized hyperglycemia and hyperinsulinemia with equal or greater potency and efficacy than pioglitazone. Treatment of hamsters with MK-0767 produced substantial reductions in blood cholesterol and triglycerides. In dogs, MK-0767 reduced serum cholesterol levels with a potency more than 10-fold greater than simvastatin. The efficacies of MK-0767 and simvastatin were additive when given together. We conclude that MK-0767 is a potent dual PPARalpha/gamma agonist with robust insulin sensitizing and hypolipidemic activities.

Animals↗
PubMed2004

Correlations between genomic GC levels and optimal growth temperatures are not 'robust'.

Musto et al. [FEBS Lett. 573 (2004) 73] studied the correlations between GC levels and optimal growth temperatures in 20 prokaryotic families. They reported that positive correlations are generally observed, and many of these are significant. Here, we have shown that these correlations are not "robust," i.e., correlation coefficients and/or significance of correlations can be considerably influenced by exclusion of very few (even as small as one) species from each dataset. The sensitivity of correlations is assumed as a result of high levels of bias in the family datasets. We concluded that solely based on these data, one cannot establish that GC contents of prokaryotic genomes increase as a result of growth temperature increments.

Adaptation, Physiological↗
PubMed2006

Robust lanthanide-based assays for the detection of anti-apoptotic Bcl-2-family protein antagonists.

Anti-apoptotic Bcl-2-family proteins (Bcl-2, Bcl-x(L), Bfl-1, Mcl-1, Bcl-W and Bcl-B) have been recently validated as drug discovery targets for cancer, owed to their ability to confer tumor resistance to chemotherapy or radiation. The anti-apoptotic activity of Bcl-2 proteins is due to their ability to heterodimerize with their pro-apoptotic counterparts (proteins such as Bad, Bim or Bid) via a conserved peptide region termed BH3. Thus, molecules that mimic pro-apoptotic BH3 domains represent a direct approach to overcoming the protective effects of anti-apoptotic proteins such as Bcl-2 and Bcl-x(L). Here, we report on the development and evaluation of two novel Lanthanide-based assays that are formatted for high-throughput screening of small molecules capable of antagonizing BH3-Bcl-2 interactions. The assay conditions, robustness and reproducibility (Z' factors) are described. These assays represent useful tools to enable further studies in the search for novel, safe and effective anti-cancer agents targeting Bcl-2-family proteins.

Amino Acid Sequence↗
PubMed2004

Robust and tissue-specific expression of TPH2 versus TPH1 in rat raphe and pineal gland.

BACKGROUND: Regulation of raphe serotonergic cells is fundamental to the prevailing hypothesis of major depression pathophysiology. Tryptophan hydroxylase (TPH) is the rate-limiting enzyme in serotonin biosynthesis, but brainstem TPH mRNA expression has been difficult to measure and study. Recently, a novel paralog of TPH, TPH2 (or neuronal TPH), was described, but its anatomic expression is unknown. METHODS: In situ hybridization histochemical survey was conducted across Sprague-Dawley rat brain for TPH1 and TPH2 mRNA. Semiquantitative techniques were used to estimate relative mRNA levels in individual cells. RESULTS: Almost exclusively, TPH2 mRNA is expressed in raphe, in a pattern overlapping the histologically defined raphe nuclei. In sharp contrast, TPH1 (the previously known TPH) is expressed predominantly in pineal gland. There is no appreciable overlap in the expression of these paralogs. The level of TPH2 mRNA expression in individual raphe cells is approximately 2.5-fold greater than the level of TPH1 expression in pinealocytes. CONCLUSIONS: TPH2 mRNA has an anatomic expression pattern consistent with brainstem raphe nuclei and is likely to be the gene giving rise to the majority of TPH activity in these cells. The robust expression of TPH2 in brainstem should facilitate studies on the transcriptional regulation of raphe serotonin biosynthesis.

Amino Acid Sequence↗
PubMed2004

Robust and emergent Physarum logical-computing.

There have been many attempts for realization of emergent computing, but the notion of emergent computing is still ambiguous. In an open system, emergence and an error cannot be specified distinctly, because they are dependent on the dis-equilibration process between local and global behaviors. To manifest such an aspect, we implement a Boolean gate as a biological device made of slime mold Physarum polycephalum. A Physarum (slime mold) Boolean gate could be an internally instable machine, while it has the potential for emergent computing. First, we examined whether Physarum Boolean gate works properly, and then examined its behaviors when the gate is collapsed in terms of hardware. The behavior of Physarum changes and self-repairing computing is achieved as a result. The self-repairing against internal failure is one of attributes of emergent and robust computing.

Animals↗