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Biomedical subjects

Matthew A Cooper

Publications and source records attributed to Matthew A Cooper.

At least 19 recordsLinked to original sources
PubMed2006

Profiling of molecular interactions in real time using acoustic detection.

Acoustic sensors that exploit resonating quartz crystals to directly detect the binding of an analyte to a receptor are finding increasing utility in the quantification of clinically relevant analytes. We have developed a novel acoustic detection technology, which we term resonant acoustic profiling (RAP). This technology builds on the fundamental basics of the "quartz crystal microbalance" or "QCM" with several key additional features including two- or four-channel automated sample delivery, in-line referencing and microfluidic sensor 'cassettes' that are pre-coated with easy-to-use surface chemistries. Example applications are described for the quantification of myoglobin concentration and its interaction kinetics, and for the ranking of enzyme-cofactor specificities.

Biosensing Techniques↗
PubMed2006

Non-optical screening platforms: the next wave in label-free screening?

The use of optical biosensors for compound screening was first demonstrated in the mid-1990s, but there has been limited uptake in the market owing to issues of limited throughput and a lack of applications for key receptor classes. Recently, several start-up and established tools companies have exploited non-optical detection modalities that seek to address the shortcomings of more established optical approaches. Platforms based on acoustic resonance, electrical impedance, microcantilevers, nanowires and differential calorimetry are beginning to appear with commercially available products targeted at post-high-throughput screening hit confirmation and mode-of-action studies. This article highlights key advances in commercial label-free analysis platforms, which complement more traditional optical system and which also allow novel assay formats for the analysis of previously intractable targets.

Biosensing Techniques↗
PubMed2006

Optical biosensors: where next and how soon?

From a direct comparison of the technical benefits of labelled reporter assays with the benefits of label-free assays, label-free appears to have significant advantages. Faster assay development times; accurate, high information content data; and less interference from labels. However, optical label-free platforms have not yet made a major impact in the drug discovery technology markets; are often viewed as having poor throughput, limited application; and are difficult to learn and use effectively.

Biosensing Techniques↗
PubMed2006

Quantification of small molecule-receptor affinities and kinetics by acoustic profiling.

The label-free RAPid 4 system that exploits resonant acoustic profiling (RAP) from Akubio (Cambridge, UK) was used to determine the affinity and kinetics for several different small molecule-receptor interactions. This was achieved by attaching the target receptor to the surface of quartz crystal resonators through a variety of specific coupling chemistries, followed by application of a small-molecular-weight ligand to the receptor via a microfluidic flow-based delivery system. Rank order of binding was determined for very weak interactions such as cofactor binding to glucose dehydrogenase. Moderate interaction affinities and binding kinetics could be determined for biotin binding to a specific antibody, and also for several low-molecular-weight sulfonamide analogues binding to human carbonic anhydrase isoform II. The equilibrium binding constants were in general agreement with the values obtained by kinetic analysis of the data, as well as with previously published values obtained using surface plasmon resonance, stopped flow fluorescence, and isothermal titration calorimetry.

Acoustics↗
PubMed2005

Direct quantification of analyte concentration by resonant acoustic profiling.

BACKGROUND: Acoustic sensors that exploit resonating quartz crystals directly detect the binding of an analyte to a receptor. Applications include detection of bacteria, viruses, and oligonucleotides and measurement of myoglobin, interleukin 1beta (IL-1beta), and enzyme cofactors. METHODS: Resonant Acoustic Profiling was combined with a microfluidic lateral flow device incorporating an internal reference control, stable linker chemistry, and immobilized receptors on a disposable sensor "chip". Analyte concentrations were determined by analyzing the rate of binding of the analyte to an appropriate receptor. RESULTS: The specificity and affinity of antibody-antigen and enzyme-cofactor interactions were determined without labeling of the receptor or the analyte. We measured protein concentrations (recombinant human IL-1beta and recombinant human myoglobin) and quantified binding of cofactors (NADP+ and NAD+) to the enzyme glucose dehydrogenase. Lower limits of detection were approximately 1 nmol/L (17 ng/mL) for both IL-1beta and human myoglobin. The equilibrium binding constant for NADP+ binding to glucose dehydrogenase was 2.8 mmol/L. CONCLUSIONS: Resonant Acoustic Profiling detects analytes in a relatively simple receptor-binding assay in <10 min. Potential applications include real-time immunoassays and biomarker detection. Combination of this technology platform with existing technologies for concentration and presentation of analytes may lead to simple, label-free, high-sensitivity methodologies for reagent and assay validation in clinical chemistry and, ultimately, for real-time in vitro diagnostics.

Acoustics↗
PubMed2005

Repeated agonistic encounters in hamsters modulate AVP V1a receptor binding.

Arginine vasopressin (AVP) regulates aggression in male Syrian hamsters. In this study, we used radioligand receptor autoradiography to examine whether changes in agonistic behavior following acute and repeated social defeat are accompanied by changes in AVP V1a receptor binding. Social defeat produced high levels of submissive behavior and a loss of territorial aggression when hamsters were subsequently tested with a novel intruder, and repeated agonistic encounters produced similar behavioral changes in subordinates. AVP V1a receptor binding was not reduced by acute social defeat but was affected by repeated agonistic encounters. Dominants had significantly more AVP V1a receptor binding in lateral portions of the ventromedial hypothalamus (VMHL) than did their subordinate opponents, but subordinates were no different from controls. In contrast, receptor binding did not differ in most other brain regions examined. The changes in receptor binding appear to be independent of testosterone levels, as testosterone levels did not differ among dominants, subordinates, and controls. Our results suggest that changes in AVP V1a receptors do not account for the changes in agonistic behavior produced by acute social defeat but AVP V1a binding in the VMHL correlates with, and may modulate, the behavioral changes that occur following repeated experiences of victory.

Aggression↗
PubMed2005

Reconciliation and relationship quality in Assamese macaques (Macaca assamensis).

A consistent conclusion in reconciliation research is that animals that reconcile are likely to have strong social bonds. This has led to the hypothesis that reconciliation occurs most often between valuable social partners. We tested this hypothesis in a group of Assamese macaques (Macaca assamensis) living near a temple in Assam, India. Using focal sample and ad libitum data collection, we recorded the occurrence of reconciliation, grooming, and agonistic aiding, and the outcomes of approach. We used matrix association methods (TauKr correlation) to correlate reconciliation with grooming, aiding, and approach outcome. Females reconciled more often with females with which they had stronger grooming and aiding relationships. The correlation between reconciliation and aiding was significant for support to the aggressor and the victim. In contrast, no such correlations with reconciliation were found for males. This study provides evidence that females reconcile most often with valuable and compatible social partners. The results do not support the relationship-quality hypothesis for males, and we suggest that future studies give more consideration to the possibility that males reconcile for reasons other than to repair relationships with valuable partners.

Aggression↗
PubMed2005

Corticotropin-releasing factor type II (CRF-sub-2) receptors in the bed nucleus of the stria terminalis modulate conditioned defeat in Syrian hamsters (Mesocricetus auratus).

In Syrian hamsters (Mesocricetus auratus), social defeat produces a subsequent increase in submissive and defensive behavior and a loss of normal territorial aggression, which the authors have called conditioned defeat. In this study, the authors investigated the effect of blocking corticotropin-releasing factor (CRF) Type I and Type II receptors on conditioned defeat. Intracerebroventricular infusion of the CRF-sub-2 receptor antagonist antisauvagine-30 prior to testing significantly reduced conditioned defeat compared with vehicle controls, whereas the CRF-sub-1 receptor antagonist CP-154,526 had no effect. Also, infusion of antisauvagine-30 into the bed nucleus of the stria terminalis (BNST) 15 min, but not immediately, prior to testing reduced conditioned defeat in a dose-dependent manner. The authors' results provide evidence that CRF-sub-2 receptors in the BNST, but not CRF-sub-1 receptors, are an important component in the neural circuitry regulating conditioned defeat.

Aggression↗
PubMed2004

A biophysical characterisation of factors controlling dimerisation and selectivity in the NF-kappaB and NFAT families.

The Rel/NF-kappaB family of eukaryotic transcription factors bind DNA with high specificity and affinity as homo- or heterodimers to mediate a diverse range of biological processes. By comparison, the nuclear factor of activated T-cells (NFAT) family has been recognised as Rel homologues due to structural similarities between the DNA-binding domains, yet they bind DNA as lower-affinity monomers. The structural and functional overlap between the NF-kappaB and NFAT families suggests that they may be evolutionarily divergent from a common, monomeric ancestor but have evolved different mechanisms to achieve high-affinity binding to their target DNA sequences. In order to understand the origin of these mechanistic differences, we constructed two chimeric proteins, based on molecular modelling, comprising the DNA-binding domain of NFAT and the dimerisation domain of NF-kappaB p50, differing only in the position of the splice site. Biophysical characterisation of the wild-type and chimeric proteins revealed that one of the chimeras bound DNA as a high-affinity, NF-kappaB-like cooperative dimer, whilst the other bound as a lower-affinity, NFAT-like monomer, demonstrating the importance of the interdomain linker in controlling the intrinsic ability of NFATc to form dimers. In addition, we have studied the rate of exchange of monomers between preformed NF-kappaB dimers and have determined, for the first time, the intrinsic homodimerisation constant for NF-kappaB p50. These data support a model in which NF-kappaB proteins bind DNA both in vitro and in vivo as high-affinity preformed homo- or heterodimers, which in an unbound form can still exchange monomer units on a physiologically relevant timescale in vivo.

Amino Acid Sequence↗
PubMed2004

A novel method of resistance for influenza against a channel-blocking antiviral drug.

Effective antivirals are few and far between, and as such, the appearance of resistance toward such treatments is an obvious medical concern. In this article, we analyze the mechanism by which influenza attains resistance toward amantadine, a blocker of the viral M2 H(+) channel. Binding analyses of amantadine to M2 peptides from different viral strains showed that the virus has developed two alternate routes to avoid blockage of its channel: (1) a conventional route, in which the channel no longer binds the blocker and, hence, the blocker cannot exert its inhibitory function; and (2) a novel mechanism, in which binding of the blocker is retained, yet the function of the protein is unaffected. Pore diameter profiles revealed the molecular mechanism by which the virus may attain this novel type of resistance: an increase in the size of the channel. Thus, despite the drug binding the channel, it may not be able to block the pore, since the channel diameter has increased. Our findings may have broad ramifications in the design of new antivirals, and of novel blockers against malfunctioning human channels implicated in disease.

Amantadine↗
PubMed2003

Design, synthesis, conformational analysis and nucleic acid hybridisation properties of thymidyl pyrrolidine-amide oligonucleotide mimics (POM).

Pyrrolidine-amide oligonucleotide mimics (POM) 1 were designed to be stereochemically and conformationally similar to natural nucleic acids, but with an oppositely charged, cationic backbone. Molecular modelling reveals that the lowest energy conformation of a thymidyl-POM monomer is similar to the conformation adopted by ribonucleosides. An efficient solution phase synthesis of the thymidyl POM oligomers has been developed, using both N-alkylation and acylation coupling strategies. 1H NMR spectroscopy confirmed that the highly water soluble thymidyl-dimer, T2-POM, preferentially adopts both a configuration about the pyrrolidine N-atom and an overall conformation in D2O that are very similar to a typical C3'-endo nucleotide in RNA. In addition the nucleic acid hybridisation properties of a thymidyl-pentamer, T5-POM, with an N-terminal phthalimide group were evaluated using both UV spectroscopy and surface plasmon resonance (SPR). It was found that T5-POM exhibits very high affinity for complementary ssDNA and RNA, similar to that of a T5-PNA oligomer. SPR experiments also showed that T5-POM binds with high sequence fidelity to ssDNA under near physiological conditions. In addition, it was found possible to attenuate the binding affinity of T5-POM to ssDNA and RNA by varying both the ionic strength and pH. However, the most striking feature exhibited by T5-POM is an unprecedented kinetic binding selectivity for ssRNA over DNA.

Base Pairing↗
PubMed2003

Label-free screening of bio-molecular interactions.

The majority of techniques currently employed to interrogate a biomolecular interaction require some type of radio- or enzymatic- or fluorescent-labelling to report the binding event. However, there is an increasing awareness of novel techniques that do not require labelling of the ligand or the receptor, and that allow virtually any complex to be screened with minimal assay development. This review focuses on three major label-free screening platforms: surface plasmon resonance biosensors, acoustic biosensors, and calorimetric biosensors. Scientists in both academia and industry are using biosensors in areas that encompass almost all areas drug discovery, diagnostics, and the life sciences. The capabilities and advantages of each technique are compared and key applications involving small molecules, proteins, oligonucleotides, bacteriophage, viruses, bacteria, and cells are reviewed. The role of the interface between the biosensor surface (in the case of SPR and acoustic biosensors) and the chemical or biological systems to be studied is also covered with attention to the covalent and non-covalent coupling chemistries commonly employed.

Binding, Competitive↗
PubMed2003

G-quadruplex-specific peptide-hemicyanine ligands by partial combinatorial selection.

G-quadruplex DNA-specific ligands were generated using a combinatorial selection of tetrapeptides which were then conjugated to a hemicyanine scaffold. The heterocycle enhanced peptide binding affinity by approximately 1000-fold to give ligands with near micromolar affinity and >40-fold discrimination for quadruplex DNA over duplex.

Carbocyanines↗
PubMed2003

Biosensor profiling of molecular interactions in pharmacology.

Techniques employed to profile the pharmacological properties of a molecule in vitro normally require some type of radio-, enzymatic- or fluorescent-labeling of the ligand and/or the receptor. In contrast, biosensor techniques do not require labeling, and they allow virtually any complex to be screened with minimal assay development. Scientists in both academia and industry are now using biosensors in areas that encompass almost all sectors of drug discovery, diagnostics and the life sciences. Assays have been developed for the analysis of small molecules, proteins, oligonucleotides, bacteriophage, viruses, bacteria and cells. In addition, novel biosensor applications are being developed for the predictive profiling of key pharmacokinetic parameters of a molecule (adsorption, distribution, metabolism, excretion and toxicity).

Animals↗
PubMed2002

Mechanism of the regulation of type IB phosphoinositide 3OH-kinase byG-protein betagamma subunits.

Type IB phosphoinositide 3OH-kinase (PI3K) is activated by G-protein betagamma subunits (Gbetagammas). The enzyme is soluble and largely cytosolic in vivo. Its substrate, PtdIns(4,5)P(2), and the Gbetagammas are localized at the plasma membrane. We have addressed the mechanism by which Gbetagammas regulate the PI3K using an in vitro approach. We used sedimentation assays and surface plasmon resonance to determine association of type IB PI3K with lipid monolayers and vesicles of varying compositions, some of which had Gbetagammas incorporated. Association and dissociation rate constants were determined. Our results indicated that in an assay situation in vitro the majority of PI3K will be associated with lipid vesicles, irrespective of the presence or absence of Gbetagammas. In line with this, a constitutively active membrane-targeted PI3K construct could still be activated substantially by Gbetagammas in vitro. We conclude that Gbetagammas activate type IB PI3K by a mechanism other than translocation to the plasma membrane.

Animals↗
PubMed2002

Counter aggression and reconciliation in Assamese macaques (Macaca assamensis).

Patterns of aggressive and affiliative behavior, such as counter aggression and reconciliation, are said to covary in the genus Macaca; this is referred to as the systematic variation hypothesis. These behavior patterns constitute a species dominance style. Van Schaik's [1989] socioecological model explains dominance style in macaques in terms of within- and between-group contest competition. Dominance style is also said to correlate with phylogeny in macaques. The present study was undertaken to examine phylogenetic and socioecological explanations of dominance style, as well as the systematic variation hypothesis. We collected data on counter aggression and reconciliation from a habituated group of Assamese macaques (Macaca assamensis) at the Tukeswari Temple in Assam, India. The proportion of agonistic episodes that involved counter aggression was relatively low. Counter aggression, however, occurred more often among males than among females, and it was most common when females initiated aggression against males. The conciliatory tendency for this group of Assamese macaques was 11.2%. The frequency of reconciliation was low for fights among males and for fights among females, but reconciliation was particularly rare for opposite-sexed opponents. Female social relationships were consistent with the systematic variation hypothesis, and suggest a despotic dominance style. A despotic dominance style in Assamese macaques weakens the correlation between dominance style and phylogeny in macaques, but it is not inconsistent with the socioecological model. Male-female relationships were not well explained by the despotic-egalitarian framework, and males may well have more tolerant social relationships than do females. Sex differences need to be considered when categorizing species according to dominance style.

Aggression↗
PubMed2002

Optical biosensors in drug discovery.

Optical biosensors that exploit surface plasmon resonance, waveguides and resonant mirrors have been used widely over the past decade to analyse biomolecular interactions. These sensors allow the determination of the affinity and kinetics of a wide variety of molecular interactions in real time, without the need for a molecular tag or label. Advances in instrumentation and experimental design have led to the increasing application of optical biosensors in many areas of drug discovery, including target identification, ligand fishing, assay development, lead selection, early ADME and manufacturing quality control. This article reviews important advances in optical-biosensor instrumentation and applications, and also highlights some exciting developments, such as highly multiplexed optical-biosensor arrays.

Animals↗