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Mark Cooper

Publications and source records attributed to Mark Cooper.

13 recordsLinked to original sources
PubMed2006

Models for navigating biological complexity in breeding improved crop plants.

Progress in breeding higher-yielding crop plants would be greatly accelerated if the phenotypic consequences of making changes to the genetic makeup of an organism could be reliably predicted. Developing a predictive capacity that scales from genotype to phenotype is impeded by biological complexities associated with genetic controls, environmental effects and interactions among plant growth and development processes. Plant modelling can help navigate a path through this complexity. Here we profile modelling approaches for complex traits at gene network, organ and whole plant levels. Each provides a means to link phenotypic consequence to changes in genomic regions via stable associations with model coefficients. A unifying feature of the models is the relatively coarse level of granularity they use to capture system dynamics. Much of the fine detail is not directly required. Robust coarse-grained models might be the tool needed to integrate phenotypic and molecular approaches to plant breeding.

Arabidopsis↗
PubMed2006

Improving whole brain structural MRI at 4.7 Tesla using 4 irregularly shaped receiver coils.

Both higher magnetic field strengths (> or =3 T) and multiple receiver "array coils" can provide increased signal-to-noise ratio (SNR) for MRI. This increase in SNR can be used to obtain images with higher resolution, enabling better visualisation of structures within the human brain. However, high field strength systems also suffer from increased B(1) non-uniformity and increased power deposition, reaching specific absorption rate (SAR) limits more quickly. For these problems to be mitigated, a careful choice of both the pulse sequence design and transmit RF coil is required. This paper describes the use of a prototype array coil consisting of 4 irregularly shaped coils within a standard configuration for neuroimaging at 4.7 T (a head transmit/receive volume coil to minimise SAR and a head gradient insert for maximum gradient performance). With a fast spin echo (FSE) pulse sequence optimised for 4.7 T, this provides dramatically increased quality and resolution over a large brain volume. Using the array coil, a SNR improvement relative to the volume coil of 1-1.5 times in central brain areas and 2-3 times in cortical regions was obtained. Array coil images with a resolution of 352 x 352 x 2000 mum had a SNR of 16.0 to 26.2 in central regions and 19.9 to 34.8 in cortical areas. Such images easily demonstrate cortical myeloarchitecture, while still covering most of the brain in a approximately 12 min scan.

Algorithms↗
PubMed2006

Management strategies for patients with hypertension and diabetes: why combination therapy is critical.

Hypertension is commonly associated and acts synergistically with diabetes in increasing the risk of macrovascular and microvascular diabetic complications. Large-scale clinical trials have demonstrated that this risk is significantly reduced by intensive antihypertensive treatment, and accordingly, the Seventh Report of the Joint National Committee on Prevention, Detection, Evaluation, and Treatment of High Blood Pressure guideline has further lowered the blood pressure goals for diabetic subjects to <130/80 mm Hg. This implies that most diabetic patients will require the combination of two or more antihypertensive agents to achieve this blood pressure target. Although the most effective combination strategy in diabetes has not yet been determined in large-scale randomized clinical trials, a combination that includes at least one agent that interrupts the renin-angiotensin system appears to not only have a good safety profile, but may also provide additional renal and cardiovascular protection. Other antihypertensive agents should be added based on the patients risk profile and overall treatment regimen to achieve blood pressure goal.

Angiotensin Receptor Antagonists↗
PubMed2004

The selective values of alleles in a molecular network model are context dependent.

Classical quantitative genetics has applied linear modeling to the problem of mapping genotypic to phenotypic variation. Much of this theory was developed prior to the availability of molecular biology. The current understanding of the mechanisms of gene expression indicates the importance of nonlinear effects resulting from gene interactions. We provide a bridge between genetics and gene network theories by relating key concepts from quantitative genetics to the parameters, variables, and performance functions of genetic networks. We illustrate this methodology by simulating the genetic switch controlling galactose metabolism in yeast and its response to selection for a population of individuals. Results indicate that genes have heterogeneous contributions to phenotypes and that additive and nonadditive effects are context dependent. Early cycles of selection suggest strong additive effects attributed to some genes. Later cycles suggest the presence of strong context-dependent nonadditive effects that are conditional on the outcomes of earlier selection cycles. A single favorable allele cannot be consistently identified for most loci. These results highlight the complications that can arise with the presence of nonlinear effects associated with genes acting in networks when selection is conducted on a population of individuals segregating for the genes contributing to the network.

Alleles↗
PubMed2003

Evolving concepts in advanced glycation, diabetic nephropathy, and diabetic vascular disease.

Advanced glycation endproducts (AGEs) have been postulated to play a role in the development of both nephropathy and large vessel disease in diabetes. However, it is still not clear which AGE subtypes play a pathogenetic role and which of several AGE receptors mediate AGE effects on cells. This review summarises the renoprotective effect of inhibitors of AGE formation, including aminoguanidine, and of cross-link breakers, including ALT-711, on experimental diabetic nephropathy and on mesenteric vascular hypertrophy. It also demonstrates similar effects of aminoguanidine and ramipril (an angiotensin converting enzyme inhibitor) on fluorescent and immunoassayable AGE levels, renal protein kinase C activity, nitrotyrosine expression, lysosomal function, and protein handling in experimental diabetes. These findings indicate that inhibition of the renin angiotensin system blocks both upstream and downstream pathways leading to tissue injury. We postulate that the chemical pathways leading to advanced glycation endproduct formation and the renin angiotensin systems may interact through the generation of free radicals, induced both by glucose and angiotensin II. There is also evidence to suggest that AGE-dependent pathways may play a role in the development of tubulointerstitial fibrosis in the diabetic kidney. This effect is mediated through RAGE and is TGF-beta and CTGF-dependent.

Albuminuria↗
PubMed2003

Advanced glycation end products activate Smad signaling via TGF-beta-dependent and independent mechanisms: implications for diabetic renal and vascular disease.

While it is thought that advanced glycation end products (AGEs) act by stimulating transforming growth factor (TGF)-beta to mediate diabetic injury, we report that AGEs can activate TGF-beta signaling, Smads, and mediate diabetic scarring directly and independently of TGF-beta. AGEs activate Smad2/3 in renal and vascular cells at 5 min, peaking over 15-30 min before TGF-beta synthesis at 24 h and occurs in TGF-beta receptor I and II mutant cells. This is mediated by RAGE and ERK/p38 mitogen-activated protein kinases (MAPKs). In addition, AGEs also activate Smads at 24 h via the classic TGF-beta-dependent pathway. A substantial inhibition of AGE-induced Smad activation and collagen synthesis by ERK/p38 MAPK inhibitors, but not by TGF-beta blockade, suggests that the MAPK-Smad signaling crosstalk pathway is a key mechanism in diabetic scarring. Prevention of AGE-induced Smad activation and collagen synthesis by overexpression of Smad7 indicates that Smad signaling may play a critical role in diabetic complications. This is further supported by the findings that activation of Smad2/3 in human diabetic nephropathy and vasculopathy is associated with local deposition of AGEs and up-regulation of RAGE. Thus, AGEs act by activating Smad signaling to mediate diabetic complications via both TGF-beta-dependent and -independent pathways, shedding new light on the pathogenesis of diabetic organ injury.

Cells, Cultured↗
PubMed2003

Ontogeny of calcitonin receptor mRNA and protein in the developing central nervous system of the rat.

In this study, the expression of receptors for calcitonin (CTR), the CTR C1a and C1b isoforms, was investigated during development of the fetal rat central nervous system (CNS) by using in situ hybridization and immunohistochemistry. Coincident expression with both techniques was evident. Immunohistochemical evidence for the expression of the C1a isoform alone was found. Expression was first observed at embryonic day 12/13 (E12/E13) within and adjacent to the ventricular zones known to include primary matrices of proliferation, in regions of the preoptic area, anterior and posterior hypothalamus, anterior and posterior pons, medulla, and spinal cord. At later times, with the decline in the density of immunoreactivity at these loci (E15), expression in primary matrices was found later at distinct loci within the ventricular zones of cerebellum (E17), and at E19, the tectum, lateral ventricle, and cortical subplate. By E19, the density of staining had increased and was widespread throughout the expanding CNS. In the rostral domains, moderate to high density was found in the external plexiform layer; the medial preoptic area and nucleus; the ventromedial, dorsomedial, and arcuate hypothalamic nuclei; and the lateral and posterior hypothalamic areas. In the midbrain, similar levels of expression were noted in the central nucleus of raphe; the deep mesencephalic, dorsal raphe, and laterodorsal tegmental nuclei; and the ventral periaqueductal gray. In the pons, positive loci included the locus coeruleus and the gigantocellular and pontine reticular nuclei. In the medulla, high expression was evident in the gigantocellular, intermediate, magnocellular, and medullary reticular, spinal trigeminal and cuneate nuclei; and the nucleus tractus solitarius. In the spinal cord, moderate to high density of staining was found in the ventral, dorsal, and lateral horns, and in the ventral, dorsal, and cuneate funiculi. On the other hand, transitory expression was found in the diagonal band, bed nucleus of the stria terminalis, amygdala, and the lateral mamillary and anterobasal nuclei of the hypothalamus. These studies indicate a role for CTR in the activation of some premigratory neuroblasts in the CNS as well as a possible role later in an undefined function associated with mature neurons of particular nuclei.

Animals↗
PubMed2003

On the determination of recombination rates in intermated recombinant inbred populations.

The recurrent intermating of F(2) individuals for some number of generations followed by several generations of inbreeding produces an intermated recombinant inbred (IRI) population. Such populations are currently being developed in the plant-breeding community because linkage associations present in an F(2) population are broken down and a population of fixed inbred lines is also created. The increased levels of recombination enable higher-resolution mapping in IRI populations relative to F(2) populations. Herein we derive relationships, under several limiting assumptions, for determining the expected recombination fraction in IRI populations from the crossover rate per meiosis. These relationships are applicable to situations where the inbreeding component of IRI population development is by either self-fertilization or full-sib mating. Additionally, we show that the derived equations can be solved for the crossover rate per meiosis if the recombination fraction is known for the IRI population. Thus, the observed recombination fraction in any IRI population can be expressed on an F(2) basis. The implications of this work on the expansion of genetic maps in IRI populations and limits for detecting linkage between markers are also considered.

Chromosome Mapping↗
PubMed2002

Effects of lerisetron, a new 5-HT3 receptor antagonist, on ipecacuanha-induced emesis in healthy volunteers.

The purpose of these studies was to evaluate the effect of lerisetron (1-phenyl-methyl-2-piperazinyl-1H-benzimidazole hydrochloride, CAS 143257-98-1, F-0930-RS2), a new 5-HT3 receptor antagonist, on ipecacuanha-induced nausea and vomiting. The ipecacuanha model of emesis has been used to test the anti-emetic activity of several different 5-HT3 antagonists and the anti-emetic doses that were effective in the ipecacuanha model have been found to correlate well with the clinically effective doses. Study 1 investigated oral doses of lerisetron from 4 mg to 40 mg. Study 2 evaluated the duration of effect of a single dose of 20 mg oral lerisetron. Study 3 evaluated intravenous doses of 18 mg and 12 mg lerisetron. In Study 1, the 40 mg dose of oral lerisetron inhibited emesis in all test subjects. The percentage of subjects who experienced an emetic episode increased as the dose of lerisetron decreased. At the lowest dose level tested five of six subjects had an emetic episode compared with four out of five in the placebo group. In Study 2, 20 mg oral lerisetron was effective up to 12 h after administration. When ipecacuanha was administered at 18 h post-dose three of seven subjects had an emetic episode and at 24 h post-dose the incidence of emesis was similar to the placebo treatment groups in the previous study. Study 3 demonstrated the effectiveness of intravenous doses of lerisetron. The 18 mg intravenous dose reduced the number of patients experiencing emetic episodes by 75% compared with placebo, doses below 12 mg i.v. were not evaluated because of the reduced efficacy of the compound at this dose level. In conclusion, lerisetron has been shown to be effective in the treatment of ipecacuanha-induced nausea and vomiting at intravenous doses of 18 mg and at oral doses of 20 mg for up to 12 hours.

Administration, Oral↗
PubMed2002

The GP problem: quantifying gene-to-phenotype relationships.

In this paper we refer to the gene-to-phenotype modeling challenge as the GP problem. Integrating information across levels of organization within a genotype-environment system is a major challenge in computational biology. However, resolving the GP problem is a fundamental requirement if we are to understand and predict phenotypes given knowledge of the genome and model dynamic properties of biological systems. Organisms are consequences of this integration, and it is a major property of biological systems that underlies the responses we observe. We discuss the E(NK) model as a framework for investigation of the GP problem and the prediction of system properties at different levels of organization. We apply this quantitative framework to an investigation of the processes involved in genetic improvement of plants for agriculture. In our analysis, N genes determine the genetic variation for a set of traits that are responsible for plant adaptation to E environment-types within a target population of environments. The N genes can interact in epistatic NK gene-networks through the way that they influence plant growth and development processes within a dynamic crop growth model. We use a sorghum crop growth model, available within the APSIM agricultural production systems simulation model, to integrate the gene-environment interactions that occur during growth and development and to predict genotype-to-phenotype relationships for a given E(NK) model. Directional selection is then applied to the population of genotypes, based on their predicted phenotypes, to simulate the dynamic aspects of genetic improvement by a plant-breeding program. The outcomes of the simulated breeding are evaluated across cycles of selection in terms of the changes in allele frequencies for the N genes and the genotypic and phenotypic values of the populations of genotypes.

Computer Simulation↗