Inference of population structure using multilocus genotype data

We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci-e.g. , seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/ approximately pritch/home. html.

A new statistical method for haplotype reconstruction from population data

Current routine genotyping methods typically do not provide haplotype information, which is essential for many analyses of fine-scale molecular-genetics data. Haplotypes can be obtained, at considerable cost, experimentally or (partially) through genotyping of additional family members. Alternatively, a statistical method can be used to infer phase and to reconstruct haplotypes. We present a new statistical method, applicable to genotype data at linked loci from a population sample, that improves substantially on current algorithms; often, error rates are reduced by > 50%, relative to its nearest competitor. Furthermore, our algorithm performs well in absolute terms, suggesting that reconstructing haplotypes experimentally or by genotyping additional family members may be an inefficient use of resources.

Association mapping in structured populations

The use, in association studies, of the forthcoming dense genomewide collection of single-nucleotide polymorphisms (SNPs) has been heralded as a potential breakthrough in the study of the genetic basis of common complex disorders. A serious problem with association mapping is that population structure can lead to spurious associations between a candidate marker and a phenotype. One common solution has been to abandon case-control studies in favor of family-based tests of association, such as the transmission/disequilibrium test (TDT), but this comes at a considerable cost in the need to collect DNA from close relatives of affected individuals. In this article we describe a novel, statistically valid, method for case-control association studies in structured populations. Our method uses a set of unlinked genetic markers to infer details of population structure, and to estimate the ancestry of sampled individuals, before using this information to test for associations within subpopulations. It provides power comparable with the TDT in many settings and may substantially outperform it if there are conflicting associations in different subpopulations.

Inferring coalescence times from DNA sequence data

The paper is concerned with methods for the estimation of the coalescence time (time since the most recent common ancestor) of a sample of intraspecies DNA sequences. The methods take advantage of prior knowledge of population demography, in addition to the molecular data. While some theoretical results are presented, a central focus is on computational methods. These methods are easy to implement, and, since explicit formulae tend to be either unavailable or unilluminating, they are also more useful and more informative in most applications. Extensions are presented that allow for the effects of uncertainty in our knowledge of population size and mutation rates, for variability in population sizes, for regions of different mutation rate, and for inference concerning the coalescence time of the entire population. The methods are illustrated using recent data from the human Y chromosome.

Coalescents and genealogical structure under neutrality

Genealogical or coalescent methods have proved very useful in interpreting and understanding a wide range of population genetic data. Our aim is to illustrate some of the central ideas behind this approach. The primary focus is genealogy in neutral genetic models, for which the effects of demography can be separated from those of mutation. We describe the coalescent for panmictic populations of fixed size, and its extensions to incorporate various assumptions about variation in population size and nonrandom mating caused by geographical population subdivision. The effects of such genealogical structure on patterns and correlations in genetic data are discussed. An urn model is useful for simulating samples at loci with complex mutation mechanisms. We give two applications of the genealogical approach. The first concerns methods for estimating the mutation rate from infinitely-many-sites data, and the second relates to inference about recent common ancestors and population history.

Case-control studies of association in structured or admixed populations

Case-control tests for association are an important tool for mapping complex-trait genes. But population structure can invalidate this approach, leading to apparent associations at markers that are unlinked to disease loci. Family-based tests of association can avoid this problem, but such studies are often more expensive and in some cases--particularly for late-onset diseases--are impractical. In this review article we describe a series of approaches published over the past 2 years which use multilocus genotype data to enable valid case-control tests of association, even in the presence of population structure. These tests can be classified into two categories. "Genomic control" methods use the independent marker loci to adjust the distribution of a standard test statistic, while "structured association" methods infer the details of population structure en route to testing for association. We discuss the statistical issues involved in the different approaches and present results from simulations comparing the relative performance of the methods under a range of models.

Copper complexes of bis(thiosemicarbazones): from chemotherapeutics to diagnostic and therapeutic radiopharmaceuticals

The molecules known as bis(thiosemicarbazones) derived from 1,2-diones can act as tetradentate ligands for Cu(II), forming stable, neutral complexes. As a family, these complexes possess fascinating biological activity. This critical review presents an historical perspective of their progression from potential chemotherapeutics through to more recent applications in nuclear medicine. Methods of synthesis are presented followed by studies focusing on their potential application as anti-cancer agents and more recent investigations into their potential as therapeutics for Alzheimer's disease. The Cu(II) complexes are of sufficient stability to be used to coordinate copper radioisotopes for application in diagnostic and therapeutic radiopharmaceuticals. Detailed understanding of the coordination chemistry has allowed careful manipulation of the metal based properties to engineer specific biological activities. Perhaps the most promising complex radiolabelled with copper radioisotopes to date is Cu(II)(atsm), which has progressed to clinical trials in humans (162 references).

Increasing Cu bioavailability inhibits Abeta oligomers and tau phosphorylation

Cognitive decline in Alzheimer's disease (AD) involves pathological accumulation of synaptotoxic amyloid-beta (Abeta) oligomers and hyperphosphorylated tau. Because recent evidence indicates that glycogen synthase kinase 3beta (GSK3beta) activity regulates these neurotoxic pathways, we developed an AD therapeutic strategy to target GSK3beta. The strategy involves the use of copper-bis(thiosemicarbazonoto) complexes to increase intracellular copper bioavailability and inhibit GSK3beta through activation of an Akt signaling pathway. Our lead compound Cu(II)(gtsm) significantly inhibited GSK3beta in the brains of APP/PS1 transgenic AD model mice. Cu(II)(gtsm) also decreased the abundance of Abeta trimers and phosphorylated tau, and restored performance of AD mice in the Y-maze test to levels expected for cognitively normal animals. Improvement in the Y-maze correlated directly with decreased Abeta trimer levels. This study demonstrates that increasing intracellular copper bioavailability can restore cognitive function by inhibiting the accumulation of neurotoxic Abeta trimers and phosphorylated tau.

Estimating recombination rates from population genetic data

We introduce a new method for estimating recombination rates from population genetic data. The method uses a computationally intensive statistical procedure (importance sampling) to calculate the likelihood under a coalescent-based model. Detailed comparisons of the new algorithm with two existing methods (the importance sampling method of Griffiths and Marjoram and the MCMC method of Kuhner and colleagues) show it to be substantially more efficient. (The improvement over the existing importance sampling scheme is typically by four orders of magnitude.) The existing approaches not infrequently led to misleading results on the problems we investigated. We also performed a simulation study to look at the properties of the maximum-likelihood estimator of the recombination rate and its robustness to misspecification of the demographic model.

Comparison of (64)Cu-complexing bifunctional chelators for radioimmunoconjugation: labeling efficiency, specific activity, and in vitro/in vivo stability

High radiolabeling efficiency, preferably to high specific activity, and good stability of the radioimmunoconjugate are essential features for a successful immunoconjugate for imaging or therapy. In this study, the radiolabeling efficiency, in vitro stability, and biodistribution of immunoconjugates with eight different bifunctional chelators labeled with (64)Cu were compared. The anti-CD20 antibody, rituximab, was conjugated to four macrocyclic bifunctional chelators (p-SCN-Bn-DOTA, p-SCN-Bn-Oxo-DO3A, p-SCN-NOTA, and p-SCN-PCTA), three DTPA derivatives (p-SCN-Bn-DTPA, p-SCN-CHX-A″-DTPA, and ITC-2B3M-DTPA), and a macrobicyclic hexamine (sarcophagine) chelator (sar-CO2H) = (1-NH2-8-NHCO(CH2)3CO2H)sar where sar = sarcophagine = 3,6,10,13,16,19-hexaazabicyclo[6.6.6]icosane). Radiolabeling efficiency under various conditions, in vitro stability in serum at 37 °C, and in vivo biodistribution and imaging in normal mice over 48 h were studied. All chelators except sar-CO2H were conjugated to rituximab by thiourea bond formation with an average of 4.9 ± 0.9 chelators per antibody molecule. Sar-CO2H was conjugated to rituximab by amide bond formation with 0.5 chelators per antibody molecule. Efficiencies of (64)Cu radiolabeling were dependent on the concentration of immunoconjugate. Notably, the (64)Cu-NOTA-rituximab conjugate demonstrated the highest radiochemical yield (95%) under very dilute conditions (31 nM NOTA-rituximab conjugate). Similarly, sar-CO-rituximab, containing 1/10th the number of chelators per antibody compared to that of other conjugates, retained high labeling efficiency (98%) at an antibody concentration of 250 nM. In contrast to the radioimmunoconjugates containing DTPA derivatives, which demonstrated poor serum stability, all macrocyclic radioimmunoconjugates were very stable in serum with <6% dissociation of (64)Cu over 48 h. In vivo biodistribution profiles in normal female Balb/C mice were similar for all the macrocyclic radioimmunoconjugates with most of the activity remaining in the blood pool up to 48 h. While all the macrocyclic bifunctional chelators are suitable for molecular imaging using (64)Cu-labeled antibody conjugates, NOTA and sar-CO2H show significant advantages over the others in that they can be radiolabeled rapidly at room temperature, under dilute conditions, resulting in high specific activity.

Randomised controlled trials of staged teaching for basic life support. 1. Skill acquisition at bronze stage

We have investigated a method of teaching community CPR in three stages instead of in a single session. These have been designated bronze, silver, and gold stages. The first involves only opening of the airway and chest compression with back blows for choking, the second adds ventilation in a ratio of compressions to breaths of 50:5, and the third is a conversion to conventional CPR. In a controlled randomised trial of 495 trainees we compared the performance in tests immediately after instruction of those who had received a conventional course and those who had had the simpler bronze level tuition. The tests were based on video recordings of simulated resuscitation scenarios and the readouts from recording manikins. Differences occurred as a direct consequence of ventilation being required in one group and not the other, some variation probably followed from unforeseen minor changes in the way that instruction was given, whilst others may have followed from the greater simplicity in the new method of training. A careful approach was followed by slightly more trainees in the conventional group whilst appreciably more in the bronze group remembered to shout for help (44% vs. 71%). A clear advantage was also seen for bronze level training in terms of those who opened the airway as taught (35% vs. 56%), for checking breathing (66% vs. 88%), and for mentioning the need to phone for an ambulance (21% vs. 32%). Little difference was observed in correct or acceptable hand position between the conventional group who were given detailed guidance and the bronze group who were instructed only to push on the centre of the chest. The biggest differences related to the number of compressions given. The mean delay to first compression was 63 s and 34 s, and the mean duration of pauses between compressions was 16 s and 9 s, respectively. Average performed rates were similar in the two groups, but more in the conventional group compressed too slowly whereas more in the bronze group compressed too rapidly. Observations were made for only three cycles of compression, but extrapolating these to the 8 min often considered a watershed for chances of survival for victims of cardiac arrest, an average of 308 compressions would be expected from those using conventional CPR compared with 675 for those using bronze level CPR. The implications of this difference are discussed.

An unusual dimeric structure of a Cu(I) bis(thiosemicarbazone) complex: implications for the mechanism of hypoxic selectivity of the Cu(II) derivatives

The electrochemical reduction of Cu(II) bis(thiosemicarbazone) complexes [Cu(II)(btsc)] is accompanied by protonation to give an unstable Cu(I) intermediate [Cu(btscH(2))](+). The nature of this intermediate was probed by reaction of bis(thiosemicarbazone) ligands with a Cu(I) precursor which gave a novel helical dimeric dicationic complex. The dependence of these reactions on the ligand backbone substituents is discussed together with their possible relevance to the use of Cu(II) bis(thiosemicarbazone) ligands as hypoxic selective imaging and therapeutic agents.

Pairwise comparisons of mitochondrial DNA sequences in subdivided populations and implications for early human evolution

We consider the effect on the distribution of pairwise differences between mitochondrial DNA sequences of the incorporation into the underlying population genetics model of two particular effects that seem realistic for human populations. The first is that the population size was roughly constant before growing to its current level. The second is that the population is geographically subdivided rather than panmictic. In each case these features tend to encourage multimodal distributions of pairwise differences, in contrast to existing, unimodal datasets. We argue that population genetics models currently used to analyze such data may thus fail to reflect important features of human mitochondrial DNA evolution. These may include selection on the mitochondrial genome, more realistic mutation mechanisms, or special population or migration dynamics. Particularly in view of the variability inherent in the single available human mitochondrial genealogy, it is argued that until these effects are better understood, inferences from such data should be rather cautious.

The hypoxia imaging agent CuII(atsm) is neuroprotective and improves motor and cognitive functions in multiple animal models of Parkinson's disease

The PET imaging agent Cu^II(atsm) improves motor and cognitive function in Parkinson’s disease.

Parkinson’s disease (PD) is a progressive, chronic disease characterized by dyskinesia, rigidity, instability, and tremors. The disease is defined by the presence of Lewy bodies, which primarily consist of aggregated α-synuclein protein, and is accompanied by the loss of monoaminergic neurons. Current therapeutic strategies only give symptomatic relief of motor impairment and do not address the underlying neurodegeneration. Hence, we have identified Cu^II(atsm) as a potential therapeutic for PD. Drug administration to four different animal models of PD resulted in improved motor and cognition function, rescued nigral cell loss, and improved dopamine metabolism. In vitro, this compound is able to inhibit the effects of peroxynitrite-driven toxicity, including the formation of nitrated α-synuclein oligomers. Our results show that Cu^II(atsm) is effective in reversing parkinsonian defects in animal models and has the potential to be a successful treatment of PD.

Copper and Alzheimer's disease

Copper is essential for some of the enzymes that have a role in brain metabolism. Sophisticated mechanisms balance copper import and export to ensure proper nutrient levels (homeostasis) while minimizing toxic effects. Several neurodegenerative diseases including Alzheimer's disease (AD) are characterized by modified copper homeostasis. This change seems to contribute either directly or indirectly to increased oxidative stress, an important factor in neuronal toxicity. When coupled to misfolded proteins, this modified copper homeostasis appears to be an important factor in the pathological progression of AD.

The mutation rate in the human mtDNA control region

The mutation rate of the mitochondrial control region has been widely used to calibrate human population history. However, estimates of the mutation rate in this region have spanned two orders of magnitude. To readdress this rate, we sequenced the mtDNA control region in 272 individuals, who were related by a total of 705 mtDNA transmission events, from 26 large Icelandic pedigrees. Three base substitutions were observed, and the mutation rate across the two hypervariable regions was estimated to be 3/705 =.0043 per generation (95% confidence interval [CI].00088-.013), or.32/site/1 million years (95% CI.065-.97). This study is substantially larger than others published, which have directly assessed mtDNA mutation rates on the basis of pedigrees, and the estimated mutation rate is intermediate among those derived from pedigree-based studies. Our estimated rate remains higher than those based on phylogenetic comparisons. We discuss possible reasons for-and consequences of-this discrepancy. The present study also provides information on rates of insertion/deletion mutations, rates of heteroplasmy, and the reliability of maternal links in the Icelandic genealogy database.

Engineering poly(ethylene glycol) particles for improved biodistribution

We report the engineering of poly(ethylene glycol) (PEG) hydrogel particles using a mesoporous silica (MS) templating method via tuning the PEG molecular weight, particle size, and the presence or absence of the template and investigate the cell association and biodistribution of these particles. An ex vivo assay based on human whole blood that is more sensitive and relevant than traditional cell-line based assays for predicting in vivo circulation behavior is introduced. The association of MS@PEG particles (template present) with granulocytes and monocytes is higher compared with PEG particles (template absent). Increasing the PEG molecular weight (from 10 to 40 kDa) or decreasing the PEG particle size (from 1400 to 150 nm) reduces phagocytic blood cell association of the PEG particles. Mice biodistribution studies show that the PEG particles exhibit extended circulation times (>12 h) compared with the MS@PEG particles and that the retention of smaller PEG particles (150 nm) in blood, when compared with larger PEG particles (>400 nm), is increased at least 4-fold at 12 h after injection. Our findings highlight the influence of unique aspects of polymer hydrogel particles on biological interactions. The reported PEG hydrogel particles represent a new class of polymer carriers with potential biomedical applications.

The coalescent process with selfing

A method of estimating the selfing rate using DNA sequence data was recently proposed by Milligan. Unfortunately, a number of errors make interpretation of his results problematic. In the present paper we first show how the usual coalescent process can be adapted to models that include selfing, and then use this result to find moment estimators as well as the likelihood surface for the selfing rate, s, and the scaled mutation rate, theta. We conclude that, regardless of the method used, large sample sizes are necessary to estimate s with any degree of certainty, and that the estimate is always highly sensitive to recent changes in the true value.

Metal complexes designed to bind to amyloid-β for the diagnosis and treatment of Alzheimer's disease

Alzheimer's disease is the most common form of age-related neurodegenerative dementia. The disease is characterised by the presence of plaques in the cerebral cortex. The major constituent of these plaques is aggregated amyloid-β peptide. This review focuses on the molecular aspects of metal complexes designed to bind to amyloid-β. The development of radioactive metal-based complexes of copper and technetium designed as diagnostic imaging agents to detect amyloid burden in the brain is discussed. Separate sections of the review discuss the use of luminescent metal complexes to act as non-conventional probes of amyloid formation and recent research into the use of metal complexes as inhibitors of amyloid formation and toxicity.

Diacetylbis(N(4)-methylthiosemicarbazonato) copper(II) (CuII(atsm)) protects against peroxynitrite-induced nitrosative damage and prolongs survival in amyotrophic lateral sclerosis mouse model

Amyotrophic lateral sclerosis (ALS) is a progressive paralyzing disease characterized by tissue oxidative damage and motor neuron degeneration. This study investigated the in vivo effect of diacetylbis(N(4)-methylthiosemicarbazonato) copper(II) (CuII(atsm)), which is an orally bioavailable, blood-brain barrier-permeable complex. In vitro the compound inhibits the action of peroxynitrite on Cu,Zn-superoxide dismutase (SOD1) and subsequent nitration of cellular proteins. Oral treatment of transgenic SOD1G93A mice with CuII(atsm) at presymptomatic and symptomatic ages was performed. The mice were examined for improvement in lifespan and motor function, as well as histological and biochemical changes to key disease markers. Systemic treatment of SOD1G93A mice significantly delayed onset of paralysis and prolonged lifespan, even when administered to symptomatic animals. Consistent with the properties of this compound, treated mice had reduced protein nitration and carbonylation, as well as increased antioxidant activity in spinal cord. Treatment also significantly preserved motor neurons and attenuated astrocyte and microglial activation in mice. Furthermore, CuII(atsm) prevented the accumulation of abnormally phosphorylated and fragmented TAR DNA-binding protein-43 (TDP-43) in spinal cord, a protein pivotal to the development of ALS. CuII(atsm) therefore represents a potential new class of neuroprotective agents targeting multiple major disease pathways of motor neurons with therapeutic potential for ALS.