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Biomedical subjects

R C Griffiths

Publications and source records attributed to R C Griffiths.

At least 19 recordsLinked to original sources
PubMed2003

The frequency spectrum of a mutation, and its age, in a general diffusion model.

General formulae are derived for the probability density and expected age of a mutation of frequency x in a population, and similarly for a mutation with b copies in a sample of n genes. A general formula is derived for the frequency spectrum of a mutation in a sample. Variable population size models are included. Results are derived in two frameworks: diffusion process models for the frequency of the mutation; and birth and death process models. The coalescent structure within the mutant gene group and the non-mutant group is considered.

Alleles↗
PubMed2001

Deficiency of 5-lipoxygenase accelerates renal allograft rejection in mice.

Acute renal allograft rejection is associated with alterations in renal arachidonic acid metabolism, including enhanced synthesis of leukotrienes (LTs). LTs, the products of the 5-lipoxygenase (5-LO) pathway, are potent lipid mediators with a broad range of biologic activities. Previous studies, using pharmacological agents to inhibit LT synthesis or activity, have implicated these eicosanoids in transplant rejection. To further investigate the role of LTs in acute graft rejection, we transplanted kidneys from CByD2F1 mice into fully allogeneic 129 mice that carry a targeted mutation in the 5lo gene. Unexpectedly, allograft rejection was significantly accelerated in 5-LO-deficient mice compared with wild-type animals. Despite the marked reduction in graft survival, the 5lo mutation had no effect on the hemodynamics or morphology of the allografts. Although LTB4 levels were reduced, renal thromboxane B2 production and cytokine expression were not altered in 5-LO-deficient allograft recipients. These findings suggest that, along with their proinflammatory actions, metabolites of 5-LO can act to enhance allograft survival.

Animals↗
PubMed2001

Coalescence time for two genes from a subdivided population.

In this paper a new form of the solution for the Laplace transform and moments of the distribution of the waiting time for two genes to coalescence is presented. The two genes are sampled from a subdivided population where migration rates between populations are constant in time. Equal subpopulation size is not assumed. For the special case of an island model with equal migration rates between islands, the Laplace transform of the coalescence time and the first and second moments are found explicitly. The new form of the solutions allows numerical calculation. The connection of how the results relate to a panmictic population when migration rates are large is illustrated using strong-migration-limit theory.

Genetics, Population↗
PubMed2000

Inference from gene trees in a subdivided population.

This paper studies gene trees in subdivided populations which are constructed as perfect phylogenies from the pattern of mutations in a sample of DNA sequences and presents a new recursion for the probability distribution of such gene trees. The underlying evolutionary model is the coalescent process in a subdivided population. The infinitely-many-sites model of mutation is assumed. Ancestral inference questions that are discussed are maximum likelihood estimation of migration and mutation rates; detection of population growth by likelihood techniques; determining the distribution of the time to the most recent common ancestor of a sample of sequences; determining the distribution of the age of the mutations on the gene tree; determining in which subpopulation the most recent common ancestor of all the sequences was; determining subpopulation ancestors, where they were, and times to them; and determining in which subpopulations mutations occurred. A computational technique of Griffiths and Tavaré used is a computer intensive Markov chain simulation, which simulates gene trees conditional on their topology implied by the mutation pattern in the sample of DNA sequences. The software GENETREE, which implements these ancestral inference techniques, is available.

Algorithms↗
PubMed1999

Deficiency of 5-lipoxygenase abolishes sex-related survival differences in MRL-lpr/lpr mice.

Leukotrienes, the 5-lipoxygenase (5LO) products of arachidonic acid metabolism, have many proinflammatory actions that have been implicated in the pathogenesis of a variety of inflammatory diseases. To investigate the role of LTs in autoimmune disease, we generated an MRL-lpr/lpr mouse line with a targeted disruption of the 5lo gene. MRL-lpr/lpr mice spontaneously develop autoimmune disease that has many features resembling human systemic lupus erythematosus, including sex-related survival differences; female MRL-lpr/lpr mice experience significant early mortality compared with males. Unexpectedly, we found that mortality was accelerated in male 5LO-deficient MRL-lpr/lpr mice compared with male wild-type MRL-lpr/lpr animals. In contrast, the 5lo mutation had no effect on survival in females. Mortality was also accelerated in male MRL-lpr/lpr mice that were treated chronically with a pharmacological inhibitor of LT synthesis. Furthermore, LT-dependent inflammatory responses are enhanced in male MRL-lpr/lpr mice compared with females, and the 5lo mutation has greater impact on these responses in males. Because immune complex-mediated glomerulonephritis is the major cause of death in MRL-lpr/lpr mice and has been related to arachidonic acid metabolites, we also assessed kidney function and histopathology. In male MRL-lpr/lpr mice, renal plasma flow was significantly reduced in the 5lo-/- compared with the 5lo+/+ group, although there were no differences in the severity of renal histopathology, lymphoid hyperplasia, or arthritis between the groups. These findings suggest that the presence of a functional 5lo gene confers a survival advantage on male MRL-lpr/lpr mice and that, when 5LO function is inhibited, either genetically or pharmacologically, this advantage is abolished.

Acute Disease↗
PubMed1999

The time to the ancestor along sequences with recombination.

In a sample of DNA sequences where recombination can occur to the ancestors of the sample, distinct parts of the sequences may have different most recent common ancestors. This paper presents a Markov chain Monte Carlo algorithm for computing the expected time to the most recent common ancestor along the sequences, conditional on where the mutations occur on the sequences.

Algorithms↗
PubMed1999

Fas on renal parenchymal cells does not promote autoimmune nephritis in MRL mice.

BACKGROUND: Although Fas on pancreatic islets promotes autoimmune diabetes in mice, the role of Fas expression on kidney parenchymal cells during autoimmune disease is unknown. METHODS: To determine whether Fas on renal parenchymal cells promotes autoimmune renal destruction, we compared apoptosis and pathology in Fas-intact and Fas-deficient kidneys in an autoimmune milieu. For this purpose, we transplanted single, normal kidneys from MRL-++ (Fas-intact) mice (3 months of age) into age-matched, congenic MRL-Faslpr (Fas-deficient) recipients after removal of nephritic kidneys. These Fas-intact kidneys were compared with Fas-deficient nephritic kidneys. RESULTS: There is a progressive increase of FasL on kidney-infiltrating cells and Fas and FasL on renal parenchymal cells in MRL-++ kidneys during engraftment (0, 2, 4-6, and 8 weeks). By comparison, we detected an increase in FasL in MRL-Faslpr kidneys (3 to 5 months of age), whereas Fas was not detectable. The engagement of T cells bearing FasL with Fas expressing tubular epithelial cells (TECs) induced TEC apoptosis in vitro. However, apoptosis and pathology were similar in kidneys (MRL-++, 8 weeks postengraftment vs. MRL-Faslpr, 5 months) with equivalent amounts of FasL-infiltrating cells or FasL TECs, regardless of Fas on renal parenchymal cells. CONCLUSION: The expression of Fas on renal parenchymal cells does not increase apoptosis or promote renal disease in MRL-++ mice. We speculate that the autoimmune milieu evokes mechanisms that mask, counter, or pre-empt Fas-FasL-initiated apoptosis in MRL kidneys.

Animals↗
PubMed1999

Ancestral Asian source(s) of new world Y-chromosome founder haplotypes.

Haplotypes constructed from Y-chromosome markers were used to trace the origins of Native Americans. Our sample consisted of 2,198 males from 60 global populations, including 19 Native American and 15 indigenous North Asian groups. A set of 12 biallelic polymorphisms gave rise to 14 unique Y-chromosome haplotypes that were unevenly distributed among the populations. Combining multiallelic variation at two Y-linked microsatellites (DYS19 and DXYS156Y) with the unique haplotypes results in a total of 95 combination haplotypes. Contra previous findings based on Y- chromosome data, our new results suggest the possibility of more than one Native American paternal founder haplotype. We postulate that, of the nine unique haplotypes found in Native Americans, haplotypes 1C and 1F are the best candidates for major New World founder haplotypes, whereas haplotypes 1B, 1I, and 1U may either be founder haplotypes and/or have arrived in the New World via recent admixture. Two of the other four haplotypes (YAP+ haplotypes 4 and 5) are probably present because of post-Columbian admixture, whereas haplotype 1G may have originated in the New World, and the Old World source of the final New World haplotype (1D) remains unresolved. The contrasting distribution patterns of the two major candidate founder haplotypes in Asia and the New World, as well as the results of a nested cladistic analysis, suggest the possibility of more than one paternal migration from the general region of Lake Baikal to the Americas.

Asia↗
PubMed1998

Out of Africa and back again: nested cladistic analysis of human Y chromosome variation.

We surveyed nine diallelic polymorphic sites on the Y chromosomes of 1,544 individuals from Africa, Asia, Europe, Oceania, and the New World. Phylogenetic analyses of these nine sites resulted in a tree for 10 distinct Y haplotypes with a coalescence time of approximately 150,000 years. The 10 haplotypes were unevenly distributed among human populations: 5 were restricted to a particular continent, 2 were shared between Africa and Europe, 1 was present only in the Old World, and 2 were found in all geographic regions surveyed. The ancestral haplotype was limited to African populations. Random permutation procedures revealed statistically significant patterns of geographical structuring of this paternal genetic variation. The results of a nested cladistic analysis indicated that these geographical associations arose through a combination of processes, including restricted, recurrent gene flow (isolation by distance) and range expansions. We inferred that one of the oldest events in the nested cladistic analysis was a range expansion out of Africa which resulted in the complete replacement of Y chromosomes throughout the Old World, a finding consistent with many versions of the Out of Africa Replacement Model. A second and more recent range expansion brought Asian Y chromosomes back to Africa without replacing the indigenous African male gene pool. Thus, the previously observed high levels of Y chromosomal genetic diversity in Africa may be due in part to bidirectional population movements. Finally, a comparison of our results with those from nested cladistic analyses of human mtDNA and beta-globin data revealed different patterns of inferences for males and females concerning the relative roles of population history (range expansions) and population structure (recurrent gene flow), thereby adding a new sex-specific component to models of human evolution.

Africa↗
PubMed1997

Enzymatic synthesis of the glycosides of calystegines B1 and B2 and their glycosidase inhibitory activities.

Several glycosides of calystegines B1 and B2 were synthesized by use of rice alpha-glucosidase and the whole cells of Rhodotorula lactosa, and their glycosidase inhibitory activities were investigated. Incubation of mixture of calystegine B1 and maltose with rice alpha-glucosidase gave 3-O-alpha-D-glucopyranosylcalystegine B1 (2, 11.3%). An enzymatic beta-transglucosylation reaction of calystegines B1 or B2 with cellobiose using the whole cells of R. lactosa gave 3-O-beta-D-glucopyranosylcalystegine B1 (1) (0.9%) or 4-O-beta-D-glucopyranosylcalystegine B2 (3, 11.2%), respectively, while similar beta-transgalactosylation of calystegine B2 from lactose gave 4-O-beta-D-galactopyranosylcalystegine B2 (4, 10.1%). The glycosylation of calystegines B1 and B2 markedly decreased or abolished their inhibition against beta-glucosidase, alpha- or beta-galactosidase. Compound 4 however retained more or less the potency of calystegine B2 against trehalase. Interestingly, compound 1 was a noncompetitive inhibitor of rice alpha-glucosidase, with a Ki value of 0.9 +/- 0.1 microM.

Animals↗
PubMed1997

A gene tree for beta-globin sequences from Melanesia.

We have analyzed allelic sequence variation in sixty-one 3-kb beta-globin sequences from the Melanesian population of Vanuatu to demonstrate the value of (1) turning to the autosomal nuclear genome for studies on the evolution of modern humans and (2) using new analytical methods based on a coalescent model. After excluding recombination events, beta-globin sequence variants were connected in a unique gene tree. A gene tree provides more information for inferences on the population genealogy than simple summary statistics such as the average pairwise sequence difference. Estimates of the time to the most recent common ancestor (MRCA) and of the ages of each mutation, conditional on the gene tree, were made using new maximum likelihood methods assuming a coalescent model. We found that allelic beta-globin variation coalesces to a single shared ancestral haplotype over a time scale of approximately 900,000 years. Three major haplotypes (A1, B1, C3) that are older than 200,000 years identify ancestral diversity contemporaneous with the single MRCA for mitochondrial variation.

Animals↗
PubMed1997

Systemic autoimmune nephritogenic components induce CSF-1 and TNF-alpha in MRL kidneys.

MRL-Faslpr mice are an appealing strain to understand the importance of cytokines in the pathogenesis of autoimmune renal destruction, since injury is rapid and predictable. Colony stimulating factor 1 (CSF-1) and tumor necrosis factor alpha (TNF-alpha) are detected in the kidney and circulation prior to renal injury and continue to increase with progressive renal damage in MRL-Faslpr, Fas deficient mice, but not the congenic Fas intact MRL-(++) strain. Delivery of CSF-1, but not TNF-alpha, into the kidney via gene transfer incites local renal injury. By comparison, dual gene transfer of CSF-1 and TNF-alpha incites autoimmune renal injury that is far more severe than CSF-1 alone. The purpose of this study was to establish whether CSF-1 and TNF-alpha incites autoimmune renal injury that is far more severe than CSF-1 alone. The purpose of this study was to establish whether CSF-1 and TNF-alpha expression in the kidney of MRL-Faslpr mice induced by a circulating stimulant resulted from a primary defect in the kidney. Therefore, we transplanted (Tx) a MRL-(++) kidney without CSF-1, TNF-alpha and renal injury into an MRL-Faslpr recipient after removing nephritic kidney expressing CSF-1 and TNF-alpha. The Tx kidneys were examined after 2, 4, 5, 6, and 12 weeks. CSF-1 and TNF-alpha were rapidly induced in the MRL-(++) Tx kidney. CSF-1 and TNF-alpha were evident by two weeks and continually increased for 12 weeks post-transplantation. Within several weeks, the rapid expansion of M phi and T cells and induction of glomerulonephritis and interstitial nephritis in the MRL-(++) Tx kidney was similar to the age-matched native MRL-Faslpr kidney. In conclusion, we have constructed an experimental transplantation system that can explore whether cytokine expression in the kidney induced by a circulating stimulant is a result of a primary defect in the kidney. Using this approach, we established that the MRL-Faslpr kidney is not defective, but rather a circulating stimulant in the MRL-Faslpr mouse can induce CSF-1, TNF-alpha and renal injury in a normal MRL-(++) kidney. Thus, we exclude an intrinsic defect in the MRL-Faslpr kidney as the pathogenic mechanism responsible for tissue damage. We suggest purging the circulation of molecules that induce CSF-1 and TNF-alpha as a therapeutic strategy for autoimmune renal injury.

Animals↗
PubMed1997

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.

Algorithms↗
PubMed1997

Archaic African and Asian lineages in the genetic ancestry of modern humans.

A 3-kb region encompassing the beta-globin gene has been analyzed for allelic sequence polymorphism in nine populations from Africa, Asia, and Europe. A unique gene tree was constructed from 326 sequences of 349 in the total sample. New maximum-likelihood methods for analyzing gene trees on the basis of coalescence theory have been used. The most recent common ancestor of the beta-globin gene tree is a sequence found only in Africa and estimated to have arisen approximately 800,000 years ago. There is no evidence for an exponential expansion out of a bottlenecked founding population, and an effective population size of approximately 10,000 has been maintained. Modest differences in levels of beta-globin diversity between Africa and Asia are better explained by greater African effective population size than by greater time depth. There may have been a reduction of Asian effective population size in recent evolutionary history. Characteristically Asian ancestry is estimated to be older than 200,000 years, suggesting that the ancestral hominid population at this time was widely dispersed across Africa and Asia. Patterns of beta-globin diversity suggest extensive worldwide late Pleistocene gene flow and are not easily reconciled with a unidirectional migration out of Africa 100,000 years ago and total replacement of archaic populations in Asia.

Africa↗
PubMed1996

Estimation in an island model using simulation.

Estimation for an island model where mutation maintains a k-allele neutral polymorphism at a single locus on each island is considered. The likelihood of an observed sample type configuration is obtained by applying a computational algorithm analogous to Griffiths and Tavaré (Theor. Popul. Biol. 46 (1994), 131-159). This allows the computation of sampling distributions in an island model and investigation of their properties. Given a sample type configuration, the maximum likelihood estimate of the migration parameter is obtained by simulating independently the likelihood at a grid of points and, also, using a surface simulation method. The latter method generates the whole likelihood trajectory in a single application of the simulation program. An estimate of variance of the estimate of the migration parameter is obtained using the likelihood trajectory. A comparison of the maximum likelihood estimates of the gene flow between subpopulations is made with those obtained by using Wright's FST statistic.

Algorithms↗
PubMed1996

Transplant approach establishes that kidneys are responsible for serum CSF-1 but require a stimulus in MRL-lpr mice.

Colony stimulating factor-1 (CSF-1) is a chemoattractant and growth factor for macrophages. In autoimmune MRL-lpr mice, CSF-1 is detected in the circulation and there is an increase in CSF-1 transcripts and macrophages in the kidney. The purpose of this study was to establish whether the MRL-lpr kidney is responsible for increasing serum CSF-1, and to determine if the expression of CSF-1 requires a circulating component in MRL-lpr mice. We transplanted a MRL-lpr kidney with nephritis [serum CSF-1 = 32.6 +/- 5.1 colony forming units (CFU)] into a bilaterally nephrectomized normal MRL-++ recipient. Circulating CSF-1 increased from 1.2 +/- CFU to 14.1 +/_ 5.6 CFU in recipients by one week. Continuous production of CSF-1 required a stimulating component since: (1) CSF-1 in the kidney and circulation disappeared several weeks after engraftment into MRL-++ mice and (2) isolated glomeruli from MRL-lpr required stimulation to express CSF-1. In the transplanted MRL-lpr kidney, hypercellularity in the glomerulus and interstitium (predominantly macrophages) returned to normal as rapidly as two weeks after engraftment into MRL-++. Thus, this study establishes that the kidney is responsible for circulating CSF-1 in MRL-lpr mice. Without the autoimmune environment CSF-1, macrophages, but not T cells, disappear and nephritis resolves.

Animals↗
PubMed1996

Ancestral inference from samples of DNA sequences with recombination.

The sampling distribution of a collection of DNA sequences is studied under a model where recombination can occur in the ancestry of the sequences. The infinitely-many-sites model of mutation is assumed where there may only be one mutation at a given site. Ancestral inference procedures are discussed for: estimating recombination and mutation rates; estimating the times to the most recent common ancestors along the sequences; estimating ages of mutations; and estimating the number of recombination events in the ancestry of the sample. Inferences are made conditional on the configuration of the pattern of mutations at sites in observed sample sequences. A computational algorithm based on a Markov chain simulation is developed, implemented, and illustrated with examples for these inference procedures. This algorithm is very computationally intensive.

Algorithms↗