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R C Griffiths

Publications and source records attributed to R C Griffiths.

At least 19 recordsLinked to original sources
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↗
PubMed1995

Unrooted genealogical tree probabilities in the infinitely-many-sites model.

The infinitely-many-sites process is often used to model the sequence variability observed in samples of DNA sequences. Despite its popularity, the sampling theory of the process is rather poorly understood. We describe the tree structure underlying the model and show how this may be used to compute the probability of a sample of sequences. We show how to produce the unrooted genealogy from a set of sites in which the ancestral labeling is unknown and from this the corresponding rooted genealogies. We derive recursions for the probability of the configuration of sequences (equivalently, of trees) in both the rooted and unrooted cases. We give a computational method based on Monte Carlo recursion that provides approximates to sampling probabilities for samples of any size. Among several applications, this algorithm may be used to find maximum likelihood estimators of the substitution rate, both when the ancestral labeling of sites is known and when it is unknown.

Biological Evolution↗
PubMed1994

Sampling theory for neutral alleles in a varying environment.

We develop a sampling theory for genes sampled from a population evolving with deterministically varying size. We use a coalescent approach to provide recursions for the probabilities of particular sample configurations, and describe a Monte Carlo method by which the solutions to such recursions can be approximated. We focus on infinite-alleles, infinite-sites and finite-sites models. This approach may be used to find maximum likelihood estimates of parameters of genetic interest, and to test hypotheses about the varying environment. The methods are illustrated with data from the mitochondrial control region sampled from a North American Indian tribe.

Alleles↗
PubMed1994

Determinants of forearm mineral density and its correlation with fracture history in women.

In order to evaluate the role of single photon absorptiometry (SPA) in the prediction of osteoporotic fracture risk, 1935 women, referred for measurement of forearm mineral density (FMD) at the distal radial site, were studied by questionnaire in a cross-sectional design. There was no significant decline in FMD until the age of 47, after which there was a linear decline with age of about 1.2% per year. There was no relationship between age and FMD, or forearm mineral content (FMC), in premenopausal women. There was a fall in FMD with the number of years since menopause, after correcting for the effects of age, of approximately 0.5% per year. Body weight was positively correlated with FMC in postmenopausal women. The duration of exposure to hormone replacement therapy (HRT) was positively correlated with FMD, and the magnitude of this effect was reduced the longer the delay between the onset of the menopause and the commencement of HRT. There was no significant association of FMD with calcium intake, weight-bearing exercise, tobacco or alcohol consumption, or family history of osteoporosis. FMD was significantly lower in postmenopausal women who reported fractures after the age of 25, after correcting for age and years postmenopause. In conclusion, a low FMD is predictive of a past history of fractures and may therefore be capable of predicting future fracture risk.

Absorptiometry, Photon↗
PubMed1993

The coalescent in two colonies with symmetric migration.

Kingman's coalescent process is extended to two colonies with symmetric migration. The mean waiting time until a sample of genes taken from two colonies coalesces to a common ancestor is obtained. The final step in the waiting time before the process is absorbed at 1 is observed to have an intriguing behaviour. The distribution of this final waiting time converges to the known distribution of the corresponding waiting time in the case of a single population as the migration rate tends to zero. The mean, however, does not converge. The waiting time until a sample has two common ancestors is modeled as a function of the migration rate. Finally bounds for the expected waiting time for the two colonies to have j > l ancestors are derived.

Genetics, Population↗
PubMed1993

The effects of surgery and acute rejection on glomerular hemodynamics in the transplanted rat kidney.

The effects of surgery and acute rejection on glomerular hemodynamics in the transplanted rat kidney are examined. Kidneys were transplanted from Munich-Wistar (MW) rats to syngeneic controls and MHC-incompatible PVG strain recipients. We report on 4 groups of animals: (1) two-kidney control MW rats; (2) unilaterally nephrectomized MW rats (UNX); (3) renal transplantation from MHC-identical MW littermates and removal of native kidneys (SYN); and (4) transplantation from MW donors to MHC-incompatible PVG rats and removal of native kidneys (ALLO). Glomerular filtration rate (GFR), single-nephron (SN)GFR, and glomerular capillary pressure (PGC) in SYN kidneys were depressed as compared to those in UNX (GFR, 1.41 +/- 0.08 vs. 0.80 +/- 0.08 ml/min; SNGFR, 67.2 +/- 4.8 vs. 44.7 +/- 6.6 nl/min; and PGC, 67 +/- 2 vs. 48 +/- 4 mmHg, UNX vs. SYN, respectively, P < 0.05). GFR and SNGFR in ALLO kidneys, however, were depressed even further (GFR, 0.40 +/- 0.05 ml/min; SNGFR, 13.8 +/- 1.8 nl/min; P < 0.05 for UNX vs. ALLO and SYN vs. ALLO). Afferent arteriolar resistance (RA) was increased greater than 4-fold (UNX, 1.01 +/- 0.15 10(10) dyn.sec.cm-5; SYN, 1.37 +/- 0.36 10(10) dyn.sec.cm-5; ALLO, 4.76 +/- 0.74 10(10) dyn.sec.cm-5 [P < 0.05, UNX vs. ALLO and SYN vs. ALLO]). This led to a precipitous fall in initial capillary flow rate in ALLO rats. These studies reveal the presence of moderate reductions in SNGFR and PGC in the nonrejecting transplanted kidney, which may relate to as yet unidentified consequences of the transplant surgery. More significantly, the principal mechanism leading to the reduced GFR characteristic of acute allograft rejection is identified as severe preglomerular vasoconstriction.

Acute Disease↗
PubMed1992

Statistical analysis of in situ hybridization data: derivation and use of the zmax test.

There are many situations in which grain distributions resulting from in situ hybridization of radioactively labeled probes to unique genes should be subjected to a statistical analysis. However, the problems posed by analysis of in situ hybridization data are not straightforward, and no completely satisfying method is currently available. We have developed a procedure in which the major and any number of minor site(s) of hybridization may be specifically located and the significance of each tested. This zmax procedure first tests the overall distribution for departure from randomness and then identifies significantly overlabeled whole chromosomes (or chromosome arms or other large segments), a process that may be repeated to pinpoint significantly overlabeled regions within these chromosomes. We describe in detail the derivation of the zmax statistic, present tables of significant zmax levels, and show with examples how zmax is used in tests of significance of in situ hybridization data.

Animals↗