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V Macaulay

Publications and source records attributed to V Macaulay.

At least 19 recordsLinked to original sources
PubMed2001

Do the four clades of the mtDNA haplogroup L2 evolve at different rates?

Forty-seven mtDNAs collected in the Dominican Republic and belonging to the African-specific haplogroup L2 were studied by high-resolution RFLP and control-region sequence analyses. Four sets of diagnostic markers that subdivide L2 into four clades (L2a-L2d) were identified, and a survey of published African data sets appears to indicate that these clades encompass all L2 mtDNAs and harbor very different geographic/ethnic distributions. One mtDNA from each of the four clades was completely sequenced by means of a new sequencing protocol that minimizes time and expense. The phylogeny of the L2 complete sequences showed that the two mtDNAs from L2b and L2d seem disproportionately derived, compared with those from L2a and L2c. This result is not consistent with a simple model of neutral evolution with a uniform molecular clock. The pattern of nonsynonymous versus synonymous substitutions hints at a role for selection in the evolution of human mtDNA. Regardless of whether selection is shaping the evolution of modern human mtDNAs, the population screening of L2 mtDNAs for the mutations identified by our complete sequence study should allow the identification of marker motifs of younger age with more restricted geographic distributions, thus providing new clues about African prehistory and the origin and relationships of African ethnic groups.

Base Sequence↗
PubMed2001

A signal, from human mtDNA, of postglacial recolonization in Europe.

Mitochondrial HVS-I sequences from 10,365 subjects belonging to 56 populations/geographical regions of western Eurasia and northern Africa were first surveyed for the presence of the T-->C transition at nucleotide position 16298, a mutation which has previously been shown to characterize haplogroup V mtDNAs. All mtDNAs with this mutation were then screened for a number of diagnostic RFLP sites, revealing two major subsets of mtDNAs. One is haplogroup V proper, and the other has been termed "pre*V," since it predates V phylogenetically. The rather uncommon pre*V tends to be scattered throughout Europe (and northwestern Africa), whereas V attains two peaks of frequency: one situated in southwestern Europe and one in the Saami of northern Scandinavia. Geographical distributions and ages support the scenario that pre*V originated in Europe before the Last Glacial Maximum (LGM), whereas the more recently derived haplogroup V arose in a southwestern European refugium soon after the LGM. The arrival of V in eastern/central Europe, however, occurred much later, possibly with (post-)Neolithic contacts. The distribution of haplogroup V mtDNAs in modern European populations would thus, at least in part, reflect the pattern of postglacial human recolonization from that refugium, affecting even the Saami. Overall, the present study shows that the dissection of mtDNA variation into small and well-defined evolutionary units is an essential step in the identification of spatial frequency patterns. Mass screening of a few markers identified using complete mtDNA sequences promises to be an efficient strategy for inferring features of human prehistory.

Africa, Northern↗
PubMed2001

Detecting errors in mtDNA data by phylogenetic analysis.

Sequencing and documenting a sample of homologous DNA stretches is prone to copying errors in a way rather analogous to the biological replication process. Previous attempts at obtaining representative mtDNA sequences, typically of the control region, for evolutionary studies or forensic purposes have yielded rather unsatisfactory results in many cases. The key ingredient in pinpointing problems with given data is the phylogenetic analysis of closely related mtDNAs within the framework of an established worldwide phylogeny that is supported by coding region information. We develop some general rules by which likely errors in data tables can readily be detected without rereading whole sequences repeatedly. Following these guidelines, one can expect to lower the error rate by at least an order of magnitude, although it will still be hard to beat the mitochondrial gamma polymerase in precision.

DNA, Mitochondrial↗
PubMed2001

Human Y-chromosome variation in the western Mediterranean area: implications for the peopling of the region.

Y-chromosome variation was analyzed in a sample of 1127 males from the Western Mediterranean area by surveying 16 biallelic and 4 multiallelic sites. Some populations from Northeastern Europe and the Middle East were also studied for comparison. All Y-chromosome haplotypes were included in a parsimonious genealogic tree consisting of 17 haplogroups, several of which displayed distinct geographic specificities. One of the haplogroups, HG9.2, has some features that are compatible with a spread into Europe from the Near East during the Neolithic period. However, the current distribution of this haplogroup would suggest that the Neolithic gene pool had a major impact in the eastern and central part of the Mediterranean basin, but very limited consequences in Iberia and Northwestern Europe. Two other haplogroups, HG25.2 and HG2.2, were found to have much more restricted geographic distributions. The first most likely originated in the Berbers within the last few thousand years, and allows the detection of gene flow to Iberia and Southern Europe. The latter haplogroup is common only in Sardinia, which confirms the genetic peculiarity and isolation of the Sardinians. Overall, this study demonstrates that the dissection of Y-chromosome variation into haplogroups with a more restricted geographic distribution can reveal important differences even between populations that live at short distances, and provides new clues to their past interactions.

Africa, Northern↗
PubMed2001

Prehistoric and historic traces in the mtDNA of Mozambique: insights into the Bantu expansions and the slave trade.

A sample of mitochondrial DNA (mtDNA) from the southeastern African population of Mozambique has been shown to have affinities with populations both to its north and south. From the north came sequences that may have been involved in the Bantu expansion (from western, through eastern, to southern Africa), such as members of haplogroups L3b, L3e1a and a subset of L1a. The dating of the major component of Mozambican mtDNAs, the subset L2a of haplogroup L2, displayed an age range compatible with the Bantu expansion. The southern influence was traced by the presence of sequence types from haplogroup L1d, a probable relict of Khoisan-speaking populations that inhabited the region prior to their displacement by the Bantu-speaking incomers. Within historical times, the forced displacement of Mozambicans as part of the slave trade, mainly documented as being to the Americas, generated a differential input of eastern African sequences into the mtDNA pools of the Americas and of Europe, as testified to by the greater number of sequence matches between Mozambique and the Americas, compared to those between Mozambique and Europe.

DNA, Mitochondrial↗
PubMed2000

Tracing European founder lineages in the Near Eastern mtDNA pool.

Founder analysis is a method for analysis of nonrecombining DNA sequence data, with the aim of identification and dating of migrations into new territory. The method picks out founder sequence types in potential source populations and dates lineage clusters deriving from them in the settlement zone of interest. Here, using mtDNA, we apply the approach to the colonization of Europe, to estimate the proportion of modern lineages whose ancestors arrived during each major phase of settlement. To estimate the Palaeolithic and Neolithic contributions to European mtDNA diversity more accurately than was previously achievable, we have now extended the Near Eastern, European, and northern-Caucasus databases to 1,234, 2, 804, and 208 samples, respectively. Both back-migration into the source population and recurrent mutation in the source and derived populations represent major obstacles to this approach. We have developed phylogenetic criteria to take account of both these factors, and we suggest a way to account for multiple dispersals of common sequence types. We conclude that (i) there has been substantial back-migration into the Near East, (ii) the majority of extant mtDNA lineages entered Europe in several waves during the Upper Palaeolithic, (iii) there was a founder effect or bottleneck associated with the Last Glacial Maximum, 20,000 years ago, from which derives the largest fraction of surviving lineages, and (iv) the immigrant Neolithic component is likely to comprise less than one-quarter of the mtDNA pool of modern Europeans.

DNA, Mitochondrial↗
PubMed2000

Median networks: speedy construction and greedy reduction, one simulation, and two case studies from human mtDNA.

Molecular data sets characterized by few phylogenetically informative characters with a broad spectrum of mutation rates, such as intraspecific control-region sequence variation of human mitochondrial DNA (mtDNA), can be usefully visualized in the form of median networks. Here we provide a step-by-step guide to the construction of such networks by hand. We improve upon a previously implemented algorithm by outlining an efficient parametrized strategy amenable to large data sets, greedy reduction, which makes it possible to reconstruct some of the confounding recurrent mutations. This entails some postprocessing as well, which assists in capturing more parsimonious solutions. To simplify the creation of the resulting network by hand, we describe a speedy approach to network construction, based on a careful planning of the processing order. A coalescent simulation tailored to human mtDNA variation in Eurasia testifies to the usefulness of reduced median networks, while highlighting notorious problems faced by all phylogenetic methods in this context. Finally, we discuss two case studies involving the comparison of characters in the two hypervariable segments of the human mtDNA control region in the light of the worldwide control-region sequence database, as well as additional restriction fragment length polymorphism information. We conclude that only a minority of the mutations that hit the second segment occur at sites that would have a mutation rate comparable to those at most sites in the first segment. Discarding the known "noisy" sites of the second segment enhances the analysis.

DNA, Mitochondrial↗
PubMed1999

Mitochondrial DNA recombination-no need to panic.

Recombination has recently been invoked as an explanation for the large amount of homoplasy observed in a collection of complete or nearly complete human mitochondrial sequences. Here we show that some of the data on which this conclusion was based are likely to be unreliable and that if these data are excluded, the results are no longer significant.

Animals↗
PubMed1999

The emerging tree of West Eurasian mtDNAs: a synthesis of control-region sequences and RFLPs.

Variation in the human mitochondrial genome (mtDNA) is now routinely described and used to infer the histories of peoples, by means of one of two procedures, namely, the assaying of RFLPs throughout the genome and the sequencing of parts of the control region (CR). Using 95 samples from the Near East and northwest Caucasus, we present an analysis based on both systems, demonstrate their concordance, and, using additional available information, present the most refined phylogeny to date of west Eurasian mtDNA. We describe and apply a nomenclature for mtDNA clusters. Hypervariable nucleotides are identified, and the relative mutation rates of the two systems are evaluated. We point out where ambiguities remain. The identification of signature mutations for each cluster leads us to apply a hierarchical scheme for determining the cluster composition of a sample of Berber speakers, previously analyzed only for CR variation. We show that the main indigenous North African cluster is a sister group to the most ancient cluster of European mtDNAs, from which it diverged approximately 50,000 years ago.

Africa, Northern↗
PubMed1998

A phase II study of bryostatin 1 in metastatic malignant melanoma.

Bryostatin 1 is a protein kinase C partial agonist which has both antineoplastic and immune-stimulatory properties, including the induction of cytokine release and expansion of tumour-specific lymphocyte populations. In phase I studies, tumour responses have been observed in patients with malignant melanoma, lymphoma and ovarian carcinoma. The dose-limiting toxicity is myalgia. Sixteen patients (age 35-76 years, median 57 years) with malignant melanoma were treated. All had received prior chemotherapy. In each cycle of treatment, patients received bryostatin 25 degrees g m(-2) weekly for three courses followed by a rest week. The drug was given in PET diluent (10 microg bryostatin ml(-1) of 60% polyethylene glycol, 30% ethanol, 10% Tween 80) and infused in normal saline over 1 h. The principal toxicities were myalgia (grade 2, eight patients and grade 3, six patients) and grade 2 phlebitis (four patients), fatigue (three patients) and vomiting (one patient). Of 15 patients evaluable for tumour response, 14 developed progressive disease. One patient developed stable disease for 9 months after bryostatin treatment. In conclusion, single-agent bryostatin appears ineffective in the treatment of metastatic melanoma in patients previously treated with chemotherapy. It should, however, be investigated further in previously untreated patients.

Adult↗
PubMed1998

Evidence from human oocytes for a genetic bottleneck in an mtDNA disease.

We have examined oocytes from a patient with Kearn-Sayre syndrome caused by mtDNA rearrangements. In mtDNA diseases, mutant and wild-type mtDNA frequently coexist in affected individuals (the condition of heteroplasmy). The proportion of mutant mtDNA transmitted from mother to offspring is variable because of a genetic bottleneck, and the "dose" of mutant mtDNA received influences the severity of the phenotype. The feasibility of prenatal diagnosis is critically dependent on the nature and timing of this bottleneck. Significant levels of rearranged mtDNA were detectable in the majority of the patient's oocytes, by use of multiplex PCR, with wide variation, in the levels of mutant and wild-type molecules, between individual oocytes. We also used length variation in a homopolymeric C tract, which is often heteroplasmic in normal controls, to identify founder subpopulations of mtDNAs in this patient's oocytes. We present direct evidence that the number of segregating units (n) is three to five orders of magnitude less than the number of mitochondria in the human female oocyte. In some cases, the best estimate of n may correspond to a single mitochondrion, if it is assumed that intergenerational transmission of mtDNA can be treated as a single sampling event. The bottleneck appears to contribute a major component of the variable transmission from mother to oocyte, in this patient and in a control. That this bottleneck had occurred by the time that oocytes were mature advances the prospects for prenatal diagnosis of mtDNA diseases.

DNA Primers↗
PubMed1996

Paleolithic and neolithic lineages in the European mitochondrial gene pool.

Phylogenetic and diversity analysis of the mtDNA control region sequence variation of 821 individuals from Europe and the Middle East distinguishes five major lineage groups with different internal diversities and divergence times. Consideration of the diversities and geographic distribution of these groups within Europe and the Middle East leads to the conclusion that ancestors of the great majority of modern, extant lineages entered Europe during the Upper Paleolithic. A further set of lineages arrived from the Middle East much later, and their age and geographic distribution within Europe correlates well with archaeological evidence for two culturally and geographically distinct Neolithic colonization events that are associated with the spread of agriculture. It follows from this interpretation that the major extant lineages throughout Europe predate the Neolithic expansion and that the spread of agriculture was a substantially indigenous development accompanied by only a relatively minor component of contemporary Middle Eastern agriculturalists. There is no evidence of any surviving Neanderthal lineages among modern Europeans.

Agriculture↗
PubMed1993

Control of aromatase in breast cancer cells and its importance for tumor growth.

Three approaches have been taken to elucidate further the biological importance of intratumoural aromatase activity. (i) MCF7 and T47D hormone-dependent breast cancer cell lines both showed detectable aromatase activity in vitro. The up-regulation of this by TGF alpha indicates the possible existence of an autocrine growth stimulatory loop involving aromatase. (ii) Both tamoxifen and cytotoxic chemotherapy caused the suppression of aromatase activity in breast carcinomas in vivo. Aromatase activity prior to treatment did not predict for clinical response to tamoxifen. (iii) Transfection of aromatase into MCF7 cells led to their growth being stimulated by low doses of androgens and this was inhibited by the aromatase inhibitor CGS 16949A.

Aromatase↗
PubMed1990

Somatostatin receptors are present in small-cell but not in non-small-cell primary lung carcinomas: relationship to EGF-receptors.

Sixteen primary human lung tumours were analysed for their content of somatostatin receptors using receptor autoradiography with somatostatin-28 and somatostatin octapeptide analogues as radio-ligands. Two out of 4 small-cell lung carcinomas were somatostatin receptor-positive, with a high density of homogeneously distributed receptors on tumour tissue only. Somatostatin receptors were characterized in one of the tumours in homogenate binding assay as saturable, high-affinity binding sites (KD = 0.53 nM) with a number of sites (Bmax) equivalent to 189 fmoles/mg protein. These sites were specific for somatostatin, since only biologically active somatostatin analogues but not unrelated peptides showed high-affinity binding. Both receptor-positive patients had limited disease; furthermore, the small-cell lung carcinoma patient with the longest survival was receptor-positive, while the one with the shortest survival was receptor-negative. None of the 12 non-small-cell lung carcinomas (5 squamous carcinomas, 7 adenocarcinomas) contained somatostatin receptors. For comparison, epidermal growth factor receptors were found in all non-small-cell lung carcinomas. Neuroendocrine features (synaptophysin, chromogranin, neuron-specific enolase, protein gene product 9.5) were present in all small-cell lung carcinomas but absent in non-small-cell lung carcinomas. Given the receptor-mediated action of somatostatin in other neuroendocrine tumours, these data may have a bearing on the clinical application of somatostatin analogues in patients with small-cell lung carcinomas.

Adult↗