Non-neutral plasma manipulation techniques in development of a high-capacity positron trap.

Preliminary experiments have been performed toward the development of a multi-cell Penning-Malmberg trap for the storage of large numbers of positrons (≥1010 e+). We introduce the master-cell test trap and the diagnostic tools for first experiments with electrons. The usage of a phosphor screen to measure the z-integrated plasma distribution and the number of confined particles is demonstrated, as well as the trap alignment to the magnetic field (B = 3.1 T) using the m = 1 diocotron mode. The plasma parameters and expansion are described along with the autoresonant excitation of the diocotron mode using rotating dipole fields and frequency chirped sinusoidal drive signals. We analyze the reproducibility of the excitation and use these findings to settle on the path for the next generation multi-cell test device.

A levitated magnetic dipole configuration as a compact charged particle trap.

As a magnetic confinement configuration for electron-positron pair-plasmas, the APEX collaboration [T. S. Pedersen et al., New J. Phys. 14, 035010 (2012)] plans to construct a compact levitated dipole experiment with a high-temperature superconducting coil. In order to realize stable levitation of the dipole field coil, a simple feedback-controlled levitation system was constructed with conventional analog circuits. We report the properties of a prototype levitation system using a permanent magnet and compare its behavior to predictions from a stability analysis. We also present a practical review needed for the construction of a compact levitated dipole trap system based on the work of Morikawa et al. [Teion Kogaku, J. Cryo. Soc. Jpn. 39, 209 (2004)]. Numerical orbit analysis suggests improved confinement properties of charged particles in a dipole field trap by replacing the permanent magnet with a levitated superconducting coil magnet. Such a compact dipole field configuration is potentially applicable to the confinement of various charged particles including positrons and electrons.

Lossless Positron Injection into a Magnetic Dipole Trap.

The high-efficiency injection of a low-energy positron beam into the confinement volume of a magnetic dipole has been demonstrated experimentally. This was accomplished by tailoring the three-dimensional guiding-center drift orbits of positrons via optimization of electrostatic potentials applied to electrodes at the edge of the trap, thereby producing localized and essentially lossless cross-field particle transport by means of the E×B drift. The experimental findings are reproduced and elucidated by numerical simulations, enabling a comprehensive understanding of the process. These results answer key questions and establish methods for use in upcoming experiments to create an electron-positron plasma in a levitated dipole device.

Confinement of Positrons Exceeding 1 s in a Supported Magnetic Dipole Trap.

An ensemble of low-energy positrons injected into a supported magnetic dipole trap can remain trapped for more than a second. Trapping experiments with and without a positive magnet bias yield confinement times up to τ_{A}=(1.5±0.1) and τ_{B}=(0.28±0.04) s, respectively. Supported by single-particle simulations, we conclude that the dominant mechanism limiting the confinement in this trap is scattering off of neutrals, which can lead to both radial transport and parallel losses onto the magnet surface. These results provide encouragement for plans to confine an electron-positron plasma in a levitated dipole trap.

Positron-Induced Luminescence.

We report on the observation that low-energy positrons incident on a phosphor screen produce significantly more luminescence than electrons do. For two different wide-band-gap semiconductor phosphors (ZnS:Ag and ZnO:Zn), we compare the luminescent response to a positron beam with the response to an electron beam. For both phosphors, the positron response is significantly brighter than the electron response, by a factor that depends strongly on incident energy (0-5 keV). Positrons with just a few tens of electron-volts of energy (for ZnS:Ag) or less (for ZnO:Zn) produce as much luminescence as is produced by electrons with several kilo-electron-volts. We attribute this effect to valence band holes and excited electrons produced by positron annihilation and subsequent Auger processes. These results demonstrate a valuable approach for addressing long-standing questions about luminescent materials.

Confinement time exceeding one second for a toroidal electron plasma.

Nearly steady-state electron plasmas are trapped in a toroidal magnetic field for the first time. We report the first results from a new toroidal electron plasma experiment, the Lawrence Non-neutral Torus II, in which electron densities on the order of 10(7) cm(-3) are trapped in a 270-degree toroidal arc (670 G toroidal magnetic field) by application of trapping potentials to segments of a conducting shell. The total charge inferred from measurements of the frequency of the m=1 diocotron mode is observed to decay on a 3 s time scale, a time scale that approaches the predicted limit due to magnetic pumping transport. Three seconds represents approximately equal to 10(5) periods of the lowest frequency plasma mode, indicating that nearly steady-state conditions are achieved.

Close genetic relationship between Semitic-speaking and Indo-European-speaking groups in Iran.

As part of a continuing investigation of the extent to which the genetic and linguistic relationships of populations are correlated, we analyzed mtDNA HV1 sequences, eleven Y chromosome bi-allelic markers, and 9 Y-STR loci in two neighboring groups from the southwest of Iran who speak languages belonging to different families: Indo-European-speaking Bakhtiari, and Semitic-speaking Arabs. Both mtDNA and the Y chromosome, showed a close relatedness of these groups with each other and with neighboring geographic groups, irrespective of the language spoken. Moreover, Semitic-speaking North African groups are more distant genetically from Semitic-speaking groups from the Near East and Iran. Thus, geographical proximity better explains genetic relatedness between populations than does linguistic relatedness in this part of the world.

Identification and analysis of genomic regions with large between-population differentiation in humans.

The primary aim of genetic association and linkage studies is to identify genetic variants that contribute to phenotypic variation within human populations. Since the overwhelming majority of human genetic variation is found within populations, these methods are expected to be effective and can likely be extrapolated from one human population to another. However, they may lack power in detecting the genetic variants that contribute to phenotypes that differ greatly between human populations. Phenotypes that show large differences between populations are expected to be associated with genomic regions exhibiting large allele frequency differences between populations. Thus, from genome-wide polymorphism data genomic regions with large allele frequency differences between populations can be identified, and evaluated as candidates for large between-population phenotypic differences. Here we use allele frequency data from approximately 1.5 million SNPs from three human populations, and present an algorithm that identifies genomic regions containing SNPs with extreme Fst. We demonstrate that our candidate regions have reduced heterozygosity in Europeans and Chinese relative to African-Americans, and are likely enriched with genes that have experienced positive natural selection. We identify genes that are likely responsible for phenotypes known to differ dramatically between human populations and present several candidates worthy of future investigation. Our list of high Fst genomic regions is a first step in identifying the genetic variants that contribute to large phenotypic differences between populations, many of which have likely experienced positive natural selection. Our approach based on between population differences can compliment traditional within population linkage and association studies to uncover novel genotype-phenotype relationships.

Genetic evidence concerning the origins of South and North Ossetians.

Ossetians are a unique group in the Caucasus, in that they are the only ethnic group found on both the north and south slopes of the Caucasus, and moreover they speak an Indo-European language in contrast to their Caucasian-speaking neighbours. We analyzed mtDNA HV1 sequences, Y chromosome binary genetic markers, and Y chromosome short tandem repeat (Y-STR) variability in three North Ossetian groups and compared these data to published data for two additional North Ossetian groups and for South Ossetians. The mtDNA data suggest a common origin for North and South Ossetians, whereas the Y-haplogroup data indicate that North Ossetians are more similar to other North Caucasian groups, and South Ossetians are more similar to other South Caucasian groups, than to each other. Also, with respect to mtDNA, Ossetians are significantly more similar to Iranian groups than to Caucasian groups. We suggest that a common origin of Ossetians from Iran, followed by subsequent male-mediated migrations from their Caucasian neighbours, is the most likely explanation for these results. Thus, genetic studies of such complex and multiple migrations as the Ossetians can provide additional insights into the circumstances surrounding such migrations.

Y chromosome and mitochondrial DNA variation in Lithuanians.

The genetic composition of the Lithuanian population was investigated by analysing mitochondrial DNA hypervariable region 1, RFLP polymorphisms and Y chromosomal biallelic and STR markers in six ethnolinguistic groups of Lithuanians, to address questions about the origin and genetic structure of the present day population. There were no significant genetic differences among ethnolinguistic groups, and an analysis of molecular variance confirmed the homogeneity of the Lithuanian population. MtDNA diversity revealed that Lithuanians are close to both Slavic (Indo-European) and Finno-Ugric speaking populations of Northern and Eastern Europe. Y-chromosome SNP haplogroup analysis showed Lithuanians to be closest to Latvians and Estonians. Significant differences between Lithuanian and Estonian Y chromosome STR haplotypes suggested that these populations have had different demographic histories. We suggest that the observed pattern of Y chromosome diversity in Lithuanians may be explained by a population bottleneck associated with Indo-European contact. Different Y chromosome STR distributions in Lithuanians and Estonians might be explained by different origins or, alternatively, be the result of some period of isolation and genetic drift after the population split.

Mitochondrial DNA and Y-chromosome variation in the caucasus.

We have analyzed mtDNA HVI sequences and Y chromosome haplogroups based on 11 binary markers in 371 individuals, from 11 populations in the Caucasus and the neighbouring countries of Turkey and Iran. Y chromosome haplogroup diversity in the Caucasus was almost as high as in Central Asia and the Near East, and significantly higher than in Europe. More than 27% of the variance in Y-haplogroups can be attributed to differences between populations, whereas mtDNA showed much lower heterogeneity between populations (less then 5%), suggesting a strong influence of patrilocal social structure. Several groups from the highland region of the Caucasus exhibited low diversity and high differentiation for either or both genetic systems, reflecting enhanced genetic drift in these small, isolated populations. Overall, the Caucasus groups showed greater similarity with West Asian than with European groups for both genetic systems, although this similarity was much more pronounced for the Y chromosome than for mtDNA, suggesting that male-mediated migrations from West Asia have influenced the genetic structure of Caucasus populations.

Poloidal E x B drift used as an effective rotational transform to achieve long confinement times in a toroidal electron plasma.

Electron plasmas with mean densities of 5.0 x 10(6) cm(-3) have been confined for as long as 18 ms in a partially toroidal trap with a purely toroidal magnetic field (B(0)=196 G, R(o)=43 cm, a=5 cm). Confinement is limited to 2.0 ms unless feedback is employed to suppress the growth of a toroidal version of the m=1 diocotron mode. The confinement time is much longer than all characteristic single-particle drift time scales and therefore confirms the existence of an equilibrium in which the space-charge-generated E x B drift acts as an effective rotational transform.

Genetic structure and affinities among tribal populations of southern India: a study of 24 autosomal DNA markers.

We describe the genetic structure and affinities of five Dravidian-speaking tribal populations inhabiting the Nilgiri hills of Tamil Nadu, in south India, using 24 autosomal DNA markers. Our goals were: (i). to examine what evolutionary forces have most significantly impacted south Indian tribal genetic variation, and (ii). to test whether the phenotypic similarities of some south Indian tribal groups to Africans represent a signature of close relationship to Africans or are due to convergence. All loci were polymorphic and average heterozygosities were substantial (range: 0.347-0.423). Genetic differentiation was high (Gst= 6.7%) and genetic distances were not significantly correlated with geographic distances. Genetic drift therefore probably played a significant role in shaping the patterns of genetic variation observed in southern Indian tribal populations. Otherwise, analyses of population relationships showed that Indian populations are closely related to one another, regardless of phenotypic characteristics, and do not show particular affinities to Africans. We conclude that the phenotypic similarities of some Indian groups to Africans do not reflect a close relationship between these groups, but are better explained by convergence.

Genetic variability and linkage disequilibrium within the HLA-DP region: analysis of 15 different populations.

In order to understand the forces governing the evolution of the genetic diversity in the HLA-DP molecule, polymerase chain reaction (PCR)-based methods were used to characterize genetic variation at the DPA1 and DPB1 loci encoding this heterodimer on 2,807 chromosomes from 15 different populations including individuals of African, Asian, Amerindian, Indian and European origin. These ethnically diverse samples represent a variety of population substructures and include small, isolated populations as well as larger, presumably admixed populations. Ten DPA1 and 39 DPB1 alleles were identified and observed on 87 distinct DP haplotypes, 34 of which were found to be in significant positive linkage disequilibrium in at least one population. Some haplotypes were found in all ethnic groups while others were confined to a single ethnic group or population. Strong positive global linkage disequilibrium (Wn) between DPA1 and DPB1 was present in all 15 populations. The African populations displayed the lowest values of Wn whereas the Amerindian populations displayed near absolute disequilibrium. Analysis of the distribution of haplotypes using the normalized deviate of the Ewens-Watterson homozygosity statistic, F, suggests that DP haplotypes encoding the functional heterodimer are subject to much lower degrees of balancing selection than other loci within the HLA region. Finally, neighbor joining tree analyses demonstrate the power of haplotype diversity for inferring the relationships between the different populations.

Human mtDNA and Y-chromosome variation is correlated with matrilocal versus patrilocal residence.

Genetic differences among human populations are usually larger for the Y chromosome than for mtDNA. One possible explanation is the higher rate of female versus male migration due to the widespread phenomenon of patrilocality, in which the woman moves to her mate's residence after marriage. To test this hypothesis, we compare mtDNA and Y-chromosome variation in three matrilocal (in which the man moves to his mate's residence after marriage) and three patrilocal groups among the hill tribes of northern Thailand. Genetic diversity in these groups shows a striking correlation with residence pattern, supporting the role of sex-specific migration in influencing human genetic variation.

Phylogenetic analysis of the Friedreich ataxia GAA trinucleotide repeat.

Friedreich ataxia is an autosomal recessive neurodegenerative disorder associated with a GAA repeat expansion in the first intron of the gene (FRDA) encoding a novel, highly conserved, 210 amino acid protein known as frataxin. Normal variation in repeat size was determined by analysis of more than 600 DNA samples from seven human populations. This analysis showed that the most frequent allele had nine GAA repeats, and no alleles with fewer than five GAA repeats were found. The European and Syrian populations had the highest percentage of alleles with 10 or more GAA repeats, while the Papua New Guinea population did not have any alleles carrying more than 10 GAA repeats. The distributions of repeat sizes in the European, Syrian, and African American populations were significantly different from those in the Asian and Papua New Guinea populations (p < 0.001). The GAA repeat size was also determined in five nonhuman primates. Samples from 10 chimpanzees, 3 orangutans, 1 gorilla, 1 rhesus macaque, 1 mangabey, and 1 tamarin were analyzed. Among those primates belonging to the Pongidae family, the chimpanzees were found to carry three or four GAA repeats, the orangutans had four or five GAA repeats, and the gorilla carried three GAA repeats. In primates belonging to the Cercopithecidae family, three GAA repeats were found in the mangabey and two in the rhesus macaque. However, an AluY subfamily member inserted in the poly(A) tract preceding the GAA repeat region in the rhesus macaque, making the amplified sequence approximately 300 bp longer. The GAA repeat was also found in the tamarin, suggesting that it arose at least 40 million years ago and remained relatively small throughout the majority of primate evolution, with a punctuated expansion in the human genome.

Haplotype diversity and linkage disequilibrium at human G6PD: recent origin of alleles that confer malarial resistance.

The frequencies of low-activity alleles of glucose-6-phosphate dehydrogenase in humans are highly correlated with the prevalence of malaria. These "deficiency" alleles are thought to provide reduced risk from infection by the Plasmodium parasite and are maintained at high frequency despite the hemopathologies that they cause. Haplotype analysis of "A-" and "Med" mutations at this locus indicates that they have evolved independently and have increased in frequency at a rate that is too rapid to be explained by random genetic drift. Statistical modeling indicates that the A- allele arose within the past 3840 to 11,760 years and the Med allele arose within the past 1600 to 6640 years. These results support the hypothesis that malaria has had a major impact on humans only since the introduction of agriculture within the past 10,000 years and provide a striking example of the signature of selection on the human genome.

Mitochondrial DNA variation and language replacements in the Caucasus.

Sequences of the first hypervariable segment of the mitochondrial DNA (mtDNA) control region were obtained from 353 individuals representing nine groups and four major linguistic families (Indo-European, Altaic and North and South Caucasian) of the Caucasus region. The diversity within and between Caucasus populations exceeded the diversity within Europe, but was less than that in the Near East. Caucasus populations occupy an intermediate position between European and Near Eastern populations in tree and principal coordinate analyses, suggesting that they are either ancestral to European populations or derived via admixture from European and Near Eastern populations. The genetic relationships among Caucasus populations reflect geographical rather than linguistic relationships. In particular, the Indo-European-speaking Armenians and Altaic-speaking Azerbaijanians are most closely related to their nearest geographical neighbours in the Caucasus, not their linguistic neighbours (i.e. other Indo-European or Altaic populations). The mtDNA evidence thus suggests that the Armenian and Azerbaijanian languages represent instances of language replacement that had little impact on the mtDNA gene pool.

Alu insertion polymorphisms and the genetic structure of human populations from the Caucasus.

An analysis of 8 Alu insertion loci (ACE, TPA25, PV92, APO, FXIIIB, D1, A25, B65) has been carried out in six populations from the Caucasus, including Indo-European-speaking Armenians; Altaic-speaking Azerbaijanians; North Caucasian-speaking Cherkessians, Darginians, and Ingushians; and South Caucasian (Kartvelian)-speaking Georgians. The Caucasus populations exhibit low levels of within-population variation and high levels of between-population differentiation, with the average Fst value for the Caucasus of 0.113, which is almost as large as the Fst value of 0.157 for worldwide populations. Maximum likelihood tree and principal coordinate analyses both group the Caucasus populations with European populations. Neither geographic nor linguistic relationships appear to explain the genetic relationships of Caucasus populations. Instead, it appears as if they have been small and relatively isolated, and hence genetic drift has been the dominant influence on the genetic structure of Caucasus populations.