Contrasting Paternal and Maternal Genetic Histories of Thai and Lao Populations.

The human demographic history of Mainland Southeast Asia (MSEA) has not been well studied; in particular, there have been very few sequence-based studies of variation in the male-specific portions of the Y chromosome (MSY). Here, we report new MSY sequences of ∼2.3 mB from 914 males and combine these with previous data for a total of 928 MSY sequences belonging to 59 populations from Thailand and Laos who speak languages belonging to three major Mainland Southeast Asia families: Austroasiatic, Tai-Kadai, and Sino-Tibetan. Among the 92 MSY haplogroups, two main MSY lineages (O1b1a1a* [O-M95*] and O2a* [O-M324*]) contribute substantially to the paternal genetic makeup of Thailand and Laos. We also analyze complete mitochondrial DNA genome sequences published previously from the same groups and find contrasting pattern of male and female genetic variation and demographic expansions, especially for the hill tribes, Mon, and some major Thai groups. In particular, we detect an effect of postmarital residence pattern on genetic diversity in patrilocal versus matrilocal groups. Additionally, both male and female demographic expansions were observed during the early Mesolithic (∼10 ka), with two later major male-specific expansions during the Neolithic period (∼4-5 ka) and the Bronze/Iron Age (∼2.0-2.5 ka). These two later expansions are characteristic of the modern Austroasiatic and Tai-Kadai groups, respectively, consistent with recent ancient DNA studies. We simulate MSY data based on three demographic models (continuous migration, demic diffusion, and cultural diffusion) of major Thai groups and find different results from mitochondrial DNA simulations, supporting contrasting male and female genetic histories.

Cultural Innovations Influence Patterns of Genetic Diversity in Northwestern Amazonia.

Human populations often exhibit contrasting patterns of genetic diversity in the mtDNA and the nonrecombining portion of the Y-chromosome (NRY), which reflect sex-specific cultural behaviors and population histories. Here, we sequenced 2.3 Mb of the NRY from 284 individuals representing more than 30 Native American groups from Northwestern Amazonia (NWA) and compared these data to previously generated mtDNA genomes from the same groups, to investigate the impact of cultural practices on genetic diversity and gain new insights about NWA population history. Relevant cultural practices in NWA include postmarital residential rules and linguistic exogamy, a marital practice in which men are required to marry women speaking a different language. We identified 2,969 SNPs in the NRY sequences, only 925 of which were previously described. The NRY and mtDNA data showed different sex-specific demographic histories: female effective population size has been larger than that of males through time, which might reflect larger variance in male reproductive success. Both markers show an increase in lineage diversification beginning ∼5,000 years ago, which may reflect the intensification of agriculture, technological innovations, and the expansion of regional trade networks documented in the archaeological evidence. Furthermore, we find similar excesses of NRY versus mtDNA between-population divergence at both the local and continental scale, suggesting long-term stability of female versus male migration. We also find evidence of the impact of sociocultural practices on diversity patterns. Finally, our study highlights the importance of analyzing high-resolution mtDNA and NRY sequences to reconstruct demographic history, since this can differ considerably between sexes.

Transmission of human mtDNA heteroplasmy in the Genome of the Netherlands families: support for a variable-size bottleneck.

Although previous studies have documented a bottleneck in the transmission of mtDNA genomes from mothers to offspring, several aspects remain unclear, including the size and nature of the bottleneck. Here, we analyze the dynamics of mtDNA heteroplasmy transmission in the Genomes of the Netherlands (GoNL) data, which consists of complete mtDNA genome sequences from 228 trios, eight dizygotic (DZ) twin quartets, and 10 monozygotic (MZ) twin quartets. Using a minor allele frequency (MAF) threshold of 2%, we identified 189 heteroplasmies in the trio mothers, of which 59% were transmitted to offspring, and 159 heteroplasmies in the trio offspring, of which 70% were inherited from the mothers. MZ twin pairs exhibited greater similarity in MAF at heteroplasmic sites than DZ twin pairs, suggesting that the heteroplasmy MAF in the oocyte is the major determinant of the heteroplasmy MAF in the offspring. We used a likelihood method to estimate the effective number of mtDNA genomes transmitted to offspring under different bottleneck models; a variable bottleneck size model provided the best fit to the data, with an estimated mean of nine individual mtDNA genomes transmitted. We also found evidence for negative selection during transmission against novel heteroplasmies (in which the minor allele has never been observed in polymorphism data). These novel heteroplasmies are enhanced for tRNA and rRNA genes, and mutations associated with mtDNA diseases frequently occur in these genes. Our results thus suggest that the female germ line is able to recognize and select against deleterious heteroplasmies.

Extensive tissue-related and allele-related mtDNA heteroplasmy suggests positive selection for somatic mutations.

Heteroplasmy in human mtDNA may play a role in cancer, other diseases, and aging, but patterns of heteroplasmy variation across different tissues have not been thoroughly investigated. Here, we analyzed complete mtDNA genome sequences at ∼3,500× average coverage from each of 12 tissues obtained at autopsy from each of 152 individuals. We identified 4,577 heteroplasmies (with an alternative allele frequency of at least 0.5%) at 393 positions across the mtDNA genome. Surprisingly, different nucleotide positions (nps) exhibit high frequencies of heteroplasmy in different tissues, and, moreover, heteroplasmy is strongly dependent on the specific consensus allele at an np. All of these tissue-related and allele-related heteroplasmies show a significant age-related accumulation, suggesting positive selection for specific alleles at specific positions in specific tissues. We also find a highly significant excess of liver-specific heteroplasmies involving nonsynonymous changes, most of which are predicted to have an impact on protein function. This apparent positive selection for reduced mitochondrial function in the liver may reflect selection to decrease damaging byproducts of liver mitochondrial metabolism (i.e., "survival of the slowest"). Overall, our results provide compelling evidence for positive selection acting on some somatic mtDNA mutations.

Colorectal endoscopic full-thickness resection using a novel, flat-base over-the-scope clip: a prospective study.

Background and study aims We aimed to evaluate the feasibility and safety of a new, flat-based over-the-scope clip (Padlock Clip) for colorectal endoscopic full-thickness resection (eFTR). Patients and methods We prospectively included 26 patients with lesions < 20 mm. Indications for eFTR were re-resection of the scar of a low risk malignant polyp (n = 11), recurrent adenoma in a non-lifting scar (n = 10), non-lifting polyp (n = 4), and an adenoma located in a diverticulum (n = 1). Results Technical success rate and full-thickness resection rate were 100 % (26/26) and 92 % (24/26), respectively. Median procedure time was 43 minutes (IQR 27 - 56). No complications occurred during the procedure; 3 complications (12 %) occurred within 48 hours, of which one was a perforation requiring laparoscopic suturing. Specimen volumes from eFTR of scar tissue where the original polyp had been ≥ 20 mm (n = 13) were smaller compared with those from non-scar resections or scars where the original polyps had been < 20 mm (n = 13) (median 0.8 vs. 1.5 cm3, P = 0.03). Conclusions In this first series of colorectal eFTR using the Padlock Clip, feasibility was demonstrated. It was relatively safe in view of surgery as the alternative treatment, but could still benefit from technical refinement. Future studies should explore for which indication this technique is most suitable. TRIAL REGISTRATION: NTR5562 (Dutch Trial Register).

Refining the Y chromosome phylogeny with southern African sequences.

The recent availability of large-scale sequence data for the human Y chromosome has revolutionized analyses of and insights gained from this non-recombining, paternally inherited chromosome. However, the studies to date focus on Eurasian variation, and hence the diversity of early-diverging branches found in Africa has not been adequately documented. Here, we analyze over 900 kb of Y chromosome sequence obtained from 547 individuals from southern African Khoisan- and Bantu-speaking populations, identifying 232 new sequences from basal haplogroups A and B. We identify new clades in the phylogeny, an older age for the root, and substantially older ages for some individual haplogroups. Furthermore, while haplogroup B2a is traditionally associated with the spread of Bantu speakers, we find that it probably also existed in Khoisan groups before the arrival of Bantu speakers. Finally, there is pronounced variation in branch length between major haplogroups; in particular, haplogroups associated with Bantu speakers have significantly longer branches. Technical artifacts cannot explain this branch length variation, which instead likely reflects aspects of the demographic history of Bantu speakers, such as recent population expansion and an older average paternal age. The influence of demographic factors on branch length variation has broader implications both for the human Y phylogeny and for similar analyses of other species.

Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal.

The expansion of the neocortex during mammalian brain evolution results primarily from an increase in neural progenitor cell divisions in its two principal germinal zones during development, the ventricular zone (VZ) and the subventricular zone (SVZ). Using mRNA sequencing, we analyzed the transcriptomes of fetal human and embryonic mouse VZ, SVZ, and cortical plate. In mouse, the transcriptome of the SVZ was more similar to that of the cortical plate than that of the VZ, whereas in human the opposite was the case, with the inner and outer SVZ being highly related to each other despite their cytoarchitectonic differences. We describe sets of genes that are up- or down-regulated in each germinal zone. These data suggest that cell adhesion and cell-extracellular matrix interactions promote the proliferation and self-renewal of neural progenitors in the developing human neocortex. Notably, relevant extracellular matrix-associated genes include distinct sets of collagens, laminins, proteoglycans, and integrins, along with specific sets of growth factors and morphogens. Our data establish a basis for identifying novel cell-type markers and open up avenues to unravel the molecular basis of neocortex expansion during evolution.

The paternal and maternal genetic history of Vietnamese populations.

Vietnam exhibits great cultural and linguistic diversity, yet the genetic history of Vietnamese populations remains poorly understood. Previous studies focused mostly on the majority Kinh group, and thus the genetic diversity of the many other groups has not yet been investigated. Here we analyze complete mtDNA genome sequences and ~2.3 Mb sequences of the male-specific portion of the Y chromosome from the Kinh and 16 minority populations, encompassing all five language families present in Vietnam. We find highly variable levels of diversity within and between groups that do not correlate with either geography or language family. In particular, the Mang and Sila have undergone recent, independent bottlenecks, while the majority group, Kinh, exhibits low levels of differentiation with other groups. The two Austronesian-speaking groups, Giarai and Ede, show a potential impact of matrilocality on their patterns of variation. Overall, we find that isolation, coupled with limited contact involving some groups, has been the major factor influencing the genetic structure of Vietnamese populations, and that there is substantial genetic diversity that is not represented by the Kinh.

Novel isolated cerebral ALlambda amyloid angiopathy with widespread subcortical distribution and leukoencephalopathy due to atypical monoclonal plasma cell proliferation, and terminal systemic gammopathy.

Neuropathologic and biochemical findings in a 34-year-old man whose disease began 2 years before death appearing as chronic progressive encephalitis and culminated in mutism are reported. Cerebrospinal fluid and serum of the patient showed a brain-restricted monoclonal lambda-light chain apparently produced by a small monoclonal immunoglobulin Glambda plasma cell population. In the preterminal stage, there was a systemic monoclonal gammopathy, the source of which could not be identified. At autopsy, there was extensive amyloid deposition in most vessels throughout the cerebral and cerebellar white matter, basal ganglia, and thalamus and diffuse leukoencephalopathy; cerebral and cerebellar cortices, other portions of the CNS, and non-CNS tissues were spared. Partial amino acid sequence analysis demonstrated that the amyloidogenic protein originated from immunoglobulin lambda-light chains which were produced by monoclonal plasma cells. There are 2 similar cases reported in the literature. The distribution of ALlambda deposits in these 3 cases indicates that widespread subcortical vascular amyloidosis with leukoencephalopathy is a novel clinicopathologic entity distinguished from other cerebral diseases with local amyloid light chain deposition, including amyloidoma, leptomeningeal vascular amyloidosis, solitary intracerebral plasmacytoma, primary intracerebral lymphoma with plasmacytic differentiation, and multiple sclerosis with demyelination-associated amyloid deposition.

Sharing of heteroplasmies between human liver lobes varies across the mtDNA genome.

Mitochondrial DNA (mtDNA) heteroplasmy (intra-individual variation) varies among different human tissues and increases with age, suggesting that the majority of mtDNA heteroplasmies are acquired, rather than inherited. However, the extent to which heteroplasmic sites are shared across a tissue remains an open question. We therefore investigated heteroplasmy in two liver samples (one from each primary lobe) from 83 Europeans, sampled at autopsy. Minor allele frequencies (MAF) at heteroplasmic sites were significantly correlated between the two liver samples from an individual, with significantly more sharing of heteroplasmic sites in the control region than in the non-control region. We show that this increased sharing for the control region cannot be explained by recent mutations at just a few specific heteroplasmic sites or by the possible presence of 7S DNA. Moreover, we carried out simulations to show that there is significantly more sharing than would be predicted from random genetic drift from a common progenitor cell. We also observe a significant excess of non-synonymous vs. synonymous heteroplasmies in the protein-coding region, but significantly more sharing of synonymous heteroplasmies. These contrasting patterns for the control vs. the non-control region, and for non-synonymous vs. synonymous heteroplasmies, suggest that selection plays a role in heteroplasmy sharing.

Contrasting maternal and paternal genetic variation of hunter-gatherer groups in Thailand.

The Maniq and Mlabri are the only recorded nomadic hunter-gatherer groups in Thailand. Here, we sequenced complete mitochondrial (mt) DNA genomes and ~2.364 Mbp of non-recombining Y chromosome (NRY) to learn more about the origins of these two enigmatic populations. Both groups exhibited low genetic diversity compared to other Thai populations, and contrasting patterns of mtDNA and NRY diversity: there was greater mtDNA diversity in the Maniq than in the Mlabri, while the converse was true for the NRY. We found basal uniparental lineages in the Maniq, namely mtDNA haplogroups M21a, R21 and M17a, and NRY haplogroup K. Overall, the Maniq are genetically similar to other negrito groups in Southeast Asia. By contrast, the Mlabri haplogroups (B5a1b1 for mtDNA and O1b1a1a1b and O1b1a1a1b1a1 for the NRY) are common lineages in Southeast Asian non-negrito groups, and overall the Mlabri are genetically similar to their linguistic relatives (Htin and Khmu) and other groups from northeastern Thailand. In agreement with previous studies of the Mlabri, our results indicate that the Malbri do not directly descend from the indigenous negritos. Instead, they likely have a recent origin (within the past 1,000 years) by an extreme founder event (involving just one maternal and two paternal lineages) from an agricultural group, most likely the Htin or a closely-related group.

New insights from Thailand into the maternal genetic history of Mainland Southeast Asia.

Tai-Kadai (TK) is one of the major language families in Mainland Southeast Asia (MSEA), with a concentration in the area of Thailand and Laos. Our previous study of 1234 mtDNA genome sequences supported a demic diffusion scenario in the spread of TK languages from southern China to Laos as well as northern and northeastern Thailand. Here we add an additional 560 mtDNA genomes from 22 groups, with a focus on the TK-speaking central Thai people and the Sino-Tibetan speaking Karen. We find extensive diversity, including 62 haplogroups not reported previously from this region. Demic diffusion is still a preferable scenario for central Thais, emphasizing the expansion of TK people through MSEA, although there is also some support for gene flow between central Thai and native Austroasiatic speaking Mon and Khmer. We also tested competing models concerning the genetic relationships of groups from the major MSEA languages, and found support for an ancestral relationship of TK and Austronesian-speaking groups.

Complete human mtDNA genome sequences from Vietnam and the phylogeography of Mainland Southeast Asia.

Vietnam is an important crossroads within Mainland Southeast Asia (MSEA) and a gateway to Island Southeast Asia, and as such exhibits high levels of ethnolinguistic diversity. However, comparatively few studies have been undertaken of the genetic diversity of Vietnamese populations. In order to gain comprehensive insights into MSEA mtDNA phylogeography, we sequenced 609 complete mtDNA genomes from individuals belonging to five language families (Austroasiatic, Tai-Kadai, Hmong-Mien, Sino-Tibetan and Austronesian) and analyzed them in comparison with sequences from other MSEA countries and Taiwan. Within Vietnam, we identified 399 haplotypes belonging to 135 haplogroups; among the five language families, the sequences from Austronesian groups differ the most from the other groups. Phylogenetic analysis revealed 111 novel Vietnamese mtDNA lineages. Bayesian estimates of coalescence times and associated 95% HPD for these show a peak of mtDNA diversification around 2.5-3 kya, which coincides with the Dong Son culture, and thus may be associated with the agriculturally-driven expansion of this culture. Networks of major MSEA haplogroups emphasize the overall distinctiveness of sequences from Taiwan, in keeping with previous studies that suggested at most a minor impact of the Austronesian expansion from Taiwan on MSEA. We also see evidence for population expansions across MSEA geographic regions and language families.

Enclaves of genetic diversity resisted Inca impacts on population history.

The Inca Empire is claimed to have driven massive population movements in western South America, and to have spread Quechua, the most widely-spoken language family of the indigenous Americas. A test-case is the Chachapoyas region of northern Peru, reported as a focal point of Inca population displacements. Chachapoyas also spans the environmental, cultural and demographic divides between Amazonia and the Andes, and stands along the lowest-altitude corridor from the rainforest to the Pacific coast. Following a sampling strategy informed by linguistic data, we collected 119 samples, analysed for full mtDNA genomes and Y-chromosome STRs. We report a high indigenous component, which stands apart from the network of intense genetic exchange in the core central zone of Andean civilization, and is also distinct from neighbouring populations. This unique genetic profile challenges the routine assumption of large-scale population relocations by the Incas. Furthermore, speakers of Chachapoyas Quechua are found to share no particular genetic similarity or gene-flow with Quechua speakers elsewhere, suggesting that here the language spread primarily by cultural diffusion, not migration. Our results demonstrate how population genetics, when fully guided by the archaeological, historical and linguistic records, can inform multiple disciplines within anthropology.

Biocompatibility and healing process of polyester meshes in the brain: in vivo examination in rats.

OBJECTIVES: To analyze the biocompatibility of multifilament polyester (PET) meshes used for the implantation of auditory brainstem implants in a standardized Wistar rat model (n=29). METHODS: The physical properties of the meshes were examined during surgery. Using a modified plastic embedding, the local tissue reaction and the stability of mesh position in the region of the fourth ventricle were evaluated in section series from day 3 to 64. The cellular reaction was further differentiated using transmission and scanning electron microscopy. RESULTS: PET meshes were stable for handling. However, sharp edges inevitably led to brainstem and cerebellar penetration in some cases. The meshes were preserved in situ in all section series. Positioning was stable with one exception. A sufficient fibroblast and collagen fiber encasement was reached after 14 days. In all cases, no further change was observed through day 64. The host-defense reaction was persistent and characterized by numerous macrophages and foreign-body giant cells. Bacterial infection occurred in three cases. CONCLUSIONS: PET meshes proved to have an acceptable biocompatibility regarding local-tissue reaction in the brain. Modified polymer structures should be developed to reduce risk of injury. Anti-inflammatory surface treatments and monofilament meshes could reduce the infection rate.

Optimization of glycol methacrylate embedding of large specimens in neurological research. Study of rat skull-brain specimens after implantation of polyester meshes.

Advances in neuroscience require better anatomical knowledge of neuronal architecture and structural details. Optimal embedding techniques are the basis for precise morphometric studies in section series as well as for the evaluation of tissue specimens or implants of differing hardness. There are very few methods for preparing large specimens by resin embedding, although resins such as polyethylene glycol (PEG) and methyl methacrylate (MMA) are presently in use. However, these methods have proven to be laborious and sometimes unsatisfactory for serial sectioning. While glycol methacrylate embedding (GMA) is suitable for smaller specimens, it results in inadequate infiltration and polymerization in blocks larger than 1 x 1 x 0.2 cm. We present an improved technique using GMA, which permits both standardized embedding of 4 x 2 x 2 cm blocks and preparation of section series. This method was developed for preserving skull-brain specimens from rats with polyester-mesh implants. The excellent preservation of cellular details allowed the assessment of local tissue reaction to foreign-body material in situ. Advantages of this method are: (1) No toxic catalysts or solvents are used (as opposed to MMA and current GMA processes); (2) Laborious routines in stretching and mounting of sections are not necessary (in contrast to PEG and MMA); (3) No deplastination is required before staining (in contrast to PEG and MMA); (4) Excellent morphologic preservation of various tissue is achieved.

Polyester meshes and adhesive materials in the brain: comparative research in rats to optimize surgical strategy.

OBJECT: The goal of this study was to determine the biocompatibility of polyester mesh electrode carriers for auditory brainstem implants with and without adhesives in a rat model. METHODS: Physical properties of the meshes were evaluated within the fourth ventricle region, both without (Group A) and with adhesives (muscle, Group B; oxidized regenerated cellulose [ORC], Group C; and fibrin glue, Group D). The stability of the mesh position, the healing process, and host defense reaction after 2 to 60 days were examined in series of tissue sections in which meshes were preserved in situ. The cellular reaction was further evaluated using electron microscopy. Although otherwise pliable, polyester meshes were too rigid when used with adhesives, especially fibrin glue or muscle. Also, the sharp edges of the meshes presented a risk of brainstem and cerebellar lesions. Regardless of the material, meshes induced persistent inflammatory tissue reactions characterized by numerous macrophages and foreign-body giant cells. After 14 days, the cellular response had resulted in sufficient fibroblast and collagen fiber encapsulation of the meshes and remained essentially unchanged thereafter. No influence of adhesives on the healing process was observed, and, unexpectedly, these substances did not reduce the risk of dislocation prior to adequate cellular encasement. In some rats in Groups A and C, purulent inflammation, in part with Gram-positive bacteria, occurred after 2 to 14 days. The ORC exhibited persistent swelling, introducing the risk of occlusive hydrocephalus and/or brainstem compression. CONCLUSIONS: Polyester meshes and various adhesives exhibited acceptable biocompatibility in terms of local tissue reaction. Adhesives reduced pliability of the meshes, however, and were ineffective in reducing the risk of dislocation. Handling characteristics could be improved by better mesh designs, and risk of infection could be reduced by both improved designs and surface treatment of the meshes with antibacterial agents.

Design and realization of the microwave cavity in the PTB caesium atomic fountain clock CSF1.

At the Physikalisch-Technische Bundesanstalt (PTB), the caesium atomic fountain clock CSF1 was developed. One key element of it is its microwave cavity, which was designed to have a low transversal phase variation across the cavity opening. This usually is achieved by using a cylindrical cavity with a TE011 field mode, having a high intrinsic quality factor, and by feeding the cavity symmetrically via two apertures at opposite position in the cavity wall. In contrast to other solutions, the CSF1 cavity is tightly coupled to the microwave feeds (Qload approximately 2000). Therefore, detuning of the cavity resonance frequency has a reduced impact on the microwave field amplitude in the cavity compared to the case of weak coupling. Thus, a temperature stabilization of the cavity can be avoided. The extent to which the tight coupling may have an impact on the transversal phase distribution was studied. This question was solved analytically for a simplified cavity model. The results were applied to define the coupling geometry of the CSF1 cylindrical cavity in such a manner that the transversal phase distribution should become minimized. The key parameter is the electric length of the waveguides that constitute the junction to the coupling apertures. The theoretical studies are presented in some detail, and steps of the practical realization of the cavity are described.

Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences.

BACKGROUND: Comparisons of maternally-inherited mitochondrial DNA (mtDNA) and paternally-inherited non-recombining Y chromosome (NRY) variation have provided important insights into the impact of sex-biased processes (such as migration, residence pattern, and so on) on human genetic variation. However, such comparisons have been limited by the different molecular methods typically used to assay mtDNA and NRY variation (for example, sequencing hypervariable segments of the control region for mtDNA vs. genotyping SNPs and/or STR loci for the NRY). Here, we report a simple capture array method to enrich Illumina sequencing libraries for approximately 500 kb of NRY sequence, which we use to generate NRY sequences from 623 males from 51 populations in the CEPH Human Genome Diversity Panel (HGDP). We also obtained complete mtDNA genome sequences from the same individuals, allowing us to compare maternal and paternal histories free of any ascertainment bias. RESULTS: We identified 2,228 SNPs in the NRY sequences and 2,163 SNPs in the mtDNA sequences. Our results confirm the controversial assertion that genetic differences between human populations on a global scale are bigger for the NRY than for mtDNA, although the differences are not as large as previously suggested. More importantly, we find substantial regional variation in patterns of mtDNA versus NRY variation. Model-based simulations indicate very small ancestral effective population sizes (<100) for the out-of-Africa migration as well as for many human populations. We also find that the ratio of female effective population size to male effective population size (Nf/Nm) has been greater than one throughout the history of modern humans, and has recently increased due to faster growth in Nf than Nm. CONCLUSIONS: The NRY and mtDNA sequences provide new insights into the paternal and maternal histories of human populations, and the methods we introduce here should be widely applicable for further such studies.