The multifaceted genomic history of Ashaninka from Amazonian Peru

Despite its crucial location, the western side of Amazonia between the Andes and the source(s) of the Amazon River is still understudied from a genomic and archaeogenomic point of view, albeit possibly harboring essential information to clarify the complex genetic history of local Indigenous groups and their interactions with nearby regions,^{1,2,3,4,5,6,7,8} including central America and the Caribbean.^9,10,11,12 Focusing on this key region, we analyzed the genome-wide profiles of 51 Ashaninka individuals from Amazonian Peru, observing an unexpected extent of genomic variation. We identified at least two Ashaninka subgroups with distinctive genomic makeups, which were differentially shaped by the degree and timing of external admixtures, especially with the Indigenous groups from the Andes and the Pacific coast. On a continental scale, Ashaninka ancestors probably derived from a south-north migration of Indigenous groups moving into the Amazonian rainforest from a southeastern area with contributions from the Southern Cone and the Atlantic coast. These ancestral populations diversified in the variegated geographic regions of interior South America, on the eastern side of the Andes, differentially interacting with surrounding coastal groups. In this complex scenario, we also revealed strict connections between the ancestors of present-day Ashaninka, who belong to the Arawakan language family,¹³ and those Indigenous groups that moved further north into the Caribbean, contributing to the early Ceramic (Saladoid) tradition in the islands.^14,15.

Ancient mitochondrial genomes from the Argentinian Pampas inform the early peopling of the Southern Cone of South America

The Southern Cone of South America (SCSA) is a key region for investigations about the peopling of the Americas. However, little is known about the eastern sector, the Argentinian Pampas. We analyzed 18 mitochondrial genomes—7 of which are novel—from human skeletal remains from 3 Early to Late Holocene archaeological sites. The Pampas present a distinctive genetic makeup compared to other Middle to Late Holocene pre-Columbian SCSA populations. We also report the earliest individuals carrying SCSA-specific mitochondrial haplogroups D1j and D1g from Early and Middle Holocene, respectively. Using these deep calibration time points in Bayesian phylogenetic reconstructions, we suggest that the first settlers of the Pampas were part of a single and rapid dispersal ∼15,600 years ago. Finally, we propose that present-day genetic differences between the Pampas and the rest of the SCSA are due to founder effects, genetic drift, and a partial population replacement ∼9,000 years ago.

•

Analysis of 18 ancient human mitochondrial genomes from the Argentinian Pampas.

•

Genetic makeup of Early-Mid Holocene Pampas distinct from later neighboring peoples.

•

Earliest individuals carrying region-specific mitochondrial haplogroups D1j and D1g.

•

First Pampean settlers were part of a single and rapid dispersal ∼15,600 years ago.

A Paleogenomic Reconstruction of the Deep Population History of the Andes

There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ∼9,000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today's genetic structure began to develop by 5,800 BP, followed by bi-directional gene flow between the North and South Highlands, and between the Highlands and Coast. We detect minimal admixture among neighboring groups between ∼2,000-500 BP, although we do detect cosmopolitanism (people of diverse ancestries living side-by-side) in the heartlands of the Tiwanaku and Inca polities. We also highlight cases of long-range mobility connecting the Andes to Argentina and the Northwest Andes to the Amazon Basin. VIDEO ABSTRACT.

Reconstructing the Deep Population History of Central and South America

We report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least ∼9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by ∼4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions.

Investigating the role of human papillomavirus in lung cancer

Lung cancer is the leading cancer worldwide among men and women with morbidity reaching 1.6 million. Human Papillomavirus is the causal factor of cervical cancer while its association with others is still under investigation. The purpose of our study is to examine the presence of HPV DNA as well as high-risk E6/E7 mRNA in patients with lung cancer.

Lung tissues were collected during bronchoscopy and tested for HPV DNA and E6/E7 mRNA.

67 lung tissue samples were analysed. The age range was 49–85 years old (y.o) with a mean age of 67.6 y.o. 9 patients were female and 58 were male. The study included 12 Small Cell Lung Cancers (SCLC) and 55 Non Small Cell Lung Cancer (NSCLC). HPV DNA was detected in 3.0% (2/67) of lung cancer cases, while no E6/E7 mRNA of five high-risk HPV types was found in tissue samples examined. The two positive patients had no prior history of an HPV related disease.

Using the mRNA test as a gold standard for the association of HPV with malignant transformation, the present results showed no association of HPV status with lung cancer. Further investigation of more lung cancer tissues is required to reach safe conclusions.

Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas

The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages.

bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS)

Summary: We present bammds, a practical tool that allows visualization of samples sequenced by second-generation sequencing when compared with a reference panel of individuals (usually genotypes) using a multidimensional scaling algorithm. Our tool is aimed at determining the ancestry of unknown samples—typical of ancient DNA data—particularly when only low amounts of data are available for those samples.

Availability and implementation: The software package is available under GNU General Public License v3 and is freely available together with test datasets https://savannah.nongnu.org/projects/bammds/. It is using R (http://www.r-project.org/), parallel (http://www.gnu.org/software/parallel/), samtools (https://github.com/samtools/samtools).

Contact:bammds-users@nongnu.org

Supplementary information:Supplementary data are available at Bioinformatics online.

Lipoplatin plus gemcitabine versus cisplatin plus gemcitabine in NSCLC: Preliminary results of a phase III trial

18028

Background: Lipoplatin is a liposomal formulation of cisplatin, designed to reduce its adverse reactions without reducing efficacy. Its nanoparticles evade immune surveillance and extravasate preferentially into tumors inducing tumor cell apoptosis; lipoplatin may also act as antiangiogenesis factor. This is the initial report of a randomized, multicenter, phase III trial comparing the two drugs. Methods: Eligibility criteria included confirmed diagnosis of inoperable/metastatic NSCLC, no previous chemotherapy, WHO PS 0–1, adequate end-organ function. Patients received Lipoplatin 120 mg/m2 D1,8,15 or cisplatin 100 mg/m2 D1, combined with gemcitabine 1,000 mg/m2 D1,8, in 3-week cycles, with disease evaluation after 3 and 6 cycles. Primary endpoints are overall survival and toxicity, with Response Rates, PFS and QOL also being evaluated. Results: 59 patients have been treated, 33 with lipoplatin and 26 with cisplatin; 17 have completed treatment. 2 lipoplatin patients had a hypersensitivity reaction during the first infusion. There were no grade 4 toxicities. Grade 3 toxicities were observed in <5% of the patients and were comparable for the two groups, except neutropenia (3% for lipoplatin, 15% for cisplatin). Main grade 1–2 toxicities were anemia (93% vs 88%), leucopenia (51% vs 38%), neutropenia (45% vs 30%), thrombocytopenia (58% vs 31%), hepatotoxicity (38% vs 46%), nausea/vomiting (13% vs 35%), asthenia (31% vs 30%) and anorexia (32% vs 34%). Concerning nephrotoxicity, grade 2 was reported in only 6% of lipoplatin patients vs 19% in cisplatin, although lipoplatin was administered without pre-hydration as a 6-hour infusion. Neurotoxicity was also markedly less in lipoplatin. So far, 32 patients have been assessed for response, 16 in each group; 4 partial responses have been reported in each group. However, difference has been observed in stable disease (23% in lipoplatin vs 12% in cisplatin) as well as progressive disease (16% vs 35%). Conclusions: Preliminary results show that lipoplatin may have a better safety and therapeutic profile than cisplatin, when combined with gemcitabine, in advanced NSCLC. Particularly important might be its significantly lower neuro- and nephro-toxicity and its administration on an outpatients basis.

No significant financial relationships to disclose.

Trisomy 6 and double minute chromosomes in a case of chronic myelomonocytic leukemia

A 65-year-old woman with chronic myelomonocytic leukemia was shown to have trisomy 6 and multiple double minute chromosomes. The patient had no history of prior exposure to any mutagenic or carcinogenic agents. To our knowledge, this is the first report for presence of only these two aberrations. The expression of several oncoproteins and onco-related proteins was detected immunohistochemically in bone marrow cells. Among them, only the bcl-2 oncoprotein was positively stained in 100% of myeloblasts. Although the c-myc oncogene is frequently reported to be overexpressed in myeloid disorders with double minutes and associated with chemotherapy resistance and disease aggressiveness, in our case, the c-myc oncoprotein was not positively expressed. The patient received chemotherapy and complete hematological remission was successfully achieved.

Rescued Account of a Vanished People

Chronicle of the Guayaki Indians . Pierre Clastres. Translated by Paul Auster. Zone Books, New York, 1998. 352 pp. $25.50, £21.95. ISBN 0-942299-77-9. Paper, Faber and Faber, London. 253 pp. £9.99. ISBN 0-571-19398-6.

Chronicle is the French political anthropologist's account of his first fieldwork, two years in the early 1960s spent with a small, now vanished, group inhabiting the Paraguayan rainforest. Clastres provides illuminating descriptions of a lost culture, transactions between cultures, and the practice of anthropology. The translation, by novelist Paul Auster, captures the original's freshness, sense of humor, and intellectual insight.

Biological dosimetry of absorbed radiation by C-banding of interphase chromosomes in peripheral blood lymphocytes

Induction of premature chromosome condensation enables direct observation of radiation-induced cytogenetic damage in non-stimulated, interphase, human peripheral blood lymphocytes. This phenomenon can be explored in radiation protection for biological dosimetry in instances of accidental exposure to ionizing radiation. Quantification of an exposure by means of this approach has been limited so far mainly to the analysis of chromosome fragments. This limitation is due to the fact that conventional Giemsa staining of prematurely condensed chromosomes (PCCs) does not allow visualization of the centromeric regions and, as a result, the identification of dicentrics, centric rings and acentric fragments. In the present report a C-banding procedure, refined to avoid swelling and chromosome distortion of freshly prepared PCCs spreads, is used to identify such aberrations in non-stimulated human lymphocytes. The method allows immediate banding of the centromeric regions and enables scoring of aberrations within a time interval (3-4 h after blood sample withdrawal) that is only a fraction of that normally required when cells stimulated to proliferate are analysed at metaphase. The dose-response for dicentrics and centric rings measured in interphase lymphocytes was found to be similar to that obtained at metaphase. Measurement of dicentrics and centric rings in prematurely condensed chromosomes of human lymphocytes would provide valuable information on radiation dose estimates, especially in cases of extreme urgency.

Human chromosome 19 confers the CD2/E rosette receptor phenotype in interspecific cell hybrids

Interspecific cell hybrids between Chinese Hamster Ovary (CHO) and phytohaemagglutinin (PHA) stimulated human T lymphocytes were purified by preparative rosetting with sheep red blood cells (SRBC). The hybrid cell clone used in the present study consisted of cells containing a complete set of the 20 CHO chromosomes and one extra human chromosome, No 19. Hybrid cells constitutively expressed high levels of human CD2 surface receptor and formed multilayer rosettes with SRBC and human erythrocytes. In addition to CD2 they produced low levels of a small number of human extracellular proteins. These findings suggest that the factor(s) responsible for CD2 expression are produced by the hybrid and that genes responsible for CD2 expression are located on chromosome 19. However, the present work cannot exclude that material of chromosome 1, where the CD2 gene has been assigned previously, is integrated somewhere in the hybrid karyotype. Further work is needed to clarify this point.

Effectiveness of radiation control program for Dornier HM3 lithotriptor

Radiation exposure during extracorporeal shock-wave lithotripsy (ESWL) was calculated using a "worst-case method" in 135 randomly selected patients. The patients were divided into four groups according to body weight: small (less than 140 pounds), medium (141-180 pounds), large (181-220 pounds), and very large (greater than 220 pounds). Average skin exposure was found to be 15.2 R (from 1.2 to 95.6 R). After implementation of a "radiation awareness program" radiation exposure was calculated in 128 cases (matched for body weight and stone burden) and average exposure was 9.5 R (from 0.9 to 33.4 R) with a reduction of 20, 37, 33, and 62 percent for each group, respectively. Radiation exposure reduction was primarily due to a reduction in the number of radiographic "snapshots" taken as a result of preferential use of special-mode fluoroscopic "stills."

Formation of multilayer rosettes in phytohemagglutinin-stimulated lymphocytes: correlation with chromatin condensation conformation in premature chromosome condensation

We found that the formation of multilayer rosettes by transformed human blood lymphocytes after phytohemagglutinin (PHA) stimulation is correlated with conformational changes of the chromatin as seen by premature chromosome condensation (PCC). The frequency distribution of grades of PCC and multilayer rosette formation suggests that changes in chromatin are a prerequisite for rosette formation. Rosette formation was most pronounced for 24-h and 48-h cultures. Chromatin decondensation and rosette formation showed identical patterns. The possibility that multilayer rosette formation is directly dependent on conformational changes of chromatin is discussed.

Cholesteatoma of the renal pelvis: endoscopic management

We report 2 cases of renal cholesteatoma, 1 of which was associated with inactive renal tuberculosis and the other with urinary stone disease. Both cases were managed by endourological techniques. The diagnosis of cholesteatoma was suspected at ureteroscopic examination of the renal pelvis and it was confirmed by histological examination of biopsy material in both cases. Treatment consisted of endoscopic extraction of the keratinous debris from the collecting system. In 1 case this was achieved with the ureteroscope and in the other case the nephroscope was used.

Ureteroscopy in management of ureteral calculi

Transurethral ureteroscopy (TUURS) for the management of ureteral stones was performed in 102 patients. Primary ureteroscopy was performed in 57 patients while in 20 cases the procedure was used for stone manipulation prior to ESWL and in 18 cases after ESWL treatment. In 7 cases, insertion of the instrument was impossible. The overall success rate was 89 per cent (85/95). Success rate in the lower ureter was 93 per cent, in the middle ureter 84 per cent, and in the upper ureter 80 per cent. There were four complications (4%) and open operation was required in 3 patients only (3%). The up-to-date ureteroscopic results suggest that ureteroscopy should be the procedure of choice in the treatment of lower ureteral calculi and a valuable alternative in the treatment of upper ureteral calculi.

3-Aminobenzamide does not affect X-ray-induced cytogenetic damage in G0 human lymphocytes

The inhibition of poly(ADP-ribose) polymerase by 3-aminobenzamide (3AB) has been reported to have very different effects on X-ray-induced chromosome aberrations in G0 human lymphocytes. One group of investigators observed a 2-3-fold increase in the yield of rings, dicentrics and chromosome breaks after X-irradiation and 3AB treatment, whereas another group found that 3AB had no effect on X-ray-induced chromosome aberrations. To resolve this discrepancy, we repeated the experiments as described by both groups and found no effect of 3 mM or 5 mM 3AB on the frequency of chromosome aberrations induced by either 1 Gy or 2 Gy of X-rays. Furthermore, we found no effect of 3AB on X-ray-induced aberration yields in C-banded prematurely condensed chromosome preparations from unstimulated human lymphocytes. These results indicate that poly(ADP-ribose) polymerase is not involved in the repair of cytogenetic damage in G0 human lymphocytes.

Proliferation of human acute leukemia cells in culture on treatment with an homo-aza-steroid

When cultures of human leukemia cells from 9 untreated patients with acute leukemia were treated with 3 beta-hydroxy-13 alpha-amino-13,17-seco-5 alpha-androstan-17-oic-13, 17-lactam, an increased proliferating activity was exhibited. The leukemia cells were cultured for 48h and the amounts of lactam (4, 12 and 24 ng/ml) were added at zero time in the continuous presence of (3H)-thymidine. Our data suggested that in high concentrations lactam acts as a toxic agent while in the lower ones it seems to stimulate proliferation of the blast cell.