scholarly journals Evaluation of DNA conservation in Nile-Saharan environment, Missiminia, in Nubia: Tracking maternal lineage of “X-Group”

2020 ◽  
Author(s):  
Yahia Mehdi Seddik Cherifi ◽  
Selma Amrani
Keyword(s):  
North Africa ◽  
Petrous Bone ◽  
Nile Valley ◽  
Maternal Lineage ◽  
Mt Dna ◽  
Sequencing Method ◽  
Dna Strands ◽  
Skeletal Samples ◽  
Saharan Environment

AbstractObjectiveWe assessed DNA conservation using a range of archaeological skeletal samples from Sudan (Missiminia in Upper Nubia, 350 B.C.E to 1400 C.E) from the unfavorable conditions of the Saharan milieu and humidity of the Nile valley by tracking maternal lineage on the ‘X-Group’ (Ballaneans).MethodWe were able to extract, amplify, and sequence mt-DNA HVS-I (Sanger sequencing method) from 11 petrous bone samples, eight for the X-Group set and three for the reference set (one Christian, one Late Meroitic, and one Meroitic).ResultsIt was possible to find the haplogroups (L1b, L2, L3, H2, N, T1a, X and W) and to carry out comparative data analysis in relation to haplogroup data cited in the literature. This investigation into the maternal lineage of X-Group (350 to 500 C.E.) origins allowed us to validate the efficiency of petrous bone sampling from ancient human remains from the Nile-Saharan milieu and established that the Ballaneans experienced an in-situ development with more admixture from the Levant region and North Africa.ConclusionsOur study used mt-DNA (HVS-I) to look for the biological origins of the X-Group from Upper-Nubia and demonstrated the feasibility of ancient DNA research on skeletons from the Nile-Saharan environment. The use of Next Sequencing Generation (NGS) should optimize and improve the detection of shorter DNA strands and their sequencing in complete genomes from ancient skeletal remains (petrous bones) from hot and humid environments.

scholarly journals Dating the End of the Neolithic in an Eastern Sahara Oasis: Modeling Absolute Chronology

Radiocarbon ◽  
2012 ◽  
Vol 54 (3-4) ◽  
pp. 305-318 ◽  
Author(s):  
Michel Wuttmann ◽  
François Briois ◽  
Béatrix Midant-Reynes ◽  
Tiphaine Dachy
Keyword(s):  
Bayesian Modeling ◽  
Liquid Scintillation ◽  
Nile Valley ◽  
Archaeological Remains ◽  
Middle Holocene ◽  
Cultural Complex ◽  
Scintillation Method ◽  
First Time ◽  
Ostrich Eggshell

The Neolithic site KS043, excavated by the Institut français d'archéologie orientale (IFAO), is situated in the southern basin of the Kharga Oasis (Egypt). It is one of the very few stratified prehistoric sites of the eastern Sahara. The archaeological remains were found near artesian springs that provided water for pastoralists during the dry Middle Holocene. In situ settlement features provided well-preserved material (charcoal, ashy sediment, ostrich eggshell) sufficient to perform radiocarbon dating in the IFAO laboratory in Cairo by the conventional liquid scintillation method. In 2 cases, ostrich eggshell and charcoal within the same in situ context gave significantly different results of, respectively, ∼600 and ∼1200 yr younger dates for the ostrich eggshells. The strong discrepancy is here highlighted for the first time and we suggest that it may be linked with postdepositional phenomena in the vicinity of the artesian springs. A thorough review of 14C dates available for the Holocene in eastern Sahara shows that ostrich eggshells have been widely used. They seem slightly more prone to be discarded than other material but were never the object of a particular study in this context. Bayesian modeling shows that the Neolithic occupation at site KS043 spans a range from 5000 to 3950 cal BC (and concentrated around 4600–4350 cal BC). Characteristic flint tools and pottery relate this occupation to the end of the Neolithic and show links with the Tasian culture, confirming the timing of the presence of this cultural complex in the desert before its appearance in the Nile Valley.

Current Research and Recent Radiocarbon Dates from Northern Africa, III

1988 ◽  
Vol 29 (2) ◽  
pp. 145-176 ◽  
Author(s):  
Angela E. Close
Keyword(s):  
North Africa ◽  
Good Evidence ◽  
Nile Valley ◽  
Archaeological Research ◽  
North African ◽  
Radiocarbon Dates ◽  
Plant Foods ◽  
Khartoum Mesolithic ◽  
Subsistence Activities ◽  
First Time

This article reports on developments in archaeological research in North Africa during the last four years, as these are reflected in the 350, or thereabouts, radiocarbon (and thermoluminescence) dates that have appeared since the last review. The number of new dates, and new data, becoming available indicate that North African archaeology is flourishing, although, in contrast to the earlier decades of this century, the focus seems now to be moving toward the eastern part of the region, and toward matters of adaptation rather than of simple classification, as exemplified by the new interpretations of the Dhar Tichitt Neolithic in Mauritania.The lower Nile Valley has yielded evidence for an intensification of subsistence activities in the Late Palaeolithic in two areas, Makhadma and Kubbaniya, both involving fish-harvesting and the latter also witnessing the use of plant-foods on a scale hitherto undocumented for this period.At the beginning of the Holocene, there is now good evidence for an eighth millennium bc Neolithic in northern Niger, complete with sophisticated ceramics, which complements the evidence already known for similar phenomena further east in the Sahara. There is even a possibility that the Khartoum Mesolithic of the central Nile Valley might be equally old. Our understanding of the Sudanese Neolithic has greatly increased. For the first time, there appears to be a development from the Khartoum Mesolithic into the Khartoum Neolithic, albeit located outside the Valley. The Khartoum Neolithic is more or less confined to the fourth millennium bc, but did give rise to the later Kadada Neolithic. After Kadada, the focus of settlement seems to have shifted outside the Valley until Meroitic times.In the protohistoric and historic periods, we have a better understanding of the chronology of the Egyptian Predynastic, although not yet of its development; what models exist will be radically modified if the pyramids are indeed as old as the dates on them now indicate. Finally, far from the Nile Valley in northern Niger, there comes detailed evidence of the development of a precocious metallurgical tradition within a Neolithic context.

Rock-paintings from the Libyan Desert. An Appendix to Dr H. A. Winklers's ‘Rock-drawings of Southern Upper Egypt II’

Antiquity ◽  
1939 ◽  
Vol 13 (52) ◽  
pp. 389-402 ◽  
Author(s):  
R. F. Peel
Keyword(s):  
North Africa ◽  
Nile Valley ◽  
Upper Egypt ◽  
Desert Oasis ◽  
Rock Paintings ◽  
Libyan Desert ◽  
Selection Of

The two volumes of rock-drawings from southern Upper Egypt collected by Dr H. A. Winkler, and published by the Egypt Exploration Society, together form a work of the utmost interest and importance to all interested in the archaeology and ethnology of North Africa. In the first volume, published in 1938, Dr Winkler included a selection of the material collected from the deserts east of the Nile and from the Nile valley itself. In the second volume, just published, the drawings and paintings are all from the deserts west of the Nile and cover three main regions : first the edges of the Nile valley itself from Qena to Aswan ; secondly the regions between the Nile and Kharga; and thirdly certain parts of the central Libyan Desert towards the extreme south-western frontiers of Egypt, in particular the mountain ‘ desert oasis ’ of Gebel ’Uweinat.

scholarly journals On the performance of satellite-based observations of <i>X</i>CO<sub>2</sub> in capturing the NOAA Carbon Tracker model and ground-based flask observations over Africa's land mass

2020 ◽  
Vol 13 (7) ◽  
pp. 4009-4033
Author(s):  
Anteneh Getachew Mengistu ◽  
Gizaw Mengistu Tsidu
Keyword(s):  
North Africa ◽  
Model Simulation ◽  
Satellite Observation ◽  
Satellite Observations ◽  
Lower Altitude ◽  
Equatorial Africa ◽  
Land Mass ◽  
Data Gap ◽  
Good Agreement

Abstract. Africa is one of the most data-scarce regions as satellite observation at the Equator is limited by cloud cover and there is a very limited number of ground-based measurements. As a result, the use of simulations from models is mandatory to fill this data gap. A comparison of satellite observation with model and available in situ observations will be useful to estimate the performance of satellites in the region. In this study, GOSAT column-averaged carbon dioxide dry-air mole fraction (XCO2) is compared with the NOAA CT2016 and six flask observations over Africa using 5 years of data covering the period from May 2009 to April 2014. Ditto for OCO-2 XCO2 against NOAA CT16NRT17 and eight flask observations over Africa using 2 years of data covering the period from January 2015 to December 2016. The analysis shows that the XCO2 from GOSAT is higher than XCO2 simulated by CT2016 by 0.28±1.05 ppm, whereas OCO-2 XCO2 is lower than CT16NRT17 by 0.34±0.9 ppm on the African land mass on average. The mean correlations of 0.83±1.12 and 0.60±1.41 and average root mean square deviation (RMSD) of 2.30±1.45 and 2.57±0.89 ppm are found between the model and the respective datasets from GOSAT and OCO-2, implying the existence of a reasonably good agreement between CT and the two satellites over Africa's land region. However, significant variations were observed in some regions. For example, OCO-2 XCO2 are lower than that of CT16NRT17 by up to 3 ppm over some regions in North Africa (e.g. Egypt, Libya, and Mali), whereas it exceeds CT16NRT17 XCO2 by 2 ppm over Equatorial Africa (10∘ S–10∘ N). This regional difference is also noted in the comparison of model simulations and satellite observations with flask observations over the continent. For example, CT shows a better sensitivity in capturing flask observations over sites located in North Africa. In contrast, satellite observations have better sensitivity in capturing flask observations in lower-altitude island sites. CT2016 shows a high spatial mean of seasonal mean RMSD of 1.91 ppm during DJF with respect to GOSAT, while CT16NRT17 shows 1.75 ppm during MAM with respect to OCO-2. On the other hand, low RMSDs of 1.00 and 1.07 ppm during SON in the model XCO2 with respect to GOSAT and OCO-2 are respectively determined, indicating better agreement during autumn. The model simulation and satellite observations exhibit similar seasonal cycles of XCO2 with a small discrepancy over Southern Africa (35–10∘ S) and during wet seasons over all regions.

Methanobrevibacter smithii Archaemia in Febrile Patients With Bacteremia, Including Those With Endocarditis

2020 ◽  
Author(s):  
Michel Drancourt ◽  
Kenza Djemai ◽  
Frédérique Gouriet ◽  
Ghiles Grine ◽  
Ahmed Loukil ◽  
...  
Keyword(s):  
Blood Culture ◽  
Bacterial Culture ◽  
Laboratory Methods ◽  
Cardiac Tissues ◽  
Methanobrevibacter Smithii ◽  
Specific Pcr ◽  
Sequencing Method ◽  
Two Samples ◽  
Staphylococcus Hominis

Abstract Background The spectrum of infections caused by methanogens remains to be described. We searched for methanogens in the blood of febrile patients using specific tools. Methods Blood culture samples routinely collected in patients with fever were prospectively screened by specific PCR assays for methanogens. Positive samples were observed by autofluorescence and electron microscopy, analyzed by metagenomics and cultured using previously developed methods. Blood culture bottles experimentally inoculated were used as controls. The presence of methanogens in vascular and cardiac tissues was assessed by indirect immunofluorescence, fluorescent in situ hybridization and PCR-based investigations. Results PCR detection attempted in 7,716 blood samples, was negative in all 1,312 aerobic bottles and 810 bacterial culture-negative anaerobic bottles. PCRs were positive in 27/5,594 (0.5%) bacterial culture-positive anaerobic bottles collected from 26 patients. Sequencing confirmed Methanobrevibacter smithii associated with staphylococci in 14 patients, Enterobacteriaceae in nine patients and streptococci in three patients. Metagenomics confirmed M. smithii in five samples, and M. smithii was isolated in broth from two samples; the genomes of these two isolates were sequenced. Blood cultures experimentally inoculated with Enterobacteriaceae, Staphylococcus epidermidis or Staphylococcus hominis yielded hydrogen, but no methane, authentifying observational data. Three patients diagnosed with infectious mitral endocarditis, were indisputably diagnosed by microscopy, PCR-based detections and culture: we showed M. smithii microscopically and by a specific PCR followed by sequencing method in two of three cardiovascular tissues. Conclusions Using appropriate laboratory methods, M. smithii is demonstrated as causing archaemia and endocarditis in febrile patients who are coinfected by bacteria.

Analysis of ASCAT, SMOS, in-situ and land model soil moisture as a regionalized variable over Europe and North Africa

2015 ◽  
Vol 170 ◽  
pp. 280-289 ◽  
Author(s):  
Nazzareno Pierdicca ◽  
Fabio Fascetti ◽  
Luca Pulvirenti ◽  
Raffaele Crapolicchio ◽  
Joaquin Muñoz-Sabater
Keyword(s):  
Soil Moisture ◽  
North Africa ◽  
Model Soil ◽  
Regionalized Variable

scholarly journals Hepatitis C Virus in North Africa: An Emerging Threat

2016 ◽  
Vol 2016 ◽  
pp. 1-11 ◽  
Author(s):  
Mohamed A. Daw ◽  
Abdallah El-Bouzedi ◽  
Mohamed O. Ahmed ◽  
Aghnyia A. Dau ◽  
Mohamed M. Agnan
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
North Africa ◽  
Treatment Strategies ◽  
Nile Valley ◽  
African Countries ◽  
Genotype 4 ◽  
Unique Region ◽  
Clinical Consequences ◽  
Context Specific

Hepatitis C virus is a major public health threat associated with serious clinical consequences worldwide. North Africa is a unique region composed of seven countries that vary considerably in the predisposing factors to microbial diseases both historically and at the present time. The dynamics of HCV in the region are not well documented. The data are both limited and controversial in most of the countries in the region. In North Africa, the epidemiology of HCV is disparate and understanding it has been hampered by regional “epidemiological homogeneity” concepts. As the dynamics of HCV vary from country to country, context-specific research is needed. In this review, we assess studies performed in each country in the general populations as well as among blood donors and groups exposed to the HCV infection. The reported prevalence of HCV ranges from 0.6% to 8.4% in the Maghreb countries and is predominated by genotype 1. In the Nile valley region, it ranges from 2.2% to 18.9% and is dominated by genotype 4. In North African countries, HCV seems to be a serious problem that is driven by different vectors even in different geographical locations within the same country. Efforts should be combined at both the national and regional levels to implement efficient preventive and treatment strategies.

Some properties of a mitochondrial endonuclease from yeast

1982 ◽  
Vol 60 (7) ◽  
pp. 757-762 ◽  
Author(s):  
R. Morosoli ◽  
C.V. Lusena
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mitochondrial Dna ◽  
Ionic Strength ◽  
Nuclear Dna ◽  
Double Helix ◽  
Endonuclease Activity ◽  
Mt Dna ◽  
Isolated Mitochondria ◽  
Modified Dna ◽  
Dna Strands

A mitochondrial endonuclease from Saccharomyces cerevisiae was previously shown to cut both strands of native DNA at opposite or nearby sites. The present studies demonstrate that the endonuclease activity is dependent on the strength of the hydrogen bonds between the DNA strands; the activity was measured at different ionic strengths, with substrates of different base compositions and also with DNA in which the double helix has been locally destabilized by ultraviolet irradiation, by depurination, and by single-stranded nicks. The activity is 30% greater with mitochondrial DNA (mt-DNA) than with nuclear DNA. At 0.08 ionic strength, the relative activities with double-stranded polydeoxyribonucleotides are 2.4:1:0.6 for poly(dA)∙poly(dU): poly(dA)∙poly(dT): poly(dG)∙poly(dC). Increasing ionic strength decreases similarly me activity with poly(dA)∙poly(dU) and poly(dA)∙poly(dT), but has little effect with poly(dG)∙poly(dC). The greater activity with poly(dA)∙poly(dU) than with poly(dA)∙poly(dT) was confirmed with nick-translated mt-DNA and with DNA synthesized in isolated mitochondria using [3H]TTP and [3H]dUTP in both cases. The endonuclease cuts modified DNA preferentially in the thymine dinner regions, at the apurirtic sites, and at sites opposite to nicks. The possible involvement of this endonuclease in the degradation of mitochondrial DNA during "petite" induction is discussed.

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