scholarly journals A genetic analysis of the Gibraltar Neanderthals

2019 ◽  
Vol 116 (31) ◽  
pp. 15610-15615 ◽  
Author(s):  
Lukas Bokelmann ◽  
Mateja Hajdinjak ◽  
Stéphane Peyrégne ◽  
Selina Brace ◽  
Elena Essel ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Nuclear Dna ◽  
Climatic Conditions ◽  
Northern Spain ◽  
Dna Preservation ◽  
Dna Library ◽  
Construction Methods ◽  
Human Dna ◽  
Western Asia ◽  
Coastal Climate

The Forbes’ Quarry and Devil’s Tower partial crania from Gibraltar are among the first Neanderthal remains ever found. Here, we show that small amounts of ancient DNA are preserved in the petrous bones of the 2 individuals despite unfavorable climatic conditions. However, the endogenous Neanderthal DNA is present among an overwhelming excess of recent human DNA. Using improved DNA library construction methods that enrich for DNA fragments carrying deaminated cytosine residues, we were able to sequence 70 and 0.4 megabase pairs (Mbp) nuclear DNA of the Forbes’ Quarry and Devil’s Tower specimens, respectively, as well as large parts of the mitochondrial genome of the Forbes’ Quarry individual. We confirm that the Forbes’ Quarry individual was a female and the Devil’s Tower individual a male. We also show that the Forbes’ Quarry individual is genetically more similar to the ∼120,000-y-old Neanderthals from Scladina Cave in Belgium (Scladina I-4A) and Hohlenstein-Stadel Cave in Germany, as well as to a ∼60,000- to 70,000-y-old Neanderthal from Russia (Mezmaiskaya 1), than to a ∼49,000-y-old Neanderthal from El Sidrón (El Sidrón 1253) in northern Spain and other younger Neanderthals from Europe and western Asia. This suggests that the Forbes’ Quarry fossil predates the latter Neanderthals. The preservation of archaic human DNA in the warm coastal climate of Gibraltar, close to the shores of Africa, raises hopes for the future recovery of archaic human DNA from regions in which climatic conditions are less than optimal for DNA preservation.

scholarly journals Mitochondrial DNA Methylation and Human Diseases

2021 ◽  
Vol 22 (9) ◽  
pp. 4594
Author(s):  
Andrea Stoccoro ◽  
Fabio Coppedè
Keyword(s):  
Dna Methylation ◽  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Nuclear Dna ◽  
Epigenetic Modification ◽  
Nuclear Genome ◽  
Epigenetic Modifications ◽  
Human Diseases ◽  
Loop Region ◽  
D Loop

Epigenetic modifications of the nuclear genome, including DNA methylation, histone modifications and non-coding RNA post-transcriptional regulation, are increasingly being involved in the pathogenesis of several human diseases. Recent evidence suggests that also epigenetic modifications of the mitochondrial genome could contribute to the etiology of human diseases. In particular, altered methylation and hydroxymethylation levels of mitochondrial DNA (mtDNA) have been found in animal models and in human tissues from patients affected by cancer, obesity, diabetes and cardiovascular and neurodegenerative diseases. Moreover, environmental factors, as well as nuclear DNA genetic variants, have been found to impair mtDNA methylation patterns. Some authors failed to find DNA methylation marks in the mitochondrial genome, suggesting that it is unlikely that this epigenetic modification plays any role in the control of the mitochondrial function. On the other hand, several other studies successfully identified the presence of mtDNA methylation, particularly in the mitochondrial displacement loop (D-loop) region, relating it to changes in both mtDNA gene transcription and mitochondrial replication. Overall, investigations performed until now suggest that methylation and hydroxymethylation marks are present in the mtDNA genome, albeit at lower levels compared to those detectable in nuclear DNA, potentially contributing to the mitochondria impairment underlying several human diseases.

scholarly journals Analysis of ancient DNA from a prehistoric Amerindian cemetery

1999 ◽  
Vol 354 (1379) ◽  
pp. 153-159 ◽  
Author(s):  
Anne C. Stone ◽  
Mark Stoneking
Keyword(s):  
Ancient Dna ◽  
Dna Analysis ◽  
Nuclear Dna ◽  
Genetic Research ◽  
Hypervariable Region ◽  
Dna Preservation ◽  
European Contact ◽  
Novel Method ◽  
High Level ◽  
Central Illinois

The Norris Farms No. 36 cemetery in central Illinois has been the subject of considerable archaeological and genetic research. Both mitochondrial DNA (mtDNA) and nuclear DNA have been examined in this 700–year–old population. DNA preservation at the site was good, with about 70% of the samples producing mtDNA results and approximately 15% yielding nuclear DNA data. All four of the major Amerindian mtDNA haplogroups were found, in addition to a fifth haplogroup. Sequences of the first hypervariable region of the mtDNA control region revealed a high level of diversity in the Norris Farms population and confirmed that the fifth haplogroup associates with Mongolian sequences and hence is probably authentic. Other than a possible reduction in the number of rare mtDNA lineages in many populations, it does not appear as if European contact significantly altered patterns of Amerindian mtDNA variation, despite the large decrease in population size that occurred. For nuclear DNA analysis, a novel method for DNA–based sex identification that uses nucleotide differences between the X and Y copies of the amelogenin gene was developed and applied successfully in approximately 20 individuals. Despite the well–known problems of poor DNA preservation and the ever–present possibility of contamination with modern DNA, genetic analysis of the Norris Farms No. 36 population demonstrates that ancient DNA can be a fruitful source of new insights into prehistoric populations.

scholarly journals High-level expression and molecular cloning of genes encoding Candida tropicalis peroxisomal proteins.

1984 ◽  
Vol 4 (10) ◽  
pp. 2136-2141 ◽  
Author(s):  
T Kamiryo ◽  
K Okazaki
Keyword(s):  
Oleic Acid ◽  
Candida Tropicalis ◽  
Nuclear Dna ◽  
Apparent Molecular Weight ◽  
Dna Library ◽  
Coding Regions ◽  
Chain Acyl ◽  
Genes Encoding ◽  
High Level ◽  
Acyl Coenzyme A

The development of peroxisomes in the cells of Candida tropicalis grown on oleic acid was accompanied by a markedly high expression of peroxisomal proteins. On the basis of this finding, the nuclear DNA library of this yeast was screened by differential hybridization, and 102 clones of oleic acid-inducible sequences were isolated. Seven coding regions were found to form clusters in three stretches of the genomic DNA. Five of the regions were identified as genes for peroxisomal polypeptides (PXPs). The coding sequence for PXP-2 hybrid selected an additional mRNA for PXP-4, the subunit of long-chain acyl coenzyme A oxidase, which was the most abundant PXP. PXP-2 and PXP-4 were close in apparent molecular weight and generated similar peptides when digested with a protease. The gene for PXP-4 was adjacent to that for PXP-2 on the genome and also hybridized to the mRNA coding for PXP-5. These and other similar results suggest that the genes for the peroxisomal proteins of this organism arose by duplication of a few ancestral genes.

Evaluating the Environmental Impact Score of a Residential Building Using Life Cycle Assessment

2021 ◽  
pp. 142-159
Author(s):  
Manish Sakhlecha ◽  
Samir Bajpai ◽  
Rajesh Kumar Singh
Keyword(s):  
Life Cycle Assessment ◽  
Life Cycle ◽  
Natural Resources ◽  
Impact Assessment ◽  
Environmental Impacts ◽  
Residential Building ◽  
Resource Depletion ◽  
Climatic Conditions ◽  
Construction Methods ◽  
Growing Economy

Buildings consume major amount of energy as well as natural resources leading to negative environmental impacts like resource depletion and pollution. The current task for the construction sector is to develop an evaluation tool for rating of buildings based on their environmental impacts. There are various assessment tools and models developed by different agencies in different countries to evaluate building's effect on environment. Although these tools have been successfully used and implemented in the respective regions of their origin, the problems of application occur, especially during regional adaptation in other countries due to peculiarities associated with the specific geographic location, climatic conditions, construction methods and materials. India is a rapidly growing economy with exponential increase in housing sector. Impact assessment model for a residential building has been developed based on life cycle assessment (LCA) framework. The life cycle impact assessment score was obtained for a sample house considering fifteen combinations of materials paired with 100% thermal electricity and 70%-30% thermal-solar combination, applying normalization and weighting to the LCA results. The LCA score of portland slag cement with burnt clay red brick and 70%-30% thermal-solar combination (PSC+TS+RB) was found to have the best score and ordinary Portland cement with flyash brick and 100% thermal power (OPC+T+FAB) had the worst score, showing the scope for further improvement in LCA model to include positive scores for substitution of natural resources with industrial waste otherwise polluting the environment.

Introducing the Oxford History of the Ancient Near East

2020 ◽  
pp. 1-26
Author(s):  
Karen Radner ◽  
Nadine Moeller ◽  
D. T. Potts
Keyword(s):  
Near East ◽  
Climatic Conditions ◽  
Ancient Near East ◽  
North African ◽  
Inter Tropical Convergence Zone ◽  
The North ◽  
Western Asia ◽  
History Of ◽  
Key Issues

With the emphasis of the Oxford History of the Ancient Near East firmly placed on the political, social, and cultural histories of the states and communities shaping Egypt and Western Asia (including the Levant, Anatolia, Mesopotamia, and Iran), this introduction to the five-volume series seeks to place the region in its environmental context. It discusses the lay of the land between the North African coast and the Hindu Kush, including the role of tectonics and geomorphology. It also considers some key issues regarding climatic conditions, focusing in particular on the significance of the Inter-Tropical Convergence Zone and the potential impact of megadroughts and pandemics.

scholarly journals Developmental Validation of a MPS Workflow with a PCR-Based Short Amplicon Whole Mitochondrial Genome Panel

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1345
Author(s):  
Jennifer Churchill Cihlar ◽  
Christina Amory ◽  
Robert Lagacé ◽  
Chantal Roth ◽  
Walther Parson ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Validation Studies ◽  
Dna Analysis ◽  
Nuclear Dna ◽  
Massively Parallel Sequencing ◽  
Whole Genome ◽  
Developmental Validation ◽  
Average Maximum ◽  
Variant Frequency ◽  
Sensitivity Specificity

For the adoption of massively parallel sequencing (MPS) systems by forensic laboratories, validation studies on specific workflows are needed to support the feasibility of implementation and the reliability of the data they produce. As such, the whole mitochondrial genome sequencing methodology—Precision ID mtDNA Whole Genome Panel, Ion Chef, Ion S5, and Converge—has been subjected to a variety of developmental validation studies. These validation studies were completed in accordance with the Scientific Working Group on DNA Analysis Methods (SWGDAM) validation guidelines and assessed reproducibility, repeatability, accuracy, sensitivity, specificity to human DNA, and ability to analyze challenging (e.g., mixed, degraded, or low quantity) samples. Intra- and inter-run replicates produced an average maximum pairwise difference in variant frequency of 1.2%. Concordance with data generated with traditional Sanger sequencing and an orthogonal MPS platform methodology was used to assess accuracy, and generation of complete and concordant haplotypes at DNA input levels as low as 37.5 pg of nuclear DNA or 187.5 mitochondrial genome copies illustrated the sensitivity of the system. Overall, data presented herein demonstrate that highly accurate and reproducible results were generated for a variety of sample qualities and quantities, supporting the reliability of this specific whole genome mitochondrial DNA MPS system for analysis of forensic biological evidence.

Phaseolus vulgaris is nodulated in northern Spain by Rhizobium leguminosarum strains harboring two nodC alleles present in American Rhizobium etli strains: biogeographical and evolutionary implications

2010 ◽  
Vol 56 (8) ◽  
pp. 657-666 ◽  
Author(s):  
Paula García-Fraile ◽  
Daniel Mulas-García ◽  
Alvaro Peix ◽  
Raúl Rivas ◽  
Fernando González-Andrés ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Rhizobium Leguminosarum ◽  
Intergenic Spacer ◽  
Climatic Conditions ◽  
Phylogenetic Group ◽  
Rhizobium Etli ◽  
Symbiotic Genes ◽  
Northern Spain ◽  
Major Producer ◽  
Core Genes

In this study a collection of rhizobial strains were isolated from effective nodules of Phaseolus vulgaris in a wide region of northern Spain, which is the major producer region of this legume in Spain. The analysis of their core genes, rrs, atpD, and recA, and the 16S–23S intergenic spacer showed that all isolates belong to the phylogenetic group of Rhizobium leguminosarum and some of them were identical to those of strains nodulating Vicia or Trifolium . None of the isolates was identified as Rhizobium etli ; however, all of them carry the nodC alleles α and γ harboured by American strains of this species. These alleles were also found in strains nodulating P. vulgaris in southern Spain identified as R. etli. These results suggest that R. etli was carried from America to Spain with common bean seeds, but that they could have found difficulties persisting in the soils of northern Spain, probably because of the climatic conditions. The symbiotic genes of this species could have been transferred, after the arrival of P. vulgaris, to strains of R. leguminosarum already present in northern Spanish soils.

scholarly journals Role of Mitochondrial Genome Mutations in Pathogenesis of Carotid Atherosclerosis

2017 ◽  
Vol 2017 ◽  
pp. 1-7 ◽  
Author(s):  
Margarita A. Sazonova ◽  
Vasily V. Sinyov ◽  
Anastasia I. Ryzhkova ◽  
Elena V. Galitsyna ◽  
Zukhra B. Khasanova ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Carotid Atherosclerosis ◽  
Nuclear Dna ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Atherosclerotic Lesions ◽  
Dna Mutations ◽  
Blood Leukocyte ◽  
Study Participants

Mutations of mtDNA, due to their higher frequency of occurrence compared to nuclear DNA mutations, are the most promising biomarkers for assessing predisposition of the occurrence and development of atherogenesis. The aim of the present article was an analysis of correlation of several mitochondrial genome mutations with carotid atherosclerosis. Leukocytes from blood of study participants from Moscow polyclinics were used as research material. The sample size was 700 people. The sample members were diagnosed with “atherosclerosis” on the basis of ultrasonographic examination and biochemical and molecular cell tests. DNA was isolated from blood leukocyte samples of the study participants. PCR fragments of DNA, containing the region of 11 investigated mutations, were pyrosequenced. The heteroplasmy level of these mutations was detected. Statistical analysis of the obtained results was performed using the software package SPSS 22.0. According to the obtained results, an association of mutations m.652delG, m.3336C>T, m.12315G>A, m.14459G>A m.15059G>A with carotid atherosclerosis was found. These mutations can be biomarkers for assessing predisposition to this disease. Additionally, two single nucleotide substitutions (m.13513G>A and m.14846G>A), negatively correlating with atherosclerotic lesions, were detected. These mutations may be potential candidates for gene therapy of atherosclerosis and its risk factors.

scholarly journals Climate change impacts on West Nile virus transmission in a global context

2015 ◽  
Vol 370 (1665) ◽  
pp. 20130561 ◽  
Author(s):  
Shlomit Paz
Keyword(s):  
Climate Change ◽  
West Nile Virus ◽  
Urban Areas ◽  
Climatic Factors ◽  
Eastern Mediterranean ◽  
Climatic Conditions ◽  
West Nile ◽  
Transmission Cycle ◽  
Western Asia ◽  
West Nile Virus Transmission

West Nile virus (WNV), the most widely distributed virus of the encephalitic flaviviruses, is a vector-borne pathogen of global importance. The transmission cycle exists in rural and urban areas where the virus infects birds, humans, horses and other mammals. Multiple factors impact the transmission and distribution of WNV, related to the dynamics and interactions between pathogen, vector, vertebrate hosts and environment. Hence, among other drivers, weather conditions have direct and indirect influences on vector competence (the ability to acquire, maintain and transmit the virus), on the vector population dynamic and on the virus replication rate within the mosquito, which are mostly weather dependent. The importance of climatic factors (temperature, precipitation, relative humidity and winds) as drivers in WNV epidemiology is increasing under conditions of climate change. Indeed, recent changes in climatic conditions, particularly increased ambient temperature and fluctuations in rainfall amounts, contributed to the maintenance (endemization process) of WNV in various locations in southern Europe, western Asia, the eastern Mediterranean, the Canadian Prairies, parts of the USA and Australia. As predictions show that the current trends are expected to continue, for better preparedness, any assessment of future transmission of WNV should take into consideration the impacts of climate change.

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