Human Prehistoric Demography Revealed by the Polymorphic Pattern of CpG Transitions.
Ontology highlight
ABSTRACT:
SUBMITTER: Liu X
PROVIDER: S-EPMC7820361 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Hypermethylation of promoter CpG islands is generally recognized epigenetic mechanism responsible for gene silencing in cancer. However, molecular details on how this epigenetic mark triggers the process of gene downregulation are still elusive. Here, we used deep bisulfite sequencing and qPCR analysis to investigate the pattern of CpG methylation of ALDH1L1 promoter region and its association with the gene expression level in 16 paired breast cancer (BC) samples of different clinical stages. Expression of ALDH1L1 gene was suppressed in all examined BC samples up to 200-fold, and average hypermethylation level of the promoter region correlated positively with ALDH1L1 downregulation. We determined the role of every individual CpG site within the ALDH1L1 promoter, including upstream untranscribed region, first untranslated exon, and the start of the first intron, in aberrant gene expression by correlation analysis. The search revealed CpG sites which methylation has the highest impact on intensity of gene transcription. The majority of such CpG sites are located in a compact region in the first intron of the ALDH1L1 gene. These results assist in unraveling of dynamic nature of CpG promoter hypermethylation as well as demonstrate the efficiency of deep bisulfite sequencing in search for novel epigenetic markers in cancer.
| S-EPMC5962711 | biostudies-literature
Project description:In many theories on the social and cultural evolution of human societies, the number and density of people living together in a given time and region is a crucial factor. Because direct data on past demographic developments are lacking, and reliability and validity of demographic proxies require careful evaluation, the topic has been approached from several different directions. This paper provides an introduction to a geostatistical approach for estimating prehistoric population size and density, the so-called Cologne Protocol and discusses underlying theoretical assumptions and upscaling transfer-functions between different spatial scale levels. We describe and compare the specifics for farming and for foraging societies and, using examples, discuss a diachronic series of estimates, covering the population dynamics of roughly 40 kyr of European prehistory. Ethnohistoric accounts, results from other approaches-including absolute (ethno-environmental models) and relative estimates (site-numbers, dates as data, etc.) allow a first positioning of the estimates within this field of research. Future enhancements, applications and testing of the Cologne Protocol are outlined and positioned within the general theoretical and methodological avenues of palaeodemographic research. In addition, we provide manuals for modelling Core Areas in MapInfo, ArcGIS, QGIS/Saga and R. This article is part of the theme issue 'Cross-disciplinary approaches to prehistoric demography'.
| S-EPMC7741091 | biostudies-literature
Project description:Paleoeconomy more than demography determined prehistoric human impact in Arctic Norway
| PRJEB56158 | ENA
Project description:Temperature-induced phase transitions in carbamazepine (CBZ) and 10,11-dihydrocarbamazepine (DHC) were studied by simultaneous differential scanning calorimetry-X-ray diffraction in this work. The transitions generally involve a transitional melt phase which is quickly followed by recrystallisation. The expansions of the unit cell as a function of temperature could be quantified and allow us to determine a directional order of stability in relation to the lattice constants. Dihydrocarbamazepine form II undergoes a conversion to form I by a localised melt phase. Carbamazepine (CBZ) form IV converts to form I at 182 °C, again by a localised intermediate melt phase. CBZ form II converted to form I at 119 °C by a pathway that appears to have included some melting, and form III underwent a part melt-recrystallisation and a part sublimation-recrystallisation to form I.
| S-EPMC6175174 | biostudies-literature
Project description:Recent theoretical investigations of high-pressure structures of diborane have yielded many intriguing predictions which have so far remained untested due to challenges of acquiring experimental data at extreme pressures. Here we report new pressure-induced polymorphic transformations of crystalline diborane observed between 36 and 88 GPa by in situ Raman spectroscopy and interpreted using electronic structure calculations. Two previously unknown phase transitions are identified near 42 and 57 GPa, as evidenced by significant changes in the Raman profiles. The corresponding new phases, labeled IV and V, consist of B2H6 molecules and have triclinic unit cells (P), as deduced through evolutionary structure search and comparison of experimental and simulated Raman spectra. Density-functional calculations suggest that, at pressures above 110 GPa, phase V will form new molecular structures consisting of one-dimensional (BH3)n chains and will become metallic near 138 GPa. Our findings make a significant contribution to the elucidation of the structures and properties of diborane in the near-megabar pressure region.
| S-EPMC4564767 | biostudies-literature
Project description:The evolution of self-fertilization from outcrossing has occurred on numerous occasions in flowering plants. This shift in mating system profoundly influences the morphology, ecology, genetics and evolution of selfing lineages. As a result, there has been sustained interest in understanding the mechanisms driving the evolution of selfing and its environmental context. Recently, patterns of molecular variation have been used to make inferences about the selective mechanisms associated with mating system transitions. However, these inferences can be complicated by the action of linked selection following the transition. Here, using multilocus simulations and comparative molecular data from related selfers and outcrossers, we demonstrate that there is little evidence for strong bottlenecks associated with initial transitions to selfing, and our simulation results cast doubt on whether it is possible to infer the role of bottlenecks associated with reproductive assurance in the evolution of selfing. They indicate that the effects of background selection on the loss of diversity and efficacy of selection occur rapidly following the shift to high selfing. Future comparative studies that integrate explicit ecological and genomic details are necessary for quantifying the independent and joint effects of selection and demography on transitions to selfing and the loss of genetic diversity.
| S-EPMC4071518 | biostudies-literature
Project description:Models of sexually-reproducing populations that consider only a single sex cannot capture the effects of sex-specific demographic differences and mate availability. We present a new framework for two-sex demographic models that implements and extends the birth-matrix mating-rule approach of Pollak. The model is a continuous-time matrix model that explicitly includes the processes of mating (which is nonlinear but homogeneous), offspring production, and demographic transitions and survival. The resulting nonlinear model converges to exponential growth with an equilibrium population composition. The model can incorporate age- or stage-structured life histories and flexible mating functions. As an example, we apply the model to analyze the effects of mating strategies (polygamy or monogamy, and mated unions composed of males and females, of variable duration) on the response to sex-biased harvesting. The combination of demographic complexity with the interaction of the sexes can have major population dynamic effects and can change the outcome of evolution on sex-related characters.
| S-EPMC6435235 | biostudies-literature
Project description:Based on GC content and the observed/expected CpG ratio (oCpGr), we found three major groups among the members of subfamily Parvovirinae: Group I parvoviruses with low GC content and low oCpGr values, Group II with low GC content and high oCpGr values and Group III with high GC content and high oCpGr values. Porcine parvovirus belongs to Group I and it features an ascendant CpG distribution by position in its coding regions similarly to the majority of the parvoviruses. The entire PPV genome remains hypomethylated during the viral lifecycle independently from the tissue of origin. In vitro CpG methylation of the genome has a modest inhibitory effect on PPV replication. The in vitro hypermethylation disappears from the replicating PPV genome suggesting that beside the maintenance DNMT1 the de novo DNMT3a and DNMT3b DNA methyltransferases can't methylate replicating PPV DNA effectively either, despite that the PPV infection does not seem to influence the expression, translation or localization of the DNA methylases. SNP analysis revealed high mutability of the CpG sites in the PPV genome, while introduction of 29 extra CpG sites into the genome has no significant biological effects on PPV replication in vitro. These experiments raise the possibility that beyond natural selection mutational pressure may also significantly contribute to the low level of the CpG sites in the PPV genome.
| S-EPMC3877397 | biostudies-literature
Project description:Over recent millennia, human populations have regularly reconstructed their subsistence niches, changing both how they obtain food and the conditions in which they live. For example, over the last 12,000 years the vast majority of human populations shifted from foraging to practicing different forms of agriculture. The shift to farming is widely understood to have impacted several aspects of human demography and biology, including mortality risk, population growth, adult body size, and physical markers of health. However, these trends have not been integrated within an over-arching conceptual framework, and there is poor understanding of why populations tended to increase in population size during periods when markers of health deteriorated. Here, we offer a novel conceptual approach based on evolutionary life history theory. This theory assumes that energy availability is finite and must be allocated in competition between the functions of maintenance, growth, reproduction, and defence. In any given environment, and at any given stage during the life-course, natural selection favours energy allocation strategies that maximise fitness. We argue that the origins of agriculture involved profound transformations in human life history strategies, impacting both the availability of energy and the way that it was allocated between life history functions in the body. Although overall energy supply increased, the diet composition changed, while sedentary populations were challenged by new infectious burdens. We propose that this composite new ecological niche favoured increased energy allocation to defence (immune function) and reproduction, thus reducing the allocation to growth and maintenance. We review evidence in support of this hypothesis and highlight how further work could address both heterogeneity and specific aspects of the origins of agriculture in more detail. Our approach can be applied to many other transformations of the human subsistence niche, and can shed new light on the way that health, height, life expectancy, and fertility patterns are changing in association with globalization and nutrition transition.
| S-EPMC7253633 | biostudies-literature
Project description:The Presenilin1 (PSEN1) gene encodes the catalytic peptide of the γ-secretase complex, a key enzyme that cleaves the amyloid-β protein precursor (AβPP), to generate the amyloid-β (Aβ) peptides, involved in Alzheimer's Disease (AD). Other substrates of the γ-secretase, such as E-cadherin and Notch1, are involved in neurodevelopment and haematopoiesis. Gene-specific DNA methylation influences PSEN1 expression in AD animal models. Here we evaluated canonical and non-canonical cytosine methylation patterns of the PSEN1 5'-flanking during brain development and AD progression, in DNA extracted from the frontal cortex of AD transgenic mice (TgCRND8) and post-mortem human brain. Mapping CpG and non-CpG methylation revealed different methylation profiles in mice and humans. PSEN1 expression only correlated with DNA methylation in adult female mice. However, in post-mortem human brain, lower methylation, both at CpG and non-CpG sites, correlated closely with higher PSEN1 expression during brain development and in disease progression. PSEN1 methylation in blood DNA was significantly lower in AD patients than in controls. The present study is the first to demonstrate a temporal correlation between dynamic changes in PSEN1 CpG and non-CpG methylation patterns and mRNA expression during neurodevelopment and AD neurodegeneration. These observations were made possible by the use of an improved bisulphite methylation assay employing primers that are not biased towards non-CpG methylation. Our findings deepen the understanding of γ-secretase regulation and support the hypothesis that epigenetic changes can promote the pathophysiology of AD. Moreover, they suggest that PSEN1 DNA methylation in peripheral blood may provide a biomarker for AD.
| S-EPMC7518704 | biostudies-literature