scholarly journals Genomic Structure and Evolution of Multigene Families: “Flowers” on the Human Genome

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Hie Lim Kim ◽  
Mineyo Iwase ◽  
Takeshi Igawa ◽  
Tasuku Nishioka ◽  
Satoko Kaneko ◽  
...  
Keyword(s):  
Human Genome ◽  
Gene Conversion ◽  
Genomic Structure ◽  
Gene Families ◽  
Protein Coding ◽  
Average Gene Density ◽  
The Mean ◽  
Average Gene ◽  
Computer Simulation Studies

We report the results of an extensive investigation of genomic structures in the human genome, with a particular focus on relatively large repeats (>50 kb) in adjacent chromosomal regions. We named such structures “Flowers” because the pattern observed on dot plots resembles a flower. We detected a total of 291 Flowers in the human genome. They were predominantly located in euchromatic regions. Flowers are gene-rich compared to the average gene density of the genome. Genes involved in systems receiving environmental information, such as immunity and detoxification, were overrepresented in Flowers. Within a Flower, the mean number of duplication units was approximately four. The maximum and minimum identities between homologs in a Flower showed different distributions; the maximum identity was often concentrated to 100% identity, while the minimum identity was evenly distributed in the range of 78% to 100%. Using a gene conversion detection test, we found frequent and/or recent gene conversion events within the tested Flowers. Interestingly, many of those converted regions contained protein-coding genes. Computer simulation studies suggest that one role of such frequent gene conversions is the elongation of the life span of gene families in a Flower by the resurrection of pseudogenes.

scholarly journals The Role of GC-Biased Gene Conversion in Shaping the Fastest Evolving Regions of the Human Genome

2011 ◽  
Vol 29 (3) ◽  
pp. 1047-1057 ◽  
Author(s):  
D. Kostka ◽  
M. J. Hubisz ◽  
A. Siepel ◽  
K. S. Pollard
Keyword(s):  
Human Genome ◽  
Gene Conversion ◽  
Biased Gene Conversion

scholarly journals ROLE OF BIASED GENE CONVERSION IN ONE-LOCUS NEUTRAL THEORY AND GENOME EVOLUTION

Genetics ◽  
1983 ◽  
Vol 105 (2) ◽  
pp. 461-468
Author(s):  
James Bruce Walsh
Keyword(s):  
Gene Conversion ◽  
Substitution Rate ◽  
Neutral Theory ◽  
Gene Families ◽  
The Family ◽  
Biased Gene Conversion ◽  
Fixation Probabilities ◽  
Time Required ◽  
New Alleles

ABSTRACT The implications of biased gene conversion acting on selectively neutral alleles are investigated for a single diallelic locus in a finite population. Even a very slight conversion bias can significantly alter fixation probabilities. We argue that most newly arising mutants will be at a conversion disadvantage, resulting in a potentially greatly decreased substitution rate of new alleles compared with predictions from strict neutral theory. Thus, conversion bias potential allows for conservation of particular alleles without having to invoke selection. Conversely, we also show that bias can be important in the maintenance of repeated gene families without altering the substitution rate at other loci that experience the same amount of conversion bias, provided that the number of genes in the family is sufficiently large. Bias can, therefore, be important at the genomic level and yet be unimportant at the populational level. Finally, we discuss the role of biased gene conversion in speciation events, concluding that this type of molecular turnover acting independently at many individual loci is very unlikely to decrease the time required for two allopatric populations to speciate.

The role of gene conversion in preserving rearrangement hotspots in the human genome

2013 ◽  
Vol 29 (10) ◽  
pp. 561-568 ◽  
Author(s):  
Jeffrey A. Fawcett ◽  
Hideki Innan
Keyword(s):  
Human Genome ◽  
Gene Conversion

DNA methylation in satellite repeats disorders

2019 ◽  
Vol 63 (6) ◽  
pp. 757-771 ◽  
Author(s):  
Claire Francastel ◽  
Frédérique Magdinier
Keyword(s):  
Dna Methylation ◽  
Human Genome ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Satellite Repeats ◽  
Tremendous Progress ◽  
Genes Encoding ◽  
Dna Elements ◽  
Near Future

Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.

Long-term dynamics and destruction of marsh vegetation in the Kolokolkova Bay of the Barents Sea

2012 ◽  
pp. 66-77 ◽  
Author(s):  
I. A. Lavrinenko ◽  
O. V. Lavrinenko ◽  
D. V. Dobrynin
Keyword(s):  
Species Composition ◽  
Plant Communities ◽  
Barents Sea ◽  
Mean Value ◽  
Marsh Vegetation ◽  
Composition And Structure ◽  
The Mean ◽  
Species Composition And Structure

The satellite images show that the area of marshes in the Kolokolkova bay was notstable during the period from 1973 up to 2011. Until 2010 it varied from 357 to 636 ha. After a severe storm happened on July 24–25, 2010 the total area of marshes was reduced up to 43–50 ha. The mean value of NDVI for studied marshes, reflecting the green biomass, varied from 0.13 to 0.32 before the storm in 2010, after the storm the NDVI decreased to 0.10, in 2011 — 0.03. A comparative analysis of species composition and structure of plant communities described in 2002 and 2011, allowed to evaluate the vegetation changes of marshes of the different topographic levels. They are fol­lowing: a total destruction of plant communities of the ass. Puccinellietum phryganodis and ass. Caricetum subspathaceae on low and middle marches; increasing role of halophytic species in plant communities of the ass. Caricetum glareosae vic. Calamagrostis deschampsioides subass. typicum on middle marches; some changes in species composition and structure of plant communities of the ass. Caricetum glareosae vic. Calamagrostis deschampsioides subass. festucetosum rubrae on high marches and ass. Parnassio palustris–Salicetum reptantis in transition zone between marches and tundra without changes of their syntaxonomy; a death of moss cover in plant communities of the ass. Caricetum mackenziei var. Warnstorfia exannulata on brackish coastal bogs. The possible reasons of dramatic vegetation dynamics are discussed. The dating of the storm makes it possible to observe the directions and rates of the succession of marches vegetation.

Seasonal trends in the stable isotopic composition of snow and meltwater runoff in a subarctic catchment at Okstindan, Norway

2004 ◽  
Vol 35 (2) ◽  
pp. 119-137 ◽  
Author(s):  
S.D. Gurney ◽  
D.S.L. Lawrence
Keyword(s):  
Isotopic Composition ◽  
Mean Value ◽  
Mean Values ◽  
Stable Isotopic Composition ◽  
Meltwater Runoff ◽  
Stable Isotopic ◽  
The Mean ◽  
The Difference ◽  
Δ18o And Δd

Seasonal variations in the stable isotopic composition of snow and meltwater were investigated in a sub-arctic, mountainous, but non-glacial, catchment at Okstindan in northern Norway based on analyses of δ18O and δD. Samples were collected during four field periods (August 1998; April 1999; June 1999 and August 1999) at three sites lying on an altitudinal transect (740–970 m a.s.l.). Snowpack data display an increase in the mean values of δ18O (increasing from a mean value of −13.51 to −11.49‰ between April and August), as well as a decrease in variability through the melt period. Comparison with a regional meteoric water line indicates that the slope of the δ18O–δD line for the snowpacks decreases over the same period, dropping from 7.49 to approximately 6.2.This change points to the role of evaporation in snowpack ablation and is confirmed by the vertical profile of deuterium excess. Snowpack seepage data, although limited, also suggest reduced values of δD, as might be associated with local evaporation during meltwater generation. In general, meltwaters were depleted in δ18O relative to the source snowpack at the peak of the melt (June), but later in the year (August) the difference between the two was not statistically significant. The diurnal pattern of isotopic composition indicates that the most depleted meltwaters coincide with the peak in temperature and, hence, meltwater production.

Non-pharmacological Strategies Against Systemic Inflammation: Molecular Basis and Clinical Evidence

2020 ◽  
Vol 26 (22) ◽  
pp. 2620-2629 ◽  
Author(s):  
Rita Del Pinto ◽  
Davide Pietropaoli ◽  
Annalisa Monaco ◽  
Giovambattista Desideri ◽  
Claudio Ferri ◽  
...  
Keyword(s):  
Human Genome ◽  
Systemic Inflammation ◽  
Clinical Evidence ◽  
Metabolic Diseases ◽  
Lifestyle Changes ◽  
Common Denominator ◽  
Active Lifestyle ◽  
Systemic Impact ◽  
Public Health Strategies

Systemic inflammation is a common denominator to a variety of cardiovascular (CV) and non-CV diseases and relative risk factors, including hypertension and its control, metabolic diseases, rheumatic disorders, and those affecting the gastrointestinal tract. Besides medications, a non-pharmacological approach encompassing lifestyle changes and other complementary measures is mentioned in several updated guidelines on the management of these conditions. We performed an updated narrative review on the mechanisms behind the systemic impact of inflammation and the role of non-pharmacological, complementary measures centered on lowering systemic phlogosis for preserving or restoring a good global health. The central role of genetics in shaping the immune response is discussed in conjunction with that of the microbiome, highlighting the interdependence and mutual influences between the human genome and microbial integrity, diversity, and functions. Several plausible strategies to modulate inflammation and restore balanced crosstalk between the human genome and the microbiome are then recapitulated, including dietary measures, active lifestyle, and other potential approaches to manipulate the resident microbial community. To date, evidence from high-quality human studies is sparse to allow the unconditioned inclusion of understudied, though plausible solutions against inflammation into public health strategies for global wellness. This gap claims further focused, well-designed research targeted at unravelling the mechanisms behind future personalized medicine.

scholarly journals Forensic Investigation of Four Monitored Green Infrastructure Inlets

Water ◽  
2021 ◽  
Vol 13 (13) ◽  
pp. 1787
Author(s):  
Leena J. Shevade ◽  
Franco A. Montalto
Keyword(s):  
Measurement Uncertainty ◽  
Green Infrastructure ◽  
Stormwater Management ◽  
Catchment Area ◽  
Low Flow ◽  
Inflow Rate ◽  
Forensic Investigation ◽  
Flow Conditions ◽  
The Mean

Green infrastructure (GI) is viewed as a sustainable approach to stormwater management that is being rapidly implemented, outpacing the ability of researchers to compare the effectiveness of alternate design configurations. This paper investigated inflow data collected at four GI inlets. The performance of these four GI inlets, all of which were engineered with the same inlet lengths and shapes, was evaluated through field monitoring. A forensic interpretation of the observed inlet performance was conducted using conclusions regarding the role of inlet clogging and inflow rate as described in the previously published work. The mean inlet efficiency (meanPE), which represents the percentage of tributary area runoff that enters the inlet was 65% for the Nashville inlet, while at Happyland the NW inlet averaged 30%, the SW inlet 25%, and the SE inlet 10%, considering all recorded events during the monitoring periods. The analysis suggests that inlet clogging was the main reason for lower inlet efficiency at the SW and NW inlets, while for the SE inlet, performance was compromised by a reverse cross slope of the street. Spatial variability of rainfall, measurement uncertainty, uncertain tributary catchment area, and inlet depression characteristics are also correlated with inlet PE. The research suggests that placement of monitoring sensors should consider low flow conditions and a strategy to measure them. Additional research on the role of various maintenance protocols in inlet hydraulics is recommended.

scholarly journals Recombination and Gene Conversion in a 170-kb Genomic Region of Arabidopsis thaliana

Genetics ◽  
2002 ◽  
Vol 161 (3) ◽  
pp. 1269-1278 ◽  
Author(s):  
Bernhard Haubold ◽  
Jürgen Kroymann ◽  
Andreas Ratzka ◽  
Thomas Mitchell-Olds ◽  
Thomas Wiehe
Keyword(s):  
Genetic Diversity ◽  
Arabidopsis Thaliana ◽  
Linkage Disequilibrium ◽  
Gene Conversion ◽  
Genomic Sequence ◽  
Genomic Region ◽  
Resistance To Herbivory ◽  
Linkage Disequilibria ◽  
Coalescent Simulations ◽  
The Mean

Abstract Arabidopsis thaliana is a highly selfing plant that nevertheless appears to undergo substantial recombination. To reconcile its selfing habit with the observations of recombination, we have sampled the genetic diversity of A. thaliana at 14 loci of ~500 bp each, spread across 170 kb of genomic sequence centered on a QTL for resistance to herbivory. A total of 170 of the 6321 nucleotides surveyed were polymorphic, with 169 being biallelic. The mean silent genetic diversity (πs) varied between 0.001 and 0.03. Pairwise linkage disequilibria between the polymorphisms were negatively correlated with distance, although this effect vanished when only pairs of polymorphisms with four haplotypes were included in the analysis. The absence of a consistent negative correlation between distance and linkage disequilibrium indicated that gene conversion might have played an important role in distributing genetic diversity throughout the region. We tested this by coalescent simulations and estimate that up to 90% of recombination is due to gene conversion.

Sign in / Sign up

Export Citation Format

Share Document