scholarly journals Measurements of spontaneous rates of mutations in the recent past and the near future

2010 ◽  
Vol 365 (1544) ◽  
pp. 1169-1176 ◽  
Author(s):  
Fyodor A. Kondrashov ◽  
Alexey S. Kondrashov
Keyword(s):  
Spontaneous Mutation ◽  
Natural Populations ◽  
Fundamental Parameter ◽  
Indirect Methods ◽  
The Past ◽  
Genome Wide ◽  
Related Individuals ◽  
Methodological Approaches ◽  
Near Future ◽  
Generation Sequencing

The rate of spontaneous mutation in natural populations is a fundamental parameter for many evolutionary phenomena. Because the rate of mutation is generally low, most of what is currently known about mutation has been obtained through indirect, complex and imprecise methodological approaches. However, in the past few years genome-wide sequencing of closely related individuals has made it possible to estimate the rates of mutation directly at the level of the DNA, avoiding most of the problems associated with using indirect methods. Here, we review the methods used in the past with an emphasis on next generation sequencing, which may soon make the accurate measurement of spontaneous mutation rates a matter of routine.

scholarly journals Mitochondria and Cancer: Past, Present, and Future

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
M. L. Verschoor ◽  
R. Ungard ◽  
A. Harbottle ◽  
J. P. Jakupciak ◽  
R. L. Parr ◽  
...  
Keyword(s):  
Holistic Approach ◽  
Complete Understanding ◽  
Mitochondrial Genomics ◽  
The Past ◽  
Body Of Knowledge ◽  
Metabolic Interactions ◽  
Nuclear Cell ◽  
Near Future ◽  
Generation Sequencing

The area of mitochondrial genomics has undergone unprecedented growth over the past several years. With the advent of the age of omics, investigations have reached beyond the nucleus to encompass the close biological communication and finely coordinated interactions between mitochondria and their nuclear cell mate. Application of this holistic approach, to all metabolic interactions within the cell, is providing a more complete understanding of the molecular transformation of the cell from normal to malignant behavior, before histopathological indications are evident. In this review the surging momentum in mitochondrial science, as it relates to cancer, is described in three progressive perspectives: (1) Past: the historical contributions to current directions of research; (2) Present: Contemporary findings, results and approaches to mitochondria and cancer, including the role of next generation sequencing and proteomics; (3) Future: Based on the present body of knowledge, the potential assets and benefits of mitochondrial research are projected into the near future.

scholarly journals Efficient genome-wide sequencing and low coverage pedigree analysis from non-invasively collected samples

2015 ◽  
Author(s):  
Noah Snyder-Mackler ◽  
William H Majoros ◽  
Michael L Yuan ◽  
Amanda O Shaver ◽  
Jacob B Gordon ◽  
...  
Keyword(s):  
Natural Populations ◽  
Pedigree Analysis ◽  
Non Invasive ◽  
The Past ◽  
Research Systems ◽  
Genome Wide ◽  
The Many ◽  
Low Coverage ◽  
Wild Baboons ◽  
Laboratory Protocol

Research on the genetics of natural populations was revolutionized in the 1990′s by methods for genotyping non-invasively collected samples. However, these methods have remained largely unchanged for the past 20 years and lag far behind the genomics era. To close this gap, here we report an optimized laboratory protocol for genome-wide capture of endogenous DNA from non-invasively collected samples, coupled with a novel computational approach to reconstruct pedigree links from the resulting low-coverage data. We validated both methods using fecal samples from 62 wild baboons, including 48 from an independently constructed extended pedigree. We enriched fecal-derived DNA samples up to 40-fold for endogenous baboon DNA, and reconstructed near-perfect pedigree relationships even with extremely low-coverage sequencing. We anticipate that these methods will be broadly applicable to the many research systems for which only non-invasive samples are available. The lab protocol and software (″WHODAD″) are freely available at www.tung-lab.org/protocols and www.xzlab.org/software, respectively.

scholarly journals Board evaluation process in Italy: How far is it from the UK standard?

2017 ◽  
Vol 13 (3) ◽  
pp. 6-18 ◽  
Author(s):  
Maria Gaia Soana ◽  
Giuseppe Crisci
Keyword(s):  
Best Practices ◽  
Review Process ◽  
Evaluation Process ◽  
Self Assessment ◽  
The Past ◽  
Corporate Governance Codes ◽  
Methodological Approaches ◽  
Board Review ◽  
The Uk ◽  
Near Future

Both the UK and the Italian Corporate Governance Codes call for boards to undertake an annual evaluation of their own performance and that of their committees. The study analyses the board review process conducted by the 25 most capitalized Italian listed companies at June 30th, 2016 and the top 25 companies included in the FTSE 100 on the same date in terms of objectives, parties involved, methodological approaches, suggestions to shareholders, board nomination and election. The Italian trends on board evaluation are compared to UK trends, as the UK is particularly advanced with regard to best practices on board self-assessment. Our analysis shows that in 2016 the most capitalized Italian companies seem to have improved their self-assessment compared to the past, in particular with regard to the disclosure of the process, the involvement of independent external consultants and the number of evaluated subjects. However, some aspects require improvement in the near future.

scholarly journals Does sex really matter? Explaining intraspecies variation in ocean acidification responses

2017 ◽  
Vol 13 (2) ◽  
pp. 20160761 ◽  
Author(s):  
Robert P. Ellis ◽  
William Davison ◽  
Ana M. Queirós ◽  
Kristy J. Kroeker ◽  
Piero Calosi ◽  
...  
Keyword(s):  
Ocean Acidification ◽  
Natural Populations ◽  
Aquatic Organisms ◽  
Life Stages ◽  
Early Life Stages ◽  
Intraspecies Variation ◽  
The Past ◽  
Males And Females ◽  
Near Future

Ocean acidification (OA) poses a major threat to marine ecosystems globally, having significant ecological and economic importance. The number and complexity of experiments examining the effects of OA has substantially increased over the past decade, in an attempt to address multi-stressor interactions and long-term responses in an increasing range of aquatic organisms. However, differences in the response of males and females to elevated p CO 2 have been investigated in fewer than 4% of studies to date, often being precluded by the difficulty of determining sex non-destructively, particularly in early life stages. Here we highlight that sex can significantly impact organism responses to OA, differentially affecting physiology, reproduction, biochemistry and ultimately survival. What is more, these impacts do not always conform to ecological theory based on differential resource allocation towards reproduction, which would predict females to be more sensitive to OA owing to the higher production cost of eggs compared with sperm. Therefore, non-sex-specific studies may overlook subtle but ecologically significant differences in the responses of males and females to OA, with consequences for forecasting the fate of natural populations in a near-future ocean.

scholarly journals 5-Methylcytosine and 5-Hydroxymethylcytosine Signatures Underlying Pediatric Cancers

Epigenomes ◽  
2019 ◽  
Vol 3 (2) ◽  
pp. 9 ◽  
Author(s):  
Shalu Jhanwar ◽  
Ajinkya Deogade
Keyword(s):  
Pediatric Cancer ◽  
Therapeutic Potential ◽  
The Past ◽  
Pediatric Cancers ◽  
Genome Wide ◽  
Recent Developments ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Shed Light

In addition to the genetic variations, recent evidence has shown that DNA methylation of both 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) underlies the pathogenesis of pediatric cancer. Given the high mortality rate, there is an urgent need to study the mechanisms contributing to the pathogenicity of pediatric cancer. Over the past decades, next-generation sequencing (NGS) has enabled us to perform genome-wide screening to study the complex regulatory mechanisms of 5mC and 5hmC underlying pediatric tumorigenesis. To shed light on recent developments on pediatric cancer predisposition and tumor progression, here we discuss the role of both genome-wide and locus-specific dysregulation of 5mC and 5hmC in hematopoiesis malignancy and neuroblastoma, the most common types of pediatric cancer, together with their therapeutic potential.

Dwindling status of Epimedium Elatum (Morren & Decne) and its geographical distribution in Kashmir Himalaya, India

2018 ◽  
pp. 47-52
Keyword(s):  
Medicinal Plant ◽  
Biological Activities ◽  
Conservation Status ◽  
Natural Populations ◽  
Culture Techniques ◽  
Kashmir Himalayas ◽  
Near Future ◽  
First Time ◽  
Tissue Culture Techniques

Epimedium elatum (Morren & Decne) of family Berberidaceace is a rare perennial medicinal plant, endemic to high altitude forests of Northwestern Himalayas in India. Ethnobotanically, it has been used as an ingredient for treatment of bone-joint disorders, impotence and kidney disorders in Kashmir Himalayas. Phytochemically, it is rich in Epimedin ABC and Icariin; all of these have been demonstrated to possess remarkable biological activities like PDE-5 inhibition (treatment of erectile dysfunction), anticancer, antiosteoporosis antioxidant and antiviral properties. The present investigation reports its traditional usage, comprehensive distribution and conservation status from twenty ecogeographical regions in Kashmir Himalayas, India. The species was reported from Gurez valley for the first time. Numerous threats like excessive grazing, deforestration, habitat fragmentation, tourism encroachment, landslides and excessive exploitation have decreased its natural populations in most of the surveyed habitats. Consequently, its existence may become threatened in near future if timely conservation steps are not taken immediately by concerned stakeholders involved in medicinal plant research. Moreover, use of plant tissue culture techniques is recommended for development of its in vitro propagation protocols. Therefore, introduction of this medicinal plant in botanical gardens, protected sites and development of monitoring programmes are needed for its immediate conservation in Northwestern Himalayas, India.

Present Status of the Salmonids Atlantic Salmon and Sea-Trout in the Dutch Part of the River Rhine

1994 ◽  
Vol 29 (3) ◽  
pp. 37-41 ◽  
Author(s):  
W. G. Cazemier
Keyword(s):  
Atlantic Salmon ◽  
Salmo Trutta ◽  
Natural Populations ◽  
River Rhine ◽  
Sea Trout ◽  
The Past ◽  
The North ◽  
Trout Population ◽  
The North Sea ◽  
Heavy Pollution

In the past, the anadromous salmonids, Atlantic salmon (Salmo salar) and sea-trout (Salmo trutta), have formed natural populations in the river Rhine. From the beginning of the nineteenth century onwards, the greater part of the drainage area of the river has been gradually altered from a more or less rural and agricultural area, into a highly industrialised one with subsequent industrialisation, river-engineering and heavy pollution. These developments are considered to be the major cause for the disappearance of the populations of anadromous salmonid fish in the 1950s. The water quality has recovered significantly during the past 25 years. From about 1975 onwards, this process gave rise to a recovery of the anadromous trout population. Results of recent studies of the sea-trout migration pattern are presented. They reveal that nowadays these salmonids can complete their up- and downstream migrations from the North Sea to places, situated at hundreds of kilometres upward the river and vica versa. The numbers of recorded Atlantic salmon and catch locations in inland waters are presented. They show a significant increase since 1989. These phenomena can be understood as promising signs of the recovery of the Rhine aquatic ecosystem.

Understanding Molecular Process and Chemotherapeutics for the Management of Breast Cancer.

2020 ◽  
Vol 14 ◽  
Author(s):  
Abhishek Kumar ◽  
Neeraj Masand ◽  
Vaishali M. Patil
Keyword(s):  
Breast Cancer ◽  
Molecular Mechanisms ◽  
Molecular Targets ◽  
Molecular Classification ◽  
Neoplastic Disease ◽  
Molecular Process ◽  
The Past ◽  
Anti Cancer ◽  
Molecular Etiology ◽  
Near Future

Abstract: Breast cancer is the most common and highly heterogeneous neoplastic disease comprised of several subtypes with distinct molecular etiology and clinical behaviours. The mortality observed over the past few decades and the failure in eradicating the disease is due to the lack of specific etiology, molecular mechanisms involved in initiation and progression of breast cancer. Understanding of the molecular classes of breast cancer may also lead to new biological insights and eventually to better therapies. The promising therapeutic targets and novel anti-cancer approaches emerging from these molecular targets that could be applied clinically in the near future are being highlighted. In addition, this review discusses some of the details of current molecular classification and available chemotherapeutics

scholarly journals The Genetic Architecture of Ovariole Number in Drosophila melanogaster: Genes with Major, Quantitative, and Pleiotropic Effects

2017 ◽  
Vol 7 (7) ◽  
pp. 2391-2403 ◽  
Author(s):  
Amanda S Lobell ◽  
Rachel R Kaspari ◽  
Yazmin L Serrano Negron ◽  
Susan T Harbison
Keyword(s):  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Natural Populations ◽  
Direct Role ◽  
Genome Wide ◽  
A Genome ◽  
Fitness Trait ◽  
Sleep Parameters ◽  
Activity Behavior ◽  
Ovariole Number

Abstract Ovariole number has a direct role in the number of eggs produced by an insect, suggesting that it is a key morphological fitness trait. Many studies have documented the variability of ovariole number and its relationship to other fitness and life-history traits in natural populations of Drosophila. However, the genes contributing to this variability are largely unknown. Here, we conducted a genome-wide association study of ovariole number in a natural population of flies. Using mutations and RNAi-mediated knockdown, we confirmed the effects of 24 candidate genes on ovariole number, including a novel gene, anneboleyn (formerly CG32000), that impacts both ovariole morphology and numbers of offspring produced. We also identified pleiotropic genes between ovariole number traits and sleep and activity behavior. While few polymorphisms overlapped between sleep parameters and ovariole number, 39 candidate genes were nevertheless in common. We verified the effects of seven genes on both ovariole number and sleep: bin3, blot, CG42389, kirre, slim, VAChT, and zfh1. Linkage disequilibrium among the polymorphisms in these common genes was low, suggesting that these polymorphisms may evolve independently.

scholarly journals Science for the Next Century: Deep Phenotyping

2021 ◽  
pp. 002203452110018
Author(s):  
J.T. Wright ◽  
M.C. Herzberg
Keyword(s):  
Health Care ◽  
Human Health ◽  
Care Delivery ◽  
The Past ◽  
Large Populations ◽  
Health And Disease ◽  
Methodological Approaches ◽  
Omic Data ◽  
Precision Health ◽  
Deep Phenotyping

Our ability to unravel the mysteries of human health and disease have changed dramatically over the past 2 decades. Decoding health and disease has been facilitated by the recent availability of high-throughput genomics and multi-omics analyses and the companion tools of advanced informatics and computational science. Understanding of the human genome and its influence on phenotype continues to advance through genotyping large populations and using “light phenotyping” approaches in combination with smaller subsets of the population being evaluated using “deep phenotyping” approaches. Using our capability to integrate and jointly analyze genomic data with other multi-omic data, the knowledge of genotype-phenotype relationships and associated genetic pathways and functions is being advanced. Understanding genotype-phenotype relationships that discriminate human health from disease is speculated to facilitate predictive, precision health care and change modes of health care delivery. The American Association for Dental Research Fall Focused Symposium assembled experts to discuss how studies of genotype-phenotype relationships are illuminating the pathophysiology of craniofacial diseases and developmental biology. Although the breadth of the topic did not allow all areas of dental, oral, and craniofacial research to be addressed (e.g., cancer), the importance and power of integrating genomic, phenomic, and other -omic data are illustrated using a variety of examples. The 8 Fall Focused talks presented different methodological approaches for ascertaining study populations and evaluating population variance and phenotyping approaches. These advances are reviewed in this summary.

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