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Advances in Genetics

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https://www.readbyqxmd.com/read/30122236/darwin-s-pangenesis-and-certain-anomalous-phenomena
#1
Yongsheng Liu
Darwin clearly described certain anomalous phenomena, including what he referred to as "the direct action of the male element on the female form" and what we now call xenia and telegony, bud variation (mutation), reversion or atavism, and the inheritance and non-inheritance of mutilation. Some phenomena, particularly xenia, telegony and the inheritance of mutilation, were considered as doubtful phenomena by such authorities as Weismann and Morgan. Over the past 150 year, however, there has been increasing evidence for xenia, which is of great interest and importance in physiological research and plant production...
2018: Advances in Genetics
https://www.readbyqxmd.com/read/30122235/darwin-s-pangenesis-and-medical-genetics
#2
Yongsheng Liu
Darwin had many close connections with medical men, and made a number of observations on inherited diseases, clearly describing the inheritance of sex-linked diseases, inherited diseases at corresponding ages, infectious disease and the causes of diseases. Darwin's Pangenesis provides an alternative explanation for cancer metastasis, and is now supported by the discovery of circulating tumour DNA. The "genometastasis hypothesis" proposed by Garcia-Olmo et al. is consistent with Pangenesis. Darwin's view of animal regeneration and his pangenetic explanation is also supported by the recent finding regarding the role of small RNAs and extracellular vesicles in regeneration...
2018: Advances in Genetics
https://www.readbyqxmd.com/read/30122234/darwin-s-pangenesis-and-graft-hybridization
#3
Yongsheng Liu
Although there were many records of graft-induced variations in ancient China, it was Darwin who coined the term "graft hybridization", the formation of hybrids between distinct species or varieties, through plant grafting, without the intervention of the sexual organs. He described many cases of the so-called "graft hybrids", in which shoots produced from grafted plants exhibited a combination of characters of both rootstock and scion, and explained their formation by his Pangenesis. Michurin invented "mentor-grafting" and "preliminary vegetative approximation" methods, which greatly increased the production of graft hybrids, thus providing a solution to Darwin's puzzle...
2018: Advances in Genetics
https://www.readbyqxmd.com/read/30122233/natural-selection-and-pangenesis-the-darwinian-synthesis-of-evolution-and-genetics
#4
Yongsheng Liu
Since the end of the 19th century, Lamarck's name has been tightly linked to the notion of the inheritance of acquired characters. Darwin regarded Lamarck as a great zoologist and a forerunner of evolution, and repeatedly expressed the opinion that "natural selection has been the main but not the exclusive means of modification." The original Darwinism not only includes natural selection, but also the inheritance of acquired characters and mutation. Neo-Darwinism considers natural selection as the one controlling process of evolution, but denies the inheritance of acquired characters...
2018: Advances in Genetics
https://www.readbyqxmd.com/read/30122232/darwin-and-mendel-the-historical-connection
#5
Yongsheng Liu
Darwin carried out a host of carefully controlled cross- and self-pollination experiments in a wide variety of plants, and made a significant and imperishable contribution to the knowledge of hybridization. He not only clearly described the phenomenon of what he called prepotency and what we now call dominance or Mendelian inheritance, but also explained it by his Pangenesis. Recent discovery of small RNAs acting as dominance modifiers supports his Pangenesis regarding the control of prepotency by gemmules...
2018: Advances in Genetics
https://www.readbyqxmd.com/read/30037394/in-search-of-darwin-s-imaginary-gemmules
#6
Yongsheng Liu
Darwin's gemmules were supposed to be "thrown off" by cells and were "inconceivably minute and numerous as the stars in heaven." They were capable of self-propagation and diffusion from cell to cell, and circulation through the system. The word "gene" coined by Wilhelm Johannsen, was derived from de Vries's term "pangen," itself a substitute for "gemmule" in Darwin's Pangenesis. Johannsen resisted the "morphological" conception of genes as particles with a certain structure...
2018: Advances in Genetics
https://www.readbyqxmd.com/read/30037393/the-influence-of-darwin-s-pangenesis-on-later-theories
#7
Yongsheng Liu
Although Darwin's Pangenesis received strong criticism and never gained any very wide acceptance, it was of great importance due to its stimulating effect on later work and thought. Nearly every major theory of heredity developed in the late 19th century began with a discussion of Darwin's Pangenesis. Darwin was shown to play a more important role in the history of genetics than hitherto attributed to him by historians through a detailed analysis of the influence of his Pangenesis on de Vries' "Intracellular Pangenesis" and "The Mutation Theory," Weismann's theory of "Continuity of the Germ-plasm," Galton's "A Theory of Heredity" and "Natural Inheritance," Brooks' "The Law of Heredity, Ross's "Graft Theory of Diseases", Haeckel's perigenesis and Kozo-Polyansky's hypothetical version of symbiogenesis...
2018: Advances in Genetics
https://www.readbyqxmd.com/read/30037392/the-criticisms-of-pangenesis-the-years-of-controversy
#8
Yongsheng Liu
When first published in 1868, Darwin's Pangenesis was almost uniformly rejected by his contemporaries. Until recently it has still been regarded as Darwin's biggest mistake or a brilliant blunder. There are three main reasons for this. First, Galton transfused the blood of one variety of rabbit into another, and then bred together the latter. The results of breeding showed no variations of characters in the offspring. Thus he concluded that Darwin's Pangenesis was incorrect. Second, there was no direct evidence for the existence of Darwin's imaginary gemmules...
2018: Advances in Genetics
https://www.readbyqxmd.com/read/30037391/darwin-s-pangenesis-and-the-lamarckian-inheritance-of-acquired-characters
#9
Yongsheng Liu
Since the earliest days of evolutionary thought, the problem of the inheritance of acquired characters has been a central debate. Darwin accepted the inheritance of acquired characters as an established fact and gave many instances. His Pangenesis was more than anything else an attempt to provide a theory for its explanation. Over the past several decades, there has been increasing evidence for the inheritance of acquired habit and immunity, and for heritable changes induced by food and fertilizer, stress, chemicals, temperature, light and other environmental factors...
2018: Advances in Genetics
https://www.readbyqxmd.com/read/30037390/darwin-s-pangenesis-a-theory-of-everything
#10
Yongsheng Liu
This chapter briefly discusses Darwin's The Origin of Species and its companion volume The Variation of Animals and Plants under Domestication. It is in the second great book that Darwin took a broad survey of the whole range of variation and heredity, and developed his Pangenesis, an expanded cell theory and a unified genetical theory that would strengthen his theory of evolution and explains the numerous phenomena of life. The essential assumption of Pangenesis is the existence of inherited particles or molecules called gemmules, and their production by cells at each stage of development...
2018: Advances in Genetics
https://www.readbyqxmd.com/read/29153406/preface
#11
EDITORIAL
Jeffrey P Townsend, Zheng Wang
No abstract text is available yet for this article.
2017: Advances in Genetics
https://www.readbyqxmd.com/read/29153405/describing-genomic-and-epigenomic-traits-underpinning-emerging-fungal-pathogens
#12
REVIEW
Rhys A Farrer, Matthew C Fisher
An unprecedented number of pathogenic fungi are emerging and causing disease in animals and plants, putting the resilience of wild and managed ecosystems in jeopardy. While the past decades have seen an increase in the number of pathogenic fungi, they have also seen the birth of new big data technologies and analytical approaches to tackle these emerging pathogens. We review how the linked fields of genomics and epigenomics are transforming our ability to address the challenge of emerging fungal pathogens. We explore the methodologies and bioinformatic toolkits that currently exist to rapidly analyze the genomes of unknown fungi, then discuss how these data can be used to address key questions that shed light on their epidemiology...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/29153404/fungal-phylogeny-in-the-age-of-genomics-insights-into-phylogenetic-inference-from-genome-scale-datasets
#13
László G Nagy, Gergely Szöllősi
The genomic era has been transformative for many fields, including our understanding of the phylogenetic relationships between organisms. The wide availability of whole-genome sequences practically eliminated data availability as a limiting factor for inferring phylogenetic trees, providing hundreds to thousands of loci for analyses, leading to molecular phylogenetics gradually being replaced by phylogenomics. The new era has also brought new challenges: systematic errors (resulting from, e.g., model violation) can be more pronounced in phylogenomic datasets and can lead to strongly supported incorrect relationships, creating significant incongruence among studies...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/29153403/advances-in-fungal-phylogenomics-and-their-impact-on-fungal-systematics
#14
Ning Zhang, Jing Luo, Debashish Bhattacharya
In the past decade, advances in next-generation sequencing technologies and bioinformatic pipelines for phylogenomic analysis have led to remarkable progress in fungal systematics and taxonomy. A number of long-standing questions have been addressed using comparative analysis of genome sequence data, resulting in robust multigene phylogenies. These have added to, and often surpassed traditional morphology or single-gene phylogenetic methods. In this chapter, we provide a brief history of fungal systematics and highlight some examples to demonstrate the impact of phylogenomics on this field...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/29153402/phylogenetics-and-phylogenomics-of-rust-fungi
#15
M Catherine Aime, Alistair R McTaggart, Stephen J Mondo, Sébastien Duplessis
Rust fungi (Pucciniales) are the most speciose and the most complex group of plant pathogens. Historically, rust taxonomy was largely influenced by host and phenotypic characters, which are potentially plastic. Molecular systematic studies suggest that the extant diversity of this group was largely shaped by host jumps and subsequent shifts. However, it has been challenging to reconstruct the evolutionary history for the order, especially at deeper (family-level) nodes. Phylogenomics offer a potentially powerful tool to reconstruct the Pucciniales tree of life, although researchers working at this vanguard still face unprecedented challenges working with nonculturable organisms that possess some of the largest and most repetitive genomes now known in kingdom fungi...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/29153401/multiple-approaches-to-phylogenomic-reconstruction-of-the-fungal-kingdom
#16
Charley G P McCarthy, David A Fitzpatrick
Fungi are possibly the most diverse eukaryotic kingdom, with over a million member species and an evolutionary history dating back a billion years. Fungi have been at the forefront of eukaryotic genomics, and owing to initiatives like the 1000 Fungal Genomes Project the amount of fungal genomic data has increased considerably over the last 5 years, enabling large-scale comparative genomics of species across the kingdom. In this chapter, we first review fungal evolution and the history of fungal genomics. We then review in detail seven phylogenomic methods and reconstruct the phylogeny of 84 fungal species from 8 phyla using each method...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/29153400/deciphering-pathogenicity-of-fusarium-oxysporum-from-a-phylogenomics-perspective
#17
REVIEW
Yong Zhang, Li-Jun Ma
Fusarium oxysporum is a large species complex of both plant and human pathogens that attack a diverse array of species in a host-specific manner. Comparative genomic studies have revealed that the host-specific pathogenicity of the F. oxysporum species complex (FOSC) was determined by distinct sets of supernumerary (SP) chromosomes. In contrast to common vertical transfer, where genetic materials are transmitted via cell division, SP chromosomes can be transmitted horizontally between phylogenetic lineages, explaining the polyphyletic nature of the host-specific pathogenicity of the FOSC...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/29153399/fungal-gene-cluster-diversity-and-evolution
#18
Jason C Slot
Metabolic gene clusters (MGCs) have provided some of the earliest glimpses at the biochemical machinery of yeast and filamentous fungi. MGCs encode diverse genetic mechanisms for nutrient acquisition and the synthesis/degradation of essential and adaptive metabolites. Beyond encoding the enzymes performing these discrete anabolic or catabolic processes, MGCs may encode a range of mechanisms that enable their persistence as genetic consortia; these include enzymatic mechanisms to protect their host fungi from their inherent toxicities, and integrated regulatory machinery...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/29153398/maximizing-power-in-phylogenetics-and-phylogenomics-a-perspective-illuminated-by-fungal-big-data
#19
Alex Dornburg, Jeffrey P Townsend, Zheng Wang
Since its original inception over 150 years ago by Darwin, we have made tremendous progress toward the reconstruction of the Tree of Life. In particular, the transition from analyzing datasets comprised of small numbers of loci to those comprised of hundreds of loci, if not entire genomes, has aided in resolving some of the most vexing of evolutionary problems while giving us a new perspective on biodiversity. Correspondingly, phylogenetic trees have taken a central role in fields that span ecology, conservation, and medicine...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/29050556/preface
#20
EDITORIAL
Stephen F Goodwin
No abstract text is available yet for this article.
2017: Advances in Genetics
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