Advances in GeneticsPub Date : 2018-01-01Epub Date: 2018-07-20DOI: 10.1016/bs.adgen.2018.05.009
Yongsheng Liu
{"title":"Darwin's Pangenesis and Certain Anomalous Phenomena.","authors":"Yongsheng Liu","doi":"10.1016/bs.adgen.2018.05.009","DOIUrl":"https://doi.org/10.1016/bs.adgen.2018.05.009","url":null,"abstract":"<p><p>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. The discoveries of cell-free fetal DNA, sperm RNAs, penetration of sperm into the somatic tissues of the female reproductive tract and the incorporation of exogenous DNA into somatic cells indicate that molecular mechanisms exist for telegony, one of the most controversial issues. Darwin's Pangenesis is the only theory that explains all the different types of phenomena.</p>","PeriodicalId":50949,"journal":{"name":"Advances in Genetics","volume":"102 ","pages":"93-120"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/bs.adgen.2018.05.009","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36410581","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Advances in GeneticsPub Date : 2018-01-01Epub Date: 2018-07-20DOI: 10.1016/bs.adgen.2018.05.006
Yongsheng Liu
{"title":"Darwin and Mendel: The Historical Connection.","authors":"Yongsheng Liu","doi":"10.1016/bs.adgen.2018.05.006","DOIUrl":"https://doi.org/10.1016/bs.adgen.2018.05.006","url":null,"abstract":"<p><p>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. Historical studies show that there is striking evidence that Mendel read Darwin's The Origin of Species, which had influenced his paper presented in 1865 and published in 1866. Although Mendel's paper has been considered a classic in the history of genetics, it generated much controversy since its rediscovery. Mendel's position as the father of genetics is being seriously challenged. Darwin's main contribution to genetics was the collection of a tremendous amount of genetic data, and the formulation of a comprehensive genetical theory for their explanation. Over the past 150 years, however, Darwin's legacy to genetics, particularly his Pangenesis, has not been considered seriously by most geneticists. It is proposed that Darwin should have been regarded as one of the most important pioneers in genetics.</p>","PeriodicalId":50949,"journal":{"name":"Advances in Genetics","volume":"102 ","pages":"1-25"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/bs.adgen.2018.05.006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36410577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Advances in GeneticsPub Date : 2018-01-01Epub Date: 2018-07-17DOI: 10.1016/bs.adgen.2018.05.004
Yongsheng Liu
{"title":"In Search of Darwin's Imaginary Gemmules.","authors":"Yongsheng Liu","doi":"10.1016/bs.adgen.2018.05.004","DOIUrl":"https://doi.org/10.1016/bs.adgen.2018.05.004","url":null,"abstract":"<p><p>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. Morgan's genes were considered to be stable entities arranged in an orderly linear pattern on chromosomes, like beads on a string. In the late 1940s, McClintock challenged the concept of the stability of the gene when she discovered that some genes could move within a chromosome and between chromosomes. In 1948, Mandel and Metais reported the presence of cell-free nucleic acids in human blood for the first time. Over the past several decades, it has been universally accepted that almost all types of cells not only shed molecules such as cell-free DNA (including genomic DNA, tumor DNA and fetal DNA), RNAs (including mRNA and small RNAs) and prions, but also release into the extracellular environment diverse types of membrane vesicles (known as extracellular vesicles) containing DNA, RNA and proteins. Thus Darwin's speculative gemmules of the 19th century have become the experimentally demonstrated circulating cell-free DNA, mobile RNAs, prions and extracellular vesicles.</p>","PeriodicalId":50949,"journal":{"name":"Advances in Genetics","volume":"101 ","pages":"87-114"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/bs.adgen.2018.05.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36335153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Advances in GeneticsPub Date : 2018-01-01Epub Date: 2018-07-17DOI: 10.1016/bs.adgen.2018.05.001
Yongsheng Liu
{"title":"Darwin's Pangenesis: A Theory of Everything?","authors":"Yongsheng Liu","doi":"10.1016/bs.adgen.2018.05.001","DOIUrl":"https://doi.org/10.1016/bs.adgen.2018.05.001","url":null,"abstract":"<p><p>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. He assumed that besides the ordinary cellular division, cells could also \"throw off\" numerous and minute gemmules, which were capable of self-replication and dormancy, diffusion from cell to cell or circulation through the body, modification by the effects of use and disuse or environmental changes, union with nascent cells, aggregation into buds and germ cells, and transmission from parent to offspring. By his Pangenesis, Darwin not only explained the general phenomena pertaining to inheritance, variation, development and reproduction, but also the inheritance of acquired characters, prepotency, graft hybridization, reversion, regeneration, xenia, telegony, transposition, sex-linked inheritance, the inheritance and non-inheritance of mutilation, and many other facts. Darwin called Pangenesis his \"beloved child\", and firmly believed that it \"will turn out true some day!\"</p>","PeriodicalId":50949,"journal":{"name":"Advances in Genetics","volume":"101 ","pages":"1-30"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/bs.adgen.2018.05.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36336266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Advances in GeneticsPub Date : 2018-01-01Epub Date: 2018-07-20DOI: 10.1016/bs.adgen.2018.05.010
Yongsheng Liu
{"title":"Natural Selection and Pangenesis: The Darwinian Synthesis of Evolution and Genetics.","authors":"Yongsheng Liu","doi":"10.1016/bs.adgen.2018.05.010","DOIUrl":"https://doi.org/10.1016/bs.adgen.2018.05.010","url":null,"abstract":"<p><p>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. Lysenkoism accepts the inheritance of acquired characters and graft hybridization, but denies the significance of Malthusism and Mutationism. It has been suggested that the \"modern synthesis\", which evolved from neo-Darwinism, needs a rethink. I propose that there is a need to go back to Darwin's own synthesis which combined his theory of evolution by natural selection with his theory of heredity and variation - Pangenesis.</p>","PeriodicalId":50949,"journal":{"name":"Advances in Genetics","volume":"102 ","pages":"121-142"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/bs.adgen.2018.05.010","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36410578","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Advances in GeneticsPub Date : 2018-01-01Epub Date: 2018-07-17DOI: 10.1016/bs.adgen.2018.05.005
Yongsheng Liu
{"title":"Darwin's Pangenesis and the Lamarckian Inheritance of Acquired Characters.","authors":"Yongsheng Liu","doi":"10.1016/bs.adgen.2018.05.005","DOIUrl":"https://doi.org/10.1016/bs.adgen.2018.05.005","url":null,"abstract":"<p><p>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. Many studies also suggest that parental age has certain influences on the characters of offspring. The current explanations include environmentally induced DNA changes (mainly DNA rearrangements and DNA methylation), RNA-mediated inheritance, and horizontal gene transfer. These mechanistic explanations are consistent with Darwin's Pangenesis.</p>","PeriodicalId":50949,"journal":{"name":"Advances in Genetics","volume":"101 ","pages":"115-144"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/bs.adgen.2018.05.005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36335150","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Advances in GeneticsPub Date : 2017-01-01Epub Date: 2017-10-03DOI: 10.1016/bs.adgen.2017.09.003
Malcolm von Schantz
{"title":"Natural Variation in Human Clocks.","authors":"Malcolm von Schantz","doi":"10.1016/bs.adgen.2017.09.003","DOIUrl":"https://doi.org/10.1016/bs.adgen.2017.09.003","url":null,"abstract":"<p><p>Our own species has a diurnal activity pattern and an average circadian period of 24.2h. Exact determination of circadian period requires expensive and intrusive protocols, and investigators are therefore using chronotype questionnaires as a proxy quantitative measure. Both measures show a normal distribution suggestive of a polygenic trait. The genetic components of the 24-h feedback loop that generates circadian rhythms within our cells have been mapped in detail, identifying a number of candidate genes which have been investigated for genetic polymorphisms relating to the phenotypic variance. Key in this mechanism is the inhibitory complex containing period and cryptochrome proteins and interacting protein kinases and ubiquitin ligases, and the stability of this complex is recognized as the major determinant of circadian periodicity. The identification of the causative mutations in familial circadian rhythms sleep disorders has shed additional light into this mechanism. Mutations in the negative feedback protein-encoding genes PER2 and CRY2 as well as the CSNK1D gene encoding casein kinase I delta have been shown to cause advanced sleep phase disorder, and a mutation in the CRY1 gene delayed sleep phase disorder. The candidate gene approach has also yielded a number of genetic associations with chronotype as determined by questionnaires. More recently, genome-wide association studies of chronotype have both confirmed associations with the candidate clock gene PER2 and identified a serious of novel genes associated with variability in circadian rhythmicity, which have yet to be explored. While considerable progress has thus been made with mapping the phenotypic diversity in human circadian rhythms and the genomic variability that causes it, studies to date have been mostly focused on individuals of European descent, and there is a strong need for research on other populations.</p>","PeriodicalId":50949,"journal":{"name":"Advances in Genetics","volume":"99 ","pages":"73-96"},"PeriodicalIF":0.0,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/bs.adgen.2017.09.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35526779","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Advances in GeneticsPub Date : 2017-01-01Epub Date: 2016-12-29DOI: 10.1016/bs.adgen.2016.11.001
T M Hammond
{"title":"Sixteen Years of Meiotic Silencing by Unpaired DNA.","authors":"T M Hammond","doi":"10.1016/bs.adgen.2016.11.001","DOIUrl":"https://doi.org/10.1016/bs.adgen.2016.11.001","url":null,"abstract":"<p><p>The filamentous fungus Neurospora crassa possesses a process called meiotic silencing by unpaired DNA (MSUD). MSUD has a remarkable ability to scan homologous chromosomes for unpaired DNA during meiosis. After unpaired DNA is identified, MSUD silences all RNA from the unpaired DNA along with any RNA transcribed from homologous sequences at other locations in the genome, regardless of their pairing state. The mechanism by which unpaired DNA is detected is unknown. Unpaired DNA segments can be as short as 1.3kb, if not shorter, and DNA sequences with only a small level of polymorphism (6%) can be considered unpaired by MSUD. MSUD research has identified nine proteins required for full efficiency of the process, three of which are homologs of the canonical RNA interference (RNAi) proteins Dicer, Argonaute, and RNA-dependent RNA polymerase. Most MSUD proteins, including the RNAi homologs, appear to dock outside of the nuclear envelope during early stages of meiosis. Only two have been observed inside the nucleus, a low number given that the identification of unpaired DNA and the triggering of silencing must begin within this location. These two proteins may participate in the unpaired DNA detection process. Recent evidence indicates that the search for unpaired DNA is spatially constrained, possibly because of restrictions on the arrangement of chromatin loops during or after homolog pairing. This review attempts to provide a complete analysis of past, present, and future directions of MSUD research, starting with its discovery during a search for a conserved regulator of fungal development and ending with some benefits the process may provide to MSUD capable organisms.</p>","PeriodicalId":50949,"journal":{"name":"Advances in Genetics","volume":"97 ","pages":"1-42"},"PeriodicalIF":0.0,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/bs.adgen.2016.11.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35347141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Advances in GeneticsPub Date : 2017-01-01Epub Date: 2017-09-11DOI: 10.1016/bs.adgen.2017.08.002
Devin M Stranford, Joshua N Leonard
{"title":"Delivery of Biomolecules via Extracellular Vesicles: A Budding Therapeutic Strategy.","authors":"Devin M Stranford, Joshua N Leonard","doi":"10.1016/bs.adgen.2017.08.002","DOIUrl":"https://doi.org/10.1016/bs.adgen.2017.08.002","url":null,"abstract":"<p><p>Extracellular vesicles (EVs) are membrane-enclosed particles that are secreted by nearly all cells and play an important role in intercellular communication by transporting protein and nucleic acids between cells. EV-mediated processes shape phenomena as diverse as cancer progression, immune function, and wound healing. The natural role of EVs in encapsulating and delivering cargo to modify cellular function highlights the potential to use these particles as therapeutic delivery vehicles. In this chapter, we describe emerging strategies for EV engineering and consider how different approaches to EV production, purification, and design may impact the efficacy of EV-based therapeutics.</p>","PeriodicalId":50949,"journal":{"name":"Advances in Genetics","volume":"98 ","pages":"155-175"},"PeriodicalIF":0.0,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/bs.adgen.2017.08.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35442734","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Advances in GeneticsPub Date : 2017-01-01Epub Date: 2017-09-02DOI: 10.1016/bs.adgen.2017.08.001
Lina Mastrangelo
{"title":"The Genetics of Parkinson Disease.","authors":"Lina Mastrangelo","doi":"10.1016/bs.adgen.2017.08.001","DOIUrl":"https://doi.org/10.1016/bs.adgen.2017.08.001","url":null,"abstract":"<p><p>The 200years of research efforts on Parkinson disease (PD) form the basis of our understanding of the second most common neurodegenerative disorder after Alzheimer disease. This journey has been marked by the revolutionary discovery of a neurotransmitter replacement therapy that provides a longer and healthier life to patients. Since 1997, the advances in the genetics of PD have expanded our understanding of this neurodegenerative disorder and they are opening up new ways to search for disease-modifying therapies. This chapter is a summary of the historical discoveries and latest progress in PD research.</p>","PeriodicalId":50949,"journal":{"name":"Advances in Genetics","volume":"98 ","pages":"43-62"},"PeriodicalIF":0.0,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/bs.adgen.2017.08.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35540743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}