Investigative genetics最新文献

{"title":"DNA fingerprinting in zoology: past, present, future.","authors":"Geoffrey K Chambers,&nbsp;Caitlin Curtis,&nbsp;Craig D Millar,&nbsp;Leon Huynen,&nbsp;David M Lambert","doi":"10.1186/2041-2223-5-3","DOIUrl":"https://doi.org/10.1186/2041-2223-5-3","url":null,"abstract":"<p><p>In 1962, Thomas Kuhn famously argued that the progress of scientific knowledge results from periodic 'paradigm shifts' during a period of crisis in which new ideas dramatically change the status quo. Although this is generally true, Alec Jeffreys' identification of hypervariable repeat motifs in the human beta-globin gene, and the subsequent development of a technology known now as 'DNA fingerprinting', also resulted in a dramatic shift in the life sciences, particularly in ecology, evolutionary biology, and forensics. The variation Jeffreys recognized has been used to identify individuals from tissue samples of not just humans, but also of many animal species. In addition, the technology has been used to determine the sex of individuals, as well as paternity/maternity and close kinship. We review a broad range of such studies involving a wide diversity of animal species. For individual researchers, Jeffreys' invention resulted in many ecologists and evolutionary biologists being given the opportunity to develop skills in molecular biology to augment their whole organism focus. Few developments in science, even among the subsequent genome discoveries of the 21st century, have the same wide-reaching significance. Even the later development of PCR-based genotyping of individuals using microsatellite repeats sequences, and their use in determining multiple paternity, is conceptually rooted in Alec Jeffreys' pioneering work. </p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"5 1","pages":"3"},"PeriodicalIF":0.0,"publicationDate":"2014-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-5-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32086248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The music of the genes.","authors":"Mark A Jobling","doi":"10.1186/2041-2223-5-2","DOIUrl":"https://doi.org/10.1186/2041-2223-5-2","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"5 1","pages":"2"},"PeriodicalIF":0.0,"publicationDate":"2014-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-5-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32059071","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DNA fingerprinting in botany: past, present, future.","authors":"Hilde Nybom, Kurt Weising, Björn Rotter","doi":"10.1186/2041-2223-5-1","DOIUrl":"10.1186/2041-2223-5-1","url":null,"abstract":"<p><p>Almost three decades ago Alec Jeffreys published his seminal Nature papers on the use of minisatellite probes for DNA fingerprinting of humans (Jeffreys and colleagues Nature 1985, 314:67-73 and Nature 1985, 316:76-79). The new technology was soon adopted for many other organisms including plants, and when Hilde Nybom, Kurt Weising and Alec Jeffreys first met at the very First International Conference on DNA Fingerprinting in Berne, Switzerland, in 1990, everybody was enthusiastic about the novel method that allowed us for the first time to discriminate between humans, animals, plants and fungi on the individual level using DNA markers. A newsletter coined \"Fingerprint News\" was launched, T-shirts were sold, and the proceedings of the Berne conference filled a first book on \"DNA fingerprinting: approaches and applications\". Four more conferences were about to follow, one on each continent, and Alec Jeffreys of course was invited to all of them. Since these early days, methodologies have undergone a rapid evolution and diversification. A multitude of techniques have been developed, optimized, and eventually abandoned when novel and more efficient and/or more reliable methods appeared. Despite some overlap between the lifetimes of the different technologies, three phases can be defined that coincide with major technological advances. Whereas the first phase of DNA fingerprinting (\"the past\") was dominated by restriction fragment analysis in conjunction with Southern blot hybridization, the advent of the PCR in the late 1980s gave way to the development of PCR-based single- or multi-locus profiling techniques in the second phase. Given that many routine applications of plant DNA fingerprinting still rely on PCR-based markers, we here refer to these methods as \"DNA fingerprinting in the present\", and include numerous examples in the present review. The beginning of the third phase actually dates back to 2005, when several novel, highly parallel DNA sequencing strategies were developed that increased the throughput over current Sanger sequencing technology 1000-fold and more. High-speed DNA sequencing was soon also exploited for DNA fingerprinting in plants, either in terms of facilitated marker development, or directly in the sense of \"genotyping-by-sequencing\". Whereas these novel approaches are applied at an ever increasing rate also in non-model species, they are still far from routine, and we therefore treat them here as \"DNA fingerprinting in the future\". </p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"5 1","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2014-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3880010/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31996315","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editors' pick: re-'colon'-ization of healthy microbiota after recurrent C. difficile infection.","authors":"Bruce Budowle","doi":"10.1186/2041-2223-4-28","DOIUrl":"https://doi.org/10.1186/2041-2223-4-28","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"4 1","pages":"28"},"PeriodicalIF":0.0,"publicationDate":"2013-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-4-28","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31957563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabarcoding avian diets at airports: implications for birdstrike hazard management planning.","authors":"Megan L Coghlan, Nicole E White, Dáithí C Murray, Jayne Houston, William Rutherford, Matthew I Bellgard, James Haile, Michael Bunce","doi":"10.1186/2041-2223-4-27","DOIUrl":"10.1186/2041-2223-4-27","url":null,"abstract":"<p><strong>Background: </strong>Wildlife collisions with aircraft cost the airline industry billions of dollars per annum and represent a public safety risk. Clearly, adapting aerodrome habitats to become less attractive to hazardous wildlife will reduce the incidence of collisions. Formulating effective habitat management strategies relies on accurate species identification of high-risk species. This can be successfully achieved for all strikes either through morphology and/or DNA-based identifications. Beyond species identification, dietary analysis of birdstrike gut contents can provide valuable intelligence for airport hazard management practices in regards to what food is attracting which species to aerodromes. Here, we present birdstrike identification and dietary data from Perth Airport, Western Australia, an aerodrome that saw approximately 140,000 aircraft movements in 2012. Next-generation high throughput DNA sequencing was employed to investigate 77 carcasses from 16 bird species collected over a 12-month period. Five DNA markers, which broadly characterize vertebrates, invertebrates and plants, were used to target three animal mitochondrial genes (12S rRNA, 16S rRNA, and COI) and a plastid gene (trnL) from DNA extracted from birdstrike carcass gastrointestinal tracts.</p><p><strong>Results: </strong>Over 151,000 DNA sequences were generated, filtered and analyzed by a fusion-tag amplicon sequencing approach. Across the 77 carcasses, the most commonly identified vertebrate was Mus musculus (house mouse). Acrididae (grasshoppers) was the most common invertebrate family identified, and Poaceae (grasses) the most commonly identified plant family. The DNA-based dietary data has the potential to provide some key insights into feeding ecologies within and around the aerodrome.</p><p><strong>Conclusions: </strong>The data generated here, together with the methodological approach, will greatly assist in the development of hazard management plans and, in combination with existing observational studies, provide an improved way to monitor the effectiveness of mitigation strategies (for example, netting of water, grass type, insecticides and so on) at aerodromes. It is hoped that with the insights provided by dietary data, airports will be able to allocate financial resources to the areas that will achieve the best outcomes for birdstrike reduction.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"4 1","pages":"27"},"PeriodicalIF":0.0,"publicationDate":"2013-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3874626/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31948406","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DNA capture and next-generation sequencing can recover whole mitochondrial genomes from highly degraded samples for human identification.","authors":"Jennifer E L Templeton,&nbsp;Paul M Brotherton,&nbsp;Bastien Llamas,&nbsp;Julien Soubrier,&nbsp;Wolfgang Haak,&nbsp;Alan Cooper,&nbsp;Jeremy J Austin","doi":"10.1186/2041-2223-4-26","DOIUrl":"https://doi.org/10.1186/2041-2223-4-26","url":null,"abstract":"<p><strong>Background: </strong>Mitochondrial DNA (mtDNA) typing can be a useful aid for identifying people from compromised samples when nuclear DNA is too damaged, degraded or below detection thresholds for routine short tandem repeat (STR)-based analysis. Standard mtDNA typing, focused on PCR amplicon sequencing of the control region (HVS I and HVS II), is limited by the resolving power of this short sequence, which misses up to 70% of the variation present in the mtDNA genome.</p><p><strong>Methods: </strong>We used in-solution hybridisation-based DNA capture (using DNA capture probes prepared from modern human mtDNA) to recover mtDNA from post-mortem human remains in which the majority of DNA is both highly fragmented (<100 base pairs in length) and chemically damaged. The method 'immortalises' the finite quantities of DNA in valuable extracts as DNA libraries, which is followed by the targeted enrichment of endogenous mtDNA sequences and characterisation by next-generation sequencing (NGS).</p><p><strong>Results: </strong>We sequenced whole mitochondrial genomes for human identification from samples where standard nuclear STR typing produced only partial profiles or demonstrably failed and/or where standard mtDNA hypervariable region sequences lacked resolving power. Multiple rounds of enrichment can substantially improve coverage and sequencing depth of mtDNA genomes from highly degraded samples. The application of this method has led to the reliable mitochondrial sequencing of human skeletal remains from unidentified World War Two (WWII) casualties approximately 70 years old and from archaeological remains (up to 2,500 years old).</p><p><strong>Conclusions: </strong>This approach has potential applications in forensic science, historical human identification cases, archived medical samples, kinship analysis and population studies. In particular the methodology can be applied to any case, involving human or non-human species, where whole mitochondrial genome sequences are required to provide the highest level of maternal lineage discrimination. Multiple rounds of in-solution hybridisation-based DNA capture can retrieve whole mitochondrial genome sequences from even the most challenging samples.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"4 1","pages":"26"},"PeriodicalIF":0.0,"publicationDate":"2013-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-4-26","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31914055","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The truth is out there.","authors":"Mark A Jobling","doi":"10.1186/2041-2223-4-24","DOIUrl":"https://doi.org/10.1186/2041-2223-4-24","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"4 ","pages":"24"},"PeriodicalIF":0.0,"publicationDate":"2013-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-4-24","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32563564","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modeling the contrasting Neolithic male lineage expansions in Europe and Africa.","authors":"Michael J Sikora,&nbsp;Vincenza Colonna,&nbsp;Yali Xue,&nbsp;Chris Tyler-Smith","doi":"10.1186/2041-2223-4-25","DOIUrl":"https://doi.org/10.1186/2041-2223-4-25","url":null,"abstract":"<p><strong>Background: </strong>Patterns of genetic variation in a population carry information about the prehistory of the population, and for the human Y chromosome an especially informative phylogenetic tree has previously been constructed from fully-sequenced chromosomes. This revealed contrasting bifurcating and starlike phylogenies for the major lineages associated with the Neolithic expansions in sub-Saharan Africa and Western Europe, respectively.</p><p><strong>Results: </strong>We used coalescent simulations to investigate the range of demographic models most likely to produce the phylogenetic structures observed in Africa and Europe, assessing the starting and ending genetic effective population sizes, duration of the expansion, and time when expansion ended. The best-fitting models in Africa and Europe are very different. In Africa, the expansion took about 12 thousand years, ending very recently; it started from approximately 40 men and numbers expanded approximately 50-fold. In Europe, the expansion was much more rapid, taking only a few generations and occurring as soon as the major R1b lineage entered Europe; it started from just one to three men, whose numbers expanded more than a thousandfold.</p><p><strong>Conclusions: </strong>Although highly simplified, the demographic model we have used captures key elements of the differences between the male Neolithic expansions in Africa and Europe, and is consistent with archaeological findings.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"4 1","pages":"25"},"PeriodicalIF":0.0,"publicationDate":"2013-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-4-25","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31888758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DNA fingerprinting in anthropological genetics: past, present, future.","authors":"Michael H Crawford,&nbsp;Kristine G Beaty","doi":"10.1186/2041-2223-4-23","DOIUrl":"https://doi.org/10.1186/2041-2223-4-23","url":null,"abstract":"<p><p>In 1985, Sir Alec Jeffreys developed the variable-number tandem repeat method used to identify individuals and giving researchers the first DNA fingerprints. These initial methods were used in anthropological genetics, a field that uses a comparative approach to answer questions about human history, including the discernment of the origin of Native American populations and the discrimination of clan affiliation from individuals in Siberia. The technological and methodological advances since this time have led to the use of many more markers, including restriction fragment length polymorphisms, Y chromosomal and autosomal short tandem repeats, single nucleotide polymorphisms, and direct sequencing not only to identify individuals, but to examine frequencies and distributions of markers (or \"prints\") of entire populations. In the field of anthropological genetics these markers have been used to reconstruct evolutionary history and answer questions concerning human origins and diaspora, migration, and the effects of admixture and adaptation to different environments, as well as susceptibility and resistance to disease. This review discusses the evolution of DNA markers since their application by Sir Alec Jeffreys and their applications in anthropological genetics. </p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"4 1","pages":"23"},"PeriodicalIF":0.0,"publicationDate":"2013-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-4-23","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31875161","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Curiosity in the genes: the DNA fingerprinting story.","authors":"Mark A Jobling","doi":"10.1186/2041-2223-4-20","DOIUrl":"https://doi.org/10.1186/2041-2223-4-20","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"4 1","pages":"20"},"PeriodicalIF":0.0,"publicationDate":"2013-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-4-20","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31876817","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}