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1
Straalen, Nico, and Dick Roelofs. Human Evolution and Development. NL Amsterdam: Amsterdam University Press, 2019. http://dx.doi.org/10.5117/9789463729208.
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Our understanding of human evolution is proceeding at an unprecedented rate over the last years due to spectacular fossil finds, reconstructions based on genome comparison, ancient DNA sequencing and new insights into developmental genetics. This book takes an integrative approach in which the development of the human embryo, the evolutionary history of our body, the structure of human populations, their dispersal over the world and their cultures are examined by integrating paleoanthropology, developmental biology, comparative zoology, population genetics and phylogenetic reconstruction. The authors discuss questions like: - What do we know about ancient humans? - What happens in the development of an embryo? - How did we manage to walk upright and why did we lose our hair? - What is the relationship between language, migration and evolution? - How does our body respond to the challenges of modern society? In addition to being a core text for the study of the life sciences, Human Evolution and Development is an easy-to-read overview for the interested layperson.
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Taberlet, Pierre, Aurélie Bonin, Lucie Zinger, and Eric Coissac. DNA sequencing. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198767220.003.0007.
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The emergence of eDNA analysis is tightly linked to the development of next-generation sequencing. Chapter 7 “DNA sequencing” gives an overview of the characteristics and limitations of the main next-generation sequencing platforms. It focuses particularly on the Illumina platform, which is the only technology currently suitable for large-scale analysis with hundreds to thousands of samples. More specifically, Chapter 7 describes the Illumina library preparation process, the generation of sequencing clusters by bridge PCR on the flow cell, and the sequencing reaction itself, based on sequencing by synthesis. Finally, detailed information is provided on the meaning and coding of quality scores of the sequencing reads.
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Walker, Dan. Korg M-One Sequencing and Recording Handbook (Korg M-One Support Series). Alexander Pub, 1988.
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4
Newman, Abraham L. Sequencing, Layering, and Feedbacks in Global Regulation. Edited by Orfeo Fioretos, Tulia G. Falleti, and Adam Sheingate. Oxford University Press, 2016. http://dx.doi.org/10.1093/oxfordhb/9780199662814.013.38.
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From banking standards to data privacy, regulation has entered the lexicon of international affairs. Unlike trade or currencies, however, there are few formal treaty-based international organizations resolving disputes or setting the rules for the world. Instead, global regulation is frequently shaped by informal networks of regulators or at times by the extraterritorial extension of domestic law by large markets. Drawing on work from historical institutionalism, this chapter argues that the global politics of regulation is in important respects the product of domestic and international institutions interacting over time and across space. In developing three mechanisms—relative sequencing, cross-national layering, and transnational feedbacks —the chapter argues that historical institutionalism helps address lacunae in extant approaches to global regulation.
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Bantekas, Ilias. Sequencing Peace and Justice in Post-Conflict Africa. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780198810568.003.0005.
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This chapter discusses the extent to which there is any conflict or harm in the ICC Prosecutor’s involvement in cases undergoing mediation by the international community, most of which are currently in Africa. The ICC Prosecutor’s discretion, as per the Court’s Statute, to hold a prosecution in abeyance in anticipation of the outcomes of mediating efforts which aim at ending a conflict is at best ambivalent. Recent practice suggests that stakeholders engaged in ending long-running African conflicts prefer the Prosecutor to decline to exercise jurisdiction in order to encourage the parties to reach some agreement. For obvious reasons, discussions on such matters are often held confidentially and not in the context of official debates. The African experience with the peace–justice nexus shows that the peace-versus-justice debate has not been resolved in favour of any camp.
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Taberlet, Pierre, Aurélie Bonin, Lucie Zinger, and Eric Coissac. DNA metabarcoding data analysis. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198767220.003.0008.
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DNA metabarcoding generates huge amounts of data containing noise introduced by molecular methods. Chapter 8 “DNA metabarcoding data analysis” discusses the analytic steps and available software to curate and evaluate DNA metabarcoding data prior to final ecological analyses. It provides command lines to perform primary analyses of Illumina sequencing data with the OBITools, ranging from read assignment to samples to the formation of molecular operational taxonomic units (MOTUs) and their assignment to a taxon through comparison against reference databases. Chapter 8 also develops several methods to further curate sequencing data from contaminants or dysfunctional PCRs by using DNA extraction, PCR, and sequencing blank controls as well as PCR/biological replicates. It also presents several classical analyses to ensure that the diversity of the sample or the study site is appropriately covered. Finally, this chapter considers what conclusions on biodiversity and ecological processes can be really drawn from metabarcoding data.
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Sadleir, Lynette G., Jozef Gecz, and Ingrid E. Scheffer. Epilepsies That Occur Predominantly in Girls. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780199937837.003.0041.
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Availability of DNA sequencing has led to an increase in the number of children being identified with mutations in specific genes in specific epilepsy phenotypes. The presence of mutations that cause epilepsy only in females is one of the discoveries revealed in the sequencing era. Mutations in PCDH19 and CDKL5 are distinctive and identifiable forms of female-only epilepsy, and clinicians should consider PCDH19 in normal girls presenting with clusters of afebrile or febrile seizures in the first 3 years of life, and CDKL5 in girls or boys presenting with severe developmental delay within the first 6 months of life followed by intractable seizures including spasms within the first 2 years.
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Taberlet, Pierre, Aurélie Bonin, Lucie Zinger, and Eric Coissac. The future of eDNA metabarcoding. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198767220.003.0019.
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Environmental DNA-based research is undergoing rapid developments, but its democratization in basic and applied research remains hampered by the biases introduced by molecular approaches, the difficulties in estimating absolute organisms’ abundances, and a lack of general consensus in molecular protocols. Chapter 19 “The future of eDNA metabarcoding” provides an overview of these current challenges and discusses how shotgun sequencing, capture-based methods, inclusion of internal standards, and development of new data repositories could alleviate these limits and facilitate cross-experiments comparisons. This chapter finally turns to open questions on the potentiality of new sequencing methods and proposes directions to improve biodiversity estimates and ecological inferences and predictions from eDNA data, and ultimately stimulate further developments and integration of eDNA metabarcoding into academic and operational ecological research and monitoring.
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Maher, Christopher J., and Elaine R. Mardis. Genomic Landscape of Cancer. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780190238667.003.0004.
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The study of cancer genomics has advanced rapidly during the last decade due to the development of next generation or massively parallel technology for DNA sequencing. The resulting knowledge is transforming the understanding of both inherited (germline) genetic susceptibility and the somatic changes in tumor tissue that drive abnormal growth and progression. The somatic alterations in tumor tissue vary depending on the type of cancer and its characteristic “genomic landscape.” New technologies have increased the speed and lowered the cost of DNA sequencing and have enabled high-volume characterization of RNA, DNA methylation, DNA-protein complexes, DNA conformation, and a host of other factors that, when altered, can contribute to the development and/or progression of the cancer. Technologic advances have greatly expanded research on somatic changes in tumor tissue, revealing both the singularity of individual cancer genomes and the commonality of genetic alterations that drive cancer in different tissues.
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Mammen, Andrew L., and Jessica R. Nance. Evaluation of hyperCKaemia. Edited by Hector Chinoy and Robert Cooper. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198754121.003.0007.
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Serum creatine kinase (CK) levels may be elevated in patients with muscle weakness or pain. In asymptomatic patients with CK elevations, the focus should be on identifying reversible causes, followed by investigation for inherited muscle diseases. In asymptomatic patients with an incidental finding of elevated CK, clinicians should look for reversible causes, then re-test the CK after 10 days of rest in the absence of potential triggers. If the CK remains markedly elevated and/or electromyography proves myopathic, a muscle biopsy should be considered. Women of childbearing age with elevation of serum CK should be evaluated for dystrophin mutation. Genetic causes of hyperCKaemia can be pursued with targeted gene sequencing, or whole exome or next generation sequencing. Patients with inherited skeletal muscle diseases may also have associated cardiac disease, so a cardiology evaluation should be considered in all patients with unexplained CK elevations.
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Ingles, Jodie, Charlotte Burns, and Laura Yeates. Genetic counselling. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198784906.003.0145.
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Cardiac genetic counselling is an emerging but important subspecialty. The qualifications of cardiac genetic counsellors depend on the country of practice, but at a minimum they are Master’s-level trained health professionals with expertise in genetics, and are integral members of the multidisciplinary inherited cardiovascular disease clinic. Though the framework is diverse in different countries, key roles include investigation and confirmation of family history details, discussion of inheritance risks and facilitation of cardiac genetic testing, communication with at-risk relatives, and increasingly, curation of genetic test results. The use of next-generation sequencing technologies has seen a recent shift in the uptake of genetic testing, due to greater availability and lowered costs. As these gene tests become more comprehensive, including large panels of genes and even whole exome or whole genome sequencing, the need for cardiac genetic counsellors to provide informed consent, appropriate pre- and post-test genetic counselling, and ongoing curation of the variants identified is evident. Finally, given the improved understanding of the psychological implications of living with a cardiovascular genetic disease, cardiac genetic counsellors are integral in delivering psychosocial care and identifying patients requiring intervention with a clinical psychologist.
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Halliday, Catriona L., and Sarah E. Kidd. Cryptococcus species. Edited by Christopher C. Kibbler, Richard Barton, Neil A. R. Gow, Susan Howell, Donna M. MacCallum, and Rohini J. Manuel. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780198755388.003.0012.
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Cryptococcus neoformans and Cryptococcus gattii are the principal pathogenic species within the genus Cryptococcus and the causative agents of cryptococcosis. Although rare, the incidence of infection due to other Cryptococcus species previously regarded as saprophytes, has increased over the last 40 years. Irrespective of the infecting species, infections are acquired following inhalation from the environment, causing localised or disseminated disease. The severity of disease is dependent on the organism’s virulence factors and the host’s immune response, and the clinical manifestations are indistinguishable. Accurate identification of the pathogenic species relies on rDNA sequencing
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Iversen, Les. 6. What can we expect in the future? Oxford University Press, 2016. http://dx.doi.org/10.1093/actrade/9780198745792.003.0006.
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‘What can we expect in the future?’ considers changing attitudes to drugs in the 21st century, the current pharmaceutical industry, and the rise of personalized medicines as a result of a greater understanding of the genetic and molecular basis of diseases and lower costs of DNA sequencing. Public attitudes to both medicinal and recreational drugs are changing: the easy availability of information and misinformation on the Internet is affecting vaccination rates in children, patients are researching new drugs, and there is a growing movement towards legalizing cannabis. The escalating costs of new medicines often makes them too expensive for most European health services and out of reach of developing countries.
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Taberlet, Pierre, Aurélie Bonin, Lucie Zinger, and Eric Coissac. Environmental DNA. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198767220.001.0001.
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Environmental DNA (eDNA), i.e. DNA released in the environment by any living form, represents a formidable opportunity to gather high-throughput and standard information on the distribution or feeding habits of species. It has therefore great potential for applications in ecology and biodiversity management. However, this research field is fast-moving, involves different areas of expertise and currently lacks standard approaches, which calls for an up-to-date and comprehensive synthesis. Environmental DNA for biodiversity research and monitoring covers current methods based on eDNA, with a particular focus on “eDNA metabarcoding”. Intended for scientists and managers, it provides the background information to allow the design of sound experiments. It revisits all steps necessary to produce high-quality metabarcoding data such as sampling, metabarcode design, optimization of PCR and sequencing protocols, as well as analysis of large sequencing datasets. All these different steps are presented by discussing the potential and current challenges of eDNA-based approaches to infer parameters on biodiversity or ecological processes. The last chapters of this book review how DNA metabarcoding has been used so far to unravel novel patterns of diversity in space and time, to detect particular species, and to answer new ecological questions in various ecosystems and for various organisms. Environmental DNA for biodiversity research and monitoring constitutes an essential reading for all graduate students, researchers and practitioners who do not have a strong background in molecular genetics and who are willing to use eDNA approaches in ecology and biomonitoring.
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Walsh, Richard A. “Are My Children at Risk, Doctor?”. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780190607555.003.0007.
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Few patients with Parkinson’s disease will be found to have a monogenic cause of their disease, even among those with early onset symptoms. The identification of a genetic etiology will in general have no implications on management but can be helpful in offering a prediction on prognosis, predicting response to treatment, and allowing genetic counseling to take place. Insights into the molecular mechanisms provided by a greater understanding of the genetics of Parkinson’s disease may offer the best hope for identifying future disease-modifying therapies. Next-generation sequencing techniques offer a more cost-effective approach to pursuing genetic testing where indicated.
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Hull, Sarah, and Andrew R. Webster. Ophthalmic Manifestations of Inherited Metabolic Diseases. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780199972135.003.0075.
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Systemic metabolic disorders can manifest in the cornea, lens, or retina with or without affecting vision. In some conditions findings are present from birth, and in others ophthalmic complications develop as the disease progresses. In some conditions in adults (for instance pseudoxanthoma elasticum (PXE), Wilson disease, Fabry and gyrate atrophy) ocular findings are pathognomic and should lead to targeted investigations such as sequencing of ABCC6 in PXE and serum ornithine levels in gyrate atrophy. Early diagnosis and treatment may improve visual outcomes. This chapter will focus on the key conditions in adults that have distinct presentations in the eye.
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Divan, Aysha, and Janice A. Royds. 2. DNA. Oxford University Press, 2016. http://dx.doi.org/10.1093/actrade/9780198723882.003.0002.
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Another significant milestone was the publication in 2003 of the complete sequence of the human genome—the entire DNA contained within the forty-six chromosomes located in the nucleus of each human somatic (body) cell. Once this was published, further worldwide projects were launched to work out what the functions of these genes and other regions of the genome actually were. ‘DNA’ outlines the components of the human genome and their organization; DNA replication; mutations and correction mechanisms; polymorphisms; and new DNA technologies, including gene cloning, the polymerase chain reaction, and sequencing methods. Finally, bioinformatics and the subsequent issues of privacy and how this information could be used are discussed.
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Lamari, Foudil, and Jean-Marie Saudubray. Disorders of Complex Lipids Synthesis and Remodeling. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780199972135.003.0066.
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Defective lipid catabolic pathways are involved in numerous inherited metabolic diseases such as lysosomal storage diseases and peroxisome biogenesis disorders. We recently described a new classification of a rapidly growing group of inherited metabolic disorders involving biosynthesis and remodeling of complex lipids including phospholipids and sphingolipids. The remarkable progress achieved over the last decade in high throughput gene sequencing and in lipid analysis technologies have enabled the description of more than 40 diseases linked to defects in enzymes involved in these pathways. Some of these defects present in infancy or childhood but most of them are diagnosed in adolescence or adulthood. In this review we focus on those with adult presentation.
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Taberlet, Pierre, Aurélie Bonin, Lucie Zinger, and Eric Coissac. Environmental DNA for functional diversity. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198767220.003.0010.
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Chapter 10 “Environmental DNA for functional diversity” discusses the potential of environmental DNA to assess functional diversity. It first focuses on DNA metabarcoding and discusses the extent to which this approach can be used and/or optimized to retrieve meaningful information on the functions of the target community. This knowledge usually involves coarsely defined functional groups (e.g., woody, leguminous, graminoid plants; shredders or decomposer soil organisms; pathogenicity or decomposition role of certain microorganisms). Chapter 10 then introduces metagenomics and metatranscriptomics approaches, their advantages, but also the challenges and solutions to appropriately sampling, sequencing these complex DNA/RNA populations. Chapter 10 finally presents several strategies and software to analyze metagenomes/metatranscriptomes, and discusses their pros and cons.
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Gorman, Gráinne S., and Patrick F. Chinnery. Mitochondrial diseases. Oxford University Press, 2015. http://dx.doi.org/10.1093/med/9780199658602.003.0011.
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This chapter critiques ten seminal papers that epitomize the advent and evolution of mitochondrial medicine from the latter half of the last century up until today. These important bodies of work span the pre-molecular and molecular eras, from when diagnostic yield was based on meticulous clinical and biochemical characterization of patients, up until now, with targeted next-generation sequencing revolutionizing our diagnostic approach. The first clinical description of a mitochondrial disorder is reviewed and the subsequent landmark papers that define current clinical and molecular understanding of human diseases caused by inherited disorders of mitochondrial dysfunction are chronicled. The chapter also charts the shift in emphasis from diagnosis to the development of treatments and novel approaches for disease prevention.
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Landreth, Anthony. The Emerging Theory of Motivation. Edited by John Bickle. Oxford University Press, 2009. http://dx.doi.org/10.1093/oxfordhb/9780195304787.003.0016.
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This article attempts to elate aspects of our commonsense understanding of motivation to an emerging, mechanistic account of motivation in neuroscience. It identifies various points in the neural process where motivational control will have an opportunity to play a role. It suggests that these points of influence occur in the early stages of planning a course of action by sequencing a set of subgoals, at the stage of action selection when the type of instrumental action to be performed is chosen and at the stage of online action correction when adjustments are made in the midst of performance. The article argues that it is possible to advance the understanding of motivational states by modeling them on reinforcement learning principles.
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Taberlet, Pierre, Aurélie Bonin, Lucie Zinger, and Eric Coissac. Analysis of bulk samples. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198767220.003.0018.
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Chapter 18 “Analysis of bulk samples” deals with the particular case of biodiversity surveys based on bulk samples. A bulk sample is an environmental sample containing mainly organisms from the taxonomic group under study, such as insect samples obtained from a Malaise trap, or eukaryote-enriched samples obtained from filtered or size-fractionated water samples. One important characteristic of bulk samples is that they usually provide good-quality DNA in high amounts. Chapter 18 presents several seminal studies based on bulk samples that aimed at monitoring arthropod, nematode, or marine metazoan diversity. The advantages and limitations of the classical barcoding COI marker versus metabarcoding markers for bulk sample analysis are also discussed. Finally, Chapter 18 reviews two alternative strategies to limit the taxonomic biases associated with the use of the COI marker (i.e., mitochondrial enrichment via differential centrifugation or capture, followed by extraction and shotgun sequencing).
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Riley, Peter. The role of the microbiology laboratory in antimicrobial stewardship. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780198758792.003.0010.
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Microbiology laboratories play an important role in antimicrobial stewardship at the level of individual patients and the population as a whole. When empiric therapy has been started, rapid results can lead to earlier targeted treatment. Accumulated results of susceptibility tests can be analysed and used to generate local or national guidelines on empiric treatment and prophylaxis. Several methods can be used to determine microbial identity and antimicrobial susceptibility, including traditional culture-based methods and newer molecular methods such as matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry, polymerase chain reaction (PCR), and whole-genome sequencing. These methods and potential advantages are reviewed. Before results are reported, expert rules are applied and results edited. At this point the laboratory can influence prescribing practices.
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Leslie, Vinjamuri. Part I Context, Challenges, and Constraints, 2 The ICC and the Politics of Peace and Justice. Oxford University Press, 2015. http://dx.doi.org/10.1093/law/9780198705161.003.0002.
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The indictment of sitting heads of state and rebel leaders during active armed conflict has radically altered the debate surrounding international justice. Despite the view now widely held that peace and justice are complementary rather than competing values, conflicts in the former Yugoslavia, Sudan, Libya, and Syria have brought home the reality that there are still significant barriers to achieving both peace and justice simultaneously, and that the prospects for enforcing justice are weak when perpetrators of atrocities remain powerful at home. Leading advocacy organizations and the ICC stress the role of international justice in delivering results, especially peace, the rule of law, and stability. This chapter discusses the shift in international justice advocacy from a principle or duty-based logic to one that is results-based. It argues that one way to promote justice may be to postpone it (e.g. through sequencing).
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Kobayashi, Bruce. Economics of Litigation. Edited by Francesco Parisi. Oxford University Press, 2017. http://dx.doi.org/10.1093/oxfordhb/9780199684250.013.006.
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This chapter examines the basic model of the law and economics of litigation, focusing on private civil litigation, in particular the litigation value of a lawsuit and the incentives for filing a suit. It begins with the one-stage single plaintiff/single defendant investment model of litigation, and describes the conditions for filing, default, settlement, and litigation. It examines the effects of litigation cost- and fee-shifting and the effects of percentage contingency fee arrangements within the standard one-stage model. The model is modified to take into account sequencing and option value. It is shown how litigation with multiple stages and the revelation of information alter the investment value of litigation, and the effects of litigation reform proposals such as fee-shifting. The chapter discusses third party or external effects and how these complications affect the outcome of litigation, the viability of a lawsuit, and the predictions of the standard model of litigation.
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Ramaswamy, Vijay, Jason T. Huse, and Yasmin Khakoo. Pediatric Brain Tumors. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780199937837.003.0140.
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Cerebellar astrocytoma of childhood most commonly refers to cerebellar pilocytic astrocytoma, a World health Organization (WHO) Grade I tumor. However, on occasion cerebellar astrocytomas may demonstrate more aggressive histology including fibrillary astrocytomas, pilomyxoid astrocytomas, and rarely malignant lesions. In the near future, the diagnosis of cerebellar astrocytomas will be simplified by molecular analysis for BRAF fusions rather than a purely morphological approach. The emergence of next-generation sequencing can be expected to identify single nucleotide variations and further expand our understanding of both pilocytic astrocytomas as well as rare variants that occur in the cerebellum. Therapies targeting BRAF (B-raf protooncogene) are currently in clinical trial for adult malignancies and will eventually reach the pediatric population, allowing a targeted approach to recurrent and surgically inaccessible cases of pilocytic astrocytomas.
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Pont Evksinskiy – 2021 : materials of XII All-Russian scientific and applied conference for young scientists on the water systems problems, dedicated to the 150 th anniversary of the Sevastopol Biological Station ‒ A. O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Sevastopol, 20–24 September, 2021. IBSS, 2021. http://dx.doi.org/10.21072/978-5-6044865-8-0.
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The book includes materials of young scientists from Russia and the Republic of Abkhazia, revealing various aspects of modern marine and freshwater biology. Abstracts highlight the results of scientific research in the field of population dynamics and genetic differentiation of aquatic organisms, the features of their life cycle. The book present works on the influence of abiotic and anthropogenic environmental factors on the physiological status of aquaculture species. A number of works describes the capabilities of modern research methods applied in marine and freshwater biological studies, such as metabarcoding, "frame" and "rake method" for detecting beach debris, NGS sequencing, and satellite monitoring. In addition, the book reveals the features of the functioning of coastal ecosystems. The book is valuable for young scientists in the field of marine and freshwater biology, water ecology, biotechnology, aquaculture, marine ecology and zoology
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Traynor, Bryan J., and Adriano Chiò. Genetic counselling: Psychological impact and concerns. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198757726.003.0006.
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Genetic counselling is the process by which the patients or relatives at risk of an inherited disorder are advised of the consequences and nature of the disorder, the probability of developing or transmitting it, and the options open to them in clinical management of their disease and family planning. Genetic counselling centres on helping patients understand the implications of their genetic test results. Advances in sequencing technology are changing the scope and practice of genetic counselling. It is likely that the role of genomics in clinical medicine will continue to grow over the next decade, and may eventually dominate the practice of health care. Genetic counselling is an increasingly important aspect in the clinical care of patients diagnosed with amyotrophic lateral sclerosis due to rapid advances in our understanding of the underlying genetics of this disorder.
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de Koning, Tom J. Serine Deficiency. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780199972135.003.0023.
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Serine deficiency is a rare cause of intractable seizures and severe psychomotor retardation in infants and young children. However, in recent years it has become clear that serine deficiency in adolescents and adults can give rise to milder forms of seizure disorders and mild mental retardation or to a phenotype with severe progressive polyneuropathy. Serine deficiency can be diagnosed on the basis of low values of serine in plasma and CSF using routine amino acid analysis. However, with the introduction of next generation sequencing in clinical diagnostics the majority of patients are diagnosed through molecular testing of the three genes of the synthesis pathway. L-serine therapy is highly effective in the treatment of seizures and improvement of wellbeing and daily activities. Early diagnosis and timely treatment are important to prevent irreversible damage to the central or peripheral nervous system.
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Chaudhry, Bill, José Luis de la Pompa, and Nadia Mercader. The zebrafish as a model for cardiac development and regeneration. Edited by José Maria Pérez-Pomares, Robert G. Kelly, Maurice van den Hoff, José Luis de la Pompa, David Sedmera, Cristina Basso, and Deborah Henderson. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198757269.003.0029.
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The zebrafish has become an established laboratory model for developmental studies and is increasingly used to model aspects of human development and disease. However, reviewers and grant funding bodies continue to speculate on the utility of this Himalayan minnow. In this chapter we explain the similarities and differences between the heart from this distantly related vertebrate and the mammalian heart, in order to reveal the common fundamental processes and to prevent misleading extrapolations. We provide an overview of zebrafish including their husbandry, development, peculiarities of their genome, and technological advances, which make them a highly tractable laboratory model for heart development and disease. We discuss the controversies around morphants and mutants, and relate the development and structures of the zebrafish heart to mammalian counterparts. Finally, we give an overview of regeneration in the zebrafish heart and speculate on the role of the model organism in next-generation sequencing technologies.
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Bliss, Catherine. A Sociogenomic World. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780190465285.003.0006.
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This chapter discusses a paradigm shift in the genomic sciences wherein scientists have gone from ignoring race to studying it. It argues that the field has adopted a sociogenomic approach to race, in which scientists understand race as a muddled mix of genetic and social factors. Scientists responsible for seminal genome projects, who have faced pressure from the US public health establishment and an array of experts on race, now prioritize race-targeted research, minority recruitment, and analysis of genomic health disparities. As a result large-scale sequencing projects, pharmaceuticals, and postgenomic research have become ever more racialized, while race has taken on an irrevocably genomic imprimatur. This paradigm shift has occurred because of changes across a number of powerful social domains of expertise within science, medicine, and policy. This chapter thus draws upon events taking place in a variety of institutional, regulatory, and normative contexts.
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Goldman, David, Zhifeng Zhou, and Colin Hodgkinson. The Genetic Basis of Addictive Disorders. Edited by Dennis S. Charney, Eric J. Nestler, Pamela Sklar, and Joseph D. Buxbaum. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780190681425.003.0042.
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Addictive disorders are moderately to highly heritable, indicating that alleles transmitted from parents are protective, or enhance risk by whatever mechanisms. However, the inheritance of addictive disorders is complex, involving hundreds of genes and variants that are both common and rare, and that vary in effect size and context of action. Genes altering risk for addictions have been identified by pathway and candidate gene studies in humans and model organisms, and genomic approaches including genome-wide association, meiotic linkage, and sequencing. Genes responsible for shared liability to different addictive disorders have been identified, as well as genes that are relatively specific in altering risk of addiction to one agent. An impediment to overarching conclusions is that most of the heritability of addictions is unexplained at the level of gene or functional locus. However, new analytic approaches and tools have created new potentials for resolution of the “missing heritability.”
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Camilletti, Elena, and Prerna Banati. Making Strategic Investments in Adolescent Well-Being. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780190847128.003.0015.
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Investing in young people is crucial to achieve inclusive development and uphold human rights. Adolescence is a unique window of opportunity whereby countries can benefit from investing in their educated, healthy, and gainfully employed young people. Evidence is needed to support how interventions are selected, implemented, and scaled up in developing countries. When nested within human rights–based policy efforts, economic appraisals such as cost–benefit and cost-effectiveness analyses can support policymakers in formulating decisions on the types and extents of investments in adolescents and in sequencing interventions while moving toward the full realization of their rights. This chapter discusses key literature on cost analyses on investments in adolescents in low- and middle-income countries in six intervention areas: education, health, violence, child marriage, child labor, and multisectoral analyses. Evidence and information gaps are then suggested, and the importance of integrating cost analyses into human rights–based approaches to development is considered.
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Renner, Tanya, Tianying Lan, Kimberly M. Farr, Enrique Ibarra-Laclette, Luis Herrera-Estrella, Stephan C. Schuster, Mitsuyasu Hasebe, Kenji Fukushima, and Victor A. Albert. Carnivorous plant genomes. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198779841.003.0011.
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Carnivorous plant genome research has focused on members of the Lamiales and Oxalidales; the most complete sequences are for Utricularia gibba and Cephalotus follicularis. The size-limited U. gibba genome highlights the importance of small-scale tandem duplications, which likely play roles in this species’ carnivorous adaptation. Sequencing of the C. follicularis genome detected adaptive changes that may explain the evolution of traits associated with attraction, trapping, digestion, and absorption. Functional consequences of genes putatively missing in the U. gibba genome, yet present in other angiosperms, may have influenced the evolution of polyploidy, physiology, and a rootless Bauplan. Additional draft nuclear genomes and transcriptomes are available for carnivorous Caryophyllales, Ericales, Lamiales, and Poales, but are limited in quantity and quality. Chloroplast genomes of carnivorous Lentibulariaceae have revealed interesting patterns of gene loss, alterations in the proportion of repeat DNA, and plastome-wide increases in substitution rates.
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Taberlet, Pierre, Aurélie Bonin, Lucie Zinger, and Eric Coissac. Diet analysis. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198767220.003.0017.
Full textAbstract:
Chapter 17 “Diet analysis” focuses on the specificities of DNA metabarcoding in the context of diet analyses. It presents the proof-of-concept study, which examined the diet of several herbivore species using next-generation sequencing for the first time. Chapter 17 reports how DNA-based analysis of bison diet helped evaluate the effect of conservation policies in a protected area. The different strategies aiming at disentangling predator and prey sequences in carnivorous diets are reviewed, including the use of a blocking oligonucleotide. Using bear diet as a study case, the issues associated with omnivorous diets are discussed, particularly that of integrating several diet components. Finally, Chapter 17 develops several important methodological and experimental factors to consider in eDNA-based diet analyses. These comprise the source of eDNA, the quantitative aspects, and the use of diet as a proxy of surrounding biodiversity (e.g., as in the case of invertebrate samplers).
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Taberlet, Pierre, Aurélie Bonin, Lucie Zinger, and Eric Coissac. DNA amplification and multiplexing. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198767220.003.0006.
Full textAbstract:
After a brief reminder of the principles underlying the polymerase chain reaction (PCR), Chapter 6 “DNA amplification and multiplexing” discusses the choice of a DNA polymerase for the PCR. In particular, it warns against the use of proofreading polymerases, that can lead to a substantial loss of PCR specificity. Chapter 6 insists on the benefits of including different types of controls in the PCR (e.g., PCR negatives and positives, tagging system controls, etc.). The most common causes of PCR failures and their solutions are addressed, as well as the precautions to take to avoid and monitor contaminations. Chapter 6 also deals with the particular case of blocking oligonucleotides, which aim at reducing the amplification of undesired sequences. It gives some valuable guidelines to design such oligonucleotides and use them efficiently. Finally, Chapter 6 presents different strategies for tagging individual samples during the amplification, to allow subsequent multiplexing during the sequencing step.
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Forsyth, Rob, and Richard Newton. Neurodiagnostic tools. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780198784449.003.0002.
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This chapter explains the principles of how best to use the main diagnostic tools in paediatric neurology in the context of evidence-based medicine. The description of neuroradiology includes the principles of DWI, SWI, MRS, ASL and fMRI, and the usefulness of ultrasound, CT and PET scanning; neuroradiological anatomy, terminology, common incidental findings and normal myelination patterns. An approach to white matter and developmental brain abnormalities is depicted. Neurogenetic testing discusses the capabilities and limitations of microarray for Comparative Genomic Hybridization (copy-number variants), gene panel testing, and whole exome and whole genome next generation sequencing. The chapter offers the theory, practicality and pitfalls of electroencephalography, peripheral neurophysiology and evoked potential testing. Common practical procedures are described, including lumbar puncture, muscle biopsy and shunt tapping with an understanding of the place of special investigations on CSF, blood, urine, and skin. The scope of neuropsychological testing is described.
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Bijankhan, Mahmood. Phonology. Edited by Anousha Sedighi and Pouneh Shabani-Jadidi. Oxford University Press, 2018. http://dx.doi.org/10.1093/oxfordhb/9780198736745.013.5.
Full textAbstract:
This chapter reviews the organization of sounds in the contemporary Persian language and discusses the issues in phoneme inventory, syllable structure, distinctive features, phonological rules, rule interaction, and prosodic structure according to the framework of the derivational phonology. Laryngeal states responsible for contrast in pairs of homorganic stops and fricatives are different in Persian. Phonological status of continuancy is controversial for the uvular obstruent. Glottal stop is distinctive at the beginning of loan-words while not at the beginning of the original Persian words. Phonotactic constraints within the codas of the syllables violate the sonority sequencing principle. Glottals are moraic in the coda position. Feature geometry is posited on the sound distinctions and patterns within phonological processes. Eleven phonological rules are explained to suggest natural classes. Interaction of some rules is derived. Laryngeal conspiracy, syllable structure, and intersegmental processes are analysed according to interaction of ranked violable constraints of optimality theory.
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Barker, Richard. The accelerating pace of biomedical advance. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780198737780.003.0002.
Full textAbstract:
Bioscience has progressed exponentially, in scientific advances and enabling technology. From quicker and much cheaper gene sequencing to the emergence of data-mining tools, the last 20 years has been unprecedented in exploitable advances brought by research. We have the tools and insights to trace disease from underlying genetics and epigenetics, through proteins that represent intervention options, to ways to create molecules, diagnostics, and devices based on those insights. The life sciences enterprise, once largely confined to Europe, the USA, and Japan, is now seeing major investment from emerging economies. We should be poised to reap the benefits of this rising tide of research with lives transformed and health systems revolutionized. However, the two million biological science papers published annully results in about 14 000 patents, only 5000 drugs in the pipeline, and a mere 30 or so actual medicines. Translation of life sciences research into usable products is hugely inefficient.
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Lurie, Peter. Queer Historiography in The Bridge. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780199797318.003.0005.
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This chapter culminates my earlier discussion of several works’ regretful looks back on U.S. history with Hart Crane’s plaintive lament over the country’s signal historical events, tempered by his hopefulness for the republic’s future. It uses sexuality theory to argue against a teleological, progressive sequencing—both in my study’s rhetorical structure and in ways of tracing history’s unfolding. It suggests the importance of textual erotics of painful empathy in the reader’s encounter with an indigenous past in its early sections, before turning to in The Bridge’s critique of U.S. aerial history and maritime trade. The poem’s account of displaced historical subjects encompasses this alterity in the figure of its peripatetic speaker across its several sections and historical eras. The chapter ends with a coda about Crane’s suicide as a response to his New Critical peers’ rejection of his nonironic, non-Eliotonian vision and of what they saw as his “undisciplined” style and sexuality.
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Purves, Alex. Homer and the Poetics of Gesture. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780190857929.001.0001.
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This book offers five readings of the Homeric poems through five different postures, actions, or gestures: falling, running, leaping, standing, and reaching. It argues for a connection between formularity and embodiment in Homeric epic by tracing, in each chapter, the story of a particular gesture through one or both of the poems. In doing so, it presents a new understanding of what the body does and suffers in Homer alongside original readings and arguments about the structure and meaning of the poems themselves. It revises our understanding of formula and type scenes in the Iliad and Odyssey by reading repetition through the body, identifying a relationship between familiar epic movements—learned through repetition, reinforced by muscle memory, and culturally engrained—and the verbal formulas through which many of the movements are conveyed. As a result, the book suggests a different way of thinking about epic repetition, both insofar as it relates to the sequencing of action through time, and in relation to the autonomy and agency of the Homeric body and its role within the narrative.
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Pezzella, Francesco, Mahvash Tavassoli, and David J. Kerr, eds. Oxford Textbook of Cancer Biology. Oxford University Press, 2019. http://dx.doi.org/10.1093/med/9780198779452.001.0001.
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The study of the biology of tumours has grown to become markedly interdisciplinary, involving chemists, statisticians, epidemiologists, mathematicians, bioinformaticians, and computer scientists alongside medical scientists. Oxford Textbook of Cancer Biology brings together the developments from different branches of research into one volume. Structured in seven sections, the book starts with a review of the development and biology of multicellular organisms, how they maintain a healthy homeostasis in an individual, and a description of the molecular basis of cancer development. The book then illustrates how, once cells become neoplastic, their signalling network is altered and pathological behaviour follows. Changes that cancer cells can induce in nearby normal tissue are explored, and the new relationship established between them and the stroma is explicated. Finally, the authors illustrate the contribution provided by high throughput techniques to map cancer at different levels, from genomic sequencing to cellular metabolic functions, and how information technology with its vast amounts of data are integrated with traditional cell biology to provide a global view of the disease. The book concludes by summarizing what we know to date about cancer, and in what direction our understanding of cancer is moving.
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Bensimon, David, Vincent Croquette, Jean-François Allemand, Xavier Michalet, and Terence Strick. Single-Molecule Studies of Nucleic Acids and Their Proteins. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198530923.001.0001.
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This book presents a comprehensive overview of the foundations of single-molecule studies, based on manipulation of the molecules and observation of these with fluorescent probes. It first discusses the forces present at the single-molecule scale, the methods to manipulate them, and their pros and cons. It goes on to present an introduction to single-molecule fluorescent studies based on a quantum description of absorption and emission of radiation due to Einstein. Various considerations in the study of single molecules are introduced (including signal to noise, non-radiative decay, triplet states, etc.) and some novel super-resolution methods are sketched. The elastic and dynamic properties of polymers, their relation to experiments on DNA and RNA, and the structural transitions observed in those molecules upon stretching, twisting, and unzipping are presented. The use of these single-molecule approaches for the investigation of DNA–protein interactions is highlighted via the study of DNA and RNA polymerases, helicases, and topoisomerases. Beyond the confirmation of expected mechanisms (e.g., the relaxation of DNA torsion by topoisomerases in quantized steps) and the discovery of unexpected ones (e.g., strand-switching by helicases, DNA scrunching by RNA polymerases, and chiral discrimination by bacterial topoII), these approaches have also fostered novel (third generation) sequencing technologies.
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Robert F, Williams. The Law of American State Constitutions. Oxford University Press, 2009. http://dx.doi.org/10.1093/acprof:oso/9780195343083.001.0001.
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This book provides complete coverage of American State Constitutional Law. It contrasts the more familiar federal Constitution and explains the importance of the differences. The book then surveys the state constitutions put in place before the adoption of the federal Constitution, together with their influences on the development of the federal Constitution. Next, it describes the broad outlines of state constitutions' evolution over the centuries, as well as the limits placed on state constitutions by federal law. Next, the book covers the growth of the New Judicial Federalism (state constitutions providing, or being interpreted to provide, more protective rights than the federal Constitution). This includes a variety of methodology issues arising in cases raising both federal and state constitutional rights arguments, such as the sequencing of arguments and development of criteria for recognizing rights beyond the federal minimum standards. The technique of interpreting state constitutional rights in “lockstep” with federal rights is analyzed and criticized. State constitutional separation or distribution of powers is discussed and contrasted with the federal doctrines. The book then explains and illustrates the unique features of each of the three branches of state governments. The book analyzes the specialized techniques of judicial interpretation applied to state constitutions. Finally, it surveys the mechanisms of state constitutional amendment and revision, together with the extensive judicial involvement in these processes.
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Jalloh, Charles Chernor, and Ilias Bantekas, eds. The International Criminal Court and Africa. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780198810568.001.0001.
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Africa has been at the forefront of contemporary global efforts towards ensuring greater accountability for international crimes. But the continent’s early embrace of international criminal justice seems to be taking a new turn with the recent pushback from some African states claiming that the emerging system of international criminal law represents a new form of imperialism masquerading as international rule of law. This work analyses the relationship and tensions between the International Criminal Court (ICC) and Africa. It traces the origins of the confrontation between African governments, acting individually or within the framework of the African Union, and the permanent Hague-based ICC. Topics examined include Africa, the ICC, and universal jurisdiction; the controversial use of the prosecutor’s proprio motu power to initiate investigations in Africa; national implementation of the ICC statute in Africa; the complementarity principle; the sequencing of justice and peace; the question of immunity of sitting heads of state; the controversial role of the UN Security Council in referring and deferring situations under ICC investigation; the role of African domestic and traditional courts in the fight against impunity as well as the recent withdrawal of some African states parties from the ICC. Leading commentators offer valuable insights on the core legal and political issues that have bedevilled the relationship between the two sides and expose the uneasy interaction between international law and international politics.
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Vaheri, Antti, James N. Mills, Christina F. Spiropoulou, and Brian Hjelle. Hantaviruses. Oxford University Press, 2011. http://dx.doi.org/10.1093/med/9780198570028.003.0035.
Full textAbstract:
Hantaviruses (genus Hantavirus, family Bunyaviridae) are rodent- and insectivore-borne zoonotic viruses. Several hantaviruses are human pathogens, some with 10-35% mortality, and cause two diseases: hemorrhagic fever with renal syndrome (HFRS) in Eurasia, and hantavirus cardiopulmonary syndrome (HCPS) in the Americas. Hantaviruses are enveloped and have a three-segmented, single-stranded, negative-sense RNA genome. The L gene encodes an RNA-dependent RNA polymerase, the M gene encodes two glycoproteins (Gn and Gc), and the S gene encodes a nucleocapsid protein. In addition, the S genes of some hantaviruses have an NSs open reading frame that can act as an interferon antagonist. Similarities between phylogenies have suggested ancient codivergence of the viruses and their hosts to many authors, but increasing evidence for frequent, recent host switching and local adaptation has led to questioning of this model. Infected rodents establish persistent infections with little or no effect on the host. Humans are infected from aerosols of rodent excreta, direct contact of broken skin or mucous membranes with infectious virus, or rodent bite. One hantavirus, Andes virus, is unique in that it is known to be transmitted from person-to-person. HFRS and HCPS, although primarily affecting kidneys and lungs, respectively, share a number of clinical features, such as capillary leakage, TNF-, and thrombocytopenia; notably, hemorrhages and alterations in renal function also occur in HCPS and cardiac and pulmonary involvement are not rare in HFRS. Of the four structural proteins, both in humoral and cellular immunity, the nucleocapsid protein appears to be the principal immunogen. Cytotoxic T-lymphocyte responses are seen in both HFRS and HCPS and may be important for both protective immunity and pathogenesis. Diagnosis is mainly based on detection of IgM antibodies although viral RNA (vRNA) may be readily, although not invariably, detected in blood, urine and saliva. For sero/genotyping neutralization tests/RNA sequencing are required. Formalin-inactivated vaccines have been widely used in China and Korea but not outside Asia. Hantaviruses are prime examples of emerging and re-emerging infections and, given the limited number of rodents and insectivores thus far studied, it is likely that many new hantaviruses will be detected in the near future.
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Kirchman, David L. Community structure of microbes in natural environments. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198789406.003.0004.
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Community structure refers to the taxonomic types of microbes and their relative abundance in an environment. This chapter focuses on bacteria with a few words about fungi; protists and viruses are discussed in Chapters 9 and 10. Traditional methods for identifying microbes rely on biochemical testing of phenotype observable in the laboratory. Even for cultivated microbes and larger organisms, the traditional, phenotype approach has been replaced by comparing sequences of specific genes, those for 16S rRNA (archaea and bacteria) or 18S rRNA (microbial eukaryotes). Cultivation-independent approaches based on 16S rRNA gene sequencing have revealed that natural microbial communities have a few abundant types and many rare ones. These organisms differ substantially from those that can be grown in the laboratory using cultivation-dependent approaches. The abundant types of microbes found in soils, freshwater lakes, and oceans all differ. Once thought to be confined to extreme habitats, Archaea are now known to occur everywhere, but are particularly abundant in the deep ocean, where they make up as much as 50% of the total microbial abundance. Dispersal of bacteria and other small microbes is thought to be easy, leading to the Bass Becking hypothesis that “everything is everywhere, but the environment selects.” Among several factors known to affect community structure, salinity and temperature are very important, as is pH especially in soils. In addition to bottom-up factors, both top-down factors, grazing and viral lysis, also shape community structure. According to the Kill the Winner hypothesis, viruses select for fast-growing types, allowing slower growing defensive specialists to survive. Cultivation-independent approaches indicate that fungi are more diverse than previously appreciated, but they are less diverse than bacteria, especially in aquatic habitats. The community structure of fungi is affected by many of the same factors shaping bacterial community structure, but the dispersal of fungi is more limited than that of bacteria. The chapter ends with a discussion about the relationship between community structure and biogeochemical processes. The value of community structure information varies with the process and the degree of metabolic redundancy among the community members for the process.