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This volume provides comprehensive dry and wet experiments, methods, and applications on nanopore sequencing. Chapters guide readers through bioinformatic procedures, genome sequencing, analysis of repetitive regions, structural variations, rapid and on-site microbial identification, epidemiology, and transcriptome analysis. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Nanopore Sequencing: Methods and Protocols aims to be comprehensive guide for researchers.
This is an introductory text and laboratory manual to be used primarily in undergraduate courses. It is also useful for graduate students and research scientists who require an introduction to the theory and methods of nanopore sequencing. The book has clear explanations of the principles of this emerging technology, together with instructional material written by experts that describes how to use a MinION nanopore instrument for sequencing in research or the classroom.At Harvard University the book serves as a textbook and lab manual for a university laboratory course designed to intensify the intellectual experience of incoming undergraduates while exploring biology as a field of concentration. Nanopore sequencing is an ideal topic as a path to encourage students about the range of courses they will take in Biology by pre-emptively addressing the complaint about having to take a course in Physics or Maths while majoring in Biology. The book addresses this complaint by concretely demonstrating the range of topics — from electricity to biochemistry, protein structure, molecular engineering, and informatics — that a student will have to master in subsequent courses if he or she is to become a scientist who truly understands what his or her biology instrument is measuring when investigating biological phenomena.
Viral infections in animals occasionally develop potentially fatal diseases that affect almost all organs. Especially in zoonotic diseases, the causative agents that usually exist in animals can be transmitted between animal species to humans directly or via a vector. Throughout recent history, disease outbreaks and pandemics including SARS, H7N9, Ebola, and COVID-19, have led to a dramatic loss of human life worldwide and harmed economic growth. The most effective strategies for the control of disease are vaccination and early diagnosis. Vaccines directed against viral and bacterial pathogens prevent catastrophic losses of life in humans, other animals, and plants, and are considered among the greatest public health achievements. Rapid and accurate detection of pathogens and identification of the aetiologic agent play a crucial role at every step of disease management. In the case of zoonotic illnesses, early detection of wildlife aids in the establishment of a surveillance system, allowing for the introduction of efficient and timely disease control interventions to prevent transmission from animal to human. At present, variations and deletions in the genome of the virus are of common occurrence during evolution, coupled with the new emerging disease and cross-species disease transmission, which are increasing the potential for the transmissibility and severity of the disease. For this reason, developing safe and effective vaccines, and enhancing the sensitivity and specificity of the diagnostic methods are urgently required. The scope of this research topic will share and discuss findings in the areas of diagnosis of viral diseases or vaccine development for all animal species, including terrestrial and aquatic mammals, fishes, insects, birds, etc.
In this book, the latest tools available for functional metagenomics research are described.This research enables scientists to directly access the genomes from diverse microbial genomes at one time and study these “metagenomes”. Using the modern tools of genome sequencing and cloning, researchers have now been able to harness this astounding metagenomic diversity to understand and exploit the diverse functions of microorganisms. Leading scientists from around the world demonstrate how these approaches have been applied in many different settings, including aquatic and terrestrial habitats, microbiomes, and many more environments. This is a highly informative and carefully presented book, providing microbiologists with a summary of the latest functional metagenomics literature on all specific habitats.
This book provides insights into the current state of sorghum genomics. It particularly focuses on the tools and strategies employed in genome sequencing and analysis, public and private genomic resources and how all this information is leading to direct outcomes for plant breeders. The advent of affordable whole genome sequencing in combination with existing cereal functional genomics data has enabled the leveraging of the significant novel diversity available in sorghum, the genome of which was fully sequenced in 2009, providing an unmatched resource for the genetic improvement of sorghum and other grass species. Cultivated grain sorghum is a food and feed cereal crop adapted to hot and dry climates, and is a staple for 500 million of the world’s poorest people. Globally, sorghum is also an important source of animal feed and forage, an emerging biofuel crop and model for C4 grasses, particularly genetically complex sugarcane.
This issue of Clinics in Laboratory Medicine, guest edited by Drs. Nicole D. Pecora and Matthew Pettengill, will cover Current Issues in Clinical Microbiology. This issue is one of four selected each year by our Editor-in-Chief, Dr. Milenko Jovan Tanasijevic. Topics discussed in this issue will include: Update in Diagnostics of Bloodstream Infections, Panels and Syndromic Testing in Clinical Microbiology, Lab Consolidation and Centralization, Update in Susceptibility Testing: Phenotypic and Genotypic Methods, Genomics in the Clinical Microbiology Laboratory, Automation in the Clinical Microbiology Laboratory, Coronavirus Detection in the Clinical Microbiology Laboratory: Are We Ready for Identifying and Diagnosing a Novel Strain?, Update on Biosafety and Emerging Infections for the Clinical Microbiology Lab, Update in Clinical Mycology, Point of Care Testing in Microbiology, Pediatric Diagnostic Microbiology, Antimicrobial Stewardship: What the Clinical Laboratory Needs to Know, Fellowship Training for the Future Clinical Microbiology Laboratory Director, Update in Diagnostics/Susceptibility of Mycobacterial Diseases, Role of the Clinical Microbiology Lab in One Health, Update in Infectious Disease Diagnosis in Surgical Pathology, and more.
Probabilistic models are becoming increasingly important in analysing the huge amount of data being produced by large-scale DNA-sequencing efforts such as the Human Genome Project. For example, hidden Markov models are used for analysing biological sequences, linguistic-grammar-based probabilistic models for identifying RNA secondary structure, and probabilistic evolutionary models for inferring phylogenies of sequences from different organisms. This book gives a unified, up-to-date and self-contained account, with a Bayesian slant, of such methods, and more generally to probabilistic methods of sequence analysis. Written by an interdisciplinary team of authors, it aims to be accessible to molecular biologists, computer scientists, and mathematicians with no formal knowledge of the other fields, and at the same time present the state-of-the-art in this new and highly important field.