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Chapter 14 - Applying enzymatic biomarkers of the in situ microbial community to assess the risk of coastal sediment
Elisamara Sabadini-Santos, Vanessa de Almeida Moreira, Angelo Cezar Borges de Carvalho, Juliana Ribeiro Nascimento, Jose V. Lopez, Luiz Francisco Fontana, Ana Elisa Fonseca Silveira, and Edison Dausacker Bidone
[Chapter Abstract] This study applied the Quality Ratio (QR) index to integrate geochemical (TOC, fine grain content, and metal concentrations) and microbiological (Esterases (EST) and Dehydrogenase (DHA) activities of the in situ microbial community) parameters in order to classify the potential ecological risk of coastal sediments in dredging activities. Total concentrations (C) of Hg, Cd, As, Pb, Cr, Cu, and Zn (indicators of the complex mixture of contaminants in sediments) were determined in sediments inside Guanabara and Sepetiba bays (Rio de Janeiro, Brazil) and in oceanic dump sites outside the bays (C0) to calculate the contamination factor (CF = C/C0) and the degree of contamination (ΣCF). Likewise, DHA and EST activities were determined—respectively, biomarkers of energy production in the cell and hydrolase of organic matter outside the cell—which are altered under adverse conditions (e.g., contamination). The QR, a function of the microbial term DHA/EST and the geochemical term (TOC × ΣCF)/fine-grained content, was able to classify the sediments into three classes of risk: low (QR ≥ 10− 1), moderate (10− 2 ≤ QR < 10− 1), and high (QR ≥ 10− 3). The QR was able to segregate the hot spots of contamination of the bays. The QR was also applied to an acute assay and successfully identified the microbial community shift under a contamination gradient when mixing with dredged sediments. Thus QR provides an accessible (low cost and fast) and efficient alternative for assessing both the quality of coastal sediments and the ex situ bioassays, as required by Brazilian legislation for dredging sediments, as well as for other developing countries.
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RNA-seq Data Analysis for Differential Expression
Navdeep Gill and Braham Dhillon
Changes in the surrounding environment are mirrored by changes in the transcript profile of an organism. In the case of a plant pathogen, host colonization would be a challenge that triggers changes in transcript expression patterns. Determining the transcriptional profile could provide valuable clues on how an organism responds to defined stimuli, in this case, how a pathogen colonizes its host. Several robust data analysis methods and pipelines are available that can identify these differentially expressed transcripts. In this chapter we outline the steps and other caveats that are needed to run one such pipeline.
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Biology 1500 Laboratory Manual
Jane Nyugen, Drew W. Mertzlufft, Sarah G. Koerner, Kevin Corneille, Aarti Raja, and Emily Schmitt
2nd Edition
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Chapter One - The mechanisms and cell signaling pathways of programmed cell death in the bacterial world
Robert Smith, Ivana Barraza, Rebecca J. Quinn, and Marla Fortoul
While programmed cell death was once thought to be exclusive to eukaryotic cells, there are now abundant examples of well regulated cell death mechanisms in bacteria. The mechanisms by which bacteria undergo programmed cell death are diverse, and range from the use of toxin-antitoxin systems, to prophage-driven cell lysis. Moreover, some bacteria have learned how to coopt programmed cell death systems in competing bacteria. Interestingly, many of the potential reasons as to why bacteria undergo programmed cell death may parallel those observed in eukaryotic cells, and may be altruistic in nature. These include protection against infection, recycling of nutrients, to ensure correct morphological development, and in response to stressors. In the following chapter, we discuss the molecular and signaling mechanisms by which bacteria undergo programmed cell death. We conclude by discussing the current open questions in this expanding field.
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Impacts of the COVID-19 Pandemic on Global Education
Santanu De
Coronavirus Infectious Disease 2019 (COVID-19) has been one of the most dreaded, recent pandemics impacting multifarious global sectors, including education. To control contagion, affected nations ordered academic campus closures and home-schooling plans. Schools, colleges, and universities underwent a paradigm shift adopting internet-based delivery of lectures, synchronously or asynchronously (recorded), with virtual labs. Medical education suffered significantly; suspending student internships in hospitals decreased practical exposure to clinical specialties, impairing students’ performance, and competency.Teachers of traditional classes, with technical assistance, undertook rigorous trainings to restructure pedagogical and assessment strategies online using web/mobile applications and other digital tools.
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Atlas of Mammalian Chromosomes
Stephen James O'Brien, Alexander S. Graphodatsky, and Polina L. Perelman
Filled with a visually exquisite collection of the banded metaphase chromosome karyotypes from some 1,000 species of mammals, the Atlas of Mammalian Chromosomes offers an unabridged compendium of the state of this genomic art form. The Atlas??contains the best karyotype produced, the common and Latin name of the species, the published citation, and identifies the contributing authors. Nearly all karyotypes are G-banded, revealing the chromosomal bar codes of homologous segments among related species. The Atlas brings together information from a range of cytogenetic literature and features high-quality karyotype images for nearly every mammal studied to date.
When the Atlas was first published, only three mammals were sequenced. Today, that number is over 300. Now in its second edition, this book contains extensive revisions and major additions such as new karyotypes that employ G- and C- banding to represent euchromatin and heterochromatin genome composition, new phylogenetic trees for each order, homology segment chromosome information on published aligned chromosome painting. Summaries of the painting data for some species indicate conserved homology segments among compared species. An invaluable resource for today's comparative genomics era, this comprehensive collection of high-resolution chromosome photographs:
- Assembles information previously scattered throughout the cytogenetics literature in one comprehensive volume
- Provides chromosome information and illustrations for the karyotypes of 300 new species
- Addresses the mandate of the Human Genome Project to annotate the genomes of other organisms
- Serves as a basis for chromosome-level genome assemblies
- Offers a detailed summation of three decades of ZooFish (chromosome painting)
- Presents high-resolution photos of karyotypes that represent more than 1,000 mammal species
Written for geneticists, mammalogists, and biologists, the Atlas of Mammalian Chromosomes offers a step forward for an understanding of species formation, of genome organization, and of DNA script for natural selection.
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After the Taxonomic Identification Phase: Addressing the Functions of Symbiotic Communities Within Marine Invertebrates
Jose Lopez
Characterizations of the identity and diversity of microbial symbiotic communities (“microbiomes”) within different sponges have advanced considerably over the last two decades. Thousands of microbes, mostly unculturable, operational taxonomic units (OTUs) have been identified through the advances of high-throughput DNA sequencing. However, in spite of compelling data pointing to bona fide symbioses between many microbes and the sponge host, determination of specific microbial symbiont functions remains difficult to pinpoint and equivocal in many cases. In this chapter, I highlight past and present approaches toward addressing the potential functions of microbial symbionts (mostly bacterial) found in marine sponges and invertebrates. In an interesting irony, one barrier to effective definition of some symbiont microbial functions stems from their obligate dependence on their host. Investigations suggest that microbes significantly contribute to fundamental processes such as elemental cycling, anabolism, and catabolism. An additional likely role for symbionts is the biosynthesis of unique secondary metabolites (SMs) and vitamins, exhibited in many sponge species. These can be used as defensive or communication factors increasing fitness and thus benefiting the holobiont, which appears more and more reminiscent of a vibrant community than the traditional notion of an individual sponge. One approach to circumvent the dearth of empirical evidence on specific symbiont functions is to apply modern -omics methods: for example, sequencing the entire sponge holobiont (host and microbiome) as a metagenome and metatranscriptome can reveal potential functional genetic information. Together with computational tools, one can infer function from biological sequence data, although rigorous experimentation is still needed for verifications. Newer combinations of older, sophisticated technologies such as fluorescence in situ hybridization-correlative light and electron microscopy (FISH-CLEM), stable isotope tracking, and nanoscale secondary ion mass spectrometry (NanoSIMS) now promise to reveal more potential symbiont functions. Metaproteomics will also help further advance the understanding of the relationships within the holobiont community, but its wide applicability still remains mostly on the horizon. Other pervasive questions on the origins, coevolution, and fitness of specific symbiont-host partners include relevant microbiome functions within their orbit.
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Chapter 8: Ancient DNA in the Study of Ancient Disease
Anne C. Stone and Andrew T. Ozga
The study of ancient disease can now include direct analyses of all or part of the genomes of pathogens through ancient DNA techniques. Such analyses are challenging since due to several factors including preservation, pathogen load and location in the body, environmental microbial contamination, and current understanding of microbial pathogenicity. When successful, ancient DNA analyses have provided insight into the evolutionary history of a number of human and animal pathogens. In addition, recent microbiome analyses have shed light on how cultural and environmental changes have altered microbial profiles across the human body and impacted host health. In this chapter, we summarize the history and current state of the field as well as posit future directions for research associated with the study of ancient disease.
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Chapter 6: Genetic and Microscopic Analysis of Human Dental Calculus from Swift Water Place
Christina Warinner, Andrew T. Ozga, Anita Radini, Krithivasan Sankaranarayanan, and Cecil M. Lewis Jr.
Full Book Description: This is a multidisciplinary study of the early contact period of Alaskan Native history that follows a major hunting and fishing Inupiaq group at a time of momentous change in their lifeways. The Amilgaqtau yaagmiut were the most powerful group in the Kobuk River area. But their status was forever transformed thanks to two major factors. They faced a food shortage prompted by the decline in caribou, one of their major foods. This was also the time when European and Asian trade items were first introduced into their traditional society. The first trade items to arrive, a decade ahead of the Europeans themselves, were glass beads and pieces of metal that the Inupiat expertly incorporated into their traditional implements. This book integrates ethnohistoric, bio-anthropological, archaeological, and oral historical analyses.
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The Hawk-Dove Model
Omar T. Eldakar
This Encyclopedia provides a comprehensive overview of individual differences within the domain of personality, with major sub-topics including assessment and research design, taxonomy, biological factors, evolutionary evidence, motivation, cognition and emotion, as well as gender differences, cultural considerations, and personality disorders. It is an up-to-date reference for this increasingly important area and a key resource for those who study intelligence, personality, motivation, aptitude and their variations within members of a group.
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Feralisation - The Understudied Counterpoint to Domestication
R. Henriksen, Eben Gering, and Dominic Wright
Feralisation is a complex process that occurs when a domestic population is returned to the wild. It impacts species invasion biology, speciation, conservation and hybridisation and can be thought of as the reverse of domestication. Domestication has been an area of intense interest and study ever since Darwin, and useful as a model for evolution and the effects of strong directional selection. Despite domestication being used to study genes affecting a large number of traits that change with selection, little is known about the genomic changes associated with feralisation. Much of the current work on the genetics of feralisation has focused on the detection of early hybrids (F1 or F2) between wild and domestic populations. Feralisation can lead to large changes in morphology, behaviour and many other traits, with the process of feralisation involving the sudden return of both natural and sexual selection. Such evolutionary forces influence predatory, foraging and male choice decisions and exert strong effects on once domesticated, now feral, individuals. As such, feralisation provides a unique opportunity to observe the genomic and phenotypic responses to selection from a known (domesticated) standpoint and identify the genes underlying these selective targets. In this review, we summarise what is known in particular regarding the genomics of feralisation, and also the changes that feralisation has induced on brain size and behaviour.
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Conclusion: DNA-Based Authentication of Shark Products and Implications for Conservation and Management
Robert H. Hanner, Amanda M. Naaum, and Mahmood Shivji
Given long generation times and relatively slow reproductive rates, elasmobranchs (sharks and rays) are particularly prone to overexploitation. The unrelenting demand for shark products is unsustainable and many shark fisheries are collapsing. Because of the urgency of addressing this situation, this book concludes with an overview of how DNA-based tools are being deployed for the identification of shark products in commercial trade and summarize the relevance of this information for conservation and management. Advances in reference sequence library construction, population-level identification methods, and instrumentation platforms, together with declining costs of conducting molecular diagnostic tests, will enhance the uptake of these tools for seafood authentication and traceability. However, as this text has demonstrated, they are already improving our ability to monitor patterns of exploitation and yield greater transparency in the industry. The results highlight the urgency of enforcing existing regulations and promoting additional measures to conserve the world's shark fisheries.
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Tissue-Specific DNA Methylation Patterns in Forensic Samples Detected by Pyrosequencing®
Joana Antunes, Kuppareddi Balamurugan, George Duncan, and Bruce McCord
In certain circumstances the outcome of a trial may hinge on the ability of a forensic laboratory to determine the identity of biological stains present at crime scenes. An example of such a situation would be the detection of blood, saliva, vaginal fluid, or other body fluid in a specific location whereby its presence would reinforce the victim’s or suspect’s version of the events that happened during the commission of a crime. However, current serological methods used for identifying body fluids may lack the sensitivity and specificity to identify these fluids, particularly for trace levels. New procedures using proteomic methods and RNA-based gene expression show promise in addressing this issue; however, concerns about stability and relative levels of gene expression remain. An alternative approach is to utilize patterns of epigenetic DNA methylation. DNA methylation is an epigenetic mechanism that regulates the specificity of genes being expressed or silenced in cells. Regions in the human genome referred to as tissue-specific differentially methylated regions account for unique patterns of DNA methylation that are specific for each cell type. This chapter addresses the application of bisulfite-modified PCR combined with Pyrosequencing® to detect tissue-specific DNA methylation patterns and perform trace serological analysis. The quantitative nature and precision available with Pyrosequencing presents major advantages in these studies as it permits detection of and contrast between cells with differential levels of methylation. The procedure can be applied to a variety of biological fluids which may be present at crime scenes.
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Group Selection
Omar T. Eldakar
This Encyclopedia is a comprehensive A-Z reference that defines sexuality from a broad biocultural perspective and show the diversity of human sexual behavior and belief systems.
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Chapter 12: Engineering Cell-to-Cell Communication to Explore Fundamental Questions in Ecology and Evolution
Robert P. Smith, Lauren Boudreau, and Lingchong You
Synthetic biology has created countless examples of gene circuits that lead to novel behavior in cells. While the technological applications of these circuits, in terms of their use in medicine, industry, and to study systems biology has been acknowledged, synthetic biology is increasingly used to explore questions in evolution and ecology. Traditionally, evolutionary and ecological studies have taken two separate approaches to address scientific questions. One traditional approach uses mathematical modeling to capture the essential aspects of the dynamic or relationship under study. Research is performed in silico, allowing the researcher to explore multiple parameters in a well-defined system, as compared to studying the relationship in its natural setting. However, predictions generated by mathematical models are often not verified experimentally, leading to questions regarding their validity. On the other hand, studying a single dynamic in a natural setting offers its own set of challenges. Here, the single dynamic of interest may be subject to multiple interacting factors, which may obscure its true contribution to the relationship under study. Synthetic biology thus offers a well-rounded intermediate between these two approaches; modeling predictions are verified in living, experimental systems. This dual approach has allowed for the study of ecological and evolutionary dynamics that would be nearly impossible to study in the natural environment. Indeed, the number of studies that have utilized synthetic biology to study such relationships is growing quickly.
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Protein 14-3-3 (YWHA) isoforms and their roles in regulating mouse oocyte maturation
Santanu De
The 14-3-3 (YWHA) is a highly conserved, ubiquitously expressed protein family regulating important cellular processes including cell cycle. This work, for the first time, explored the differential expression and roles of 14-3-3 isoforms during mouse oocyte maturation.
All seven mammalian 14-3-3 isoforms were identified in mouse eggs and ovarian follicular cells including oocytes, by Western blotting. Immunocytochemical and immunohistochemical staining confirmed the presence of all 14-3-3 isoforms in oocytes, eggs and ovarian follicles with characteristic similarities and differences in their distributions.
Mammalian oocytes are arrested at meiosis prophase I by an inhibitory phosphorylation on Cyclin-Dependent Kinase I (CDK1), released by CDC25B phosphatase which is bound and inactivated in phosphorylated form by 14-3-3 in oocyte cytoplasm. Here, in situ Proximity Ligation Assays (PLA) revealed that all 14-3-3 isoforms interact with CDC25B in oocytes, with reduced interactions in eggs. Phosphorylation of CDC25B at Ser-149 was found to be reduced in eggs compared to oocytes. Microinjection of a translation-blocking morpholino oligonucleotide against 14-3-3eta mRNA caused germinal vesicle breakdown in significantly higher percentage of oocytes compared to oocytes injected with morpholinos targeting other 14-3-3 isoforms. Thus, interaction of 14-3-3eta with CDC25B is required for maintaining prophase I arrest in oocytes.
Protein 14-3-3eta was observed to accumulate and co-localize with alpha-tubulin at both meiosis I and II spindles during mouse oocyte maturation in vivo as well as in vitro. It interacts directly with alpha-tubulin with an accumulation of the interactions at meiotic spindles, detected by in situ PLA. In a significant 76% of mouse oocytes microinjected with the morpholino against 14-3-3eta mRNA, meiotic spindles were deformed or absent with clumped chromosomes, no accumulation of 14-3-3eta and no polar body formation. All control eggs showed normal, bipolar spindles with accumulation of 14-3-3eta. Therefore, 14-3-3eta is essential for normal meiotic spindle formation during in vitro maturation of mouse oocytes, in part by interacting with alpha-tubulin, to regulate the assembly of microtubules.
These studies reveal 14-3-3 isoform-specific interactions with key proteins involved in mouse oocyte maturation, such as CDC25B and alpha-tubulin. The results help to elucidate the roles of 14-3-3 proteins in mammalian oogenesis and reproductive development. -
Chapter 12: Forensic Animal DNA Analysis
Marilyn Menotti-Raymond, Victor A. David, Stephen J. O'Brien, Sree Kanthaswamy, Petar Projic, Vedrana Skaro, Gordan Lauc, and Adrian Linacre
Forensic DNA Applications: An Interdisciplinary Perspective was developed as an outgrowth of a conference held by the International Society of Applied Biological Sciences. The topic was human genome–based applications in forensic science, anthropology, and individualized medicine. Assembling the contributions of contributors from numerous regions around the world, this volume is designed as both a textbook for forensic molecular biology students and a reference for practitioners and those in the legal system.
The book begins with the history and development of DNA typing and profiling for criminal and civil purposes. It discusses the statistical interpretation of results with case examples, mitochondrial DNA testing, Y single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs), and X SNP and STR testing. It also explores low copy number DNA typing, mixtures, and quality assurance and control.
The second section examines the collection and preservation of biological evidence under a variety of different circumstances and the identification of human remains—including in mass disaster settings. It discusses applications to bioterrorism investigations, animal DNA testing in criminal cases, pedigree questions and wildlife forensic problems, applications in forensic entomology, and forensic botany.
The third section explores recent developments and new technologies, including the rigorous identification of tissue of origin, mtDNA profiling using immobilized probe strips, chips and next-generation sequencing, the use of SNPs to ascertain phenotypic characteristics, and the "molecular autopsy" that looks at aspects of toxicogenetics and pharmacogenetics.
The book concludes with a discussion on law, ethics, and policy. It examines the use of DNA evidence in the criminal justice system in both the United States and Europe, ethical issues in forensic laboratory practices, familial searches, DNA databases, ancestry searches, physical phenotyping, and report writing. The contributors also examine DNA applications in immigration and human trafficking cases and international perspectives on DNA databases.
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Pluripotent Adult Stem Cells: A Potential Revolution in Regenerative Medicine and Tissue Engineering
Tsz Kin Ng, Daniel Pelaez, Veronica R. Fortino, Jordan Greenberg, and Herman S. Cheung
Stem cells have generated a lot of excitement among the researchers, clinicians and the public alike. Various types of stem cells are being evaluated for their regenerative potential. Marginal benefit resulting by transplanting autologus stem cells (deemed to be absolutely safe) in various clinical conditions has been proposed to be a growth factor effect rather than true regeneration. In contrast, various pre-clinical studies have been undertaken, using differentiated cells from embryonic stem cells or induced pluripotent stem cells have shown promise, functional improvement and no signs of teratoma formation. The scientists are not in a rush to reach the clinic but a handful of clinical studies have shown promise. This book is a collection of studies/reviews, beginning with an introduction to the pluripotent stem cells and covering various aspects like derivation, differentiation, ethics, etc., and hence would provide insight into the recent standing on the pluripotent stem cells biology. The chapters have been categorized into three sections, covering subjects ranging from the generation of pluripotent stem cells and various means of their derivation from embryonic as well as adult tissues, the mechanistic understanding of pluripotency and narrating the potential therapeutic implications of these in vitro generated cells in various diseases, in addition to the associated pros and cons in the same.
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Chapter 13: Synthetic Microbial Consortia and their Applications
Robert P. Smith, Yu Tanouchi, and Lingchong You
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Synthetic Microbial Consortia and Their Applications
Robert P. Smith, Y. Tanouchi, and L. You
Synthetic Biology provides a framework to examine key enabling components in the emerging area of synthetic biology. Chapters contributed by leaders in the field address tools and methodologies developed for engineering biological systems at many levels, including molecular, pathway, network, whole cell, and multi-cell levels. The book highlights exciting practical applications of synthetic biology such as microbial production of biofuels and drugs, artificial cells, synthetic viruses, and artificial photosynthesis. The roles of computers and computational design are discussed, as well as future prospects in the field, including cell-free synthetic biology and engineering synthetic ecosystems.
Synthetic biology is the design and construction of new biological entities, such as enzymes, genetic circuits, and cells, or the redesign of existing biological systems. It builds on the advances in molecular, cell, and systems biology and seeks to transform biology in the same way that synthesis transformed chemistry and integrated circuit design transformed computing. The element that distinguishes synthetic biology from traditional molecular and cellular biology is the focus on the design and construction of core components that can be modeled, understood, and tuned to meet specific performance criteria and the assembly of these smaller parts and devices into larger integrated systems that solve specific biotechnology problems.
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Laboratory Exercises in Biology
Edward O. Keith, Charles Messing, Emily F. Schmitt Lavin, and Joshua Stephen Feingold
Third edition
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Chapter 19: Quantitative Analysis of the Spatiotemporal Dynamics of a Synthetic Predator–Prey Ecosystem
Stephen Payne, Robert P. Smith, and Lingchong You
A major focus in synthetic biology is the rational design and implementation of gene circuits to control dynamics of individual cells and, increasingly, cellular populations. Population-level control is highlighted in recent studies which attempt to design and implement synthetic ecosystems (or engineered microbial consortia). On the one hand, these engineered systems may serve as a critical technological foundation for practical applications. On the other hand, they may serve as well-defined model systems to examine biological questions of broad relevance. Here, using a synthetic predator-prey ecosystem as an example, we illustrate the basic experimental techniques involved in system implementation and characterization. By extension, these techniques are applicable to the analysis of other microbial-based synthetic or natural ecosystems.
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Case Study: Elasmobranch Bycatch in the Pelagic Longline Fishery off the Southeastern United States, 1992-1997
Lawrence R. Beerkircher, Enric Cortes, and Mahmood Shivji
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Case Study: Rapid Species Identification of Pelagic Shark Tissues Using Genetic Approaches
Mahmood Shivji, Melissa Pank, Lisa Natanson, Nancy Kohler, and Michael Stanhope
