Isolation and Genome Analysis of an Amoeba-Associated Bacterium \u3ci\u3eDyella terrae\u3c/i\u3e Strain Ely Copper Mine From Acid Rock Drainage in Vermont, United States

Protozoa play important roles in microbial communities, regulating populations via predation and contributing to nutrient cycling. While amoebae have been identified in acid rock drainage (ARD) systems, our understanding of their symbioses in these extreme environments is limited. Here, we report the first isolation of the amoeba Stemonitis from an ARD environment as well as the genome sequence and annotation of an associated bacterium, Dyella terrae strain Ely Copper Mine, from Ely Brook at the Ely Copper Mine Superfund site in Vershire, Vermont, United States. Fluorescent in situ hybridization analysis showed this bacterium colonizing cells of Stemonitis sp. in addition to being outside of amoebal cells. This amoeba-resistant bacterium is Gram-negative with a genome size of 5.36Mbp and GC content of 62.5%. The genome of the D. terrae strain Ely Copper Mine encodes de novo biosynthetic pathways for amino acids, carbohydrates, nucleic acids, and lipids. Genes involved in nitrate (1) and sulfate (7) reduction, metal (229) and antibiotic resistance (37), and secondary metabolite production (6) were identified. Notably, 26 hydrolases were identified by RAST as well as other biomass degradation genes, suggesting roles in carbon and energy cycling within the microbial community. The genome also contains type IV secretion system genes involved in amoebae resistance, revealing how this bacterium likely survives predation from Stemonitis sp. This genome analysis and the association of D. terrae strain Ely Copper Mine with Stemonitis sp. provide insight into the functional roles of amoebae and bacteria within ARD environments

From Immortality to Borrowed Time: Correlates and Challenges

The history of the human race is marked by the entrance of corruption, which also represents the loss of immortality. After the Fall, humans, and animals experienced death. By contrast, unfeeling organisms/cells may have several design functions. Plants, for example, photosynthesize and then are eaten and digested; unsuccessful sperm and ova are discarded and decay. These examples were in God’s original plan. Following the entrance of sin, adverse events such as environmental, genetic, and ecological changes, alterations in human attitudes, and manipulation of germplasm occurred. The image of God found in humans at the beginning was marred by the Fall and accounts for the adverse human attitude changes noted today. Despite this, God offers all individuals a make-over in their physical, intellectual, emotional, and spiritual/moral domains. Acceptance of the offer in its fullness would result in focused attention to health and efforts to repair and restore the environment, among other valuable outcomes. Keywords: Immortality, corruption, aging, design function, environmental change

Biohacking and code convergence : a transductive ethnography

Cette thèse se déploie dans un espace de discours et de pratiques revendicatrices, à l’inter- section des cultures amateures informatiques et biotechniques, euro-américaines contempo- raines. La problématique se dessinant dans ce croisement culturel examine des métaphores et analogies au coeur d’un traffic intense, au milieu de voies de commmunications imposantes, reliant les technologies informatiques et biotechniques comme lieux d’expression médiatique. L’examen retrace les lignes de force, les médiations expressives en ces lieux à travers leurs manifestations en tant que codes —à la fois informatiques et génétiques— et reconnaît les caractères analogiques d’expressivité des codes en tant que processus de convergence. Émergeant lentement, à partir des années 40 et 50, les visions convergentes des codes ont facilité l’entrée des ordinateurs personnels dans les marchés, ainsi que dans les garages de hackers, alors que des bricoleurs de l’informatique s’en réclamaient comme espace de liberté d’information —et surtout d’innovation. Plus de cinquante ans plus tard, l’analogie entre codes informatiques et génétiques sert de moteur aux revendications de liberté, informant cette fois les nouvelles applications de la biotechnologie de marché, ainsi que l’activité des biohackers, ces bricoleurs de garage en biologie synthétique. Les pratiques du biohacking sont ainsi comprises comme des individuations : des tentatives continues de résoudre des frictions, des tensions travaillant les revendications des cultures amateures informatiques et biotechniques. Une des manières de moduler ces tensions s’incarne dans un processus connu sous le nom de forking, entrevu ici comme l’expérience d’une bifurcation. Autrement dit, le forking est ici définit comme passage vers un seuil critique, déclinant la technologie et la biologie sur plusieurs modes. Le forking informe —c’est-à-dire permet et contraint— différentes vi- sions collectives de l’ouverture informationnelle. Le forking intervient aussi sur les plans des iii semio-matérialités et pouvoirs d’action investis dans les pratiques biotechniques et informa- tiques. Pris comme processus de co-constitution et de différentiation de l’action collective, les mouvements de bifurcation invitent les trois questions suivantes : 1) Comment le forking catalyse-t-il la solution des tensions participant aux revendications des pratiques du bioha- cking ? 2) Dans ce processus de solution, de quelles manières les revendications changent de phase, bifurquent et se transforment, parfois au point d’altérer radicalement ces pratiques ? 3) Quels nouveaux problèmes émergent de ces solutions ? L’effort de recherche a trouvé ces questions, ainsi que les plans correspondants d’action sémio-matérielle et collective, incarnées dans trois expériences ethnographiques réparties sur trois ans (2012-2015) : la première dans un laboratoire de biotechnologie communautaire new- yorkais, la seconde dans l’émergence d’un groupe de biotechnologie amateure à Montréal, et la troisième à Cork, en Irlande, au sein du premier accélérateur d’entreprises en biologie synthétique au monde. La logique de l’enquête n’est ni strictement inductive ou déductive, mais transductive. Elle emprunte à la philosophie de la communication et de l’information de Gilbert Simondon et découvre l’épistémologie en tant qu’acte de création opérant en milieux relationnels. L’heuristique transductive offre des rencontres inusitées entre les métaphores et les analogies des codes. Ces rencontres étonnantes ont aménagé l’expérience de la conver- gence des codes sous forme de jeux d’écritures. Elles se sont retrouvées dans la recherche ethnographique en tant que processus transductifs.This dissertation examines creative practices and discourses intersecting computer and biotech cultures. It queries influential metaphors and analogies on both sides of the inter- section, and their positioning of biotech and information technologies as expression media. It follows mediations across their incarnations as codes, both computational and biological, and situates their analogical expressivity and programmability as a process of code conver- gence. Converging visions of technological freedom facilitated the entrance of computers in 1960’s Western hobbyist hacker circles, as well as in consumer markets. Almost fifty years later, the analogy drives claims to freedom of information —and freedom of innovation— from biohacker hobbyist groups to new biotech consumer markets. Such biohacking practices are understood as individuations: as ongoing attempts to resolve frictions, tensions working through claims to freedom and openness animating software and biotech cultures. Tensions get modulated in many ways. One of them, otherwise known as “forking,” refers here to a critical bifurcation allowing for differing iterations of biotechnical and computa- tional configurations. Forking informs —that is, simultaneously affords and constrains— differing collective visions of openness. Forking also operates on the materiality and agency invested in biotechnical and computational practices. Taken as a significant process of co- constitution and differentiation in collective action, bifurcation invites the following three questions: 1) How does forking solve tensions working through claims to biotech freedom? 2) In this solving process, how can claims bifurcate and transform to the point of radically altering biotech practices? 3) what new problems do these solutions call into existence? This research found these questions, and both scales of material action and agency, in- carnated in three extensive ethnographical journeys spanning three years (2012-2015): the first in a Brooklyn-based biotech community laboratory, the second in the early days of a biotech community group in Montreal, and the third in the world’s first synthetic biology startup accelerator in Cork, Ireland. The inquiry’s guiding empirical logic is neither solely deductive or inductive, but transductive. It borrows from Gilbert Simondon’s philosophy of communication and information to experience epistemology as an act of analogical creation involving the radical, irreversible transformation of knower and known. Transductive heuris- tics offer unconvential encounters with practices, metaphors and analogies of code. In the end, transductive methods acknowledge code convergence as a metastable writing games, and ethnographical research itself as a transductive process

Whole-Body Regeneration

This Open Access volume provides a comprehensive overview of the latest tools available to scientists to study the many facets of whole-body regeneration (WBR). The chapters in this book are organized into six parts. Part One provides a historical overview on the study of the WBR phenomena focusing on the primary challenges of this research. Parts Two and Three explore a series of non-vertebrate zoological contexts that provide experimental models for WBR, showing how they can be approached with cellular tools. Parts Four, Five, and Six discuss the future advancements of WBR, reporting about the cutting-edge techniques in genetics and omics used to dissect the underlying mechanisms of WBR, and systems biology approaches to reach a synthetic view of WBR. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and thorough, Whole-Body Regeneration: Methods and Protocols is a valuable resource for scientists and researchers who want to learn more about this important and developing field

Whole-Body Regeneration

This Open Access volume provides a comprehensive overview of the latest tools available to scientists to study the many facets of whole-body regeneration (WBR). The chapters in this book are organized into six parts. Part One provides a historical overview on the study of the WBR phenomena focusing on the primary challenges of this research. Parts Two and Three explore a series of non-vertebrate zoological contexts that provide experimental models for WBR, showing how they can be approached with cellular tools. Parts Four, Five, and Six discuss the future advancements of WBR, reporting about the cutting-edge techniques in genetics and omics used to dissect the underlying mechanisms of WBR, and systems biology approaches to reach a synthetic view of WBR. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and thorough, Whole-Body Regeneration: Methods and Protocols is a valuable resource for scientists and researchers who want to learn more about this important and developing field

Microbiology for Allied Health Students

This open textbook is a remix of Openstax Microbiology, CC-BY 4.0, and created through an Affordable Learning Georgia Round Six Textbook Transformation Grant. The textbook has the following supplemental materials within this repository: This is a collection of instructional materials for the following open textbook and lab manual: Microbiology for Allied Health Students Lab Manual Microbiology for Allied Health Students Instructional Materials Authors\u27 Description: Microbiology for Allied Health Students is designed to cover the scope and sequence requirements for the single semester Microbiology course for non-majors and allied health students. The book presents the core concepts of microbiology with a focus on applications for careers in allied health. The pedagogical features of Microbiology for Allied Health Students make the material interesting and accessible to students while maintaining the career-application focus and scientific rigor inherent in the subject matter. The scope and sequence of Microbiology for Allied Health Students has been developed and vetted with input from numerous instructors at institutions across the U.S. It is designed to meet the needs of most microbiology courses allied health students. With these objectives in mind, the content of this textbook has been arranged in a logical progression from fundamental to more advanced concepts. The opening chapters present an overview of the discipline, with individual chapters focusing on cellular biology as well as each of the different types of microorganisms and the various means by which we can control and combat microbial growth. The focus turns to microbial pathogenicity, emphasizing how interactions between microbes and the human immune system contribute to human health and disease. The last several chapters of the text provide a survey of medical microbiology, presenting the characteristics of microbial diseases organized by body system. Accessible files with optical character recognition (OCR) and auto-tagging provided by the Center for Inclusive Design and Innovation.https://oer.galileo.usg.edu/biology-textbooks/1015/thumbnail.jp

The Unnaming of Aliass

The Unnaming of Aliass performs a paradoxical quest for wildly “untold” stories in the company of one special donkey companion, a femammal of the species Equus asinus and, significantly, a registered “American Spotted Ass.” Beast of burden that she is, this inscrutable companion helped carry a ridiculous load of human longings and quandaries into a maze of hot, harrowing miles, across the US South from Mississippi to Virginia, in the summer of 2002 -- all the while carrying her own onerous and unreckoned burdens and histories. Over two decades, the original journey evolved -- from the cracking-open of a quasi-Western novel-that-never-was by an implosive pun, into an ongoing philosophical and assthetic adventure: a hybrid roadside- and barnyard-based living-art practice, wherein “Aliass” un/names something much harder to grasp than the body of a lovely little ass: protagonist, setting, and traditional Western narratives turn inside-out around this “name-that-ain’t.” Through a deeply dug-in questioning of its own authorial assumptions, The Unnaming of Aliass makes space for untold autobiographies and bright dusty lacunae, tracing ineffable tales through the tangled shapes and shadows that interweave in any environment

Ornamental bulb crops as sources of medicinal and industrial natural products

Plants produce many diverse chemical compounds that are used in various industries. The aim of this thesis was to obtain an understanding of what is needed to convert an ornamental crop to a pharmaceutical crop. This included knowledge about regulatory issues and expectations from the industry regarding quality and safety of such crops. Based on this knowledge, a further aim was to determine how the cultivation practices of the model ornamental crop Narcissus pseudonarcissus, which contains the medicinal compound galanthamine, needed to be adapted. Some key points in the cultivation process were identified that may need to be adapted in the production of Narcissus bulbs as raw material for the pharmaceutical industry. These points were investigated in field experiments using NMR-based metabolomics as the main analytical tool. This contributed to a validated production chain of Narcissus pseudonarcissus bulbs suita ble for use as raw material for the extraction of galanthamine. Results from exploratory investigations into other ornamental bulb material for novel industrial products are also presented.UBL - phd migration 201

Diseases of Edible Oilseed Crops

Diseases of Edible Oilseed Crops presents an unprecedentedly thorough collection of information on the diseases of cultivated annual oilseed crops, including peanut, rapeseed-mustard, sesame, soybean, sunflower, and safflower. Written by internationally recognized researchers, this book covers and integrates worldwide literature in the field up to 2014, setting it apart from other books that are only of regional importance. The book focuses on major diseases of economic importance to each crop. Each chapter is devoted to a type of crop and a profile of affecting diseases according to geographical occurrence, epidemiology, symptoms, causal pathogens, host-pathogen interactions, biotechnological aspects, and the latest approaches to understanding host-pathogen interactions. It also includes discussions on developments on controversial subjects in research in order to stimulate thinking and further conversation with an eye toward improvements and resolutions. Research on oilseed crop diseases has expanded tremendously in the past 30 years, primarily as an effort to reduce losses to various stresses, including crop diseases. In the war against hunger and malnutrition, it is necessary to enhance and update knowledge about crop diseases and managing them. By compiling decades of information from previously scattered research into a single globally minded volume, Diseases of Edible Oilseed Crops provides these much-needed updates and enhancements

Mathematical model of interactions immune system with Micobacterium tuberculosis

Tuberculosis (TB) remains a public health problem in the world, because of the increasing prevalence and treatment outcomes are less satisfactory. About 3 million people die each year and an estimated one third of the world's population infected with Mycobacterium Tuberculosis (M.tb) is latent. This is apparently related to incomplete understanding of the immune system in infection M.tb. When this has been known that immune responses that play a role in controlling the development of M.tb is Macrophages, T Lymphocytes and Cytokines as mediators. However, how the interaction between the two populations and a variety of cytokines in suppressing the growth of Mycobacterium tuberculosis germ is still unclear. To be able to better understand the dynamics of infection with M tuberculosis host immune response is required of a model.One interesting study on the interaction of the immune system with M.tb mulalui mathematical model approach. Mathematical model is a good tool in understanding the dynamic behavior of a system. With the mediation of mathematical models are expected to know what variables are most responsible for suppressing the growth of Mycobacterium tuberculosis germ that can be a more appropriate approach to treatment and prevention target is to develop a vaccine. This research aims to create dynamic models of interaction between macrophages (Macrophages resting, macrophages activated and macrophages infected), T lymphocytes (CD4 + T cells and T cells CD8 +) and cytokine (IL-2, IL-4, IL-10,IL-12,IFN-dan TNF-) on TB infection in the lung. To see the changes in each variable used parameter values derived from experimental literature. With the understanding that the variable most responsible for defense against Mycobacterium tuberculosis germs, it can be used as the basis for the development of a vaccine or drug delivery targeted so hopefully will improve the management of patients with tuberculosis. Mathematical models used in building Ordinary Differential Equations (ODE) in the form of differential equation systems Non-linear first order, the equation contains the functions used in biological systems such as the Hill function, Monod function, Menten- Kinetic Function. To validate the system used 4th order Runge Kutta method with the help of software in making the program Matlab or Maple to view the behavior and the quantity of cells of each population