The molecular and genetic manipulation of nitrogen fixation

1981 ◽  
Vol 292 (1062) ◽  
pp. 589-599 ◽  
Keyword(s):  
Biological Process ◽  
Genetic Manipulation ◽  
Plant Genome ◽  
Population Pressure ◽  
Major Advance ◽  
Regulated Expression ◽  
Substantial Progress ◽  
World Agriculture ◽  
Physiological Background

The fundamental importance of dinitrogen fixation for world agriculture, in relation to projected energy supplies, population pressure and food requirements over the next decades, obliges scientists to reconsider ways of exploiting this biological process. Genetic manipulation offers several options in principle. Existing symbiotic systems such as the legumes and seemingly inefficient systems such as the grass associations could be improved; new symbioses could be developed by nif gene transfer to rhizosphere commensals or by somatic hybridization of appropriate plants. A major advance would be to render plants independent of microbes by manipulation of expressable nif into the plant genome. This goal is discussed. It requires the complete genetic and physical characterization of nif in particular its regulation, and an understanding of the physiological background within which nif can be expressed, as well as the ability to fuse nif to alien genetic systems. Substantial progress in these directions has been made by using the n if genes of Klebsiella pneumoniae this progress is reviewed. Strategies for the further manipulation of nif towards regulated expression in the plant genome are considered.

Physical Ultrasonics of Composites

2011 ◽  
Author(s):  
Dale Chimenti ◽  
Stanislav Rokhlin ◽  
Peter Nagy
Keyword(s):  
Composite Laminates ◽  
Stiffness Matrix ◽  
Composite Plates ◽  
Anisotropic Media ◽  
Anisotropic Materials ◽  
Ultrasonic Waves ◽  
Laminated Plates ◽  
Structure Characteristic ◽  
Major Advance

Physical Ultrasonics of Composites is a rigorous introduction to the characterization of composite materials by means of ultrasonic waves. Composites are treated here not simply as uniform media, but as inhomogeneous layered anisotropic media with internal structure characteristic of composite laminates. The objective here is to concentrate on exposing the singular behavior of ultrasonic waves as they interact with layered, anisotropic materials, materials which incorporate those structural elements typical of composite laminates. This book provides a synergistic description of both modeling and experimental methods in addressing wave propagation phenomena and composite property measurements. After a brief review of basic composite mechanics, a thorough treatment of ultrasonics in anisotropic media is presented, along with composite characterization methods. The interaction of ultrasonic waves at interfaces of anisotropic materials is discussed, as are guided waves in composite plates and rods. Waves in layered media are developed from the standpoint of the "Stiffness Matrix", a major advance over the conventional, potentially unstable Transfer Matrix approach. Laminated plates are treated both with the stiffness matrix and using Floquet analysis. The important influence on the received electronic signals in ultrasonic materials characterization from transducer geometry and placement are carefully exposed in a dedicated chapter. Ultrasonic wave interactions are especially susceptible to such influences because ultrasonic transducers are seldom more than a dozen or so wavelengths in diameter. The book ends with a chapter devoted to the emerging field of air-coupled ultrasonics. This new technology has come of age with the development of purpose-built transducers and electronics and is finding ever wider applications, particularly in the characterization of composite laminates.

scholarly journals Modernized Tools for Streamlined Genetic Manipulation and Comparative Study of Wild and Diverse Proteobacterial Lineages

mBio ◽  
2018 ◽  
Vol 9 (5) ◽  
Author(s):  
Travis J. Wiles ◽  
Elena S. Wall ◽  
Brandon H. Schlomann ◽  
Edouard A. Hay ◽  
Raghuveer Parthasarathy ◽  
...  
Keyword(s):  
Comparative Study ◽  
Molecular Mechanisms ◽  
Genetic Manipulation ◽  
Functional Characterization ◽  
Symbiotic Bacteria ◽  
Bacterial Isolates ◽  
Major Barrier ◽  
Allelic Exchange ◽  
Genetic Techniques

ABSTRACTCorrelating the presence of bacteria and the genes they carry with aspects of plant and animal biology is rapidly outpacing the functional characterization of naturally occurring symbioses. A major barrier to mechanistic studies is the lack of tools for the efficient genetic manipulation of wild and diverse bacterial isolates. To address the need for improved molecular tools, we used a collection of proteobacterial isolates native to the zebrafish intestinal microbiota as a testbed to construct a series of modernized vectors that expedite genetic knock-in and knockout procedures across lineages. The innovations that we introduce enhance the flexibility of conventional genetic techniques, making it easier to manipulate many different bacterial isolates with a single set of tools. We developed alternative strategies for domestication-free conjugation, designed plasmids with customizable features, and streamlined allelic exchange using visual markers of homologous recombination. We demonstrate the potential of these tools through a comparative study of bacterial behavior within the zebrafish intestine. Live imaging of fluorescently tagged isolates revealed a spectrum of distinct population structures that differ in their biogeography and dominant growth mode (i.e., planktonic versus aggregated). Most striking, we observed divergent genotype-phenotype relationships: several isolates that are predicted by genomic analysis andin vitroassays to be capable of flagellar motility do not display this trait within living hosts. Together, the tools generated in this work provide a new resource for the functional characterization of wild and diverse bacterial lineages that will help speed the research pipeline from sequencing-based correlations to mechanistic underpinnings.IMPORTANCEA great challenge in microbiota research is the immense diversity of symbiotic bacteria with the capacity to impact the lives of plants and animals. Moving beyond correlative DNA sequencing-based studies to define the cellular and molecular mechanisms by which symbiotic bacteria influence the biology of their hosts is stalling because genetic manipulation of new and uncharacterized bacterial isolates remains slow and difficult with current genetic tools. Moreover, developing tools de novo is an arduous and time-consuming task and thus represents a significant barrier to progress. To address this problem, we developed a suite of engineering vectors that streamline conventional genetic techniques by improving postconjugation counterselection, modularity, and allelic exchange. Our modernized tools and step-by-step protocols will empower researchers to investigate the inner workings of both established and newly emerging models of bacterial symbiosis.

scholarly journals Hidden in plain sight: What remains to be discovered in the eukaryotic proteome?

2018 ◽  
Author(s):  
Valerie Wood ◽  
Antonia Lock ◽  
Midori A. Harris ◽  
Kim Rutherford ◽  
Jürg Bähler ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Fission Yeast ◽  
Genome Sequencing ◽  
Large Scale ◽  
Biological Process ◽  
Blind Spot ◽  
Model Organisms ◽  
Biological Processes ◽  
Health And Disease

AbstractThe first decade of genome sequencing stimulated an explosion in the characterization of unknown proteins. More recently, the pace of functional discovery has slowed, leaving around 20% of the proteins even in well-studied model organisms without informative descriptions of their biological roles. Remarkably, many uncharacterized proteins are conserved from yeasts to human, suggesting that they contribute to fundamental biological processes. To fully understand biological systems in health and disease, we need to account for every part of the system. Unstudied proteins thus represent a collective blind spot that limits the progress of both basic and applied biosciences.We use a simple yet powerful metric based on Gene Ontology (GO) biological process terms to define characterized and uncharacterized proteins for human, budding yeast, and fission yeast. We then identify a set of conserved but unstudied proteins in S. pombe, and classify them based on a combination of orthogonal attributes determined by large-scale experimental and comparative methods. Finally, we explore possible reasons why these proteins remain neglected, and propose courses of action to raise their profile and thereby reap the benefits of completing the catalog of proteins’ biological roles.

scholarly journals Emerging characterization of the role of SIRT3-mediated mitochondrial protein deacetylation in the heart

2011 ◽  
Vol 301 (6) ◽  
pp. H2191-H2197 ◽  
Author(s):  
Michael N. Sack
Keyword(s):  
Posttranslational Modification ◽  
Genetic Manipulation ◽  
Mitochondrial Protein ◽  
Pressure Overload ◽  
Therapeutic Agents ◽  
Redox Stress ◽  
Lysine Residues ◽  
Term Objective

Studies to quantify the protein acetylome show that lysine-residue acetylation rivals phosphorylation in prevalence as a posttranslational modification. Interesting, this posttranslational modification is modified by nutrient flux and by redox stress and targets the vast majority of metabolic pathway proteins in the mitochondria. Furthermore, the mitochondrial deacetylase enzyme SIRT3 appears to be regulated by exercise in skeletal muscle and in response to pressure overload in the heart. The alteration of protein lysine residues by acetylation and the enzymes controlling deacetylation are beginning to be explored as important regulatory events in the control of mitochondrial function and homeostasis. This review focuses on the mitochondrial targets of SIRT3 that are functionally implicated in heart biology and pathology and on the direct cardiac consequences of the genetic manipulation of SIRT3. As therapeutic modulators of other SIRT isoforms have been identified, the longer-term objective of our understanding of this biology would be to identify SIRT3 modulators as putative cardiac therapeutic agents.

The development and use of a spatial database for the determination and characterization of the state of the German Baltic small-scale fishery sector

2012 ◽  
Vol 69 (8) ◽  
pp. 1480-1490 ◽  
Author(s):  
Eva A. Papaioannou ◽  
Athanasios T. Vafeidis ◽  
Martin F. Quaas ◽  
Jörn O. Schmidt
Keyword(s):  
Spatial Database ◽  
The State ◽  
Primary Data ◽  
Small Scale ◽  
Substantial Progress ◽  
Technical Specifications ◽  
Data Deficient ◽  
Agriculture And Food ◽  
Operational Range

Abstract Papaioannou, E. A., Vafeidis, A. T., Quaas, M. F., and Schmidt, J. O. 2012. The development and use of a spatial database for the determination and characterization of the state of the German Baltic small-scale fishery sector. – ICES Journal of Marine Science, 69: . Although substantial progress has been made in the acquisition and analysis of fishery data, the small-scale fishery (SSF) sector is frequently data deficient, with relevant primary data often being fragmented and incomplete. Also, in contrast to the case of the larger scale sector, a coherent methodological framework for the assessment of the SSF has, in most cases, not been formulated. In the present study, the methodology of developing a database for the German Baltic SSF sector is presented. The aim of the database is to combine fishery primary data effectively and enable the sound determination and characterization of the German Baltic SSF sector. Data used include, among others, fleet data derived from the European Community Fleet Register (CFR) database and logbook data from the German Federal Office for Agriculture and Food (BLE). The database includes information on the technical specifications of SSF vessels (length, engine power, etc.); the sector's operational range; main target species; fishing grounds; landing ports; and weight and price of landings. Results of employing the database for profiling the state of the SSF sector (in 2008) are presented. The results demonstrate the benefits of such an approach within the framework of managing coastal fish resources and fishing activities.

scholarly journals The identification and characterization of zebrafish hematopoietic stem cells

Blood ◽  
2011 ◽  
Vol 118 (2) ◽  
pp. 289-297 ◽  
Author(s):  
Dongdong Ma ◽  
Jing Zhang ◽  
Hui-feng Lin ◽  
Joseph Italiano ◽  
Robert I. Handin
Keyword(s):  
Danio Rerio ◽  
Genetic Manipulation ◽  
Transplant Recipients ◽  
Adult Zebrafish ◽  
Hematopoietic Progenitors ◽  
Hematopoietic Stem ◽  
Proliferation And Differentiation ◽  
Identification And Characterization

Abstract HSCs are defined by their ability to self-renew and maintain hematopoiesis throughout the lifespan of an organism. The optical clarity of their embryos and the ease of genetic manipulation make the zebrafish (Danio rerio) an excellent model for studying hematopoiesis. Using flow cytometry, we identified 2 populations of CD41-GFP+ cells (GFPhi and GFPlo) in the whole kidney marrow of Tg(CD41:GFP) zebrafish. Past studies in humans and mice have shown that CD41 is transiently expressed in the earliest hematopoietic progenitors and is then silenced, reappearing in the platelet/thrombocyte lineage. We have transplanted flow-sorted GFPhi and GFPlo cells into irradiated adult zebrafish and assessed long-term hematopoietic engraftment. Transplantation of GFPhi cells did not reconstitute hematopoiesis. In contrast, we observed multilineage hematopoiesis up to 68 weeks after primary and secondary transplantation of GFPlo cells. We detected the CD41-GFP transgene in all major hematopoietic lineages and CD41-GFP+ cells in histologic sections of kidneys from transplant recipients. These studies show that CD41-GFPlo cells fulfill generally accepted criteria for HSCs. The identification of fluorescent zebrafish HSCs, coupled with our ability to transplant them into irradiated adult recipients, provide a valuable new tool to track HSC homing, proliferation, and differentiation into hematopoietic cells.

scholarly journals Ebola vaccine–induced protection in nonhuman primates correlates with antibody specificity and Fc-mediated effects

2021 ◽  
Vol 13 (602) ◽  
pp. eabg6128
Author(s):  
Michelle Meyer ◽  
Bronwyn M. Gunn ◽  
Delphine C. Malherbe ◽  
Karthik Gangavarapu ◽  
Asuka Yoshida ◽  
...  
Keyword(s):  
Nonhuman Primates ◽  
Ebola Virus ◽  
Mucosal Vaccine ◽  
Protective Mechanisms ◽  
Degree Of Protection ◽  
Mediated Effects ◽  
Immune Correlates ◽  
Substantial Progress ◽  
Linear Epitopes

Although substantial progress has been made with Ebola virus (EBOV) vaccine measures, the immune correlates of vaccine-mediated protection remain uncertain. Here, five mucosal vaccine vectors based on human and avian paramyxoviruses provided nonhuman primates with varying degrees of protection, despite expressing the same EBOV glycoprotein (GP) immunogen. Each vaccine produced antibody responses that differed in Fc-mediated functions and isotype composition, as well as in magnitude and coverage toward GP and its conformational and linear epitopes. Differences in the degree of protection and comprehensive characterization of the response afforded the opportunity to identify which features and functions were elevated in survivors and could therefore serve as vaccine correlates of protection. Pairwise network correlation analysis of 139 immune- and vaccine-related parameters was performed to demonstrate relationships with survival. Total GP-specific antibodies, as measured by biolayer interferometry, but not neutralizing IgG or IgA titers, correlated with survival. Fc-mediated functions and the amount of receptor binding domain antibodies were associated with improved survival outcomes, alluding to the protective mechanisms of these vaccines. Therefore, functional qualities of the antibody response, particularly Fc-mediated effects and GP specificity, rather than simply magnitude of the response, appear central to vaccine-induced protection against EBOV. The heterogeneity of the response profile between the vaccines indicates that each vaccine likely exhibits its own protective signature and the requirements for an efficacious EBOV vaccine are complex.

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