Advances in biotechnology and genomics of switchgrass

Switchgrass (Panicum virgatum L.) is a C4 perennial warm season grass indigenous to the North American tallgrass prairie. A number of its natural and agronomic traits, including adaptation to a wide geographical distribution, low nutrient requirements and production costs, high water use efficiency, high biomass potential, ease of harvesting, and potential for carbon storage, make it an attractive dedicated biomass crop for biofuel production. We believe that genetic improvements using biotechnology will be important to realize the potential of the biomass and biofuel-related uses of switchgrass. Tissue culture techniques aimed at rapid propagation of switchgrass and genetic transformation protocols have been developed. Rapid progress in genome sequencing and bioinformatics has provided efficient strategies to identify, tag, clone and manipulate many economically-important genes, including those related to higher biomass, saccharification efficiency, and lignin biosynthesis. Application of the best genetic tools should render improved switchgrass that will be more economically and environmentally sustainable as a lignocellulosic bioenergy feedstock

Sensitivity of a real-time PCR method for the detection of transgenes in a mixture of transgenic and non-transgenic seeds of papaya (\u3cem\u3eCarica papaya\u3c/em\u3e L.)

Background Genetically engineered (GE) ringspot virus-resistant papaya cultivars ‘Rainbow’ and ‘SunUp’ have been grown in Hawai’i for over 10 years. In Hawai’i, the introduction of GE papayas into regions where non-GE cultivars are grown and where feral non-GE papayas exist have been accompanied with concerns associated with transgene flow. Of particular concern is the possibility of transgenic seeds being found in non-GE papaya fruits via cross-pollination. Development of high-throughput methods to reliably detect the adventitious presence of such transgenic material would benefit both the scientific and regulatory communities. Results We assessed the accuracy of using conventional qualitative polymerase chain reaction (PCR) as well as real-time PCR-based assays to quantify the presence of transgenic DNA from bulk samples of non-GE papaya seeds. In this study, an optimized method of extracting high quality DNA from dry seeds of papaya was standardized. A reliable, sensitive real-time PCR method for detecting and quantifying viral coat protein (cp) transgenes in bulk seed samples utilizing the endogenous papain gene is presented. Quantification range was from 0.01 to 100 ng/μl of GE-papaya DNA template with a detection limit as low as 0.01% (10 pg). To test this system, we simulated transgene flow using known quantities of GE and non-GE DNA and determined that 0.038% (38 pg) GE papaya DNA could be detected using real-time PCR. We also validated this system by extracting DNA from known ratios of GE seeds to non-GE seeds of papaya followed by real-time PCR detection and observed a reliable detection limit of 0.4%. Conclusions This method for the quick and sensitive detection of transgenes in bulked papaya seed lots using conventional as well as real-time PCR-based methods will benefit numerous stakeholders. In particular, this method could be utilized to screen selected fruits from maternal non-GE papaya trees in Hawai’i for the presence of transgenic seed at typical regulatory threshold levels. Incorporation of subtle differences in primers and probes for variations in cp worldwide should allow this method to be utilized elsewhere when and if deregulation of transgenic papaya occurs

Sensitivity of a real-time PCR method for the detection of transgenes in a mixture of transgenic and non-transgenic seeds of papaya (Carica papaya L.)

BACKGROUND: Genetically engineered (GE) ringspot virus-resistant papaya cultivars ‘Rainbow’ and ‘SunUp’ have been grown in Hawai’i for over 10 years. In Hawai’i, the introduction of GE papayas into regions where non-GE cultivars are grown and where feral non-GE papayas exist have been accompanied with concerns associated with transgene flow. Of particular concern is the possibility of transgenic seeds being found in non-GE papaya fruits via cross-pollination. Development of high-throughput methods to reliably detect the adventitious presence of such transgenic material would benefit both the scientific and regulatory communities. RESULTS: We assessed the accuracy of using conventional qualitative polymerase chain reaction (PCR) as well as real-time PCR-based assays to quantify the presence of transgenic DNA from bulk samples of non-GE papaya seeds. In this study, an optimized method of extracting high quality DNA from dry seeds of papaya was standardized. A reliable, sensitive real-time PCR method for detecting and quantifying viral coat protein (cp) transgenes in bulk seed samples utilizing the endogenous papain gene is presented. Quantification range was from 0.01 to 100 ng/μl of GE-papaya DNA template with a detection limit as low as 0.01% (10 pg). To test this system, we simulated transgene flow using known quantities of GE and non-GE DNA and determined that 0.038% (38 pg) GE papaya DNA could be detected using real-time PCR. We also validated this system by extracting DNA from known ratios of GE seeds to non-GE seeds of papaya followed by real-time PCR detection and observed a reliable detection limit of 0.4%. CONCLUSIONS: This method for the quick and sensitive detection of transgenes in bulked papaya seed lots using conventional as well as real-time PCR-based methods will benefit numerous stakeholders. In particular, this method could be utilized to screen selected fruits from maternal non-GE papaya trees in Hawai’i for the presence of transgenic seed at typical regulatory threshold levels. Incorporation of subtle differences in primers and probes for variations in cp worldwide should allow this method to be utilized elsewhere when and if deregulation of transgenic papaya occurs

Implementation of Balanced Scorecard Method in an Engineering Company

Import 23/08/2017Cílem diplomové práce je navrhnout konkrétní formu implementace Balanced Scorecard do systému řízení pro podnik PMB – ZOS, s.r.o., která povede ke zvýšení výkonnosti a konkurenceschopnosti této společnosti. V části teoreticko – metodologické budou definovány principy metody Balanced Scorecard zahrnující specifikaci jednotlivých perspektiv, popis implementace včetně omezení a bariér aplikace této metody. Praktická část se pak již bude zabývat provedením analýz u jednotlivých čtyř perspektiv a následným vytvořením konkrétního návrhu implementace dané metody do podniku. Závěr práce budou tvořit návrhy a doporučení pro podnik včetně vyčíslení nákladů na zavedení této metody.The aim of the diploma thesis is to propose a specific form of implementation of the Balanced Scorecard management system for the company PMB - ZOS, s.r.o., which can promote the increasing of the efficiency and competitiveness of the company. In the theoretical - methodological part will be defined principles of the Balanced Scorecard method comprising the specification of individual perspectives, including description of implementation barriers and limitations of application of this method. The practical part will be engaged in performance analyzes for each of the four perspectives and the subsequent creation of a specific design of the implementation of the method for this company. The final part of this diploma thesis will include proposals and recommendations for this company, including costings for implementation of the method.152 - Katedra podnikohospodářskávýborn

Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP

The Leguminosae has emerged as a model for studying angiosperm plastome evolution because of its striking diversity of structural rearrangements and sequence variation. However, most of what is known about legume plastomes comes from few genera representing a subset of lineages in subfamily Papilionoideae. We investigate plastome evolution in subfamily Mimosoideae based on two newly sequenced plastomes (Inga and Leucaena) and two recently published plastomes (Acacia and Prosopis), and discuss the results in the context of other legume and rosid plastid genomes. Mimosoid plastomes have a typical angiosperm gene content and general organization as well as a generally slow rate of protein coding gene evolution, but they are the largest known among legumes. The increased length results from tandem repeat expansions and an unusual 13 kb IR-SSC boundary shift in Acacia and Inga. Mimosoid plastomes harbor additional interesting features, including loss of clpP intron1 in Inga, accelerated rates of evolution in clpP for Acacia and Inga, and dN/dS ratios consistent with neutral and positive selection for several genes. These new plastomes and results provide important resources for legume comparative genomics, plant breeding, and plastid genetic engineering, while shedding further light on the complexity of plastome evolution in legumes and angiosperms.This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Nature Publishing Group. The published article can be found at: http://www.nature.com/articles/srep1695

Advances in Biofuels and Bioenergy

The worldwide consumption of fossil fuel continues to increase at unsustainable levels, which will lead to progressive scarcity, if immediate and innovative measures are not taken for its sustainable use. This scarcity necessitates the development of renewable and sustainable alternatives for fossil fuels. A possible solution to today's energy challenges can be provided by biofuels. This book intends to provide the reader with a comprehensive overview of the current status and the future implications of biofuels. Diverse and aptly covered comprehensive information in this book will directly enhance both basic and applied research in biofuels and will particularly be useful for students, scientists, breeders, growers, ecologists, industrialists and policy makers. It will be a valuable reference point to improve biofuels in the areas of ecologically and economically sustainable bioenergy research

Breeding and Health Benefits of Fruit and Nut Crops

The fruit and nut crops are laden with health benefits. As people are becoming more conscious about their health and nutritional uptake, the worldwide demand and consumption of fruit and nut crops are steadily increasing. This has made it hard to keep pace between the rate of fruit and nut production and its consumption. To meet this increasing demand, there is a need to produce improved, better yielding, and high-quality fruit and nut crops. This book intends to provide the reader with a comprehensive overview of the current status and future prospects of fruit and nut crops. Such information covered in this book will directly enhance both basic and applied research in fruit and nut crops and will particularly be useful for students, scientists, researchers, teachers, breeders, policy-makers, and growers

Tropical Forests - New Edition

Tropical forests occupy only one-tenth of the world's land area but are home to more than half of the world's flora and fauna. They comprise extremely complex labyrinth of ecological interactions. The astounding richness and biodiversity of tropical forests are rapidly dwindling. There is a fear that the burgeoning human population and industrialization, where a majority of these tropical forests are found, may lead to the clearing or modification or may be a complete disappearance of the remaining tropical forests within few decades. This has severely altered the vital biogeochemical cycles of carbon, phosphorus, nitrogen, and so on and has led to the change in global climate and pristine natural ecosystems. Hence, there is an urgent need to protect, restore, conserve, and improve the forest resources before they are irrevocably lost. In this second edition of the book Tropical Forests, the chapters share the above issues and help in understanding, educating, and creating awareness on the role of ""tropical forests"" for the very survival of mankind, climate change, and the diversity of biota across the globe. This book will be of great use and could be useful to students, scientists, ecologists, population and conservation biologists, and forest managers across the globe

Tropical Forests

The astounding richness and biodiversity of tropical forests is rapidly dwindling. This has severely altered the vital biogeochemical cycles of carbon, phosphorus, nitrogen etc. and has led to the change in global climate and pristine natural ecosystems. In this elegant book, we have defined ""Tropical Forests"" broadly, into five different themes: (1) tropical forest structure, synergy, synthesis, (2) tropical forest fragmentation, (3) impact of anthropogenic pressure, (4) Geographic Information System and remote sensing, and (5) tropical forest protection and process. The cutting-edge synthesis, detailed current reviews, several original data-rich case studies, recent experiments/experiences from leading scientists across the world are presented as unique chapters. Though, the chapters differ noticeably in the geographic focus, diverse ecosystems, time and approach, they share these five important themes and help in understanding, educating, and creating awareness on the role of ""Tropical Forests"" for the very survival of mankind, climate change, and the diversity of biota across the globe. This book will be of great use to the students, scientists, ecologists, population and conservation biologists, and forest managers across the globe. The publication of this book was supported by the Secretariat of the Convention on Biological Diversity, United Nations </span