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Advances in Biochemical Engineering/biotechnology

Kelley M Heffner, Qiong Wang, Deniz Baycin Hizal, Özge Can, Michael J Betenbaugh
Mammalian expression systems such as Chinese hamster ovary (CHO), mouse myeloma (NS0), and human embryonic kidney (HEK) cells serve a critical role in the biotechnology industry as the production host of choice for recombinant protein therapeutics. Most of the recombinant biologics are glycoproteins that contain complex oligosaccharide or glycan attachments representing a principal component of product quality. Both N-glycans and O-glycans are present in these mammalian cells, but the engineering of N-linked glycosylation is of critical interest in industry and many efforts have been directed to improve this pathway...
March 13, 2018: Advances in Biochemical Engineering/biotechnology
Bradley J Till, Sneha Datta, Joanna Jankowicz-Cieslak
Gene space: the final frontier in plant functional genomics. These are the voyages of TILLING, the reverse-genetics strategy that sought to boldly go where no-one had gone before by combining high-density chemical mutagenesis with high-throughput mutation discovery. Its 18-year mission has been to explore new technologies such as next generation sequencing and to seek out new strategies like in silico databases of catalogued EMS-induced mutations from entire mutant plant populations. This chapter is a clip show highlighting key milestones in the development of TILLING...
March 8, 2018: Advances in Biochemical Engineering/biotechnology
Pradeep R Marri, Liang Ye, Yi Jia, Ke Jiang, Steven D Rounsley
DNA sequencing technologies have changed the face of biological research over the last 20 years. From reference genomes to population level resequencing studies, these technologies have made significant contributions to our understanding of plant biology and evolution. As the technologies have increased in power, the breadth and complexity of the questions that can be asked has increased. Along with this, the challenges of managing unprecedented quantities of sequence data are mounting. This chapter describes a few aspects of the journey so far and looks forward to what may lie ahead...
March 8, 2018: Advances in Biochemical Engineering/biotechnology
M Saba Rahim, Himanshu Sharma, Afsana Parveen, Joy K Roy
Previously, association mapping (AM) methodology was used to unravel genetic complications in animal science by measuring the complex traits for candidate and non-candidate genes. Nowadays, this statistical approach is widely used to clarify the complexity in plant breeding program-based genome-wide breeding strategies, marker development, and diversity analysis. This chapter is particularly focused on methodologies with limitations and provides an overview of AM models and software used up to now. Association or linkage disequilibrium mapping has become a very popular method for discovering candidate and non-candidate genes and confirmation of quantitative trait loci (QTL) on various parts of the genome and in marker-assisted selection for breeding...
March 7, 2018: Advances in Biochemical Engineering/biotechnology
James Cockram, Ian Mackay
Fine mapping of quantitative trait loci (QTL) is the route to more detailed molecular characterization and functional studies of the relationship between polymorphism and trait variation. It is also of direct relevance to breeding since it makes QTL more easily integrated into marker-assisted breeding and into genomic selection. Fine mapping requires that marker-trait associations are tested in populations in which large numbers of recombinations have occurred. This can be achieved by increasing the size of mapping populations or by increasing the number of generations of crossing required to create the population...
February 23, 2018: Advances in Biochemical Engineering/biotechnology
Arindam Ghatak, Palak Chaturvedi, Wolfram Weckwerth
Metabolomics is an essential technology for functional genomics and systems biology. It plays a key role in functional annotation of genes and understanding towards cellular and molecular, biotic and abiotic stress responses. Different analytical techniques are used to extend the coverage of a full metabolome. The commonly used techniques are NMR, CE-MS, LC-MS, and GC-MS. The choice of a suitable technique depends on the speed, sensitivity, and accuracy. This chapter provides insight into plant metabolomic techniques, databases used in the analysis, data mining and processing, compound identification, and limitations in metabolomics...
February 23, 2018: Advances in Biochemical Engineering/biotechnology
Ismail Ocsoy, Didar Tasdemir, Sumeyye Mazicioglu, Weihong Tan
The integration of nanotechnology in medicine has had a tremendous impact in the past few decades. The discovery of synthesis of nanomaterials (NMs) and their functions as versatile tools promoted various applications in nano-biotechnology and nanomedicine. Although the physical and chemical methods are still considered as commonly used methods, they introduce several drawbacks such as the use of toxic chemicals (solvent, reducing, and capping agents) and poor control of size, size distribution, and morphology, respectively...
February 21, 2018: Advances in Biochemical Engineering/biotechnology
Rajeev K Varshney, Manish K Pandey, Annapurna Chitikineni
The rapidly evolving technologies can serve as a potential growth engine in agriculture as many of these technologies have revolutionized several industries in the recent past. The tremendous advancements in biotechnology methods, cost-effective sequencing technology, refinement of genomic tools, and standardization of modern genomics-assisted breeding methods hold great promise in taking the global agriculture to the next level through development of improved climate-smart seeds. These technologies can dramatically increase our capacity to understand the molecular basis of traits and utilize the available resources for accelerated development of stable high-yielding, nutritious, input-use efficient, and climate-smart crop varieties...
February 16, 2018: Advances in Biochemical Engineering/biotechnology
Pawan L Kulwal
Quantitative trait loci (QTL) mapping in crop plants has now become a common practice due to the advances made in the area of molecular markers as well as that of statistical genomics. Consequently, large numbers of QTLs have been identified in different crops for a variety of traits. Several computational tools are now available that suit the type of mapping population and the trait(s) to be studied for QTL analyses as well as the objective of the program. These methods are comprised of simpler approaches like single marker analysis and simple interval mapping to relatively exhaustive inclusive composite interval mapping and Bayesian interval mapping...
February 13, 2018: Advances in Biochemical Engineering/biotechnology
Naghmeh Nejat, Abirami Ramalingam, Nitin Mantri
The current global population of 7.3 billion is estimated to reach 9.7 billion in the year 2050. Rapid population growth is driving up global food demand. Additionally, global climate change, environmental degradation, drought, emerging diseases, and salty soils are the current threats to global food security. In order to mitigate the adverse effects of these diverse agricultural productivity constraints and enhance crop yield and stress-tolerance in plants, we need to go beyond traditional and molecular plant breeding...
February 2, 2018: Advances in Biochemical Engineering/biotechnology
Abhishek Rathore, Vikas K Singh, Sarita K Pandey, Chukka Srinivasa Rao, Vivek Thakur, Manish K Pandey, V Anil Kumar, Roma Rani Das
Agricultural disciplines are becoming data intensive and the agricultural research data generation technologies are becoming sophisticated and high throughput. On the one hand, high-throughput genotyping is generating petabytes of data; on the other hand, high-throughput phenotyping platforms are also generating data of similar magnitude. Under modern integrated crop breeding, scientists are working together by integrating genomic and phenomic data sets of huge data volumes on a routine basis. To manage such huge research data sets and use them appropriately in decision making, Data Management Analysis & Decision Support Tools (DMASTs) are a prerequisite...
January 26, 2018: Advances in Biochemical Engineering/biotechnology
Armin Scheben, Jacqueline Batley, David Edwards
In the past decade, the application of high-throughput sequencing to crop genotyping has given rise to novel platforms capable of genotyping tens of thousands of genome-wide DNA markers. Coupled with the decreasing costs of sequencing, this rapid increase in markers allows accelerated and highly accurate genotyping of entire crop populations and diversity sets using single nucleotide polymorphisms (SNPs). These revolutionary advances accelerate crop improvement by facilitating a more precise connection of phenotype to genotype through association studies, linkage mapping and diversity analysis...
January 23, 2018: Advances in Biochemical Engineering/biotechnology
Chandra Bhan Yadav, Garima Pandey, Mehanathan Muthamilarasan, Manoj Prasad
The genetic material DNA in association with histone proteins forms the complex structure called chromatin, which is prone to undergo modification through certain epigenetic mechanisms including cytosine DNA methylation, histone modifications, and small RNA-mediated methylation. Alterations in chromatin structure lead to inaccessibility of genomic DNA to various regulatory proteins such as transcription factors, which eventually modulates gene expression. Advancements in high-throughput sequencing technologies have provided the opportunity to study the epigenetic mechanisms at genome-wide levels...
January 23, 2018: Advances in Biochemical Engineering/biotechnology
Monica Jara Avaca, Ina Gruh
Engineered cardiac tissue might enable novel therapeutic strategies for the human heart in a number of acquired and congenital diseases. With recent advances in stem cell technologies, namely the availability of pluripotent stem cells, the generation of potentially autologous tissue grafts has become a realistic option. Nevertheless, a number of limitations still have to be addressed before clinical application of engineered cardiac tissue based on human stem cells can be realized. We summarize current progress and pending challenges regarding the optimal cell source, cardiomyogenic lineage specification, purification, safety of genetic cell engineering, and genomic stability...
2018: Advances in Biochemical Engineering/biotechnology
De-Chuan Meng, Guo-Qiang Chen
Microbial polyhydroxyalkanoates (PHA) are a family of biodegradable and biocompatible polyesters which have been extensively studied using synthetic biology and metabolic engineering methods for improving production and for widening its diversity. Synthetic biology has allowed PHA to become composition controllable random copolymers, homopolymers, and block copolymers. Recent developments showed that it is possible to establish a microbial platform for producing not only random copolymers with controllable monomers and their ratios but also structurally defined homopolymers and block copolymers...
2018: Advances in Biochemical Engineering/biotechnology
Markus Schmidt, Lei Pei, Nediljko Budisa
The basic chemical constitution of all living organisms in the context of carbon-based chemistry consists of a limited number of small molecules and polymers. Until the twenty-first century, biology was mainly an analytical science and has now reached a point where it merges with engineering science, paving the way for synthetic biology. One of the objectives of synthetic biology is to try to change the chemical compositions of living cells, that is, to create an artificial biological diversity, which in turn fosters a new sub-field of synthetic biology, xenobiology...
2018: Advances in Biochemical Engineering/biotechnology
Weihua Guo, Jiayuan Sheng, Xueyang Feng
Metabolic engineering of industrial microorganisms to produce chemicals, fuels, and drugs has attracted increasing interest as it provides an environment-friendly and renewable route that does not depend on depleting petroleum sources. However, the microbial metabolism is so complex that metabolic engineering efforts often have difficulty in achieving a satisfactory yield, titer, or productivity of the target chemical. To overcome this challenge, (13)C Metabolic Flux Analysis ((13)C-MFA) has been developed to investigate rigorously the cell metabolism and quantify the carbon flux distribution in central metabolic pathways...
2018: Advances in Biochemical Engineering/biotechnology
Timothy L Turner, Heejin Kim, In Iok Kong, Jing-Jing Liu, Guo-Chang Zhang, Yong-Su Jin
To mitigate global climate change caused partly by the use of fossil fuels, the production of fuels and chemicals from renewable biomass has been attempted. The conversion of various sugars from renewable biomass into biofuels by engineered baker's yeast (Saccharomyces cerevisiae) is one major direction which has grown dramatically in recent years. As well as shifting away from fossil fuels, the production of commodity chemicals by engineered S. cerevisiae has also increased significantly. The traditional approaches of biochemical and metabolic engineering to develop economic bioconversion processes in laboratory and industrial settings have been accelerated by rapid advancements in the areas of yeast genomics, synthetic biology, and systems biology...
2018: Advances in Biochemical Engineering/biotechnology
Judith Becker, Gideon Gießelmann, Sarah Lisa Hoffmann, Christoph Wittmann
Since its discovery 60 years ago, Corynebacterium glutamicum has evolved into a workhorse for industrial biotechnology. Traditionally well known for its remarkable capacity to produce amino acids, this Gram-positive soil bacterium, has become a flexible, efficient production platform for various bulk and fine chemicals, materials, and biofuels. The central turnstile of all these achievements is our excellent understanding of its metabolism and physiology. This knowledge base, together with innovative systems metabolic engineering concepts, which integrate systems and synthetic biology into strain engineering, has upgraded C...
2018: Advances in Biochemical Engineering/biotechnology
Tobias Baumann, Matthias Exner, Nediljko Budisa
To date, the two systems most extensively used for noncanonical amino acid (ncAA) incorporation via orthogonal translation are based on the Methanococcus jannaschii TyrRS/tRNA CUA(Tyr) and the Methanosarcina barkeri/Methanosarcina mazei PylRS/tRNA CUA(Pyl) pairs. Here, we summarize the development and usage of the pyrrolysine-based system for orthogonal translation, a process that allows for the recombinant production of site-specifically labeled proteins and peptides. Via stop codon suppression in Escherichia coli and mammalian cells, genetically encoded biomolecules can be equipped with a great diversity of chemical functionalities including click chemistry handles, post-translational modifications, and photocaged sidechains...
2018: Advances in Biochemical Engineering/biotechnology
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