Webinars

Genetic Engineering Technologies & Applications | Next-Generation Sequencing Technologies & Applications | Metagenomics | Immunology |




Genetic Engineering Technologies & Applications

Protein Engineering: Gene Synthesis Applications

Presenter: Sumit Kumar, PhD

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Protein engineering is the design of new enzymes or proteins with desired functions. The DNA sequence used to encode a polypeptide can have dramatic effects on its expression. Due to advances in recombinant DNA technology, synthetic biology, and high-throughput screening techniques, protein engineering methods and applications are becoming increasingly important and widespread. A variety of protein engineering applications have emerged ranging from agriculture, environmental, medical, and nanobiotechnology applications. In this webinar, we will discuss how these new synthetic DNA tools are being applied and how they circumvent the constraints of previous approaches. We will also highlight some of the promising results emerging from the developing field of protein engineering.

Interrogating Tumor Immunology By Genomics & Genome Engineering Tools

Presenter: Le Cong, Ph.D., Postdoctoral Associate, Broad Institute of MIT and Harvard, CRISPR pioneer

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Advances in genome sequencing and related technology have led to unprecedented pace at which we can identify genomic and epigenetic changes associated with human diseases. For this purpose, genome editing tools adapted from CRISPR-Cas system can be employed for modifying genomic sequences at massive scale. I discuss here how genome engineering technology based on the CRISPR system can be deployed as versatile discovery and therapeutics tool. I will focus on the power and precision of novel technology development and describing its potential ex vivo and in vivo applications. In addition, I will highlight the emerging trend on how genomics analysis could be integrated to transform our ability to understand and treat human diseases, particularly complex diseases such as cancer via tumor immunology approaches.

A Synthetic Biology Approach to Enzyme Engineering

Presenter: Daniela Quaglia, PhD, Postdoctoral Researcher in Biocatalysis at Université de Montréal

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"Effective mutagenesis strategies in enzyme engineering are often dependent on the generation of small and targeted, high-quality libraries of mutants. Such 'smart' libraries are consistent with practical constraints imposed by the screening effort; while point-mutant libraries are readily screened, we need creative solutions to improve our capacity to explore the combinatorial complexity of sequence space." In this webinar, Dr. Quaglia will talk about how she used a flexible approach based on directed evolution and the Golden Gate cloning strategy to target three distinct regions of Candida antarctica lipase A (Cal-A) generating a series of diverse libraries. Screening to improve discrimination of short-chain versus long-chain fatty acid substrates was aided by the development of a general, automated method that allowed for visual discrimination in the hydrolysis of varied substrates in whole cells.

Gene Synthesis: Process & Applications

Presenter: Krithika Vaidyanathan, Ph.D., Scientist I, Project Management, GENEWIZ

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This webinar focuses on Gene Synthesis and why it has become the most convenient alternative to cloning. Codon optimization, the advantages of Gene Synthesis over PCR Cloning, and GENEWIZ case studies on complex projects will all be explored in this presentation. Dr. Vaidyanathan will also be answering questions about Gene Synthesis and its various applications.

Fine-tuning a Genetically Encoded Metabolite Biosensor for High-throughput Screening of Synthetic Yeast Cell Factories

Presenter: Thomas C. Williams, PhD, Macquarie University, Sydney, Australia

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The emerging field of synthetic genomics involves the redesign and construction of entire genomes. This approach to synthetic biology will enable an unparalleled understanding of minimal biological modules and genome organisation, as well as the construction of superior industrial strains. As part of the global ‘Yeast 2.0’ consortium, the Macquarie University team is contributing to the field of synthetic genomics by building chromosomes XIV and XVI of the synthetic Saccharomyces cerevisiae genome. A defining feature of the synthetic yeast genome is an inducible genome shuffling system that is facilitated by the flanking of every non-essential gene with Cre recombinase LoxP recognition sites. This Synthetic Chromosome Recombination and Modification by LoxP mediated Evolution (SCRaMbLE) system can facilitate deletion, inversion, duplication, and translocation events between LoxP sites upon Cre recombinase induction. After the synthetic yeast genome is complete, we will be able to generate millions of different versions that vary in genomic architecture and content using SCRaMbLE. The tools of systems biology can then be used to elucidate novel genome design principles that are common to SCRaMbLEd genomes with superior industrial properties.

Rewriting Natural Decoding Rules by De Novo Genome Synthesis

Presenter: Kaihang Wang, PhD, Senior Investigator Scientist, Jason Chin's Lab at MRC Laboratory of Molecular Biology and Julius Fredens, PhD, Postdoctoral Fellow, Jason Chin's Lab at the MRC Laboratory of Molecular Biology

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Genetic incorporation of unnatural amino acids allows expansion of the chemical, physical, and biological properties of proteins and thereby of life itself. One possible way of expanding incorporation to several unnatural amino acids simultaneously is by synthesising a new genome with artificially re-defined decoding rules. This requires the de novo construction of a viable, synthetic, recoded genome, with a reduced number of codons. To facilitate the synthesis of a whole genome, we have developed an efficient, specific, and iterative method in E. coli to replace defined genomic fragments with synthetic DNA (replicon excision enhanced recombination, REXER). We have employed this method to empirically test several codon compression schemes in vivo and the method should allow replacement of the entire 4.6-Mb E. coli genome in around 15 or less iterated REXER steps.

Genome-wide Synthetic Biology: From Pathways to Genomes

Presenter: Marc Güell, PhD, Wyss Institute Technology Development Fellow at Harvard University (George Church Lab)

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Advances in the first decade of 2000s enabled not only edits to genes but also to pathways. Synthetic biologists developed gene circuits to carry out sophisticated functions in cells such as synthesis of complex molecules (artemisinin, erythromycin, etc.), or biosensing. Technological advances in gene synthesis and genome engineering have radically upgraded the scope of synthetic biology applications. Gene synthesis costs have dropped exponentially, and genetic engineering has flourished with a powerful repertoire of new technologies, including MAGE and CRISPR/cas9. These new tools have enabled researchers to address genome-wide properties which alter an organism’s most fundamental features such as genetic code or transspecies differences.

Creation of Hypomorphic Alleles for Functional Gene Studies

Presenter: Sergej Djuranovic, PhD, Assistant Professor, Department of Cell Biology and Physiology, Washington University School of Medicine

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Manipulation of gene expression and activity is a standard approach to evaluate gene function in living organisms. However, current genetic tools for manipulation of gene expression are rather tuned towards complete loss of gene function; they are organism specific, show unpredictable alterations in gene activity (dependent on tissue or cell types within the organism) and change spatial-temporal regulation of gene expression. Hypomorphic mutations, partial loss of gene function, are a valuable tool for both genetic analysis of gene function and for synthetic biology applications. I will present a simple and predictable method to generate hypomorphic mutations in model organisms that targets specific step of translation cycle - translation elongation. This method is dependent on addition of polyA tracks, runs of consecutive adenosine nucleotides, to the gene coding sequence of interest. The consequence of this addition is decrease in translation elongation efficiency, and in all tested cell cultures and model organisms, this decreases mRNA stability and protein expression. As such this method can be used in industry for control of biosynthetic pathways in production of useful secondary metabolites, antibiotics or recombinant antibodies; in synthetic biology for introduction of controllable retrosynthetic and fully engineered pathways; as well as in basic research for ultimate control of gene regulatory pathways in the modelling of diseases.

Organism Making and Modding

Presenter: Mike Fero, Ph.D., CEO and Founder at TeselaGen Biotechnology

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Until recently, modifying microbes to improve production of chemicals and enzymes via fermentation has been a slow and somewhat artisanal process. With advances in recombinant methods and DNA synthesis, systems can now be put in places that vastly accelerate product development of everything from fragrances to future fuels. In this webinar, we will review the progress made and show how systems can be implemented that completely automate organism modification R&D.

Next Generation Sequencing Technologies & Applications

Emerging Next-Generation Sequencing Technologies and Applications

Presenter: Chris Mozdzierz, PhD, Associate Manager, Next-Generation Sequencing, GENEWIZ

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The most cutting-edge and powerful NGS platforms on the market are revolutionizing the way scientists do genomics. The HiSeq X Series makes the $1000 genome a reality – this platform offers the most cost-effective approach for large genome sequencing, allowing researchers to expand their population genetic studies. The PacBio Sequel is the industry-leading platform for long read lengths, allowing researchers to completely close smaller bacterial genomes and greatly aids in larger genome assemblies and structural variant discovery. The 10X Genomics Chromium is a revolutionary platform that allows for cost-effective, true single-cell analysis of up to ~50K cells. This platform’s applications include gene expression analysis from mixed samples, variant phasing, and haplotyping. This presentation will focus on how the aforementioned platforms work, their detailed applications, and some new platforms on the horizon.

Emergence of High-Throughput, Single-Cell RNA-Seq Technologies

Presenter: David Corney, Ph.D., Sr. Scientist, Next Generation Sequencing

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Traditional RNA-seq produces a representative snapshot of the transcriptional state averaged across all cells. The caveat with traditional RNA-seq is the resolution of individual cells and cellular subpopulations are lost. Various single-cell RNA-seq techniques have emerged to allow researchers to not only identify cellular subpopulations, but to fully interrogate them. In this webinar, we will review the applications of popular single-cell RNA-seq approaches. We will then highlight case studies using a microdroplet technology, the 10x Genomics Chromium™. This platform is driving the evolution of single-cell RNA-seq, offering high-throughput, cost-effective and interactive analysis.

PacBio Sequencing Overview and Applications

Presenter: Haythem Latif, Ph.D., Business and Strategic Partnership Manager at GENEWIZ

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PacBio long reads offer a distinctive advantage over short reads in that they can span long repeat regions, link variants spanning multiple kilobase, and offer higher consensus accuracy. Here, we will focus on how researchers are leveraging the benefits of long reads to complement or replace short reads. The Sequel system enables multiplexed, high quality, small genome assemblies to be produced from a single SMRT cell while also allowing for large genome de novo assemblies to be completed quickly. Low coverage human whole genome sequencing has facilitated analysis and discovery of a myriad of large structural variants. Multiplexed targeted resequencing on the Sequel allows extending amplicon sequencing to several kilobases thereby spanning highly complex, highly variable regions. Lastly, the various isoforms naturally present in the transcriptome can be interrogated using the Iso-Seq workflow. Collectively, the Sequel is enabling exploration of the complexities of the genome and transcriptome in new and valuable ways.

Rapid and Sensitive Validation of Gene Editing with Novel NGS Assays

Presenter: Chris Mozdzierz, Ph.D., Manager, Next Generation Sequencing at GENEWIZ

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The discovery and advancements of nucleases, including CRISPR-Cas9, have revolutionized the accuracy and downstream potential of targeted genomic manipulations. Despite these advancements, identification of correctly targeted events remains a significant bottleneck. Simple, fast, and cost-effective techniques, such as RFLP and Sanger sequencing, have traditionally been used for screening. However, both techniques lack sensitivity and scalability. Next-generation sequencing provides ultra-sensitive results, but requires extensive bioinformatics expertise to interpret data. Furthermore, scalability was mitigated by limitations in off-the-shelf library preparation kits. This webinar will describe the differences amongst various screening techniques and focus on recent advancements in the utility of next-generation sequencing.

Solving Forgotten Disorders: Gene Discovery for Cerebellar Malformations

Presenter: Kimberly Aldinger, PhD, Research Scientist at the Center for Integrative Brain Research at Seattle Children’s Research Institute

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Next generation sequencing has revolutionized medical genetics, identifying the genetic causes for hundreds of disorders. One notable exception is cerebellar disorders, which have eluded gene discovery for several reasons: cerebellum is often not assessed in children with other diagnosed neurodevelopmental disorders, clinical and neuroimaging features of specific cerebellar malformations overlap considerably, and non-genetic causes of cerebellar damage, such as prenatal hemorrhage, often cannot be distinguished from likely genetic-caused cerebellar disruption. We are examining DNA from the largest collection of patients with cerebellar malformations using exome and genome sequencing together with cell-type specific RNA-sequencing of fetal cerebellum to identify the genetic causes for phenotypes with primary effects on cerebellar structure and function that are often overlooked.

Effective & Efficient Approaches to Cell Line Engineering in CHO Cells

Presenter: Stephanie Sandefur, Consultant Biologist in the Molecular & Cellular Biology Group at Eli Lilly and Company

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Over the past decade, considerable progress has been made in improving the effectiveness and efficiency of generating highly-productive recombinant CHO cell lines. These improvements are now the underpinning of bioprocess development and involve both advancements in cell line generation and cell culture process development. While these efforts have been primarily centered on driving cell culture productivity, more recently, focus has turned to approaches to impact product quality. Specifically, host engineering capabilities have been directed to successfully edit CHO cell lines to improve product quality profiles of bio-therapeutic proteins. Given the labor-intensive, inefficient and time-consuming nature of such capability application, a significant need exists to find creative approaches to maximize the effectiveness, while minimizing the impact of such efforts to timelines. This presentation will describe potential approaches to maximizing the effectiveness of host cell engineering and reducing the time to successfully impact bio-therapeutic product quality profiles.

Population-specific Transcriptional Analysis Methods for Brain Tissue

Presenter: Hope Kronman, Graduate Student in Neuroscience at Icahn School of Medicine, Mount Sinai

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The brain is an intricate web of specialized neurons, with sub-populations of these neurons expressing unique markers and serving distinct biochemical - and behavioral - roles. The cutting edge of transcriptional analysis in the brain has gotten sharper in recent years, and neuroscientists are moving from broad, whole-tissue experiments to more refined analyses of neuronal cell types. This webinar will discuss the technical elements of dissociating, sorting and analyzing brain tissue according to two different protocols - whole cell and nuclear extraction. It will also touch upon the challenges and promises of moving to single-cell analysis of neuronal transcription.



Metagenomics

Metagenomics for Biomarker Discovery: Precision Medicine Applications

Presenter: Edward Messick, Bioinformatics Analyst at GENEWIZ

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Metagenomics, the study of all genetic material within a community of microbes, can be applied broadly to research across many industries. The field of microbiome research is booming and will continue to expand into both new and existing areas of research and development, including medicine. In this webinar, I will discuss how metagenomics can be used to develop microbiome-based biomarkers. Such biomarkers may be applied to precision medicine, direct-to-consumer applications, and agriculture. Medical studies of the human microbiome can be leveraged in developing diagnostic tools, new therapies, and even as an indicator of success in a surgical procedure. Direct to consumer applications of metagenomics are helping reveal links between our microbiome and health, diet, or lifestyle. Microbiome-based biomarkers can also be developed in other fields like agriculture to help understand plant health or to improve crop yield. As the number of microbiome based studies continues to grow, the applications of metagenomics will as well. This webinar introduces bioinformatics techniques for metagenomic analysis and discuss several exciting applications for this new class of biomarkers, highlighting the current and future developments within precision medicine.

Metagenomics as a Window into the Microbial World: Medical Implications of the Gut Microbiome & Other Applications

Presenter: Gilead Kedem, M.D., Senior Bioinformatics Analyst, GENEWIZ

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Microbial communities abound everywhere and exert powerful effects on their surroundings. For example, variations in the gut microbiome—the trillions of bacteria in the human gut—are associated with disorders ranging from diabetes mellitus and obesity to inflammatory bowel disease to cancer.This webinar will describe how metagenomic sequencing and bioinformatics are being applied to a range of industries, including microbiome-based diagnostics and therapeutics, infectious disease diagnostics and agriculture.



Immunology

Immuno-sequencing Analysis and its Clinical Applications

Presenter: Dr. Antonina Silkov, Bioinformatics Analyst at GENEWIZ

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B and T cells are major players of an adaptive immune system that protects organisms against pathogenic hazards. B and T cell receptor repertoires are highly diverse due to V(D)J rearrangement and somatic mutations. This diversity enables recognition of a wide range of antigens. High-throughput sequencing empowers B and T cell receptor repertoire profiling, which provides insights into the adaptive immune response in healthy individuals and in those with a wide range of diseases.

Automated Microfluidic Platform for Circulating Tumor Cell Capture

Presenter: Yixin Wang, Ph.D., Chief Scientific Officer at Celsee Diagnostics

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Cancer is comprised of heterogeneous cell populations, and research is increasingly becoming dependent on the ability to isolate rare cells, both enriched populations as well as individual, single cells. Employing advanced molecular and cytogenetic technologies to analyze isolated rare cells, such as circulating tumor cells, provides a unique opportunity to interrogate the cancer biomarkers.