Minor Tweak, Major Impact

Cori Bargmann is a neuroscientist and geneticist. She received a BS in biochemistry from the University of Georgia and a Ph.D. from the Massachusetts Institute of Technology. Cori has studied the relationships between genes, circuits, and behaviors in the genetically tractable nematode worm Caenorhabditis elegans as a faculty member at the University of California, San Francisco (1991-2004) and at the Rockefeller University as the Torsten N. Wiesel Professor and Head of the Lulu and Anthony Wang Laboratory of Neural Circuits and Behavior (2004-present). Cori’s work has been recognized by scientific honors including a 2012 Kavli Prize in Neuroscience, the 2013 Breakthrough Prize in Life Sciences, and she also co-chaired the NIH working group to the Advisory Committee to the NIH Director for President Obama’s Brain Initiative. In 2016, Cori joined the Chan Zuckerberg Initiative as its first Head of Science. CZI Science has the mission of supporting the science and technology that will make it possible to cure, prevent, or manage all diseases by the end of the century. Referenced Links: HCA Method Development Community - https://www.protocols.io/workspaces/hca COVID-19 Cell Atlas - https://www.covid19cellatlas.org/ CZI Science - https://chanzuckerberg.com/science/

Ross has recently completed his PhD at the Manchester Institute of Biotechnology. Ross has worked on modern tools for fine-tuned regulation of gene expression in bacteria, with a focus on applying statistical modelling techniques and QbD and Design of Experiments to rapidly engineer and optimise genetic toolkits. Ross is currently working at the University of Manchester as a postdoctoral research associate in the lab of Dr. Neil Dixon, but will shortly be starting a new position at Syngenta as an Automation Scientist. In this episode we’re talking with Ross about his work, Design of Experiments, Computer-Aided Biology, the impact of the coronavirus pandemic and more. Referenced Links Survey and CAB website: https://www.computeraidedbiology.com/cab-survey https://www.computeraidedbiology.com Paper explaining why we need DoE: https://pubmed.ncbi.nlm.nih.gov/26505134 Synthace articles on DoE: https://synthace.com/blog/2020/6/4/heres-why-you-should-stop-doing-science-like-you-were-taught-in-high-school-part-1 https://synthace.com/blog/2020/6/29/heres-why-you-should-stop-doing-science-like-you-were-taught-in-high-school-part-2

Richard Harris has been a science correspondent at National Public Radio since 1986. He took a break from that to write Rigor Mortis – a book about rigor and reproducibility in biomedical research, which was published in 2017. Rigor Mortis was a finalist for the 2018 National Academies Communication Award. In this episode we’re talking to Richard about his experience as a science writer, the Rigor Mortis book and Minor Tweak Major Impact stories that it covers, as well as the impact of the coronavirus pandemic. Referenced Links: Book “Rigor Mortis: How Sloppy Science Creates Worthless Cures, Crushes Hope, and Wastes Billions” https://www.amazon.com/Rigor-Mortis-Science-Worthless-Billions/dp/0465097901

Juita Martinez is a wildlife conservationist and a 3rd year BOR-SREB doctoral fellow at the University of Louisiana at Lafayette. For her dissertation research she is studying the effects of barrier & bay island restoration on Brown Pelican (Pelecanus occidentalis) demography and reproductive ecology in coastal Louisiana. She focuses on utilizing non-invasive techniques to gain a better understanding of how organisms utilize their natural habitats. Juita’s work aims to aid in the conservation of her study organisms and communicate ways to inspire generations after her to do the same. Referenced Links: Juita's Twitter - https://twitter.com/JuitaMartinez Juita’s Website - https://juitamartinez.weebly.com/

Dr. Shai Silberberg is the Director of Research Quality at the NIH National Institute of Neurological Disorders and Stroke (NINDS) leading the Institute efforts to increase the excellence of science and the completeness of research reporting. Prior to joining NINDS, Dr. Silberberg was an Associate Professor at Ben-Gurion University of the Negev in Israel, investigating the biophysical functions and physiological roles of ion channels.

Naomi is a senior staff scientist in the DNA pipelines research and development team at the Sanger Institute. Thirteen years ago, her PhD included researching improvements to multiplex PCR – an integral method to many of the processes she has since been involved with at Sanger. Discovering this experience would be extremely useful in the midst of a pandemic is something she didn’t see coming.. Referenced Links: Josh Quick 2020. nCoV-2019 sequencing protocol. dx.doi.org/10.17504/protocols.io.bbmuik6w COVID-19 ARTIC v3 Illumina library construction and sequencing protocol. dx.doi.org/10.17504/protocols.io.bgxjjxkn Naomi’s Tweet https://twitter.com/SequencingPark/status/1263802155816947715?s=20

Dr. Matthew DeGennaro’s laboratory at Florida International University studies the molecular genetics of mosquito host detection and the vector ecology of Aedes aegypti. During his postdoctoral training at Rockefeller University with Leslie Vosshall, he used the first mosquito mutant to study behavior in yellow fever mosquito, Aedes aegypti. His work has explored how mosquitoes sense human sweat, choose a host, and avoid repellents like DEET. Matt’s current goal is to identify the critical olfactory receptors that mosquitoes need to find humans and use these genes to identify new attractants and repellents. Referenced Links: DeGennaro Lab http://www.degennarolab.org/

Rebecca Nance is a research assistant and PhD student in Dr. Bruce Smith's lab in the Scott-Ritchey Research Center at the Auburn University College of Veterinary Medicine in Auburn, Alabama. Rebecca is involved in modifying Canine Adenovirus Type 2 to explore targeted oncolytic virotherapy in dogs. Using a transcriptomic sequencing approach, the team aims to identify potential targets that are unique to cancerous tissue when compared to the corresponding tissue of origin. In this show, she discusses simple protocol modifications that allowed the isolation of moderately intact RNA from the dense, brittle, and hypocellular bone matrix of canine phalanges, with minimal contamination from connective tissue and marrow, in a quantity and quality suitable for transcriptomic sequencing. Referenced Links: A method for isolating RNA from canine bone, BioTechniques. https://doi.org/10.2144/btn-2019-0153 A method for isolating RNA from canine bone, protocols.io. dx.doi.org/10.17504/protocols.io.bf9vjr66

Dr. Lenny Teytelman has over a decade of computational and experimental biology experience. He did his graduate studies at UC Berkeley, and it was his struggle with correcting a published research method as a postdoc at MIT that led him to cofound protocols.io. Lenny brings to protocols.io a strong passion for open access, sharing knowledge, and improving research efficiency through technology. Referenced Links: Fixation of yeast cells for RNA-FISH V.1 https://www.protocols.io/view/Fixation-of-yeast-cells-for-RNA-FISH-fbjbikn/abstract Modified protocol for URA3 counter-selection at highly expressed regions of Saccharomyces cerevisiae https://www.protocols.io/view/modified-protocol-for-ura3-counter-selection-at-hi-bf7njrme/abstract

Dr. Kenneth Yamada has been an NIH Distinguished Investigator since 2011. He has been a Section Chief at the National Cancer Institute and currently at the National Institute for Dental and Craniofacial Research at NIH. His research focuses on discovering novel mechanisms of cell interactions with the extracellular matrix and their roles in cell migration and tissue reorganization in embryonic development and cancer. He has published more than 400 papers that are highly cited. His Additional interests include research reproducibility, enhancing diversity, and mentoring the next generation of researchers. Referenced Links: NIH Rigor and Reproducibility Best Practices https://www.nih.gov/research-training/rigor-reproducibility 2016 NIH Case Study on Research Reproducibility https://oir.nih.gov/sites/default/files/uploads/sourcebook/documents/ethical_conduct/case_studies-2016.pdf