Category Archives: Molecular Genetics

image:Testis tissue section from a wild-type mouse stained for meiotic markers (in pink and green) and DNA (in blue). view more

Credit: Courtesy of Devanshi Jain

Researchers at Rutgers University, Memorial Sloan Kettering Cancer Center, Rockefeller University, and Cornell University are teaming up to examine how the processes that regulate gene expression and chromosome behaviors can lead to health issues, including cancer, birth defects, miscarriage, and infertility.

Cells undergo a remarkable transformation process to form eggs and sperm, which upon fertilization can form an entire organism. A key step of this transformation involves meiosis, a cell division that halves the genome content of cells. During early stages of egg and sperm development, cells divide by mitosis, the process used by most cells in our body. They then undergo a complete remodeling of the gene expression landscape, and switch to meiosis. Mis-regulation of the mitosis-to-meiosis switch can lead to tumor-like growth, depletion of the reproductive cell pool or failure to complete meiosis.

In the new Rutgers-led study in the journal Genes & Development, the researchers applied powerful methods for mapping genome-wide protein-RNA interactions and innovative genetic mouse mutants to define how the RNA helicase, YTHDC2, binds RNA and controls gene expression to regulate meiosis. YTHDC2 and its interacting protein partners form an essential pathway that controls the mitosis-to-meiosis switch. Prior to this study, little was known about the mechanisms regulating this switch in mammals.

Our work sheds light on the genetic and molecular mechanisms that are required for normal meiosis, which is an essential step towards understanding how and why these processes go wrong and lead to reproductive disorders, said Devanshi Jain, a principal investigator of the study and an Assistant Professor of Genetics at the School of Arts and Sciences (SAS) at Rutgers University-New Brunswick. Additionally, as YTHDC2 has been implicated in multiple diseases, especially cancers, our work will have broad implications on those fields as well.

Jain said this new study, along with ongoing research at the Rutgers-housed Jain Lab, explores the genetic and molecular mechanisms of meiosis, and the processes that regulate gene expression and chromosome behaviors. Researchers at the Jain Lab use the mouse model system to explore these fundamental aspects of cell biology.

Understanding meiosis is of paramount importance to reproductive health as errors in meiosis can lead to reproductive cell death and infertility, said Jain. Going forward, we plan to delve deeper into the molecular mechanisms of the YTHDC2 pathway and its control of gene expression. We also continue to study other fundamental aspects of how meiosis is regulated.

Genes & Development

YTHDC2 control of gametogenesis requires helicase activity but not m6A binding

20-Jan-2022

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.

Originally posted here:
New research sheds light on causes of reproductive disorders, infertility, miscarriage, birth defects - EurekAlert

Bioinformatics jobs involve analyzing and interpreting biology-related data. These professionals' work benefits hospitals and medical clinics, healthcare and pharmaceutical companies, biotechnology firms, and research institutions.

As a bioinformatics professional, you're equipped to design and develop the tools, methods, and systems to work with data. Bioinformaticians aid life-saving medicine development, study genes, improve crop productivity, and more.

Bioinformatics professionals work full-time in labs, offices, and research settings. They use statistics, programming, data management, and machine learning skills. They also understand biology and may specialize in a subdiscipline, like genomics or molecular biology.

The federal government, private corporations, and the public sector all employ bioinformatic professionals to analyze and interpret biological data. They also hire individuals who can create software and hardware to manage and assess large datasets.

Bioinformatics jobs may allow you to work remotely, depending on the position and employer.

According to Payscale, the average base salary in informatics is $87,000 per year as of March 2022. Education level, experience, industry, and location influence pay.

You can find top-paying bioinformatics jobs in companies and agencies focused on biotechnological research. Research scientists took home average salaries above $91,000 in 2021. Senior research scientists in biotechnology earned nearly $110,000 on average in early 2022.

Additional education and training prepare you for advanced and managerial bioinformatics positions and may boost your earning potential. Certificates and advanced degrees, such as a computer science master's degree, increase your knowledge.

By gaining insight into emerging technologies through continued education, you position yourself to grow in the field.

Earning a bioinformatics degree may lead to a job in agriculture and wildlife, computer technology, research, or biotechnology.

Bioinformatics jobs are varied and may be highly specialized. You'll find some of the more prominent jobs below.

Bioinformatics jobs in agriculture, zoology, microbiology, and wildlife biology involve assessing data related to plants, crops, and animal health.

You apply knowledge of statistics, computer science, and information technology at companies or in the public sector.

Bioinformaticians in these fields protect and study living organisms, optimizing interactions among them. Depending on the setting, you may work to increase food production, assess genetic variations, or improve land productivity.

Some roles include:

Bioinformatics jobs in computer and data science put your computational and analytical skills to work. In this discipline, you design new hardware and software to assess biological data.

Research and development, technology firms, and healthcare informatics companies may hire bioinformatics specialists to create proprietary software. You may also qualify to work as a biological data scientist in industrial settings.

Common jobs include:

Bioinformatics professionals in pharmaceuticals serve a vital role in the creation, development, and testing of new medications. Bioinformaticians in biotechnology might assess data needed to develop gene therapies and advance immunology.

You may improve existing processes and technologies and establish new data analysis methods. In both pharma and biotech roles, you work alongside fellow scientists and computational biologists to contribute to the field at theoretical and practical levels.

Pharma and biotech roles include:

Clinical bioinformatics data analyst

Project manager for bioinformatics

Human genetics bioinformatics scientist

Public-sector bioinformaticians may work for federal, state, and local governments to address public health and safety issues. The government also employs bioinformaticians in agriculture and wildlife-related roles.

In public sector roles, you may work to improve your environment and the world. Public sector bioinformatics positions also advance military medicine, inform national and regional policies, and contribute to agricultural production.

Job options include:

Bioinformatics scientist with the National Institute of Health

Bioinformatics analyst with a state hospital system

Computational biologist with a local or state department of public health

Research and academic bioinformatics jobs extend from the lab to the classroom. Colleges and universities may employ bioinformatics researchers in labs and as instructors.

Bioinformaticians at colleges and universities often work with public agencies and private companies. Through grants and collaboration, bioinformatics researchers and academics work with funders to tackle projects. For example, you might map the genes that cause a poorly understood disease.

Roles include:

Bioinformatics blends science and technology. You may find jobs in the private and public sectors with a bioinformatics degree.

Bioinformatics jobs involve interpreting data to address vital issues. Sound rewarding? If so, bioinformatics might be the right field for you.

Nicole Galan is a registered nurse who started in a general medical/surgical care unit and then moved into infertility care, where she worked for almost 10 years. She has also worked for over 13 years as a freelance writer, specializing in consumer health sites and educational materials for nursing students. Galan currently works as a full-time freelancer and recently earned her master's degree in nursing education from Capella University.

Nicole Galan is a paid member of the Red Ventures Education freelance review network.

Last reviewed March 22, 2022. Unless otherwise noted, salary data is drawn from Payscale as of March 24, 2022.

Read more:
Bioinformatics jobs: All of your options - ZDNet

Gennady Bratslavsky, MD, spoke about the evolution for treatments in renal cell carcinoma and how surgery may play a role.

The role of surgery for renal cell carcinoma (RCC) and strategies used for treatment are ever evolving. As options for systemic therapies continually improve, many clinicians are opting to spare patients from undergoing procedures.

Gennady Bratslavsky, MD, professor and chair of the Department of Urology and director of the Prostate Cancer Program at Upstate Medical University in Syracuse, New York, recently hosted a presentation on the role of surgical in management in RCC at the 15th Annual Interdisciplinary Prostate Cancer Congress and Other Genitourinary Malignancies, hosted by Physicians Education Resource, LLC (PER).

I still think that there will be appropriately selected patients [for whom] surgery will remain the first and potentially the main type of treatment. We may even include metastasectomy [for some as] that has been used for years, said Bratslavsky.

In an interview with CancerNetwork, Bratslavsky spoke about what role surgery currently plays in RCC, new strategies on the horizon, and trials he is most excited to see read out.

This is an evolving landscape. We are going to try to operate less on patients who we can avoid surgery, were going to try to prognosticate better and see who can be spared. The term intervention-free survival is something that will hopefully be used more and more. Some trials are being designed, for example, in a role for renal biopsy where type of surgery or timing of surgery may be affected.

The role of surgery for more advanced disease is also ever changing. Obviously, the dogma that every metastatic kidney cancer can be removed is wrong, [but] his can still render patients disease free and offer a durable long-term survival.

The adjuvant [therapy] space is finally having some promise with the recently published KEYNOTE-564 trial [NCT03142334]. Adjuvant pembrolizumab [Keytruda] certainly [provides] an opportunity for us to expect and hope for disease-free survival [DFS]. Most of the adjuvant trials to date have not been more successful [than KEYNOTE-564]. Even in the S-TRAC [NCT00375674] trial of adjuvant [sunitnib; Sutent] utilization for a year after nephrectomy in patients with the kidney cancer that were found to be high risk, the presence of DFS never translated into overall survival [OS].

While KEYNOTE-564 is yet to matureto demonstrate whether its use in the adjuvant setting would help with OS is yet to be determinedthere is certainly quite a bit of hope that after 2 years of follow up, were starting to see a promise and a strong signal that this DFS may translate into OS, although this has yet to be seen. The recently completed PROSPER trial [NCT03055013] is bringing another opportunity for us to evaluate the role of immunotherapy in the neoadjuvant as well as the adjuvant setting for high-risk patients. There are many unanswered questions. Even if we identify an agent that is effective in improving DFS, we will always question the patients who would have not recurred and still would be subjected to therapy. There is still an ongoing need for better identification of these patients that are most likely to recur beyond our standard clinical variables that have been traditionally used in designing the trials for both neoadjuvant and an adjuvant therapy.

Any research [conducted] has an enormous impact [on] the molecular subcategorization of renal neoplasms, the understanding of genetics, branched evolution, our ability to detect the circulating tumor DNA, and the numerous structures that still contain many of the genetic material and prognostic information. All of this has an enormous potential [for clinical impact].

Were continuously learning about new pathways that may bring in more systemic options, with the biggest breakthrough [being] in our continued appreciation of how heterogeneous kidney cancer is as a disease, how heterogeneous the molecular characteristics are, and how heterogeneous the clinical course and the metastatic potential of each tumor is. These are not tumors that are created equal. They possess very different clinical behaviors and opportunities for targeted or immunotherapies. Research is strong.

Our lab at SUNY Upstate Medical University focuses on the role of molecular chaperones in identification of potential targets and how activity of chaperones can be modified. Our lab has been creating new avenues for therapeutics. Numerous centers and laboratories are doing a great job in identifying these new avenues into how this cancer can be targeted or identified, and even the identification of some biomarkers for better disease response. [There are many paths] that were trying to tackle from different angles.

Choueiri TK, Tomczak P, Park SH, et al. Adjuvant pembrolizumab after nephrectomy in renal-cell carcinoma. N Engl J Med. 2021;385(8):683-694. doi:10.1056/NEJMoa2106391

View post:
The Changing Treatment Landscape and the Role of Surgery in RCC - Cancer Network

Most people are familiar with the cell nucleus from grade school biology as a storage compartment for DNA. But the nucleus also contains several distinct structurescalled nuclear bodies or domains and some of them are brimming with genes messages, also known as RNA transcripts.

Scientists are just now beginning to understand these structures, with University of Toronto researchers recently reportingthe first large-scale survey of RNA transcripts that are associated with different nuclear bodies in human cells.

The work, published in the journalMolecular Cell, suggests that the structures act as hubs to co-ordinate gene regulation and cell division.

It was known that some nuclear domains contain RNA, but the composition of that RNA was not systematically probed in previous studies, saidBenjamin Blencowe, senior author on the study and a professor of molecular genetics in the Donnelly Centre for Cellular and Biomolecular Researchat the Temerty Faculty of Medicine.

Our data has shed light not only on the RNA composition of different nuclear domains, but also provides clues as to the functions of some of these domains.

Until now, the information on nuclear body composition has trickled in piecemeal because there were no methods enabling a systematic survey of RNA localized to these structures. But post-doctoral researcher Rasim Barutcuand graduate studentMingkun Wurealized they could apply a method called APEX-Seq, which had been developed by scientists at Stanford University and the University of California, Berkeley.

APEX is an enzyme that can be fused to any protein of interest and allows labeling of RNAsand other biomoleculesin its proximity. The labeled RNAs can then be isolated and identified by sequencing. By fusing APEX to various marker proteins residing in the different nuclear bodies, Barutcu and Wu were able to create RNA maps for each.

The pair collaborated withUlrich Braunschweig, a senior research associate in Blencowes lab, and with the groups of:Anne-Claude Gingras, a senior scientist at the Lunenfeld-Tanenbaum Research Institute,Sinai Health System, and professor of molecular genetics;Philipp Maass, a scientist at TheHospital for Sick Children andassistant professor of molecular genetics;andRobert Weatheritt,a principal investigator at theGarvan Institute of Medical Research inAustralia.

The team discovered swaths of novel RNAs from several hundred to thousands across the nuclear bodies. Previously, only a handful of transcripts were known to be associated with some of these structures, said Barutcu, whose research was supported by the Banting Postdoctoral Fellowship and a fellowship from the Canadian Institutes of Health Research (CIHR).

One piece of data immediately struck the researchers: The nuclear bodies known as speckles were associated with surprisingly high numbers of RNA transcripts with retained introns segments that do not code for proteins. When a gene is transcribed into RNA, introns must be spliced out in the nucleus before the transcript can be released into the cells interior to serve as a template for making proteins.

The finding led them to realize that speckles are associated with a class of introns with delayed splicing. The nature of the transcripts provided a clue to their function. They were transcribed from genes that control various aspects of gene regulation and the cell division cycle. Genes controlling cell cycle progression must be activated in a timely manner so that their protein products are made only when they are needed. Errors in this process are well known drivers of cancer.

The researchers came up with a model in which the role of the speckles might be to co-ordinate intron removal from transcripts in order to regulate their release from the nucleus, and their subsequent translation into protein factors required for gene regulation and the cell cycle. This mechanism would help ensure a rapid response to cellular signals to make the right kinds of proteins at the right time.

Furthermore, when speckles were disrupted, this altered the splicing of the retained introns, including those located in genes that are directly involved in control of the cell cycle, supporting the idea that the speckles are linked to cell cycle progression.

The model opens up new ways of thinking about cell cycle regulation with implications for cancer research, said Blencowe, who holds a Canada Research Chair in RNA Biology and Genomics and Banbury Chair in Medical Research.

Weve uncovered a mechanism involving differential intron retention linked to speckle integrity that could play an important role in not just normal cell division but also how it goes wrong in cancers, he said, noting that the project was made possible by the now defunct CIHR Foundation grant scheme, which provided long-term research funding.

In addition to the speckles, the team also found large numbers of intron-retained transcripts associated with the nuclear lamina, which forms at the periphery of the nucleus. However,the functional significance of this observation remains unclear.

The researchers said they hope others in the field will take advantage of their datasets and open new avenues of research into nuclear body function where many questions remain.

Read the original here:
RNA map of cell nucleus reveals new insights into gene regulation and cell division - University of Toronto

The School of Biological Sciences

Batley Lab Crop Genomics

About the team

The School of Biological Sciences is a large, multidisciplinary School with over 80 high-calibre staff delivering world-class education and research programs to approximately 600 undergraduate and postgraduate coursework students and is responsible for the supervision of ~100 PhD students. The School is research-intensive with expertise in the disciplines of Computational Biology, Ecology & Conservation, Evolutionary Biology, Neuroscience and Science Communication.

The Batley lab studies genetics and genomics on a range of crop and pathogen species, including subterranean clover, soybean, wheat, banana and chickpea, with other projects on a wide range of species including parasitic plants and pearl oyster, however our primary research focus is on the agricultural oilseed crop Brassica napus (canola), and its interactions with the disease-causing fungus Leptosphaeria maculans (blackleg).

Related research projects include identification of blackleg disease resistance genes in canola using next-generation sequencing and high-throughput molecular marker approaches. New projects are investigating the role of structural variation in the Brassica genomes, specifically in relation to disease resistance and understanding the evolution of disease resistance genes. In conjunction with this our lab continues to work on development of genomes and pan genomes.

About the role

You, as the successful appointee, will be responsible for research projects investigating plant pathogen interactions and evolution of disease resistance genes and preparing and publishing scientific publications with a focus on crop plants.

You will also be involved in project planning, execution of molecular experiments, data analysis and interpretation, preparation of scientific manuscripts for publication and participation in the supervision of other research personnel engaged in the projects.

To be considered for this role, you will demonstrate:

Full details of the position's responsibilities and the selection criteria are outlined in the position description.

Closing date:Friday, 20 May 2022

This position is open to international applicants.

Application Details: Please apply online via the Apply Now button.

Our commitment to inclusion and diversity

UWA is committed to a diverse workforce. We celebrate inclusion and diversity and believe gender equity is fundamental to achieving our goal of being a top 50 university by 2050.

See the original post:
Research Associate, Crop Genomics job with UNIVERSITY OF WESTERN AUSTRALIA | 286656 - Times Higher Education

Three Minute Thesis (3MT), a spoken-word thesis competition held annually at Stony Brook, is an opportunity for graduate students to present their dissertation research findings to a general audience in three minutes with only one PowerPoint slide. The goal is for students to engage all their communication skills to make their research vivid and engaging while emphasizing its key point without technical terminology or field-specific jargon.

Graduate students receive specialized coaching and professional development that uses a cohort approach to encourage peer feedback and support. The Alumni Association sponsors prizes for the best talks: First Prize: $1,000, Second Prize: $700, Third Prize: $500 and Peoples Choice: $300. Talks are evaluated by a panel of judges from a range of backgrounds and disciplines for how well the speaker engages a general audience of non-specialists and can convey the excitement and innovation of their research without jargon or distortion.

The final round of this years competition will be held live via Zoom on Wednesday, April 6, at 4 pm and streamed on stonybrook.edu/3mt.

The 2022 3MT competitors are:

Farzana Ali, Biomedical Engineering, Advisor: Christine DeLorenzoCaitlyn Cardetti, Molecular and Cellular Pharmacology, Advisor: Daniel Bogenhagen Allen Chen, Neuroscience, Advisor: Qiaojie XiongXinan Chen, Applied Mathematics and Statistics, Advisor: Allen TannenbaumMarcy Ekanayake-Weber, Interdepartmental Doctoral Program in Anthropological Sciences, Advisor: Andreas KoenigShrin Feiz-Disfani, Computer Science, Advisor: IV RamakrishnanLesia Guinn, Biomedical Engineering, Advisor: Gabor BalazsiMoises Hassan Bendahan, Hispanic Languages and Literature, Advisor: Kathleen VernonJessica Hautsch, English, Advisor: Amy CookKathryn Hill, Neuroscience, Advisor: Ramin ParseyErwei Huang, Chemistry, Advisor: Ping Liu (BNL)Samruddhi Jewlikar, Biochemistry and Structural Biology, Advisor: Peter TongeSin-ying Lin, Clinical Psychology, Advisor: Nicholas Eaton Yu Chung Lin, Materials Science and Chemical Engineering, Advisor: Miriam RafailovichXiaoyang Liu, Materials Science and Chemical Engineering, Advisor: Yu-Chen Karen Chen-WiegartDevon Lukow, Genetics, Advisor: Jason SheltzerAlok Mishra, Computer Science, Advisor: Barbara ChapmanPhilip Opsasnick, Philosophy, Advisor: Anne OByrneGiancarlo Pasquini, Social and Health Psychology, Advisor: Stacey ScottDerek Pope, Science/STEM Education, Advisor: Angela KellyAnthony Ripa, Computer Science, Advisor: Aaditya RanganDeborah Rupert, Neuroscience, Advisor: Stephen SheaHeidi Schneider, Music, Advisor: Jeremy LittleDamion Scott, Philosophy, Advisor: Harvey CormierAlyssa Stansfield, Atmospheric Science, Advisor: Kevin ReedLiu Yang, Electrical Engineering, Advisor: Petar Djuric

The winner of Stony Brooks 3MT 2022 competition will have the opportunity to represent Stony Brook in the Northeastern regional competition.

Read story "Three Minute Thesis Competition Final is April 6" on SBU News

More:
Research - Stony Brook University

PHILADELPHIA--(BUSINESS WIRE)-- Ceptur Therapeutics, Inc. (Ceptur), a biotechnology company focused on developing targeted oligonucleotide therapeutics based on U1 Adaptor technology, today announced the completion of a $75M Series A financing. The round was co-led by venBio Partners and Qiming Venture Partners USA with participation by new investors Perceptive Xontogeny Venture (PXV) Fund, Bristol Myers Squibb and Janus Henderson Investors along with existing Seed investors Affinity Asset Advisors, Boxer Capital and LifeSci Venture Partners.

We are extremely grateful for the support of our new and existing investors, said Ceptur Therapeutics co-founder, President and CEO P. Peter Ghoroghchian, MD, PhD. In 2021, we in-licensed and internally expanded our foundational IP portfolio on U1 Adaptor technology; we further recruited a world-class scientific advisory board, comprising academic and industry leaders in oligonucleotide therapeutics. Moving forward, Ceptur will use the proceeds of this financing round to advance our broad discovery pipeline of differentiated genetic medicines.

U1 Adaptors are bivalent oligonucleotides that engage sequence-specific mRNA and the U1 small nuclear ribonuclear protein (U1 snRNP), which is a ubiquitous intracellular machine that regulates transcription and splicing. U1 Adaptor therapeutics control gene expression at the pre-mRNA level within the nucleus, affording advantageous properties for drugging difficult targets.

Therapeutic approaches that target RNA have become an essential treatment modality for patients with genetic diseases and a priority for many biopharma companies; we believe that the U1 Adaptor technology is a differentiated approach to RNA regulation that has multiple potential advantages over current technologies, said Aaron Royston, M.D., M.B.A., Managing Partner at venBio Partners. We are excited to further build out Cepturs team and capabilities, to demonstrate these unique applications, and, ultimately, to advance novel therapeutics for patients with genetic diseases.

Colin Walsh, Ph.D., Partner at Qiming Venture Partners USA, added, RNA-based drugs have already become an essential tool in our therapeutic arsenal; and, we strongly believe that this modality will continue to deliver meaningful new therapies for patients. Cepturs use of synthetic oligonucleotides that engage U1 snRNP offers the ability to co-opt this master regulator of the transcriptome to regulate mRNA in a highly targeted fashion. We are thrilled to support Cepturs next phase of growth as they apply this disruptive approach for novel therapeutic applications.

With this financing, Aaron Royston, M.D., M.B.A., and Colin Walsh, Ph.D., join Cepturs Board of Directors.

Daniel Heller, M.S., M.B.A., General Partner and Chief Investment Officer at Affinity Asset Advisors, continued, In leading the Series Seed round, we identified early the potential of U1 Adaptor technology. Over the past year, we have worked closely with Peter and the Ceptur team and are delighted at the progress that has been made towards establishing the platform. In this financing round, we have significantly expanded upon our initial commitment and are inspired to partner with our new investor syndicate to advance U1 Adaptors for unmet patient needs.

To realize the revolutionary potential of the U1 Adaptor technology, several new members join Samuel Gunderson, Ph.D., co-founder of Ceptur, Professor of Molecular Biology at Rutgers University, and a leading expert on U1 snRNP biology, on Cepturs Scientific Advisory Board:

Thomas Andresen, Ph.D. Dr. Thomas L. Andresen is the CEO of T-Cypher Bio and the former CSO of Torque Therapeutics, now Repertoire Immune Medicines. While at Torque, he led the companys cellular immunotherapy programs from early-stage discovery to CMC scaling and through to clinical development. Dr. Andresen is a serial entrepreneur, having founded several US and EU life-science companies that further include Nanovi A/S and Monta Biosciences. His company creation track record spans early discovery to commercial and maps across multiple immunotherapy approaches for oncology. Dr. Andresen sits on several boards/advisory boards, including for Tidal Therapeutics (acquired by Sanofi), Monta Biosciences, and Nanovi; in academia, hes further founded the Institute of Health Technology at the Technical University of Denmark, where he maintains a professorial position. Dr. Andresen has co-authored over >200 research articles, has been listed as an inventor on >45 patent applications, and has received multiple research prizes, including the Elite Research Price from the Danish Ministry of Science.

Dennis Benjamin, Ph.D. Dr. Dennis Benjamin is the former SVP of Research at Seagen where he was a key developer of the companys ADC technology and clinical pipeline. Prior, he worked at Praecis Pharmaceuticals and Genetics Institute, advancing DNA encoded libraries and working in protein and small molecule discovery. Over his career, he has led teams that have discovered 25 biologics and small molecules that entered clinical trials and has contributed to 4 drug approvals. He is currently an advisor and SAB member at several start-up biotechnology companies.

Steven Dowdy, Ph.D. Dr. Steven F. Dowdy is a Professor of Cellular & Molecular Medicine at the UCSD School of Medicine and a cancer biologist, specializing in the development and delivery of RNA therapeutics as well as in G1 cell cycle control in cancer. The Dowdy lab is focused on the molecular details of delivery of RNA therapeutics across the endosomal lipid bilayer as well as the synthesis of endosomal escape domains to overcome this rate-limiting and billion year-old delivery challenge; its members were the first to synthesize bioreversible, charge neutralizing phosphotriester backbone RNAi prodrug triggers that increase metabolic stability, that augment pharmacokinetics and that enhance endosomal escape. Dr. Dowdy currently serves on five Science Advisory Boards for biotech companies and is an elected member of the Oligonucleotide Therapeutics Society (OTS) Board of Directors.

Sridhar Ganesan, M.D., Ph.D. Dr. Shridar Ganesan is the Associate Director for Translational Science, Chief of the Section of Molecular Oncology, and the co-Leader of the Clinical Investigations and Precision Therapeutics Program at the Rutgers Cancer Institute of New Jersey; he is also the Omar Boraie Chair in Genomic Science and Professor of Medicine at the Rutgers Robert Wood Johnson Medical School. Dr. Ganesan is a medical oncologist with clinical expertise in triple-negative breast cancer, hereditary breast cancer and rare cancer. His research interests include the characterization of DNA repair abnormalities in cancer with a focus on the BRCA1 tumor suppressor gene, the multi-modal molecular characterizations of different cancers, and the identification of biomarkers of response and resistance in early phase clinical trials. He has authored or co-authored over 120 publications, serves on multiple national and international grant review committees and is an Associate Editor of JCO-Precision Oncology.

Adrian Krainer, Ph.D. Dr. Adrian Krainer is the St Giles Professor at Cold Spring Harbor Laboratory (CSHL) and Deputy Director of Research of the CSHL Cancer Center. A world-renowned biochemist recognized for his basic work on RNA splicing and the development of its mechanism-based therapeutic applications, his seminal work with antisense oligonucleotides in mouse models of spinal muscular atrophy led to the development of nusinersen (Spinraza), which is the first FDA-approved drug for this disease; he is also a co-founder and a member of the Board of Directors at Stoke Therapeutics (NASDAQ: STOK). Dr. Krainer is the recipient of the Life Sciences Breakthrough Prize, the RNA Societys Lifetime Achievement Award, the Reemtsma Foundation International Prize in Translational Neuroscience, the Speiser Award in Pharmaceutical Sciences, and the Ross Prize in Molecular Medicine, amongst others. He previously served as the President of the RNA Society and is a member of the National Academy of Sciences, the National Academy of Medicine, the National Academy of Inventors, and the American Academy of Arts & Sciences.

Iain Mattaj, Ph.D. Dr. Iain Mattaj is the founding Director of Fondazione Human Technopole in Milan, Italy. Dr. Mattaj has made seminal contributions to the fields of transcription, RNA metabolism, nucleocytoplasmic transport and cell division. His prominent standings in these fields are underlined by his election as the past President of the RNA Society, Fellow of the Royal Society (London), Fellow of the Royal Society of Edinburgh, elected Member of the German Academy of Sciences Leopoldina, Member of Academia Europea, Foreign Honorary Member of the American Academy of Arts and Science, Fellow of the Academy of Medical Sciences (London) and Foreign Associate of the National Academy of Sciences (US). Dr. Mattaj was previously awarded the prestigious Louis-Jeantet Prize for Medicine in 2001. He is further a member of the European Molecular Biology Organization (EMBO) and helped to make The EMBO Journal a highly successful international publication, acting as Executive Editor from 1990 to 2004. Prior to his current appointment, Dr. Mattaj was a member of EMBL Heidelberg, Germany, serving as Group Leader (1985-1990), Coordinator of the Gene Expression Unit (1990-1999), and, subsequently, as the institutes Scientific Director (1999-2005) and Director General (2005-2018).

Henrik Oerum, Ph.D. Dr. Henrik Oerum the co-founder and CSO of Civi BioPharma and has previously founded 3 other oligonucleotide companies. Dr. Oerum has over 25 years of experience in the development and commercialization of oligonucleotide therapeutics, has authored >70 peer reviewed publications, and has been listed as an inventor on numerous patents in the field. In 1993, he founded PNA Diagnostics A/S, where he was also the CSO until 1999. During his tenure at PNA, the company was sold to Boehringer Mannheim (1994) and later to Hoffman-La Roche (1997). In 1996, Dr. Oerum cofounded Exiqon A/S, a nucleic acid diagnostics company that was floated on the Copenhagen Stock Exchange in 2007 (CSE:EXQ). In 2000, he co-founded the LNA-oligotherapeutics company Santaris Pharma A/S, where he served as CSO and VP of Business Development until its acquisition by Roche in 2014. Thereafter, he worked for Roche Pharma as Global Head of RNA therapeutics until March 2016, where he left to pursue new opportunities, leading to his founding of CiVi.

Thomas Tuschl, Ph.D. Dr. Thomas Tuschl is a Professor of RNA Molecular Biology at Rockefeller University. Dr. Tuschl is world renown for his research on the regulation of RNA and has discovered small interfering RNAs (siRNAs), microRNAs (miRNAs) and piwi-interacting RNAs (piRNAs). He is a member of the German National Academy of Sciences and the recipient of numerous awards, including the NIH Directors Transformative Research Project Award, the Ernst Jung Prize, the Max Delbrck Medal, the Molecular Bioanalytics Prize, the Meyenburg Prize, the Wiley Prize and the AAAS Newcomb Cleveland Prize. He is also the co-founder and a former Director of Alnylam Pharmaceuticals (NASDAQ: ALNY).

About Ceptur Therapeutics, Inc. Headquartered in Hillsborough New Jersey, Ceptur Therapeutics is a pre-clinical stage biotechnology company focused on developing targeted oligonucleotide therapeutics based on U1 Adaptor technology. For more information about Ceptur Therapeutics, please visit http://www.cepturtx.com or follow http://www.linkedin.com/company/ceptur-therapeutics/ on Linkedin.

View source version on businesswire.com: https://www.businesswire.com/news/home/20220119005064/en/

Excerpt from:
Ceptur Therapeutics Launches with $75M Series A Financing to Advance RNA Therapeutics Based on Proprietary U1 Adaptor Technology - BioSpace

After much of Los Angeles went dark in the spring of 2020 amid the growing SARS-CoV-2 threat, two UCLA scientists and their small teambegan working late nights on the fifth floor of the Gonda (Goldschmied) Neuroscience and Genetics Research Center, developing technology that would pave the way for the UCLA community to safely return to campus.

The safer-at-home orders had shut down all but the few core campus activities and services deemed essential. While that meant the suspension of most laboratory research, it didnt apply to a new project led by Valerie Arboleda M.D. 14,Ph.D. 14, assistant professor of pathology and human genetics, and Joshua Bloom 06, a research scientist in human genetics and an adjunct professor in computational biology. Through their collaboration with Octant Bio, a biotech company founded and incubated at UCLA; faculty in UCLAs departments of human genetics and computational medicine; UCLA Health; and other academic institutions across the country, their research ultimately found its way from the high-tech lab Arboleda and Bloom named SwabSeq to vending machines across campus.UCLA faculty, staff and students returning last fall were able to easily access the free COVID-19 test kits, with picking up a testas simple as grabbing a snack: Users simply register for the SwabSeq test by scanning a QR code with their smartphone, retrieve the kit and collect their saliva sample, then deposit the kit in a drop box next to the machine. An email or text notifies them when they can access a secure website for their result.

Diagnosing COVID-19 typically involves polymerase chain reaction (PCR) testing, but as a tool for mass screening of asymptomatic individuals, the approach is limited in its capacity. To run tens of thousands of tests simultaneously, SwabSeq harnesses the power of next-generation DNA sequencing a revolutionary technology thats come of age in the last 15 years and enables the processing of millions of DNA fragments at a time. The testing platform also bypasses a step typically required in the PCR method that of extracting RNA from samples, which can take days to process.

Im thrilled that SwabSeq helped put us back on campus and that my students and I are able to come into the lab.

Valerie Arboleda

SwabSeq attaches a piece of DNA that acts like a molecular barcode to each persons sample, enabling the labs scientists to combine large batches of samples in a genomic sequencing machine. Viewing the barcodes in the resulting sequence, the technology can quickly identify the samples that have the coronavirus that causes COVID-19. SwabSeq can return individual test results in about 24 hours, with highly accurate results the false-positive rate is just 0.2%.

Michal Czerwonka

Rachel Young, laboratory supervisor and clinical laboratory scientist for the COVID-19 SwabSeq lab

SwabSeq has now tested more than half a million specimens from UCLA, as well as from a handful of other universities in Southern California and from the Los Angeles Unified School District. A $13.3 million contract recently awarded by the National Institutes of Health sets the stage for an expansion of SwabSeqs efforts.

This is an innovative use of genomic sequencing for COVID-19 testing that is uniquely scalable to thousands of samples per day, [and that is] sensitive and fast a combination that is challenging to find in diagnostic testing, Arboleda says. Its not cost-effective as a test for a few people, or if you have someone in the hospital who needs an immediate result, but its very effective as a screening tool for large asymptomatic populations.

Neither Arboleda nor Bloom could have predicted they would one day find themselves leading a major element of UCLAs research response to a once-in-a-century pandemic.

Arboleda entered the David Geffen School of Medicine at UCLA intending to become a full-time clinician, but when she took a year off from her medical school studies to work in a lab, she found her true calling. She enrolled in the UCLA Medical Student Training Program, graduating in 2014 with both an M.D. and a Ph.D. in human genetics. As a faculty member, she now devotes about 80% of her time to research, with much of the focus on rare genetic syndromes.

Bloom, trained as a geneticist and a computational biologist, has used model systems such as yeast to develop experimental and computational methods for identifying the heritable genetic factors underlying gene expression differences and other complex traits in large populations. Ive worked on some really abstract problems. Diagnostic testing in a pandemic is definitely not something I thought Id ever be involved in, he says, smiling.

Michal Czerwonka

A machine in the SwabSeq laboratory

Like most of their UCLA colleagues and much of the rest of the world, Bloom and Arboleda saw their work routines upended by the pandemic. Bloom was grappling with the new reality when he received a call from Sri Kosuri, a UCLA assistant professor of chemistry and biochemistry and co-founder/CEO of Emeryville, California-based Octant Bio, the startup where Bloom was a consultant and where early pilot studies for SwabSeq were conducted.

He suggested we could turn the drug-screening technology Octant was using into a COVID test, and asked if I could help with the computational work, Bloom recalls. There were other people at UCLA who were also thinking that with all these smart people here, we should be able to develop a test. From there we began to have large group meetings involving multiple universities sharing information.

When Arboleda heard about the nascent project from a faculty colleague, she knew she could be helpful. In addition to the expertise in molecular biology she could apply to setting up the experiments, her training in pathology gave her the experience with regulatory matters that would need to be addressed once the test was developed. She agreed to collaborate with Bloom, who used his expertise in informatics to optimize the automated DNA sequencing process toward the goal of producing accurate diagnostic readouts.

The two spent a good part of April and May 2020 in the lab. We would do the assay and put it on the sequencer, then Josh would analyze it as soon as it came off the machine, Arboleda says. Based on that, the next day we would adjust a couple of parameters and rerun the experiment.

PreCOVID-19, she had become accustomed to a supervisory role as a principal investigator overseeing a team of scientists. I hadnt gone back to the lab in a while, she says. It was a wild two months, where I felt like a grad student again!

The number and pace of the iteration cycles a new one every 24 hours made this research project unlike any other Bloom had seen. The sequencing technology enables that, because you can tweak a bunch of things and get readouts for them all at once, he says.

But more than that, he credits the speed with which SwabSeq moved from concept to reality to an all-hands-on-deck approach befitting the urgency of the need. We had senior faculty, including department heads, engaged and excited to help, Bloom says.

One of those department heads isEleazar Eskin,chair of the Department of Computational Medicine,a departmentaffiliated with both UCLA Samueli School of Engineering and the medical school. He hascoordinatedlogistics and business operations to ensure that the lab operates efficiently and remainsflexibleenough toadapt to changing circumstances, such asthe appearance of theomicron variant of the virus.Eskinalso built the custom software for SwabSeq'slab-information management system.

Adds Arboleda: Everyone knew it was important and contributed in whatever way would support the mission, whether it was getting space, fundingor institutional review board approvals. And since only people who were doing COVID work could come to campus, I had people on my team who said, OK, Ill put on a mask and do whats needed.

Michal Czerwonka

Hard at work in the SwabSeq lab

The SwabSeq lab now occupies an entire floor in the Center for Health Sciences South Tower. The space is divided into three rooms, each dedicated to a portion of the test. One room is for handling samples; a second is used as a clean room and storage area; and a third, its walls lined with high-level sequencers, is for post-PCR sequencing. All over, freezers and refrigerators store enough reagents for millions of tests. The lab isnt necessarily a one-off Arboleda notes that the technology can be applied to general infectious disease testing and surveillance. Its flexible protocol can rapidly scale up testing and provide a solution to the need for population-wide testing to stem future pandemics, she says.

For now, aside from regular meetings to discuss SwabSeq development and high-level technical issues, the scientists have returned to the work they were doing before everything changed in March 2020. Im thrilled that SwabSeq helped put us back on campus and that my students and I are able to come into the lab, Arboleda says. Now if someone tests positive, no one worries because that person can stay home, and we know we can all easily get tested.

See the original post:
SwabSeq: Scalable, Sensitive and Fast COVID-19 Testing - UCLA Newsroom

Combined group to enable better public health outcomes through innovation in diagnostics and laboratory informatics technology

TUCSON, Arizona, Jan. 18, 2022 /PRNewswire/ -- CliniSys is announcing the recent acquisition of HORIZON Lab Systems and the combination with Sunquest Information Systems, as CliniSys.This acquisition and Sunquest combination creates one of the world's largest organizations dedicated to diagnostic and laboratory informatics.

CliniSys' vision is to go beyond the walls of the clinical laboratory to embrace a new wave of digital diagnostics and laboratories across the continuum of care and community to improve public health. HORIZON Lab Systems is critical to this vision with its advanced cloud-based laboratory solutions and unsurpassed knowledge and expertise in Environmental, Water Quality Testing, Public Health, Toxicology and Agriculture laboratory solutions.

Together, CliniSys, Sunquest and HORIZON Lab Systems are over 1,300 employees living in 12 different countries, representing 19 diverse cultures, speaking 21 different languages with unsurpassed global knowledge of the complex laboratory and diagnostics sector.

CliniSys is positioned to deliver the benefits of cloud transformation and apply new technologies such as advanced analytics, AI, and machine learning, to empower laboratory professionals with better diagnostic capabilities and tools to work more effectively and improve public health worldwide.

Laboratories around the globe monitor and safeguard health across multiple determinants of health from medical care, genetics, environmental to physical influences and CliniSys has the proven ability to deliver 100s of millions of medical results a month to enable pandemic-scale population disease surveillance across the globe.

Michael Simpson, CliniSys CEO, commented, "Public health is a major concern for all governments and citizens.With HORIZON's advanced cloud-based solutions and unsurpassed knowledge and expertise in Environmental, Water Quality Testing, Public Health, Toxicology and Agriculture, CliniSys can now provide organizations and governments at all levels, and across different sectors of the public health ecosystem, solutions to improve health at population scale."

About CliniSys

CliniSys, headquartered in Chertsey, England and Tucson, Arizona, is one of the largest providers of laboratory information systems, order entry and result consultation, and public health solutions in disease surveillance and outbreak management across the United Kingdom, Europe, and the United States.For 40 years, successfully specializing in complex and the wide scale delivery of comprehensive laboratory and public health solutions in over 3,000 laboratories across 34 countries using CliniSys solutions.

Our combined cross-discipline expertise provides customers with solutions to support laboratory workflow across clinical, histology, molecular, genetics, including order management, reporting and results delivery.Additionally, we serve laboratories in environmental testing, water quality, agriculture, and toxicology.

http://www.clinisys.com(UK & Europe)

http://www.sunquestinfo.com(North America)

http://www.horizonlims.com(HORIZON)

CliniSys Media Contact:

Linden GregoryMetia Group+44 (0) 7525 926 435 [emailprotected]

SOURCE CliniSys

Read the original here:
CliniSys acquires HORIZON Lab Systems and combines with Sunquest Information Systems to create one of the world's largest organizations dedicated to...

Significance

We present a model of biogenic magnetite formation in eukaryotes and hypothesize this genetic mechanism is used by broad forms of life for geomagnetic sensory perception. Countering previous assertions that salmon olfactory tissues lack biogenic magnetite, we determine that it is present in the form of compact crystal clusters and show that a subset of genes differentially expressed in candidate magnetoreceptor cells, compared to nonmagnetic olfactory cells, are distant homologs to a core suite of genes utilized by magnetotactic bacteria for magnetite biomineralization. This same core gene suite is common to a broad array of eukaryotes and the Asgard clade archaea Lokiarchaeta. Findings have implications for revising our understanding of eukaryote magnetite biomineralization, sensory perception of magnetic fields, and eukaryogenesis.

Animals use geomagnetic fields for navigational cues, yet the sensory mechanism underlying magnetic perception remains poorly understood. One idea is that geomagnetic fields are physically transduced by magnetite crystals contained inside specialized receptor cells, but evidence for intracellular, biogenic magnetite in eukaryotes is scant. Certain bacteria produce magnetite crystals inside intracellular compartments, representing the most ancient form of biomineralization known and having evolved prior to emergence of the crown group of eukaryotes, raising the question of whether magnetite biomineralization in eukaryotes and prokaryotes might share a common evolutionary history. Here, we discover that salmonid olfactory epithelium contains magnetite crystals arranged in compact clusters and determine that genes differentially expressed in magnetic olfactory cells, contrasted to nonmagnetic olfactory cells, share ancestry with an ancient prokaryote magnetite biomineralization system, consistent with exaptation for use in eukaryotic magnetoreception. We also show that 11 prokaryote biomineralization genes are universally present among a diverse set of eukaryote taxa and that nine of those genes are present within the Asgard clade of archaea Lokiarchaeota that affiliates with eukaryotes in phylogenomic analysis. Consistent with deep homology, we present an evolutionary genetics hypothesis for magnetite formation among eukaryotes to motivate convergent approaches for examining magnetite-based magnetoreception, molecular origins of matrix-associated biomineralization processes, and eukaryogenesis.

Diverse animals utilize the Earths magnetic field for orientation and navigation cues; however, the receptor mechanism that underlies this sensory ability remains a fundamental question in sensory biology (13). A leading hypothesis posits that specialized sensory organelles containing crystals of magnetite physically interact with Earthstrength magnetic fields to transduce geomagnetic information into neural signals (1, 47). These crystals are predicted to be similar in shape and size (47) to iron mineral crystals biosynthesized by magnetotactic bacteria (MTB) for use in magnetotaxis, passive alignment to geomagnetic fields (8). MTB are the most ancient and simple organisms known to biomineralize (79), with biologically controlled iron-based (Fe3O4 and Fe3S4) iron mineral formation in the domain Bacteria proposed to have originated 3 to 2 gigaannum (Ga) (911). Magnetite biomineralization thus predates the emergence of the crown group of eukaryotes (1.8 to 1.2 Ga), based on the fossil record and molecular clock estimates (7, 912). Like other forms of nonskeletal biomineralization, formation of crystals occurs in intracellular compartments bounded by membranes, underpinned by local expression of genes that guide precipitation (13). The mechanisms that control magnetite biomineralization in prokaryotes have been studied for decades, and numerous associated proteins are well characterized (1417).

Presence of magnetite in eukaryotes has mainly been affirmed through magnetic remanence measurements in magnetosensitive species, e.g., honeybees, birds, mice, fish (reviewed by ref. 6), yet direct evidence for intracellular magnetite is scant, the evolutionary origins are poorly understood, and no magnetite-based receptor has been confirmed in situ (1, 18, 19). Iron-rich structures detected in the upper beak of pigeons were once proposed as magnetoreceptors (20) but later were identified as phagocytosed debris in cells presenting major histocompatibility complex II, probably macrophages(18). Still, multiple lines of evidence support a universal magnetite-based magnetoreceptor (4, 5): The trigeminal nerve of fish exhibits neural responses to magnetic treatment (4), neurons associated with the avian trigeminal brainstem complex show magnetic activation (2), and behavioral responses to pulse magnetization are exhibited by birds, sea turtles, and bats (2123). Thus, the magnetite hypothesis for geomagnetic receptivity holds and is believed to provide sensory information that differs from the cryptochrome-based model, which is unaffected by magnetic pulse (3).

Pacific and Atlantic salmon (Oncorhynchus and Salmo) possess an innate guidance mechanism utilized for long-distance migration and homing to natal rivers (24). Navigational cues include geomagnetic intensity and inclination, as shown by exposing juvenile salmon to simulated magnetic displacements (25, 26). Although magnetite is present in salmon tissues, no deposits have been directly associated with sensory transduction and in most cases are unlikely to represent the magnetoreceptor site (6). An important exception is occurrence of magnetite in olfactory epithelial tissue (refs. 1, 5, and 27; but see ref. 19), innervated by the magnetically responsive superficial ophthalmic branch of the trigeminal nerve (4). We extend the hypothesis that magnetite-containing cells have a universal genetic basis and role in magnetoreception through 1) in situ magnetic measurements, microscopies, and transcriptomic characterization of magnetite-containing cells of salmonids; 2) assessing whether magnetite biomineralization in eukaryotes could have ancient prokaryotic origins by comparing the genome contents of a salmon, 12 additional eukaryotes, and one archaea against an MTB magnetosome protein sequence database; and 3) proposing an evolutionary genetics hypothesis for eukaryote biomineralization and magnetoreception predicated on transcriptomic and comparative genomic findings.

The physical properties of magnetite in salmon olfactory epithelium were characterized using a combination of ferromagnetic resonance spectrum (FMR) and atomic and magnetic force microscopies (AFM/MFM). The FMR analysis, conducted on intact olfactory rosette (OR) tissues (Fig. 1A), provides in situ information relating to the size and physical arrangement of magnetite particles. The rainbow trout (Oncorhynchus mykiss) broad FMR spectrum (Fig. 1B; SI Appendix, Fig. S1) seen in the electron spin resonance spectrum is different from that reported for linear chains of magnetosome crystals in MTB and rather resembles the FMR spectra of strongly interacting magnetic particle systems (28). Consistent with that finding, visualized under AFM, magnetic particles extracted from digests of Atlantic salmon (Salmo salar) olfactory epithelium appear as uniformly sized and ellipsoid shaped clusters, with each cluster containing a compact arrangement of individual particles. Clusters range in size from 200 to 300 nm (Fig. 1 CG) and are estimated to contain 100 to 200 individual particles with diameters that range from approximately 30 to 60 nm. As an example, a profile of a single cluster (Fig. 1D) marked by the white bar in Fig. 1C, is 300 nm in diameter and contains crystals with a maximum diameter of 60 nm. Individual crystals can also be visualized in the higher resolution image shown in Fig. 1E. Using images taken from a different sample location, to demonstrate the magnetic properties of particle clusters, a switch from AFM (Fig. 1F) to MFM measurements performed in a near-zero field show an attractive interaction between the magnetic probe tip and the magnetite, which results from magnetostatic interactions and is indicated by a dark contrast (Fig. 1G; SI Appendix, Fig. S2). Our images of magnetite are strikingly similar to those obtained by Diebel etal. (5) (see their figure 2), who used confocal microscopy and AFM/MFM to visualize a cluster of intracellular magnetite in a rainbow trout olfactory epithelium cell. In our case, we can rule out bacteria and commercially prepared magnetite contaminants by differences in particle size and aggregation patterns visualized by AFM/MFM (SI Appendix, Figs. S2 and S3).

Candidate magnetoreceptor cell characteristics. (A) Schematic representation of a salmonid head showing OR location. (B) Broad electron spin resonance spectrum of rainbow trout (O. mykiss) ORs demonstrates presence of ferromagnetic material. The sharp edge at a magnetic field strength H = 3 kOe corresponds to a paramagnetic signal (SI Appendix, Fig. S1). (C, E, and F) AFM images of magnetite clusters extracted from Atlantic salmon (S. salar) ORs (SI Appendix, Fig. S2). (D) Dimensional profile of the magnetite cluster (x axis) and maximum diameter of individual magnetite particles (y axis) marked by the white line in (C). (E) Individual particles can be visualized under higher magnification. (G) Magnetic force microscopy image obtained at 0.5 mT; image directly corresponds to F. (HJ) Chinook salmon (O. tshawytscha) transcriptome profiles of three blood, muscle, and whole OR samples obtained from three fish (n = 9 transcriptomes), a single pair of deep-sequenced ORs (ORds) sampled from a fourth fish (n = 1 transcriptome), and MAG and NM cells obtained through three replicate MAG cell isolation experiments, each using dissociated ORs from 3 to 5 fish (n = 3 MAG and n = 3 NM transcriptomes). (H) Multidimensional scaling plot and (I) heatmap of top 500 most abundantly expressed genes across the 16 transcriptomes. ORs in the color keys are demarcated with dark outlines. (J) M (log ratio) versus A (mean average) plot of the log2 fold ratio of modeled gene expression values (y axis) and average log2 counts per million (x axis) between magnetic (negative y axis) and nonmagnetic (positive y axis) cell isolates, with red dots indicating DEGs (at FDR < 0.05) and black dots indicating no significant difference in gene expression.

After confirming the presence of biogenic magnetite in salmonid olfactory epithelium, we then determined candidate magnetoreceptor genes of Chinook salmon (Oncorhynchus tshawytscha) by contrasting transcriptome profiles of magnetic (MAG) and nonmagnetic (NM) olfactory cells and blood and muscle tissues. Briefly, three replicate MAG cell isolation experiments were conducted by dissociating OR cells, followed by collection of MAG cells using a magnet with a pointed tip placed on the outside, upper portion of the sample vial and allowing the NM cells to settle to the bottom of the vial through gravitational forces. The pellet of MAG cells that accumulated inside the vial at the tip of the magnet and NM cells from the bottom of the vial were aspirated and transferred into new vials for messenger RNA (mRNA) isolation. Because of MAG cell scarcity, three to five sets of ORs were combined for each cell isolation experiment. The MAG and NM samples, plus three sets of ORs, blood, and muscle tissues from three additional fish and a set of ORs from a fourth fish (for a total of 16 transcriptomes), were subjected to Illumina sequencing for transcriptome profiling. Adjusting for false discovery rates (FDRs) < 0.05, this experiment revealed 610 differentially expressed genes (DEGs) more highly expressed in the MAG relative to the NM cell type and considerably greater difference between MAG and blood and muscle tissues (Fig. 1 HJ; SI Appendix, Fig. S4 and Table S1). In the latter two cases, >11,000 DEGs were more highly expressed in each binary comparison. Consistent with DEG results, multidimensional scaling plots show well separated clusters of points by tissue type or experimental condition (Fig. 1H). Two of the three MAG samples clustered together, positioned distinct from their NM sample counterparts, while the third MAG sample grouped between the other MAG samples and its NM experimental counterpart. The NM samples were positioned intermediate between the MAG and nontreated olfactory samples. A heatmap of the top 500 most variable genes shows that at this high level, samples from MAG and NM experimental trials group together (Fig. 1I), which masks expression differences between these two OR cell subtypes. Overall, differences in gene expression fold-differences and transcript abundance are less for the MAGNM contrast compared to MAGblood and MAGmuscle contrasts, as visualized in MA plots, in which red and black dots depict genes with significant or nonsignificant levels of expression, respectively (Fig. 1J MAGNM contrast; MAGblood and MAGmuscle contrasts available in SI Appendix, Fig. S4).

Discrete differential gene expression distinctions observed repeatedly when comparing MAG and NM cell findings in our study are only consistent with the conclusion that salmon olfactory tissue magnetic properties result from the intracellular presence of biogenic magnetite. With macrophages ruled out (SI Appendix), a random assortment of MAG material attached to NM cells could not provide the data observed here.

To broadly characterize the molecular functions of MAG cells, we relaxed the threshold FDR < 0.1 and focused on the 1,588 DEGs more highly expressed within the MAG sample contrasted to the NM sample. These candidate genes were overrepresented in 80 Gene Ontology (GO)categories, including anatomical structure and cell maturation/development, mitotic cell cycle, protein modification, protein binding, and bounding membrane of an organelle (Dataset S1). Among the DEGs were proteins involved in iron uptake and transport (14, <1% of DEGs) and iron ion binding (6, <1% of DEGs), including ferritin. Also present were proteins associated with keywords actin (84, 5.3% of DEGs), microtubule (24, 1.5% of DEGs), and cytoskeleton (36, 2.3% of DEGs). These results are consistent with the production or maintenance of an organelle, possibly one produced through a cellular machinery process that somehow shares commonalities with mitosis and that involves iron.

To examine the hypothesis that genetic mechanisms controlling magnetite biomineralization in prokaryotes and eukaryotes might share common, ancient origins, we compared the genome contents of 13 eukaryotes (five protostomes and eight deuterostomes; SI Appendix, Table S2) to a database of magnetite biomineralization genes (Dataset S2). We found that 11 MTB magnetosome gene homologs (MGHs) are universally present (uMGHs) in eukaryotes, defined as having bidirectional Basic Local Alignment Search Tool protein (BLASTp)matches across at least 12 of the 13 animal genomes (>92%, Fig. 2A and Datasets S2 and S3). Furthermore, 9 of these 11 uMGHs were contained in genome contents of the Asgard archaea clade Lokiarchaeota (Fig. 2A; Datasets S2 and S3), which shows monophyly with eukaryotes (29, 30). The MamE homolog, an HTRA-like serine protease, exhibits exceptionally high levels of conservation in Chinook salmon and other magnetically sensitive animals (Fig. 2; Dataset S4 and SI Appendix).

Comparative genomics. Data are presented for reciprocal BLASTp matches between magnetotactic bacterial biomineralization proteins and genome contents of eukaryotes and the archaea Lokiarchaeota. (A) Numbers of eukaryote proteins with reciprocal BLASTp match to 11 proteins known for involvement in prokaryote iron biomineralization (numbers of genes in prokaryote database in parenthesis). (BG) Scatterplots of alignment lengths and percent identities scores for unidirectional BLASTp matches between genome contents of five magnetic responsive eukaryote taxa and the MTB magnetosome gene dataset (gray background circles). Proteins showing homology to the MTB gene MamE (HtrA-like serine protease) with E-value < 1 10e5 are color highlighted. (B) All taxa (CG combined), (C) zebra finch, Taeniopygia guttata (red); (D) naked mole-rat Heterocephalus glaber (cyan); (E) Chinook salmon, O. tshawytscha (blue); (F) little brown bat, Myotis lucifugus (black); and (G) honeybee, Apis mellifera (yellow). (H) A partial (66 amino acid) MamE alignment displays high levels of conservation across the five eukaryote taxa (CG) and four MTB (1 to 4: UniprotKB accessions L0R6S4, Desulfamplus magnetovallimortis; C5JBP1, uncultured bacterium; A0A0F3GW16, Candidatus Magnetobacterium bavaricum; C5JAJ2, uncultured bacterium). Arrows in panels C to G point to the gene included in the multispecies alignment, with the red arrow indicating a gene differentially and more highly expressed in salmonid candidate magnetoreceptor cells, indicated by e* in the alignment. A full alignment is available from Dataset S4. Genome details are available from SI Appendix, Table S2.

A previous survey of MTB Nitrospirae and Proteobacteria genomes indicates they share a core set of five MTB magnetosome genes, MamABEKP (10). The 11 uMGHs identified in our study include four of these five core genes, with only MamP missing from eukaryotes (and Lokiarchaeota; Fig. 2A; Dataset S3). MamP contains an iron-binding residue with a role in iron oxidation (31), but this protein is not essential for crystal formation, possibly because of functional compensation by other magnetosome proteins (15, 31). These core genes, along with MamH and MamN (6 of the 11 uMGHs), are part of the MamAB operon (1416), the only operon solely capable of supporting magnetite crystallization (14, 17). We found no support for the presence of MGHs belonging to three other magnetosome-associated, operon-like gene clusters, MamGFDC, MamXY, and mms6 (Datasets S2 and S3). Those gene clusters are generally present in magnetotactic Alphaproteobacteria (14, 17, 32) but absent from magnetotactic Deltaproteobacteria and Nitrospirae (10, 16, 33) (Datasets S2 and S3). Of the remaining five uMGHs, Mad9, 17, 25, 29 are present in genomes of magnetotactic Deltaproteobacteria and Nitrospirae, the latter also containing Man6 (10, 16). At a broader view, a meta-analysis of MTB genomes indicated that Mad genes are present in Nitrospirae, Omnitropha, and Deltaproteobacteria but absent from Proteobacteria classes Alpha, Eta, and Zeta and that Man genes are only contained in genomes of Nitrospirae (34). Thus, presence of the Man6 uMGH in eukaryote genomes, in conjunction with generally high proportions of eukaryote gene matches to individual Nitrospirae MTB proteins (SI Appendix, Table S3), is most parsimonious with a magnetite biomineralization gene transfer to eukaryotes having involved a Nitrospirae ancestor.

After identifying the 11 universally conserved uMGH proteins, we then cataloged their complete repertoire (homologs and paralogs) within genomes of zebrafish (Danio rerio) and Chinook salmon, which amounted to a total of 244 and 367 genes encoding uMGHs. Of those Chinook salmon genes, 332 matched to 181 zebrafish orthologs and corresponding Zebrafish Information Network (ZFIN) gene codes (35), a 45% reduction most likely explained by salmonids whole genome duplication event (36). In contrast, the zebrafish gene dataset was only marginally reduced (to 226 ZFIN gene codes) after accounting for a small number of paralogs. The number of fish genes encoding uMGHs varied across the 11 uMGH categories, with MamA, MamE, and MamK having the greatest number of matches (Table 1). Using PANTHER (37) and ZFIN gene codes to leverage the well-annotated zebrafish genome (35), notable protein classes included oxidoreductase, protein chaperones, matrix proteins, serine proteases, and transporters. Despite the diversity of protein classes, gene ontology analysis for these two sets of fish uMGHs indicated significant overrepresentation and exceptionally high fold-enrichment values across several categories; as an example, the molecular function term protein folding chaperone is 90 enriched in zebrafish and 63 enriched in Chinook salmon. Other notably enriched ontology categories include protein folding and refolding; divalent inorganic cation transmembrane transporter activity; four iron, four sulfur cluster binding; zinc ion transport, activity, and response; cellular response to heat (mostly heat shock proteins); and actin-based cell projection (SI Appendix, Table S4; hierarchical ontologies available from Dataset S5). Consistent with these findings, significantly overrepresented reactome pathways include zinc efflux and compartmentalization by the SLC30 family; signal transduction; laminin interactions; and the anaphase promoting complex/cyclosome, which regulates progression through the mitotic phase of the of the cell cycle (38). Several magnetite biomineralization proteins of bacteria have been functionally categorized, yet the roles of some proteins are not yet well understood, especially within the magnetotactic Nitrospirae and Deltaproteobacteria (Table 1). A list of genes encoding fish uMGHs, their ZFIN codes, and protein class annotations are provided in Dataset S6.

Summary data for the complete repertoire of fish genes encoding distant homologs of 11 MTB biomineralization proteins

Considering the full repertoire of uMGHs in Chinook salmon, we then examined whether these genes may be engaged with putative magnetite presence in salmonid olfactory cells, and thus biomineralization, in light of the DEG findings at threshold FDR < 0.1. Based on the full repertoire of protein-coding uMGHs in the salmon genome, 12.5 MGHs are expected to occur by chance in a random sample equally sized to the MAG DEG dataset. We found 18 uMGHs were among the differentially expressed genes, which approaches statistical significance (P = 0.0675, one-tailed proportion test, P value threshold = 0.05). This indicates that uMGHs may show up-regulated expression in the MAG cell sample. The 18 genes were distributed across 7 of the 11 universally conserved categories and included MamABEK, Mad9, Mad25, and Man6 (SI Appendix, Table S5 and SI Appendix). The differentially expressed MamE homolog shows an exceptional level of conservation to MTB proteins (Fig. 2 E and H; Dataset S4).

The widespread distribution of magnetite and retention of distant homologs of bacterial magnetite biomineralization genes in eukaryote genomes is interpreted by us as an indication that biologically controlled magnetite precipitation is a fundamental feature of eukaryotic biology and was at one time present in the last common ancestor of extant eukaryotes and some archaea. All but two of the core set of genes we identified as universally present in eukaryotes are detectible in genome contents of Lokiarchaeota, a member of the Asgard superphylum of archaea that forms a monophyletic group with eukaryotes in phylogenomic analyses and whose genome encodes an expanded repertoire of eukaryotic signature proteins (actin and tubulin, which form the core of the cytoskeleton), suggestive of sophisticated membrane remodeling capabilities (29, 30). Our results are thus consistent with eukaryotes having evolved from within the archaea (3942).

Could ancient serial endosymbiosis events explain magnetite biomineralization in complex life forms (9, 43) (Fig. 3)? Since the now widely accepted symbiotic origin for some eukaryotic organelles was proposed, a wealth of secondary and even tertiary symbioses events within eukaryotes have been cataloged (reviewed by refs. 44, 45). Here, observed commonality of core biomineralization genes between prokaryotes and eukaryotes is consistent with an ancient endosymbiosis event (9), although an ancient horizontal gene transfer event cannot be ruled out. Regardless of gene acquisition mechanisms, retention of uMGHs in eukaryote genomes (and Lokiarchaeota) signifies that these particular genes are essential features of eukaryotic biology. Our results are parsimonious with the hypothesis that magnetite biomineralization represents deep homology, a latent but plesiomorphic ability (genetic and cellular) to form structures (46), and exaptation of magnetite biomineralization for magnetoreception (7, 43).

Conceptual schematic of the magnetite evolutionary hypothesis. The timing of ancient serial endosymbiosis events (stylistically adapted from ref. 45) are detailed in refs. 9, 10, and 12 and described in the main text. Uncertainty surrounding timing of eukaryogenesis is depicted by the box.

The importance of endosymbiosis in the evolution of eukaryotic complexity has become firmly established through accumulation of evidence that mitochondria and plastids (double bilayer membrane-bound organelles) evolved from bacteria (44, 45). A necessary intermediary to endosymbiosis is formation of obligate hostsymbiont associations, with numerous examples known to occur at various levels of interdependence and integration, e.g., endosymbiotic bacteria found in cells of insects, nitrogen-fixing spheroid bodies found in some diatoms, and zooxanthellae in marine invertebrates (47). Symbiosis is suspected to occur between members of the Asgard clade of archaea and a candidate division of bacteria (TA06) (40) and was recently documented to occur between MTB and a unicellular eukaryote. In that case, excavate protists (Symbiontida, Euglenozoa) and ectosymbiotic Deltaproteobacteria biomineralizing ferrimagnetic nanoparticles formed a mutualistic relationship based on collective magnetotactic motility with division of labor and interspecies hydrogen-transferbased syntrophy (48). These assemblages were identified in multiple locations around the northern and southern hemispheres of the globe, and congruence in topology of hostsymbiont phylogenetic trees indicates that these partners coevolved and diversified from a single ancestral magnetotactic symbiosis event. Symbiosis between MTB and other forms of life potentially carry a selective advantage, perhaps through a dedicated molecular machinery to sequester excess iron, or perhaps through the physical properties of magnetite, be it a magnetic dipole moments for magnetotaxis of the host [as suggested for a marine protist (48) and for larvae of a marine mollusc (49)], density for adjusting buoyancy in the water column, mechanical stability similar to silica-based phytoliths in grasses and other land plants, hardness for providing protection against grazing, or protection against ultraviolet radiation (50). Consistent with endosymobiosis, mutualistic symbiosis assemblages composed of microbial eukaryotes and bacteria that biomineralize magnetosomes have been observed in multiple locations around the globe (48).

Previous searches for candidate magnetoreceptors in dissociated salmonid ORs using a microscope with an applied rotating magnetic field identified cells with magnetic properties (27). However, in a follow-up study (19), cells isolated in a similar way showed an absence of intracellular magnetite and presence of extracellular contaminants, leading some researchers to question whether olfactory tissues indeed even harbor biogenic magnetite at all (51). Why our search for magnetite was successful in contrast to the cell-spinning approach may be explained by the constraining effect of solution viscosity on spinning properties, with trade-offs between levels of dissociation. Gentle dissociation produces whole cells as necessary for quantifying intracellular components but increases the probability of cells remaining in intact clumps that may not spin, while strong dissociation risks membrane rupture and loss of magnetic contents that are invisible under light microscopy. Alternatively, putative magnetic particle structures from ruptured trigeminal nerve terminals in the OR were released into the cell suspension and adhered to other cells, making them magnetic.

Our findings are a transformative advance to generate convergent approaches that may illuminate the mysterious sixth sense of magnetoreception. Equipped with genomic findings, genetic tools coupled with those of physics, behavior, anatomy, and physiology can be developed to validate associations between candidate magnetoreceptor cells and neural signal transduction. Whether the ancient biomineralization system we nominate here bears a relationship to the numerous other matrix-mediated biomineralization systems found in living organisms (7, 13) or played a role in eukaryogenesis further warrants advancing convergent approaches to resolve the complex innovations that embody lifes diversity.

To minimize contamination by nontarget magnetic particles, the tools used for animal termination and dissection were iron-free and nonmagnetic (made of titanium, ceramic, or glass). All tools and labware used for microscopy protocols, if not presterilized, were cleaned in HCl or ultrasonic bath in EtOH. The tools and labware used for magnetic cell isolation/transcriptomics experiments were cleaned in HCl, with the exception of filter tips used in RNA liquid handling. That work was performed inside a hood equipped with a high-efficiency particulate air filterwhenever possible, and tools were covered with plastic wrap as a dust preventative measure. All reagents were ultrapure, molecular biologygrade buffers made with Milli-Q water, and powdered (e.g., papain and L-cysteine [Sigma-Aldrich]) reagents were hydrated in molecular-grade water and filtered through a 0.22-m membrane using an HCl-cleaned syringe. Fish were obtained from local fish farms/markets or hatchery operations and killed in accordance with European and German regulations or under the authority of permit issued to Oregon State University (ACUP 4421).

To assess in situ magnetic properties, the olfactory epithelium of rainbow trout (O. mykiss, n = 10) was isolated bilaterally and frozen for measurement of FMR absorption spectra acquired using an X-band ESR spectrometer (JEOL, JES-FA 200), at a microwave frequency of 9.07 GHz, 4-mW input power, and a magnetic field sweep rate of 200 mT/min. For lock-in detection, the applied magnetic field was modulated with a 0.4-mT magnetic field of 100 kHz frequency. Findings were compared to experimentally observed FMR spectra of MTB quantitatively explained using the theoretical model developed in Charilaou etal. (52).

To study biogenic magnetism at the nanoscale, the physical and magnetic features of salmonid and bacteria magnetite particles were determined using a custom-designed scanning probe microscope with AFM and MFM modes. Biogenic magnetite particles were extracted from Atlantic salmon olfactory epithelium and the MTB Magnetospirillum gryphiswaldense MSR-1 and compared to a commercial ferrofluid (sample preparation details available from SI Appendix, Extended Methods). The scanning probe microscope (Veeco Digital Instruments) was equipped with a small, super-sharp AFM/MFM tip attached to a commercially produced cantilever (53). The tip, with a curvature radius less than 10 nm, was made from a microfabricated silicon probe selectively coated with 30 nm Co85Cr15. The tip and cantilever had a resonant frequency of 75 kHz and a spring constant of 3 N/m for measurement of topography and magnetic signals using MFM tapping and lift modes, setting the lift height in MFM measurements to 20 nm. External in-plane magnetic fields were generated by a pair of solenoids. The field strength was enhanced by a pair of iron cores, with a maximum field in the middle of two iron cores measured as 370 mT. The sweeping function of the magnetic field within the MFM was realized by the combination of a function generator (HP 33120A) and a self-made voltage to current converter with a maximum current of 8 A for the employed solenoid. The salmon magnetite sample was visualized in external fields applied normal (z axis) to the sample surface at field strengths of 0.5, 3.5, 7, 15, and 35 mT. The externally applied magnetic fields orients all particle magnetic moments partially or even completely along the field direction. Since the probe magnetization is also partially aligned, attractive magnetostatic interactions between probe and magnetic nanoparticles result. These interactions are specifically measured upon lifting the probe in the MFM mode of operation and they manifest themselves in terms of a dark contrast. In the tapping mode of operation, the oscillating probe is periodically almost in contact with the sample, which results in a topographical image irrespectively of the nanoparticle magnetic configurations. Additional microscope details are available from (53).

Rainbow trout olfactory epithelium and MTB were examined using reflectance mode of the confocal microscope, based on previously developed protocols (5, 54) and described in SI Appendix, Extended Methods. A sample of competent Escherichia coli (DH-5) was used as a nonmagnetic control. The MTB were obtained from mud samples collected in the Rhin Tortu, Strasbourg, France (483259.1N, 74538.0E). Samples were imaged using a Leica TCS SP5 II Laser Scanning Confocal microscope with a 63 oil immersion objective (numerical aperture 1.40). fn1-43fx was excited at 488 nm and emitted light collected using a 500 long pass filter. DAPI was excited at 405 nm. The reflectance mode option of the confocal microscope was calibrated using the MTB reflectance. Further analysis and image presentation were performed using ImageJ software (55). Confocal microscopy was performed at the invitro imaging core facility (CNRS UPS3156) located at the Institute of Cellular and Integrative Neuroscience, Centre National de la Recherche Scientifique, Strasbourg, France.

Tissues for RNA isolation were sourced from Chinook salmon reared in a single tank at the Fish Research Laboratory, Corvallis, OR (443352.4N, 231543.4W). 15 fish were sampled for OR tissues used in magnetic cell isolation experiments, one fish was sampled for OR deep transcriptome sequencing, and three fish were each sampled for muscle tissue, blood, and additional pairs of ORs. Muscle tissue was used as a negative control to rule out potential presence of contaminants during magnetic cell isolation experiments. For olfactory MAG and NM transcriptome profiling, three replicate experiments were conducted by enzymatically dissociating olfactory tissues, then isolating MAG cells by conducting magnetic collection (using a fine-point magnet placed on the exterior of a glass vial), during which NM cells collected on the bottom of the vial through gravitational forces (SI Appendix, Extended Methods). Given the scarcity of MAG cells in olfactory tissues, three to five sets of ORs were combined in each experiment to obtain sufficient material for visualization of the magnetic pellet under a dissecting microscope. The magnetic cell pellet was aspirated and placed in a RNase-free vial with 20 L buffer, followed by transfer of an aliquot (20 L) of the nonmagnetic cells to a separate RNase-free vial. All other transcriptome samplesn = 3 muscle, n = 3 blood, and n = 4 pairs of ORswere individually processed. The fish fork lengths ranged from 10 to 15 cm.

In the presence of QIAzol Lysis Reagent (Qiagen), solid tissues (untreated ORs and muscle) were mechanically homogenized and lysed with an electronic mortar and pestle, while blood and dissociated MAG and NM OR cells were homogenized and lysed by pipetting. Total RNA was isolated from lysed materials using a Qiagen RNEasy Mini kit following manufacturers protocols. Samples were submitted to Oregon State Universitys Center for Genome Research and Biocomputing core facility for messenger RNA isolation, Illumina library preparation, individual indexing for demultiplexing, and sequencing on an Illumina HiSeq2000. Each experimental pair of MAG and NM samples was sequenced in a single Illumina lane using 101 cycles and paired-end protocols, with one lane also including the additional snap-frozen single OR sample for deep sequencing. The other nine samplesblood, muscle, and OR tissueswere single-end sequenced in a single lane using 50 cycles.

The raw Illumina reads were quality processed with Trimmomatic (56) (version 0.32), removing adapter contaminants and low-quality sequences and retaining reads 25 nucleotides in length with an average sequencing quality of phred 20 across 4 nucleotide sliding windows. Reads were mapped with Bowtie2 version 2.2.1 (57) (setting: very sensitive) to a Chinook salmon reference transcriptome based on a Chinook salmon genome (36) having a total sequence length of 2.54 Gb (National Center for Bioinformatic Information Accession GCF_002872995.1). This genomes companion *rna.fna file contains 81,329 predicted RNA transcripts that correspond to 73,277 predicted proteins and their variants. The longest RNA transcript per gene (n = 47,921 transcripts) was selected for inclusion in the reference transcriptome used for read-mapping, differential gene expression analysis, and bidirectional BLASTp comparison to MTB biomineralization proteins (MTB accessions available from Dataset S3).

Differential gene expression was modeled using a generalized linear model likelihood ratio test implemented in EdgeR (58). With focus on MAG samples, pairwise contrasts were made to NM experimental counterparts, blood, and muscle tissues. Magnetoreceptors are presumed to be absent from the latter two sample types, and their expression profiles may be useful for making general inferences about gene functions. Data inputs for EdgeR included counts of mapped forward reads (to match single-end sequenced samples) extracted from *bam files. Transcripts were filtered for low expression using a minimum of two count-per-million reads across at least three of the 16 samples, adjusting for high expressed reads using trimmed mean of M componentread normalization (59). Postfilter, per-sample mapped read numbers ranged from 8.6 to 46.0 million (average 21.7 million; SD 9.0 million). A total of 38,598 (81% of 47,921) RNA transcripts were considered in differential gene expression analysis. Statistical significance was adjusted for multiple tests using BenjaminiHochberg (B-H) (60) FDR-corrected P values with a threshold cutoff of FDR < 0.05 for broad contrasts between MAG and all tissue types and FDR < 0.1 for analysis of genes differentially expressed in the MAGNM contrast. Broad relationships among gene expression profiles were visualized and inspected through multidimensional scaling plots (EdgeR function plotMDS) and heatmaps (gplot version 3.0.1 function heatmap.2) generated in EdgeR version 3.12.1 with R version 3.2 (61).

The molecular functions of zebrafish and Chinook salmon genes encoding uMGHs and genes differentially expressed in the MAG cell sample (contrasted to NM cell sample, FDR < 0.1) were annotated using the Protein ANalysis THrough Evolutionary Relationships classification system (37) (PANTHER version 13.1, release date February 3, 2018). To leverage well-characterized gene ontology terms from a model fish species, the Chinook salmon mRNA transcripts were BLASTx matched to zebrafish (D. rerio) orthologs (ENSEMBL genome version GRCz11, file Danio_rerio.GRCz11.pep.all.fa; last modified March 8, 2018) to identify PANTHER-compatible ZFIN identifiers (35). Nonspecific BLASTx matches were filtered by applying a threshold cutoff E < 1e5. Of the 1,588 MAG DEGs, 1,333 zebrafish ZDB gene identifiers were procured. Statistical tests for overrepresentation across GO complete categories (Overrepresentation Release 20181113; GO database release January 1, 2019) and reactome pathways (Reactome version 65, released June 12, 2018) were assessed on the basis of fold-enrichment values, dividing the observed by expected numbers of per GO or pathway term. This denominator is based on the zebrafish background genome and considers the number of genes in the input file. The zebrafish genome was used as a background genome. Statistical significance was adjusted for multiple tests using PANTHERs built-in B-H FDR correction function. Individual zebrafish and Chinook salmon genes encoding uMGHs (see below) were also categorized by PANTHER family/subfamily groups and protein classes, based on ZFIN identifiers (35), using the 2020_04 release of the ReferenceProteome dataset. Protein names of individual DEGs were also obtained from the Chinoook salmon RefSeq genome feature table (GCF_002872995.1).

Macrophages, a type of immune system cell that can precipitate and store iron deposits (62), were evaluated as a potential explanation for the observed magnetic properties of dissociated cells used for transcriptome experiments. Genes annotated as macrophage (n = 261 ZDB genes) in the ZFIN data repository (35) were matched to annotations for NM and MAG DEGs (at FDR < 0.05) and evaluated for statistical overrepresentation using a one-sided proportion test with a threshold significance value of P = 0.05.

Whether distant homologs of MTB biomineralization proteins are universally present among eukaryote genomes was assessed by comparing genome contents of 13 phylogenetically diverse eukaryote taxa (SI Appendix, Table S2) to a database of magnetosome proteins of distantly related phyla including Nitrospirae and Proteobacteria (classes Alpha, Delta, and Gamma; Uniprot-KB SWISS-PROT database download date 9/12/2018; search term name = magnetosome) (accessions provided in Dataset S3). An MGH was classified as universal (uMGH) in eukaryote genomes if a bidirectional BLASTp match to a named MGH occurred across at least 12 of the 13 eukaryote genomes (>92%), allowing for one missed protein product annotation or gene loss. Nonspecific matches were filtered by applying a threshold cutoff Expect value (E) of E < 1e3, considered reliable for inferring gene descendants with distant homology (63), in the eukaryote/archaea to bacteria comparison. The MTB protein database contained 106 named magnetosome genes (similarly named genes were kept separate, e.g., MamK and its paralog MamK2; ref. 64) represented by 594 sequences meeting a threshold minimum length of 100 amino acids (Dataset S3). Genes labeled as Unknown (n = 7) were excluded from consideration as uMGHs. To account for evolutionary distance, the Lokiarchaeota uMGH assessment included matches to uMGHs and similarly named MTB homologs.

The full repertoire of genes encoding uMGHs in zebrafish and Chinook salmon was identified through unidirectional BLASTp queries of fish genome contents to the magnetosome protein database, applying a threshold E < 1e3 filter to remove nonspecific matches (63). As the objective here was to identify the complete repertoire of genes with distant homology to MTB magnetite biomineralization genes, we retained both matches to named uMGHs and matches to their homologs and grouped them under a single gene identifier (i.e., MamK and MamK2 were retained and grouped as MamK). Based on the full uMGH repertoire of Chinook salmon, whether the relative frequency of DEGs characterized as uMGHs was greater than expected was tested using a one-tailed proportion test (without Yates continuity correction). The background global frequency of uMGHs was calculated by dividing the number of protein-coding uMGHs (n = 367) by the genome-wide number of protein-coding genes (n = 42,215). Only DEGs characterized as protein coding were considered in this analysis (n = 1,433 of 1,588 DEGs). Calculations were made in R package stats version 3.2.1 (61), with statistical significance set to P < 0.05.

The RNA sequencing data used for differential gene expression modeling are available through National Center for Biotechnology Information BioProject accession no. PRJNA614978. All other data are available from SI Appendix, Datasets S1S6, and public repositories as described within the text.

Chinook salmon rearing facilities were provided by the Oregon Department of Fish and Wildlife at Nestucca Hatchery, the National Oceanic and Atmospheric Administration, Northwest Fishery Science Center Newport Aquaculture Facility (Mary Arkoosh), and the Corvallis Research Group (Rob Chitwood, David Noakes, and Joseph ONeil). David Jacobson of Coastal Oregon Marine Experiment Station, Oregon State University, contributed research advice. The authors acknowledge Benot Rose for technical assistance and StephanEder for assistance with FMR measurements. M.R.B. and M.A.B. received funding from Coastal Oregon Marine Experiment Station, Project CROOS, Collaborative Research on Oregon Ocean Salmon funded by Oregon Watershed Enhancement Board and Klamath Disaster Relief Funds (National Oceanic Atmospheric Administration grant NA07NMF4540337) and other National Marine Fisheries Service funds administered through the Cooperative Institute of Marine Resources Studies. M.R.B. received support from Oregon State University scholarships (Dr. Hari S. and Dr. Renuka R. Sethi, H. Richard Carlson, Neil Armantrout, and Oregon Lottery) and Mamie Markham Research Awards administered by the Hatfield Marine Science Center. H.C. received support from the University of Strasbourg Institute for Advanced Studies. M.W. acknowledges funding from the Deutsche Forschungsgemeinschaft, grant 395940726SFB 1372 Magnetoreception and Navigation in Vertebrates. Oregon State University, Center for Genome Research and Biocomputing core facility provided RNA-seq sequencing services and advanced computing resources. Advanced computing resources were also provided by the University of HawaiiInformation Technology ServicesCyberinfrastructure, funded in part by the NSF MRI award no. 1920304. We are grateful for insightful comments by two reviewers whose recommendations substantially improved the presentation of our findings.

Author contributions: M.R.B., J.W., U.H., H.C., M.W., and M.A.B. designed research; M.R.B., J.W., U.H., H.C., and M.W. performed research; M.R.B., J.W., U.H., H.C., M.W., and M.A.B. contributed new reagents/analytic tools; M.R.B., J.W., U.H., H.C., and M.W. analyzed data; and M.R.B., J.W., U.H., H.C., M.W., and M.A.B. wrote the paper.

The authors declare no competing interest.

This article is a PNAS Direct Submission.

This article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2108655119/-/DCSupplemental.

Read more here:
Conservation of magnetite biomineralization genes in all domains of life and implications for magnetic sensing - pnas.org