Here Comes the Sun: How to Protect Yourself and the Coral Reefs

Sunscreen usage is increasing, with more people using SPF to prevent the very real threats of skin cancer and early signs of aging. While slathering on the sunscreen is unarguably important to protect your skin from the sun, new concerns arise linking sunscreen chemicals to coral reef bleaching, as an estimated “14,000 tons of sunscreen is believed to be deposited in the oceans annually.”

Coral reefs are the most productive marine ecosystem known. Coral reefs protect coastlines from storm surge and support commercial and recreational fisheries and tourism. Unfortunately, certain chemicals in sunscreen are causing coral reefs to bleach; thus, becoming more susceptible to viral infections. The reefs eventually turn white and die. Coral reef bleaching is the leading cause of coral reef deaths worldwide. This conversation is an important one to discuss leading up to the celebration of World Oceans Day on June 8.

Chemical recreational sunscreen contains oxybenzone, a toxic synthetic molecule. Oxybenzone is prevalent in the majority of mainstream sunscreen brands. This ingredient results in extreme harm to marine organisms. The Ocean Foundation emphasized that, “A single drop of this compound in more than 4 million gallons of water is enough to endanger organisms.” Even if you do not physically go in the water, the chemical can be washed into the ocean through the sand.

In response to this issue, many countries and resorts are banning “reef-toxic” sunscreen. Hawaii and Key West recently passed a bill banning the sale and distribution of any sunscreen that contains 10 toxic ingredients, including oxybenzone. This bill goes into effect January 2021. Many dermatologists are concerned for public safety, highlighting that banning certain sunscreens will decrease overall use. Unprotected sun exposure it the most preventable risk factor for skin cancer. From the perspective of a customer, it is important to be actively informed on what constitutes a “reef-safe” sunscreen. Oxybenzone can pop-up in many moisturizers, primers, and foundations that contain SPF. Reef-friendly options include: any version of chemical sunscreen that does not contain oxybenzone.

With a commitment to protect the environment, Promega has pledged $3 million over the next three years to the Revive and Restore Catalyst Science fund. Organization founders and scientists are focused on an extremely long-term view of wildlife conservation. This fund invests in proof-of-concept research projects that offer innovative solutions for conservation challenges and threatened ecosystems. Marine biologist Steve Palumbi was awarded the first Fund grant to investigate the triggers that may cause corals to bleach. Palumbi reflects on his research in an interview with Stanford News stating, “The report reflects a sense of urgency. We need to start helping corals now, so that as the climate gets worse—and it will inevitably get worse—we’re a little bit in front of the problem. There’s this amazing sense that we all have to just jump in and try ideas and fail so that, eventually, someone comes up with the answers we need.”

MSI Analysis and the Application of Therapies Based on 2018 Nobel Immuno-Oncology Work

The 2018 Nobel Prize in Physiology and Medicine was awarded to James P. Allison of the United States and Tasuku Honjo of Japan for their work to identify pathways in the immune system that can be used to attack cancer cells (1). Although immunotherapy for cancer has been a goal for many decades, Dr. Allison and Dr. Honjo succeeded through their manipulation of “checkpoint inhibitor” pathways to target cancer cells.

Immune checkpoint inhibitor drugs have been effective in cancers such as aggressive metastatic melanoma, some lung cancers, kidney, bladder and head and neck cancers. These therapies have succeeded in pushing many aggressive cancers below detectable limits, though these cases are notably not relapse-free or necessarily “cured” (2,3).

One challenge in implementing immunotherapy in a cancer treatment regime is the need to understand the genetic makeup of the tumor. Certain tumors, with specific genetic features, are far more likely to respond to immune checkpoint therapy than others. For this reason, Microsatellite Instability (MSI) analysis has become an increasingly relevant tool in genetic and immuno-oncology research.

What is MSI Analysis?

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“GenEthics” – The Implications of Genomic Data

I majored in genetics because I love Punnett Squares. Don’t get me wrong, I was fascinated by the groundbreaking research going on in fields like oncology and agriculture, but there was something about the simple and logical nature of calculating inheritance patterns that really drew me in. At the time when I confusingly wandered into my advisor’s office to make this life changing academic decision, I had no idea that this degree would help me see the more complicated, “gray area”, of science, changing the way that I look at the world today.

What is “GenEthics” ?

As I’m sure you’ve already guessed, “GenEthics” is the intersection between the fields of genetics and ethics. A broad term involving questions related to the implications of a variety of different topics in genetic research; “GenEthics” covers everything from the modification of stem cells, to gene therapy and GMOs. Since this term encompasses such a large array of topics, I’m going to focus on some of the ethical questions related to your genome.

Genomic data and its applications

If you’ve ever heard of 23andMe or Ancestry.com then you’ve already had an introduction to genomic data. These direct-to-consumer genetic testing companies are a result of advancements in technology that have made the genotyping process relatively cheap and quick. When you submit a sample, they send it to a lab, extract the DNA, and test it for various markers. What’s returned to you is a report of what markers (alleles) you do and don’t have. These reports can tell you everything from what percent German you are, to your status for any of the many alleles of several genes that may increase risk for Alzheimer’s disease. Genomic data has affected a variety of fields; knowledge of the genome has allowed us to catch famous criminals like the Golden State Killer and has provided us with diagnostic markers for serious diseases. But even with all the good that genomic data has done and will do, there is a “gray area” where many questions regarding safety, equality, and privacy lie.

Safety – Should everyone have their genomes sequenced?

Some believe this is the future of healthcare, that everyone will have their genomes sequenced at birth and put into a national database. This would have amazing implications in the research world; access to endless data, and the ability to form conclusions about everything from human disease to intelligence.

This question also brings up a plethora of others, some pertaining to identity safety. In particular, what if this fictitious database is hacked? There have already been smaller-scale database breaches, the most recent being on the MyHeritage website. These breaches are potentially dangerous; the entirety of your personal health information is housed in your genome. With proper scientific guidance, hackers could infer your: gender, ethnicity, disease status, etc. DNA is not like a credit card, there is no way to obtain a new set of genes.

Equality – How do we ensure that everyone benefits from the advancements that genomic data has to offer?

There are many studies being done with the goal of eradicating cancer using precision medicine. This involves finding common tumor-causing variants in patients’ DNA sequences, and treating them based on their genes. These types of studies have the potential to contribute greatly to the field of personalized medicine, but caution needs to be taken to ensure that multiple populations are represented in the study. Ethnic groups have evolved on separate continents and their genetic sequences contain different variations, one set of conclusions about a disease might not apply to all populations.

Privacy: Who has a right to your genetic information?

The Genetic Nondiscrimination Act (GINA) was passed in 2008 to prevent your genetic test results from affecting your qualification for health insurance, or employment prospects. However, this is but a scratch on the surface of possible genomics-related legal issues; the ownership of a DNA sequence is a complete question mark at this time. There are no laws regarding an organization or family members’ right to an individual’s sequence.

Genomic data has the ability to save lives and prevent devastating disease, but it also can cause disputes within families, and between organizations and individuals. The question of DNA ownership brings up many others: if you test positive for a condition, should you inform other at risk family members? Do you have sole claim on your DNA when you have family members that share most of your sequence? When you submit your DNA to an organization what ownership rights do they have?

The Future…

We have come a long way since completion of the Human Genome Project back in 2003, and we will continue to make amazing advances thanks to the field of genetics. The questions I have posed are just a few that lie in the “gray area” we will be venturing into in the future. These questions may seem as if they are just for researchers, doctors, and lawyers, but they really are for everyone. The social and ethical implications of science affect us all; it’s important that we all join the conversation!

Questions of Genome Privacy and Protection

In April 2018, law enforcement officials announced the arrest of a suspect in the Golden State Killer case (New York Times 4/27/2018 ). Shortly after the announcement, those same law enforcement officers explained that detectives had used a public forensic genealogy web site to help identify the killer.

What does it mean when a law enforcement agency accesses a public genetic genealogy database to search for a suspect in a crime?

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The Pan-Cancer Atlas: “The End of the Beginning”

In April 2018, a series of 27 papers representing the most comprehensive genomic analysis of human cancers to date was published in Cell Press journals.

The collection constitutes the final outputs from the Cancer Genome Atlas (TCGA) project, a collaboration between the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI) involving analysis of over 11,000 tumors representing 33 different cancers. The many research teams involved analyzed tumor DNA, mRNA, miRNA and chromatin, comparing them to matched normal cellular genomes to perform a complete molecular characterization of cancer-specific changes. The results have been presented with much hope that open access to this type of comprehensive analysis will build on recent advances in understanding tumor biology and spur further progress in developing new approaches to treatment. (See this news item for more detail).

The Pan-Cancer Atlas results are collected on a cell.com portal, where they are presented in three collections grouped by topic: Cell of Origin, Oncogenic Processes and Signaling Pathways. Each collection is accompanied by a “Flagship” paper introducing the topic and summarizing the findings. It seems fitting that these findings have been published in #HumanGenomeMonth. This comprehensive analysis of the genomic and metagenomic profiles of tumors illustrates one powerful application of the type of genomic analysis pioneered by the original Human Genome Project, and shows just how much has been made possible since the initial publication of the human genome fifteen years ago.

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A Surprising New Role for Body Fat?

This cloaked fat cell just might be a superhero.

Forty-some years ago fat was just fat. And it was regarded with disdain, to say the least.

An entire industry existed to help get rid of fat, using what was then the latest mass media technology, television. If you wanted to get rid of fat you could exercise with Jack LaLanne as he worked out on television. We exercised in elementary school PE class to a vinyl recording of “Chicken Fat”. You could strap into a device that employed shaking to get rid of the fat from your “hips”, or eat a piece of chocolate fudge with a hot beverage before meals to curb your appetite.

Fat was not our friend. We knew long before the current diabetes epidemic that being overweight was not good for our health.

Fast forward to the 21st century, where we’ve learned that some forms of fat are actually good for you–important in metabolism, growth and immunity. The variety of types of mammalian fat include brown adipose tissue, beige adipose tissue and white adipose tissue, and it’s possible to convert one to the other under certain conditions. For details on these types of adipose tissue, read this article —after you finish this blog.

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The Bacteria that are Good for Us

Chains of Streptococci

Salmonella. Streptococcus. Shigella. The most well-known bacteria are those that cause disease. Our relationship with them is one of combat. With good reason, we look for ways to avoid encountering them and to eliminate them when we do meet.

But not all bacteria are bad for us. Of course we have known for years that we are colonized by harmless bacteria, but recently, studies on the human microbiome have revealed many surprising things about these bacterial tenants. Studies are showing that the teeming multitudes of organisms living in and on the human body are not just harmless bystanders, but complex, interrelated communities that can have profound effects on our health.

Three studies published in Science in 2018 add more to the growing body of microbiome surprises, showing that certain gut bacteria are not only good for us, but may even be required for the effectiveness of some anti-cancer immunotherapies.

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Promega Partnering with UC-Davis Drought-Resistant Rice Project

The Foundation for Food and Agriculture Research (FFAR) announced on November 30 that they are awarding $1M to a project based at the University of California, Davis, to study protein kinases of rice plants. The team is led by Dr. Pamela Ronald, a leading expert in plant genetics who has engineered disease- and flood-resistant rice. This project aims to address the growing agricultural problem of water scarcity by gaining a better understanding of the role kinases play in enabling drought-resistance. Promega will be supporting this research by providing NanoBRET™ products to help characterize kinase inhibitors.

Principal Investigator Pamela Ronald, Ph.D. Photo Credit: Deanne Fitzmaurice

The research team will begin by screening over 1,000 human kinase inhibitors to determine which ones do interact with the plant kinome and, if applicable, which kinase(s) they inhibit. Once the compound library has been established, the team will assess the inhibitors’ phenotypic effects on rice to identify kinases that, when inhibited, positively impact root growth and development. The long-term goal is to use these findings to engineer drought-resistant rice.

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Where Would DNA Sequencing Be Without Leroy Hood?

There have been many changes in sequencing technology over the course of my scientific career. In one of the research labs I rotated in as a graduate student, I assisted a third-year grad student with a manual radioactive sequencing gel because, I was told, “every student should run at least one in their career”. My first job after graduate school was as a research assistant in a lab that sequenced bacterial genomes. While I was the one creating shotgun libraries for the DNA sequencing pipeline, the sequencing reaction was performed using dideoxynucleotides labeled with fluorescent dyes and amplified in thermal cyclers. The resulting fragments were separated by manual loading on tall slab polyacrylamide gels (Applied Biosystems ABI 377s) or, once the lab got them running, capillary electrophoresis of four 96-well plates at a time (ABI 3700s).

Sequencing throughput has only increased since I left the lab. This was accomplished by increasing well density in a plate and number of capillaries for use in capillary electrophoresis, but more importantly, with the advent of the short read, massively parallel next-generation sequencing method. The next-gen or NGS technique decreased the time needed to sequence because many sequences were determined at the same time, significantly accelerating sequencing capacity. Instruments have also decreased in size as well as the price per base pair, a measurement used when I was in the lab. The long-prophesized threshold of $1,000 per genome has arrived. And now, according to a recent tweet from a Nanopore conference, you can add a sequencing module to your mobile device:

Welcome to the future – DNA sequencing on your mobile phone – imagine where and how you can use it. Hats off to the @nanopore team for getting this to work at this form factor, voltage and watts. https://t.co/Tm6A5fj8M4

— Ewan Birney (@ewanbirney) November 30, 2017

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Ancient Images of Dogs Include Restraints?

This dog is wearing a leash.

You, like me, may occasionally find youself in need of a canine control device. While I’m not a fan of the dog tie out, I do walk dogs on leash—as is required by our county and city government here in Madison, WI.

If you have read Temple Grandin’s books about dogs, you might feel a tug at your heartstrings while enduring a tug on the leash. Aren’t dogs meant to run freely? Don’t we love to watch them run? Are leashes humane?

When walking dogs I feel the need to protect them, but also a desire to let them live like dogs, sniffing, marking and other behaviors that are all limited when the dog is leashed.

When a report in Science last week showed evidence that our ancient ancestors were using leashes 8,000-9,000 years ago I was: 1) surprised; and 2) felt vindicated from self-imposed dog owner guilt.

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