Millions of Pickles, Pickles in the Sea

For a few years beginning late in 2013, warmer ocean conditions in the eastern Pacific prompted the appearance of unexpected species and toxic algal blooms that devastated others. When temperatures cooled in 2017, the marine ecosystems seemed to be returning to normal. Except for the pyrosomes. Although these previously rare organisms did start to wash up on beaches during the periods of warming, they began to appear by the millions from Oregon to Alaska that spring.

Pyrosomes

Photo by Steven Grace.

Some combination of ideal conditions led pyrosomes to multiply, dominate the ocean surface and wash up on beaches along the US and Canadian Pacific Coasts. Pyrosomes typically exist offshore, far below the surface in warm, tropical waters all over the world. Their sudden proliferation in other areas is likely due to the warm, Pacific ocean “blob,” although atypical sea currents and changes in pyrosome diet have been offered as other possible explanations.

While the appearance of pyrosomes impeded the efforts of fisherman by clogging nets and filling hooks, greater ecological effects have yet to be observed. As we celebrate World Oceans Month, pyrosomes offer a mesmerizing example of the astounding biological diversity our oceans have to offer and, perhaps, a cautionary tale of the impact climate change can have on those marine lifeforms.

The pyrosome species common in the NE Pacific, Pyrosoma atlanticum, goes by a few other colorful names. Each name reveals something captivating about these creatures. Commonly called “sea pickles” due their size, shape and bumpy texture (like a transparent cucumber), these are not single organisms, but colonies formed by hundreds or thousands of individual multicellular animals call zooids.

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High-Throughput Purification with Experts Included

Implementing automated nucleic acid purification or making changes to your high-throughput (HT) workflow can be complicated and time-consuming. There are also many barriers to success such as challenging samples types and maintaining desirable downstream results that can add to the stress, not to mention actually getting the robotic instrumentation to do what you want it to. All of this makes it easy to understand why many labs avoid automating or own expensive instrumentation that goes unused. Continue reading

Reflections of a Thankful Former Teacher

Today is the start of Teacher Appreciation Week in the United States, punctuated tomorrow by National Thank a Teacher Day. I used to be on the receiving end of the various expressions of gratitude bestowed upon our educators: platters of brownies or cookies from the Board of Education, free meals from restaurants, discounts at retail stores and, if you were really lucky, maybe a student or two (likely initiated by their parents) would bring a gift card or note.

I would also reflect on the teachers that I was personally thankful for: my elementary teachers through graduate school professors (I still remember most of them by name and, with few exceptions, I received what I needed from all of them to learn and grow), my colleagues (who provided mentorship, support and comradery to me and so much more to their students) and my parents (who taught my earliest and most important lessons).

But now I find myself looking at this annual celebration of teachers from the other side—it has been two years since I became a science writer after nearly a decade of teaching high school science. The transition has completely changed my life in ways I could not have imagined and has also impacted the way I think about educators.

The main impetus for this career change was burnout. I had spent countless early mornings, late nights and weekends grading, planning lessons, completing professional development requirements and simply worrying about what challenges I would face the next morning, week or class period. The pressures of each school year would crescendo to a near breaking point every May, and then be swiftly wiped away by the arrival of summer break.

This cycle seemed inevitable, but I had been conditioned by the cultural narrative about teachers to consider it a tolerable tradeoff to the enviable benefits of teaching: holidays and summers “off”, ending the workday before 4 (even I groaned while typing that), great (read: better than average American, worse than someone with similar level of education and experience) benefits & retirement.

Unfortunately, this wasn’t sustainable for me. Moreover, legislative changes and budget cuts exacerbated the ever-present stress to new levels during my last few years as an educator. The strain was taking a toll on my mental health and my ability to be present with family and friends, especially my children.

In my new position, I have been met with intellectual challenges equal to those I encountered as a teacher but face a manageable amount of stress and few threats to work-life balance. Ending my teaching career was probably one of the best decisions I have ever made for my personal well-being. But despite this newfound joie de vivre, I am left with a feeling of guilt that resurfaces whenever issues I used to be so connected with make their way to the national spotlight.

Two of these have been in the news a lot this year—repercussions from budget cuts to education and gun violence in schools. I shouldered the burden of helping my students’ process school shootings and personally dealing with the reality that I could be in the middle of such a tragedy. Similar to the recent wave of teacher walkouts, budget measures that targeted educators brought me to the state capitol in protest.

Yet, I don’t have to face these issues with the sense of urgency I used to. My guilt is rooted in the fact that being a good teacher required selflessness and I chose to be selfish and leave because I couldn’t meet that expectation. It is perhaps because of this nagging feeling that I now feel a gratitude toward teachers that I didn’t before. I am still thankful to all the teachers in my past, but now my appreciation also extends to those that are and will become the future of education.

This year for Teacher Appreciation Week I want to express special gratitude for all of the teachers who feel the same pressures I did and are able to persist. I admire those of you already in the classroom and know you are putting your students’ needs ahead of your own. I’m grateful for all of you who are studying to become teachers, looking past all of the reasons you shouldn’t go into education and focusing instead on the impact you’ll have on future generations.

At a time when it is increasingly difficult to be optimistic about the future, knowing that there are still teachers willing to fight for themselves and their students gives me all the hope I need. Thank you teachers, this week and every week, for all you do!

Evaluating the Costs of Endotoxin Testing

http://www.eniscuola.net/en/mediateca/king-crab/

Recently, I had the opportunity to attend a fascinating symposium held at Promega featuring conservationist Steward Brand, where he described some of the projects developed by his foundation, Revive & Restore.

The organization’s mission is to apply emerging biotechnology techniques to endangered and extinct species with the intent to increase genetic diversity, provide disease resistance and facilitate adaptation to changing climates. Although the overall message of enhancing biodiversity through the application of new genetic technology was inspiring, the project that resonated most for me was related to the plight of horseshoe crabs.

Horseshoe crabs, often referred to as living fossils, include four extant species with origins dating back about 450 million years. Although they look like crabs, they belong to their own subphylum and are more closely related to spiders. When horseshoe crabs spawn, they leave their usual habitat on the ocean floor and migrate to shore in large numbers. As a result, they have been exploited for bait and fertilizer for decades.

Enter endotoxins, an indicator for bacterial contamination in biologicals, drugs and medical devices. U.S. Food & Drug Administration regulations dictate that finished products be tested for the presence of endotoxins. These pyrogenic compounds, found in the cell wall of Gram-negative bacteria, can cause fever and affect a wide range of biological activity, possibly leading to aseptic shock and death. The most common method for testing is the gel clot and Limulus Amebocyte Lysate (LAL) Test.

I first learned about the LAL test during graduate school, where it was presented as a ubiquitous and standard requirement for testing bacterial contamination in injectable drugs. I remember being fascinated that horseshoe crabs (Limulus sp.), contain a substance that could be used to detect endotoxins. Although the instructors mentioned the need to collect blood from horseshoe crabs in order to produce the test, the method or scale of this harvest wasn’t discussed, nor were the true costs of using this method of endotoxin testing.

The LAL test has served as a faster, more inexpensive replacement for the rabbit pyrogens test for the past 35 years. Every year during mating season horseshoe crabs move to shallow water, where they are removed in huge numbers. (To get an idea of scale for the harvest and read a much more comprehensive investigation of the issue, check out this article in The Atlantic, which features an archive photo of Delaware Bay horseshoe crab harvest from 1928—for fertilizer, not pharmaceutical testing.)

After collection, the crabs end up in a lab where up to 30% of their blood is drained from a needle stuck in tissue around their heart. The LAL is extracted from the blood and can yield a product worth up to $15,000/quart. In order to avoid recollection, the crabs are returned to the ocean far from the shore where they were collected a few days before. Although it’s estimated that only 10-30% of these crabs die as a result of the process, there are indications that the horseshoe crab population and their ecosystems are impacted in other ways.

Researchers at the University of New Hampshire and Plymouth State University used accelerometers attached to recently bled female horseshoe crabs to test the hypothesis that harvesting for LAL was affecting their ability to spawn. While the research supported previous estimates with a death rate of 18%, females were found to be less likely to mate after being bled.

During his talk, Brand shared results from a study still in review that confirm the effect of over-harvesting Limulus on the survival of long distance migratory shorebirds. These birds synchronize their migration with horseshoe crab spawning, which provides a needed feast of eggs before the homestretch of their journey. Along with other ecosystem threats from climate change, the accelerated decline in the horseshoe crab population and dependency of migratory birds will likely to lead to a devastating ecological domino effect.

Fortunately, a synthetic alternative to LAL, recombinant factor C (rFC), has been available for nearly 20 years. Alas, there has been no significant shift by pharmaceutical companies away from the test based on horseshoe crab blood. rFC was patented and licensed to one company, Lonza, which Brand posited as one reason for the reluctance of drug companies to adopt its use.

Obviously, relying on one source for an essential testing reagent with no competition to temper cost is quite unattractive. But that argument has less bearing now that the patent is scheduled to expire in a few months, opening the door for additional manufacturers and creating an economic incentive for switching to the synthetic test.

Another reason may be that implementing a new test would require additional resources to validate the synthetic test for products that are already being tested with the LAL. Since the LAL has been specified in FDA guidance documents on endotoxin testing for decades, quality standards for existing products are based on the LAL, limiting momentum to change.

If both tests offered the same benefits, these arguments would make sense; however, research by one of the discoverers of rFC, Jeak Ling Ding of the National University of Singapore, shows that in many respects rFC is more efficacious than LAL. Since the raw material for the LAL test depends on an organism, there is seasonal variation in the components of the processed blood that must be taken into account. The reaction of the LAL also depends on a cascade of multiple compounds that can be affected by temperature, pH and proteins—leaving the test vulnerable to false positive results.

Although Eli Lilly is the only pharmaceutical company to date to use rFC in place of LAL, It seems the tide may be turning. According to Brand, others are interested in making the transition. It seems foolish not to, given the source for LAL shows signs of dwindling due to overexploitation. Perhaps pharmaceutical companies are beginning to see the value of a “slower/better” philosophy (the cornerstone of the Long Now Foundation, another brainchild of Brand’s), rather than “faster/cheaper.” I have certainly gained a new perspective on endotoxin testing and a deep appreciation for the work of Brand and his foundation.

Does your organization use the LAL test? What is preventing you from switching to the synthetic alternative? Let us know!

Biotechnology From the Mouths of Babes

As a science writer, much of my day entails reviewing and revising marketing materials and technical literature about complex life science research products. I take for granted the understanding that I, my colleagues and our customers have of how these technologies work. This fact really struck me as I read an article about research to improve provider-patient communication in healthcare settings.

The researchers completed an analysis revealing that patient information materials had an average readability at a high school level, while the average patient reads at a fourth-grade level. These findings inspired the researchers to conduct a study in which they enlisted the help of elementary students to revise the content of the patient literature after giving them a short lesson on the material.

The resulting content did not provide more effective ways to communicate indications, pre- and post-op care, risks or procedures—that wasn’t really the point. Instead, the study underscores the important connection between patient literacy and health outcomes. More specifically, a lack of health literacy is correlated with poor outcomes and increased healthcare costs, prompting action from the US Department of Health & Human Services.

While healthcare information can be complex and full of specific medical terminology, I recognized that a lot of the technical and marketing information we create for our products at Promega has similar features. Wouldn’t it be interesting to find out how descriptions of some of our biggest technologies translate through the eyes and mouths of children?

After enlisting some help from my colleagues, I was able to catch a glimpse of how our complex technologies are understood by the little people in our lives. The parents and I explained a technology and then had our child provide a description or drawing of what they understood. Continue reading

Choosing a Better Path for Your NGS Workflow

Imagine you are traveling in your car and must pass through a mountain range to get to your destination. You’ve been following a set of directions when you realize you have a decision to make. Will you stay on your current route, which is many miles shorter but contains a long tunnel that cuts straight through the mountains and obstructs your view? Or will you switch to a longer, more scenic route that bypasses the tunnel ahead and gets you to your destination a bit later than you wanted?

Choosing which route to take illustrates a clear trade-off that has to be considered—which is more valuable, speed or understanding? Yes, the tunnel gets you from one place to another faster. But what are you missing as a result? Is it worth a little extra time to see the majestic landscape that you are passing through?

Considering this trade-off is especially critical for researchers working with human DNA purified from formalin-fixed paraffin-embedded (FFPE) or circulating cell-free DNA (ccfDNA) samples for next-generation sequencing (NGS). These sample types present a few challenges when performing NGS. FFPE samples are prone to degradation, while ccfDNA samples are susceptible to gDNA contamination, and both offer a very limited amount of starting material to work with.

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Some Seriously Funny Science

The other night I was playing volleyball and, during a team huddle, made a joke that the only players working hard were those with two X chromosomes (a playful jab at the male players on my team). The only response I got was a single, delayed smile along with a bunch of blank looks. That joke certainly would have produced a better reaction among my scientific colleagues, even if that simply meant a bunch of immediate groans.

I happen to think science-minded folks like myself have a terrific sense of humor, it’s just tailored to a more niche audience since a lot of the jokes we tell may not be immediately understood by the average person. While I appreciate comedy in all forms, I delight in laughing at and making jokes related to science.

Since I don’t think I am alone, I thought I would share a few events in today’s blog that really highlight the humor that can be found in the scientific community.

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Better NGS Size Selection

One of the most critical parts of a Next Generation Sequencing (NGS) workflow is library preparation and nearly all NGS library preparation methods use some type of size-selective purification. This process involves removing unwanted fragment sizes that will interfere with downstream library preparation steps, sequencing or analysis.

Different applications may involve removing undesired enzymes and buffers or removal of nucleotides, primers and adapters for NGS library or PCR sample cleanup. In dual size selection methods, large and small DNA fragments are removed to ensure optimal library sizing prior to final sequencing. In all cases, accurate size selection is key to obtaining optimal downstream performance and NGS sequencing results.

Current methods and chemistries for the purposes listed above have been in use for several years; however, they are utilized at the cost of performance and ease-of-use. Many library preparation methods involve serial purifications which can result in a loss of DNA. Current methods can result in as much as 20-30% loss with each purification step. Ultimately this may necessitate greater starting material, which may not be possible with limited, precious samples, or the incorporation of more PCR cycles which can result in sequencing bias. Sample-to-sample reproducibility is a daily challenge that is also regularly cited as an area for improvement in size-selection.

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Lessons from My Kindergartener’s First Podcast

I am a podcast junkie. In a given week I will listen to 15-20 podcast episodes, while only watching a couple television shows. Podcasts allow me to partake in my favorite pastime, learning, while offering distraction from mundane and time-consuming activities.

Podcasts help me pass the time during my daily 1.5+ hour round trip commute, while running (including during races) and in waiting rooms or airport terminals. Not surprisingly, many of these include science podcasts.

So, I was ecstatic to hear about a new science podcast for kids, Wow in the World, that I could share with my 5-year-old daughter. I considered it an experiment, assuming that she would listen to one or two episodes and lose interest, not expecting her to stay engaged by 20 minutes of audio alone.

I couldn’t have been more wrong. Within a few seconds, she was singing along with the theme song and after a couple minutes she was fully engaged and asking questions about what was being discussed. In a world where our DVR is filled with a backlog of recorded shows for her to watch on TV, she had trouble understanding that we had to wait until next week for another episode. In the meantime, she enthusiastically listened to the same episode 3 or 4 times, picking up something new each time.

This particular podcast really honed in on topics sure to spark interest in kids, such as the velocity of poop, tooting cows and slug slime. But they also addressed more abstract subject matter like human origins, G-forces and space science, explaining complex new scientific discoveries in an entertaining and memorable way.

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Predicting the Future with Dirty Diapers

Microbiome research is booming right now, with more and more evidence that our personal health and environment are shaped and influenced by the microbes we harbor and encounter. One area of study I find particularly interesting is how the microbiome we acquire at birth affects our long-term health.

A flood of new findings have emerged related to infant microbiome research, leaving parents like me scratching their heads about whether the secrets to our children’s future health may exist in the seemingly endless stream of dirty diapers we change.

The human microbiome evolves and develops in utero and then during and after delivery is colonized by bacteria encountered during exposure to the external environment. The initial composition of microbes an infant is populated with influences their lifelong microbiome signature and can be influenced by many factors along the way, including the microbiome community of the mother, use of antibiotics or other antibacterial substances, breastfeeding, C-section birth. These variables have been correlated with disruption of the infant microbiome and associated with differences in cognitive development and the development of disease, such as asthma and allergies.

In general, these correlations are discovered by taking a fecal sample from an infant and analyzing the DNA sequences of the bacteria present. The microbiome composition of the individual is then compared against different individual characteristics (such as presence or absence of a disease) at the time of the sample and/or at later points in time. Finally researchers look for statistically significant patterns among individuals with similar characteristics or microbiome communities. This type of study can reveal associations between the microbiome and individual traits, but further experiments are needed to show causation. Continue reading