Get Out and Count: The Great Backyard Bird Count of 2018

2018 has been designated “The Year of the Bird”, and beginning today, Friday, February 16, 2018, bird lovers around the world will grab their binoculars, fill their bird feeders, update their eBird app, and look toward the skies. The 21st Annual Great Backyard Bird Count, one of the largest and longest running citizen science projects, begins today, and you can be part of this grand event of data collection.

All it takes is a mobile device (or computer) to log your results, an account at gbbc.birdcount.org , and 15 minutes of your time during the four-day event.

Can’t tell a red-tailed hawk from a red-winged black bird? That’s okay. The GBBC web site provides a handy online bird guide.  The web site also provides a guide for tricky bird IDs, including: Which Red Finch is it, Identifying Some Common Sparrows, and Identifying Doves.

I recently spent some time talking to Brian Schneider, one of the educators at the Aldo Leopold Nature Center in Monona, WI, to get some tips for first-time birders. Continue reading

Black-Footed Ferrets: Back from the Brink

Bff = black footed ferret

Giving some love to a BFF (Black-Footed Ferret).

Today is Valentine’s Day (February 14) and our thoughts turn to doing something special for a significant other (so),  a best friend (bf) or best friend forever (bff).  In this blog we consider doing something special for a bff, but the bff at focus here is not human.

This bff is the black-footed ferret.

That’s correct—we’re talking about the weasel-like critter with the black mask, black tail tip and black feet. This small, wiry animal, with the help of some particularly dedicated humans, has had an amazing come-back story since the 1970s, when these ferrets were believed to be extinct.

About the BFF (Black-Footed Ferret)
The black-footed ferret, Mustela nigripes, is a member of the family Mustelidae, which includes mink, badger, marten, fisher, polecat and wolverine (of course domestic ferrets are also members of this family). Like mink and other members of the mustelidae, bff are long, slender animals that average 18 to 24 inches in length. Black-footed ferrets weigh 1½ –2½ lbs. Female ferrets are “jills”, males are “hobs” and juvenile ferrets are “kits”. The average life span of a black-footed ferret in the wild is 1–3 years. Continue reading

Mass Spec Analysis of PTMs Using Minimal Sample Material

DNA is organized by protein:DNA complexes called nucleosomes in eukaryotes. Nucleosomes are composed of 147 base pairs of DNA wrapped around a histone octamer containing two copies of each core histone protein. Histone proteins play significant roles in many nuclear processes including transcription, DNA damage repair and heterochromatin formation. Histone proteins are extensively and dynamically post-translationally modified, and these post-translational modifications (PTMs) are thought to comprise a specific combinatorial PTM profile of a histone that dictates its specific function.  Abnormal regulations of PTM may lead to developmental disorders and disease development such as cancer.

Antibodies have been widely used to characterize histones and histone PTMs. However, antibody-based techniques have several limitations. Mass spectrometry (MS) has therefore emerged as the most suitable analytical tool to quantify proteomes and protein PTMs.  The most commonly used strategy is still bottom-up MS, and the most widely adopted protocol includes derivatization of lysine residues in histones to allow trypsin to generate Arg-C like peptides (4–20 aa). However, samples such as primary tissues, complex model systems, and biofluids are hard to retrieve in large quantities. Because of this, it is critical to know whether the amount of sample available would lead to an exhaustive analysis if subjected to MS.

In a recent publication, Guo, et al. examined (1) the reproducibility in quantification of histone PTMs using a wide range of starting material: from 50,000 to 5,000,000 cells. They used four different cell lines: HeLa, 293T, human embryonic stem cells (hESCs), and myoblasts. Their results demonstrated that an accurate quantification of abundant histone PTMs can be efficiently obtained by using low-resolution MS and as low as 50,000 cells as starting material Low abundance histone marks showed more variability in quantification when comparing different amounts of starting material, so a larger amount of starting material (at least 500,000 cells) is recommended.

Reference

Guo, Q. et al. (2017) Assessment of Quantification Precision of Histone Post-Translational Modifications by Using an Ion Trap and down To 50,000 Cells as Starting Material. J. Proteome Res. 17, 234–42.

Celebrating Women in Science

By US Environmental Protection Agency [Public domain], via Wikimedia Commons

February 11 is the International Day of Women and Girls in Science, a reminder that there is still a gender gap in science. Despite the obstacles that women need to overcome, their contributions to field of science have benefited not only their fellow researchers but also their fellow humans. From treatments for diseases to new discoveries that opened up entire fields, women have advanced knowledge across the spectrum of science. Below is a sampling of the achievements of just a few women. What other living female scientist or inventor might you add?

Hate malaria? You can thank Tu Youyou for discovering artemisinin and dihydroartemisinin, compounds that are used to treat the tropical disease and save numerous lives. Her discovery was so significant, she received the 2015 Nobel Prize in Physiology or Medicine. Continue reading

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!

Announcing the 13th Annual Wisconsin Stem Cell Symposium

20 Years of Human Pluripotent Stem Cells: Current Clinical Trials and Regulatory Framework

April 18, 2018 | Madison, WI

Picture of Stem Cell Booth display from last year's meetingOver the years, the BTC Institute has partnered with the Stem Cell & Regenerative Medicine Center, at the University of Wisconsin-Madison to offer this packed day of excellent talks and opportunities to interact with renowned speakers, poster session presenters, sponsor representatives and other attendees.

Our UW-Madison committee members define each year’s content and pull together a strong group of presenters.  This year, we’re working with Timothy J. Kamp, M.D. (Professor, Medicine, Cell and Regenerative Biology; Co-director, Stem Cell and Regenerative Medicine Center), William L. Murphy, Ph.D. (Professor, Biomedical Engineering, Orthopedics & Rehabilitation; Co-director, Stem Cell & Regenerative Medicine Center) and James Thomson, Ph.D. (John D. MacArthur Professor, Director, Regenerative Biology, Morgridge Institute for Research; Professor, Department of Molecular, Cellular, & Developmental Biology, University of California – Santa Barbara).

Attendees at last year's stem cell symposiumOur 2018 symposium brings together leading researchers advancing human pluripotent stem cell products to clinical applications for a range of degenerative diseases. Progress in clinical trials, as well as major barriers for developing these revolutionary new therapies will be discussed.

As Dr. Kamp notes, “This will be a remarkable meeting highlighting the emerging field of regenerative medicine which has grown from the pioneering discovery of human embryonic stem cells 20 years ago.” Continue reading

Feminization and Mass Die Offs: The Effects of Changes in Climate

Say the words “climate change” in a room full of people and you are bound to inspire some passion in the response—and very likely start an argument. There is no question that emotions and opinions run high whenever this topic is introduced. Most often the debate centers around who or what might be causing changes in the earth’s climate and what should be done about it. So for the sake of everyone’s blood pressure, I want to set some expectations around this blog.

This is not a blog about the causes of climate change. I am not going to talk about who or what might be causing it, nor am I going to discuss ways the changes could be stopped, slowed down or altered.

The earth’s climate has warmed and cooled before. Looking at ice-core and geological records, we know that the earth has been much warmer than it is now, and we know that it has been much colder. Climate is dynamic, there are always fluctuations in temperature and moisture from year to year and decade to decade. Some of these fluctuations become trends where the changes consistently track in one direction, and some are anomalies, with more extreme climate conditions and less predictable patterns. Plant and animal populations are unquestionably affected by both the year-to-year fluctuations and the long-term trends. In this blog I am going to talk about two rather dramatic examples of the effects climate change. One example looks at the impact of warming global temperatures over time on the breeding populations of green sea turtles. The other is an example of the devastating results of one warm, remarkably humid, spring on the calving aggregations of the saiga antelope.

Continue reading

Encouraging, Supporting, and Advocating for Diversity in Science

On December 27, 2017, the life sciences community lost a pioneer in neurobiology and an advocate for equality in science. Dr. Ben A. Barres passed away at the age of 63. His work focused on the critical role of glia (non-neuronal cells) in the brain and how they interface with neurons to maintain cognitive function.

Equally remarkable was the more personal side of his life. In 1997, Dr. Barbara Barres transitioned from female to male and lived the remainder of his life as Ben Barres. I read a number of the articles that Dr. Barres wrote and came across one that particularly caught my attention. Continue reading

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

A Virus-like Neural Pathway Hints at the Origins of the Mammalian Brain

The mammalian brain is extremely complex. We know that it processes and stores information through synaptic connections within a complicated neural network. But how exactly do neurons communicate with each other? And how did this neural network come to exist? A recent paper published in Cell may provide some answers. It describes a previously unknown signaling pathway–with surprising origins–that transports RNA between neurons. Continue reading