Your New Best Research Partner: The Structural Genomics Consortium

Research surrounding drug discovery has historically been highly competitive and expensive. Unfortunately, many late-stage drug failures have occurred over recent years, often due to lack of efficacy. These failures have left the industry searching for new means by which to improve early drug discovery efforts aimed at understanding the drug target and its role in disease. One idea that is gaining traction is partnerships to openly share information at the early, precompetitive stages of drug discovery.

I used to think of open access only in terms of publishing data and information—online sites where you could freely access data without a subscription or membership, and without payment.

Structural Genomics Consortium logo.

Meet the Structural Genomics Consortium (SGC), the international partnership that’s taking open access to a new level in order to advance scientific research for scientists working in a variety of disciplines—structural genomics and beyond. The SGC might just become your new, best laboratory research partner. Continue reading

Cytotoxicity Testing of 9,667 Tox21 Compounds using Two Real-Time Assays by Promega

A recent paper in PLOS One demonstrated real-time cytotoxicity profiling of approximately 10,000 chemical compounds in the Tox21 compound library, using two Promega assays, RealTime-Glo™ MT Cell Viability Assay and CellTox™ Green Cytotoxicity Assay. This is exciting to me, a science writer working at Promega; exciting because it’s tricky figuring out how to write about the utility of our products without sounding like an evangelist.

I don’t know about you, but I tend to shut out evangelists and their messages.

Instead of me telling you about real-time viability and cytotoxicity assays from Promega, here is an example of their use in Tox21 chemical compound library research.

What is the Tox21 compound library?
As described in the article by Hsieh, J-H. et al. (2017) in PLOS One:
“The Toxicology in the 21st Century (Tox21) program is a federal collaboration among the National Institutes of Health, including the National Toxicology Program (NTP) at the National Institute of Environmental Health Sciences and the National Center for Advancing Translational Sciences, the Environmental Protection Agency, and the Food and Drug Administration. Tox21 researchers utilize a screening method called high throughput screening (HTS) that uses automated methods to quickly and efficiently test chemicals for activity across a battery of assays that target cellular processes. These assays are useful for rapidly evaluating large numbers of chemicals to provide insight on potential human health effects.” Continue reading

Findings May Reveal Earliest Evidence of Selective Dog Breeding

Image showing DeLong chain of islands.

Zhokhov Island is part of the DeLong chain of islands off the north coast of Siberia. Image courtesy of Wikimedia Commons.

A report in the June 2, 2017 edition of Science magazine digs into findings from an ancient archaeological site on the very remote and very, very cold Zhokhov Island, to show that the locals, hardy human hunters, not only lived and worked with dogs, but also quite probably selectively bred the dogs for certain traits.

Archaeologist Vladmir Pitulko with the Russian Academy of Sciences has been excavating on Zhokhov Island since 1989, where he has found dog bones as well as remnants of wooden sleds. With archaezoologist Aleksey Kasparov, also of the RAS, they’ve compared two of the most complete dog skulls found to those of contemporary Siberian Huskies and wolves.

Pitulko and Kasparov wanted to first determine if the skulls were those of dogs or wolves. They first employed two key skull ratios: snout height to skull length and cranium height to skull length. Using these ratios, they were able to reliably distinguish between skulls of a modern wolf and husky. Continue reading

Real-Time Analysis for Cell Viability, Cytotoxicity and Apoptosis: What Would You Do with More Data from One Sample?

You are studying the effects of a compound(s) on your cells. You want to know how the compound affects cell health over a period of hours, or even days. Real-time assays allow you to monitor cell viability, cytotoxicity and apoptosis continuously, to detect changes over time.

Why use a real-time assay?
A real-time assay enables you to repeatedly measure specific events or conditions over time from the same sample or plate well. Repeated measurement is possible because the cells are not harmed by real-time assay reagents. Real-time assays allow you to collect data without lysing the cells.

Advantages of  Real-Time Measurement
Real-time assays allow you to: Continue reading

In Healthy Eating Less is More: The Science Behind Intermittent Fasting

Mix a love of eating with a desire to live a long, healthy life what do you get? Probably the average 21st century person looking for a way to continue enjoying food despite insufficient exercise and/or an age-related decline in caloric needs.

Enter intermittent fasting, a topic that has found it’s way into most news sources, from National Institutes of Health (NIH) and Proceedings of the National Academy of Sciences publications to WebMD and even the popular press. For instance, National Public Radio’s “The Salt” writers have tried and written about their experiences with dietary restriction.

While fasting has enjoyed fad-like popularity the past several years, it is not new. Fasting, whether purposely not eating or eating a restricted diet, has been practiced for 1,000s of years. What is new is research studies from which we are learning the physiologic effects of fasting and other forms of decreased nutrient intake.

You may have heard the claims that fasting makes people smarter, more focused and thinner? Researchers today are using cell and animal models, and even human subjects, to measure biochemical responses at the cellular level to restricted nutrient intake and meal timing, in part to prove/disprove such claims (1,2). Continue reading

Widening the Proteolysis Bottleneck: A New Protein Sample Preparation Tool

The poster featured in this blog provides background information and data on development of Rapid Digestion-Trypsin.

The poster featured in this blog provides background information and data on development of Rapid Digestion-Trypsin.

Improvements in Protein Bioprocessing

As more and more protein-based therapeutics enter research pipelines, more efficient protocols are needed for characterization of protein structure and function, as well as means of quantitation. One main step in this pipeline, proteolysis of these proteins into peptides, presents a bottleneck and can require optimization of multiple steps including reduction, alkylation and digestion time.

We have developed a new trypsin reagent, Rapid Digestion–Trypsin, that streamlines the protein sample preparation process, reducing the time to achieve proteolysis to about 1 hour, a remarkable improvement over existing overnight sample preparation times.

How Does it Work?

With this new trypsin product, proteolysis is performed at 70°C, incorporating both denaturation and rapid digestion. The protocol can be used with multiple protein types, including pure proteins and complex mixtures, and is compatible with digestion under native, reduced or nonreduced conditions.

Continue reading

Gut Microbes and Hypertension: Demonstrating a Causal Link

Most of us are aware that the human body is covered by and full of microorganisms. And we understand that most of these microorganisms are helpful, both in terms of competition with and protection against invading microorganisms, and in the gut, as agents of digestion.

Bacillus subtilis, an example of Firmicutes, and not a good gut microbe. By Y tambe (original uploader) - Own work, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=49528

Bacillus subtilis, an example of Firmicutes, and not a good gut microbe. By Y tambe (original uploader) – Own work, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=49528

In the past decade, however, research has brought compelling details implicating gut microbes in obesity, cancer, insulin resistance and such central nervous system disorders as depression, austism spectrum disorder and multiple sclerosis (Adnan, S. et al.). Yet the mechanisms and details of these associations have not been fully demonstrated.

Gut bacteria have been proven to be connected to thickening of heart vasculature, known as atherosclerosis. Researchers have demonstrated that bacteria metabolize choline and L-carnitine from food to trimethylamine, which crosses the gut barrier into circulation and reaches the liver. In the liver, trimethylamine is metabolized to the atherogenic molecule triethylamine-N-oxide (Gregory, J.C. et al., Brown and Hazen). These studies are among the few that provide a direct connection between gut microbes and a pathological condition. Continue reading

The Wide World of Bioprocessing: Science for the Greater Good

My former research career was spent in academic laboratories, and I don’t have first-hand experience in the world of bioprocessing. However in my current job as a science writer/copy editor, I create product information and literature about products that are useful to bioprocessing engineers and technicians, and thus wanted to learn more about this diverse area, where discovery and processing of biomaterials results in better therapeutic drugs, better biofuels and even healthier foods.

Bioprocessing is a combination of biological science and chemistry, and a burgeoning science field. Burgeoning is an understatement. Exploding is a much more apt description.

This 2011 Science magazine careers article defines bioprocessing thusly:

“Bioprocessing is an expanding field encompassing any process that uses living cells or their components (e.g., bacteria, enzymes, or chloroplasts) to obtain desired products, such as biofuels and therapeutics.”

Continue reading

To Quilt, Perchance to Discover

What is it about Quilting?

Not yet a quilt, this is a stock photo image.

Not yet a quilt, this is a stock photo image.

There is a really big quilt show going on in town right now. The annual Wisconsin Quilt Expo runs Thursday through Saturday, September 8–10, 2016 here in Madison, WI.

This quilt expo is the State Fair for quilters. It is to quilters, what Summerfest, or a Lollapalooza festival is to music fans. It is the Stitch-Stitch fest for those with thimbles (and fabric, of course).

To give you another idea of the size of Quilt Expo, busloads of quilters and quilt fans come to this expo, and there are awards for the best quilt in each of ten categories. Can you imagine the time it takes to judge quilts in 10 different categories?

Quilt Expo is sponsored by Wisconsin Public Television and quilter-in-chief Nancy Zieman, host of the popular public television show “Sewing with Nancy”. Her store, Nancy’s Notions is a destination quilting shop in Beaver Dam, WI. I’ve been to this store twice, both times with dedicated quilters. Each time, my quilter counterpart stopped talking immediately upon entering the store. They looked around once, took a cart and went deep into shopping. I gave up on attempts at conversation, due to a lack of response. Continue reading

Seeing the Sites: Summer Travel Close to Home

As the July heat and humidity builds, my mind wanders to good wandering places, including natural historical sites close to home.

Don’t get me wrong, there is nothing like a cross-country adventure, but if I drive 700 miles to a family gathering, and cannot converse on the state parks and historical attractions near my adopted home in southern Wisconsin, then what kind of a traveler—or Wisconsin resident for that matter—am I?

You know what I mean. You drive a full day to a family reunion, only to have someone there tell you how they loved a historical attraction minutes from your home, an attraction you’ve never seen—a conversation stopper to be sure.

Effigy Mounds National Monument, IA, US.

Effigy Mounds National Monument, IA, US.

Case in point: Wisconsin has one of the highest numbers of Native American Indian burial mounds in the US. In case it’s on your way to Wisconsin, our neighbor to the west, Iowa, is home of Effigy Mounds National Monument, part of the National Park Service!

Let’s start with ancient effigy mounds close to home; Here in Madison, Wisconsin, there are mounds on the University of Wisconsin campus, both on Observatory Drive and closer to the Picnic Point path. The web site for the Lakeshore Nature Preserve along Lake Mendota provides some fascinating detail and historical accounts of some of these ancient burial sites, attributed to the Woodland Indians.

Continue reading