Hot Wings and Snow Birds: A Study of Genetic Selection in Chickens

African chicken breed Boschvelder. Image copyright ICBH GROUP.

This past summer, I visited the county fair and stopped by the animal barn to look at some of the poultry on display. Specifically, I wanted to see examples of the breeds of chickens available that I may be interested in adding to my flock. Rather than each chicken in their display cage being labeled with a bird’s breed, each cage listed the geographic origin of the chicken within such as Asiatic, Continental or American. This did not benefit my search for potential new members of my flock, but intrigued me enough that I wanted to find out how my flock of 19 hens and pullets would be characterized. Using the classes delineated by the Wisconsin State Fair, my feathered ladies break down to 12 American, 4 English and 3 Continental chickens. There are also classes for Mediterranean and Asiatic (and Other). I live in a part of the United States that gets cold, snowy weather for what seems like six months out of the year, weather that my chickens seem to take in stride. But in other places in the world, heat is the name of the game for the poultry strutting there. In a Genes, Genomics, Genetics publication, Fleming et al. wanted to know if there were genetic differences in Northern European and African chickens that might be caused by their environment. Continue reading

Reveal More Biology: How Real-Time Kinetic Cell Health Assays Prove Their Worth

What if you could uncover a small but significant cellular response as your population of cells move toward apoptosis or necrosis? What if you could view the full picture of cellular changes rather than a single snapshot at one point? You can! There are real-time assays that can look at the kinetics of changes in cell viability, apoptosis, necrosis and cytotoxicity—all in a plate-based format. Seeking more information? Multiplex a real-time assay with endpoint analysis. From molecular profiling to complementary assays (e.g., an endpoint cell viability assay paired with a real-time apoptosis assay), you can discover more information hidden in the same cells during the same experiment.

Whether your research involves screening a panel of compounds or perturbing a regulatory pathway, a more complete picture of cellular changes gives you the benefit of more data points for better decision making. Rather than assessing the results of your experiment using a single time point, such as 48 hours, you could monitor cellular changes at regular intervals. For instance, a nonlytic live-cell reagent can be added to cultured cells and measurements taken repeatedly over time. Pairing a real-time cell health reagent with a detection instrument that can maintain the cells at the correct temperature means you can automate the measurements. These repeated measurements over time reveal the kinetic changes in the cells you are testing, giving a real-time status update of the cellular changes from the beginning to the end of your experiment. Continue reading

Postcards from the Northern Roman Empire

Some of the thin wood tablets found at Vindolanda in Northumberland, England. Image Copyright The Vindolanda Trust.

Correspondence whether via postcard or letter has been a method of human communication likely since people became literate. Old letters and postcards have been uncovered in attics, basements and garages, offering depth and richness to historical events or adding context to how humans lived in the past. But what about finding correspondence from more than a few hundred years ago?

Interestingly, archeologists were excavating in a Roman fort just south of Hadrian’s Wall and discovered well-preserved thin slices of wood with ink writing dating to the 1st century. While these 25 postcard-sized correspondence, found in a line about 3–4 meters long, are just the latest uncovered at the Vindolanda fort, the documents add to the history of Romans in Britain.

Many of the newly discovered wooden wafer postcards seemed to contain complete messages and could be read without the need for infrared photography. This treasure “hoard” of ancient Roman writing tablets offer insights such as a man named Masclus asking for leave. His previously discovered correspondence also from the Roman fort at Vindolanda included asking his commanding officer to supply more beer to his outpost.

The announcement of these 25 new Roman messages by the sponsors of the fort excavation are only preliminary overview of the find. In fact, archeologists are working on conserving and deciphering messages on the wooden tablets and plan on using infrared photography to reveal if there is any more writing on these postcards from the past.

Read more in the Vindolanda Trust Press Release.

Six (and a Half) Reasons to Quantitate Your DNA

Knowing how much DNA you have is fundamental to successful experiments. Without a firm number in which you are confident, the DNA input for subsequent experiments can lead you astray. Below are six reasons why DNA samples should be quantitated.

6. Saving time by knowing what you have rather than repeating experiments. Without quantitating your DNA, how certain can you be that the same amount of DNA is consistently added? Always using the same volume for every experiment does not guarantee the same DNA amount goes into the assay. Continue reading

Revealing Time of Death: The Microbiome Edition

Forensic analysts have long sought precision when determining time of death. While on crime scene investigation television shows, the presence of insects always seems to reveal when a person died, there are many elements to account for, and the probable date may still not be accurate. Insects arrive days after death if at all (e.g., if the body is found indoors or after burial), and the stage of insect activity is influenced by temperature, weather conditions, seasonal variation, geographic location and other factors. All this makes it difficult to estimate the postmortem interval (PMI) of a body discovered an unknown time after death. One way to make estimating PMI less subjective would be to have calibrated molecular markers that are easy to sample and are not altered by environmental variabilities.

Bacterial communities called microbiomes have been frequently in the news. The influence of these microbes encompass living creatures and the environment. Not surprisingly, research has focused on the influence of microbiomes on humans. For example, changes in gut microbiome seem to affect human health. Intriguingly, microbiomes may also be a key to determining time of death. The National Institute of Justice (NIJ) has funded several projects focused on the forensic applications of microbiomes. One focus involves the necrobiome, the community of organisms found on or around decomposing remains. These microbes could be used as an indicator of PMI when investigating human remains. Recent research published in PLOS ONE examined the bacterial communities found in human ears and noses after death and how they changed over time. The researchers were interested in developing an algorithm using the data they collected to estimate of time of death. Continue reading

Preventing Viral Infection by Blocking Cellular Receptors with a Tethered Antibody

Cross section of mature HIV. Copyright David S. Goodsell, The Scripps Research Institute.

Cross section of mature HIV. Copyright David S. Goodsell, The Scripps Research Institute.

Finding a way to neutralize or block infection by HIV has long been pursued by viral researchers. Various treatments have been developed, driven by the need to find effective drugs to manage HIV in infected individuals. The ultimate goal is to develop a vaccine to prevent HIV from even taking hold in the body. With all of our knowledge about the cellular receptors HIV needs to enter the cell, there has to be a method to prevent a viral particle from binding and being internalized. Many researchers are pursuing neutralizing antibodies to the virus as one method. What about antibodies that target the cellular receptor recognized by the virus? In a recently published article in Proceedings of the National Academy of Sciences, antibodies to cellular receptors for rhinovirus and HIV were tethered to the plasma membrane and tested for the ability to prevent infection. Continue reading

Pollinator-Plant Interactions, Neanderthal Teeth, Desiccated Tardigrades and Blood Typing: Science News This Week

Keeping up with the pace of scientific discoveries being published each week can be difficult. Here I share a few scientific publications that piqued my interest over the past week:

Pollinators influence evolution of plant traits

Brassica rapa cv. By I, KENPEI [GFDL (http://www.gnu.org/copyleft/fdl.html), CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0/) or CC BY-SA 2.5-2.0-1.0 (http://creativecommons.org/licenses/by-sa/2.5-2.0-1.0)], via Wikimedia Commons

Brassica rapa cv. By I, KENPEI [GFDL (http://www.gnu.org/copyleft/fdl.html), CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0/) or CC BY-SA 2.5-2.0-1.0 (http://creativecommons.org/licenses/by-sa/2.5-2.0-1.0)], via Wikimedia Commons

To explore the plant-pollinator relationship, researchers studied field mustard, a relative of oilseed rape, under the influence of three pollination conditions: by hand, by bumblebee and by hoverfly. After nine generations, the plants were visually changed. The ones pollinated by bumblebees were taller than the original plant; the ones pollinated by hoverflies, shorter. In addition, the bumblebee-pollinated field mustard developed more fragrant floral compounds and more UV-reflecting petals while the hoverfly-pollinated plants became more self-pollinated. While this experimental was done in isolation from other plants, the research suggests a pollinator can influence the traits evolved by a plant.

Read the Nature Communications research article.

Calculus from Neanderthals reveal diet and probable self-medication

The calcified plaque on teeth of five Neanderthal skulls was scraped, PCR amplified and sequenced to examine what could be learned of diet, behavior and disease. One specimen was eliminated because the DNA did not amplify, one due to environmental contamination, leaving two specimens from Spain and one from Belgium that were used for analysis. The Belgian individual had rhinoceros, sheep and mushrooms caught in its teeth while the Spanish Neanderthals consumed mushrooms, pine nuts, forest moss, and poplar as well as plant fungus. The last two items were of interest because these sequences were found in the Neanderthal suffering from a dental abscess. Poplar contains the active ingredient in aspirin and the fungus was Penicillium from which the first antibiotic was derived. Researchers also compared the bacterial sequences of oral microbes across hominid species and sequenced a draft genome of the 48,000-year-old oral bacterium Methanobrevibacter oralis subsp. neandertalensis.

Read the research article in Nature.

The desiccation tolerance of water bears explained

Scanning electron micrograph of an adult tardigrade (water bear). By Goldstein lab - tardigrades (originally posted to Flickr as water bear) [CC BY-SA 2.0 (http://creativecommons.org/licenses/by-sa/2.0)], via Wikimedia Commons

Adult tardigrade (water bear). By Goldstein lab – tardigrades (originally posted to Flickr as water bear) [CC BY-SA 2.0 (http://creativecommons.org/licenses/by-sa/2.0)], via Wikimedia Commons

The microscopic tardigrades are a creature that inspire microbiologists and others with their cuteness (hence the nickname water bears) and their resilience under dry conditions. However, little was known why they can survive desiccation. New research reveals that unlike other organisms that use sugar to resist drying, tardigrades use disordered proteins to protect itself. These proteins lack stable 3D structures and form glass-like protection under desiccation. Not surprisingly, these proteins are called tardigrade-specific intrinsically disordered proteins or TDPs. By transferring TDPs into yeast, researchers were able to increase yeast tolerance to drying as well as enhance survival.

Read a summary of the research in The Scientist (contains link to research article).

Blood type determined in 30 seconds using a paper-based assay

Matching blood type usually involves centrifuging blood samples to test both red blood cells and plasma, and takes about 30 minutes. However, a rapid test would be useful in emergencies while an alternate test for those without the funds for lab facilities would be beneficial. What about paper infused with dye that could show blood type in seconds, no centrifugation needed? In fact, researchers have developed a paper-based assay that uses microliter volumes of whole blood to determine blood type with a visual indicator. Using immobilized antibodies and a green dye, the blood will clump in the presence of an antibody that is recognized, turning the paper blue to show it has the marker for A (left side of chip) or B (right side of chip). Type AB will have both markers while type O has neither, turning the paper brown on both sides of the chip. Rare blood types and five Rhesus markers can also be analyzed using this paper-based chip assay, starting with a small sample of whole blood.

Read a summary of the research and watch a video of the paper assay chip in Science (contains link to research article).

From Whence You Came, Honey Bee?

Apis melliferaWestern honey bee. By Ivar Leidus (Own work) [CC BY-SA 4.0 (http://creativecommons.org/licenses/by-sa/4.0)], via Wikimedia Commons

Apis mellifera Western honey bee. By Ivar Leidus (Own work) [CC BY-SA 4.0 (http://creativecommons.org/licenses/by-sa/4.0)], via Wikimedia Commons

As a new beekeeper, I never really considered much about the origins of honey bees. I knew they were not native to the United States, most are from Europe and the ones that sting in a swarm are called Africanized. Local beekeepers talk about ordering Italians or Carniolans to populate hives, and during a recent local beekeeper’s association presentation, Asian honey bees were mentioned. From where Apis mellifera, the Western honey bee arose, I did not know.

As it turns out, the origin of honey bees is a highly debated topic. Some say they arose from Asia; others say Africa. Recently, researchers from the University of California—Davis used short nucleotide polymorphisms (SNPs) and two sets of previously published whole genome data, included additional sequenced genomes and applied multiple computational methods to analyze honey bee population genetics. They published their conclusions in Genome Biology and Evolution. Continue reading

A Big Protective Step Forward for A Rare Bee

A rusty-patched bumblebee on Culver’s root in the UW–Madison Arboretum. Photo Copyright: SUSAN DAY/UW-MADISON ARBORETUM

A rusty-patched bumblebee on Culver’s root in the UW–Madison Arboretum. Photo Copyright: SUSAN DAY/UW-MADISON ARBORETUM

Bees have been in the news many times over the past several years. Much of the concern has been focused on the collapse of honey bee colonies because these bees collect nectar to create honey and can be transported for use as pollinators for farmers. Alongside the plight of the honey bee are the declines in the population of native bees in the United States. These bees include insects like the big, fuzzy bumble bees, tiny, iridescent green sweat bees and dark blue mason bees. The native bees live in different conditions. They may be solitary, have a small colony or even nest close together in a communal arrangement, but never in the numbers likely to be seen for a honey bee colony. These lower-density populations can make seeing a change in native bee numbers more difficult. While honey bees have gained the majority of bee decline attention, native bees have suffered dramatic population loss with long-term consequences for the plants they pollinate and the animals that depend upon those plants.

On January 11, 2017, in a landmark decision by the United States Fish and Wildlife Service, the one of the rarest native bees called the rusty-patched bumble bee (Bombus affinis) has been listed as threatened, and this designation will go into effect February 10, 2017. This is the first bee in the U.S. that has been placed on the Endangered Species list. The rusty-patched bumble bee derived its name from the rust-colored patch found on its back. Continue reading

Making It Easier to Investigate PGTs

Introduction

Studying cellular molecules can be challenging. Some processes are troublesome to study due to the lack of an assay or a complicated assay exists but lacks sensitivity. Membrane proteins in particular are difficult to isolate and characterize. Phosphoglycosyltransferases (PGTs) are transmembrane proteins that transfer phosphosugars onto phospholipids, initiating the synthesis of oligosaccharides in bacterial cell walls. This transfer creates a diphosphate link between a lipid and a sugar and generates UMP as a byproduct. Once this lipid–P–P–sugar linkage occurs, more sugars can be added by glycosyltransferases, generating membrane-based polysaccharides (e.g., peptidoglycan) used for signaling, recognition and defense.

While PGTs have been studied biochemically and an X-ray structure of one member exists, much is still unknown about these enzymes. Overexpressing and purifying membrane proteins remains a challenge, and the conventional PGT assay requires isotope labeled-UDP-sugar donors and is based on the solubility difference between substrate and product to determine enzyme turnover using extraction-based or chromatographic methods. While there are other assays that use fluorescent modified substrates or multienzyme analysis, none of the methods can be applied to all of the diverse PGT enzymes.

All PGTs generate UMP as a byproduct of the transfer of a phosphosugar to a phospholipid. Based on the principle of the luminescent UDP-Glo™ Glycosyltransferase Assay where UDP released during the glycosyltransferase reaction was quantitated, a new luminescent assay called UMP-Glo™ Assay is able to measure the activity of PGT enzymes by adding a single reagent to detect UMP. Das et al. validated this assay by testing PglC, a PGT from Campylobacter jejuni, as well as PglC from Helicobacter pullorum and WecA from Thermatoga maritime and published the results in Scientific Reports. Continue reading