The Simplex Things In Life: Utilizing Artificial Intelligence Models to Better Understand Autism

Autism Spectrum Disorder, or ASD, is nothing if not unique.

The way ASD manifests itself in people is unique; although it most often presents as some form of variable impairment in social interaction and communication, each individual has behaviors and habits that are as unique to them as snowflakes are to one another.

ASD has also proven itself to be a uniquely challenging disorder to study. In the past decade, de novo (new) mutations have been identified as key contributors to causality of ASD. However, the majority of these identified de novo mutations are located in protein-coding genes, which comprise only 1–2% of the entire human genome.

Up to this point, a majority of previous research has focused on identifying mutations located in the 20,000 identified genes in the protein-coding region, which would seem like a promising approach. Genes are the genetic blueprints for creating proteins, which control and perform crucial tasks in our bodies, such as fighting off infections, communicating between your organs, tissues, and cells as chemical messengers, and regulating your blood sugar levels. It seems like basic math: Genes + Mutations = Mutated Proteins. Mutated Proteins = Disrupted Protein Function.

However, it has been observed that all the known genes that are ASD-associated can explain only a minor fraction of new autism cases, and it is estimated that known de novo mutations in the protein-coding region contribute to not more than 30% of cases for individuals who have no family history of autism (better known as simplex ASD). This provides evidence to suggest mutations contributing to autism must additionally occur elsewhere in the genome. Continue reading “The Simplex Things In Life: Utilizing Artificial Intelligence Models to Better Understand Autism”

What Packaging Dog Food Can Teach You About Science Writing and Other Tales

Cartoon drawing of two workers drinking coffee

Believe it or not, the most unglamorous jobs teach us all a thing or two about life. I asked Promega staff members to discuss the most impactful lessons they learned at their first jobs. Check it out.

Continue reading “What Packaging Dog Food Can Teach You About Science Writing and Other Tales”

When Proteins Get Together: Shedding (Blue) Light on Cellular LOV

NanoBRETNo protein is an island. Within a cell, protein-protein interactions (PPIs) are involved in highly regulated and specific pathways that control gene expression and cell signaling. The disruption of PPIs can lead to a variety of disease states, including cancer.

Two general approaches are commonly used to study PPIs. Real-time assays measure PPI activity in live cells using fluorescent or luminescent tags. A second approach includes methods that measure a specific PPI “after the fact”; popular examples include a reporter system, such as the classic yeast two-hybrid system.

Continue reading “When Proteins Get Together: Shedding (Blue) Light on Cellular LOV”

What Makes a “Good” Buffer?

Buffers are often overlooked and taken for granted by laboratory scientists, until the day comes when a bizarre artifact is observed and its origin is traced to a bad buffer.

The simplest definition of a buffer is a solution that resists changes in hydrogen ion concentration as a result of internal and environmental factors. Buffers essentially maintain pH for a system. The effective buffering range of a buffer is a factor of its pKa, the dissociation constant of the weak acid in the buffering system. Many things, such as changes in temperature or concentration, can affect the pKa of a buffer.

In 1966, Norman Good and colleagues set out to define the best buffers for biochemical systems (1). By 1980, Good and his colleagues identified twenty buffers that set the standard for biological and biochemical research use (2,3).  Good set forth several criteria for the selection of these buffers: Continue reading “What Makes a “Good” Buffer?”

Evaluating CAR NK Immunotherapy in Patient-Derived Colorectal Organoids

In recent years, great advances have been made in the field of immunotherapy to treat cancer. One of the most promising treatments involves engineering immune cells to express chimeric antigen receptors (CAR). These receptors are carefully designed to recognize antigens expressed on the surface of tumor cells. Once the target is recognized, the CAR-engineered immune cells can attack and kill the tumor cells. CAR T cells have been successfully used to treat certain blood cancers—three CAR T therapies for lymphoma and leukemia have gained US FDA approval. In these cases, T cells were taken from individual patients, grown and genetically-altered in the lab, then reintroduced into the same patient. Continue reading “Evaluating CAR NK Immunotherapy in Patient-Derived Colorectal Organoids”

Meet the Mighty Masked Masters of Measurement: #WorldMetrologyDay

Scientific investigation is an iterative process, for which reproducibility is key. Reproducibility, in turn, requires accuracy and precision—particularly in measurement. The unsung superheroes of accuracy and precision in the research lab are the members of your local Metrology Department. According to Promega Senior Metrologist, Keela Sniadach, it’s good when the metrology department remains unsung and behind the scenes because that means everything is working properly.

Holy Pipettes, Scientists! We have a metrology department?! Wait…what’s metrology again?

Callibration technician checks out a multipipettorMetrology (the scientific study of measurement) got its start in France, when it was proposed that an international length standard be based on a natural source. It was from this start that the International System of Units (SI), the modern metric system of measurement, was born.

Metrology even has its own day: May 20, which is the anniversary of day the International Bureau of Weights and Measures (BIPM) was created by the Meter Convention in Paris in 1875. The job of BIPM is to ensure worldwide standards of measurement.

For life scientists, metrology centers around making sure the equipment used everyday—from pipettes to heating blocks to centrifuges—is calibrated and measuring correctly. Continue reading “Meet the Mighty Masked Masters of Measurement: #WorldMetrologyDay”

Making Research More Sustainable, One Lab at a Time

Do you love your research job? What if you couldn’t do that work anymore? What if future researchers couldn’t have the opportunity to build from what you have accomplished and feel the same joy you do about their research?

Unfortunately, these may become more than hypotheticals for the next generation of scientists due to the impact humans are having on the earth. Scientific research has an outsized impact on some aspects of our unsustainable use of resources. Academic research buildings can use four times more energy than a typical office building and can be responsible for one-third of all waste generated on campus. So, can you make scientific research more sustainable? Continue reading “Making Research More Sustainable, One Lab at a Time”

Research-Based Training for Sustainable Use and Management of Marine Ecosystems in Namibia

In my science blog research/writing, news reports are usually pulled from US sources. But interesting scientific research is obviously being conducted in many places around the globe. When this story from Namibia came along, there was so much I didn’t know. It was time to catch up.

relief map of Namibia
Relief map of Namibia. Image by Natural Earth and Kbh3rd with permission under Wikimedia commons.

Namibia is Exactly Where in Africa?

Namibia is one of the world’s youngest countries, having gained independence from South Africa in 1990. Situated northwest of the country of South Africa on the Atlantic Ocean, Namibia is arid, composed largely of desert.

This blog is about research conducted at the Sam Nujoma Research Center, University of Namibia, on Henties Bay. Henties Bay (not shown on this map) is in the region of Erongo, located in the center of Namibia along the coast. Henties Bay has become a tourist destination in part due to the abundance of fish and marine life found there.

Sam Nujoma Research center.
The Sam Nujoma Research Center of University of Namibia, located near Henties Bay.

Continue reading “Research-Based Training for Sustainable Use and Management of Marine Ecosystems in Namibia”

Studying Autophagy in Flies Using CRISPR

 

Transcribed RNA can be used to study RNA structure and how it relates to function or how proteins and RNA interact. It can also be used for gene silencing using RNAi (studied more often as a possible therapeutic option) or simply serve as a molecular standard in Real-time RT-PCR. Transcribed RNA is also used in Class 2 Clustered Regularly Interspaced Short Palindromic Repeat systems, or CRISPR.

The CRISPR system, which is naturally occurring in bacteria, has been manipulated to perform gene editing in a laboratory environment. To perform CRISPR in the laboratory environment, you need two main reagents:

  1. The Brains: Guide RNA (gRNA or sgRNA) – Small piece of RNA containing a nucleotide sequence that is capable of binding the chosen Cas Protein, and contains a portion of the sequence that can bind the DNA the researcher intends to modify – the target DNA.
  2. The Brawn: CRISPR-associated endonuclease (Cas Protein) – The protein that cleaves the target DNA; the most popular Cas protein is called Cas9. The Cas protein is guided by the (gRNA).

Recently, Guo et al. used Promega’s RiboMAX™ Large-Scale RNA Production System to produce gRNA to be used in CRISPR for their study to determine the effects of the loss of, or mutations in, a specific gene in fruit flies (1).  Atg101 is a gene that plays an important role in autophagy, an intracellular pathway for removing toxins or damaged parts of cells. Continue reading “Studying Autophagy in Flies Using CRISPR”

Celebrating Bike-to-Work Week 2019

Every day at the Promega Headquarters in Madison, Wisconsin, many Promega employees trade the crowded Beltline Highway for a scenic route along the bike trails. As our colleagues wind around the lakes and prairies of south-central Wisconsin, they’re reducing greenhouse gas emissions and getting some fun exercise in the process. This week, during National Bike-to-Work week, we’re taking time to recognize our colleagues who opt for a healthier and more sustainable commute. In the video below, hear about how Promega supports our bike commuters from Sam Jackson, an avid biker and Multimedia Specialist at Promega.