Will Artificial Intelligence (AI) Transform the Future of Life Science Research?

Artificial intelligence (AI) is not a new technological development. The idea of intelligent machines has been popular for several centuries. The term “artificial intelligence” was coined by John McCarthy for a workshop at Dartmouth College in 1955 (1), and this workshop is considered the birthplace of AI research. Modern AI owes much of its existence to an earlier paper by Alan Turing (2), in which he proposed the famous Turing Test to determine whether a machine could exhibit intelligent behavior equivalent to—or indistinguishable from—that of a human.

The explosive growth in all things AI over the past few years has evoked strong reactions from the general public. At one end of the spectrum, some people fear AI and refuse to use it—even though they may have unwittingly been using a form of AI in their work for years. At the other extreme, advocates embrace all aspects of AI, regardless of potential ethical implications. Finding a middle ground is not always easy, but it’s the best path forward to take advantage of the improvements in efficiency that AI can bring, while still being cautious about widespread adoption. It’s worth noting that AI is a broad, general term that covers a wide range of technologies (see sidebar).

AI personified looking at a dna double helix against an abstract cosmic background
Image generated with Adobe Firefly v.2.

For life science researchers, AI has the potential to address many common challenges; a previous post on this blog discussed how AI can help develop a research proposal. AI can help with everyday tasks like literature searches, lab notebook management, and data analysis. It is already making strides on a larger scale in applications for lab automation, drug discovery and personalized medicine (reviewed in 3–5). Significant medical breakthroughs have resulted from AI-powered research, such as the discovery of novel antibiotic classes (6) and assessment of atherosclerotic plaques (7). A few examples of AI-driven tools and platforms covering various aspects of life science research are listed here.

Continue reading “Will Artificial Intelligence (AI) Transform the Future of Life Science Research?”

Cell-Based Target Engagement and Functional Assays for NLRP3 Inhibitor Profiling Help Identify Successes and Failures

Identifying Inflammasome Inhibitors: What’s Missing
The NLRP3 inflammasome is implicated in a wide range of diseases. The ability to inhibit this protein complex could provide more precise, targeted relief to inflammatory disease sufferers than current broad-spectrum anti-inflammatory compounds, potentially without side effects.

Studies of NLRP3 inflammasome inhibitors have relied on cell-free assays using purified NLRP3. But cell-free assays cannot assess physical engagement of the inhibitor and target in the cellular micro-environment. Cell-free assays cannot show if an NLRP3 inhibitor enters the cell, binds the target and how long the inhibitor binding lasts.

Cell-based assays that interrogate the physical interaction of the NLRP3 target and inhibitor inside cells are needed.

Continue reading “Cell-Based Target Engagement and Functional Assays for NLRP3 Inhibitor Profiling Help Identify Successes and Failures”

Addressing the Problem of Dosing in Gene Therapy

One key obstacle to crafting effective gene therapies is the ability to tailor dosing according to a patient’s needs. This can be tricky because even if protein production is successful, staying within the therapeutic window is paramount—too much of a protein could be toxic, and too little will not produce the desired effect. This balance is difficult to achieve with current technologies. In a study recently published in Nature Biotechnology, researchers at Baylor College of Medicine investigated a possible solution to this problem, engineering a molecular “on/off” switch that could regulate gene expression and maintain protein production at dose-dependent, therapeutic levels.

Continue reading “Addressing the Problem of Dosing in Gene Therapy”

Transformative Gene Therapies Greenlit for Sickle Cell Disease

In sickle cell anemia, red bloods cells elongate into an abnormal “sickled” shape

Sickle cell disease is a debilitating blood disorder that causes recurrent pain crises and severe health effects, and can drastically impact quality of life. Recently, Vertex Pharmaceuticals and CRISPR Therapeutics introduced Casgevy, or exa-cel, a novel form of gene therapy that could radically change the management of sickle cell disease. On the heels of exa-cel’s approval in Britain, this groundbreaking therapy was also recently approved in the U.S.

Continue reading “Transformative Gene Therapies Greenlit for Sickle Cell Disease”

Designing Science: A Behind-the-Scenes Look at Our Recent Journal Cover Art

A 3D illustration showing RAF inhibitor LXH254 engages BRAF or CRAF protomers (orange), but spares ARAF (red). Unoccupied ARAF is competent to trigger downstream mitogenic signaling, which is demonstrated with lightning bolts. Red cells in the background are fluorescently labeled RAS proteins, expressed in live cells. The Cell Chemical Biology cover type superimposes the image.
Image adapted from original artwork by iSO-FORM LLC.

We made the cover! Of Cell Chemical Biology, that is.

This July, Cell Chemical Biology editors accepted a study from Promega scientists and invited the research team to submit cover art for the issue. The study in question details a BRET-based method to quantify drug-target occupancy within RAF-KRAS complexes in live cells. Promega scientists Matt Robers and Jim Vasta collaborated with one of our talented designers, Michael Stormberg, to craft an image that accurately represents the science in a dynamic and engaging way.

You can check out the paper and cover art in the November 16 issue of Cell Chemical Biology.

I spoke with Michael Stormberg to learn more about the creative process that went into creating this cover art and how he worked with the research team and other collaborators.

Continue reading “Designing Science: A Behind-the-Scenes Look at Our Recent Journal Cover Art”

Uncovering the Neuroscience of Imagination Using a Virtual Reality World for Rats

Imagination is often considered a uniquely human trait. Simply put, it is what allows us to think about things that aren’t happening in that moment, and it plays an integral part in our day-to-day lives. We use it when we think through our calendar for the day, consider restaurant options for dinner, or visualize the best route. It turns out this trait might not be as unique to humans as we thought. In fact, a study published in Science suggests that we might share this ability with rats (1).

Rats are the most divisive of rodents. Some people see disease-carrying scourges; some see intelligent, affectionate creatures with larger-than-life personalities; and still others simply can’t get past their bare tails and small eyes. Love them or hate them, science has shown that there is more to these creatures than meets the eye. They are intelligent, ticklish and empathetic; and the study in Science suggests, imaginative.

Continue reading “Uncovering the Neuroscience of Imagination Using a Virtual Reality World for Rats”

Shocking Revelation about Starfish Anatomy: Just a Head

Two starfish on the beach
Recent research reveals that starfish anatomy is even stranger than previously thought

Most animals in the world are what biologists refer to as “bilateral”—their left and right sides mirror one another. It is also typically easy to tell which part of most animals is the top and which is the bottom. The anatomical arrangements of certain other animals, however, are slightly more confounding, for instance in the case of echinoderms, which include sea urchins, sand dollars and starfish. These animals are “pentaradial”, with five identical sections of the body radiating from a central axis. The question of how these creatures evolved into such a state has been a puzzle pondered by many a biologist, with little progress made until recently. In a new study published in Nature, scientists closely examining the genetic composition of starfish point to some key evidence that suggests a starfish is mostly just a head.

Starfish are a deuterostome, belonging to the superphylum Deuterostomia. Most deuterostomes are bilateral, leading scientists to believe that, despite their peculiar body plan, starfish evolved from a bilateral ancestor. This is supported by the fact that starfish larvae actually start out bilateral, and eventually transform into the characteristic star shape. But where the head of the starfish is, or whether it even has one, has proved difficult for scientists to parse out, especially since their outward structure offers no real clues.

There have been a number of theories posited, such as the duplication hypothesis—where each of the five sections of a starfish could be considered “bilateral”, placing the head at the center—and the stacking hypothesis, which asserts that the body is stacked atop the head. In a bilateral body plan, anterior genes broadly code for the front, or the head-region, and posterior genes are primarily responsible for the tail. The torso, or “trunk”, is the result of complex interplay between both anterior and posterior, as well as other types of genes. Researchers in this new study looked at the expression of these genes throughout the body plan as a possible source of clarity as to which part of the starfish is its head and which parts comprise the body.

To this end, researchers used advanced molecular and genetic sequencing techniques including RNA tomography and in situ hybridization. RNA tomography allowed them to create a three-dimensional map of gene expression throughout the limbs of the sea star Patiria miniate. In situ hybridization is a fluorescent staining technique that offered them a means by which to examine where exactly anterior or posterior genes are expressed in the sea star’s tissue, providing a clearer picture of genetic body patterning.

Remarkably, scientists found that anterior or head-coding genes were expressed in the starfish’s skin, including head-like regions appearing in the center, or midline, of each arm, while tail-coding genes were only seen at the outer edges of the arms. Perhaps even more remarkable was the lack of genetic patterning accounting for a trunk or torso, leading scientists to the conclusion that starfish are, for the most part, just heads.

Whether this holds true for other echinoderms remains to be proven, and further investigations into starfish anatomy may seek to pinpoint where in the timeline the trunk was lost. Overall, research like this helps scientists understand how life came to look the way it does. Oddly shaped creatures like the humble starfish can offer insight into the strange evolutionary processes that result in such rich biodiversity across the animal kingdom.


Works cited:

  1. ‘A disembodied head walking about the sea floor on its lips’: Scientists finally work out what a starfish is | Live Science
  2. Molecular evidence of anteroposterior patterning in adult echinoderms | Nature
  3. Starfish Are Heads–Just Heads – Scientific American
  4. Study reveals location of starfish’s head | Stanford News

Reviewing the Importance of circRNA

In recent years following the COVID-19 pandemic, RNA has gained attention for its successes and potential use in vaccines and therapeutics. One avenue of interest in RNA research is a non-coding class of RNA first identified almost 50 years ago, circular RNA (circRNA).

In 1976, Sanger et al. first identified circRNA in plant viroids, and later additions to the field found them in mice, humans, nematodes, and other groups. Unlike linear RNA, circRNA are covalently closed loops that don’t have a 5′ cap or 3′ polyadenylated tail. Following its discovery, researchers thought circRNA was the product of a rare splicing event caused by an error in mRNA formation leading to low interest in researching the subject (1).

In the early 2010s, following the development of high throughput RNA sequencing technology, Salzman et al. determined that circRNAs were not a result of misplicing, but a stable, conserved, and widely sourced form of RNA with biological importance. Since noncoding RNA makes up the majority of the transcriptome it’s an incredibly important field of study. We now recognize circRNAs for their potential as disease biomarkers and importance in researching human disease (2).

Continue reading “Reviewing the Importance of circRNA”

For Frogs, Surviving the Heat Could Come Down to What Is in Their Gut

Amphibians are the most threatened vertebrate class worldwide. Because they lack the ability to regulate their own temperature and moisture levels, climate change is playing a significant role in this growing peril (1). Climate change impacts amphibian survival in several ways. In addition to habitat loss, growing drought conditions make maintaining body moisture levels challenging and warming temperatures restrict activity periods needed for reproduction as well as increasing the risk of heat stress.

Heat tolerance varies by species, and understanding what influences these differences could help predict species survival. The gut microbiota is known to affect a wide range of functions in host animals, and recently studies have begun to investigate its role in host thermal tolerance (2).

Continue reading “For Frogs, Surviving the Heat Could Come Down to What Is in Their Gut”

Treating Solid Tumors: Combining CAR-T Cell Therapy with Probiotics

Chimeric Antigen Recepter (CAR)-T cell therapy is a personalized immunotherapy that harnesses the patient’s own immune system to combat cancer. It is done by engineering the patient’s T cells to specifically target and attack cancer cells in their body, and it has shown great success in treating various blood cancers such as leukemia.

Treating solid tumors with CAR-T cells, however, has proved much more challenging. This is mainly because solid tumors contain a heterogeneous population of cells, expressing a variety of antigens—many of which are also expressed in healthy cells. Therefore, T cells targeting solid tumors could potentially attack healthy tissue, resulting in serious side effects. In addition, solid tumors create a hostile microenvironment that is difficult for CAR-T cells to infiltrate.

Continue reading “Treating Solid Tumors: Combining CAR-T Cell Therapy with Probiotics”