The Tiniest Test Tube: Studying Cell-Specific Protein Secretion

Free floating single cells, blue
Researchers explore an innovative method for single-cell analysis

Cells produce proteins that serve different purposes in maintaining human health. These bioactive secretions range from growth factors to antibodies to cytokines and vary between different types of cells. Even within a certain cell type, however, there are individual cells that produce more secretions than others, a phenomenon that especially interests scientists studying cell-based therapies. In contrast to molecular therapies, which typically involve specific genes or proteins, a primary challenge to crafting cell therapies is the wide range of functional outputs seen in cells that have the same genetic template. This leads to the question of what molecular properties, from a genomic and transcriptomic perspective, would lead one cell to produce more of a protein than its companions. 

There have been few investigative strategies put forth that allow scientists to connect a cell’s characteristics and genetic coding with its secretions. In July 2023 a team of scientists published a paper in Nature Communications outlining an innovative solution: little hydrogel particles, or “nanovials”, that essentially serve as tiny test tubes and can be used to measure protein secretion, track transcriptome data, and identify relevant surface markers in a single cell.

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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.

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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.

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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 code for the trunk, or the “torso”, and tail. 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

Custom in vitro Transcription Reagents for Manufacturing RNA Therapeutics

Doctor filling syringe

Research into vaccines based on RNA began decades ago when scientists theorized that they could harness RNA to produce viral proteins within a cell, prompting a protective immune response. RNA vaccine research drew scientists’ attention during the development of SARS-CoV-2 vaccines during the COVID-19 pandemic, which opened the door for research targeting other diseases with RNA-based therapeutics.

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Ancient Worm Reveals Simple Hack for Remaining Ageless After 46,000 Years

If you could, would you enter a suspended metabolic state for the chance to reawaken 46,000 years from now, as you are today? For one nematode discovered in Siberian permafrost, the answer is a resounding “yes”. A study published in late July of this year details recent research that expands on a paper published in 2018 wherein scientists announced that they successfully reanimated a small but resilient nematode, or roundworm, who remained alive for tens of thousands of years in a state called cryptobiosis after being frozen in extreme Arctic soil conditions.

Blue roundworm on a black background
Caenorhabditis elegans, a type of roundworm whose dauer larvae are capable of cryptobiosis
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Streamlining Disease Diagnostics to Protect Potato Crops

A potato farmer holds a handful of potatoes. Scientists are working to protect potato crops from disease.
The WSPCP works to provide seed potato growers with healthy planting stock

The mighty potato—the Midwest’s root vegetable of choice—is susceptible to a variety of diseases that, without proper safeguards, can spell doom for your favorite side dishes. Founded in 1913 and housed in the Department of Plant Pathology at the University of Wisconsin-Madison, the Wisconsin Seed Potato Certification Program (WSPCP) helps Wisconsin seed potato growers maintain healthy, profitable potato crops year-to-year through routine field inspections, a post-harvest grow-out and laboratory testing.

While WSPCP conducts visual inspections for various seed potato pathogens, their diagnostic laboratory testing is primarily focused on viruses such as Potato virus Y (PVY), which can cause yield reduction and tuber defects, along with select bacteria such as Dickeya and Pectobacterium species that cause symptoms like wilting, stem rot and tuber decay.

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Confronting an Emerging Pathogen: Candida auris

Candida auris illustration
Candida auris is a fungal infection sweeping through healthcare sites across the U.S.

HBO’s The Last of Us has successfully brought fungal pathogens to the forefront of the pandemic discourse, raising questions as to whether a fungus could really pose a significant threat to humans. While scientists agree that the fungus featured in the show, cordyceps, won’t be making the required inter-species jump any time soon, there is a fungal pathogen that has been taking root in hospitals across the U.S. which gives some cause for concern: Candida auris.

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Shifting Gears: Repurposing Instruments for Changing Needs

Sarah Teter operates the Tecan Freedom EVO 150 liquid handler
Sarah Teter operates the Tecan Freedom EVO 150

The thought of an expensive instrument falling out of use and gathering dust on the shelf is enough to bring a tear to any lab manager’s eye. An instrument that once served a key purpose and now functions only as a “paperweight” is a tragic waste of valuable resources. Fortunately, it is sometimes possible to breathe new life into neglected tools and to retrofit or repurpose equipment to meet the new needs that will inevitably arise in a changing lab environment.  

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Promega qPCR Grant Funds Genetic Database for Antarctic Krill

Boasting a biomass of roughly 400 million tons, Antarctic krill are a key source of food for a wide array of marine life, including sea birds, seals, penguins and whales. As with the rest of the oceanic ecosystem, krill are subject to rapidly shifting climate conditions, prompting scientists to seek a deeper understanding of how they might adapt to a changing environment.

Facing a general lack of genetic information on the species, Professors Cristiano De Pittà and Gabriele Sales from the Department of Biology at the University of Padova in Italy set out to define the krill transcriptome, or sequences of ribonucleic acid (RNA), and in doing so facilitated the discovery of key gene sequences that may play important roles in krill reproduction and survival.

In recent years, there have been concerns about potential impacts to the krill population from ocean warming and commercial fishing operations. Mapping the krill transcriptome may offer scientists crucial insight into the effects of climate change and anthropogenic activity on the dynamics of the Antarctic ecosystem. Doing so is no small feat. Though krill may be miniscule, their genome is 15 times the size of the human genome.

To this end, the research groups of De Pittà and Sales established the database KrillDB, providing a single resource where scientists can access a comprehensive catalogue of krill genes and RNA transcripts. This database represented a powerful bioinformatic tool for examining molecular processes in krill. Funded in part by the Promega 2019 qPCR Grant Program, researchers subsequently rolled out an updated database, KrillDB2, which includes improvements to the quality and breadth of the sequences covered and the information associated. Their corresponding study, published summer 2022 in Scientific Reports, identified a series of genes involved in the krill molting cycle, the reproductive process and sexual maturation, and included never-before reported insights into the expression of microRNA precursors and their effect on krill physiology.

The 2019 Promega qPCR Grant Program offered recipients $10,000 in free PCR reagents and related products, as well as access to Promega technical services and training teams. 

Researcher and awardee Alberto Biscontin said of the grant’s impact on their project: “RNA sequencing approaches allow us to determine the level of expression of thousands of genes with a single experiment. The standard in the field is to define transcript expression levels by quantitative RT-PCR to technically validate RNA-seq results. We have been relying on the GoTaq® qPCR solutions by Promega for years.” He added, “We have used the GoTaq® 1-Step RT-qPCR System to compare the level of expression of candidate genes with those obtained from RNA-seq analysis. This allowed us to verify at any time the reliability of our bioinformatics pipelines.”

In the future, researchers plan to maintain the KrillDB2 database with the latest genome and transcriptome sequencing data, to provide the most comprehensive integrative analysis possible. They intend to develop a multi-crustaceans database to support future comparative genomics studies. The KrillDB2 database may also serve as a model to develop other databases for similar species.

Learn more about the GoTaq® 1-Step RT-qPCR System.

Read more about the 2019 qPCR Grant winners.  


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