Streamlining Research: The Merits of Adaptive Clinical Trials

Clinical trials are arguably the backbone of medical advancement. But the trials most worth doing are usually large, costly and time-intensive, demanding extensive resources and personnel. During the COVID-19 pandemic, there has been a marked uptick in the number of clinical trials, many of which are woefully flawed with issues ranging from insufficient sample size to bad design. The published research that follows is often redundant or inconclusive.

So how can scientists designing and running clinical trials streamline their efforts to reduce waste and achieve more useful outcomes? The answer could be adaptive clinical trials.

Adaptive clinical trials are designed so they can be modified as data are being collected
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A One-Two Punch to Knock Out HIV

This schematic of HIV life cycle summarizes years of research to understand HIV and get to a potential cure for HIV infection
HIV-1 lifecycle illustration. Copyright Promega Corporation.

Scientists investigating the human immunodeficiency virus (HIV) have learned much about the retrovirus’s lifecycle, but their ultimate goals were to discover a cure and prevent infection. In the decades since HIV was discovered, basic research and pharmaceutical drug development have expanded the antiviral toolbox, but these HIV treatments do not provide a functional cure, only manage the infection. However, two techniques may offer a potential cure for HIV infection using CRISPR and a possible vaccine using mRNA.

CRISPR-Based Therapy May Cure HIV Infection

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Seeing is Believing: How NanoLuc® Luciferase Illuminates Virus Infections

Artists interpretation of in vivo imaging of viral infections in mice using NanoLuc luciferase.

Wearing blue surgical gowns and white respirator hoods, research scientist Pradeep Uchil and post-doctoral fellow Irfan Ullah carry an anesthetized mouse to the lab’s imaging unit. Two days ago, the mouse was infected with a SARS-CoV-2 virus engineered to produce a bioluminescent protein. After an injection of a bioluminescence substrate, a blue glow starts to emanate from within the mouse’s nasal cavity and chest, visible to the imaging unit’s camera and Uchil’s eyes.

“We were never able to see this kind of signal with retrovirus infections.” Uchil is a research scientist at the Yale School of Medicine whose work focuses on the in vivo imaging of retroviral infections. Normally, the mouse would have to be sacrificed and “opened up” for viral bioluminescent signals from internal tissues to be imaged directly.

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From Drug Use to Viral Outbreaks, How Monitoring Sewage Can Save Lives

Most of us, after we flush the toilet, don’t think twice about our body waste. To us, it’s garbage. To epidemiologists, however, wastewater can provide valuable information about public health and help save lives.

History of Wastewater-Based Epidemiology

Wastewater-based epidemiology (WBE) is the analysis of wastewater to monitor public health. The term first emerged in 2001, when a study proposed the idea of analyzing wastewater in sewage-treatment facilities to determine the collective usage of illegal drugs within a community. At the time, this idea to bridge environmental and social sciences seemed radical, but there were clear advantages. Monitoring wastewater is a nonintrusive and relatively inexpensive way to obtain real-time data that accurately reflects community-wide drug usage while ensuring the anonymity of individuals.

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Rice-Based Cholera Vaccine

Oral vaccines are a great strategy and are especially beneficial in areas with poor sanitation. This form of vaccine distribution could help control the acute diarrheal disease caused by Vibrio cholera. There are an estimated 1.3 to 4 million cases and 21,000 to 143,000 deaths from cholera each year. A recent study from The Lancet Microbe finds new hope in a rice-based cholera vaccine that will fight against the diarrheal toxin without severe adverse events.

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What You Should Know About The Delta Variant

The Delta Variant poses a unique challenge to global health. We’ve compiled answers to some of the most common questions about Delta and other SARS-CoV-2 variants.

What is a variant?

A variant is a form of a virus that is genetically distinct from the original form.

“All organisms have mutation rates,” says Luis A Haddock, a graduate student at University of Wisconsin – Madison. “Unfortunately for us, viruses have one of the highest mutation rates of everything that currently exists. And even more unfortunately, RNA viruses have the highest mutation rates even among viruses.”

Luis works in the Friedrich Lab at UW-Madison, which has been sequencing SARS-CoV-2 genomes from positive test samples since the beginning of the pandemic. SARS-CoV-2 is constantly evolving, and sequencing can help us follow it through time and space. Most of the variants don’t behave any differently. A single nucleotide substitution might not even change the amino acid sequence of an encoded protein. However, occasionally a mutation will alter the structure or function of a protein.

Learn more about SARS-CoV-2 sequencing in the article “From Primate Models to SARS-CoV-2 Sequencing and Testing,” featuring David and Shelby O’Connor, two collaborators of the Friedrich Lab.

What is a Variant of Concern?

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How Promega Helped Our Lab Scale Up Drug Discovery for Bloodborne Pathogens

This blog was written by Sebastien Smick, Research Technician in Dr. Jacquin Niles’ laboratory at Massachusetts Institute of Technology (MIT)

Our lab is heavily focused on the basic biology and drug discovery of the human bloodborne pathogen Plasmodium falciparum, which causes malaria. We use the CRISPR/Cas9 system, paired with a TetR protein fused to a native translational repressor alongside a Renilla luciferase reporter gene, to conditionally knock down genes of interest to create modified parasites. We can then test all kinds of compounds as potential drug scaffolds against these gene-edited parasites. Our most recent endeavor, one made possible by Promega, is a medium-low throughput robotic screening pipeline which compares conditionally-activated or-repressed parasites against our dose-response drug libraries in a 384-well format. This process has been developed over the past few years and is a major upgrade for our lab in terms of data production. Our researchers are working very hard to generate new modified parasites to test. Our robots and plate readers rarely get a day’s rest!

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NAD: A Renaissance Molecule and its Role in Cell Health

NAD is a pyridine nucleotide. It provides the oxidation and reduction power for generation of ATP by mitochondria. For many years it was believed that the primary function of NAD/NADH in cells was to harness and transfer energy  from glucose, fatty and amino acids through pathways like glycolysis, beta-oxidation and the citric acid cycle.

Promega NAD/NADH-Glo system and how to prepare samples for  identification of NAD or NADH.
Promega NAD/NADH-Glo system and how to prepare samples for identification of NAD or NADH.

However NAD also is recognized as an important cell signaling molecule and substrate. The many regulatory pathways now known to use NAD+ in signaling include multiple aspects of cellular homeostasis, energy metabolism, lifespan regulation, apoptosis, DNA repair and telomere maintenance.

This resurrection of NAD importance is due in no small part to the discovery of NAD-using enzymes, especially the sirtuins.

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A SARS-CoV-2 NanoLuc® Reporter Virus for Rapid Screening of Antivirals

nanoluc invivo imaging

Before the COVID-19 global pandemic began, Dr. Xuping Xie, Assistant Professor of the University of Texas Medical Branch at Galveston, TX has been studying viruses, such as Dengue and Zika, for more than 10 years. Once the pandemic hit in early 2020, he was prepared to join the fight against the virus. “There was an urgent need to know: Is there a quicker way to develop therapeutics or antibodies to target SARS-CoV-2?” says Dr. Xie. “That’s why we immediately launched our SARS-CoV-2 project.”

His goal was to create an assay that could 1) screen for antiviral drugs and 2) quickly measure neutralizing antibody levels. The assay could be used to determine the immune status of previously infected individuals and to evaluate various vaccines under development. To achieve this, he wanted to create a reporter virus that is genetically stable and replicates similarly to the wild-type virus in cell culture. 

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Firefly Luciferase Sheds Light on Development of New Malaria Treatments

field of fireflies at night; researchers are using firefly luciferase as a tool to power screening assays for new malaria treatments

Despite significant advancements in antimalarial drugs and widespread efforts to prevent transmission over the past decade, deaths from malaria remain high, particularly in younger children. New drugs with novel modes of action are urgently needed to continue reducing mortality and address drug resistance in the malaria parasite, Plasmodium falciparum. While tens of thousands of compounds have been identified as potential candidates through massive screening efforts, scalable methods for identifying the most effective compounds are needed.

The goal is to find a drug that is potent during all stages in the life cycle of P. falciparum and kills the parasite quickly. Focusing on assessing whether a compound can rapidly eliminate initial parasite burden, Paul Horrocks, PhD, and his colleagues developed a validated bioluminescence-based assay that rapidly determines the initial rate of kill for discovery antimalarials. One key to developing their assay was figuring out how to monitor when the parasite dies after introducing the drug. While measuring DNA content can be used to monitor parasite burden, it is too stable to use for a relevant time course assay.

See how Dr. Paul Horrocks uses a firefly luciferase-based system to understand the dynamics of drug action in the development of new malaria treatments.

Enter firefly luciferase, a dynamic reporter tool to investigate drug action. By creating transgenic P. falciparum that express the luc reporter gene, the researchers could monitor drug action over time. When the parasite is killed, it stops making the luciferase reporter. Since there is no new production of luciferase, levels fall quickly after the parasite dies, and a luciferase assay can determine how fast each drug killed the parasite.

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