Durham Wheat Genome Sequenced, Protecting Pasta's Future

International team decodes the durum wheat genome

“An international consortium has sequenced the entire genome of durum wheat--the source of semolina for pasta, a food staple for the world's population, according to an article published today in Nature Genetics.

Durham Wheat Genome Sequenced, Protecting Pasta's Future

The team has also discovered how to significantly reduce cadmium levels in durum grain, ensuring the safety and nutritional value of the grain through selective breeding.

"This ground-breaking work will lead to new standards for durum breeding and safety of durum-derived products, paving the way for production of durum wheat varieties better adapted to climate challenges, with higher yields, enhanced nutritional quality, and improved sustainability," said Luigi Cattivelli of Italy's Council for Agricultural Research and Economics (CREA).”


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Pharma-Investor's Perspective on Gene Therapy

The Future of Cell and Gene Therapy

“Each passing year, the success of cell and gene therapy (CGT) becomes clearer, more widely covered in the media, and is increasingly the focus of a rapidly growing society of researchers. Making sense of this extensive ecosystem is no small feat, but by using a data-driven approach, we can get closer to determining what the future holds for CGT.

Pharma-Investor's Perspective on Gene Therapy

CGT has emerged as one of the most exciting areas of biotechnology. Its buzz can be attributed to the hope these therapies hold for patients with rare and often deadly inherited diseases; the scientific promise and intrigue of gene editing; and the business opportunity that these revolutionary therapies with lucrative price tags hold.

But what do we really know about cell and gene therapy? What proverbial gold will be found at the end of this rainbow?“


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Positive coverage of a study linking genetics to beauty, will be savagely critiqued soon

Researchers identify 'beauty spots' in the genome

Genome-wide association study suggests variants underlying facial beauty varies by sex and claims to detect meaningful signal for these variants. This is an interesting study, but expect it to be attacked soon given recent work that highlights how population stratification can be misinterpreted as significant variant effects (e.g. Sohail, eLIFE, 2019). —RPR

Positive coverage of a study linking genetics to beauty, will be savagely critiqued soon

“Genes play a role in determining the beauty of a person's face, but that role varies with the person's sex, according to a new study by Qiongshi Lu and colleagues at the University of Wisconsin-Madison, published 4th April in PLOS Genetics.

Humans tend to be preoccupied with beauty -- a person's attractiveness is associated with academic performance, career success and economic mobility. But despite its importance, scientists know little about the genetic basis for having a pretty face. In the current work, researchers performed a genome-wide association study using genetic information from 4,383 individuals to pinpoint parts of the genome linked to facial beauty. They had volunteers score yearbook photos based on attractiveness from participants with European ancestry and compared the scores to each person's genetic information. The researchers identified several genes related to facial attractiveness, but their roles and relatedness to other human traits varied by sex. In women, certain genetic variations linked to beauty also appeared to be related to genes impacting body mass, while in males, variants were linked to genes affecting blood cholesterol levels.”



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CRISPR DNA "shredder"

New DNA 'shredder' technique goes beyond CRISPR's scissors

CRISPR DNA "shredder"

An international team has unveiled a new CRISPR-based tool that acts more like a shredder than the usual scissor-like action of CRISPR-Cas9. The new approach, based on Type I CRISPR-Cas3, is able to wipe out long stretches of DNA in human cells with programmable targeting, and has been shown to work in human cells for the first time.


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New Database of Dog Genomes

Researchers create the largest global catalog of variations in the dog genome

By Prabarna Ganguly, Ph.D.
Science Writer/Editor, NHGRI

New Database of Dog Genomes

In 2019, 'King' the Wire Fox Terrier won the Westminster Dog Show in Madison Square Garden, having competed against 2,800 dogs from 203 breeds. The sheer number of dog breeds points toward the major role played by genetics in shaping such variation in dogs.

In a new study, researchers at the National Human Genome Research Institute (NHGRI) have generated the largest catalog of genetic variants associated with physical traits for domesticated dog breeds. The findings, published in Nature Communication, will help researchers assess if variants associated with dog body structure, behavior and life span could also be implicated in related human diseases.

"This study included data from more than 722 dogs and 144 modern breeds," says Dr. Ostrander, NIH Distinguished Investigator and senior author of the paper. "Through the results, we've learned some of the fascinating genetics behind the variability observed in the world's 450 dog breeds."

After humans initially selected for specific traits during dog breeding centuries ago, dogs have since formed traits and characteristics spontaneously over time. Jocelyn Plassais, a postdoctoral researcher in Dr. Ostrander's laboratory and lead author of the study explained that dogs naturally develop disorders that are common to humans, such as various forms cancers, infections and even diabetes. In addition, a vast number of regions within the dog genome remain similar to the human genome. Thus, dog genomes can provide insight into the biological mechanisms of human health and disease.

The researchers used whole genome sequencing and genome-wide association studies to identify genomic variants associated with sixteen observable characteristics. Most of the blood samples from dogs were taken via The Dog Genome Project, a citizen science initiative that relies on donations from motivated dog owners.


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Gene-Expression Profiling to Understand Cancers of Unknown Origins

Phase 2 Trial Examines Gene-Expression Profiling for Cancer of Unknown Primary Site

A randomized phase 2 trial examining the assignment of treatment based on gene-expression profiling compared with standard chemotherapy for patients with cancer of unknown primary site showed no improvement in the 1-year survival rate with the more tailored approach. However, several caveats may limit the relevance of the findings. A report of this study was published in the Journal of Clinical Oncology.1

Gene-Expression Profiling to Understand Cancers of Unknown Origins

Cancer of unknown primary site (CUP) refers to malignancies in which the originating tumor type cannot be identified. As a result, determining the best treatment for this cancer, diagnosed in approximately 31,000 people in the US each year, is extremely difficult.2 In recent years, oncologists have looked to genetic testing to identify the cancer type as a way to improve care.

In the current study, a molecular analysis of biopsied tissue predicted the originating cancer site for all of the 101 patients treated. The analysis identified a total of 16 sites; cancers of the pancreas (21% of participants), gastric system (21% of participants), and malignant lymphomas (20% of patients) were the 3 most common sites to be predicted as the primary site of malignancy. The Japan-based researchers then randomized the patients to receive therapy appropriate to the predicted site of origin (50 patients) or the standard, empiric treatment of paclitaxel plus carboplatin (51 patients).


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PacBio sequencing improves some transplant outcomes

HLA typing with PacBio Shown to Improve Transplant Outcomes

By Bio-IT World Staff

April 5, 2019 | Scientists at the Anthony Nolan Research Institute in the UK have demonstrated that ultra-high-resolution HLA typing performed with PacBio sequencing identified stronger matches associated with improved survival rates among patients who received hematopoietic stem cell transplants. The retrospective study was published this week in the Journal of Biology of Blood and Marrow Transplantation.

PacBio sequencing improves some transplant outcomes

HLA typing involves analysis of the genes found in the human leukocyte antigen region of the human genome. For stem cell transplants, HLA typing is used to find the best donor/recipient match for the strongest chance of a positive outcome for transplant patients. The HLA genes are highly polymorphic and complex, making them very difficult to resolve fully with conventional technologies. They are also known to be important in immune-related diseases and drug hypersensitivity.

The Anthony Nolan Research Institute, which is funded by Anthony Nolan, a registered UK charity that maintains the world's oldest stem cell registry, has implemented Single Molecule, Real-Time (SMRT) Sequencing from PacBio to fully phase and characterize HLA genes with high accuracy. In this retrospective study, the scientists aimed to determine whether high-resolution HLA typing enabled by SMRT Sequencing would have made a difference for previously matched donors and recipients.


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Catastrophic loss of amphibian biodiversity

Scientists Uncover the Most Devastating Disease-Afflicted Biodiversity Loss Known to Science


A recent paper published in Science revealed the shocking results of a global disease transmission assessment: A fungal disease affecting amphibians has been identified as the most devastating recorded example of biodiversity loss attributable to a single disease. The analysis was made possible by an extensive collaboration involving experts from 36 institutions.

Over the past half century, the amphibian chytridiomycosis panzootic, an infectious disease that affects amphibians worldwide, has resulted in 90 presumed extinctions as well as the decline of at least 501 amphibian species.

This fungus was identified in amphibian populations about 20 years ago as the cause of death and species extinction at a global scale. The last similar analysis that assessed global amphibian decline was published in 2007 but was mainly focused on the regions that suffered the most decline.

Catastrophic loss of amphibian biodiversity

One of the two Cornell affiliates in the study, Prof. Kelly Zamudio, ecology and evolutionary biology, has worked in Panama, Brazil and the United States studying the effect of frog-killing chytrid fungus Batrachochytrium dendrobatidis using population genetics.

Zamudio said the idea for the global epidemiological analysis started from a conversation going around the amphibians researcher community: “How bad is this? How much have we really lost?”


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Be Your Own Fountain of Youth: Using Your Cells for Regenerative Medicine

Chasing the Holy Grail of Cell Therapy

Helen Albert, Labtech.eu

Be Your Own Fountain of Youth: Using Your Cells for Regenerative Medicine

Biotech entrepreneur Darrin Disley, ex-CEO and co-founder of the successful Cambridge gene editing biotech Horizon Discovery, has a new quest — creating the perfect cell therapy. He spoke to me about his position as CEO of new biotech Mogrify and why he thinks now is a good time to get into cell therapy.

Following the meteoric rise of Horizon Discovery from a small startup in 2007 to a company of 500 people and a market cap of more than €445M, Disley decided to step down as CEO of the gene editing company in February 2018. After taking a year off to travel and “get fit and healthy” he is now back in Cambridge and firmly back on the biotech scene to head up a new cell therapy biotech.

Mogrify, which has recently raised a seed round of €3.3M to kick start its technology development, specializes in transforming one type of cell into another. The key difference from other cell transformation methods is that the company can find the chemical recipe needed to flip one adult cell into another adult cell type, without transforming it into a stem cell first.

“If you could take a cell from one part of the body and turn it into any other cell at any other stage of development for another part of the body, you effectively have the Holy Grail of regenerative medicine,” enthused Disley.


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Genome of Extreme-Tolerant Fungus from Portugal Church Sequenced

High-Quality Draft Genome Sequence of the Microcolonial Black Fungus Aeminium ludgeri DSM 106916

João Trovão, Igor Tiago, Fabiana Soares, Diana Sofia Paiva, Nuno Mesquita, Catarina Coelho, Lídia Catarino, Francisco Gil, and António Portugal

Christina Cuomo, Microbiology Resource Announcements

Genome of Extreme-Tolerant Fungus from Portugal Church Sequenced

ABSTRACTAeminium ludgeri is an extremotolerant microcolonial black fungus isolated from a biodeteriorated limestone art piece in the Old Cathedral of Coimbra, Portugal (a UNESCO World Heritage Site). The high-quality draft genome sequence of Aeminium ludgeri presented here represents the first sequenced genome for both the recently described fungal family Aeminiaceae and the genus Aeminium.


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Institutional investors active with Invesco Dynamic Biotechnology & Genome ETF

Invesco Dynamic Biotechnology & Genome ETF (PBE) Shares Bought by Stifel Financial Corp

Stifel Financial Corp boosted its holdings in Invesco Dynamic Biotechnology & Genome ETF (NYSEARCA:PBE) by 34.4% during the 4th quarter, according to its most recent disclosure with the Securities & Exchange Commission. The institutional investor owned 21,776 shares of the company’s stock after buying an additional 5,578 shares during the quarter. Stifel Financial Corp owned approximately 0.40% of Invesco Dynamic Biotechnology & Genome ETF worth $1,025,000 at the end of the most recent reporting period.

money-2558681_1280.jpg

A number of other large investors have also added to or reduced their stakes in PBE. SG Americas Securities LLC acquired a new position in shares of Invesco Dynamic Biotechnology & Genome ETF in the third quarter worth about $452,000. Morgan Stanley boosted its holdings in shares of Invesco Dynamic Biotechnology & Genome ETF by 6.5% in the third quarter. Morgan Stanley now owns 153,962 shares of the company’s stock worth $9,153,000 after buying an additional 9,391 shares during the period. Carnegie Capital Asset Management LLC boosted its holdings in shares of Invesco Dynamic Biotechnology & Genome ETF by 10.7% in the third quarter. Carnegie Capital Asset Management LLC now owns 5,330 shares of the company’s stock worth $271,000 after buying an additional 515 shares during the period. B. Riley Financial Inc. boosted its holdings in shares of Invesco Dynamic Biotechnology & Genome ETF by 14.4% in the third quarter. B. Riley Financial Inc. now owns 6,982 shares of the company’s stock worth $415,000 after buying an additional 880 shares during the period. Finally, YHB Investment Advisors Inc. boosted its holdings in shares of Invesco Dynamic Biotechnology & Genome ETF by 19.0% in the fourth quarter. YHB Investment Advisors Inc. now owns 25,395 shares of the company’s stock worth $1,195,000 after buying an additional 4,050 shares during the period.


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Consumer Genomics Breast Cancer Test FAIL

23andMe DTC Breast and Ovarian Cancer Risk Test Misses Almost 90 Percent of BRCA Mutation Carriers

Julia Karow, GenomeWeb

Consumer Genomics Breast Cancer Test FAIL

SEATTLE (GenomeWeb) – A study led by researchers at Invitae has found that 23andMe's direct-to-consumer BRCA test, which tests for three common variants in the BRCA1 and BRCA2 genes and is authorized by the US Food and Drug Administration, misses almost 90 percent of BRCA mutation carriers, both in those with and those without a personal or family history of cancer. 

In addition, it misses almost 20 percent of BRCA mutations in those of self-reported Ashkenazi Jewish descent because it doesn't test for them.

The results of the study, which looked at data from almost 125,000 de-identified individuals who had been referred to Invitae for diagnostic testing with one of the firm's cancer risk tests, was presented yesterday at the American College of Medical Genetics and Genomics annual meeting by Edward Esplin,Dian a clinical geneticist at Invitae.

Esplin told GenomeWeb that the study, which did not mention 23andMe by name, was meant to criticize a screening strategy with an FDA-authorized DTC test that appears to have limited clinical utility rather than to criticize 23andMe for offering the test.

In his presentation, he pointed out that the FDA's authorization for the test last year "sounds more like a warning than an approval." FDA cautioned that the test, which examines three founder mutations in the BRCA genes that are common in the Ashkenazi Jewish population, does not assess more than 1,000 other known BRCA mutations, so a negative result does not rule out someone is a mutation carrier. It also advises that positive test results should not be used to determine any treatments without confirmatory testing and genetic counseling. 


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Bacteria deploy viruses to trick the immune system

Viruses act as decoys, study finds, helping bacteria evade the immune system

Eric Boodman, Stat News

Bacteria deploy viruses to trick the immune system

These viruses weren’t supposed to affect humans. They were supposed to ride along inside bacteria — unobtrusive hitchhikers taking advantage of another microbe’s machinery. But that wasn’t what Dr. Paul Bollyky and his colleagues saw in their lab dishes three or four years ago. The viruses seemed to be changing the behavior of human immune cells. Instead of gobbling up bacteria as they normally did, white blood cells just sat there.

“They basically don’t eat anything. They don’t move around much either,” said Bollyky, an immunologist and infectious disease specialist at Stanford University. “They would just ignore … the bacteria that were in the dish with them.”

Now, with a paper published Thursday in Science, what began as a chance observation has yielded a startling window into the inner lives of infections — one in which viruses tag-team with bacteria to trick the immune system by providing a decoy. Bollyky describes it as having someone trip the fire alarm so that the rest of the team can pull off a robbery in the chaos that ensues.


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Cancer evading the Immune System, covered in the New York Times

Cancer’s Trick for Dodging the Immune System

Matt Richtel, The New York Times

Cancer evading the Immune System, covered in the New York Times

Cancer immunotherapy drugs, which spur the body’s own immune system to attack tumors, hold great promise but still fail many patients. New research may help explain why some cancers elude the new class of therapies, and offer some clues to a solution.

The study, published on Thursday in the journal Cell, focuses on colorectal and prostate cancer. These are among the cancers that seem largely impervious to a key mechanism of immunotherapy drugs.

The drugs block a signal that tumors send to stymie the immune system. That signal gets sent via a particular molecule that is found on the surface of some tumor cells.

The trouble is that the molecule, called PD-L1, does not appear on the surface of all tumors, and in those cases, the drugs have trouble interfering with the signal sent by the cancer.


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Long non-coding RNA triggers Cancer Resistance

Long non-coding RNA GBCDRlnc1 induces chemoresistance of gallbladder cancer cells by activating autophagy

Qiang Cai, Shouhua Wang, Longyang Jin, Mingzhe Weng, Di Zhou, Jiandong Wang, Zhaohui Tang and Zhiwei Quan

Molecular Cancer (Research Article)

Background

Gallbladder cancer is the most common biliary tract malignancy and not sensitive to chemotherapy. Autophagy is an important factor prolonging the survival of cancer cells under chemotherapeutic stress. We aimed to investigate the role of long non-coding RNAs (lncRNAs) in autophagy and chemoresistance of gallbladder cancer cells.

Methods

We established doxorubicin (Dox)-resistant gallbladder cancer cells and used microarray analysis to compare the expression profiles of lncRNAs in Dox-resistant gallbladder cancer cells and their parental cells. Knockdown or exogenous expression of lncRNA combined with in vitro and in vivo assays were performed to prove the functional significance of lncRNA. The effects of lncRNA on autophagy were assessed by stubRFP-sensGFP-LC3 and western blot. We used RNA pull-down and mass spectrometry analysis to identify the target proteins of lncRNA.

Results

The drug-resistant property of gallbladder cancer cells is related to their enhanced autophagic activity. And we found a lncRNA ENST00000425894 termed gallbladder cancer drug resistance-associated lncRNA1 (GBCDRlnc1) that serves as a critical regulator in gallbladder cancer chemoresistance. Furthermore, we discovered that GBCDRlnc1 is upregulated in gallbladder cancer tissues. Knockdown of GBCDRlnc1, via inhibiting autophagy at initial stage, enhanced the sensitivity of Dox-resistant gallbladder cancer cells to Dox in vitro and in vivo. Mechanically, we identified that GBCDRlnc1 interacts with phosphoglycerate kinase 1 and inhibits its ubiquitination in Dox-resistant gallbladder cancer cells, which leads to the down-regulation of autophagy initiator ATG5-ATG12 conjugate.

Conclusions

Our findings established that the chemoresistant driver GBCDRlnc1 might be a candidate therapeutic target for the treatment of advanced gallbladder cancer.

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Gene Regulatory Networks for Key Nutrient Responses Revealed

Scientists Develop Methods to Validate Gene Regulation Networks

A team of biologists and computer scientists has mapped out a network of interactions for how plant genes coordinate their response to nitrogen, a crucial nutrient and the main component of fertilizer.

Findings Reveal How Plants Respond to Key Nutrient in Fertilizer

A team of biologists and computer scientists has mapped out a network of interactions for how plant genes coordinate their response to nitrogen, a crucial nutrient and the main component of fertilizer. The work, published in the journal Nature Communications, offers a potential framework and more efficient methods that can be used to investigate a wide-range of vital pathways in any organism.

“The sequencing of whole genomes has transformed life sciences, leading to breakthroughs in medicine, agriculture, and basic research,” explains Matthew Brooks, an NIH-postdoctoral fellow in New York University’s Department of Biology and the paper’s lead author. “The challenge now is to determine how the genes that are encoded by an organism are regulated and work together in networks that allow plants and animals to respond to their environment.”

The scientists, working in NYU’s Center for Genomics and Systems Biology, focused on gene regulatory networks, which consist of transcription factors and the target genes that they regulate. These gene regulatory networks enable organisms to adapt to fluctuating surroundings.

Potential progress for Pancreatic Cancer treatment

CRI-Sponsored Trial Reveals Promising Potential of Immunotherapy Combination in Metastatic Pancreatic Cancer

Arthur N. Brodsky, Cancer Research Institute Blog

A novel combination of immunotherapy and chemotherapy shows promise as a first-line option in patients with metastatic pancreatic cancer, according to interim results from a Cancer Research Institute-funded clinical trial that are being revealed today at the 2019 Annual Meeting of the American Association for Cancer Research (AACR19) in Atlanta.

This phase Ib trial is the first to emerge from the partnership between the Cancer Research Institute (CRI), the Parker Institute for Cancer Immunotherapy (PICI), and Bristol-Myers Squibb (BMS) that was formed in 2017 in order to accelerate promising immunotherapy to benefit the patients who need them most.

In this study, patients were treated with combinations of four different drugs, including two standard-of-care chemotherapies and two immunotherapies—one that inhibits the PD-1 immune checkpoint (nivolumab, BMS) and an experimental treatment that activates the CD40 pathway (APX005M, Apexigen).

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Use It and Never Loose It: Embryonic Enhancers Remain Available

Cells recall the way they were

Jessica Lau, HSCRB Communications

When cells grow up, they remember their childhoods.

Use It and Never Loose It: Embryonic Enhancers Remain Available

A new study has found that adult cells keep a record of which genes were activated during their early development. Even more surprisingly, the memory is retrievable: Under certain lab conditions, cells can play the story of their development in reverse, switching on genes that were active before. The study, by researchers at the Dana-Farber Cancer Institute (DFCI), Brigham and Women’s Hospital, Harvard Medical School, and the Harvard Stem Cell Institute, was published in Molecular Cell.

“We discovered that adult cells maintain a catalog of all of the genes used early in development — a record when organs and tissues are formed within the embryo,” said senior author Ramesh Shivdasani, professor of medicine at Harvard Medical School and DFCI, and faculty member of the Harvard Stem Cell Institute.

“Beyond the sheer existence of this archive, we were surprised to find that it doesn’t remain permanently locked away but can be accessed by cells under certain conditions,” he said. “This discovery has potentially profound implications for how we think about cells’ capabilities, and for the future treatment of degenerative and other diseases.”


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Looking Everywhere for Cancer Drugs

Nature’s Bounty: Revitalizing the Discovery of New Cancer Drugs from Natural Products

Cancer Currents Blog

Dr. Grkovic has spent the last several years intimately involved in improving processes for analyzing products of nature—from marine creatures to soil-dwelling fungi to plant leaves—to see whether chemical compounds within them might be starting blocks for new cancer drugs. (The Natural Products Support Group is part of the Frederick National Laboratory for Cancer Research, an NCI-sponsored contractor-operated facility.)

Looking Everywhere for Cancer Drugs

The work has been part of an ambitious, Cancer MoonshotSM-funded initiative, called the NCI Program for Natural Products Discovery (NPNPD), to make it easier for other researchers to mine nature for leads on new cancer drugs.

A big part of that story has taken place in the well-worn home of NCI’s Natural Products Branch, on the NCI campus in Frederick, MD.


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Even viruses get viruses...

Even Viruses Can Get Infected With Other Viruses

Three tiny, newly described viruses—named Larry, Curly, and Moe—target bigger viruses.

SARAH ZHANG, The Atlantic

Even viruses get viruses...

In a single drop of water from Lake Ontario, you can find an abundance of algae. In these algae, scientists in 2015 found a new virus belonging to an enigmatic group called giant viruses. And nested inside these giant viruses, scientists have now found yet more novel viruses—three tiny ones that they have named CpV-PLV Larry, Curly, and Moe.

“I originally named them to see if I can get away with it,” says Joshua Stough, now a postdoctoral research fellow at the University of Michigan. He’s a co-author of a new paper describing and naming the Three Stooges, so, in fact, he has gotten away with it.


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