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Report Finds Microsoft Excel Causes Errors in 20 Percent of Genomics Studies

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Microsoft Excel, that ubiquitous tool for data crunching, has been playing an unexpected role in the scientific world. The program has been screwing with data in genomics studies. A new report in the journal Genome Biology estimates that around 20 percent of scientific papers published in leading genome-focused journals that include gene lists from Excel contain errors due to the program’s default autocorrect settings, Slate reports.

The problem is, several genes have symbols that look a lot like dates. The program has a tendency to convert gene symbols like SEPT2 (Septin 2) and MARCH1 (Membrane Associated Ring-CH-Type Finger) into what Excel thinks is proper date form—turning them into 2-Sept and 1-Mar instead. In some, SEPT2 became “2006/09/02.”

"Inadvertent gene symbol conversion is problematic because these supplementary files are an important resource in the genomics community that are frequently reused," the paper’s authors write. They reviewed the supplementary gene list Excel files from 18 journals, examining studies published between 2005 and 2015—Excel’s gene-typo issue was first reported in 2004—for date formatting within lists of genes. The analysis was performed by a program that flagged supplementary materials that seemed to be lists of genes, then searched them for date formatting. Out of more than 35,000 supplementary files, they confirmed 987 files with gene errors that were published as part of 704 studies.

Overall, 19.6 percent of papers in the 18 journals contained gene name errors caused by Excel’s autocorrect function, but some journals were worse than others. High-impact journals, typically the most respected outlets to publish research in, actually had more affected gene lists, which the researchers speculate may be because studies published in these journals are more likely to have larger and more numerous data sets.

The highest proportion of gene lists with errors (more than 20 percent) came from the journals Nucleic Acids Research, Genome Biology, Nature Genetics, Genome Research, Genes and Development, and Nature; conversely, the journals Molecular Biology and Evolution, Bioinformatics, DNA Research, and Genome Biology and Evolution showed errors in less than 10 percent of genomics papers.

While this isn’t the worst scientific error to end up in a journal, since it’s pretty clear that 2006/09/02 isn’t a gene symbol, it’s also fairly disturbing that this many papers could make it through the editing process without anyone noticing that they contained lists of nonexistent genes.

The researchers highlight Google Sheets as a potential alternative for Excel, because it doesn’t suffer from the same symbol-date mixup, and it seems that when you open Sheets documents in other programs like Excel, the data is protected from Excel’s default autocorrection. They suggest that journal editors and reviewers should look out for these errors, pasting gene name lists into blank files and sorting them so that any dates that have been mistakenly inserted will become apparent.

[h/t Slate]

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Scientists Create Three Puppy Clones of 'Snuppy,' the World's First Cloned Dog
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Snuppy, the world's first cloned dog, died in 2015, but his genetic legacy lives on. As the National Post reports, South Korean scientists recently described in the journal Scientific Reports the birth of three clone puppies, all of which are identical replicas of the famous Afghan hound.

Those who lived through the 1990s might remember Dolly, the Scottish sheep that gained fame for being the very first mammal to be cloned from an adult cell. Following Dolly's 1996 cloning, scientists managed to replicate other animals, including cats, mice, cows, and horses. But dog cloning initially stymied scientists, Time reports, as their breeding period is limited and their eggs are also hard to extract.

Ultimately, researchers ended up using somatic cell nuclear transfer (SCNT) to clone a dog, the same method that was used to make Dolly. In the early 2000s, a team of South Korean scientists inserted DNA harvested from an Afghan hound's skin cells into a dog egg from which the DNA had been removed. The egg divided, which produced multiple cloned embryos.

The scientists implanted 1095 of these embryos in 123 dogs, an exhaustive initiative that yielded just three pregnancies, according to NPR. Of these, Snuppy—whose name is a combination of "puppy" and Seoul National University's initials—was the only survivor.

Snuppy died from cancer in April 2015, just shortly after his 10th birthday. To celebrate his successful life, the same South Korean researchers decided to re-clone him using mesenchymal stem cells from the dog's belly fat, which were taken when he was five. This time around, they transferred 94 reconstructed embryos to seven dogs. Four clones were later born, although one ended up dying shortly after birth.

The tiny Snuppy clones are now more than a year old, and researchers say that they don't think that the pups face the risk of accelerated aging, nor are they more disease-prone than other dogs. (Dolly died when she was just six years old, while cloned mice have also experienced shorter lifespans.) Snuppy's somatic cell donor, Tai, lived just two years longer than Snuppy, dying at age 12, the average lifespan of an Afghan hound.

Researchers say that this new generation of Snuppys will yield new insights into the health and longevity of cloned animals. Meanwhile, in other animal cloning news, a Texas-based company called ViaGen Pets is now offering to clone people's beloved pets, according to CBS Pittsburgh—a service that costs a cool $50,000 for dogs.

[h/t National Post]

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Researchers Pinpoint the Genes Behind the Durian's Foul Stench
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Durian is a popular fruit in parts of southeast Asia. It's also known for having the most putrid, off-putting odor of any item sold in the produce section. Even fans of durian know why the fruit gets a bad rap, but what exactly causes its divisive scent is less obvious. Determined to find the answer, a team of researchers funded by "a group of anonymous durian lovers" mapped the fruit's genome, as reported by the BBC.

The study, published in the journal Nature Genetics [PDF], contains data from the first-ever complete genetic mapping of a durian fruit. It confirms that durian's excess stinkiness comes from sulfur, a chemical element whose scent is often compared to that of rotten eggs.

Analysis of the fruit's chemical makeup has been done in the past, so the idea that sulfur is a major contributor to its signature smell is nothing new. What is new is the identification of the specific class of sulfur-producing genes. These genes pump out sulfur at a "turbocharged" rate, which explains why the stench is powerful enough to have durian banned in some public areas. It may seem like the smell is a defense mechanism to ward off predators, but the study authors write that it's meant to have the opposite effect. According to the paper, "it is possible that linking odor and ripening may provide an evolutionary advantage for durian in facilitating fruit dispersal." In other words, the scent attracts hungry primates that help spread the seeds of ripe durian fruits by consuming them.

The revelation opens the door to genetically modified durian that are tweaked to produce less sulfur and therefore have a milder taste and smell. But such a product would likely inspire outrage from the food's passionate fans. While the flavor profile has been compared to rotten garbage and dead animal meat, it's also been praised for its "overtones of hazelnut, apricot, caramelized banana, and egg custard" by those who appreciate its unique character.

[h/t BBC]

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