In 2003, the Human Genome Project finished sequencing every bit of human DNA, remembers MIT News.

“Now, over two decades later, MIT Professor Jonathan Weissman and colleagues have gone beyond the sequence to present the first comprehensive functional map of genes that are expressed in human cells.”
The data from this project, published online June 9 in Cell, ties each gene to its job in the cell, and is the culmination of years of collaboration on the single-cell sequencing method Perturb-seq.

The data are available for other scientists to use. “It’s a big resource in the way the human genome is a big resource, in that you can go in and do discovery-based research,” says Weissman, who is also a member of the Whitehead Institute and an investigator with the Howard Hughes Medical Institute….

“I think this dataset is going to enable all sorts of analyses that we haven’t even thought up yet by people who come from other parts of biology, and suddenly they just have this available to draw on,” says former Weissman Lab postdoc Tom Norman, a co-senior author of the paper.

The announcement credits the single-sequencing tool Perturb-seq and CRISPR-Cas9 genome editing which introduced genetic changes into cells and then captured information about which RNAs expressed (uses single-cell RNA sequencing).

The researchers scaled the method to the entire genome using human blood cancer cell lines and noncancerous cells derived from the retina, ultimately using Perturb-seq across more than 2.5 million cells.

Thanks to Slashdot reader Hmmmmmm for sharing the news.

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New submitter blackprint writes: The City of Austin released a memo saying that Samsung released as much as 763,000 gallons of sulfuric acid waste into a Northeast Austin creek over a period as long as 106 days. They confirmed the leak has stopped, but no fish or macro invertebrates survived in the impacted area. They don’t know if there are any long-term impacts, but pH levels in the area have returned close to normal. According to the memo, “Public access to this area is limited, and there are no nearby parks.”

They have not stated the cause of the spill. “Spill investigators and scientists took a look at the area Jan. 18-19 and saw iron staining in the tributary channel consistent with a low pH environment,” reports local news station KXAN, citing the memo. “WPD says it was in this tributary stretch from the Samsung plant to the main branch of Harris Branch Creek that WPD staff found no surviving aquatic life, including fish.”

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After deliberating for more than 40 hours over six days, jurors in the Elizabeth Holmes criminal trial have found Holmes guilty on four of 11 charges of defrauding the company’s investors and patients. She was found not guilty on four counts. NPR reports: When the verdict was read, Holmes had no visible reaction. She sat masked in the courtroom and later hugged members of her family in the front row of the court. Holmes could face up to 20 years in prison, although legal experts say her sentence is likely to be less than that. During the nearly four-month federal trial in San Jose, jurors heard from over 30 witnesses called by prosecutors. Together, they painted Holmes as a charismatic entrepreneur who secured hundreds of millions of dollars in investment for a medical device that never delivered on her promises. When Theranos’ technology fell short, the government argued, Holmes covered it up and kept insisting that the machines would transform how diseases are diagnosed through blood tests. The jury’s decision followed seven days of deliberations. Still, the jury could not reach a unanimous decision on three charges, which will be resolved at a later date..

Holmes took the witness stand for more than 20 hours to defend herself. She accused her ex-boyfriend and former deputy at Theranos, Ramesh “Sunny” Balwani, of sexual abuse, saying that clouded her sense of judgement. Balwani faces a separate fraud trial in the same court in February. Holmes also showed remorse on the stand. She said she wished she had handled some key business matters differently. But she blamed others for the downfall of Theranos. She said lab directors whom she had trusted were the ones closest to the technology. And she said Balwani, not her, oversaw the company’s financial forecasts, which were later discovered to be grossly inflated. Yet the government offered evidence that Holmes had an iron grip on Theranos’ operations. Prosecutors argued she did not stop — and even helped spread — falsehoods about the company that misled investors into pouring millions into the startup. Theranos’ value, once estimated at more than $9 billion, was ultimately squandered.

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A sugar additive used in several foods could have helped spread a seriously dangerous superbug around the US, according to a 2018 study. ScienceAlert reports: The finger of blame is pointed squarely at the sugar trehalose, found in foods such as nutrition bars and chewing gum. If the findings are confirmed, it’s a stark warning that even apparently harmless additives have the potential to cause health issues when introduced to our food supply. In this case, trehalose is being linked with the rise of two strains of the bacterium Clostridium difficile, capable of causing diarrhea, colitis, organ failure, and even death. The swift rise of the antibiotic-resistant bug has become a huge problem for hospitals in recent years, and the timing matches up with the arrival of trehalose.

“In 2000, trehalose was approved as a food additive in the United States for a number of foods from sushi and vegetables to ice cream,” said one of the researchers, Robert Britton from the Baylor College of Medicine in Texas, back in January 2018. “About three years later the reports of outbreaks with these lineages started to increase. Other factors may also contribute, but we think that trehalose is a key trigger.”

The C. difficile lineages Britton is referring to are RT027 and RT078. When the researchers analysed the genomes of these two strains, they found DNA sequences that enabled them to feed off low doses of trehalose sugar very efficiently. In fact, these particular bacteria need about 1,000 times less trehalose to live off than other varieties of C. difficile, thanks to their genetic make-up. […] It’s still not certain that trehalose has contributed to the rise of C. difficile, but the study results and the timing of its approval as an additive are pretty compelling. More research will now be needed to confirm the link. According to figures from the CDC, “C. difficile was responsible for half a million infections across the year and 29,000 deaths within the first 30 days of diagnosis,” adds ScienceAlert. The findings were published in the journal Nature.

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