WELCOME TO The Biotechnology REPORT
Biotech: As Cheap as They Come
BEN LEVISOHN | July 20, 2016
Exosome Diagnostics, Inc. is commercializing minimally invasive molecular diagnostics in blood and urine to enable doctors to select optimal therapies for cancer and other diseases.
Article | February 12, 2020
In our lab, we focus on the impact of the gut microbiome on human health and disease. To evaluate this relationship, it’s important to understand the particular functions that different bacteria have. As bacteria are able to exchange, duplicate, and rearrange their genes in ways that directly affect their phenotypes, complete bacterial genomes assembled directly from human samples are essential to understand the strain variation and potential functions of the bacteria we host. Advances in the microbiome space have allowed for the de novo assembly of microbial genomes directly from metagenomes via short-read sequencing, assembly of reads into contigs, and binning of contigs into putative genome drafts. This is advantageous because it allows us to discover microbes without culturing them, directly from human samples and without reference databases. In the past year, there have been a number of tour de force efforts to broadly characterize the human gut microbiota through the creation of such metagenome-assembled genomes (MAGs)[1–4]. These works have produced hundreds of thousands of microbial genomes that vastly increase our understanding of the human gut. However, challenges in the assembly of short reads has limited our ability to correctly assemble repeated genomic elements and place them into genomic context. Thus, existing MAGs are often fragmented and do not include mobile genetic elements, 16S rRNA sequences, and other elements that are repeated or have high identity within and across bacterial genomes.
Article | April 20, 2021
With advances in data analytics and machine learning, the move from descriptive and diagnostic analytics to predictive and prescriptive analytics and controls—allowing us to better forecast and understand what will happen and thus optimize process outcomes—is not only feasible but inevitable, according to Bonnie Shum, principal engineer, pharma technical innovation, technology & manufacturing sciences and technology at Genentech.
“Well-trained artificial intelligence systems can help drive better decision making and how data is analyzed from drug discovery to process development and to manufacturing processes,” she says.
Those advances, though, only really matter when they improve the lives of patients. That’s exactly what Shum expects.
“The convergence of digital transformation and operational/processing changes will be critical for the facilities of the future and meeting the needs of our patients,” she continues. “Digital solutions may one day provide fully automated bioprocessing, eliminating manual intervention and enabling us to anticipate potential process deviations to prevent process failures, leading to real-time release and thus faster access for patients.”
To turn Bioprocessing 4.0 into a production line for precision healthcare, real-time release and quickly manufacturing personalized medicines will be critical. Adding digitization and advanced analytics wherever possible will drive those improvements. In fact, many of these improvements, especially moving from descriptive to predictive bioprocessing, depend on more digitization.
Article | April 9, 2020
World traveler‘s will rejoice at the idea of a seemingly magical device that would guarantee they never suffer from the all-too-familiar stomach issues that come from traveling internationally while reducing jet lag at the same time. But it’s not just privileged globetrotters that would benefit from a device that eliminates the bacteria associated with the so-called Montezuma’s Revenge. In 2016, more than 230,000 children around the world died from some of the same types of bacteria as those that cause traveler’s diarrhea, and the bacteria mainly come from unsafe “drinking water, poor sanitation and malnutrition,” according to Oxford University’s Our World In Data portal. On Monday, DARPA announced it was researching an “implantable or ingestible bioelectronic carrier” that would eliminate the five major bacteria associated with traveler’s diarrhea.
Article | March 18, 2020
Scientists at the Perelman School of Medicine at the University of Pennsylvania discovered early on in each cell, FoxA2 simultaneously binds to both the chromosomal proteins and the DNA, opening the flood gates for gene activation. The discovery, “Gene network transitions in embryos depend upon interactions between a pioneer transcription factor and core histones,” published in Nature Genetics, helps untangle mysteries of how embryonic stem cells develop into organs, according to the researchers. “Gene network transitions in embryos and other fate-changing contexts involve combinations of transcription factors. A subset of fate-changing transcription factors act as pioneers; they scan and target nucleosomal DNA and initiate cooperative events that can open the local chromatin. However, a gap has remained in understanding how molecular interactions with the nucleosome contribute to the chromatin-opening phenomenon,” write the investigators.
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