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.
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 | February 24, 2020
The big question at the start of 2019 was whether the IPO window would stay open for biotech companies, particularly those seeking to pull off ever-larger IPOs at increasingly earlier stages of development. The short answer is yes—kind of. Here’s the long answer: In the words of Renaissance Capital, the IPO market had “a mostly good year.” The total number of deals fell to 159 from 192 the year before, but technology and healthcare companies were standout performers. The latter—which include biotech, medtech and diagnostics companies—led the pack, making up 43% of all IPOs in 2019. By Renaissance’s count, seven companies went public at valuations exceeding $1 billion, up from five the year before
Article | February 11, 2020
In today’s biotechnology landscape, to be competitive, meet regulations, and achieve market demands, “we must apply Bioprocessing 4.0,” said Igor Fisch, PhD, CEO, Selexis. In fact, in the last decade, “Selexis has evolved from cloning by limiting dilution to automated cell selection to nanofluidic chips and from monoclonality assessment by statistical calculation to proprietary bioinformatic analysis,” he added. Single-use processing systems are an expanding part of the biomanufacturing world; as such, they are a major component of Bioprocessing 4.0. “At Selexis, we use single use throughout our cell line development workflow. Currently, we have incorporated single-use automated bioprocessing systems such as ambr® and the Beacon® optofluidic platform for accelerated cell line development. By using these systems and optimizing our parameters, we were able to achieve high titers in shake flasks. Additionally, the Beacon systems integrate miniaturized cell culture with high-throughput liquid handling automation and cell imaging. This allows us to control, adjust, and monitor programs at the same time,” noted Fisch.