Cell biology & Biotechnology

| June 18, 2012

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Stem cells & its preservation

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Closing bacterial genomes from the human gut microbiome using long-read sequencing

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.

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Learning How FoxA2 Helps Turn Stem Cells into Organs

Article | February 12, 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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Pfizer, BioNTech Plan Clinical Trial for COVID-19 mRNA Vaccine Candidate

Article | February 12, 2020

Pfizer and BioNTech plan to begin human clinical trials on their lead COVID-19 therapeutic candidate, an mRNA vaccine, by the end of this month, the companies said today, through a collaboration that could generate up to $748 million for the German biotech. The companies announced plans last month to partner on BNT162, the first treatment to emerge from BioNTech’s accelerated COVID-19-focused development program, “Project Lightspeed.” BioNTech and Pfizer established collaboration intended to draw upon BioNTech’s proprietary mRNA vaccine platforms, and Pfizer’s expertise in vaccine research and development, regulatory capabilities, and global manufacturing and distribution network.

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Cell Out? Lysate-Based Expression an Option for Personalized Meds

Article | February 12, 2020

Cell-free expression (CFE) is the practice of making a protein without using a living cell. In contrast with cell line-based methods, production is achieved using a fluid containing biological components extracted from a cell, i.e., a lysate. CFE offers potential advantages for biopharma according to Philip Probert, PhD, a senior scientist at the Centre for Process Innovation in the U.K.

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