Biotech Weekly
"Once accidentally took a scanning electron microscopy image of a beard hair. Was studying carbon nanotubes. Set me back a few days debugging" - Justin Silverman
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How markets, Marx, and provincial elites created world literature to fight both empire and nationalism

Stem Cells

Gene-edited embryos enable researchers to unpick role of a crucial gene, with more studies likely to follow.

See also a discussion of this paper on The Niche: https://ipscell.com/2017/09/1st-knockout-human-embryos-made-crispr-take-pub/

Who are the major regenerative medicine and stem cell influencers?

If you’re seeking a resource to help you transition into tissue engineering and regenerative medicine, look no further. *Engineering Neural Tissue from Stem Cells* fulfills a need for an informative, but accessible, introduction to these exciting fields. It is far more detailed than a typical textbook, but slightly less specific than a review paper.

Taken together our data indicate that the patient specific iPSC model provides a robust platform for understanding the role of complement activation in AMD, evaluating new therapies based on complement modulation and drug testing. 

Genetics
Here we report a method to capture in situ global RNA interactions with DNA by deep sequencing (GRID-seq), which enables the comprehensive identification of the entire repertoire of chromatin-interacting RNAs and their respective binding sites. In human, mouse, and Drosophila cells, we detected a large set of tissue-specific coding and non-coding RNAs that are bound to active promoters and enhancers, especially super-enhancers. 

The brilliant, intricate patterns on butterfly wings — from haunting eye spots to iridescent splashes of blue — look as if they were painted on by teams of artists. Researchers thought that a complex collection of genes might be responsible, interacting to build up the final pattern. But two studies now suggest that two genes play an outsize role in determining the wing’s lines and colours. Turning off these 'master' genes disrupts the canvas, dulling the colours or turning the insects monochromatic.

We construct genomic predictors for heritable and extremely complex human quantitative traits (height, heel bone density, and educational attainment) using modern methods in high dimensional statistics (i.e., machine learning). Replication tests show that these predictors capture, respectively, ~40, 20, and 9 percent of total variance for the three traits. [...] The variance captured for height is comparable to the estimated SNP heritability from GCTA (GREML) analysis, and seems to be close to its asymptotic value (i.e., as sample size goes to infinity), suggesting that we have captured most of the heritability for the SNPs used. Thus, our results resolve the common SNP portion of the "missing heritability" problem - i.e., the gap between prediction R-squared and SNP heritability.

People used to say this couldn't be done...

Bioengineering

We provide the first empirical evidence that gene synthesis is leading biologists and bioengineers to sample more broadly across the rich genetic diversity of life, increasingly making that functionality available for industrial or biomedical advances.

Synthetic biology is typified by developing novel genetic constructs from the assembly of reusable synthetic DNA parts, which contain one or more features such as promoters, ribosome binding sites, coding sequences and terminators. While repositories of such parts exist to promote their reuse, there is still a need to design novel parts from scratch. PartsGenie, freely available at http://parts.synbiochem.co.uk, is introduced to facilitate the computational design of such synthetic biology parts.

Cells can be programmed like a computer to fight cancer, influenza and other serious health conditions – breakthrough research by University of Warwick

OA | Model-based design of RNA hybridization networks implemented in living cells

https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkx698

Cell and Molecular

Networks of nanotubes may allow cells to share everything from infections and cancer to dementia-linked proteins.

Here we explore the dynamics of T7 phage epidemics in structured and unstructured Escherichia coli populations consisting of differing mixtures of susceptible and resistant individuals harboring CRISPR immunity to the phage. Using both experiments and mathematical modelling we describe the conditions under which herd immunity arises in bacterial populations.

General Science

At the University of Chicago, biochemists, molecular biologists, and geneticists in Joseph Thornton’s lab are examining why things in biology have turned out as they have and not some other way. They note that “history leaves no trace of the roads it did not take” and ask: is the current state of things inevitable?

In September 1957, Francis Crick gave a lecture in which he outlined key ideas about gene function, in particular what he called the central dogma. These ideas still frame how we understand life. This essay explores the concepts he developed in this influential lecture, including his prediction that we would study evolution by comparing sequences.

The study of languages has long been prone to nonsense. Why is linguistics such a magnet for dilettantes and crackpots?

Bioinformatics skills have become essential for many research areas; however, the availability of qualified researchers is usually lower than the demand and training to increase the number of able bioinformaticians is an important task for the bioinformatics community.

In Other News...

I no longer doubt the research. Though simple, this is an incredibly powerful memory tool. Inspired by my success with the lukasa, I have also created songlines for more than a kilometre around my home. I have a location on my walk for each of the 244 countries and dependent territories in the world. I walk through them from the most populous in China to little Pitcairn Island. I also walk through time from 4,500 million years ago until the present, nodding to the dinosaurs, meeting our hominid ancestors and greeting numerous characters from history. My memory has been hugely expanded by using this ancient mnemonic technique.

A number of authors interested in how to translate evidence into policy identify the importance of policy narrative and argue that advocates of scientific evidence need to tell good stories to grab the attention and appeal to the emotions of policymakers. Yet, this general call for better narratives is incomplete without concrete examples and evidence of their effectiveness. This article shows how these processes are described in the “grey” literature—defined as literature which is produced by all levels of government, academics, business and industry, but which is not controlled by commercial publishers.

When we experience art, we feel connected to something larger. Why? A new field of science has the answers to some of art’s enduring mysteries.

Hope you enjoyed your week and this issue of Biotech Weekly! If you think someone would like this collection of biotech related news and recent research publications, just forward them this email. Thank you! - Kate the Great
Kate Busse · 2111 Manchester Ave · Encinitas CA 92007 · USA
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