Biotech Weekly
This weekend, I'm visiting the BODIES Exhibit in LA. If you've never heard, it's a showcase of preserved human bodies dissected to display bodily systems!
Expression quantitative trait locus (eQTL) analysis is an approach for identifying how genetic variation between individuals contributes to inter-individual differences in gene expression. This "SnapShot" describes the basic principles of eQTL analysis and its applications to diverse molecular traits of the cell measured by genomics and proteomics assays.

Passive stretch affects the structural and functional maturation of EHMs. Based on our predictive computational modeling, we show how to optimize cell alignment and calcium dynamics within EHMs. These findings provide a basis for the rational design of EHMs, which enables future scale-up productions for clinical use in cardiovascular tissue engineering.

Stem Cells

CD34-positive hematopoietic cells are the gold standard for stem cell therapy and transplantation of stem cell–enriched grafts. However, most of the cells within this population will not contribute to engraftment. Using a robust nonhuman primate transplantation model, Radtke et al. identified a stem cell–enriched subpopulation of CD34-positive cells that was exclusively responsible for multilineage engraftment.

Believed to be the first of its kind in Canada, the technology enables human embryonic stem cells to self-organize into a structure with embryo-like features, including the early precursors of organs such as the brain, the heart and the liver.

Stem cell therapy has great potential for curing cartilage damage. However, it has remained unclear whether stem cells are responsible for regeneration or whether they trigger the process. Researchers at the Vetmeduni Vienna have been able to resolve this issue by tracking the effects in a new, natural model. After injection, stem cells orchestrate the healing effect of endogenous cells but are not responsible for cartilage regeneration. The breakthrough is published in JCI-Insight and was enabled by preventing the normal immune response to the molecule required to trace the injected cells.

In a new study published in Cell Stem Cell, UNC School of Medicine neuroscientist Juan Song and colleagues discovered a long-distance brain circuit that controls the production of new neurons in the hippocampus.

A team led by Young-sup Yoon, MD, PhD developed a new method for generating endothelial cells, which make up the lining of blood vessels, from human induced pluripotent stem cells.. When endothelial cells are surrounded by a supportive gel and implanted into mice with damaged blood vessels, they become part of the animals' blood vessels, surviving for more than 10 months.

Our previous study has shown that three-dimensional (3D) culture decreases mesenchymal stem cell (MSC) size, leading to enhanced trafficking ability and reduced lung vascular obstructions. However, the underlying mechanisms are unclear. In this study, we proposed that 3D culture reduces MSC size by increasing vesicle excretion.

“We knew the gecko’s spinal cord could regenerate, but we didn’t know which cells were playing a key role,” said Vickaryous, lead author of the study recently published in the Journal of Comparative Neurology. “Humans are notoriously bad at dealing with spinal cord injuries, so I’m hoping we can use what we learn from geckos to coax human spinal cord injuries into repairing themselves.”


Psychiatric disorders can be debilitating and often involve a genetic component, yet, evolution hasn’t weeded them out. Now, recent work is beginning to reveal the role of natural selection — offering a peek at how the genetic underpinnings of mental illness has changed over time.

After years of studying advanced cancers, researchers are now training their DNA sequencers on precancerous growths to learn more about how they develop into the full-blown disease.

Senescence is a terminal differentiation program that halts the growth of damaged cells and must be circumvented for cancer to arise. Here we describe a panel of genetic screens to identify genes required for replicative senescence. We uncover a role in senescence for the potent tumor suppressor and ATM substrate USP28.

Biological systems rely on complex networks, such as transcriptional circuits and protein-protein interaction networks, to perform a variety of functions e.g. responding to stimuli, directing cell fate, or patterning an embryo. Mathematical models are often used to ask: given some network, what function does it perform? However, we often want precisely the opposite i.e. given some circuit - either observed in vivo, or desired for some engineering objective - what biological networks could execute this function? Here, we adapt optimization algorithms from machine learning to rapidly screen and design gene circuits capable of performing arbitrary functions. We demonstrate the power of this approach by designing circuits (1) that recapitulate important in vivo phenomena, such as oscillators, and (2) to perform complex tasks for synthetic biology, such as counting noisy biological events. Our method can be readily applied to biological networks of any type and size, and is provided as an open-source and easy-to-use python module, GeneNet.

Cell and Molecular
Our mucosal tissues represent the first barrier against microbial invaders. Using advanced intravital live imaging, researchers discover a sophisticated system regulating the dynamic behavior of IELs, the most common type of immune cells surveying the gut mucosa.

This one comes with a video abstract! 
Synapses are specialized junctions between neurons in brain that transmit and compute information, thereby connecting neurons into millions of overlapping and interdigitated neural circuits. Here, we posit that the establishment, properties, and dynamics of synapses are governed by a molecular logic that is controlled by diverse trans-synaptic signaling molecules. Neurexins, expressed in thousands of alternatively spliced isoforms, are central components of this dynamic code. Presynaptic neurexins regulate synapse properties via differential binding to multifarious postsynaptic ligands, such as neuroligins, cerebellin/GluD complexes, and latrophilins, thereby shaping the input/output relations of their resident neural circuits. Mutations in genes encoding neurexins and their ligands are associated with diverse neuropsychiatric disorders, especially schizophrenia, autism, and Tourette syndrome. Thus, neurexins nucleate an overall trans-synaptic signaling network that controls synapse properties, which thereby determines the precise responses of synapses to spike patterns in a neuron and circuit and which is vulnerable to impairments in neuropsychiatric disorders.
General Science

Using alien natural selection as a framework, the authors of a new paper in International Journal of Astrobiology speculated about how complexity will arise in space. Species complexity has increased on the Earth as a result of a handful of events, known as major transitions. These transitions occur when a group of separate organisms evolve into a higher-level organism - when cells become multi-cellular organisms, for example. Both theory and empirical data suggest that extreme conditions are required for major transitions to occur. 

The team has found preliminary evidence of an effect that was theorized only a few years ago1: a quantum boost that would push the diamond's power output above the level prescribed by classical thermodynamics. If the results hold up, they will be a tangible boon for the study of quantum thermodynamics, a relatively new field that aims to uncover the rules that govern heat and energy flow at the atomic scale.

In Other News...

This year marks the 40th anniversary of DNA sequencing technology (Gilbert and Maxam, 1977; Sanger et al., 1977)1 The Sanger technique soon took over and by the 1990s it was the only technique used to sequence DNA. The development of reliable sequencing machines meant the end of those large polyacrylamide gels that we all hated.

Beautiful photographs from microscopes!

Open scholarship, such as the sharing of articles, code, data, and educational resources, has the potential to improve university research and education as well as increase the impact universities can have beyond their own walls. To support this perspective, I present evidence from case studies, published literature, and personal experiences as a practicing open scholar.

Three ideas have emerged to explain the origin of viruses: 1. viruses evolved first on Earth, before cells, and when cells evolved, the viruses became their genetic parasites; 2. viruses are cells that lost many genes and became intracellular parasites; 3. viruses are collections of genes that escaped from cells. Missing from these hypothesis is how nucleic acids became virus particles – that is, how they acquired structural proteins. It seems likely that viral structural proteins originated from cellular genes.

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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