Daily Science Podcast

Nature, 2017, Vol 547, p345-349

By George Church out of the Department of Genetics and the Wyss Institute for Biologically Inspired Engineering at Harvard University

This project was funded primary by multiple NIH grants

DNA is an excellent medium for archiving data. Recent efforts have illustrated the potential for information storage in DNA using synthesized oligonucleotides assembled in vitro1–6. A relatively unexplored avenue of information storage in DNA is the ability to write information into the genome of a living cell by the addition of nucleotides over time. Using the Cas1–Cas2 integrase, the CRISPR–Cas microbial immune system stores the nucleotide content of invading viruses to confer adaptive immunity. When harnessed, this system has the potential to write arbitrary information into the genome8. Here we use theCRISPR–Cas system to encode the pixel values of black and white images and a short movie into the genomes of a population of living bacteria. In doing so, we push the technical limits of this information storage system and optimize strategies to minimize those limitations. We also uncover underlying principles of theCRISPR–Cas adaptation system, including sequence determinants of spacer acquisition that are relevant for understanding both the basic biology of bacterial adaptation and its technological applications. This work demonstrates that this system can capture and stably store practical amounts of real data within the genomes of populations of living cells.

My takeaways:

1. While the application they demonstrated in the main manuscript is cool, the real value of this paper is in the details of how they were able to achieve data reading and writing using DNA. They conducted many more control and mechanistic experiments than the actual reading and writing of data experiments. They identified a viable pathway to using bacteria and DNA to store information. This will have many obvious applications in data storage and protection.

2. While the technology is exciting, it is still very much in its infancy. I don’t expect to see this technology hit the markets for at least a decade.

Nature Materials, 2017, Vol16, p 489-496

James Moon and Anna Schwendeman of the Department of Pharmaceutical Sciences and Biointerfaces Institute at the University of Michigan

They were funded by the NIH, AHA, the UM MTRAC for Life Sciences, and the UM College of Pharmacy faculty start-up fund. Additionally, they found funding from the DoD Congressionally directed medical research program peer reviewed cancer research program and the NSF.

Despite the tremendous potential of peptide-based cancer vaccines, their efficacy has been limited in humans. Recent innovations in tumour exome sequencing have signaled the new era of personalized immunotherapy with patient-specific neoantigens, but a general methodology for stimulating strong CD8α+ cytotoxic T-lymphocyte (CTL) responses remains lacking Here we demonstrate that high-density lipoprotein-mimicking nanodiscs coupled with antigen (Ag) peptides and adjuvants can markedly improve Ag/adjuvant co-delivery to lymphoid organs and sustain Ag presentation on dendritic cells Strikingly, nanodiscs elicited up to 47-fold greater frequencies of neoantigen-specific CTLs than soluble vaccines and even 31-fold greater than perhaps the strongest adjuvant in clinical trials (that is, CpG in Montanide). Moreover, multi-epitope vaccination generated broad-spectrum T-cell responses that potently inhibited tumour growth. Nanodiscs eliminated established MC-38 and B16F10 tumours when combined with anti-PD-1 and anti-CTLA-4 therapy. These findings represent a new powerful approach for cancer immunotherapy and suggest a general strategy for personalized nanomedicine.

My takeaways:

1. The researchers leverage the two successful developing cancer treatment strategies - immunotherapy and personalized medicine - to demonstrate excellent cancer treatment and prevention in mice. I like how they used an established nanoparticle, the synthetic HDL particles - that are currently under investigation by CSL limited for preventing the recurrence of cardiovascular events. By doing this they avoid developing their own good manufacturing practices and safety profiles required for regulatory approval.

2. I’m excited to hear about the startup that the researchers formed for this product in 2016: EVOQ Therapeutics. They have a long pathway ahead of them with fundraising, pre-clinical efficacy and safety testing, and establishing their own GMP manufacturing methods. And that is just to get to first-in-human testing.

The company CSL demonstrated that HDL-ApoA1 particles have received positive results from a clinical trial on recurrence of cardiovascular events in a phase 2 clinical trial recently.

Competing financial interests

A patent application for nanodisc vaccines has been filed, with J.J.M., A.S. and R.K. as inventors, and J.J.M. and A.S. are co-founders of EVOQ Therapeutics, LLC., that develops the nanodisc technology for vaccine applications.

Found EVOQ Therapeutics in 2016.

Public funding for science is critical to the development of promising technologies and products. Highly targeted funding of areas of science, like what is being done in France with climate change, are integral in making rapid progress in those areas. The US has many programs similar to the one highlighted by France; such as the cancer moonshot seeking to make progress quicker on cancer prevention, detection and treatment; the BRAIN initiative seeking to treat, cure, and prevent brain disorders, the CRAN initiative focusing on addition; and the precision medicine initiative, among many other successful programs in the past. It may appear to be a significant win for science with the House of Representatives rejecting President Trump’s proposed 18% reduction in the NIH budget; However, the reality is that the new budget proposed by the house will only increase the NIH budget by 3.2%. My hope is that the minor increase in funding combined with the presidents vision of a more efficient and less wasteful government will lead to more innovations within the NIH framework. Here, it is important for the long term success of science and research public programs to place everything into context; such as the France initiative where they are creating this fund for climate change, but at the same time significantly reducing their overall science and research budget. So my final opinion is that it is great that the US House of representatives and the world supports scientific research, however, we need to continuously market and publicize scientific measures of success and why the scientific community affects the US and the global economy through these successes. This in turn will continue to build confidence in scientific funding.

After paralyzing spinal cord injury the adult nervous system has little ability to ‘heal’ spinal connections, and it is assumed to be unable to develop extra-spinal recovery strategies to bypass the lesion. We challenge this assumption, showing that completely spinalized adult rats can recover unassisted hindlimb weight support and locomotion without explicit spinal transmission of motor commands through the lesion. This is achieved with combinations of pharmacological and physical therapies that maximize cortical reorganization, inducing an expansion of trunk motor cortex and forepaw sensory cortex into the deafferented hindlimb cortex, associated with sprouting of corticospinal axons. Lesioning the reorganized cortex reverses the recovery. Adult rat scan thus develop a novel cortical sensorimotor circuit that bypasses the lesion, probably through biomechanical coupling, to partly recover unassisted hindlimb locomotion after complete spinal cord injury.

My takeaways:

1. This early basic research demonstrates a method for paralyzed individuals to recover function in their limbs following spinal cord injury.

eLife science, vol 6, e23532

Karen Moxon in the School of Biomedical Engineering at Drexel University and the Department of Biomedical Engineering at UC Davis

Her work was funded by the National Science Foundation, National Institute of Health, and Shriners Hospital for Children

Proteins fold into unique native structures stabilized by thousands of weak interactions that collectively overcome the entropic cost of folding. Although these forces are“encoded” in the thousands of known protein structures, “decoding” them is challenging because of the complexity of natural proteins that have evolved for function, not stability. We combined computational protein design, next-generation gene synthesis, and a high-throughput protease susceptibility assay to measure folding and stability for more than 15,000 de novo designed mini proteins, 1000 natural proteins, 10,000 point mutants, and 30,000 negative control sequences. This analysis identified more than 2500 stable designed proteins in four basic folds—a number sufficient to enable us to systematically examine how sequence determines folding and stability in uncharted protein space. Iteration between design and experiment increased the design success rate from 6% to 47%, produced stable proteins unlike those found in nature for topologies where design was initially unsuccessful, and revealed subtle contributions to stability as designs became increasingly optimized. Our approach achieves the long-standing goal of a tight feedback cycle between computation and experiment and has the potential to transform computational protein design into a data-driven science.

My takeaways:

1. This is the first successful case of researchers designing proteins in a rational method using data driven-science. Going through 4 iterations of design improvements, they were able to identify over 2500 sequences of stable protein assemblies with 4 unique structures. For reference, for a 44 amino acid protein, the total number of possible sequences is 1 with 57 zeros after it.

2. The knowledge gained by the technique they developed is going to be critical to designing therapeutic formulations for various diseases. Additionally, the methods they developed and knowledge gained on the impact of protein structure on stability will allow scientists the ability to create more stable proteins for a wide array of applications in medicine, electronics, sensing, energy, and more.

3. This type of protein design is really only possible with the help of their Hyak Supercomputer at the University of Washington. This means that while the methods they developed are an important first step, there are still many hurdles to designing functional proteins.

Science 2017, Vol 357, p 168-175

David Baker from Department of Biochemistry and Institute for Protein Design at the University of Washington

Funding is from Howard Hughes Medical Institute

The development of methods for the 3D printing of multifunctional devices could impact areas ranging from wearable electronics and energy harvesting devices to smart prosthetics and human–machine interfaces. Recently, the development of stretchable electronic devices has accelerated, concomitant with advances in functional materials and fabrication processes. In particular, novel strategies have been developed to enable the intimate biointegration of wearable electronic devices with human skin in ways that bypass the mechanical and thermal restrictions of traditional microfabrication technologies. Here, a multimaterial, multiscale, and multifunctional 3D printing approach is employed to fabricate 3D tactile sensors under ambient conditions conformally onto freeform surfaces. The customized sensor is demonstrated with the capabilities of detecting and differentiating human movements including pulse monitoring and finger motions. The custom 3D printing of functional materials and devices opens new routes for the biointegration of various sensors in wearable electronics systems, and toward advanced bionic skin applications.

My takeaways:

1. The researchers build a functioning piezoelectric sensor on a flexible substrate. The novelty is in the ink formulations and manufacturing methods they used to create these sensitive materials.

2. The future potential of this material is exciting because of how it can be adopted to areas including artificial skin and wearable devices able to track a variety of biomarkers. For example, I am developing glucose sensors that could easily be incorporated into the sensing layer of this flexible electronic for non-invasive glucose sensing in sweat.

Advanced Materials, 2017, vol 29, 1701218

Michael McAlpine from the Department of Mechanical Engineering at the University of Minnesota

Funding is through NIH (NIBIB)

Bacteria can be engineered to function as diagnostics or therapeutics in the mammalian gut but commercial translation of technologies to accomplish this has been hindered by the susceptibility of synthetic genetic circuits to mutation and unpredictable function during extended gut colonization. Here, we report stable, engineered bacterial strains that maintain their function for 6 months in the mouse gut. We engineered a commensal murine Escherichia coli strain to detect tetrathionate, which is produced during inflammation. Using our engineered diagnostic strain, which retains memory of exposure in the gut for analysis by fecal testing, we detected tetrathionate in both infection-induced and genetic mouse models of inflammation over 6 months. The synthetic genetic circuits in the engineered strain were genetically stable and functioned as intended overtime. The durable performance of these strains confirms the potential of engineered bacteria as living diagnostics.

My takeaways:

1. We are all aware of the growing impact that having and maintaining a healthy gut microbiome can have a person’s overall health. The results presented here are exciting because of the potential to engineer bacteria to both non-invasively track a disease, but also the potential to engineer bacteria to treat various diseases.

2. The exciting finding, while preliminary, is that these researcher found a way to get engineered bacterial to colonize in the gut and remain there for over 6 months. This is the major breakthrough in this paper.

Nature Biotechnology, 2017, Vol 35, p 653-658

Pamela Silver from the Department of Systems Biology in Harvard Medical School and the Wyss Institute for Biologically Inspired Engineering at Harvard University

Her work is supported by the NIH

The Trump administration has not built up their Office of Science and Technology Policy (OSTP) after taking over 6 months ago. It currently has 35 staffers with no defined leadership. The previous administration anticipated this sluggishness and According to previous Director of OSTP, John Holdren, says the plunge in staff levels is normal during a presidential transition. “But what’s shocking is that, this far into the new administration, the numbers haven’t gone back up”. "Holdren says his staff - substantially larger than OSTP’s under Bush and twice its previous peak under former President Bill Clinton - reflected Obama’s desire to elevate science and technology in his administration. “The president was so interested in knowing what science could do to advance his agenda, be it on economic recovery, energy and climate change, or national security,” Holdren says. In contrast, Holdren says, “right now I think OSTP is just hanging on.””

My opinion as a scientist is that it saddens me that the priority of this administration is to cut the budgets of scientists across all disciplines and research development level (basic vs applied). I think that advancements in science and technology have been and will be the greatest drivers of US economic success in the future years and decades to come. The hardest part for short term politicians is that science and technology progress takes a lot of time, often spanning multiple administrations from the tops of the government down to mayors of cities.

Inflammatory bowel diseases are chronic gastrointestinal inflammatory disorders that affect millions of people worldwide.Genome-wide association studies have identified 200 inflammatory bowel disease-associated loci, but few have been conclusively resolved to specific functional variants. Here we report fine-mapping of 94 inflammatory bowel disease loci using high-density genotyping in 67,852 individuals. We pinpoint 18 associations to a single causal variant with greater than 95% certainty, and an additional 27 associations to a single variant with greater than 50% certainty. These45 variants are significantly enriched for protein-coding changes (n = 13), direct disruption of transcription-factor binding sites (n = 3), and tissue-specific epigenetic marks (n = 10), with the last category showing enrichment in specific immune cells among associations stronger in Crohn’s disease and in gut mucosa among associations stronger in ulcerative colitis. The results of this study suggest that high-resolution fine-mapping in large samples can convert many discoveries from genome-wide association studies into statistically convincing causal variants, providing a powerful substrate for experimental elucidation of disease mechanisms.

Extended daytime and nighttime activities are major contributors to the growing sleep deficiency epidemic, as is the high prevalence of sleep disorders like insomnia. The consequences of chronic insufficient sleep for health remain uncertain. Sleep quality and duration predict presence of pain the next day in healthy subjects, suggesting that sleep disturbances alone may worsen pain, and experimental sleep deprivation in humans supports this claim. We demonstrate that sleep loss, but not sleep fragmentation, in healthy mice increases sensitivity to noxious stimuli (referred to as ‘pain’)without general sensory hyper-responsiveness. Moderate daily repeated sleep loss leads to a progressive accumulation of sleep debt and also to exaggerated pain responses, both of which are rescued after restoration of normal sleep. Caffeine and modafinil, two wake promoting agents that have no analgesic activity in rested mice, immediately normalize pain sensitivity in sleep-deprived animals, without affecting sleep debt The reversibility of mild sleep-loss-induced pain by wake-promoting agents reveals an unsuspected role for alertness insetting pain sensitivity. Clinically, insufficient or poor-quality sleep may worsen pain and this enhanced pain may be reduced not by analgesics, whose effectiveness is reduced, but by increasing alertness or providing better sleep.