2016/2017 Recipients

Integrating mini-­arrays of low-­cost accelerometers in earthquake early warning systems

Richard Allen, Department of Earth and Planetary Science, UC Berkeley
Alon Ziv, Department of Geosciences, Tel Aviv University

Current Earthquake Early Warning Systems (EEWS) acquire data with networks of single seismic stations, and compute source parameters assuming earthquakes to be point sources. For large events, the point-­source assumption leads to an underestimation of magnitude, and the use of single stations leads to large uncertainties in the locations of event outside the network. We propose to test the use of mini-­arrays -­ a cluster of seismic stations in a small area -­ to improve earthquake early warning systems. Mini-­arrays could: (a) estimate reliable hypocentral locations by beam forming (FK-­analysis) techniques;; (b) characterize the rupture dimensions and account for finite-­source effects, leading to reliable estimates for large magnitudes. Previously the high cost of multiple sensors has been inhibitive. However, we propose to setup mini-­arrays of a new low-­cost (<$150) high-­performance MEMS accelerometers around conventional seismic stations and test their performance for EEWS. We will assess the benefits of such mini-­arrays for real-­time location and magnitude determination. The expected benefits of such an approach include improving real-­time shaking predictions and mitigating false alarms. This research program was developed during a workshop held in Berkeley (September 2015) with TAU and UCB research groups. It merges and extends the expertise of both research groups: TAU uses its array of mini-­arrays to monitor earthquakes and to develop array-­based location algorithms, UCB has developed EEWS algorithms and is testing these algorithms around the world.

Illuminating microbial dark matter with a pinch of salt - towards the first cultivation of Nanohaloarchaea

Jillian Banfield, Departments of Earth and Planetary Science, and Environmental Science, Policy and Management, UC Berkeley
Uri Gophna, Department of Molecular Microbiology and Biotechnology, Tel Aviv University

A major challenge in microbiology is to understand the ecology and physiology of organisms that cannot be grown in culture. Recent metagenomics-based studies has shown that uncultivated lineages commonly known as "microbial dark matter", represent a large fraction of earth's biodiversity. In particular, multiple diverse groups composed exclusively of very small cells with very small genomes have remained almost totally unexplored and their ecological roles await discovery. Here we propose to combine the strength of the Banfield lab (UCB) in metagenomics and the Gophna lab's (TAU) expertise in microbiology of halophilic archaea and growth media prediction, to isolate and characterize the first representatives of a large uncultured archaeal group - the nano-haloarchaea (NH). We will achieve this goal by first identifying sampling sites where NH are abundant and obtaining their metagenomes. From these metagenomes we can obtain near-complete genomes of NH and reconstruct their metabolic pathways. These metagenomes will also help identify additional microorganisms that may interact with NH in symbiotic relationships. We will then design genome-guided growth media for cultivating NH based on the metabolic predictions and attempt to grow them in pure culture. As a complementary approach, we will identify their closest interaction partners by fluorescent in situ hybridization (FISH), and obtain co-cultures of NH and their symbionts. Once isolated we will characterize the physiology and biochemistry of NH cells and expect this to be a breakthrough in understanding the ecological role of microbial dark matter in the ecology of our planet.

Biomechanical determinants of stem cell asymmetric division

Irina Conboy, Department of Bioengineering, UC Berkeley
Ayelet Lesman, School of Mechanical Engineering, Tel Aviv University

When stem cells divide asymmetrically by cell fate, one daughter cell is a replacement stem while the other is fated to differentiate toward a particular cell lineage. One pole of the dividing cell physically touches a specific cell or tissue layer and the other orients away from this source of orientation, and the daughter cells of differing fate end up at opposite ends after cytokinesis (1). The daughter cells inherit different macromolecules: proteins, centrosomes and even epigenetically modified DNA of different age (2-5), and this is essential to establish the different fates of the daughters. This situation suggests that mechanical sensation of the extracellular matrix (ECM) regulate asymmetric fates of the daughter cells. We hypothesize that asymmetric divisions of mouse and human ESCs correlate with and are regulated by the asymmetric mechanical forces generated between cells and their environment. Furthermore, we suggest that mechanical changes of the microenvironment, which feed-back to control the cellular forces (6, 7, 8) influence the differentiation fate of the daughters. Such a mechanical feedback between asymmetrically dividing cells and their environment might be a key determinant in organ formation. Our collaborative teams will study how the forces applied by embryonic stem cells onto their surrounding environment correlate with the daughter cell fates. We will also evaluate the effect of matrices with asymmetric rigidity on mouse and human ESC asymmetric divisions. Our study will provide the first exploration of asymmetric bio-mechanical forces in regulating asymmetric divisions of pluripotent stem cells, leading to novel ways to control tissue and organ formation.

Context-dependent viral mutations as signatures of innate immune evasion

Rasmus Nielsen, Department of Integrative Biology, UC Berkeley
Adi Stern, Department of Molecular Microbiology and Biotechnology, Tel Aviv University

Viral genomes are often extremely compact, and revealing the factors that drive the composition of these genomes is central to understanding viral evolution. Surprisingly, substantial biases in nucleotide composition exist for many viruses. For example as shown herein, many viruses are strongly depleted of the dinucleotides CpG and UpA. This has led to the hypothesis that these dinucleotides trigger innate immune defenses, leading to strong selection against these dinucleotides in the viral genome. Here we propose to develop a statistical framework in order to examine how the context of viral polymorphisms affects their presence in viral genomes. This framework will expand upon the dinucleotide context in order to determine whether enrichment or depletion of longer sequence signatures is driven by mutation or by selection. We will use this new framework to examine synonymous polymorphisms in a unique experimental system of polioviruses, where viral mutations can be directly observed as they arise. Results of this analysis will allow us to decipher the powerful arsenal of tools used by innate immunity to curb viral replication, potentially allowing enhanced vaccine design and novel therapeutic strategies.