Adam Marblestone

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Measuring Cation Dependent DNA Polymerase Fidelity Landscapes by Deep Sequencing

PLoS One Jan

High-throughput recording of signals embedded within inaccessible micro-environments is a technological challenge. The ideal recording device would be a nanoscale machine capable of quantitatively transducing a wide range of variables into a molecular recording medium suitable for long-term storage and facile readout in the form of digital data. We have recently proposed such a device, in which cation concentrations modulate the misincorporation rate of a DNA polymerase (DNAP) on a known template, allowing DNA sequences to encode information about the local cation concentration. In this work we quantify the cation sensitivity of DNAP misincorporation rates, making possible the indirect readout of cation concentration by DNA sequencing. Usin

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Designing Tools for Assumption-Proof Brain Mapping

NEURON Sep

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Conneconomics: the economics of large-scale neural connectomics

BioRXiv Dec

We analyze the scaling and cost-performance characteristics of current and projected connectomics approaches, with reference to the potential implications of recent advances in diverse contributing fields. Three generalized strategies for dense connectivity mapping at the scale of whole mammalian brains are considered: electron microscopic axon tracing, optical imaging of combinatorial molecular markers at synapses, and bulk DNA sequencing of trans-synaptically exchanged nucleic acid barcode pairs. Due to advances in parallel-beam instrumentation, whole mouse brain electron microscopic image acquisition could cost less than $100 million, with total costs presently limited by image analysis to trace axons through large image stacks. Optical

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Highly Multiplexed Subcellular RNA Sequencing in Situ

Science Feb

Understanding the spatial organization of gene expression with single-nucleotide resolution requires localizing the sequences of expressed RNA transcripts within a cell in situ. Here, we describe fluorescent in situ RNA sequencing (FISSEQ), in which stably cross-linked cDNA amplicons are sequenced within a biological sample. Using 30-base reads from 8742 genes in situ, we examined RNA expression and localization in human primary fibroblasts with a simulated wound-healing assay. FISSEQ is compatible with tissue sections and whole-mount embryos and reduces the limitations of optical resolution and noisy signals on single-molecule detection. Our platform enables massively parallel detection of genetic elements, including gene transcripts and m

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The Atoms of Neural Computation

Science Oct

The human cerebral cortex is central to a wide array of cognitive functions, from vision to language, reasoning, decision-making, and motor control. Yet, nearly a century after the neuroanatomical organization of the cortex was first defined, its basic logic remains unknown. One hypothesis is that cortical neurons form a single, massively repeated “canonical” circuit, characterized as a kind of a “nonlinear spatiotemporal filter with adaptive properties” (1). In this classic view, it was “assumed that these…properties are identical for all neocortical areas.” Nearly four decades later, there is still no consensus about whether such a canonical circuit exists, either in terms of its anatomical basis or its function. Likewise, there is little

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Rapid Prototyping of 3D DNA Origami Nanostructure with caDNAno

Nucleic Acids Research Jan

DNA nanotechnology exploits the programmable specificity afforded by base-pairing to produce self-assembling macromolecular objects of custom shape. For building megadalton-scale DNA nanostructures, a long ‘scaffold’ strand can be employed to template the assembly of hundreds of oligonucleotide ‘staple’ strands into a planar antiparallel array of cross-linked helices. We recently adapted this ‘scaffolded DNA origami’ method to producing 3D shapes formed as pleated layers of double helices constrained to a honeycomb lattice. However, completing the required design steps can be cumbersome and time-consuming. Here we present caDNAno, an open-source software package with a graphical user interface that aids in the design of DNA sequences for fo

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Rosetta Brains: A Strategy for Molecularly Annotated Connectomics

ArXiv Apr

We propose a neural connectomics strategy called Fluorescent In-Situ Sequencing of Barcoded Individual Neuronal Connections (FISSEQ-BOINC), leveraging fluorescent in situ nucleic acid sequencing in fixed tissue (FISSEQ). FISSEQ-BOINC exhibits different properties from BOINC, which relies on bulk nucleic acid sequencing. FISSEQ-BOINC could become a scalable approach for mapping whole-mammalian-brain connectomes with rich molecular annotations.

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Statistical Analysis of Molecular Signal Recording

PLoS Computational Biology Jul

Recording of physiological signals from inaccessible microenvironments is often hampered by the macroscopic sizes of current recording devices. A signal-recording device constructed on a molecular scale could advance biology by enabling the simultaneous recording from millions or billions of cells. We recently proposed a molecular device for recording time-varying ion concentration signals: DNA polymerases (DNAPs) copy known template DNA strands with an error rate dependent on the local ion concentration. The resulting DNA polymers could then be sequenced, and with the help of statistical techniques, used to estimate the time-varying ion concentration signal experienced by the polymerase. We develop a statistical framework to treat this inv

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Signal-to-pump back action and self-oscillation in double-pump Josephson parametric amplifier

Physical Review B

We present the theory of a Josephson parametric amplifier employing two-pump sources. Our calculations are based on input-output theory, and can easily be generalized to any coupled system involving parametric interactions. We analyze the operation of the device, taking into account the feedback introduced by the reaction of the signal and noise on the pump power, and in this framework, compute the response functions of interest—signal and idler gains, internal gain of the amplifier, and self-oscillation signal amplitude. To account for this back action between signal and pump, we adopt a mean-field approach and self-consistently explore the boundary between amplification and self-oscillation. The coincidence of bifurcation and self-oscilla

Multiplexed Neural Recording Down a Single Optical Fiber via Optical Reflectometry with Capacitive Signal Enhancement

arXiv

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Frequently Asked Questions for: The Atoms of Neural Computation

ArXiv Oct

Based on a survey of the literature, we attempt to answer Frequently Asked Questions on issues of cortical uniformity vs. non-uniformity, the neural mechanisms of symbolic variable binding, and other issues highlighted in (Marcus, Marblestone and Dean. "The Atoms of Neural Computation". Science. 31 October 2014. Vol 346. Issue 6209).

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Exponential Quantum Enhancement for Distributed Addition with Local Nonlinearity

Quantum Information Processing Jan

We consider classical and entanglement-assisted versions of a distributed computation scheme that computes nonlinear Boolean functions of a set of input bits supplied by separated parties. Communication between the parties is restricted to take place through a specific apparatus which enforces the constraints that all nonlinear, nonlocal classical logic is performed by a single receiver, and that all communication occurs through a limited number of one-bit channels. In the entanglement-assisted version, the number of channels required to compute a Boolean function of fixed nonlinearity can become exponentially smaller than in the classical version. We demonstrate this exponential enhancement for the problem of distributed integer addition.

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Multiplexed in vivo his-tagging of enzyme pathways for in vitro single-pot multienzyme catalysis

ACS synthetic biology

Protein pathways are dynamic and highly coordinated spatially and temporally, capable of performing a diverse range of complex chemistries and enzymatic reactions with precision and at high efficiency. Biotechnology aims to harvest these natural systems to construct more advanced in vitro reactions, capable of new chemistries and operating at high yield. Here, we present an efficient Multiplex Automated Genome Engineering (MAGE) strategy to simultaneously modify and co-purify large protein complexes and pathways from the model organism Escherichia coli to reconstitute functional synthetic proteomes in vitro. By application of over 110 MAGE cycles, we successfully inserted hexa-histidine sequences into 38 essential genes in vivo that encode

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Gene Assembly from Chip-Synthesized Oligonucleotides

Current Protocols in Chemical Biology

De novo synthesis of long double-stranded DNA constructs has a myriad of applications in
biology and biological engineering. However, its widespread adoption has been hindered
by high costs. Cost can be significantly reduced by using oligonucleotides synthesized
on high-density DNA chips. However, most methods for using off-chip DNA for gene
synthesis have failed to scale due to the high error rates, low yields, and high chemical
complexity of the chip-synthesized oligonucleotides. We have recently demonstrated
that some commercial DNA chip manufacturers have improved error rates, and that the
issues of chemical complexity and low yields can be solved by using barcoded primers
to accurately and effici

Molecular Threading: Mechanical Extraction, Stretching and Placement of DNA Molecules from a Liquid-Air Interface

PLOS ONE

We present “molecular threading”, a surface independent tip-based method for stretching and depositing single and double-stranded DNA molecules. DNA is stretched into air at a liquid-air interface, and can be subsequently deposited onto a dry substrate isolated from solution. The design of an apparatus used for molecular threading is presented, and fluorescence and electron microscopies are used to characterize the angular distribution, straightness, and reproducibility of stretched DNA deposited in arrays onto elastomeric surfaces and thin membranes. Molecular threading demonstrates high straightness and uniformity over length scales from nanometers to micrometers, and represents an alternative to existing DNA deposition and linearization

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Physical Principles for Scalable Neural Recording

Frontiers in Computational Neuroscience Jun

Adam H. Marblestone●, Bradley M. Zamft●, Yael G. Maguire, Mikhail G. Shapiro, Thaddeus R. Cybulski, Joshua I. Glaser, Ben Stranges, Reza Kalhor, David A. Dalrymple, Dongjin Seo, Elad Alon, Michel M. Maharbiz, Jose Carmena, Jan Rabaey, Edward S. Boyden●●, George M. Church●●, Konrad P. Kording●●

Simultaneously measuring the activities of all neurons in a mammalian brain at millisecond resolution is a challenge beyond the limits of existing techniques in neuroscience. Entirely new approaches may be required, motivating an analysis of the fundamental physical constraints on the problem. We outline the physical principles governing brain activity mapping using optical, electrical,magnetic resonance, and molecular modalities of neural

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Adam Marblestone

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