23 papers · ranked by Valyu relevance
Graham Bell
The authors of this paper were interested to see whether the expression of three proteins (A, B and C) was altered in a knockout mouse model of a gene encoding Protein X. Each experiment measured the expression of a different protein and the results seem to show a clear increase in protein expression in the mutant…
Yajie Yang, Justin Fear, Jianhong Hu, Irina Haecker + 4 more
'Rolf Renne' 'David Bloom' 'Lauren M McIntyre'] ChIP-seq experiments identify genome-wide profiles of DNA-binding molecules including transcription factors, enzymes and epigenetic marks. Biological replicates are critical for reliable site discovery and are required for the deposition of data in the ENCODE and…
Pedro A. Peres, Heather Bracken-Grissom
The pelagic deep sea is challenging to investigate due to logistical constraints regarding access and collection of samples, however environmental DNA (eDNA) can potentially revolutionize our understanding of this ecosystem. Although advancements are being made regarding technology and eDNA samplers, many countries and…
Jie Xue, Xinfan Zhou, Jing Yang, Adan Niu + 1 more
Single-cell RNA sequencing (scRNA-seq) is a high-throughput experimental technique for studying gene expression at the single-cell level. As a key component of single-cell data analysis, differential expression analysis (DEA) serves as the foundation for all subsequent secondary studies. Despite the fact that…
Jamie Irvine, Jigyasa Arora, Jonathan N.V. Martinson, Jaymin R. Patel + 3 more
While generative artificial intelligence has shown promise for biological design, no computational system has yet created sequences proven capable of replication. Focusing on plasmids as minimal replicating systems, we develop OriGen, a language model that generates novel plasmid origins of replication while…
Scott Federhen
There is a striking visual symmetry between the 'paradoxical combinator' (which implements recursion in the mathematical theory of computation) and the biological replication fork (which implements reproduction in the living cell). Can this mean anything? Living organisms are information processors – the genome encodes…
Mio Yumura, Natsuko Yamamoto, Katsushi Yokoyama, Hirotada Mori + 3 more
'Tetsuya Yomo' 'Norikazu Ichihashi' 'Sukesh R. Bhaumik'] Construction of a complex artificial self-replication system is challenging in the field of in vitro synthetic biology. Recently, we developed a translation-coupled RNA replication system, wherein an artificial genomic RNA replicates with the Qβ RNA replicase…
Lorenzo Olivi, Mareike Berger, Ramon N. P. Creyghton, Nicola De Franceschi + 5 more
'Nicola De Franceschi' 'Cees Dekker' 'Bela M. Mulder' 'Nico J. Claassens' 'Pieter Rein ten Wolde' 'John van der Oost'] Recent developments in synthetic biology may bring the bottom-up generation of a synthetic cell within reach. A key feature of a living synthetic cell is a functional cell cycle, in which DNA…
Steve Minchin, Julia Lodge
Nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), carry genetic information which is read in cells to make the RNA and proteins by which living things function. The well-known structure of the DNA double helix allows this information to be copied and passed on to the next generation. In this…
Amit Kahana, Lior Segev, Doron Lancet
The origin of life must have involved an unlikely transition from chaotic chemistry to reproducing supramolecular structures. Previous quantitative analyses of reproducing mutually catalytic networks made of simple molecules have led to increasing popularity of this pre-RNA scenario for life’s origin. Here, we…
Atsushi Kamimura, Yoshiya J. Matsubara, Kunihiko Kaneko, Nobuto Takeuchi
'Nobuto Takeuchi'] 1 Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo 153-8902 Japan 2 Research Center for Complex Systems Biology, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo 153-8902 Japan 3…
Guanzhong Zhai, Pantelitsa Dimitriou, Jason Sengel, Mark Ian Wallace
A defining feature of living cells is their ability to self-replicate; but creating artificial cells with this capability remains challenging, due to the complexity of biological division machinery. Rather than seeking to reconstitute this machinery, here we take direct control of DNA replication and compartment…
Antony M Jose
Living systems transmit heritable information using the replicating gene sequences and the cycling regulators assembled around gene sequences. Here I develop a framework for heredity and development that includes the cycling regulators parsed in terms of what an organism can sense about itself and its environment by…
A. S. Bratus, S. Drozhzhin, T. Yakushkina
This chapter is an overview of foundational results in the mathematical theory of replicator systems. Its primary aim is to provide a unified framework for the mathematical formalisation of evolutionary processes in the spirit of generalised Darwinism -- that is, for any system in which heredity, variability, and…
Authors not listed
Self-organizing tissues, such as organoids, offer transformative potential beyond healthcare by enabling the sustainable production of advanced materials. Resource scarcity and global warming drive the need for innovative fabrication solutions. This prospective review explores developmental biology as a manufacturing…
Atsushi Kamimura, Kunihiko Kaneko
All life, including cells and artificial protocells, must integrate diverse molecules into a single unit in order to reproduce. Despite expected pressure to evolve a simple system with the fastest replication speed, the mechanism by which the use of the great variety of components, and the coexistence of diverse…
Dzmitry G. Batrakou, Emma D. Heron, Conrad A. Nieduszynski
Genomes are replicated in a reproducible temporal pattern. Current methods for assaying allele replication timing are time consuming and/or expensive. These include high-throughput sequencing which can be used to measure DNA copy number as a proxy for allele replication timing. Here, we use droplet digital PCR to study…
Nobuto Takeuchi, Kunihiko Kaneko
The Central Dogma of molecular biology, as originally proposed by Crick, asserts that information passed into protein cannot flow back out. This principle has been interpreted as underpinning modern understandings of heredity and evolution, implying the unidirectionality of information flow from nucleic acids to…
Sonja J. Messerschmidt, Daniel Schindler, Celine M. Zumkeller, Franziska S. Kemter + 2 more
'Franziska S. Kemter' 'Nadine Schallopp' 'Torsten Waldminghaus'] Learning by building is one of the core ideas of synthetic biology research. Consequently, building synthetic chromosomes is the way to fully understand chromosome characteristics. The last years have seen exciting synthetic chromosome studies. We had…
Anna Matuszyńska, Oliver Ebenhöh, Matias D. Zurbriggen, Daniel C. Ducat + 1 more
Synthetic biology designs and constructs new biological parts, devices and systems with predetermined functionalities. With the unlimited ability to synthesise any DNA and RNA and transfer it to almost any organism, we are at the dawn of a new era in which biology is being recreated in ways never before possible. It…
Cheng Bi
The essence of life is a frequency distribution conversion process of molecules accompanied by changes in information. In wet-dry cycling hot springs, RNA of different sequences continuously undergoes polymerization and decomposition reactions, products with stable configurations will accumulate their frequency among…
Michel G. Gauthier, Antoine Dubé, John Bechhoefer
We present a calculation technique for modeling inhomogeneous DNA replication kinetics, where replication factors such as initiation rates or fork speeds can change with both position and time. We can use our model to simulate data sets obtained by molecular combing, a widely used experimental technique for probing…
Authors not listed
DNA polymerases are essential enzymes responsible for accurate genome replication and repair, with divalent metal cofactors playing a crucial role in their catalytic function. Polymerase gamma (Pol γ) is the primary DNA polymerase in mitochondria, ensuring the faithful replication of mitochondrial DNA. The choice of…