Issues with data reuse have been recognized in synthetic biology and the broader scientific community. Policies and standards fall short as machine reasoning is not emphasised and enforcement is ...lacking. We discuss the progress, remaining challenges, and possible solutions.
The mammalian ionotropic glutamate receptor family encodes 18 gene products that coassemble to form ligand-gated ion channels containing an agonist recognition site, a transmembrane ion permeation ...pathway, and gating elements that couple agonist-induced conformational changes to the opening or closing of the permeation pore. Glutamate receptors mediate fast excitatory synaptic transmission in the central nervous system and are localized on neuronal and non-neuronal cells. These receptors regulate a broad spectrum of processes in the brain, spinal cord, retina, and peripheral nervous system. Glutamate receptors are postulated to play important roles in numerous neurological diseases and have attracted intense scrutiny. The description of glutamate receptor structure, including its transmembrane elements, reveals a complex assembly of multiple semiautonomous extracellular domains linked to a pore-forming element with striking resemblance to an inverted potassium channel. In this review we discuss International Union of Basic and Clinical Pharmacology glutamate receptor nomenclature, structure, assembly, accessory subunits, interacting proteins, gene expression and translation, post-translational modifications, agonist and antagonist pharmacology, allosteric modulation, mechanisms of gating and permeation, roles in normal physiological function, as well as the potential therapeutic use of pharmacological agents acting at glutamate receptors.
Synthetic biology (SynBio) is a field at the intersection of biology and engineering. Inspired by engineering principles, researchers use defined parts to build functionally defined biological ...circuits. Genetic design automation (GDA) allows scientists to design, model, and analyze their genetic circuits in silico before building them in the lab, saving time, and resources in the process. Establishing SynBio’s future is dependent on GDA, since the computational approach opens the field to a broad, interdisciplinary community. However, challenges with part libraries, standards, and software tools are currently stalling progress in the field. This review first covers recent advancements in GDA, followed by an assessment of the challenges ahead, and a proposed automated genetic design workflow for the future.
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•Synthetic biology aims to apply engineering principles in biology.•Insufficient part libraries, standards, and software are challenges to the field.•Working on the challenges will move genetic design automation forward.•Goal is a fully automated workflow for design, build, and test of genetic circuits.
Cells interact with their environment, communicate among themselves, track time and make decisions through functions controlled by natural regulatory genetic circuits consisting of interacting ...biological components. Synthetic programmable circuits used in therapeutics and other applications can be automatically designed by computer-aided tools. The Cello software designs the DNA sequences for programmable circuits based on a high-level software description and a library of characterized DNA parts representing Boolean logic gates. This process allows for design specification reuse, modular DNA part library curation and formalized circuit transformations based on experimental data. This protocol describes Cello 2.0, a freely available cross-platform software written in Java. Cello 2.0 enables flexible descriptions of the logic gates' structure and their mathematical models representing dynamic behavior, new formal rules for describing the placement of gates in a genome, a new graphical user interface, support for Verilog 2005 syntax and a connection to the SynBioHub parts repository software environment. Collectively, these features expand Cello's capabilities beyond Escherichia coli plasmids to new organisms and broader genetic contexts, including the genome. Designing circuits with Cello 2.0 produces an abstract Boolean network from a Verilog file, assigns biological parts to each node in the Boolean network, constructs a DNA sequence and generates highly structured and annotated sequence representations suitable for downstream processing and fabrication, respectively. The result is a sequence implementing the specified Boolean function in the organism and predictions of circuit performance. Depending on the size of the design space and users' expertise, jobs may take minutes or hours to complete.
Objective: Recent advancements demonstrate the significant role of digital microfluidics in automating laboratory work with DNA and on-site viral testing. However, since commercially available ...instruments are limited to droplet manipulation, our work addresses the need for accelerated integration of other components, such as temperature control, that can expand the application domain. Methods: We developed PhageBox- an accessible device that can be used as a biochip extension. At hardware level, PhageBox integrates temperature and electromagnetic control modules. At software level, PhageBox is controlled by embedded software containing a unique model for bio-protocol programming, and a graphical user interface for visual device feedback and operation. Results: To evaluate PhageBox's efficacy for biomedical applications, we performed functional testing. Similarly, we validated the temperature control using thermography, obtaining a range of <inline-formula><tex-math notation="LaTeX">\pm</tex-math></inline-formula> 0.2 <inline-formula><tex-math notation="LaTeX">^\circ C</tex-math></inline-formula> . The electromagnets produced a magnetic force of 15 milliTesla, demonstrating precise immobilization of magnetic beads. We show the potential of PhageBox for bacteriophage research through three initial protocols: a universal framework for PCR, T7 bacteriophage restriction enzyme digestion, and concentrating <inline-formula><tex-math notation="LaTeX">\phi X174</tex-math></inline-formula> RF genomic DNA. Conclusion: Our work presents an open-source hardware and software extension for digital microfluidics devices. This extension integrates temperature and electromagnetic modules, demonstrating efficacy in biomedical applications and potential for bacteriophage research. Significance: We developed PhageBox to be accessible: the components are off-the-shelf at a low cost (<inline-formula><tex-math notation="LaTeX">\leq</tex-math></inline-formula>200), and the hardware designs and software code are open-source. With the long aim of ensuring reproducibility and accelerating collaboration, we also provide a DIY-build document. ( GitHub : https://github.com/Dreycey/PhageBox )
The ability to search for a part by its sequence is crucial for a large repository of parts. Prior to this work, however, this was not possible on SynBioHub. Sequence-based search is now integrated ...into SynBioHub, allowing users to find a part by a sequence provided in plain text or a supported file format. This sequence-based search feature is accessible to users via SynBioHub's web interface, or programmatically through its API. The core implementation of the tool uses VSEARCH, an open source, global alignment search tool, and it is integrated into SBOLExplorer, an open source distributed search engine used by SynBioHub. We present a new approach to scoring part similarity using SBOLExplorer, which takes into account both the popularity and percentage match of parts.
Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for ...representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Release 2 of Version 2 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. Release 2 corrects some errors and clarifies some ambiguities discovered in Release 1. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project website at http://sbml.org/.
Hexanucleotide expansions in C9ORF72 are the most frequent genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia. Disease mechanisms were evaluated in mice expressing C9ORF72 ...RNAs with up to 450 GGGGCC repeats or with one or both C9orf72 alleles inactivated. Chronic 50% reduction of C9ORF72 did not provoke disease, while its absence produced splenomegaly, enlarged lymph nodes, and mild social interaction deficits, but not motor dysfunction. Hexanucleotide expansions caused age-, repeat-length-, and expression-level-dependent accumulation of RNA foci and dipeptide-repeat proteins synthesized by AUG-independent translation, accompanied by loss of hippocampal neurons, increased anxiety, and impaired cognitive function. Single-dose injection of antisense oligonucleotides (ASOs) that target repeat-containing RNAs but preserve levels of mRNAs encoding C9ORF72 produced sustained reductions in RNA foci and dipeptide-repeat proteins, and ameliorated behavioral deficits. These efforts identify gain of toxicity as a central disease mechanism caused by repeat-expanded C9ORF72 and establish the feasibility of ASO-mediated therapy.
•C9ORF72 repeat expansions cause age-, repeat-size-, and expression-dependent toxicity•Acquired toxicity, not loss of function, is a major contributor to C9orf72 disease•Absence of C9ORF72 in mice produces splenomegaly and enlarged cervical lymph nodes•ASO-induced decreases in repeat RNA mitigate C9ORF72-associated phenotypes in vivo
Hexanucleotide expansions in C9ORF72 are the most frequent genetic cause of ALS and FTD. Jiang et al. establish gain of toxicity from repeat-containing RNA, and not loss of C9ORF72 function, as a central disease mechanism and establish the feasibility of ASO-mediated therapy.
Information is the cornerstone of research, from experimental (meta)data and computational processes to complex inventories of reagents and equipment. These 10 simple rules discuss best practices for ...leveraging laboratory information management systems to transform this large information load into useful scientific findings.
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