Tao, Terence. “What Is Good Mathematics?,” February 13, 2007. http://arxiv.org/abs/math/0702396.
Variations of this can also be applied to other fields, like history. What makes good history, good historians, good history teachers, etc.?
Tao, Terence. “What Is Good Mathematics?,” February 13, 2007. http://arxiv.org/abs/math/0702396.
Variations of this can also be applied to other fields, like history. What makes good history, good historians, good history teachers, etc.?
advances in prompt engineering1, agents2, retrieval-augmented generation (RAG)3, and fine-tuning4
LLM advances
Over the last 25 years, shotgun metagenomic sequencing1 and associated computational methods have developed as robust, efficient ways to study the taxonomic composition
Read to figure out benefits compared to marker genes profiling such as 16S?
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comment / summary
epiphany
triggering homologous recombination and creating genetic instability10,11,12,13
approaches, which typically encapsulate bacteria in hydrogels, have produced deployable optical sensors for explosives14, heavy metals15 and chemical inducers16,17
current state-of-the-art whole-cell biosensors for field applications34,35, such as hydrogel-based20,36 and liquid-in-a-cartridge devices37
Translocation to a cell’s surface utilizes a signal peptide (for inner membrane translocation) and AIDAc as an outer membrane autotransporter pore
AHL communication modules with functional devices built from the biological components of the las18, tra18, rpa18, rhl19, cin19 and esa20 quorum-sensing systems
programming environmental microbes have been applied to a wide range of organisms. Some examples of newly-programmable microbes include
good citations of engineering non-model organisms
To date, serine integrases have not been used extensively in plant systems
although they have been shown to work in principle in Arabidopsis23, Nicotiana benthamiana2421, barley25 and wheat26
A survey of 230 diverse bacterial and archaeal genomes found evidence of DNA methylation in 93% of genomes, with a diverse array of methylated motifs (834 distinct motifs; average of three motifs per organism)
conjugative plasmids have broad-host ranges23, are resistant to restriction-modification systems24, are easy to engineer with large coding capacities25, and do not require a cellular receptor26 that would provide a facile mechanism for bacterial resistance.
Bacterial cells are typically one thousandth the volume of mammalian cells, which places them near the edge of instrument detection. At this size it can be challenging to differentiate viable cells from debris of similar size
Detailed descriptions, assumptions, limitations and test cases of many popular statistical methods for ecological research can be found in the GUSTAME server (Buttigieg and Ramette, 2014), and in the review by Paliy and Shankar (2016).
condensing the information into two- or three-dimensional spaces. A very good overview of techniques to achieve this was written by Paliy and Shankar (2016).
There are several widely used tool collections, e.g., QIIME 2 [13], mothur [14], usearch [15], and vsearch [16], and 1-stop pipelines, e.g., LotuS [17], with new approaches continually being developed, e.g., OCToPUS [18] and PEMA [19]
Recently, redox-responsive biomolecules such as phenazines have been used in several electrochemical strategies to interrogate a range of biological activities30,31 and to control gene expression in living cells32,33, where the redox status of the biomolecules could be measured or manipulated by application of electronic potentials
cellular data recorders offer the capacity to measure biologically relevant signals15,16,17,18,19 in places that are otherwise difficult to access, such as inside the body20,21, and over time22