Top 10 Biorxiv Papers Today in Synthetic Biology


2.023 Mikeys
#1. A model for the spatio-temporal design of gene regulatory circuits
Ruud Stoof, Alexander Wood, Angel Goni-Moreno
The design of increasingly complex gene regulatory networks relies upon mathematical modelling to link the gap that goes from conceptualisation to implementation. An overarching challenge is to update modelling abstractions and assumptions as new mechanistic information arises. Although models of bacterial gene regulation are often based on the assumption that the role played by intracellular physical distances between genetic elements is negligible, it has been shown that bacteria are highly ordered organisms, compartmentalizing their vital functions in both time and space. Here, we analysed the dynamical properties of regulatory interactions by explicitly modelling spatial constraints. Key to the model is the combined search by a regulator for its target promoter via 1D sliding along the chromosome and 3D diffusion through the cytoplasm. Moreover, this search was coupled to gene expression dynamics, with special attention to transcription factor-promoter interplay. As a result, promoter activity within the model depends on its...
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Alexis_Verger: #365papers 1⃣8⃣ A model for the spatio-temporal design of gene regulatory circuits by @ruud_stoof and coll https://t.co/aDjKNbpNM7 https://t.co/1ADgVRw2J8
SynBio3D: Highlights of our latest preprint 👇 https://t.co/SVZoR9kQBn
_BiotechWatcher: A model for the spatio-temporal design of gene regulatory circuits | bioRxiv https://t.co/q5QoE6Jlju, see more https://t.co/zOIpwYL5Ef
vdlorenzo_CNB: RT @biorxivpreprint: A model for the spatio-temporal design of gene regulatory circuits https://t.co/0WdnOcKU0G #bioRxiv
jmarlesw: RT @SynBio3D: Highlights of our latest preprint 👇 https://t.co/SVZoR9kQBn
hsalis: RT @SynBio3D: Highlights of our latest preprint 👇 https://t.co/SVZoR9kQBn
jijzarco: RT @SynBio3D: Highlights of our latest preprint 👇 https://t.co/SVZoR9kQBn
claudiaevickers: RT @SynBio3D: Highlights of our latest preprint 👇 https://t.co/SVZoR9kQBn
AngelGMoreno: RT @SynBio3D: Highlights of our latest preprint 👇 https://t.co/SVZoR9kQBn
rintukutum: RT @biorxivpreprint: A model for the spatio-temporal design of gene regulatory circuits https://t.co/0WdnOcKU0G #bioRxiv
SynBio3D: RT @biorxivpreprint: A model for the spatio-temporal design of gene regulatory circuits https://t.co/0WdnOcKU0G #bioRxiv
ajfedorec: RT @biorxivpreprint: A model for the spatio-temporal design of gene regulatory circuits https://t.co/0WdnOcKU0G #bioRxiv
ajfedorec: RT @SynBio3D: Highlights of our latest preprint 👇 https://t.co/SVZoR9kQBn
faguilgen: RT @biorxivpreprint: A model for the spatio-temporal design of gene regulatory circuits https://t.co/0WdnOcKU0G #bioRxiv
fabsandroses: RT @biorxivpreprint: A model for the spatio-temporal design of gene regulatory circuits https://t.co/0WdnOcKU0G #bioRxiv
GoetschPhD: RT @biorxivpreprint: A model for the spatio-temporal design of gene regulatory circuits https://t.co/0WdnOcKU0G #bioRxiv
ruud_stoof: RT @SynBio3D: Highlights of our latest preprint 👇 https://t.co/SVZoR9kQBn
ZongyingY: RT @biorxivpreprint: A model for the spatio-temporal design of gene regulatory circuits https://t.co/0WdnOcKU0G #bioRxiv
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Authors: 3
Total Words: 9362
Unqiue Words: 2721

1.996 Mikeys
#2. Measuring amber initiator tRNA orthogonality in a genomically recoded organism
Russel M. Vincent, Bradley W. Wright, Paul R. Jaschke
Using engineered initiator tRNA for precise control of protein translation within cells has great promise within future orthogonal translation systems to decouple housekeeping protein metabolism from that of engineered genetic systems. Previously, E. coli strain C321.ΔA exp lacking all UAG stop codons was created, freeing this 'amber' stop codon for other purposes. An engineered 'amber initiator' tRNACUAfMet that activates translation at UAG codons is available, but little is known about this tRNA's orthogonality. Here, we combine for the first time the amber initiator tRNACUAfMet in C321.ΔA. exp and measure its cellular effects. We found that the tRNACUAfMet expression resulted in a nearly 200-fold increase in fluorescent reporter expression with a unimodal population distribution and no apparent cellular fitness defects. Proteomic analysis revealed upregulated ribosome-associated, tRNA degradation, and amino acid biosynthetic proteins, with no evidence for off-target translation initiation. In contrast to previous work, we show...
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Authors: 3
Total Words: 2183
Unqiue Words: 902

0.0 Mikeys
#3. Discovery and Characterization of Novel Lignocellulose-Degrading Enzymes from the Porcupine Microbiome by Synthetic Metagenomics
Mackenzie Thornbury, Jacob Sicheri, Patrick Slaine, Landon Getz, Emma Finlayson-Trick, Jamie Cook, Caroline Guinard, Nicholas Boudreau, David Jakeman, John Rohde, Craig McCormick
Plant cell walls are composed of cellulose, hemicellulose, and lignin, collectively known as lignocellulose. Microorganisms degrade lignocellulose to liberate sugars to meet metabolic demands. Using a metagenomic sequencing approach, we previously demonstrated that the microbiome of the North American porcupine (Erethizon dorsatum) is replete with lignocellulose-degrading enzymes. Here, we report the identification, synthesis and partial characterization of four novel genes from the porcupine microbiome encoding putative lignocellulose-degrading enzymes; β-glucosidase, α-L-arabinofuranosidase, β-xylosidase, and an endo-1,4-β-xylanase. These genes were identified via conserved catalytic domains associated with cellulose- and hemicellulose-degradation, and phylogenetic trees were created to depict relatedness to known enzymes. The candidate synthesized genes were cloned into the pET26b(+) plasmid to enable inducible expression in Escherichia coli (E. coli). Each candidate gene was cloned as a fusion protein bearing an amino-terminal...
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Authors: 11
Total Words: 8296
Unqiue Words: 3235

0.0 Mikeys
#4. Role of interaction network topology in controlling microbial population in consortia
Xinying Ren, Richard M Murray
Engineering microbial consortia is an important new frontier for synthetic biology given its efficiency in performing complex tasks and endurance to environmental uncertainty. Most synthetic circuits regulate populational behaviors via cell-to-cell interactions, which are affected by spatially heterogeneous environments. Therefore, it is important to understand the limits on controlling system dynamics and provide a control strategy for engineering consortia under spatial structures. Here, we build a network model for a fractional population control circuit in two-strain consortia, and characterize the cell-to-cell interaction network by topological properties, such as symmetry, locality and connectivity. Using linear network control theory, we relate the network topology to system output's tracking performance. We analytically and numerically demonstrate that the minimum network control cost for good tracking depends on locality difference between two cell population's spatial distributions and how strongly the controller node...
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O_Borkowski: Role of interaction network topology in controlling microbial population in consortia https://t.co/9eCqxW5SD8
GeneMods: RT @O_Borkowski: Role of interaction network topology in controlling microbial population in consortia https://t.co/9eCqxW5SD8
willigo09: RT @O_Borkowski: Role of interaction network topology in controlling microbial population in consortia https://t.co/9eCqxW5SD8
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Authors: 2
Total Words: 5989
Unqiue Words: 1637

0.0 Mikeys
#5. Complete decoupling of bacterial growth from biopolymer production through proteolytic control of enzyme levels
Gonzalo Durante-Rodriguez, Victor de Lorenzo, Pablo Ivan Nikel
Most current methods for controlling the rate of formation of a key protein or enzyme in cell factories rely on the manipulation of target genes within the pathway. In this article, we present a novel synthetic system for post-translational regulation of protein levels, FENIX, which provides both independent control of the steady-state protein level and inducible accumulation of targeted proteins. The device is based on the constitutive, proteasome-dependent degradation of the target polypeptide by tagging with a short synthetic, hybrid NIa/SsrA amino acid sequence in the C-terminal domain. The protein degradation process can be reversed by activating the system via addition of an orthogonal inducer (e.g. 3-methylbenzoate) to the culture medium. The system was benchmarked in Escherichia coli by tagging two fluorescent proteins (GFP and mCherry) and further exploited for engineering poly(3-hydroxybutyrate) (PHB) accumulation completely uncoupled from bacterial growth. By tagging PhaA (3-ketoacyl-CoA thiolase, first step of the...
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SeqComplete: #igem #synbio Complete decoupling of bacterial growth from biopolymer production through proteolytic control of enzyme levels | bioRxiv https://t.co/D0ceOueT0q, see more https://t.co/1FYAl6h91B
vdlorenzo_CNB: One more smart tool for programming bacteria to do amazing things: in this case, complete decoupling of growth from production by playing with proteases & proteosomes. Starring ⁦@PabloINik⁩ & ⁦@Gonnyita⁩ https://t.co/Yru3kQ7ZYQ
DrLeoRios: “Complete decoupling of #bacterial growth from #biopolymer production through proteolytic control of #enzyme levels” Nice! A proteasome #synbio tag is fused to the enzyme, so it is constantly degraded until the tag is cleaved by an induced protease https://t.co/fpylvOOOFW https://t.co/wHht4vdYBm
PabloINik: Re-purposing proteases with #SynBio! In this collaboration with @Gonnyita and @vdlorenzo_CNB we engineered a #cell #factory for #polymer production uncoupled from growth. The #tool is portable and can be adapted to other targets, too! https://t.co/AuI3tTOB5P https://t.co/SBGb6MVSE1
_BiotechWatcher: Complete decoupling of bacterial growth from biopolymer production through proteolytic control of enzyme levels | bioRxiv https://t.co/aCjngIuzw5, see more https://t.co/zOIpwYL5Ef
ProtifiLlc: Complete decoupling of bacterial growth from biopolymer production through proteolytic control of enzyme levels https://t.co/rf2cklx2d7
PromPreprint: Complete decoupling of bacterial growth from biopolymer production through proteolytic control of enzyme levels https://t.co/exVw0wbFPW
O_Borkowski: Complete decoupling of bacterial growth from biopolymer production through proteolytic control of enzyme levels https://t.co/RyaXifSRas
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Authors: 3
Total Words: 12635
Unqiue Words: 3314

0.0 Mikeys
#6. Direct purification of CRISPR/Cas ribonucleoprotein from E. coli in a single step
siyu lin, jie qiao, lixin ma, yi liu
CRISPR/Cas ribonucleoprotein (RNP) complexes have been recently used as promising biological tools with plenty of applications, however, there are by far no efficient methods to prepare them at large scale and low cost. Here, we present a simple method to directly produce and purify Cas RNP, including the widely used Cas9 and Cas12a nuclease, from E.coli in a single step using an ultra-high-affinity CL7/Im7 purification system. The prepared Cas RNP shows high stability, solid nuclease activity in vitro, and profound genome editing efficiency in vivo. Our method is convenient, cost-effective, and applicable to prepare other CRISPR associated nucleases.
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biorxivpreprint: Direct purification of CRISPR/Cas ribonucleoprotein from E. coli in a single step https://t.co/DicufRpzDG #bioRxiv
ScienceCrisp: Direct purification of CRISPR/Cas ribonucleoprotein from E. coli in a single step. Lin S, Qiao J, Ma L, Liu Y. bioRxiv 2018 Jul 26. https://t.co/OyjVcg4cuv
RhondaMel2016: Scientists at Hubei University in China successfully used the CL7/Im7 purification system licensed by TriAltus Bioscience to purify Cas9 and Cas12a CRISPR-associated-proteins from E.coli in a single step. #protein #purification https://t.co/aOAnv1jlxL
JambenSloom: Direct purification of CRISPR/Cas ribonucleoprotein from E. coli in a single step https://t.co/6XBE52AxdL
ribo_doc: Direct purification of CRISPR/Cas ribonucleoprotein from E. coli in a single step https://t.co/wTGyb8FMmA
andy_utoronto: RT @biorxivpreprint: Direct purification of CRISPR/Cas ribonucleoprotein from E. coli in a single step https://t.co/DicufRpzDG #bioRxiv
Aashiq_Kachroo: RT @biorxivpreprint: Direct purification of CRISPR/Cas ribonucleoprotein from E. coli in a single step https://t.co/DicufRpzDG #bioRxiv
MaryRuberry: RT @biorxivpreprint: Direct purification of CRISPR/Cas ribonucleoprotein from E. coli in a single step https://t.co/DicufRpzDG #bioRxiv
jamesapoulter: RT @biorxivpreprint: Direct purification of CRISPR/Cas ribonucleoprotein from E. coli in a single step https://t.co/DicufRpzDG #bioRxiv
Juli_Bla: RT @biorxivpreprint: Direct purification of CRISPR/Cas ribonucleoprotein from E. coli in a single step https://t.co/DicufRpzDG #bioRxiv
SteveRees16: RT @biorxivpreprint: Direct purification of CRISPR/Cas ribonucleoprotein from E. coli in a single step https://t.co/DicufRpzDG #bioRxiv
DhritiNagar: RT @biorxivpreprint: Direct purification of CRISPR/Cas ribonucleoprotein from E. coli in a single step https://t.co/DicufRpzDG #bioRxiv
DanielDayeh: RT @ribo_doc: Direct purification of CRISPR/Cas ribonucleoprotein from E. coli in a single step https://t.co/wTGyb8FMmA
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Authors: 4
Total Words: 3274
Unqiue Words: 1242

0.0 Mikeys
#7. Transforming Insect Population Control with Precision Guided Sterile Males
Nikolay P Kandul, Junru Liu, Hector M Sanchez, Sean L Wu, John M Marshall, Omar S Akbari
The sterile insect technique (SIT) is an environmentally safe and proven technology to suppress wild populations. To further advance its utility, a novel CRISPR-based technology termed precision guided SIT (pgSIT) is described. PgSIT mechanistically relies on a dominant genetic technology that enables simultaneous sexing and sterilization, facilitating the release of eggs into the environment ensuring only sterile adult males emerge. Importantly, for field applications, the release of eggs will eliminate burdens of manually sexing and sterilizing males, thereby reducing overall effort and increasing scalability. To demonstrate efficacy, we systematically engineer multiple pgSIT systems in Drosophila which consistently give rise to 100% sterile males. Importantly, we demonstrate that pgSIT-generated males are fit and competitive. Using mathematical models, we predict pgSIT will induce substantially greater population suppression than can be achieved by currently-available self-limiting suppression technologies. Taken together,...
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biorxivpreprint: Transforming Insect Population Control with Precision Guided Sterile Males https://t.co/kCcriZ8Grk #bioRxiv
Stollovo: Steril Insect Technology Paper on BioRxiv: "Transforming Insect Population Control with Precision Guided Sterile Males“: Researchers demonstrate that pgSIT-generated drosophila males are steril, fit and competitive: https://t.co/dzkOYaLKK6
Omar_Akbari_: @RobertHWoodman @julemieux1 @quantabiodesign @GENbio @kesvelt @ValentinoGantz https://t.co/K86XMPvfqX. #pgSIT
Omar_Akbari_: One insect factory to service the world to suppress disease spreading pests?? Read More Here: #pgSIT https://t.co/K86XMPvfqX https://t.co/Zexl9PPIzR
Omar_Akbari_: Please RT - Transforming Insect Population Control with Precision Guided Sterile Males! https://t.co/K86XMPvfqX
gusmcfarlane: Precision Guided Sterile Males for Insect Population Control #CRISPR #innovation https://t.co/9ueJzhYPUL
SynBioNaut: Cool two strain genetic system for simultaneous sex sorting and production of sterile males for biocontrol by @Omar_Akbari lab Transforming Insect Population Control with Precision Guided Sterile Males https://t.co/nfiFieyiFu
ChipDelMal: New @Omar_Akbari_ & John Marshall labs' collaboration preprint!: "Transforming Insect Population Control with Precision Guided Sterile Males" https://t.co/gWF8NY4Pf4
ValentinoGantz: Amazing data from the Akbari Lab @ UCSD see preprint on Transforming Insect Population Control with Precision Guided Sterile Males https://t.co/n4ir2jTVBB
NikolayKandul: Please RT, #pgSIT. https://t.co/dkxOny3GC9 we are looking for comments on the research. https://t.co/ZHyKq5L6jI
NikolayKandul: there are many ways to mess up Dipteran females. #pgSIT https://t.co/T5RzSUJzlF https://t.co/Pe6GQ58QQm
EileenChoffnes: Transforming Insect Population Control with Precision Guided Sterile Males https://t.co/MBnXx8ARqS
PromPreprint: Transforming Insect Population Control with Precision Guided Sterile Males https://t.co/N5vSdJ9ixR
UCR_ScienceNews: RT @Omar_Akbari_: Please RT - Transforming Insect Population Control with Precision Guided Sterile Males! https://t.co/K86XMPvfqX
JackLScanlan: RT @NikolayKandul: there are many ways to mess up Dipteran females. #pgSIT https://t.co/T5RzSUJzlF https://t.co/Pe6GQ58QQm
vectorgen: RT @Omar_Akbari_: Please RT - Transforming Insect Population Control with Precision Guided Sterile Males! https://t.co/K86XMPvfqX
ProfGemmell: RT @Omar_Akbari_: Please RT - Transforming Insect Population Control with Precision Guided Sterile Males! https://t.co/K86XMPvfqX
skryazhi: RT @Omar_Akbari_: Please RT - Transforming Insect Population Control with Precision Guided Sterile Males! https://t.co/K86XMPvfqX
skryazhi: RT @NikolayKandul: Please RT, #pgSIT. https://t.co/dkxOny3GC9 we are looking for comments on the research. https://t.co/ZHyKq5L6jI
rmwaterhouse: RT @Omar_Akbari_: Please RT - Transforming Insect Population Control with Precision Guided Sterile Males! https://t.co/K86XMPvfqX
Lord_of_Flyz: RT @NikolayKandul: Please RT, #pgSIT. https://t.co/dkxOny3GC9 we are looking for comments on the research. https://t.co/ZHyKq5L6jI
Omar_Akbari_: RT @NikolayKandul: there are many ways to mess up Dipteran females. #pgSIT https://t.co/T5RzSUJzlF https://t.co/Pe6GQ58QQm
gsiwo: RT @Omar_Akbari_: Please RT - Transforming Insect Population Control with Precision Guided Sterile Males! https://t.co/K86XMPvfqX
Lena_Riab: RT @Omar_Akbari_: Please RT - Transforming Insect Population Control with Precision Guided Sterile Males! https://t.co/K86XMPvfqX
carvunis: RT @NikolayKandul: Please RT, #pgSIT. https://t.co/dkxOny3GC9 we are looking for comments on the research. https://t.co/ZHyKq5L6jI
EntomosOswin: RT @Omar_Akbari_: Please RT - Transforming Insect Population Control with Precision Guided Sterile Males! https://t.co/K86XMPvfqX
anfarauti: RT @Omar_Akbari_: Please RT - Transforming Insect Population Control with Precision Guided Sterile Males! https://t.co/K86XMPvfqX
e_levashina: RT @biorxivpreprint: Transforming Insect Population Control with Precision Guided Sterile Males https://t.co/kCcriZ8Grk #bioRxiv
geryterry: RT @Omar_Akbari_: Please RT - Transforming Insect Population Control with Precision Guided Sterile Males! https://t.co/K86XMPvfqX
capsiannum: RT @Omar_Akbari_: Please RT - Transforming Insect Population Control with Precision Guided Sterile Males! https://t.co/K86XMPvfqX
capsiannum: RT @NikolayKandul: there are many ways to mess up Dipteran females. #pgSIT https://t.co/T5RzSUJzlF https://t.co/Pe6GQ58QQm
nikiwind: RT @Omar_Akbari_: Please RT - Transforming Insect Population Control with Precision Guided Sterile Males! https://t.co/K86XMPvfqX
phiC32: RT @Omar_Akbari_: Please RT - Transforming Insect Population Control with Precision Guided Sterile Males! https://t.co/K86XMPvfqX
LSTM_VectorGene: RT @Omar_Akbari_: Please RT - Transforming Insect Population Control with Precision Guided Sterile Males! https://t.co/K86XMPvfqX
YamanakaNaoki: RT @Omar_Akbari_: Please RT - Transforming Insect Population Control with Precision Guided Sterile Males! https://t.co/K86XMPvfqX
PrimoPasquale: RT @Omar_Akbari_: Please RT - Transforming Insect Population Control with Precision Guided Sterile Males! https://t.co/K86XMPvfqX
lewishun929: RT @Omar_Akbari_: Please RT - Transforming Insect Population Control with Precision Guided Sterile Males! https://t.co/K86XMPvfqX
IlianoCoutinho: RT @Omar_Akbari_: Please RT - Transforming Insect Population Control with Precision Guided Sterile Males! https://t.co/K86XMPvfqX
elena_DB87: RT @Omar_Akbari_: Please RT - Transforming Insect Population Control with Precision Guided Sterile Males! https://t.co/K86XMPvfqX
s_verkuijl: RT @Omar_Akbari_: Please RT - Transforming Insect Population Control with Precision Guided Sterile Males! https://t.co/K86XMPvfqX
Yijin228: RT @Omar_Akbari_: Please RT - Transforming Insect Population Control with Precision Guided Sterile Males! https://t.co/K86XMPvfqX
prasadnp: RT @Omar_Akbari_: Please RT - Transforming Insect Population Control with Precision Guided Sterile Males! https://t.co/K86XMPvfqX
Brockman_AI: RT @Omar_Akbari_: Please RT - Transforming Insect Population Control with Precision Guided Sterile Males! https://t.co/K86XMPvfqX
Alex___Nash: RT @Omar_Akbari_: Please RT - Transforming Insect Population Control with Precision Guided Sterile Males! https://t.co/K86XMPvfqX
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Sample Sizes : [3628, 28, 4371, 30, 540, 7, 942, 14, 517, 7, 5747, 36, 24, 1697, 24, 1791, 24, 4231, 48, 32, 20, 12, 252, 6, 2191, 27, 2640, 27, 3019, 36, 782, 24, 0, 4, 556, 8, 2, 1490, 36, 6, 5, 199]
Authors: 6
Total Words: 11388
Unqiue Words: 3289

0.0 Mikeys
#8. Chemical Characterization of Interacting Genes in Few Subnetworks of Alzheimer's Disease
Antara Sengupta, Pabitra Pal Choudhury, Hazel Nicolette Manners, Swarup Roy
A number of genes have been identified as a key player in Alzheimers disease (AD). Topological analysis of co-expression network reveals that key genes are mostly central or hub genes. The association between a hub gene and its neighbour genes can be derived easily using relative abundance of their expression levels. However, it is still unexplored fact that whether any hub and its neighbour genes within a subnetwork exhibits any kind of proximity with respect to their chemical properties of the DNA sequences or not, that code for a sequence of amino acids. In this work, we try to make a quantitative investigation of the underlying biological facts in DNA sequential and primary protein level in mathematical paradigm. It may gives a holistic view of the interrelationships existing between hub genes and neighbour genes in few selective AD subnetworks. We define a mapping model from physicochemical properties of DNA sequence to chemical characterization of amino acid sequences. We use distribution of chemical groups present in a...
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Total Words: 4314
Unqiue Words: 1519

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#9. TnClone: high-throughput clonal analysis using Tn5-mediated library construction and de novo assembly
Byungjin Hwang, Sunghoon Heo, Namjin Cho, Duhee Bang
A typical molecular cloning procedure requires Sanger sequencing for validation, which becomes cost-prohibitive and labour intensive for large-scale clonal analysis of genotype phenotype studies. Here we present a Tn5 mediated clonal analysis platform TnClone, which uses next-generation sequencing (NGS) to rapidly and cost-effectively analyze a large number of clones. We also developed a user-friendly graphical user interface and have provided general guidelines for conducting validation experiments. Using TnClone, we achieved more than 20-fold cost reduction compared with the cost incurred using conventional Sanger sequencing and detected low-frequency mutant clones (~10%) in mixed samples. We tested our programme and achieved 99.4% sensitivity. Our platform provides rapid turnaround with minimal hands-on time for secondary evaluation as NGS technology continues to evolve.
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TnClone: High-throughput clonal analysis using Tn5-mediated library construction and de novo assembly

Repository: tnclone
User: tahuh
Language: Python
Stargazers: 0
Subscribers: 2
Forks: 1
Open Issues: 1
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Authors: 4
Total Words: 2579
Unqiue Words: 1068

0.0 Mikeys
#10. Establishing Synthesis Pathway-Host Compatibility via Enzyme Solubility
Sara A Amin, Venkatesh Endalur Gopinarayanan, Nikhil Unni Nair, Soha Hassoun
Current pathway synthesis tools identify possible pathways that can be added to a host to produce a desired target molecule through the exploration of abstract metabolic and reaction network space. However, not many of these tools do explore gene-level information required to physically realize the identified synthesis pathways, and none explore enzyme-host compatibility. Developing tools that address this disconnect between abstract reactions/metabolic design space and physical genetic sequence design space will enable expedited experimental efforts that avoid exploring unprofitable synthesis pathways. This work describes a workflow, termed Probabilistic Pathway Assembly with Solubility Scores (ProPASS), which links synthesis pathway construction with the exploration of the physical design space as imposed by the availability of enzymes with characterized activities within the host. Predicted protein solubility propensity scores are used as a confidence level to quantify the compatibility of each pathway enzyme with the host (E....
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O_Borkowski: Establishing Synthesis Pathway-Host Compatibility via Enzyme Solubility https://t.co/UF3O831TWp https://t.co/kAp4wL9T1H
maskot1977: Establishing Synthesis Pathway-Host Compatibility via Enzyme Solubility https://t.co/DdWVZKLz8w
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Authors: 4
Total Words: 7973
Unqiue Words: 2331

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