Top 10 Biorxiv Papers Today in Synthetic Biology


2.0 Mikeys
#1. Towards feedback control of the cell-cycle across a population of yeast cells
Giansimone Perrino, Davide Fiore, Sara Napolitano, Mario di Bernardo, Diego di Bernardo
Cells are defined by their unique ability to self-replicate through cell division. This periodic process is known as the cell-cycle and it happens with a defined period in each cell. The budding yeast divides asymmetrically with a mother cell generating multiple daughter cells. Within the cell population each cell divides with the same period but asynchronously. Here, we investigate the problem of synchronising the cell-cycle across a population of yeast cells through a microfluidics-based feedback control platform. We propose a theoretical and experimental approach for cell-cycle control by considering a yeast strain that can be forced to start the cell-cycle by changing growth medium. The duration of the cell-cycle is strictly linked to the cell volume growth, hence a hard constraint in the controller design is to prevent excessive volume growth. We experimentally characterised the yeast strain and derived a simplified phase-oscillator model of the cell-cycle. We then designed and implemented three impulsive control strategies...
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biorxivpreprint: Towards feedback control of the cell-cycle across a population of yeast cells https://t.co/62HCfFGuxK #bioRxiv
diegodidibi: Out our New preprint in bioarxiv with my brother’s lab ⁦@mdiberna⁩ ⁦on feedback control of cell cycle part of Fet Open project @cosybio⁩. Comments welcome :) https://t.co/5NvHSCe8Ug
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Sample Sizes : [3, 8, 12]
Authors: 5
Total Words: 5654
Unqiue Words: 1672

1.982 Mikeys
#2. Overcoming bottlenecks for in vitro synthesis and initial structural insight of ice nucleating protein InaZ
Irina V Novikova, Swarup China, James E Evans
Unlike inorganic or other synthetic alternatives, ice nucleating proteins (INPs) remain the most efficient ice nuclei today. Their potential applications in cryo-preservation, biomedicine, food industry and in the modulation of climate are widespread. Nevertheless, over several decades, cell-based recombinant methods have experienced multiple difficulties expressing these large proteins in full-length and in necessary yields while retaining functionality. As a result, our understanding of the structure and ice nucleation mechanism for this class of proteins is incomplete, and, most importantly, the full extent of possible applications unrealized. Using a wheat-germ cell-free expression pipeline, we successfully expressed and purified full-length ice nucleating protein InaZ from Pseudomonas syringae, known as a model INP. High protein yield and solubility has been achieved using this system. Ice nucleation experiments inside a dynamic environmental scanning electron microscope (ESEM) confirmed that the produced InaZ products remain...
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Sample Sizes : None.
Authors: 3
Total Words: 6670
Unqiue Words: 2620

0.0 Mikeys
#3. Validating genome-wide CRISPR-Cas9 function in the non-conventional yeast Yarrowia lipolytica
Cory Schwartz, Jan-Fang Cheng, Robert Evans, Christopher A Schwartz, James M Wagner, Scott Anglin, Adam Beitz, Weihua Pan, Stefano Lonardi, Mark Blenner, Hal S Alper, Yasuo Yoshikuni, Ian Wheeldon
Genome-wide mutational screens are central to understanding the genetic underpinnings of evolved and engineered phenotypes. The widespread adoption of CRISPR-Cas9 genome editing has enabled such screens in many organisms, but identifying functional sgRNAs still remains a challenge. To address this limitation, we developed a methodology to quantify the cutting efficiency of each sgRNA in a genome-scale library in the biotechnologically important yeast Yarrowia lipolytica . Screening in the presence and absence of native DNA repair enabled high-throughput quantification of sgRNA function leading to the identification of high efficiency sgRNAs that cover 94% of genes. Library validation enhanced the classification of essential genes by identifying inactive guides that create false negatives and mask the effects of successful disruptions. Quantification of guide effectiveness also creates a dataset from which functional determinants of CRISPR-Cas9 can be identified. Finally, application of the library identified mutations that led to...
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rnomics: Top #tweeted story in #bioscience: Validating genome-wide CRISPR-Cas9 function … https://t.co/nw68MfFeZn, see more https://t.co/kME3G1o122
MarkBlenner: Our @biorxivpreprint in collaboration with the Wheeldon & Alper labs, and with @jgi is now available. @ClemsonResearch #BlennerLab https://t.co/9tU60zAzBb
ScienceCrisp: RT @biorxivpreprint: Validating genome-wide CRISPR-Cas9 function in the non-conventional yeast Yarrowia lipolytica https://t.co/LojLsx5ViC…
Shlee84299380: RT @biorxivpreprint: Validating genome-wide CRISPR-Cas9 function in the non-conventional yeast Yarrowia lipolytica https://t.co/LojLsx5ViC…
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Sample Sizes : None.
Authors: 13
Total Words: 10222
Unqiue Words: 3045

0.0 Mikeys
#4. 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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Sample Sizes : None.
Authors: 4
Total Words: 2579
Unqiue Words: 1068

0.0 Mikeys
#5. A quasi-integral controller for adaptation of genetic modules to variable ribosome demand
Hsin-Ho Huang, Yili Qian, Domitilla Del Vecchio
The behavior of genetic circuits is often poorly predictable. A gene's expression level is not only determined by the intended regulators, but also largely dictated by changes in ribosome availability imparted by activation or repression of other genes. To address this problem, we design a quasi-integral biomolecular feedback controller that enables the expression level of any gene of interest (GOI) to adapt to changes in available ribosomes. The feedback is implemented through a synthetic small RNA (sRNA) that silences the GOI's mRNA, and uses orthogonal extracytoplasmic function (ECF) sigma factor to sense the GOIs mRNA and to activate sRNA transcription. Without the controller, the expression level of the GOI is reduced by 50% when a resource competitor is activated. With the controller, by contrast, gene expression level is practically unaffected by the competitor. This feedback controller allows adaptation of genetic modules to variable ribosome demand and thus aids modular construction of complicated circuits.
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Sample Sizes : None.
Authors: 3
Total Words: 8504
Unqiue Words: 2571

0.0 Mikeys
#6. Start-Stop Assembly: a functionally scarless DNA assembly system optimised for metabolic engineering.
George M. Taylor, Pawel M. Mordaka, John T. Heap
DNA assembly allows individual DNA constructs or designed mixtures to be assembled quickly and reliably. Most methods are either: (i) Modular, easily scalable and suitable for combinatorial assembly, but leave undesirable 'scar' sequences; or (ii) bespoke (non-modular), scarless but less suitable for construction of combinatorial libraries. Both have limitations for metabolic engineering. To overcome this trade-off we devised Start-Stop Assembly, a multi-part, modular DNA assembly method which is both functionally scarless and suitable for combinatorial assembly. Crucially, 3 bp overhangs corresponding to start and stop codons are used to assemble coding sequences into expression units, avoiding scars at sensitive coding sequence boundaries. Building on this concept, a complete DNA assembly framework was designed and implemented, allowing assembly of up to 15 genes from up to 60 parts (or mixtures); monocistronic, operon-based or hybrid configurations; and a new streamlined assembly hierarchy minimising the number of vectors. Only...
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biorxivpreprint: Start-Stop Assembly: a functionally scarless DNA assembly system optimised for metabolic engineering. https://t.co/DZLfkL1RSE #bioRxiv
MehdiGoudarzi80: Start-Stop Assembly framework allows assembly of 15 genes (from up to 60 parts or mixtures) in monocistronic, operon-based or hybrid configurations. https://t.co/JTiBwSk6JM https://t.co/SoSxA2borP
johntheap: Start-Stop Assembly as seen at #ME12 @CBMNet_NIBB @PHYCONET is now in bioRxiv. Ideal for metabolic pathways, combinatorial libraries and diverse organisms. https://t.co/N1f1HvGlXh @biorxivpreprint
druanogallego: EEUU es el país https://t.co/BXmnXGDkDW
O_Borkowski: Start-Stop Assembly: a functionally scarless DNA assembly system optimised for metabolic engineering. https://t.co/lpa3EDHgrG
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Sample Sizes : None.
Authors: 3
Total Words: 13878
Unqiue Words: 3721

0.0 Mikeys
#7. Synthetic negative feedback circuits using engineered small RNAs
Ciarán L. Kelly, Andreas W. K. Harris, Harrison Steel, Edward J. Hancock, John T. Heap, Antonis Papachristodoulou
Negative feedback is known to endow biological and man-made systems with robust performance in the face of uncertainties and disturbances. To date, synthetic biological feedback circuits have relied upon protein-based, transcriptional regulation to control circuit output. Small RNAs (sRNAs) are non-coding RNA molecules which can inhibit translation of target messenger RNAs (mRNAs). In this paper, we designed, modelled and built two synthetic negative feedback circuits that use rationally-designed sRNAs for the first time. The first circuit builds upon the well characterised tet-based autorepressor, incorporating an externally-inducible sRNA to tune the effective feedback strength. This allows more precise fine-tuning of the circuit output in contrast to the sigmoidal input-output response of the autorepressor alone. In the second circuit, the output is a transcription factor that induces expression of an sRNA which negatively regulates the translation of the mRNA encoding this output, creating direct, closed-loop, negative...
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kellier13: 10 months after the first version was submitted, this paper has finally been revised! New modelling, new plasmids, new experiments and new writing! https://t.co/NjU1gA3kif Now to resubmit to journal! #synbio https://t.co/K2tVYsSGXd
julio_r_banga: Synthetic biological circuits that utilise small RNAs for control purposes - https://t.co/W00vB5600H
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Sample Sizes : None.
Authors: 6
Total Words: 11386
Unqiue Words: 3148

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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Authors: 4
Total Words: 4314
Unqiue Words: 1519

0.0 Mikeys
#9. 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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Sample Sizes : None.
Authors: 11
Total Words: 8296
Unqiue Words: 3235

0.0 Mikeys
#10. A synthetic system that senses Candida albicans and inhibits virulence factors
Michael Tscherner, Tobias W Giessen, Laura Markey, Carol A Kumamoto, Pamela A Silver
Due to a limited set of antifungals available and problems in early diagnosis invasive fungal infections caused by Candida species are among the most common hospital-acquired infections with staggering mortality rates. Here, we describe an engineered system able to sense and respond to the fungal pathogen Candida albicans , the most common cause of candidemia. In doing so, we identified hydroxyphenylacetic acid (HPA) as a novel molecule secreted by C. albicans . Furthermore, we engineered E. coli to be able to sense HPA produced by C. albicans . Finally, we constructed a sense-and-respond system by coupling the C. albicans sensor to the production of an inhibitor of hypha formation thereby reducing filamentation, virulence factor expression and fungal-induced epithelial damage. This system could be used as a basis for the development of novel prophylactic approaches to prevent fungal infections.
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westr: A synthetic system that senses #Candida albicans and inhibits virulence factors https://t.co/ok2OeA0lHo #synbio #pathogenic #fungi
Francois_Mayer1: A synthetic system that senses Candida albicans and inhibits virulence factors https://t.co/XwzaFpgpDf
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Sample Sizes : None.
Authors: 5
Total Words: 11309
Unqiue Words: 3289

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