Altering traits and fates of wild populations with Mendelian DNA sequence modifying Allele Sails.

Population-scale genome modification can alter the composition or fate of wild populations. Synthetic gene drives provide one set of tools, but their use is complicated by scientific, regulatory, and social issues associated with transgene persistence and flow. Here we propose an alternative approach. An Allele Sail consists of a genome editor (the Wind) that introduces DNA sequence edits, and is inherited in a Mendelian fashion. Meanwhile, the edits (the Sail) experience an arithmetic, Super-Mendelian increase in frequency. We model this system and identify contexts in which a single, low frequency release of an editor brings edits to a very high frequency. We also identify conditions in which manipulation of sex determination can bring about population suppression. In regulatory frameworks that distinguish between transgenics (GMO) and their edited non-transgenic progeny (non-GMO) Allele Sails may prove useful since the spread and persistence of the GM component can be limited.

Gene synthesis design: a pythonic approach.

Researchers often need to synthesize genes of interest in this era of synthetic biology. Gene synthesis by PCR assembly of multiple DNA fragments is a quick and economical method that is widely applied. Up to now, there have been a few software solutions for designing fragments in gene synthesis. However, some of these software solutions use programming languages that are not popular now, other software products are commercial or require users to visit servers. In this study, we propose a Python program to design DNA fragments for gene synthesis. The algorithm is designed to meet the experimental needs. Also, the source code with detailed annotation is freely available for all users. Furthermore, the feasibility of the algorithm and the program is validated by experiments. Our program can be useful for the design of gene synthesis in the labs and help the study of gene structure and function.

Two teams supercharge gene spread in plants.

First synthetic "gene drive" for plants could help tame weeds-or transform them.

Synthetic gene circuit evolution: Insights and opportunities at the mid-scale.

Directed evolution focuses on optimizing single genetic components for predefined engineering goals by artificial mutagenesis and selection. In contrast, experimental evolution studies the adaptation of entire genomes in serially propagated cell populations, to provide an experimental basis for evolutionary theory. There is a relatively unexplored gap at the middle ground between these two techniques, to evolve in vivo entire synthetic gene circuits with nontrivial dynamic function instead of single parts or whole genomes. We discuss the requirements for such mid-scale evolution, with hypothetical examples for evolving synthetic gene circuits by appropriate selection and targeted shuffling of a seed set of genetic components in vivo. Implementing similar methods should aid the rapid generation, functionalization, and optimization of synthetic gene circuits in various organisms and environments, accelerating both the development of biomedical and technological applications and the understanding of principles guiding regulatory network evolution.

[Closed-loop synthetic gene circuits for cell-based therapies]. / Les circuits synthétiques de gènes fonctionnant en boucle fermée - Concept et dernières avancées.

Recent advances in synthetic biology have paved the way for new cellular therapies, using cells capable of autonomously treating chronic diseases. These cells integrate a set of genes functioning in a closed-loop synthetic circuit, delivering a therapeutic effector in response to a specific pathological signal. While promising in mice, these therapies face clinical challenges related to safety and feasibility of in vivo implementation. The latest generations of synthetic circuits aim to address these issues through advanced bioengineering strategies outlined in this article.

Title: Les circuits synthétiques de gènes fonctionnant en boucle fermée - Concept et dernières avancées. Abstract: Les progrès récents de la biologie synthétique ont ouvert la voie à de nouvelles thérapies fondées sur des cellules rendues aptes à produire de manière autonome des substrats afin de traiter des maladies chroniques. Ces cellules modifiées intègrent un ensemble de gènes fonctionnant en circuit synthétique à boucle fermée, qui permettent de délivrer un effecteur thérapeutique en réponse à un signal pathologique déterminé. Bien que prometteuses chez la souris, ces thérapies font face à des obstacles cliniques liés à leur sûreté et à leur implémentation in vivo. Les dernières générations de circuits synthétiques cherchent à résoudre ces problèmes grâce à des stratégies de bioingénierie avancées, que nous présentons dans cet article.

Engineering a synthetic gene circuit for high-performance inducible expression in mammalian systems.

Inducible gene expression systems can be used to control the expression of a gene of interest by means of a small-molecule. One of the most common designs involves engineering a small-molecule responsive transcription factor (TF) and its cognate promoter, which often results in a compromise between minimal uninduced background expression (leakiness) and maximal induced expression. Here, we focus on an alternative strategy using quantitative synthetic biology to mitigate leakiness while maintaining high expression, without modifying neither the TF nor the promoter. Through mathematical modelling and experimental validations, we design the CASwitch, a mammalian synthetic gene circuit based on combining two well-known network motifs: the Coherent Feed-Forward Loop (CFFL) and the Mutual Inhibition (MI). The CASwitch combines the CRISPR-Cas endoribonuclease CasRx with the state-of-the-art Tet-On3G inducible gene system to achieve high performances. To demonstrate the potentialities of the CASwitch, we apply it to three different scenarios: enhancing a whole-cell biosensor, controlling expression of a toxic gene and inducible production of Adeno-Associated Virus (AAV) vectors.

A coarse-grained bacterial cell model for resource-aware analysis and design of synthetic gene circuits.

Within a cell, synthetic and native genes compete for expression machinery, influencing cellular process dynamics through resource couplings. Models that simplify competitive resource binding kinetics can guide the design of strategies for countering these couplings. However, in bacteria resource availability and cell growth rate are interlinked, which complicates resource-aware biocircuit design. Capturing this interdependence requires coarse-grained bacterial cell models that balance accurate representation of metabolic regulation against simplicity and interpretability. We propose a coarse-grained E. coli cell model that combines the ease of simplified resource coupling analysis with appreciation of bacterial growth regulation mechanisms and the processes relevant for biocircuit design. Reliably capturing known growth phenomena, it provides a unifying explanation to disparate empirical relations between growth and synthetic gene expression. Considering a biomolecular controller that makes cell-wide ribosome availability robust to perturbations, we showcase our model's usefulness in numerically prototyping biocircuits and deriving analytical relations for design guidance.

dCas12a:Pre-crRNA: A New Tool to Induce mRNA Degradation in Saccharomyces cerevisiae Synthetic Gene Circuits.

We describe a new way to trigger mRNA degradation in Saccharomyces cerevisiae synthetic gene circuits. Our method demands to modify either the 5'- or the 3'-UTR that flanks a target gene with elements from the pre-crRNA of type V Cas12a proteins and expresses a DNase-deficient Cas12a (dCas12a). dCas12a recognizes and cleaves the pre-crRNA motifs on mRNA sequences. Our tool does not require complex engineering operations and permits an efficient control of protein expression via mRNA degradation.

Synthetic reversed sequences reveal default genomic states.

Pervasive transcriptional activity is observed across diverse species. The genomes of extant organisms have undergone billions of years of evolution, making it unclear whether these genomic activities represent effects of selection or 'noise'1-4. Characterizing default genome states could help understand whether pervasive transcriptional activity has biological meaning. Here we addressed this question by introducing a synthetic 101-kb locus into the genomes of Saccharomyces cerevisiae and Mus musculus and characterizing genomic activity. The locus was designed by reversing but not complementing human HPRT1, including its flanking regions, thus retaining basic features of the natural sequence but ablating evolved coding or regulatory information. We observed widespread activity of both reversed and native HPRT1 loci in yeast, despite the lack of evolved yeast promoters. By contrast, the reversed locus displayed no activity at all in mouse embryonic stem cells, and instead exhibited repressive chromatin signatures. The repressive signature was alleviated in a locus variant lacking CpG dinucleotides; nevertheless, this variant was also transcriptionally inactive. These results show that synthetic genomic sequences that lack coding information are active in yeast, but inactive in mouse embryonic stem cells, consistent with a major difference in 'default genomic states' between these two divergent eukaryotic cell types, with implications for understanding pervasive transcription, horizontal transfer of genetic information and the birth of new genes.

Enzymatic Assembly of Small Synthetic Genes with Repetitive Elements.

Gene synthesis efficiency has greatly improved in recent years but is limited when it comes to repetitive sequences, which results in synthesis failure or delays by DNA synthesis vendors. This represents a major obstacle for the development of synthetic biology since repetitive elements are increasingly being used in the design of genetic circuits and design of biomolecular nanostructures. Here, we describe a method for the assembly of small synthetic genes with repetitive elements: First, a gene of interest is split in silico into small synthons of up to 80 base pairs flanked by Golden-Gate-compatible overhangs. Then, synthons are made by oligo extension and finally assembled into a synthetic gene by Golden Gate Assembly. We demonstrate the method by constructing eight challenging genes with repetitive elements, e.g., multiple repeats of RNA aptamers and RNA origami scaffolds with multiple identical aptamers. The genes range in size from 133 to 456 base pairs and are assembled with fidelities of up to 87.5%. The method was developed to facilitate our own specific research but may be of general use for constructing challenging and repetitive genes and, thus, a valuable addition to the molecular cloning toolbox.

Synthetic Genes For Dynamic Regulation Of DNA-Based Receptors.

We present a strategy to control dynamically the loading and release of molecular ligands from synthetic nucleic acid receptors using in vitro transcription. We demonstrate this by engineering three model synthetic DNA-based receptors: a triplex-forming DNA complex, an ATP-binding aptamer, and a hairpin strand, whose ability to bind their specific ligands can be cotranscriptionally regulated (activated or inhibited) through specific RNA molecules produced by rationally designed synthetic genes. The kinetics of our DNA sensors and their genetically generated inputs can be captured using differential equation models, corroborating the predictability of the approach used. This approach shows that highly programmable nucleic acid receptors can be controlled with molecular instructions provided by dynamic transcriptional systems, illustrating their promise in the context of coupling DNA nanotechnology with biological signaling.

Context-dependent redesign of robust synthetic gene circuits.

Cells provide dynamic platforms for executing exogenous genetic programs in synthetic biology, resulting in highly context-dependent circuit performance. Recent years have seen an increasing interest in understanding the intricacies of circuit-host relationships, their influence on the synthetic bioengineering workflow, and in devising strategies to alleviate undesired effects. We provide an overview of how emerging circuit-host interactions, such as growth feedback and resource competition, impact both deterministic and stochastic circuit behaviors. We also emphasize control strategies for mitigating these unwanted effects. This review summarizes the latest advances and the current state of host-aware and resource-aware design of synthetic gene circuits.

Protein design meets biosecurity.

The power and accuracy of computational protein design have been increasing rapidly with the incorporation of artificial intelligence (AI) approaches. This promises to transform biotechnology, enabling advances across sustainability and medicine. DNA synthesis plays a critical role in materializing designed proteins. However, as with all major revolutionary changes, this technology is vulnerable to misuse and the production of dangerous biological agents. To enable the full benefits of this revolution while mitigating risks that may emerge, all synthetic gene sequence and synthesis data should be collected and stored in repositories that are only queried in emergencies to ensure that protein design proceeds in a safe, secure, and trustworthy manner.

Synthetic Gene Circuits for Regulation of Next-Generation Cell-Based Therapeutics.

Arming human cells with synthetic gene circuits enables to expand their capacity to execute superior sensing and response actions, offering tremendous potential for innovative cellular therapeutics. This can be achieved by assembling components from an ever-expanding molecular toolkit, incorporating switches based on transcriptional, translational, or post-translational control mechanisms. This review provides examples from the three classes of switches, and discusses their advantages and limitations to regulate the activity of therapeutic cells in vivo. Genetic switches designed to recognize internal disease-associated signals often encode intricate actuation programs that orchestrate a reduction in the sensed signal, establishing a closed-loop architecture. Conversely, switches engineered to detect external molecular or physical cues operate in an open-loop fashion, switching on or off upon signal exposure. The integration of such synthetic gene circuits into the next generation of chimeric antigen receptor T-cells is already enabling precise calibration of immune responses in terms of magnitude and timing, thereby improving the potency and safety of therapeutic cells. Furthermore, pre-clinical engineered cells targeting other chronic diseases are gathering increasing attention, and this review discusses the path forward for achieving clinical success. With synthetic biology at the forefront, cellular therapeutics holds great promise for groundbreaking treatments.

Producción y evaluación del antígeno recombinante TES-30 de Toxocara canis para el inmunodiagnóstico de toxocariasis / Production and evaluation of the recombinant antigen TES-30 of Toxocara canis for the immunodiagnosis of toxocariasis

Introducción. Toxocara canis es un nematodo patógeno de cánidos que accidentalmente puede ser transmitido a los humanos. A pesar de la importancia de la serología para el diagnóstico de esta zoonosis, los kits diagnósticos usan antígenos crudos de excreción-secreción, en su mayoría glucoproteínas que no son específicas de especie, por lo cual pueden presentarse reacciones cruzadas con anticuerpos generados contra otros parásitos. Objetivos. Producir el antígeno recombinante TES-30 de T. canis y evaluarlo para el inmunodiagnóstico de la toxocariasis. Materiales y métodos. Se clonó el gen que codifica TES-30 en el vector de expresión pET28a (+), usando oligonucleótidos de cadena sencilla unidos mediante reacción en cadena de la polimerasa (PCR). La proteína rTES-30 se purificó por cromotografia de afinidad (Ni 2+ ). La reacción serológica de rTES-30 se evaluó mediante immunoblot . Teniendo en cuenta que no existe una prueba de referencia , se observó el comportamiento del antigeno en comparación con la prueba de rutina para el inmunodiagnóstico de la toxocariasis, es decir, la técnica ELISA convencional con antígenos de excreción-secreción. Resultados. El rTES-30 se produjo a partir de un cultivo de Escherichia coli LB, con un rendimiento de 2,25 mg/l y 95 % de pureza. La concordancia de la reacción entre el immunoblot rTES-30 y la ELISA convencional, fue de 73 % (46/63) y de 100 % con los 21 sueros no reactivos. De los 21 sueros con diagnóstico de otras parasitosis, 19 fueron reactivos con ELISA, mientras que tan solo siete fueron positivos con el immunoblot rTES-30. La concordancia entre la ELISA y el immunoblot fue moderada (índice kappa de 0,575; IC 95% 0,41-0,74). Conclusiones. Los datos presentados respaldan la utilidad del immunoblot r TES-3 0 para la confirmación de los posibles positivos por ELISA, no solo en los estudios epidemiológicos, sino también, como candidato para el desarrollo de pruebas diagnósticas de la toxocariasis ocular en Colombia.

Introduction: Toxocara canis is a pathogenic nematode of canines which can be accidentally transmitted to humans. Although serology is the most important diagnostic tool for this zoonosis, diagnostic kits use crude excretion/secretion antigens, most of them being glycoproteins which are not species-specific and may cross-react with antibodies generated against other parasites. Objectives: To produce the rTES-30 recombinant antigen of Toxocara canis and evaluate it in the immunodiagnosis of toxocariasis. Materials and methods: The gene that codes for TES-30 was cloned in the expression vector pET28a (+) using single-stranded oligonucleotides united by PCR. The protein rTES-30 was purified by Ni 2+ affinity chromotography. Seroreactivity of rTES-30 was evaluated by immunoblot. Given that there is no gold standard test, the behaviour of the antigen was compared with the method that is routinely used to immunodiagnose toxocariasis, i.e., the conventional ELISA technique using excretion/secretion antigens. Results: The rTES-30 was produced from an Escherichia coli LB culture which yielded 2.25 mg/L of the antigen with a purity of 95%. The results obtained showed 73% (46/63) concordance of reactivity between the rTES-30 immunoblot and the conventional ELISA, and 100% concordance with the non-reactive sera (21). Nineteen of the 21 sera positive for other parasitoses reacted with ELISA, while only seven of these were positive with the rTES-30 immunoblot. Concordance between the ELISA and the immunoblot was moderate (kappa coefficient: 0.575; 95% CI: 0.41- 0.74). Conclusions: The data presented show the potential of the rTES-30 inmunoblot for confirmation of possible ELISA positives, not only in epidemiological studies, but also as a candidate for the development of diagnostic tests for ocular toxocariasis in Colombia.

T-DNA transfer from Agrobacterium tumefaciens to the ectomycorrhizal fungus Pisolithus microcarpus / Transferencia de T-DNA de Agrobacterium tumefaciens al hongo ectomicorrícico Pisolithus microcarpus

The model ectomycorrhizal fungus Pisolithus microcarpus isolate 441 was transformed by using Agrobacterium tumefaciens LBA1100 and AGL-1. The selection marker was the Shble gene of Streptoallotecius hidustanus, conferring resistance to phleomycin, under the control of the gpd gene promoter and terminator of Schizophyllum commune. Transformation resulted in phleomycin resistant clones which were confirmed by PCR to contain the resistance cassette. A. tumefaciens-mediated gene transfer would allow the development of RNA interference technology in P. microcarpus.

El hongo ectomicorrícico modelo Pisolithus microcarpus aislamiento 441 fue transformado utilizando Agrobacterium tumefaciens LBA 1100 y AGL-1. El marcador de selección fue el gen Shble de Streptoallotecius hidustanus, el cual confiere resistencia a fleomicina, bajo el control del promotor y terminador del gen gpd de Schizophyllum commune. La transformación resultó en clones resistentes a fleomicina comprobándose por PCR la presencia del transgen. La transferencia génica mediada por Agrobacterium podría permitir el desarrollo de la tecnología de interferencia por ARN en P. microcarpus.

Terapia génica / Gene therapy

La aplicación de la genética molecular a la biología de la enfermedad humana tiene un profundo efecto en la comprensión de los mecanismos moleculares de la patogénesis de la enfermedad. En esta revisión se proporciona una introducción y bosquejo de la terapia génetica, y se presentan y discuten las técnicas más actualizadas para hacer la entrega de genes asi como las hazañas clínicas y experimentales realizadas hasta la fecha. El desarrollo de métodos de entrega de genes a células de mamífero lleva a la posibilidad de tratar la enfermedad humana a través de terapias basadas en genes. Como resultado, conceptos y métodos que podían considerarse ciencia ficción hace 50 años se aplican ahora en el tratamiento de diversas enfermedades. La aplicación de la terapia génica está rompiendo las fronteras tradicionales en la cual la medicina moderna ha estado sumergida. Sin embargo, no obstante los progresos, un gran número de dificultades técnicas necesitan ser resueltas antes de que la terapia génica pueda ser segura y eficientemente aplicada en la clínica. Los desarrollos tecnológicos, particularmente la entrega de genes y el trasplante celular, son críticos para la práctica exitosa de la terapia génica

Síntesis total del gen de la ertropoyetina humana / Total synthesis of the human erythropoietin gene

En el presente trabajo se reporta la síntesis total del gen que codifica para la eritropoyetina humana, hormona glicoproteica de 166 aminoácidos, que constituye la hormona principal para la regulación y el mantenimiento, a niveles fisiològicos, de la masa de eritrocitos circulantes el la sangre. El diseño del gen sitético 620 pb, incluye la secuencia que codifica para el péptido señal de 27 aminoácidos, la secuencia consenso CCACC,los sitios de restricción Bgl LL y EcoR l en los extremos 5' y 3' y los codones más frecuentes en eucariotas. Fueron sintetizados en fase sólida, por el método del ß-cianoetilfosforamidito, 54 oligonuleótidos. El gen sintetizado, uno d4 los mayores reportados sin el uso de subclonajes de fragmentos, fue insertado en un vector de expresión para células de mamíferos y secuenciado con el método Sanger