Predicting DNA toehold-mediated strand displacement rate constants using a DNA-BERT transformer deep learning model.

Dynamic DNA nanotechnology is driving exciting developments in molecular computing, cargo delivery, sensing and detection. Combining this innovative area of research with the progress made in machine learning will aid in the design of sophisticated DNA machinery. Herein, we present a novel framework based on a transformer architecture and a deep learning model which can predict the rate constant of toehold-mediated strand displacement, the underlying process in dynamic DNA nanotechnology. Initially, a dataset of 4450 DNA sequences and corresponding rate constants were generated in-silico using KinDA. Subsequently, a 1D convolution neural network was trained using specific local features and DNA-BERT sequence embedding to produce predicted rate constants. As a result, the newly trained deep learning model predicted toehold-mediated strand displacement rate constants with a root mean square error of 0.76, during testing. These findings demonstrate that DNA-BERT can improve prediction accuracy, negating the need for extensive computational simulations or experimentation. Finally, the impact of various local features during model training is discussed, and a detailed comparison between the One-hot encoder and DNA-BERT sequences representation methods is presented.

Strategic concept paper for bioeconomy in Poland: executive summary.

The main objective of the proposed approach is to accelerate the transition of the bioeconomy towards a knowledge-based sustainable system, covering key biobased sectors strongly linked to agriculture in Poland, in line with the European Green Deal. The proposed model of a bioeconomy development strategy, with a special focus on agriculture, is based on two pillars: (1) strengthening traditional, relevant (in terms of economic indicators) sectors of the economy and improving their 'sustainability' by implementing the proposed transformation pathways; and (2) developing economic activities or 'niche or novel sectors' that are prospective accelerators of change in the face of climate challenge, and ensuring their upscaling. This approach forms the basis for policy planning at national and regional level in these European Union (EU) countries, where bioeconomy development strategies have been initiated through dialogue between science, administration and industry stakeholders. The strategic actions we propose are grouped in three areas; (1) Market intervention mainly by introducing sustainability criteria for the national production system; (2) Research, innovation and education that significantly strengthen the relationship between business and science and educational activities in the field of sustainability and climate change, and (3) Governance and policy actions to enforce the relationship between the main sub-sectors of bioeconomy and niche sectors in frame of bio-economy strategy or action plan that will profits by added value of products from bioeconomy sectors and increasing number of newly created jobs.

Cotranscriptional Folding of a Bio-orthogonal Fluorescent Scaffolded RNA Origami.

The scaffolded origami technique is an attractive tool for engineering nucleic acid nanostructures. This paper demonstrates scaffolded RNA origami folding in vitro in which, for the first time, all components are transcribed simultaneously in a single-pot reaction. Double-stranded DNA sequences are transcribed by T7 RNA polymerase into scaffold and staple strands able to correctly fold in a high synthesis yield into the nanoribbon. Synthesis is successfully confirmed by atomic force microscopy, and the unpurified transcription reaction mixture is analyzed by an in gel-imaging assay where the transcribed RNA nanoribbons are able to capture the specific dye through the reconstituted split Broccoli aptamer showing a clear green fluorescent band. Finally, we simulate the RNA origami in silico using the nucleotide-level coarse-grained model oxRNA to investigate the thermodynamic stability of the assembled nanostructure in isothermal conditions over a period of time. Our work suggests that the scaffolded origami technique is a viable, and potentially more powerful, assembly alternative to the single-stranded origami technique for future in vivo applications.

Efficiency under different methods for incorporating undesirable outputs in an LCA+DEA framework: A case study of winter wheat production in Poland.

Incorporating undesirable outputs in the operational assessments through the integration of Life Cycle Assessment (LCA) and Data Envelopment Analysis (DEA) has received great attention recently. There are many studies throughout literature that apply various methods to integrate LCA and DEA. In this case study, the six most common approaches were employed to assess the winter wheat cropping system in Poland. These six methods were: a) ignoring undesirable outputs, b) treating undesirables as inputs to the DEA model, c) data transformation, d) impact rate, e) ratio model, and f) slack based measurement DEA with undesirable outputs. The environmental impact of wheat production was assessed by determining its carbon footprint (CF). The mean CF equalled 0.45 kg CO2eq per kg wheat grain (ranging from 0.25 to 0.67). According to the model comparison results, a slack based measurement DEA with undesirable outputs could better reflect the performance of undesirable outputs, and was selected as the most appropriate method to maximize the efficiency of winter wheat production while minimizing undesirable outputs. The advantage of applying the slack based model with undesirable outputs was that the targets presented by this model were based on existing efficient farms, as opposed to theoretical results; thus achieving these targets are feasible. The average efficiency score equalled 0.43, whereby few farms were classified as efficient farms. The results of the proposed integrated model showed a high reduction potential for mineral fertilizers (up to 595 kg ha-1 y-1), seed (up to 37 kg ha-1 y-1), and fuel (up to 75 L ha-1 y-1) in winter wheat farms. These results help farmers to obtain a realistic and reliable usage pattern for inputs in a winter wheat production system, whereby the greatest production can be achieved in conjunction with the lowest possible environmental impact.

Linking Engineered Cells to Their Digital Twins: A Version Control System for Strain Engineering.

As DNA sequencing and synthesis become cheaper and more easily accessible, the scale and complexity of biological engineering projects is set to grow. Yet, although there is an accelerating convergence between biotechnology and digital technology, a deficit in software and laboratory techniques diminishes the ability to make biotechnology more agile, reproducible, and transparent while, at the same time, limiting the security and safety of synthetic biology constructs. To partially address some of these problems, this paper presents an approach for physically linking engineered cells to their digital footprint-we called it digital twinning. This enables the tracking of the entire engineering history of a cell line in a specialized version control system for collaborative strain engineering via simple barcoding protocols.

Molecular chracterisation of porcine group A rotaviruses: Studies on the age-related occurrence and spatial distribution of circulating virus genotypes in Poland.

Rotaviruses of group A (RVAs) commonly occur in farm animals. In pigs, they cause acute gastrointestinal disease which is considered as significant factor of economic losses in pig farming. The aim of the study was an assessment of the prevalence of rotavirus (RV) infections in farmed pigs in Poland, genotype identification of the virus strains in conjunction with their age-related occurrence and regional (province) distribution pattern in pig herds. In total, 920 pig faecal samples were collected from pigs between the ages of one week and two years old from 131 farms. RVAs were detected using ELISA and molecular methods followed by a sequence-based identification of G (VP7) and P (VP4) virus genotypes. RV antigen was found in 377 (41%) of pig faecal samples. The correlation between pig age and frequency of RV infections was shown. In the Polish pig population, 145 RVA strains representing 33 GP genotypes were identified. Subsequent molecular analysis revealed an age-dependent and regional diversity in distribution of genotypes and virus strains. Besides typical pig RVA strains, novel strains such as G5P [34], G9P[34], and human G1P[8] were identified in this animal host. Findings from this study showed a change over time in the genotype occurrence of circulating pig RVAs in Poland. The high genetic variability of RV strains and acquisition of new virus genotypes have led to the emergence of novel, genetically distinct RVAs. The changes in the genotype occurrence of RVA strains in pigs indicate the need for their continuous epidemiological surveillance.

Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon.

RNA presents intringuing roles in many cellular processes and its versatility underpins many different applications in synthetic biology. Nonetheless, RNA origami as a method for nanofabrication is not yet fully explored and the majority of RNA nanostructures are based on natural pre-folded RNA. Here we describe a biologically inert and uniquely addressable RNA origami scaffold that self-assembles into a nanoribbon by seven staple strands. An algorithm is applied to generate a synthetic De Bruijn scaffold sequence that is characterized by the lack of biologically active sites and repetitions larger than a predetermined design parameter. This RNA scaffold and the complementary staples fold in a physiologically compatible isothermal condition. In order to monitor the folding, we designed a new split Broccoli aptamer system. The aptamer is divided into two nonfunctional sequences each of which is integrated into the 5' or 3' end of two staple strands complementary to the RNA scaffold. Using fluorescence measurements and in-gel imaging, we demonstrate that once RNA origami assembly occurs, the split aptamer sequences are brought into close proximity forming the aptamer and turning on the fluorescence. This light-up 'bio-orthogonal' RNA origami provides a prototype that can have potential for in vivo origami applications.

Designing Uniquely Addressable Bio-orthogonal Synthetic Scaffolds for DNA and RNA Origami.

Nanotechnology and synthetic biology are rapidly converging, with DNA origami being one of the leading bridging technologies. DNA origami was shown to work well in a wide array of biotic environments. However, the large majority of extant DNA origami scaffolds utilize bacteriophages or plasmid sequences thus severely limiting its future applicability as a bio-orthogonal nanotechnology platform. In this paper we present the design of biologically inert (i.e., "bio-orthogonal") origami scaffolds. The synthetic scaffolds have the additional advantage of being uniquely addressable (unlike biologically derived ones) and hence are better optimized for high-yield folding. We demonstrate our fully synthetic scaffold design with both DNA and RNA origamis and describe a protocol to produce these bio-orthogonal and uniquely addressable origami scaffolds.