An Alternative Approach to Geometric Harmonization of the Great Mosque in Córdoba

This research constitutes an alternative to proportional composition studies of the original Great Mosque and its four extensions in Córdoba, based on diagonals of a square and rectangles in ratio 1:√2 and 1:√3 (Fernández-Puertas, 2000, 2008). The method for this alternative research consists of graphic analyses by iteration of hypothetical products of the golden section in AutoCAD 2D software conducted on architectural drawings of the original Great Mosque and its four extensions, in reconstruction, according to measurements from the relevant literature. The alternative method insists on geometric harmonization derived from only one starting length in all drawings of same scale. It resulted in the production of a single harmonization pattern based on the golden section, with an additional sequence of a√2/Φn, successively developed for the original monument and its four extensions. It also includes otherwise excluded basic composition elements (minarets) and reveals otherwise hidden proportional qualities. The alternative approach enabled a deduction of algebraic expressions having only one variable for all drawings of the same scale. Their arithmetic values and deviations from real dimensions are calculated. Geometric harmonization by golden section with another starting length is applied to the drawing of the elevation at a different scale.

Chloroplast transit peptides often require downstream unstructured sequence in Chlamydomonas reinhardtii

The N-terminal sequence stretch that defines subcellular targeting for most nuclear encoded chloroplast proteins is usually considered identical to the sequence that is cleaved upon import. Yet here this study shows that for nine out of ten tested Chlamydomonas chloroplast transit peptides, additional sequence past the cleavage site is required to enable chloroplast targeting. Using replacements of native post-cleavage residues with alternative sequences points to a role for unstructured sequence at mature protein N-termini.

Infection, recovery and re-infection of farmed mink with SARS-CoV-2

Mink, on a farm with about 15,000 animals, became infected with SARS-CoV-2. Over 75% of tested animals were positive for SARS-CoV-2 RNA in throat swabs and 100% of tested animals were seropositive. The virus responsible had a deletion of nucleotides encoding residues H69 and V70 within the spike protein gene as well as the A22920T mutation, resulting in the Y453F substitution within this protein, seen previously in mink. The infected mink recovered and after free-testing of 300 mink (a level giving 93% confidence of detecting a 1% prevalence), the animals remained seropositive. During further follow-up studies, after a period of more than 2 months without any virus detection, over 75% of tested animals again scored positive for SARS-CoV-2 RNA. Whole genome sequencing showed that the viruses circulating during this re-infection were most closely related to those identified in the first outbreak on this farm but additional sequence changes had occurred. Animals had much higher levels of anti-SARS-CoV-2 antibodies in serum samples after the second round of infection than at free-testing or during recovery from initial infection, consistent with a boosted immune response. Thus, it was concluded that following recovery from an initial infection, seropositive mink were readily re-infected by SARS-CoV-2.

RNA Helix Thermodynamics: The End Game

Nearest neighbor parameters for estimating the folding stability of RNA secondary structures are in widespread use. For helices, current parameters penalize terminal AU base pairs relative to terminal GC base pairs. We curated an expanded database of helix stabilities determined by optical melting experiments. Analysis of the updated database shows that terminal penalties depend on the sequence identity of the adjacent penultimate base pair. New nearest neighbor parameters that include this additional sequence dependence accurately predict the measured values of 271 helices in an updated database with a correlation coefficient of 0.982. This refined understanding of helix ends facilitates fitting terms for base pair stacks with GU pairs. Prior parameter sets treated 5'GGUC/3'CUGG separately from other 5'GU/3'UG stacks. The improved understanding of helix end stability, however, makes the separate treatment unnecessary. Introduction of the additional terms was tested with three optical melting experiments. The average absolute difference between measured and predicted free energy changes at 37° C for these three duplexes containing terminal adjacent AU and GU pairs improved from 1.38 to 0.27 kcal/mol. This confirms the need for the additional sequence dependence in the model.

Single-Molecule Detection of SARS-CoV-2 by Plasmonic Sensing of Isothermally Amplified Nucleic Acids

Single-molecule detection of pathogens such as SARS-CoV-2 is key to combat infectious diseases outbreak and pandemic. Currently colorimetric sensing with loop-mediated isothermal amplification (LAMP) provides simple readouts but suffers from intrinsic non-template amplification. Herein, we report that plasmonic sensing of LAMP amplicons via DNA hybridization allows highly specific and single-molecule detection of SARS-CoV-2 RNA. Our work has two important advances. First, we develop gold and silver alloy (Au-Ag) nanoshells as plasmonic sensors that have 4-times stronger extinction in the visible wavelengths and give 20-times lower detection limit for oligonucleotides than Au nanoparticles. Second, we demonstrate that the diagnostic method allows cutting the complex LAMP amplicons into short repeats that are amendable for hybridization with oligonucleotide-functionalized nanoshells. This additional sequence identification eliminates the contamination from non-template amplification. The detection method is a simple and single-molecule diagnostic platform for virus testing at its early representation.Table of Content

Efficient linear dsDNA tagging using deoxyuridine excision

Site-specific strategies for exchanging segments of dsDNA are important for DNA library construction and molecular tagging. Deoxyuridine (dU) excision is an approach for generating 3′ ssDNA overhangs in gene assembly and molecular cloning procedures. Unlike approaches that use a multi-base pair motif to specify a DNA cut site, dU excision requires only a dT→dU substitution. Consequently, excision sites can be embedded in biologically active DNA sequences by placing dU substitutions at non-perturbative positions. In this work, I describe a molecular tagging method that uses dU excision to exchange a segment of a dsDNA strand with a long synthetic oligonucleotide. The core workflow of this method, called deoxyUridine eXcision-tagging (dUX-tagging), is an efficient one-pot reaction: strategically positioned dU nucleotides are excised from dsDNA to generate a 3′ overhang so that additional sequence can be appended by annealing and ligating a tagging oligonucleotide. The tagged DNA is then processed by one of two procedures to fill the 5′ overhang and remove excess tagging oligo. To facilitate its widespread use, all dUX-tagging procedures exclusively use commercially available reagents. As a result, dUX-tagging is a concise and easily implemented approach for high-efficiency linear dsDNA tagging.

Infection, recovery and re-infection of farmed mink with SARS-CoV-2

Mink, on a farm with about 15,000 animals, became infected with SARS-CoV-2. Over 75% of tested animals were positive for SARS-CoV-2 RNA in throat swabs and 100% of tested animals were seropositive. The virus responsible had a deletion of nucleotides encoding residues H69 and V70 within the spike protein gene. The infected mink recovered and after free-testing of the mink, the animals remained seropositive. During follow-up studies, after a period of more than 2 months without virus detection, over 75% of tested animals scored positive again for SARS-CoV-2 RNA. Whole genome sequencing showed that the virus circulating during this re-infection was most closely related to the virus identified in the first outbreak on this farm but additional sequence changes had occurred. Animals had much higher levels of anti-SARS-CoV-2 antibodies after re-infection than at free-testing. Thus, following recovery from an initial infection, seropositive mink rapidly became susceptible to re-infection by SARS-CoV-2.

A large-scale comparative study on peptide encodings for biomedical classification

Owing to the great variety of distinct peptide encodings, working on a biomedical classification task at hand is challenging. Researchers have to determine encodings capable to represent underlying patterns as numerical input for the subsequent machine learning. A general guideline is lacking in the literature, thus, we present here the first large-scale comprehensive study to investigate the performance of a wide range of encodings on multiple datasets from different biomedical domains. For the sake of completeness, we added additional sequence- and structure-based encodings. In particular, we collected 50 biomedical datasets and defined a fixed parameter space for 48 encoding groups, leading to a total of 397 700 encoded datasets. Our results demonstrate that none of the encodings are superior for all biomedical domains. Nevertheless, some encodings often outperform others, thus reducing the initial encoding selection substantially. Our work offers researchers to objectively compare novel encodings to the state of the art. Our findings pave the way for a more sophisticated encoding optimization, for example, as part of automated machine learning pipelines. The work presented here is implemented as a large-scale, end-to-end workflow designed for easy reproducibility and extensibility. All standardized datasets and results are available for download to comply with FAIR standards.

Energisation Method For Offshore Wind Farms Connected To HVdc Via Diode Rectifiers

Diode rectifiers (DRs) have been recently suggested as a viable alternative for connecting offshore wind farms (OWFs) to HVdc, eliciting growing interest from both industry and academia. However, energisation of DR-connected OWFs is not straightforward. The present study constitutes a proof of concept of a novel energisation method for DR-connected OWFs, in which auxiliary power is provided from the shore through the HVdc link and the dc bus bar of one or more WTs. The proposed method provides an alternative with minimal additional hardware, which can be easily extended to more WTs in the OWF, increasing reliability by providing redundancy. The study includes coinciding auxiliary loads with active and reactive power components and a semi-aggregated OWF model, in which every WT is individually represented in the string containing the energising WT. An additional sequence of simulation events is considered following the initial energisation sequence. Such sequence comprises wind power taking over the provision of the auxiliary power. The simulation results indicate that the proposed method is a suitable alternative for energising OWFs connected to HVdc via DRs.<br><br>The manuscript has been submitted to the CIGRÉ Symposium 2021.

Energisation Method for Offshore Wind Farms Connected to HVdc via Diode Rectifiers

Diode rectifiers (DRs) have been recently suggested as a viable alternative for connecting offshore wind farms (OWFs) to HVdc, eliciting growing interest from both industry and academia. However, energisation of DR-connected OWFs is not straightforward. The present study constitutes a proof of concept of a novel energisation method for DR-connected OWFs, in which auxiliary power is provided from the shore through the HVdc link and the dc bus bar of one or more WTs. The proposed method provides an alternative with minimal additional hardware, which can be easily extended to more WTs in the OWF, increasing reliability by providing redundancy. The study includes coinciding auxiliary loads with active and reactive power components and a semi-aggregated OWF model, in which every WT is individually represented in the string containing the energising WT. An additional sequence of simulation events is considered following the initial energisation sequence. Such sequence comprises wind power taking over the provision of the auxiliary power. The simulation results indicate that the proposed method is a suitable alternative for energising OWFs connected to HVdc via DRs.<br><br>The manuscript has been submitted to the CIGRÉ Symposium 2021.