The jumping spider Saitis barbipes lacks a red photoreceptor to see its own sexually dimorphic red coloration

Examining the role of color in mate choice without testing what colors the study animal is capable of seeing can lead to ill-posed hypotheses and erroneous conclusions. Here, we test the seemingly reasonable assumption that the sexually dimorphic red coloration of the male jumping spider Saitis barbipes is distinguishable, by females, from adjacent black color patches. Using microspectrophotometry, we find clear evidence for photoreceptor classes with maximal sensitivity in the UV (359 nm) and green (526 nm), inconclusive evidence for a photoreceptor maximally sensitive in the blue (451 nm), and no evidence for a red photoreceptor. No colored filters within the lens or retina could be found to shift green sensitivity to red. To quantify and visualize whether females may nevertheless be capable of discriminating red from black color patches, we take multispectral images of males and calculate photoreceptor excitations and color contrasts between color patches. Red patches would be, at best, barely discriminable from black, and not discriminable from a low-luminance green. Some color patches that appear achromatic to human eyes, such as beige and white, strongly absorb UV wavelengths and would appear as brighter “spider-greens” to S. barbipes than the red color patches. Unexpectedly, we discover an iridescent UV patch that contrasts strongly with the UV-absorbing surfaces dominating the rest of the spider. We propose that red and black coloration may serve identical purposes in sexual signaling, functioning to generate strong achromatic contrast with the visual background. The potential functional significance of red coloration outside of sexual signaling is discussed.

Rider and Sunflower optimization-driven neural network for image classification

Image classification is the classical issue in computer vision, machine learning, and image processing. The image classification is measured by differentiating the image into the prescribed category based on the content of the vision. In this paper, a novel classifier named RideSFO-NN is developed for image classification. The proposed method performs the image classification by undergoing two steps, namely feature extraction and classification. Initially, the images from various sources are provided to the proposed Weighted Shape-Size Pattern Spectra for pattern analysis. From the pattern analysis, the significant features are obtained for the classification. Here, the proposed Weighted Shape-Size Pattern Spectra is designed by modifying the gray-scale decomposition with Weight-Shape decomposition. Then, the classification is done based on Neural Network (NN) classifier, which is trained using an optimization approach. The optimization will be done by the proposed Ride Sunflower optimization (RideSFO) algorithm, which is the integration of Rider optimization algorithm (ROA), and Sunflower optimization algorithm (SFO). Finally, the image classification performance is evaluated using RideSFO-NN based on sensitivity, specificity, and accuracy. The developed RideSFO-NN method achieves the maximal accuracy of 94%, maximal sensitivity of 93.87%, and maximal specificity of 90.52% based on K-Fold.

Tannic Acid-Capped Gold Nanoparticles as a Novel Nanozyme for Colorimetric Determination of Pb2+ Ions

In this study, tannic acid-modified gold nanoparticles were found to have superior nanozyme activity and catalyze the oxidation reaction of 3,3′,5,5′-tetramethylbenzidine in the presence of hydrogen peroxide. Enhancing the catalytic activity of the nanozyme by Pb2+ ions caused by selectively binding metal ions by the tannic acid-capped surface of gold nanoparticles makes them an ideal colorimetric probe for Pb2+. The parameters of the reaction, including pH, incubation time, and concentration of components, were optimized to reach maximal sensitivity of Pb2+ detection. The absorption change is directly proportional to the Pb2+ concentration and allows the determination of Pb2+ ions within 10 min. The colorimetric sensor is characterized by a wide linear range from 25 to 500 ng×mL−1 with a low limit of detection of 11.3 ng×mL−1. The highly sensitive and selective Pb2+ detection in tap, drinking, and spring water revealed the feasibility and applicability of the developed colorimetric sensor.

DEPENDENCE OF MAXIMAL SENSITIVITY OF THE MAGNETIC FIELD HALL SENSORS BASED ON GRAPHENE ON TEMPERATURE

A theory of graphene-based magnetic field Hall sensors sensitivity dependence on temperature is summarized. The existence of low-temperature range with sensitivity, almost independent on temperature, is predicted; at higher temperatures, when thermally-induced carrier concentration in graphene prevails, the sensitivity decreases with temperature. The experimental studies of the temperature dependence of magnetic sensitivity of Hall sensors on single layer graphene base were carried in temperature range from 300 °K to 430 °K. The values of sensitivity, obtained for room temperatures ~ 230 V·А‑1·Т‑1 exceed essentially the maximum sensitivity of the traditional Hall sensors on silicon base ~ 100 V·А‑1·Т‑1.

The ATP bioluminescence assay: a new application and optimization for viability testing in the parasitic nematode Haemonchus contortus

The parasitic gastrointestinal nematode Haemonchus contortus causes serious economic losses to agriculture due to infection and disease in small ruminant livestock. The development of new therapies requires appropriate viability testing, with methods nowadays relying on larval motility or development using procedures that involve microscopy. None of the existing biochemical methods, however, are performed in adults, the target stage of the anthelmintic compounds. Here we present a new test for the viability of H. contortus adults and exsheathed third-stage larvae which is based on a bioluminescent assay of ATP content normalized to total protein concentration measured using bicinchoninic acid. All the procedure steps were optimized to achieve maximal sensitivity and robustness. This novel method can be used as a complementary assay for the phenotypic screening of new compounds with potential antinematode activity in exsheathed third-stage larvae and in adult males. Additionally, it might be used for the detection of drug-resistant isolates.

Amplification-free RNA detection with CRISPR–Cas13

CRISPR-based nucleic-acid detection is an emerging technology for molecular diagnostics. However, these methods generally require several hours and could cause amplification errors, due to the pre-amplification of target nucleic acids to enhance the detection sensitivity. Here, we developed a platform that allows “CRISPR-based amplification-free digital RNA detection (SATORI)”, by combining CRISPR-Cas13-based RNA detection and microchamber-array technologies. SATORI detected single-stranded RNA targets with maximal sensitivity of ~10 fM in <5 min, with high specificity. Furthermore, the simultaneous use of multiple different guide RNAs enhanced the sensitivity, thereby enabling the detection of the SARS-CoV-2 N-gene RNA at ~5 fM levels. Therefore, we hope SATORI will serve as a powerful class of accurate and rapid diagnostics.

Evaluation of a Broad Panel of SARS-CoV-2 Serological Tests for Diagnostic Use

Serological testing is crucial in detection of previous infection and in monitoring convalescent and vaccine-induced immunity. During the Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) pandemic, numerous assay platforms have been developed and marketed for clinical use. Several studies recently compared clinical performance of a limited number of serological tests, but broad comparative evaluation is currently missing. Within this study, a panel of 161 sera from SARS-CoV-2 infected, seasonal CoV-infected and SARS-CoV-2 naïve subjects was enrolled to evaluate 16 ELISA/ECLIA-based and 16 LFA-based tests. Specificities of all ELISA/ECLIA-based assays were acceptable and generally in agreement with the providers’ specifications, but sensitivities were lower as specified. Results of the LFAs were less accurate as compared to the ELISAs, albeit with some exceptions. We found a sporadic unequal immune response for different antigens and thus recommend the use of a nucleocapsid protein (N)- and spike protein (S)-based test combination when maximal sensitivity is necessary. Finally, the quality of the immune response in terms of neutralization should be tested using S-based IgG tests.

Specific residues in the cytoplasmic domain modulate photocurrent kinetics of channelrhodopsin from Klebsormidium nitens

Channelrhodopsins (ChRs) are light-gated ion channels extensively applied as optogenetics tools for manipulating neuronal activity. All currently known ChRs comprise a large cytoplasmic domain, whose function is elusive. Here, we report the cation channel properties of KnChR, one of the photoreceptors from a filamentous terrestrial alga Klebsormidium nitens, and demonstrate that the cytoplasmic domain of KnChR modulates the ion channel properties. KnChR is constituted of a 7-transmembrane domain forming a channel pore, followed by a C-terminus moiety encoding a peptidoglycan binding domain (FimV). Notably, the channel closure rate was affected by the C-terminus moiety. Truncation of the moiety to various lengths prolonged the channel open lifetime by more than 10-fold. Two Arginine residues (R287 and R291) are crucial for altering the photocurrent kinetics. We propose that electrostatic interaction between the rhodopsin domain and the C-terminus domain accelerates the channel kinetics. Additionally, maximal sensitivity was exhibited at 430 and 460 nm, the former making KnChR one of the most blue-shifted ChRs characterized thus far, serving as a novel prototype for studying the molecular mechanism of color tuning of the ChRs. Furthermore, KnChR would expand the optogenetics tool kit, especially for dual light applications when short-wavelength excitation is required.

VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

Background Viruses are a significant player in many biosphere and human ecosystems, but most signals remain “hidden” in metagenomic/metatranscriptomic sequence datasets due to the lack of universal gene markers, database representatives, and insufficiently advanced identification tools. Results Here, we introduce VirSorter2, a DNA and RNA virus identification tool that leverages genome-informed database advances across a collection of customized automatic classifiers to improve the accuracy and range of virus sequence detection. When benchmarked against genomes from both isolated and uncultivated viruses, VirSorter2 uniquely performed consistently with high accuracy (F1-score > 0.8) across viral diversity, while all other tools under-detected viruses outside of the group most represented in reference databases (i.e., those in the order Caudovirales). Among the tools evaluated, VirSorter2 was also uniquely able to minimize errors associated with atypical cellular sequences including eukaryotic genomes and plasmids. Finally, as the virosphere exploration unravels novel viral sequences, VirSorter2’s modular design makes it inherently able to expand to new types of viruses via the design of new classifiers to maintain maximal sensitivity and specificity. Conclusion With multi-classifier and modular design, VirSorter2 demonstrates higher overall accuracy across major viral groups and will advance our knowledge of virus evolution, diversity, and virus-microbe interaction in various ecosystems. Source code of VirSorter2 is freely available (https://bitbucket.org/MAVERICLab/virsorter2), and VirSorter2 is also available both on bioconda and as an iVirus app on CyVerse (https://de.cyverse.org/de).

Development of an Automated Chemiluminescence Assay System for Quantitative Measurement of Multiple Anti-SARS-CoV-2 Antibodies

ObjectivesSerological tests for COVID-19 have been instrumental in studying the epidemiology of the disease. However, the performance of the currently available tests is plagued by the problem of variability. We have developed a high-throughput serological test capable of simultaneously detecting total immunoglobulins (Ig) and immunoglobulin G (IgG) against nucleocapsid protein (NP) and spike protein (SP) and report its performance in detecting COVID-19 in clinical samples.MethodsWe designed and prepared reagents for measuring NP-IgG, NP-Total Ig, SP-IgG, and SP-Total Ig (using N-terminally truncated NP (ΔN-NP) or receptor-binding domain (RBD) antigen) dedicated automated chemiluminescent enzyme immunoassay analyzer AIA-CL1200. After determining the basal thresholds based on 17 sera obtained from confirmed COVID-19 patients and 600 negative sera, the clinical validity of the assay was evaluated using independent 202 positive samples and 1,000 negative samples from healthy donors.ResultsAll of the four test parameters showed 100% specificity individually (1,000/1,000; 95%CI, 99.63–100). The sensitivity of the assay increased proportionally to the elapsed time from symptoms onset, and all the tests achieved 100% sensitivity (153/153; 95%CI, 97.63–100) after 13 days from symptoms onset. NP-Total Ig was the earliest to attain maximal sensitivity among the other antibodies tested.ConclusionOur newly developed serological testing exhibited 100% sensitivity and specificity after 13 days from symptoms onset. Hence, it could be used as a reliable method for accurate detection of COVID-19 patients and to evaluate seroprevalence and possibly for surrogate assessment of herd immunity.