Structural Insights Into the 5′UG/3′GU Wobble Tandem in Complex With Ba2+ Cation

G•U wobble base pair frequently occurs in RNA structures. The unique chemical, thermodynamic, and structural properties of the G•U pair are widely exploited in RNA biology. In several RNA molecules, the G•U pair plays key roles in folding, ribozyme catalysis, and interactions with proteins. G•U may occur as a single pair or in tandem motifs with different geometries, electrostatics, and thermodynamics, further extending its biological functions. The metal binding affinity, which is essential for RNA folding, catalysis, and other interactions, differs with respect to the tandem motif type due to the different electrostatic potentials of the major grooves. In this work, we present the crystal structure of an RNA 8-mer duplex r[UCGUGCGA]2, providing detailed structural insights into the tandem motif I (5′UG/3′GU) complexed with Ba2+ cation. We compare the electrostatic potential of the presented motif I major groove with previously published structures of tandem motifs I, II (5′GU/3′UG), and III (5′GG/3′UU). A local patch of a strongly negative electrostatic potential in the major groove of the presented structure forms the metal binding site with the contributions of three oxygen atoms from the tandem. These results give us a better understanding of the G•U tandem motif I as a divalent metal binder, a feature essential for RNA functions.

Novel Centromeric and Subtelomeric Repetitive DNA Sequences for Karyotyping the Bambara Groundnut (Vigna subterranea L. Verdc.)

Bambara groundnut (<i>Vigna subterranea</i> L. Verdc.) is an un­derutilized minor legume crop with climate resilience and great potential use in world agriculture. This study aimed to cytogenetically characterize the genome and chromosome properties of Bambara groundnut. We cloned, sequenced, and mapped a 50-bp centromere-specific tandem repeat on all chromosomes. In addition, a 400-bp subtelomeric repeat was discovered and mapped on a single pair of chromosomes. A Bambara groundnut karyotype was constructed using these novel repeats along with ribosomal RNA genes (45S and 5S) and telomeric DNA sequences. This study provides the first analysis of the genome and chromosome properties of Bambara groundnut. We discuss our findings in relation to genetic improvement of Bambara groundnut and centromere evolution in legume species.

Effects of Water Removal from Palm Oil Reactant by Electrolysis on the Fuel Properties of Biodiesel

Biodiesel, which is composed of mono-alkyl esters of long carbon-chained fatty acids, is used as an alternative fuel to petro-diesel. The water content of the reactant mixture of feedstock oil influences the extent of transesterification and thus the fuel characteristics. Lower water content in feedstock oil is generally suggested for successful transesterification. This experimental study removed water from the reactant mixture of feedstock palm oil and methanol during transesterification using various systems composed of either electrodes or molecular sieves with rotary vibration. The effect of input electrical energy, number of electrodes, vibration modes, and operating time on the amount of water removed from the reactant mixture and the fuel properties of the final biodiesel product were analyzed and compared with those achieved using molecular sieves. The results show that the biodiesel—after water was removed during transesterification—appeared to have increased kinematic viscosity, cetane index, distillation temperature, and acid value, while the heating value, flash point, ignition point, and water content decreased with an increase in the input electrical energy of the electrodes responsible for electrolyzing water away. Electrolysis by the double-pair electrodes was more effective at reducing acid value and water content than that performed by the single-pair electrodes under the same input electrical energy. The biodiesel was found to have the lowest water content (0.0304 wt.%) and the highest water-removal rate (0.011 wt.%) when water was removed during transesterification by the double-pair electrodes with an input electrical energy of 9 J/(g palm oil). The water-removal rate of the rotary-vibrating molecular sieves was 11.24 times that of the single-pair electrodes. The biodiesel was found to have increased kinematic viscosity with higher input electrical energy, reaching 5.15 mm2/s when the double-pair electrodes with an input electrical energy of 11 J/(g palm oil) were used. Longer carbon-chained fatty acids, ranging from C20 to C24, amounted to 0.74 wt.% of the biodiesel produced using the double-pair electrodes, which was greater than that seen for the single-pair electrodes. However, the molecular sieve method consumed more energy than the double-pair electrodes did to remove the same amount of water from the palm oil reactant mixture via transesterification.

MCKAT: a multi-dimensional copy number variant kernel association test

Background Copy number variants (CNVs) are the gain or loss of DNA segments in the genome. Studies have shown that CNVs are linked to various disorders, including autism, intellectual disability, and schizophrenia. Consequently, the interest in studying a possible association of CNVs to specific disease traits is growing. However, due to the specific multi-dimensional characteristics of the CNVs, methods for testing the association between CNVs and the disease-related traits are still underdeveloped. We propose a novel multi-dimensional CNV kernel association test (MCKAT) in this paper. We aim to find significant associations between CNVs and disease-related traits using kernel-based methods. Results We address the multi-dimensionality in CNV characteristics. We first design a single pair CNV kernel, which contains three sub-kernels to summarize the similarity between two CNVs considering all CNV characteristics. Then, aggregate single pair CNV kernel to the whole chromosome CNV kernel, which summarizes the similarity between CNVs in two or more chromosomes. Finally, the association between the CNVs and disease-related traits is evaluated by comparing the similarity in the trait with kernel-based similarity using a score test in a random effect model. We apply MCKAT on genome-wide CNV datasets to examine the association between CNVs and disease-related traits, which demonstrates the potential usefulness the proposed method has for the CNV association tests. We compare the performance of MCKAT with CKAT, a uni-dimensional kernel method. Based on the results, MCKAT indicates stronger evidence, smaller p-value, in detecting significant associations between CNVs and disease-related traits in both rare and common CNV datasets. Conclusion A multi-dimensional copy number variant kernel association test can detect statistically significant associated CNV regions with any disease-related trait. MCKAT can provide biologists with CNV hot spots at the cytogenetic band level that CNVs on them may have a significant association with disease-related traits. Using MCKAT, biologists can narrow their investigation from the whole genome, including many genes and CNVs, to more specific cytogenetic bands that MCKAT identifies. Furthermore, MCKAT can help biologists detect significantly associated CNVs with disease-related traits across a patient group instead of examining each subject’s CNVs case by case.

Single candidates: Ensuring a path to victory in local elections

This article analyzes the phenomenon of single candidates in Indonesia's 2020 local elections, where the number increased compared to the previous local elections. Although initially local elections with single candidates were not intended, by a ruling of the Constitutional Court a local election must still be carried out even if there is only a single pair of candidates. The number of single candidates has increased, as it becomes an easier and cheaper way to ensure victory, particularly for incumbents. This condition is strengthened by the culture of political parties that tend to provide support to candidates who possess a greater chance of winning in order to take control of the government and form political cartels. Although presently it has not been indicated that single candidates are a form of oligarchic rule and political dynasty, it may become an easy way to obtain political power.

On transmission Zeros of piezoelectric structures

The evaluation of transmission zeros is of great importance for the control engineering applications. The structures equipped with piezoelectric patches are complex to model and usually require finite element approaches supplemented by model reduction. This study rigorously investigates the influence of mesh size, model reduction, boundary conditions (free and clamped), and sensor/actuator configuration (collocated and non-collocated) on the evaluation of transmission zeros of the piezoelectric structures. The numerical illustrations are presented for a thin rectangular plate equipped with a single pair of piezoelectric voltage sensor/ voltage actuator. Through the examples considered in this study, a link is presented between the static response (or static deflected shape) and the transmission zeros of the piezoelectric structures. This interesting observation forms the basis of: (i) a local mesh refinement strategy for computationally efficient estimation of the transmission zeros and (ii) a physical interpretation of the pole-zero pattern in the case of piezoelectric structures. The physical interpretation developed in this study helps in qualitatively explaining the pole-zero patterns observed for different configurations. It is also shown that this understanding of the relation between the static deformed shape and the transmission zeros can be used by the practitioners to modify the pole-zero pattern through a careful selection of the orientation and the size of the piezoelectric patches.

Genetic Analysis of Yield and Quality Traits in Switchgrass Based on Population Crosses

Obtaining greater genetic gains, particularly for biomass yield, requires a good understanding of the gene action governing the inheritance of traits with economic importance in switchgrass (Panicum virgatum L.). Individual genotypes from three different accessions were crossed in single-pair matings with reciprocals to assess the relative importance of additive to nonadditive genetic variation and the potential of using inter-ecotypic crosses to improve dry matter yield (DMY), in vitro dry matter digestibility (IVDMD), lignin content (ADL and KL), and ethanol yield (ETOH). Crosses and four reference populations were planted in a randomized complete block design with eight replications of single family-rows plots, with five-plants each and 1 m spacings. A linear mixed model was applied as per the restricted maximum likelihood method, integrated with a pedigree tracing back to the original founders of these parental populations, and augmented with the designation of four genetic groups. Variation due to SCA (specific combining ability) was predominant for all traits, contributing from 20% to 57% of the total phenotypic variation and with Baker’s ratios (GCA/SCA) varying from 0.003 to 0.67. Heritability values calculated at the fullsib-family mean level were moderate to very high. Variation due to GCA (general combining ability) was detected with a lesser significance for DMY and ETOH. A reciprocal GCA effect was present in the form of maternal inheritance for DMY, suggesting the use of the highest biomass-yielding parent as female in inter-ecotypic breeding. Selecting and deploying fullsib families, deploying clonal hybrids, and adopting an introgression breeding approach are all possibilities available to switchgrass breeders to exploit the complementary genes from this germplasm and capitalize on the non-additive genetic variation present in these crosses.

Migrationskonzept zur Einführung von Ethernet TSN in die Feldebene

Zusammenfassung Anwendungen, wie z. B. eine datengetriebene Prozessüberwachung oder eine für die Fertigung kundenindividueller Produkte notwendige wandlungsfähige Produktionstechnik, erzeugen neue und zusätzliche Anforderungen an die Industrielle Kommunikation. Die Kommunikation muss stoßfrei rekonfiguriert werden können, um Plug-and-Play-Dienste zu ermöglichen und so skalierbar und sicher sein, dass eine vertikale Kommunikation vom Sensor bis zur Cloud möglich wird. Als Basis für ein skalierbares Kommunikationsnetzwerk, welches von verschiedenen echtzeitfähigen oder nicht-echtzeitfähigen Protokollen konvergent genutzt werden kann und so die bisher harte Grenze zwischen IT und Feldebene durchlässig macht, soll Ethernet TSN verwendet werden. Um auch einfache Sensoren ohne Gateways anzuschließen, sollen neue physikalische Übertragungstechnologien, Single Pair Ethernet (SPE) eingesetzt werden. Lange Lebenszyklen von Produktionsanlagen und Automatisierungstechnik führen allerdings dazu, dass die Einführung und Verbreitung neuer Technologien nur langsam erfolgt. Dabei unterliegt die Einführung der genannten Technologien unterschiedlichen Einflüssen: So ist die Einführung von TSN als Netzwerktechnologie gegenüber einer Physical Layer-Technologie, wie Single Pair Ethernet, oder einer Protokolleinführung, wie OPC UA, besonders schwer, da TSN nur dann genutzt werden kann, wenn alle Geräte eines Netzwerkes TSN auch unterstützen. Migrationsstrategien für Feldgeräte sind heute häufig unzureichend. Ein neuer Ansatz für eine verbesserte Migrationsstrategie für Feldgeräte, der die Einführung von Ethernet TSN in die Feldebene ermöglicht, ist der Ethernet Bridge-Modus „Time Aware Forwarding“. Time Aware Forwarding vereinfacht die Umsetzung von TSN in Feldgeräte mit zwei Ports. Bestehende PROFINET-Hardware und -Geräte erlangen mit diesem Verfahren die geforderten Funktions- und Leistungsmerkmale, wie Synchronität und geplanter Datenverkehr, um mit TSN-Netzwerken zusammenarbeiten zu können.

Neuronally Produced Betaine Acts via a Novel Ligand Gated Ion Channel to Control Behavioural States

Trimethyl glycine, or betaine, is an amino acid derivative found in diverse organisms, from bacteria to plants and animals. It can function as an osmolyte to protect cells against osmotic stress, and building evidence suggests betaine may also play important functional roles in the nervous system. However, despite growing interest in betaine's roles in the nervous system, few molecular mechanisms have been elucidated. Here we identify the expression of betaine synthesis pathway genes in the nervous system of the nematode worm, C. elegans. We show that betaine, produced in a single pair of interneurons, the RIMs, can control complex behavioural states. Moreover, we also identify and characterise a new betaine-gated inhibitory ligand gated ion channel, LGC-41, which is required for betaine related behavioural changes. Intriguingly we observed expression of LGC-41 in punctate structures across several sensory and interneurons, including those synaptically connected to the RIMs. Our data presents a neuronal molecular mechanism for the action of betaine, via a specific receptor, in the control of complex behaviour within the nervous system of C. elegans. This may suggest a much broader role for betaine in the regulation of animal nervous systems than previously recognised.