Search

Establishment of oak seedlings, which is an important factor in forest restoration, is affected by drought that hampers the survival, growth, and development of seedlings. Therefore, it is necessary to understand how seedlings respond to and recover from water-shortage stress. We subjected seedlings of two oak species, Quercus acutissima and Quercus palustris, to drought stress for one month and then rewatered them for six days to observe physiological and genetic expression changes. Phenotypically, the growth of Q. acutissima was reduced and severe wilting and recovery failure were observed in Q. palustris after an increase in plant temperature. The two species differed in several physiological parameters during drought stress and recovery. Although the photosynthesis-related indicators did not change in Q. acutissima, they were decreased in Q. palustris. Moreover, during drought, content of soluble sugars was significantly increased in both species, but it recovered to original levels only in Q. acutissima. Malondialdehyde content increased in both the species during drought, but it did not recover in Q. palustris after rewatering. Among the antioxidant enzymes, only superoxide dismutase activity increased in Q. acutissima during drought, whereas activities of ascorbate peroxidase, catalase, and glutathione reductase increased in Q. palustris. Abscisic acid levels were increased and then maintained in Q. acutissima, but recovered to previous levels after rewatering in Q. palustris. RNA samples from the control, drought, recovery day 1, and recovery day 6 treatment groups were compared using transcriptome analysis. Q. acutissima exhibited 832 and 1076 differentially expressed genes (DEGs) related to drought response and recovery, respectively, whereas Q. palustris exhibited 3947 and 1587 DEGs, respectively under these conditions. Gene ontology enrichment of DEGs revealed “response to water,” “apoplast,” and “Protein self-association” to be common to both the species. However, in the heatmap analysis of genes related to sucrose and starch synthesis, glycolysis, antioxidants, and hormones, the two species exhibited very different transcriptome responses. Nevertheless, the levels of most DEGs returned to their pre-drought levels after rewatering. These results provide a basic foundation for understanding the physiological and genetic expression responses of oak seedlings to drought stress and recovery.

Tuberculosis (TB) is a global health challenge associated with considerable levels of illness and mortality worldwide. The development of innovative therapeutic strategies is crucial to combat the rise of drug-resistant TB strains. DNA Gyrase A (GyrA) and serine/threonine protein kinase (PknB) are promising targets for new TB medications. This study employed techniques such as similarity searches, molecular docking analyses, machine learning (ML)-driven absolute binding-free energy calculations, and molecular dynamics (MD) simulations to find potential drug candidates. By combining ligand- and structure-based methods with ML principles and MD simulations, a novel strategy was proposed for identifying small molecules. Drugs with structural similarities to existing TB therapies were assessed for their binding affinity to GyrA and PknB through various docking approaches and ML-based predictions. A detailed analysis identified six promising compounds for each target, such as DB00199, DB01220, DB06827, DB11753, DB14631, and DB14703 for GyrA; and DB00547, DB00615, DB06827, DB14644, DB11753, and DB14703 for PknB. Notably, DB11753 and DB14703 show significant potential for both targets. Furthermore, MD simulations’ statistical metrics confirm the drug–target complexes’ stability, with MM-GBSA analyses underscoring their strong binding affinity, indicating their promise for TB treatment even though they were not initially designed for this disease.

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is crucial in plant metabolism and responses to various abiotic stresses. In the glycolysis pathway, glyceraldehyde-3-phosphate (G3P) is oxidized to 1,3-bisphosphate glycerate (1,3-BPG) through the catalytic action of GAPDH. However, the GAPDH gene family in Quercus rubra has been minimally researched. In this study, we identified 13 GAPDH-encoding genes in Q. rubra through a bioinformatics analysis of genomic data. Evolutionary studies suggest that these QrGAPDH genes are closely related to those in Glycine max and Triticum aestivum. We conducted a comprehensive whole-genome study, which included predictions of subcellular localization, gene structure analysis, protein motif identification, chromosomal placement, and analysis of cis-acting regions. We also examined the expression of GAPDH proteins and genes in various tissues of Q. rubra and under drought stress. The results indicated diverse expression patterns across different tissues and differential expression under drought conditions. Notably, the expression of Qurub.02G290300.1, Qurub.10G209800.1, and Qrub.M241600.1 significantly increased in the leaf, stem, and root tissues under drought stress. This study provides a systematic analysis of QrGAPDH genes, suggesting their pivotal roles in the drought stress response of trees.

Progress in the manufacturing sector resulted in the need for products with enhanced mechanical properties, corrosion, and heat resistance. Thus, superalloy was produced with desired mechanical properties. Monel Alloy is one of those nickel-based superalloys, commonly used in industry for its high strength and resistance to corrosion. Monel is also acid- and saltwater resistant. Some properties such as gummy behavior and job hardening make machining superalloys by traditional methods difficult. For this purpose, in this analysis, near-dry wire electric discharge machining (WEDM) is chosen for Monel machining. The present research explores the feasibility of nearly dry Monel alloy WEDM using air and deionized water in nebulous or mist form to achieve the optimal surface finish and resolve environmental issues associated with wet WEDM. This work reflects the study of the influence of various input parameters on the output calculated in terms of the rate of material removal (MRR) and surface roughness (Ra). On an inference, near-dry WEDM formed a smooth surface on Monel alloy over traditional WEDM; however, ranges of MRR still elevate their support to wet WEDM. [ABSTRACT FROM AUTHOR]

The glycolytic pathway involves phosphofructokinase (PFK), a rate-limiting enzyme that catalyzes the phosphorylation of fructose-6-phosphate. In plants, the two PFK members are ATP-dependent phosphofructokinase (PFK) and pyrophosphate-fructose-6-phosphate phosphotransferase (PFP). However, the functions of the PFK family members in Quercus rubra are not well understood. The purpose of this study was to investigate the genome-wide distribution of the PFK family members and their roles in Q. rubra by performing a systematic study of the phylogenetic relationships, molecular characteristics, motifs, chromosomal and subcellular locations, and cis-elements of QrPFKs. We identified 14 QrPFK genes in the genome of Q. rubra, followed by examining their expression in different tissues, including the roots, stems, and leaves. The phylogenetic tree divided the 14 QrPFK genes into two groups: 11 belonging to PFK and three belonging to PFP. The expression profiles of all 14 proteins were relatively the same in leaves but differed between stems and roots. Four genes (Qurub.02G189400.1, Qurub.02G189400.2, Qurub.09G134300.1, and Qurub.09G134300.2) were expressed at very low levels in both stems and roots, while two (Qurub.05G235500.1 and Qurub.05G235500.1) were expressed at low levels and the others showed relatively high expression in all tissues.

Abstract Background Grading of cancer histopathology slides requires more pathologists and expert clinicians as well as it is time consuming to look manually into whole-slide images. Hence, an automated classification of histopathological breast cancer sub-type is useful for clinical diagnosis and therapeutic responses. Recent deep learning methods for medical image analysis suggest the utility of automated radiologic imaging classification for relating disease characteristics or diagnosis and patient stratification. Methods To develop a hybrid model using the convolutional neural network (CNN) and the long short-term memory recurrent neural network (LSTM RNN) to classify four benign and four malignant breast cancer subtypes. The proposed CNN-LSTM leveraging on ImageNet uses a transfer learning approach in classifying and predicting four subtypes of each. The proposed model was evaluated on the BreakHis dataset comprises 2480 benign and 5429 malignant cancer images acquired at magnifications of 40×, 100×, 200× and 400×. Results The proposed hybrid CNN-LSTM model was compared with the existing CNN models used for breast histopathological image classification such as VGG-16, ResNet50, and Inception models. All the models were built using three different optimizers such as adaptive moment estimator (Adam), root mean square propagation (RMSProp), and stochastic gradient descent (SGD) optimizers by varying numbers of epochs. From the results, we noticed that the Adam optimizer was the best optimizer with maximum accuracy and minimum model loss for both the training and validation sets. The proposed hybrid CNN-LSTM model showed the highest overall accuracy of 99% for binary classification of benign and malignant cancer, and, whereas, 92.5% for multi-class classifier of benign and malignant cancer subtypes, respectively. Conclusion To conclude, the proposed transfer learning approach outperformed the state-of-the-art machine and deep learning models in classifying benign and malignant cancer subtypes. The proposed method is feasible in classification of other cancers as well as diseases.

The Lily database is an online genomic resource which is composed of a Korean Lily germplasm collection, transcriptome sequences, molecular markers, transcription factors (TFs) and DEGs (Differentially Expressed Genes) data. A total of ~0.23 gb of RNA-sequencing data were used for gene identification, marker development and gene expression analysis. As a result, 103,929 genomic, 47,863 EST-SSR, 20,929 SNP and 1213 COS-marker were developed. A total of 1327 TF genes were identified and characterized. This is the first unique, user-friendly, genomic resource database for Lilium species. It is a relational database based on a ‘three-tier architecture’ that catalogs all the information in a MySQL table and a user-friendly query interface and data visualization page developed using JavaScript, PHP and HTML code. The search parameters are highly flexible; users can retrieve data by using either single or multiple search parameters. Data present in this database can be used for germplasm characterization, gene discovery, population structure analysis, QTL mapping, and accelerating lily variety improvements.

Staphylococcus aureus is a pathogen that causes a variety of infectious diseases such as pneumonia, endocarditis, and septic shock. Methicillin-resistant S. aureus (MRSA) evades virtually all available treatments, creating the need for an alternative control strategy. Although we previously demonstrated the inhibitory effect of sodium propionate (NaP) on MRSA, the regulatory mechanism of this effect remains unclear. In this study, we investigated the regulatory mechanism responsible for the inhibitory effect of NaP on MRSA using RNA-Seq analysis. Total RNAs were isolated from non-treated and 50 mM NaP-treated S. aureus USA300 for 3 h and transcriptional profiling was conducted by RNA-Seq analysis. A total of 171 differentially expressed genes (DEGs) with log2 fold change ≥2 and p

The Internet of Things (IoT) is no longer a fanciful vision. It is very much with us, in everything from factory automation to on-demand entertainment. Yet by most accounts, the full potential of interconnected systems and intelligent devices for changing the way we work and live has barely been tapped. As a long-established industry leader in enabling wireless connectivity Solutions offers the industry's broadest spectrum of products and services to accelerate your product development and succeed in the market. global team of engineers, developers, and support professionals have helped countless customers bring innovative wireless products to market spanning Wi-Fi, Bluetooth, BLE, LoRa, Zigbee, 802.15.4, custom point-to-point implementations, and more Embedded for Medical Devices This Embedded technology, which is being widely accepted and proven technology in the field of Medical Device manufacture and production. The highlight some of the crucial features and application areas for Medical Instrumentation and control. [ABSTRACT FROM AUTHOR]

The Routing Protocol for Low Power and Lossy Networks (RPL) is operated by gadgets comprised of many devices of embedded type with limited energy, memory as well as resources that do their process. The improvements in the life of the network and energy conservation are the key challenging features in Low Power and Lossy Networks (LLN). Obviously, the LLN has a key strategic part in routing. The Internet of Things (IoT) device is expected to make the apt choice. In LLN, the poor routing choice leads to traffic congestion, reduction in power as well as packet loss ratio. The task in the proposal analyzes Delay (D), Load (L) and Battery Discharge Index (BDI) pivoted Energy Efficient Composite Metric Routing (EECMR) protocol for LLN. The performance of the work in the proposal is evaluated by the COOJA simulator. It outperforms with respect to Network Lifetime (NL), Delay as well as Packet Delivery Ratio (PDR) contrasted to the routing metrics like Traffic Load (TL), Link Quality (LQ), Residual Energy (RE), RE-Battery Discharge Index (RE-BDI) and Hop Count (HC).

Abstract Lily belongs to family liliaceae, which mainly propagates vegetatively. Therefore, sufficient number of polymorphic, informative, and functional molecular markers are essential for studying a wide range of genetic parameters in Lilium species. We attempted to develop, characterize and design SSR (simple sequence repeat) markers using online genetic resources for analyzing genetic diversity and population structure of Lilium species. We found di-nucleotide repeat motif were more frequent (4684) within 0.14 gb (giga bases) transcriptome than other repeats, of which was two times higher than tetra-repeat motifs. Frequency of di-(AG/CT), tri-(AGG/CTT), tetra-(AAAT), penta-(AGAGG), and hexa-(AGAGGG) repeats was 34.9%, 7.0%, 0.4%, 0.3%, and 0.2%, respectively. A total of 3607 non-redundant SSR primer pairs was designed based on the sequences of CDS, 5′-UTR and 3′-UTR region covering 34%, 14%, 23%, respectively. Among them, a sub set of primers (245 SSR) was validated using polymerase chain reaction (PCR) amplification, of which 167 primers gave expected PCR amplicon and 101 primers showed polymorphism. Each locus contained 2 to 12 alleles on average 0.82 PIC (polymorphic information content) value. A total of 87 lily accessions was subjected to genetic diversity analysis using polymorphic SSRs and found to separate into seven groups with 0.73 to 0.79 heterozygosity. Our data on large scale SSR based genetic diversity and population structure analysis may help to accelerate the breeding programs of lily through utilizing different genomes, understanding genetics and characterizing germplasm with efficient manner.

Biliary tract cancer (BTC) is constituted by a heterogeneous group of malignant tumors that may develop in the biliary tract, and it is the second most common liver cancer. Human ribonucleotide reductase M1 (hRRM1) has already been proven to be a potential BTC target. In the current study, a de novo design approach was used to generate novel and effective chemical therapeutics for BTC. A set of comprehensive pharmacoinformatics approaches was implemented and, finally, seventeen potential molecules were found to be effective for the modulation of hRRM1 activity. Molecular docking, negative image-based ShaEP scoring, absolute binding free energy, in silico pharmacokinetics, and toxicity assessments corroborated the potentiality of the selected molecules. Almost all molecules showed higher affinity in comparison to gemcitabine and naphthyl salicylic acyl hydrazone (NSAH). On binding interaction analysis, a number of critical amino acids was found to hold the molecules at the active site cavity. The molecular dynamics (MD) simulation study also indicated the stability between protein and ligands. High negative MM-GBSA (molecular mechanics generalized Born and surface area) binding free energy indicated the potentiality of the molecules. Therefore, the proposed molecules might have the potential to be effective therapeutics for the management of BTC.

Abstract Background Plasmodiophora brassicae is a soil-borne plant pathogen that causes clubroot disease, which results in crop yield loss in cultivated Brassica species. Here, we investigated whether a quantitative trait locus (QTL) in B. rapa might confer resistance to a Korean P. brassicae pathotype isolate, Seosan. We crossed resistant and susceptible parental lines and analyzed the segregation pattern in a F2 population of 348 lines. We identified and mapped a novel clubroot resistance QTL using the same mapping population that included susceptible Chinese cabbage and resistant turnip lines. Forty-five resistant and 45 susceptible F2 lines along with their parental lines were used for double digest restriction site-associated DNA sequencing (ddRAD-seq). High resolution melting (HRM)-based validation of SNP positions was conducted to confirm the novel locus. Results A 3:1 ratio was observed for resistant: susceptible genotypes, which is in accordance with Mendelian segregation. ddRAD-seq identified a new locus, CRs, on chromosome A08 that was different from the clubroot resistance (CR) locus, Crr1. HRM analysis validated SNP positions and constricted CRs region. Four out of seventeen single nucleotide polymorphisms (SNPs) positions were within a 0.8-Mb region that included three NBS-LRR candidate genes but not Crr1. Conclusion The newly identified CRs locus is a novel clubroot resistance locus, as the cultivar Akimeki bears the previously known Crr1 locus but remains susceptible to the Seosan isolate. These results could be exploited to develop molecular markers to detect Seosan-resistant genotypes and develop resistant Chinese cabbage cultivars.

Clubroot is one of the most economically important diseases of the Brassicaceae family. Clubroot disease is caused by the obligate parasite Plasmodiophora brassicae, which is difficult to study because it is non-culturable in the laboratory and its races are genetically variable worldwide. In Korea, there are at least five races that belongs to four pathotype groups. A recent study conducted in Korea attempted to develop molecular markers based on ribosomal DNA polymorphism to detect P. brassicae isolates, but none of those markers was either race-specific or pathotype-specific. Our current study aimed to develop race- and isolate-specific markers by exploiting genomic sequence variations. A total of 119 markers were developed based on unique variation exists in genomic sequences of each of the races. Only 12 markers were able to detect P. brassicae strains of each isolate or race. Ycheon14 markers was specific to isolates of race 2, Yeoncheon and Hoengseong. Ycheon9 and Ycheon10 markers were specific to Yeoncheon isolate (race 2, pathotype 3), ZJ1-3, ZJ1-4 and ZJ1-5 markers were specific to Haenam2 (race 4) isolate, ZJ1-35, ZJ1-40, ZJ1-41 and ZJ1-49 markers were specific to Hoengseong isolate and ZJ1-56 and ZJ1-64 markers were specific to Pyeongchang isolate (race 4, pathotype 3). The PCR-based sequence characterized amplified region (SCAR) markers developed in this study are able to detect five Korean isolates of P. brassicae. These markers can be utilized in identifying four Korean P. brassicae isolates from different regions. Additional effort is required to develop race- and isolate-specific markers for the remaining Korean isolates.

Fleshy fruits are the most demanded fruits because of their organoleptic qualities and nutritional values. The genus Prunus is a rich source of diversified stone/drupe fruits such as almonds, apricots, plums, sweet cherries, peaches, and nectarines. The fruit-ripening process in Prunus involves coordinated biochemical and physiological changes resulting in changes in fruit texture, aroma gain, color change in the pericarp, sugar/organic acid balance, fruit growth, and weight gain. There are different varieties of peaches with unique palatable qualities and gaining knowledge in the genetics behind these quality traits helps in seedling selection for breeding programs. In addition, peaches have shorter post-harvest life due to excessive softening, resulting in fruit quality reduction and market loss. Many studies have been executed to understand the softening process at the molecular level to find the genetic basis. To summarize, this review focused on the molecular aspects of peach fruit quality attributes and their related genetics to understand the underlying mechanisms.

Classical antibiotics are the foremost treatment strategy against microbial infections. Overuse of this has led to the evolution of antimicrobial resistance. Antimicrobial peptides (AMPs) are natural defense elements present across many species including humans, insects, bacteria, and plants. Insect AMPs are our area of interest, because of their stronger abilities in host defense. We have deciphered AMPs from an endangered species Parnassius bremeri, commonly known as the red spotted apollo butterfly. It belongs to the second largest insect order Lepidoptera, comprised of butterflies and moths, and lives in the high altitudes of Russia, China, and Korea. We aimed at identifying the AMPs from the larvae stages. The rationale of choosing this stage is that the P. bremeri larvae development occurs at extremely low temperature conditions, which might serve as external stimuli for AMP production. RNA was isolated from larvae (L1 to L5) instar stages and subjected to next generation sequencing. The transcriptomes obtained were curated in in-silico pipelines. The peptides obtained were screened for requisite AMP physicochemical properties and in vitro antimicrobial activity. With the sequential screening and validation, we obtained fifteen candidate AMPs. One peptide TPS–032 showed promising antimicrobial activity against Porphyromonas gingivalis, a primary causative organism of periodontitis.

Context: Alzheimer’s disease (AD) is the most common form of dementia affecting the aged population and neuroinflammation is one of the most observed AD pathologies. NF-κB is the central regulator of inflammation and inhibitor κB kinase (IKK) is the converging point in NF-κB activation. Celastrol is a natural triterpene used as a treatment for inflammatory conditions. Objective: This study determines the neuroprotective and inhibitory effect of celastrol on amyloid beta1-42 (Aβ1-42) induced cytotoxicity and IKKβ activity, respectively. Materials and methods: Retinoic acid differentiated IMR-32 cells were treated with celastrol (1 μM) before treatment with Aβ1-42 (IC30 10 μM) for 24 h. The cytotoxicity and IKK phosphorylation were measured by MTT and western blotting analysis, respectively. We screened 36 celastrol analogues for the IKKβ inhibition by molecular docking and evaluated their drug like properties to delineate the neuroprotective effects. Results: Celastrol (1 μM) inhibited Aβ1-42 (10 μM) induced IκBα phosphorylation and protected IMR-32 cells from cell death. Celastrol and 25 analogues showed strong binding affinity with IKKβ as evidenced by strong hydrogen-bonding interactions with critical active site residues. All the 25 analogues displayed strong anti-inflammatory properties but only 11 analogues showed drug-likeness. Collectively, molecule 15 has highest binding affinity, CNS activity and more drug likeness than parent compound celastrol. Discussion and conclusion: The decreased expression of pIκBα in celastrol pretreated cells affirms the functional representation of inhibited IKKβ activity in these cells. The neuroprotective potentials of celastrol and its analogues may be related to IKK inhibition.

An insect’s innate immune system is the front line of defense against many invading microorganisms. One of the important components of this defense system is antimicrobial peptides (AMPs). Papiliocin is a well-studied antimicrobial peptide (AMP) isolated from the swallowtail butterfly, Papilio xuthus, and it was previously reported to be effective against Gram-positive bacteria, Gram-negative bacteria, and fungi, particularly in drug resistant Gram-negative bacteria. Hence, we aimed to identify novel AMPs from Papilio xuthus using its transcriptome. We immunized the swallowtail butterfly with Escherichia coli, Staphylococcus aureus, Candida albicans, and the total RNA was isolated. De novo transcriptome assembly and functional annotations were conducted, and AMPs were predicted using an in-silico pipeline. The obtained 344,804,442 raw reads were then pre-processed to retrieve 312,509,806 (90.6%) total clean reads. A total of 38,272 unigenes were assembled with the average length of 1010 bp. Differential gene expression analysis identified 584 and 1409 upregulated and downregulated genes, respectively. The physicochemical, aggregation, and allergen propensity were used as filtration criteria. A total of 248 peptides were predicted using our in-house pipeline and the known AMPs were removed, resulting in 193 novel peptides. Finally, seven peptides were tested in vitro and three peptides (Px 5, 6, and 7) showed stronger antimicrobial activity against Gram-negative bacteria and yeast. All the tested peptides were non-allergens. The identified novel AMPs may serve as potential candidates for future antimicrobial studies.

Antimicrobial peptides (AMPs) are the frontline innate defense system evolutionarily preserved in insects to combat invading pathogens. These AMPs could serve as an alternative to classical antibiotics to overcome the burden of treating multidrug resistant bacteria. Psacotheasin, a knottin type AMP was isolated from Psacothea hilaris and shown to exhibit antimicrobial activity, especially against fungi through apoptosis mediated cell death. In this study, we aimed to identify novel probable AMPs from Psacothea hilaris, the yellow spotted longicorn beetle. The beetle was immunized with the two bacterial strains (E. coli and S. aureus), and the yeast strain C. albicans. After immunization, total RNA was isolated and sequenced in Illumina platform. Then, beetle transcriptome was de novo assembled and searched for putative AMPs with the known physiochemical features of the AMPs. A selection of AMP candidates were synthesized and tested for antimicrobial activity. Four peptides showed stronger activity against E. coli than the control AMP, melittin while one peptide showed similar activity against S. aureus. Moreover, four peptides and two peptides showed antifungal activity stronger than and similar to melittin, respectively. Collectively one peptide showed both antibacterial and antifungal activity superior to melittin; thus, it provides a potent antimicrobial peptide. All the peptides showed no hemolysis in all the tested concentrations. These results suggest that in silico mining of insects’ transcriptome could be a promising tool to obtain and optimize novel AMPs for human needs.

Background: Adipocytes, which are the main cellular component of adipose tissue, are the building blocks of obesity. The nuclear hormone receptor PPARγ is a major regulator of adipocyte differentiation and development. Obesity, which is one of the most dangerous yet silent diseases of all time, is fast becoming a critical area of research focus. Methods: In this study, we initially aimed to investigate whether the ginsenoside Rf, a compound that is only present in Panax ginseng Meyer, interacts with PPARγ by molecular docking simulations. After we performed the docking simulation the result has been analyzed with several different software programs, including Discovery Studio, Pymol, Chimera, Ligplus, and Pose View. All of the programs identified the same mechanism of interaction between PPARγ and Rf, at the same active site. To determine the drug-like and biological activities of Rf, we calculate its absorption, distribution, metabolism, excretion, and toxic (ADMET) and prediction of activity spectra for substances (PASS) properties. Considering the results obtained from the computational investigations, the focus was on the in vitro experiments. Results: Because the docking simulations predicted the formation of structural bonds between Rf and PPARγ, we also investigated whether any evidence for these bonds could be observed at the cellular level. These experiments revealed that Rf treatment of 3T3-L1 adipocytes downregulated the expression levels of PPARγ and perilipin, and also decreased the amount of lipid accumulated at different doses. Conclusion: The ginsenoside Rf appears to be promising compound that could prove useful in antiobesity treatments.

Onion (Allium cepa L.) is an economically important vegetable crop around the world. Genetic and genomic research into various onion accessions will provide insights into the onion genome to enhance breeding strategies and improve crops. However, the onion's large genome size means that studies of molecular markers are limited in onion. This study aimed to discover high quality single nucleotide polymorphisms (SNPs) from 192 onion inbred lines relating to short-day cultivation in Korea. Paired-end (PE) double digested restriction site-associated DNA sequencing (ddRAD-seq) was used to discover SNPs in onion. A total of 538,973,706 reads (25.9 GB), with an average of 2,658,491 high-quality reads, were generated using ddRAD-seq. With stringent filtering, 1904 SNPs were discovered based on onion reference scaffolds. Further, population structure and genetic relationship studies suggested that two well-differentiated sub-populations exist in onion lines. SNP-associated flanking sequences were also compared with a public non-redundant database for gene ontology and pathway analysis. To our knowledge, this is the first report to identify high-quality SNPs in onion based on reference sequences using the ddRAD-seq platform. The SNP markers identified will be useful for breeders and the research community to deepen their understanding, enhance breeding programs, and support the management of onion genomic resources.

Maintenance optimization has received special attention among the wind energy research community over the past two decades. This is mainly because of the high degree of uncertainties involved in the execution of operation and maintenance (O&M) activities throughout the lifecycle of wind farms. The increasing complexity in offshore maintenance execution demands applied research and brings forth a need to develop problem-specific maintenance decision-making models. In this paper, a mathematical model is proposed to assist wind farm stakeholders in making critical resource- related decisions for corrective maintenance at offshore wind farms (OWFs), considering uncertainties in turbine failure information.

Onions (Allium cepa L.) are a medicinally and economically important vegetable species rich in sulphur compounds, polyphenols, and antioxidants. In Korea, most of the onion cultivars are of the open-pollinated, heterozygous, short duration, and early spring type, which are generally harvested in April. Precise varietal identification is crucially important to warrant the authenticity of supreme onion genotypes, which aid in affirming the genetic identity of breeding materials at both the breeders and farmers levels. A set of markers identified from the double-digest restriction-site associated DNA sequencing (ddRAD-seq) database of Allium cepa L. and involving single nucleotide polymorphisms (SNPs) were deployed for genotyping deoxyribonucleic acid (DNA) samples extracted from seven genetically diverse onion cultivars collected in Korea and Japan. The validation process led us to designating 43 SNPs out of 48 that unequivocally identified all seven genotypes with high statistical validity (p < 0.001). Phylogenetic relationships and varietal identity among the cultivars were ascertained by Bayesian clustering and ordination analyses. Two genotypes, Singsingball and Taegeukhwang of Korean origin, showed a greater genetic distance from the five other onion cultivars. The SNP markers deployed in this study effectively authenticated the DNA fingerprints of the early spring onion cultivars utilizing a high-throughput genotyping protocol. The method exploited in this study provides an efficient pathway of verifying genetic identity of onion genotypes for their quality control. The markers developed are highly useful in the management and conservation of elite onion breeding materials at the farmers’ level.

Bulb onion (Allium cepa) is the second most widely cultivated and consumed vegetable crop in the world. During winter, cold injury can limit the production of bulb onion. Genomic resources available for bulb onion are still very limited. To date, no studies on heritably durable cold and freezing tolerance have been carried out in bulb onion genotypes. We applied high-throughput sequencing technology to cold (2°C), freezing (-5 and -15°C), and control (25°C)-treated samples of cold tolerant (CT) and cold susceptible (CS) genotypes of A. cepa lines. A total of 452 million paired-end reads were de novo assembled into 54,047 genes with an average length of 1,331 bp. Based on similarity searches, these genes were aligned with entries in the public non-redundant (nr) database, as well as KEGG and COG database. Differentially expressed genes (DEGs) were identified using log10 values with the FPKM method. Among 5,167DEGs, 491 genes were differentially expressed at freezing temperature compared to the control temperature in both CT and CS libraries. The DEG results were validated with qRT-PCR. We performed GO and KEGG pathway enrichment analyses of all DEGs and iPath interactive analysis found 31 pathways including those related to metabolism of carbohydrate, nucleotide, energy, cofactors and vitamins, other amino acids and xenobiotics biodegradation. Furthermore, a large number of molecular markers were identified from the assembled genes, including simple sequence repeats (SSRs) 4,437 and SNP substitutions of transition and transversion types of CT and CS. Our study is the first to provide a transcriptome sequence resource for Allium spp. with regard to cold and freezing stress. We identified a large set of genes and determined their DEG profiles under cold and freezing conditions using two different genotypes. These data represent a valuable resource for genetic and genomic studies of Allium spp.

Powdery mildew is one of the most common fungal diseases in the world. This disease frequently affects melon (Cucumis melo L.) and other Cucurbitaceous family crops in both open field and greenhouse cultivation. One of the goals of genomics is to identify the polymorphic loci responsible for variation in phenotypic traits. In this study, powdery mildew disease assessment scores were calculated for four melon accessions, 'SCNU1154', 'Edisto47', 'MR-1', and 'PMR5'. To investigate the genetic variation of these accessions, whole genome re-sequencing using the Illumina HiSeq 2000 platform was performed. A total of 754,759,704 quality-filtered reads were generated, with an average of 82.64% coverage relative to the reference genome. Comparisons of the sequences for the melon accessions revealed around 7.4 million single nucleotide polymorphisms (SNPs), 1.9 million InDels, and 182,398 putative structural variations (SVs). Functional enrichment analysis of detected variations classified them into biological process, cellular component and molecular function categories. Further, a disease-associated QTL map was constructed for 390 SNPs and 45 InDels identified as related to defense-response genes. Among them 112 SNPs and 12 InDels were observed in powdery mildew responsive chromosomes. Accordingly, this whole genome re-sequencing study identified SNPs and InDels associated with defense genes that will serve as candidate polymorphisms in the search for sources of resistance against powdery mildew disease and could accelerate marker-assisted breeding in melon.

Chemical synthesis of unconventional topologically close-packed intermetallic nanocrystals (NCs) remains a considerable challenge due to the limitation of large volume asymmetry between the components. Here, a series of unconventional intermetallic Frank-Kasper C15 phase Ir 2 M (M = rare earth metals La, Ce, Gd, Tb, Tm) NCs is successfully prepared via a molten-salt assisted reduction method as efficient electrocatalysts for hydrogen evolution reaction (HER). Compared to the disordered counterpart (A1-Ir 2 Ce), C15-Ir 2 Ce features higher Ir-Ce coordination number that leads to an electron-rich environment for Ir sites. The C15-Ir 2 Ce catalyst exhibits excellent and pH-universal HER activity and requires only 9, 16, and 27 mV overpotentials to attain 10 mA cm -2 in acidic, alkaline, and neutral electrolytes, respectively, representing one of the best HER electrocatalysts ever reported. In a proton exchange membrane water electrolyzer, the C15-Ir 2 Ce cathode achieves an industrial-scale current density of 1 A cm -2 with a remarkably low cell voltage of 1.7 V at 80 °C and can operate stably for 1000 h with a sluggish voltage decay rate of 50 µV h -1 . Theoretical investigations reveal that the electron-rich Ir sites intensify the polarization of *H 2 O intermediate on C15-Ir 2 Ce, thus lowering the energy barrier of the water dissociation and facilitating the HER kinetics., (© 2024 Wiley‐VCH GmbH.)

Similarities and differences in brain structure and function across species are of major interest in systems neuroscience, comparative biology, and brain mapping. Recently, increased emphasis has been placed on tertiary sulci, which are shallow indentations of the cerebral cortex that appear last in gestation, continue to develop after birth, and are largely either human or hominoid specific. While tertiary sulcal morphology in lateral prefrontal cortex (LPFC) has been linked to functional representations and cognition in humans, it is presently unknown if small and shallow LPFC sulci also exist in non-human hominoids. To fill this gap in knowledge, we leveraged two freely available multimodal datasets to address the following main question: Can small and shallow LPFC sulci be defined in chimpanzee cortical surfaces from human predictions of LPFC tertiary sulci? We found that 1-3 components of the posterior middle frontal sulcus (pmfs) in the posterior middle frontal gyrus are identifiable in nearly all chimpanzee hemispheres. In stark contrast to the consistency of the pmfs components, we could only identify components of the paraintermediate frontal sulcus (pimfs) in two chimpanzee hemispheres. Putative LPFC tertiary sulci were relatively smaller and shallower in chimpanzees compared to humans. In both species, two of the pmfs components were deeper in the right compared to the left hemisphere. As these results have direct implications for future studies interested in the functional and cognitive role of LPFC tertiary sulci, we share probabilistic predictions of the three pmfs components to guide the definitions of these sulci in future studies., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Developing efficient and anti-corrosive oxygen reduction reaction (ORR) catalysts is of great importance for the applications of proton exchange membrane fuel cells (PEMFCs). Herein, we report a novel approach to prepare metal oxides supported intermetallic Pt alloy nanoparticles (NPs) via the reactive metal-support interaction (RMSI) as ORR catalysts, using Ni-doped cubic ZrO 2 (Ni/ZrO 2 ) supported L1 0 -PtNi NPs as a proof of concept. Benefiting from the Ni migration during RMSI, the oxygen vacancy concentrations in the support are increased, leading to an electron enrichment of Pt. The optimal L1 0 -PtNi-Ni/ZrO 2 -RMSI catalyst achieves remarkably low mass activity (MA) loss (17.8 %) after 400,000 accelerated durability test cycles in a half-cell and exceptional PEMFC performance (MA=0.76 A mg Pt -1 at 0.9 V, peak power density=1.52/0.92 W cm -2 in H 2 -O 2 /-air, and 18.4 % MA decay after 30,000 cycles), representing the best reported Pt-based ORR catalysts without carbon supports. Density functional theory (DFT) calculations reveal that L1 0 -PtNi-Ni/ZrO 2 -RMSI requires a lower energetic barrier for ORR than L1 0 -PtNi-Ni/ZrO 2 (direct loading), which is ascribed to a decreased Bader charge transfer between Pt and *OH, and the improved stability of L1 0 -PtNi-Ni/ZrO 2 -RMSI compared to L1 0 -PtNi-C can be contributed to the increased adhesion energy and Ni vacancy formation energy within the PtNi alloy., (© 2024 Wiley-VCH GmbH.)