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Potato late blight caused by Phytophthora infestans is a destructive disease in Korea. To elucidate the genomic variation of the mitochondrial (mt) genome, we assembled its complete mt genome and compared its sequence among different haplotypes. The mt genome sequences of four Korean P. infestans isolates were revealed by Illumina HiSeq. The size of the circular mt genome of the four major genotypes, KR_1_A1, KR_2_A2, SIB-1, and US-11, was 39,872, 39,836, 39,872, and 39,840 bp, respectively. All genotypes contained the same 61 genes in the same order, comprising two RNA-encoding genes, 16 ribosomal genes, 25 transfer RNA, 17 genes encoding electron transport and ATP synthesis, 11 open reading frames of unknown function, and one protein import-related gene, tatC. The coding region comprised 91% of the genome, and GC content was 22.3%. The haplotypes were further analyzed based on sequence polymorphism at two hypervariable regions (HVRi), carrying a 2 kb insertion/deletion sequence, and HVRii, carrying 36 bp variable number tandem repeats (VNTRs). All four genotypes carried the 2 kb insertion/deletion sequence in HVRi, whereas HVRii had two VNTRs in KR_1_A1 and SIB-1 but three VNTRs in US-11 and KR_2_A2. Minimal spanning network and phylogenetic analysis based on 5,814 bp of mtDNA sequences from five loci, KR_1_A1 and SIB-1 were classified as IIa-6 haplotype, and isolates KR_1_A2 and US-11 as haplotypes IIa-5 and IIb-2, respectively. mtDNA sequences of KR_1_A1 and SIB-1 shared 100% sequence identity, and both were 99.9% similar to those of KR_2_A2 and US-11.

Abstract Characterizing the genetic diversity and population structure of breeding materials is essential for breeding to improve crop plants. The potato is an important non-cereal food crop worldwide, but breeding potatoes remains challenging owing to their auto-tetraploidy and highly heterozygous genome. We evaluated the genetic structure of a 110-line Korean potato germplasm using the SolCAP 8303 single nucleotide polymorphism (SNP) Infinium array and compared it with potato clones from other countries to understand the genetic landscape of cultivated potatoes. Following the tetraploid model, we conducted population structure analysis, revealing three subpopulations represented by two Korean potato groups and one separate foreign potato group within 110 lines. When analyzing 393 global potato clones, country/region-specific genetic patterns were revealed. The Korean potato clones exhibited higher heterozygosity than those from Japan, the United States, and other potato landraces. We also employed integrated extended haplotype homozygosity (iHS) and cross-population extended haplotype homozygosity (XP-EHH) to identify selection signatures spanning candidate genes associated with biotic and abiotic stress tolerance. Based on the informativeness of SNPs for dosage genotyping calls, 10 highly informative SNPs discriminating all 393 potatoes were identified. Our results could help understanding a potato breeding history that reflects regional adaptations and distinct market demands.

Abstract Interspecific somatic hybridization has been performed in potato breeding experiments to increase plant resistance against biotic and abiotic stress conditions. We analyzed the mitochondrial and plastid genomes and 45S nuclear ribosomal DNA (45S rDNA) for the cultivated potato (S. tuberosum, St), wild potato (S. commersonii, Sc), and their somatic hybrid (StSc). Complex genome components and structure, such as the hybrid form of 45S rDNA in StSc, unique plastome in Sc, and recombinant mitogenome were identified. However, the mitogenome exhibited dynamic multipartite structures in both species as well as in the somatic hybrid. In St, the mitogenome is 756,058 bp and is composed of five subgenomes ranging from 297,014 to 49,171 bp. In Sc, it is 552,103 bp long and is composed of two sub-genomes of 338,427 and 213,676 bp length. StSc has 447,645 bp long mitogenome with two subgenomes of length 398,439 and 49,206 bp. The mitogenome structure exhibited dynamic recombination mediated by tandem repeats; however, it contained highly conserved genes in the three species. Among the 35 protein-coding genes of the StSc mitogenome, 21 were identical for all the three species, and 12 and 2 were unique in Sc and St, respectively. The recombinant mitogenome might be derived from homologous recombination between both species during somatic hybrid development.

This study is designed to discover current energy-related research trends as evidence inherent in big data and obtain future agendas and new insights to reshape global energy strategy considering environmental change globally in the era of COVID-19. To this end, vast amounts of unstructured text data on energy demand from 4 top journals in the energy field over the past year (2020–2021) were collected. This study used a semantic network analysis in big data analytics. As a result, this study obviously shows that research evidence on traditional energy sources such as fossil fuels and gas is still essential in the current situation where climate change and global warming are intensifying worldwide. Simultaneously, research on renewable energy is positioned as a critical agenda by providing sufficient evidence to draw practical implications concerning overall global energy companies' strategy and each government's new energy policy in line with the rapid changes in the global environment. Consequently, this study proposes that a decision-maker or leader can exert the remarkable power of reshaping global energy strategy for future sustainability, taking into account the recognizable trends inherent in big data.

Abstract Along with the big data era, digital transformation has had a transformative effect on modern education tremendously in higher education. It transforms an institutional core value of education to better meet students’ needs by leveraging big data and digital technology. Based on this background, this study attempts to catch the principal trends, or new directions, paradigms as predictors with an association of each topic by discovering the up-to-date research trends on teaching and learning in higher education via text mining techniques. For this, 285 research articles in the area of teaching and learning in higher education were collected from several big databases (distinguishable publishers’ web platforms) through search engines for 2 years in 2018–2019. Then it was analyzed using a semantic network analysis that processes natural human language. Consequently, research results show a relatively high connection with ‘student’ or ‘student-centered/led’ rather than ‘teacher-led.’ Moreover, it exhibits that the practice and assessment in learning can be attained via diverse learning activities, containing community or outreach activities. Besides, research in academic contexts, experience-based classes, the effect of group activities, how students’ feelings or perceptions, and relationships affect learning outcomes were addressed as the main topics through topic modeling of LDA, a machine learning algorithm. This study proposes that educators, researchers, and even academic leaders can exert extraordinary power to reshape educational quality programs for future education and in a timely manner with recognizable trends or agendas in teaching and learning of higher education.

Although the potato chip industry is booming, and distinct chip-processing clones have been released over the past 60 years, the genetic architecture of their chip-processing characteristics remains largely unknown. Case-control genome-wide association studies (GWAS) with SolCAP SNP array data for chip-processing clones versus all other market classes in the 393-line potato diversity panel were performed using the GWASpoly R package, enabling detection of significant signals on chromosome 10. Our results were replicated using internal replication of a strata-corrected 190-line panel. Furthermore, the genomic scans employing selective sweep approaches such as the cross-population composite likelihood ratio method (XP-CLR) and PCAdapt redetected the same signals as those in our GWAS. Through applications of four selective sweep approaches, various genetic variants were found across the genome that had been differentially selected. These genomic regions under selection along with transcriptomic data analysis are involved in carbohydrate metabolism-related genes or loci and transcription factors, indicating to be associated with the improvement of chip-processing performance of potato cultivars. Kompetitive allele-specific PCR (KASP) assays were designed for the causal SNPs to use in validating the chip-processing clones. The results could have implications for genomics-assisted breeding of the promising chip-processing cultivars in potato.

Heart valve disease is a growing problem worldwide. Though very common in older adults, the mechanisms behind the development of the disease aren’t well understood, and at present the only therapeutic option is valve replacement. Valvular interstitial cells (VICs) may hold the answer. These cells can undergo pathological differentiation into contractile myofibroblasts or osteoblasts, leading to thickening and calcification of the valve tissue. Our study aimed to characterise the effect of fibroblast growth factor 2 (FGF-2) on the differentiation potential of VICs. We isolated VICs from diseased human valves and treated these cells with FGF-2 and TGF-β to elucidate effect of these growth factors on several myofibroblastic outcomes, in particular immunocytochemistry and gene expression. We used TGF-β as a positive control for myofibroblastic differentiation. We found that FGF-2 promotes a ‘quiescent-type’ morphology and inhibits the formation of α-smooth muscle actin positive myofibroblasts. FGF-2 reduced the calcification potential of VICs, with a marked reduction in the number of calcific nodules. FGF-2 interrupted the ‘canonical’ TGF-β signalling pathway, reducing the nuclear translocation of the SMAD2/3 complex. The panel of genes assayed revealed that FGF-2 promoted a quiescent-type pattern of gene expression, with significant downregulations in typical myofibroblast markers α smooth muscle actin, extracellular matrix proteins, and scleraxis. We did not see evidence of osteoblast differentiation: neither matrix-type calcification nor changes in osteoblast associated gene expression were observed. Our findings show that FGF-2 can reverse the myofibroblastic phenotype of VICs isolated from diseased valves and inhibit the calcification potential of these cells.

Abstract Background Alternative grafts are needed to improve the healing of bone non-union. Here, we assessed a bovine bone product which retains the inorganic and organic components of bone, as an alternative bone graft. Methods Bovine bone matrix proteins (BBMPs) were isolated from bovine bone particulates (BBPs) and tested in vitro. Primary rat osteoblast viability, differentiation, and mineralisation were assessed with alamarBlue®, real-time PCR, and von Kossa staining assays, respectively. Osteoclast formation was assessed in primary murine bone marrow cultures with TRAP staining. Human osteoblast growth and differentiation in the presence of BBPs was evaluated in 3D collagen gels in vitro using alamarBlue® and real-time PCR, respectively. The efficacy of BBPs as an alternative bone graft was tested in a rat critical-size calvarial defect model, with histology scored at 4 and 12 weeks post-surgery. Results In vitro, the highest concentration of BBMPs increased mineral deposition five-fold compared to the untreated control group (P

Solanum demissum is a wild tuber-bearing species belonging to Solanaceae family. The complete chloroplast genome of S. demissum was constituted by de novo assembly using a small amount of whole genome sequencing data. The chloroplast genome of S. demissum was circular DNA molecule with a length of 155,558 bp and consisted of 85,999 bp of large single copy, 18,373 bp of small single copy, and 25,593 bp of a pair of inverted repeat regions. A total of 158 genes were annotated including 105 protein-coding genes, 45 tRNA genes, and 8 rRNA genes. Maximum likelihood phylogenetic analysis with 30 Solanaceae species revealed that S. demissum is most closely grouped with S. hougasii and S. stoloniferum.

Solanum hougasii is a wild tuber-bearing species belonging to the family Solanaceae. The complete chloroplast genome of S. hougasii was constituted by de novo assembly, using a small amount of whole genome sequencing data. The chloroplast genome of S. hougasii was a circular DNA molecule with a length of 155,549 bp and consisted of 85,990 bp of large single copy, 18,373 bp of small single copy, and 25,593 bp of a pair of inverted repeat regions. A total of 158 genes were annotated, including 105 protein-coding genes, 45 tRNA genes, and eight rRNA genes. Maximum likelihood phylogenetic analysis with 25 Solanaceae species revealed that S. hougasii is most closely grouped with S. tuberosum.

Solanum chacoense is a wild tuber-bearing species belonging to Solanaceae family. The chloroplast genome of the species was completed by de novo assembly using a small amount of whole genome sequencing data. The genome is the circular DNA molecule with a length of 155,532 bp containing 159 predicted genes totally, including 105 protein-coding, 45 tRNA and eight rRNA genes. Maximum-likelihood phylogenetic analysis with 26 species in Solanaceae revealed that S. chacoense is the most closely grouped with S. commersonii.

We report two complete mitochondrial genome sequences of a tuber-bearing wild potato species (Solanum commersonii). The genomes are circular DNA molecules with lengths of 213,676 bp and 338,427 bp containing 80 nonredundant genes totally, including 34 protein-coding genes, 25 hypothetical open reading frames, 18 tRNA genes, and 3 rRNA genes. Phylogenetic analysis using common protein-coding sequences confirmed that S. commersonii belongs to the Solanoideae subfamily in the Solanaceae family.

Potato (Solanum tuberosum) from the Solanaceae is the fourth most important food crop worldwide. In this study, five complete mitochondrial genome sequences of S. tuberosum were characterized through de novo assembly of whole genome sequencing data. The resulting circular mitochondrial DNA molecules ranged from 49,171 bp to 297,014 bp in size and contained a total of 80 non-redundant genes, comprising 34 protein-coding genes, 24 hypothetical open reading frames, 19 tRNA genes, and 3 rRNA genes. Phylogenetic analysis using common protein-coding sequences confirmed that S. tuberosum belongs to the Solanoideae subfamily in the Solanaceae family.

Abstract P53 and its family member p63 play important roles in cellular senescence and organismal aging. In this study, p53 and p63 immunoreactivity were examined in the hippocampus of young, adult and aged mice by using immunohistochemistry. In addition, neuronal distribution and degeneration was examined by NeuN immunohistochemistry and fluoro-Jade B fluorescence staining. Strong p53 immunoreactivity was mainly expressed in pyramidal and granule cells of the hippocampus in young mice. p53 immunoreactivity in the pyramidal and granule cells was significantly reduced in the adult mice. In the aged mice, p53 immunoreactivity in the pyramidal and granule cells was more significantly decreased. p63 immunoreactivity was strong in the pyramidal and granule cells in the young mice. p63 immunoreactivity in these cells was apparently and gradually decreased with age, showing that p63 immunoreactivity in the aged granule cells was hardly shown. However, numbers of pyramidal neurons and granule cells were not significantly decreased in the aged mice with normal aging. Taken together, this study indicates that there are no degenerative neurons in the hippocampus during normal aging, showing that p53 and p63 immunoreactivity in hippocampal neurons was progressively reduced during normal aging, which might be closely related to the normal aging processes.

Purpose: Although several cases of anatomical variants of the proximal portion of the long head of the biceps brachii tendon have been reported, most are case reports on single patients; few studies have investigated the classification and incidence of this phenomenon. We aimed to classify the variants of the long head of the biceps brachii tendon by their morphology and characterize them in regard to incidence, demography, and the relationship with biceps tendon or other shoulder diseases. Methods: We retrospectively reviewed 760 arthroscopic images spanning 31 months from October 2008 and found 45 variations of the proximal portion of the long head of the biceps brachii tendon. We classified the variants using Dierickx classification system and calculated the incidence of each subtype. We investigated age, gender, bicipital morbidity rate, procedure rate, and the frequency of related shoulder disease among the variant groups using patient data and compared the groups to normal patients. Results: The overall incidence of variants was 6.5% (67.4%, mesotenon; 32.6%, adherent; 0% split (SPL); and 0% absent (ABS) type). Morbidity and procedure rates of the long head of the biceps (LHB) tendon in the variant group (27.9% and 25.6%, respectively) were lower than in the normal group (40.5% and 38.9%, respectively), but the difference was not statistically significant ( p = 0.102 and 0.082, respectively). Rotator cuff tear was significantly less common in the mesotenon (44.8%) group than in the normal group (62.4%; p = 0.004). Shoulder joint instability was more prevalent in the mesotenon (27.6%) group than in the normal group (14.9%), but the difference was not significant ( p = 0.305). The distribution of other shoulder diseases in the adherent group was similar to that in the normal group. Conclusions: The incidence of variants of the long head of the biceps brachii tendon was 6.5%, and most variants were mesotenon or adherent type. The SPL and ABS types were rare. Morbidity and procedure rates of the LHB were not significantly different between the variant group and the normal group, and rotator cuff tear was less common in the mesotenon group.

Clematis mandshurica RUPR. (CMR) and Erigeron annuus (L.) PERS. (EALP) have pharmacological effects including anti-inflammatory activity and been used in traditional medicines in Asia. However, neuroprotective effects of CMR and/or EALP extracts against brain ischemic insults have never been addressed. Thus, the aim of this study was to examine neuroprotective effects of YES-10, a combination of extracts from CMR and EALP (combination ratio, 1:1), in the hippocampus following ischemia/reperfusion in gerbils. Protection of neurons was investigated by cresyl violet staining, fluoro-jade B histofluorescence staining and immunohistochemistry for neuronal nuclei. In addition, attenuation of gliosis was studied by immunohistochemistry for astrocytic and microglial markers. Treatments with 50 or 100 mg/kg YES-10 failed to protect neurons in the hippocampus after ischemia/reperfusion injury. However, administration of 200 mg/kg YES-10 protected neurons from ischemia/reperfusion injury and attenuated reactive gliosis. These findings strongly suggest that a combination of extracts from CMR and EALP can be used as a prevention approach/drug against brain ischemic damage.

Oxcarbazepine, an antiepileptic drug, has been reported to modulate voltage-dependent sodium channels, and it is commonly used in epilepsy treatment. In this study, we investigated the neuroprotective effect of oxcarbazepine in the hippocampus after transient ischemia in gerbils. Gerbils randomly received oxcarbazepine 100 or 200 mg/kg before and after transient ischemia. We examined its neuroprotective effect in the cornu ammonis 1 subfield of the gerbil hippocampus at 5 days after transient ischemia by using cresyl violet staining, neuronal nuclei immunohistochemistry and Fluoro-Jade B histofluorescence staining for neuroprotection, and by using glial fibrillary protein and ionized calcium-binding adapter molecule 1 immunohistochemistry for reaction of astrocytes and microglia, respectively. Pre- and post-treatment with 200 mg/kg of oxcarbazepine, but not 100 mg/kg of oxcarbazepine, protected pyramidal neurons of the cornu ammonis 1 subfield from transient ischemic damage. In addition, pre- and post-treatment with oxcarbazepine (200 mg/kg) significantly ameliorated astrocytes and microglia activation in the ischemic cornu ammonis 1 subfield. In brief, our current results indicate that post-treatment as well as pre-treatment with 200 mg/kg of oxcarbazepine can protect neurons from ischemic insults via attenuation of the glia reaction.