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The seedlessness of grape derived from stenospermocarpy is one of the most prized traits of table or raisin grapes. It is controlled by a complex genetic system containing one major dominant gene and multiple minor recessive genes. Here, we collected dense variation data from high-depth resequencing data of seeded, seedless, and wild relative grape genomes sequenced to > 37x mean depth. Variant calls were made using a modified variant calling pipeline that was suitable for highly diverse interspecific grape accessions. The modified pipeline enabled us to call several million more variants than the commonly recommended pipeline. The quality was validated by Sanger sequencing data and subsequently supported by the genetic population structure and the phylogenetic tree constructed using the obtained variation data, results of which were generally consistent with known pedigree and taxonomic classifications. Variation data enabled us to confirm a major dominant gene and identify minor recessive loci for seedlessness. Incidentally, we found that grape cultivar Rizamat contains an ancestral chromosomal region of the major gene in Sultanina, a predominant seedlessness donor cultivar. Furthermore, we predicted new candidate causal genes including Vitvi01g00455, Vitvi08g01528, and Vitvi18g01237 associated with the minor seedless-regulating loci, which showed high homology with genes that regulate seed development in Arabidopsis. This study provides fundamental insights relevant to variant calling from genome resequencing data of diverse interspecific hybrid germplasms such as grape and will accelerate future efforts aimed at crop improvement.

Massive resequencing efforts have been undertaken to catalog allelic variants in major crop species including soybean, but the scope of the information for genetic variation often depends on short sequence reads mapped to the extant reference genome. Additional de novo assembled genome sequences provide a unique opportunity to explore a dispensable genome fraction in the pan-genome of a species. Here, we report the de novo assembly and annotation of Hwangkeum, a popular soybean cultivar in Korea. The assembly was constructed using PromethION nanopore sequencing data and two genetic maps, and was then error-corrected using Illumina short-reads and PacBio SMRT reads. The 933.12 Mb assembly was annotated 79,870 transcripts for 58,550 genes using RNA-Seq data and the public soybean annotation set. Comparison of the Hwangkeum assembly with the Williams 82 soybean reference genome sequence revealed 1.8 million single-nucleotide polymorphisms, 0.5 million indels, and 25 thousand putative structural variants. However, there was no natural megabase-scale chromosomal rearrangement. Incidentally, by adding two novel groups, we found that soybean contains four clearly separated groups of centromeric satellite repeats. Analyses of satellite repeats and gene content suggested that the Hwangkeum assembly is a high-quality assembly. This was further supported by comparison of the marker arrangement of anthocyanin biosynthesis genes and of gene arrangement at the Rsv3 locus. Therefore, the results indicate that the de novo assembly of Hwangkeum is a valuable additional reference genome resource for characterizing traits for the improvement of this important crop species.

Elucidation of the genomic organizations of transgene insertion sites is essential for the genetic studies of transgenic plants. Herein, we establish an analysis pipeline that identifies the transgene insertion sites as well as the presence of vector backbones, through de novo genome assembly with high-throughput sequencing data in two transgenic soybean lines, AtYUCCA6-#5 and 35S-UGT72E3/2-#7. Sequencing data of approximately 28× and 29× genome coverages for each line generated by high-throughput sequencing were de novo assembled. The databases generated from the de novo assembled sequences were used to search contigs that contained putative insertion sites and their flanking sequences (integration sites) of transgene fragments using transgenic vector sequences as queries. The predicted integration site sequences, which are located at three annotated genes that might regulate plant development or confer disease resistance, were then confirmed by local alignment against the soybean reference genome and PCR amplification. As results, we revealed the precise transgene-flanking sequences and sequence rearrangements at insertion sites in both the transgenic lines, as well as the aberrant insertion of a transgene fragment. Consequently, relative to experimental or enrichment technologies, our approach is straightforward and time-effective, providing an alternative method for the identification of insertion sites in transgenic plants.

The recent extensive spread of Zika virus has led to increased interest in the development of early diagnostic tests. To the best of our knowledge, this is the first study to demonstrate the successful use of phage display to identify affinity peptides for quantitative analysis of AXL, a tyrosine kinase receptor involved in Zika virus entry. Biopanning of M13 phage library successfully identified a high affinity peptide, with the sequence AHNHTPIKQKYL. To study the feasibility of using free peptides for molecular recognition, we synthesized a series of amino acid-substituted peptides and examined their binding affinity for AXL using electrochemical impedance spectroscopy and square wave voltammetry. Most synthetic peptides had non-identical random coil structures based on circular dichroism spectroscopy. Of the peptides tested, AXL BP1 exhibited nanomolar binding affinity for AXL. To verify whether AXL BP1 could be used as a peptide inhibitor at the cellular level, two functional tests were carried out: a WST assay for cell viability and qRT-PCR for quantification of RNA levels in Zika virus-infected Huh7 cells. The results showed that AXL BP1 had low cytotoxicity and could block Zika virus entry. These results indicate that newly identified affinity peptides could potentially be used for the development of Zika virus entry inhibitors.

Globally, soybean is a major protein and oil crop. Enhancing our understanding of the soybean domestication and improvement process helps boost genomics-assisted breeding efforts. Here we present a genome-wide variation map of 10.6 million single-nucleotide polymorphisms and 1.4 million indels for 781 soybean individuals which includes 418 domesticated (Glycine max), 345 wild (Glycine soja), and 18 natural hybrid (G. max/G. soja) accessions. We describe the enhanced detection of 183 domestication-selective sweeps and the patterns of putative deleterious mutations during domestication and improvement. This predominantly selfing species shows 7.1% reduction of overall deleterious mutations in domesticated soybean relative to wild soybean and a further 1.4% reduction from landrace to improved accessions. The detected domestication-selective sweeps also show reduced levels of deleterious alleles. Importantly, genotype imputation with this resource increases the mapping resolution of genome-wide association studies for seed protein and oil traits in a soybean diversity panel., The accumulation of recombination events in selfing species may lead to a rapid fixation of both beneficial and deleterious mutations. Here, the authors resequence 781 soybean accessions, show purging of deleterious mutation during domestication, and report genome-wide associations for seed protein and oil traits.

As a predominant plant protein and oil source for both food and feed, soybean is unique in that both domesticated and wild types are predominantly selfing. Here we present a genome-wide variation map of 781 soybean accessions that include 418 domesticated (Glycine max) and 345 wild (Glycine soja) accessions and 18 of their natural hybrids. We identified 10.5 million single nucleotide polymorphisms and 5.7 million small indels that contribute to within- and between-population variations. We describe improved detection of domestication-selective sweeps and drastic reduction of overall deleterious alleles in domesticated soybean relative to wild soybean in contrast to the cost of domestication hypothesis. This resource enables the marker density of existing data sets to be increased to improve the resolution of association studies.

Dengue virus type 2 NS1 (DENV2 NS1) is a specific and sensitive protein biomarker for dengue fever diagnosis. In this study we used polyvalent phage display to identify unique affinity peptides that can bind NS1 protein. Cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) were used to investigate the binding interactions. The potential affinity peptide-displayed phage from these methods was selected; its sequence was EHDRMHAYYLTR (R3#10). Amino acid sequence analysis showed that the peptide was rich in basic residues (two His and Arg). Among all the peptides tested, R3#10 showed the greatest decrease in current in CV and increase in impedance in EIS upon binding to NS1 proteins. EIS revealed that R3#10 phage clones were more specific towards NS1 proteins, as compared to bovine serum albumin or the M13 wild type used as control. Detection of NS1 proteins is in accordance with the electron-transfer resistance (Rct) value of the sensor layer, which is confirmed by EIS, and the Kd value of the R3#10 peptide while binding to the phage particles was measured. To the best of our knowledge, this is the first example of identification and characterization of NS1 binding affinity peptides using phage display technology and electrochemical methods. We concluded that these new peptide-displayed phages or free peptides from phages may have potential applications in dengue diagnosis.

In this study, we developed an electrochemical biosensor coated with a peptide that can detect the protein hemagglutinin (HA) present in the envelope of the influenza virus (H5N1). Using phage display, high-affinity peptide-displaying phage particles (GHPHYNNPSLQL) with specific binding abilities for HA were identified, which were evaluated using enzyme-linked immunosorbent assays (ELISAs). Based on the molecular structure identified by the functional studies, six newly designed peptides were chemically synthesized, and their binding interactions with HA proteins were characterized by atomic force microscopy (AFM), scanning electron microscopy (SEM), isothermal titration calorimetry (ITC), and surface plasmon resonance spectroscopy (SPR). Square wave voltammetry (SWV) revealed the presence of a linear relationship between the change in current and concentration of HA protein. From these observations, we selected IFA BP1 peptide as a potential molecular receptor and confirmed that the limit of detection (LOD) was found to be 3.26 nM. In addition, our electrochemical sensor successfully detected HA spiked in human plasma samples. Furthermore, good results for reproducibility and recovery using this biosensor were observed within a range of 31.2–500 nM concentrations and 82.3–111.5%, respectively. Importantly, the levels of HA proteins in the samples of human plasma measured using this sensor system corresponded well with those determined using a commercial ELISA method and also offered advantages such as low cost of fabrication, faster analysis, and use of lower sample volumes, suggesting that it could be applied for rapid and effective detection of the influenza virus antigen.

Cultivated soybean [Glycine max (L.) Merr.] flowers are either white or purple, whereas nearly all wild soybean (G. soja Sieb. and Zucc.) accessions have purple flowers. As a result, the soybean flower color phenotype has attracted the attention of plant breeders, biochemists, and population geneticists. Here, we report genetic mapping of a novel recessive white flower gene in YWS415, a wild soybean accession collected in Korea. The W1 locus, which is the major locus determining purple (W1) or white (w1) flower color, encodes flavonoid 3′ 5′-hydroxylase in YWS415, which was more similar to the common W1-type sequences than w1-type sequences. Subsequent mapping results using an F₂ population from a cross between the ‘Hwangkeum’ (purple flower) and YWS415 variants indicated that the white flower color was controlled by a recessive allele at the W4 locus that encodes dihydroflavonol-4-reductase 2 (DFR2). The w4 allele arose through insertion of a 5584-bp nonautonomous transposon member of soybean GM_CACTA_33 family into the second intron of DFR2. It was designated as GM_CACTA_33_w4. Results from this study will enhance our understanding of soybean white flower inheritance and facilitate marker-assisted selection for the antioxidative anthocyanins in soybeans.

Retinoic acid (RA), a metabolite of vitamin A, has been found to influence regeneration in the adult central nervous system (CNS). There may be an effect of RA in the recovery/repair in multiple sclerosis (MS), an autoimmune and neurodegenerative disease of the CNS. We hypothesized that RA is a regulator of the further differentiation of oligodendrocyte precursor cells (OPCs) – cells key to the remyelination process in MS. We conducted studies utilizing RNA-sequencing in human embryonic stem cell (hESC)-derived neural stem cells (NSCs) and OPCs so as to understand the role of transcriptional regulators during transition from both ESCs to NSCs and NSCs to OPCs. We identified that expression of retinoic acid receptors β and γ (RARβ and RARγ ) was significantly increased following the transition from NSCs to OPCs. We also demonstrated that long term in vitro culture of hESC-derived OPC with different isoforms of RA led to the significant up-regulation of two known transcriptional inhibitors of oligodendrocyte differentiation: Hes5 following prolonged treatment with all-trans-RA, 9-cis RA and 13-cis RA; and Id4 following treatment with 13cisRA. These results suggest that long term exposure to certain RA isoforms may impact the continued differentiation of this population., Highlights • Retinoic acid (ATRA) might have an effect on generation of oligodendrocyte precursor cells (OPC) in the CNS. • RNA-sequencing used for identification of up-regulation of RARβ and RARɣ expression during OPC differentiation. • Activation of RARβ and RARɣ by using three different agonists led increase expression of Hes5 and Id4.

Inflammasomes are caspase-1-activating molecular platforms that produce active interleukin (IL)-1β and are implicated in various central nervous system (CNS) diseases. These multi-protein complexes can be activated by exposure of cells to low osmolality. The inflammasome nucleotide-binding and oligomerization domain-like receptor pyrin domain-containing protein 3 (NLRP3) is hereby the main sensor of cellular osmolality. IL-1β was found to stimulate the secretion of antidiuretic hormone (ADH) from the posterior pituitary gland either by action of prostaglandins or indirectly by causing the release of IL-6. Based on these findings, we hypothesize that the hyponatremia caused by a wide range of CNS diseases is able to induce significant cell swelling with induction of a hyposmotic intracellular environment, which activates the NLRP3 inflammasome, causing the release of IL-1β and induced by IL-1β, IL-6, which increases the production of ADH that leads to more profound hyponatremia. Supportive evidence for this hypothesis is the finding that IL-1 injection can induce ADH release and hyposmotic effect of ADH induced hyponatremia can, via the mechanical effect of cell swelling, activate transient receptor potential channels, which via transforming growth factor β-activated kinase 1 activate NLRP3. Implications of this hypothesis, if confirmed, would include that hyponatremia can be exacerbated through this vicious cycle but also that the inflammasomes are key mediators of this process. Confirmation of this hypothesis would have implications for prevention and clinical management of changes in patients sodium levels related to syndrome of inappropriate antidiuretic hormone secretion (SIADH) with interventions targeting inflammatory mediator production and function of inflammasomes with the potential of prevention of permanent brain damage in a wide range of CNS diseases.

Discovery of new germplasm sources and identification of haplotypes for the durable Soybean mosaic virus resistance gene, Rsv 4, provide novel resources for map-based cloning and genetic improvement efforts in soybean. The Soybean mosaic virus (SMV) resistance locus Rsv4 is of interest because it provides a durable type of resistance in soybean [Glycine max (L.) Merr.]. To better understand its molecular basis, we used a population of 309 BC3F2 individuals to fine-map Rsv4 to a ~120 kb interval and leveraged this genetic information in a second study to identify accessions 'Haman' and 'Ilpumgeomjeong' as new sources of Rsv4. These two accessions along with three other Rsv4 and 14 rsv4 accessions were used to examine the patterns of nucleotide diversity at the Rsv4 region based on high-depth resequencing data. Through a targeted association analysis of these 19 accessions within the ~120 kb interval, a cluster of four intergenic single-nucleotide polymorphisms (SNPs) was found to perfectly associate with SMV resistance. Interestingly, this ~120 kb interval did not contain any genes similar to previously characterized dominant disease resistance genes. Therefore, a haplotype analysis was used to further resolve the association signal to a ~94 kb region, which also resulted in the identification of at least two Rsv4 haplotypes. A haplotype phylogenetic analysis of this region suggests that the Rsv4 locus in G. max is recently introgressed from G. soja. This integrated study provides a strong foundation for efforts focused on the cloning of this durable virus resistance gene and marker-assisted selection of Rsv4-mediated SMV resistance in soybean breeding programs.

On the basis of vegetation data by point quarter sampling method, the natural forest of Jirisan(Mt.)was classified into eight forest types by cluster analysis. They were Quercus mogolica forest type, Fraxinusmandshurica – Betula costata forest type, Mixed mesophytic forest type, Abies koreana forest type, Carpinuslaxiflora forest type, Quercus serrata forest type, Pinus densiflora forest type, and Quercus variabilis foresttype. Then, succession index was estimated for each forest type so as to evaluate succession processcomparatively among forest types. The results showed that Carpinus laxiflora forest type had highest successionindex of 219.7, followed by Mixed mesophytic forest type with little difference of the index of 218.3. Pinusdensiflora forest type had lowest index. Succession indices were hardly correlated with species diversity indicesof forest types. We presumed that the higher value of succession index a forest type had, the closer toward theclimax forest. However, the estimated index was not supposed to be absolute level of successional stage, but itcould play a role of comparative assessment in the position of the seral stage among forest types.Key words: forest type classification, forest succession, Jirisan, succession index, species diversity

This study was conducted to evaluate the ecological characteristics of forest cover types which were classified by cluster analysis in the natural forest of Sobaeksan on the basis of the vegetation data from the point-quarter sampling method. Recognized forest cover types were 1) Mixed mesophytic forest, 2) Taxus cuspidata forest, 3) Fraxinus rhynchophylla-Quercus mongolica forest, 4) Betula ermanii forest, 5) Pinus densiflora forest, 6) Quercus mongolica mixed forest, and 7) Quercus mongolica pure forest. For those of classified types, the species composition was expressed by importance value (IV) to describe the community floristically. The species diversity was quantified using the Shannon's diversity index. The results showed that the forest cover types were characteristically different from one another in growing species and compositional rates, depending upon the type which was formed by a number of similar vegetational sample points. Species diversity indices (H') of total and overstory both were the highest in the mixed mesophytic forest (3.530 and 2.880, respectively), and lowest in the Q. mongolica pure forest (2.122 and 0.000, respectively) with only one canopy species. The highest species diversity in the mixed mesophytic forest may due to the relatively high species richness and evenness in the forest cover types. The description on ecological characteristics were suggested to understand the formation and development of forest cover types in this study area.Key Words: cluster analysis, forest cover type, importance value, species diversity, sobaeksan

Globally, c. 0.8–1.2 million species of insects exist, with Coleoptera making up about 40% of this total. Pitfall traps for collecting ground beetles were installed at 11 study plots in Baekdudaegan mountain of Gangwon-do. Individual trapped species were counted and analyzed at each study area. This study has been carried out to provide basic data for analyzing forest health and investigating the competitive distribution among biological species in the forest environment through a field investigation on the species composition, diversity, and dominance rate of Coleoptera. Carabidae were collected using pitfall traps at the study area in Backdudaegan Mountain of Gangwon-do, and the individual number of collected species was counted. Collected ground beetles in the study area comprised 837 individuals, 14 genus, and 32 species. In this study, 217, 303, 144, and 209 individuals were found in Jinburyung, Mt. Odaesan, Mt. Taebaeksan, and Mt. Dutasan area, respectively. The abundance of ground beetles was relat...

The purpose of this study was to classify current forest cover types, and to investigate stand development patterns for natural forests in six areas in northern Baekdudaegan, South Korea. Twenty-eight independent forest communities were aggregated into eight forest cover types by species composition in the overstory of each forest community. The forest cover types were of mixed mesophytic, “others” deciduous, Quercus mongolica dominant, Q. mongolica pure, Pinus densiflora–Q. mongolica, P. densiflora, Betula ermanii, and Q. mongolica–P. koraiensis. The ecological information was organized by importance value and species diversity for each forest type. Based on the correlation between species diversity index and the abundance of Q. mongolica plus P. densiflora for corresponding forest cover types, we compared the developmental process and approximate successional pathway between each cover type. The P. densiflora forest cover type changes into the P. densiflora–Q. mongolica cover type, followed by the Q. mongolica dominant cover type through continuous invasion of the oak trees. Furthermore, the Q. mongolica pure cover type would spread toward the Q. mongolica dominant cover type with a mixture of various deciduous tree species. The Q. mongolica dominant cover type progresses through the other deciduous cover types to the mixed mesophytic cover type with diversified composition and structure. On the mid to lower slopes, with loamy soils and good moisture conditions, various deciduous forest types should progress, by ecological succession, toward the mixed mesophytic cover type without any further disturbance.

Delta neutrophil index (DNI) is the fraction of circulating immature granulocytes, which reflects severe bacterial infections and septic condition but has not been studied in urinary tract infection (UTI). Here, we evaluated the value of DNI in predicting acute pyelonephritis (APN) or vesicoureteral reflux (VUR) using the data of 288 patients. Conventional inflammatory markers (white blood cell [WBC] count, erythrocyte sedimentation rate [ESR], C-reactive protein [CRP]), and DNI were measured. WBC, CRP, ESR and DNI were higher in APN than in lower UTI (p P P P P

A high-resolution genetic map that was constructed for the Lf1 -residing region will provide valuable information for map-based cloning and genetic improvement efforts in soybean. Changes in leaf architecture as photosynthesis factories remain a major challenge for the improvement of crop productivity. Unlike most soybeans, which have compound leaves comprising three leaflets, the soybean Lf1 mutant has a high frequency of compound leaves with five leaflets in a partially dominant manner. Here, we generated a fine genetic map to determine the genetic basis of this multifoliolate leaf trait. A five-leaflet variant Dusam was found in a recently collected landrace cultivar. Phenotypic data were collected from the F2 population of a cross between the Dusam and three-leaflet cultivar V94-5152. The mapping results generated using public markers indicated that the five-leaflet determining gene in Dusam is an allele of the previously studied Lf1 gene on chromosome 8. A high-resolution map delimited the genomic region controlling the leaflet number trait to a sequence length of 49 kb. AP2 domain-containing Glyma.08g281900 annotated in this 49 kb region appeared to be a strong candidate for the Lf1-encoding gene, as members of the AP2-type transcription factor family regulate lateral organ development. Dusam additionally exhibits visually distinct phenotypes for shattering and seed-coat cracking traits. However, the two traits were clearly unlinked to the Lf1 gene in our mapping population. Interestingly, the mapping results suggest that the Lf1 gene most likely exerts a pleiotropic effect on the number of seeds per pod. Thus, our results provide a strong foundation towards the cloning of this compound leaf development gene and marker-assisted selection of the seeds per pod trait.

We investigated the effect of fire disturbance on short-term soil respiration in birch (Betula platyphylla Suk.) and larch (Larix gmelinii Rupr.) forests in Greater Xing’an range, northeastern China for further understanding of its effect on the carbon cycle in ecosystems. Our study show that post-fire soil respiration rates in B. platyphylla and L. gmelinii forests were reduced by 14% and 10%, respectively. In contrast, the soil heterotrophic respiration rates in the two types of forest were similar in post-fire and control plots. After fire, the contribution of root respiration to total soil respiration was dramatically reduced. Variation in soil respiration rates was explained by soil moisture (W) and soil temperature (T) at a depth of 5 cm. Exponential regression fitted T and W models explained Rs rates in B. platyphylla control and post-fire plots (83.1% and 86.2%) and L. gmelinii control and post-fire plots (83.7% and 88.7%). In addition, the short-term temperature coefficients in B. platyphylla control and post-fire plots were 5.33 and 5, respectively, and 9.12, and 5.26 in L. gmelinii control and post-fire plots, respectively. Our results provide an empirical baseline for studying the effect of fire disturbance on soil carbon balance and estimation of soil carbon flux in boreal forest.

The correlation between disturbance intensity and stand development was evaluated on the basis of natural forest community type classification in areas of Baekhaksan (more disturbed area) and Hwangaksan (less disturbed area). The vegetation data were collected by point-centered quarter sampling method, and they were subjected to cluster analysis for classifying community types and to analysis of species composition and species diversity for reviewing ecological characteristics. By the method of cluster analysis, natural forests of Baekhaksan were classified into Quercus forest community, Pinus densiflora community, Q. variabilis community, and Q. mongolica community. Those of Hwangaksan were divided into P. densiflora community, Q. mongolica community, Q. forest community, and Mixed mesophytic community. It is presumed that more developed and less disturbed forest area shows multiple species community pattern and more diversified structure than less developed and more disturbed forest area. In Korean peninsula, the abundance of red pine may play an important indicator to estimate the developmental pattern of the forest after artificial disturbance. The overall evaluation indicated that less disturbed Hwangaksan area had more developed stand pattern with mixed mesophytic community, more complicated species composition, and higher species diversity than Baekhaksan area.

Objectives/Hypothesis The study evaluated the relationship between the position that initially provoked vertigo and the affected semicircular canal (SCC) in patients with benign paroxysmal positional vertigo (BPPV), and aimed to predict the side affected by BPPV through history taking regarding the provoking position. Study Design Prospective study at a tertiary hospital. Methods A total of 521 patients with BPPV involving the posterior or horizontal SCCs performed questionnaires at initial visit asking to choose the initial provoking position among the 10 positions corresponding to one of the three planes (roll, pitch, or yaw). After excluding 45 patients showing signs of simultaneous multiple canal or anterior canal involvement, the frequency of the provoking positions and the correlation between the side of the provoking position and the ear affected by BPPV were analyzed. Results There were 239 patients with posterior SCC BPPV (p-BPPV) and 237 patients with horizontal SCC BPPV (h-BPPV). The waking-up position was the most common provoking position in both types of BPPV. Statistically significant correlation was demonstrated between the side of the provoking position at the onset of vertigo and the affected side by BPPV (P < .01) in patients with p-BPPV as well as h-BPPV (geotropic type [Geo]), but not in patients with h-BPPV (apogeotropic type [Apo]). Conclusions History taking regarding the side of provoking position at the onset of vertigo may help predict the side affected by BPPV in p-BPPV and h-BPPV (Geo). When h-BPPV (Apo) is suspected, further detailed examinations using additional localization methods should be performed. Level of Evidence 2b. Laryngoscope, 123:2259–2263, 2013

Objective Several copy number variations (CNVs) have been found to be associated with systemic lupus erythematosus (SLE) through the target gene approach. However, genome-wide features of CNVs and their role in the risk of SLE remain unknown. The aim of this study was to identify SLE-associated CNVs in Korean women. Methods Genome-wide assessments of CNVs were performed in 382 SLE patients and 191 control subjects, using an Illumina HumanHap610 BeadChip genotyping platform. SLE-associated CNV regions that were identified by genome-wide association study (GWAS) were replicated in quantitative polymerase chain reaction (PCR) and deletion-typing PCR analyses in an independent sample set comprising 564 SLE patients and 511 control subjects. Results Of 144 common CNV regions, 3 deletion-type CNV regions in 1q25.1, 8q23.3, and 10q21.3 were found to be significantly associated with SLE by GWAS analysis. In the independent replication, the CNV regions in 1q25.1 (RABGAP1L) and 10q21.3 were successfully replicated (odds ratio [OR] 1.30, P = 0.038 and OR 1.90, P = 3.6 × 10−5, respectively), and the associations were confirmed again by deletion-typing PCR. The CNV region in the C4 gene, which showed a potential association in the discovery stage, was included in the replication analysis and was found to be significantly associated with the risk of SLE (OR 1.88, P = 0.01). Through deletion-typing PCR, the exact sizes and breakpoint sequences of the deletions were defined. Individuals with the deletions in all 3 loci (RABGAP1L, 10q21.3, and C4) had a much higher risk of SLE than did those without any deletions in the 3 loci (OR 5.52, P = 3.9 × 10−4). Conclusion These CNV regions can be useful to identify the pathogenic mechanisms of SLE, and might be used to more accurately predict the risk of SLE by taking into consideration their synergistic effects on disease susceptibility.

The aim of this study was to determine whether decreased serum sodium concentration could be associated with the disease activity in SLE. We retrospectively analyzed the data of the two independent cohorts of children and adults with SLE in two centers. Hyponatremia was associated with serum chloride (p = 0.004), albumin (p = 0.002) and SLE disease activity index (SLEDAI) (p = 0.026) in children with SLE. Serum sodium levels were correlated negatively with ESR (p =0.001) and positively with serum albumin levels (p

The aim of this study was to evaluate the influence of cyclosporine A (CsA) on glomerular growth and the effect of mizoribine (MZR) and losartan (LSAR) on CsA-induced nephropathy in young rats. Six-week-old male Sprague-Dawley rats maintained on a low salt diet were given CsA (15 mg/kg), CsA and LSRT (30 mg/kg/day), CsA and MZR (5 mg/kg), or a combination of CsA, LSRT, and MZR for 4 and 7 weeks (two experiments) and compared with control group (olive oil-treated). Histopathology and glomerular size, inflammatory and fibrotic factors were studied. The score of acute CsA toxicity significantly decreased in the CsA + MZR group compared to the CsA group (p

Background The UBA6-specific E2 conjugating enzyme 1 (USE1) ubiquitin enzyme cascade is a poorly characterized arm of the ubiquitin-proteasome system. We investigated whether the UBA6-USE1 enzyme cascade plays a role in lung cancer tumorigenesis. Methods USE1 expression was assessed in tumor-normal paired samples from 106 lung cancer patients by immunoblot. USE1 was stably overexpressed and knocked down in lung cancer cell lines to evaluate cell proliferation, colony formation, and invasion. Xenograft models were used to determine the effects of USE1 on tumor growth (n = 7). Proteomics analysis was used to identify proteins interacting with USE1. The USE1 gene was sequenced in lung cancer patients, and missense mutations of USE1 were generated to evaluate its function. All statistical tests were two-sided. Results USE1 proteins were frequently overexpressed in lung cancer patients (92.5%) Stable overexpression of USE1 increased cell proliferation ( P = .002), migration ( P < .001), and invasion ( P < .001), whereas knockdown of USE1 reduced cell proliferation ( P < .001), migration ( P = .003), and invasion in lung cancer cells and xenograft models ( P < .001). USE1 was found to have a conserved D-box domain, and the level of the protein was regulated by the anaphase-promoting complex. Several missense mutations in USE1 identified in patients prolong the stability of the protein. Conclusions USE1 proteins are frequently overexpressed in lung cancer, and missense mutations in USE1 prolong the half-life of the protein, promoting tumor formation. Our findings reveal novel roles for USE1 in lung cancer and the possible use of USE1 as a novel biomarker and therapeutic target for lung cancer treatment.

Little information is currently available on the development of tubulointerstitial lesions in children with Henoch–Schonlein nephritis (HSN). To identify the impact of the development of tubulointerstitial changes in HSN, we retrospectively analyzed renal biopsies obtained from children with HSN. Twenty-eight children with HSN from whom serial renal biopsies had been obtained before and after immunosuppressive therapy were enrolled in the study. The patients were divided into two groups according to the observed change in tubulointerstitial lesion development: group I (n = 15), with stable or improved tubulointerstitial lesions, and group II (n = 13), with worsened tubulointerstitial lesions. Group II patients had longer duration of proteinuria than group I patients (3.7 ± 3.7 years vs. 1.7 ± 1.7 years, p = 0.052). The change in serum albumin level was negatively correlated with the change in tubulointerstitial scores before and after treatment (γ = −0.444, p = 0.018). Group II patients showed a significant decrease in immunoglobulin G (IgG) and IgA deposits after treatment (p = 0.039 and 0.003, respectively), while group II patients did not (p = 0.458 and 0.506, respectively). Although the International Study of Kidney Disease in Children classification of HSN does not include tubulointerstitial lesions, they can progress during treatment and could have significant clinical implications in association with the duration of proteinuria.

Leaf senescence is a finely regulated complex process; however, evidence for the involvement of epigenetic processes in the regulation of leaf senescence is still fragmentary. Therefore, we chose to examine the functions of DRD1, a SWI2/SNF2 chromatin remodeling protein, in epigenetic regulation of leaf senescence, particularly because drd1-6 mutants exhibited a delayed leaf senescence phenotype. Photosynthetic parameters such as Fv/Fm and ETRmax were decreased in WT leaves compared to leaves of drd1-6 mutants after dark treatment. The WT leaves remarkably lost more chlorophyll and protein content during dark-induced senescence (DIS) than the drd1-6 leaves did. The induction of senescence-associated genes was noticeably inhibited in the drd1-6 mutant after 5-d of DIS. We compared changes in epigenetic regulation during DIS via quantitative expression analysis of 180-bp centromeric (CEN) and transcriptionally silent information (TSI) repeats. Their expression levels significantly increased in both the WT and the drd1-6 mutant, but did much less in the latter. Moreover, the delayed leaf senescence was observed in ddm1-2 mutants as well as the drd1-6, but not in drd1-p mutants. These data suggest that SWI2/SNF2 chromatin remodeling proteins such as DRD1 and DDM1 may influence leaf senescence possibly via epigenetic regulation.

This study was conducted to estimate climax index by eco-morphology for major 36 tree and sub-tree species in natural deciduous forests so as to interpret seral position of each species in the forest community. Fourteen eco-morphological characters which were considered to be associated with successional gradient in the forest were selected for the study. Four levels per character for each species were given on a standardized scale of increasing climax, and the index was computed by the proportion of the sum of total scores, expressed by percent values. With calculated mean value of 54.8 for all indices, Carpinus cordata had the highest index value of 90.5, and Populus davidiana recorded the lowest of 13.2. The most climax group, greater than 70 of the index, contained only 8 species, intermediate group, between 41 to 70 of the index, had 23 species, and the most pioneer group, less than 40 of the index comprised 5 species. The result has noticed that the large number of species would take advantage of most diverse resource and niche in the intermediate stage of the sere in the forest. By cluster analysis all 36 species were subjected to be classified into several species groups which had common similar eco-morphological characteristics. The indices were additionally plotted on the two dimensional graph to recognize the positions related to the light absorption factor and reproduction factor. The climax index of tree and sub-tree species developed by this study could be applied to understand the present status of successional stage on the basis of species composition by the method of summing up the indices. And comparison of forest successional stage among various forest communities could be done by summing up the climax indices of composed species in each community. However, this kind of applied methodology should be limited to the forest of similar species composition and site condition.

We evaluated whether cytochrome c oxidase subunit I (COI) barcodes that have been previously suggested for birds are useful for identifying species of the genus Larus, which are resident or migratory birds in Korea. We found 31 intra- or interspecific COI haplotypes from 12 of 13 Larus species in Korea. Haplotype analyses showed that the COI barcodes could not distinguish some interspecific haplotypes from 6 of 12 Larus species because there were no nucleotide substitutions among their COI haplotypes. The neighbor-joining tree formed shallow branches in the clades expected for L. saundersi, L. crassirostris, L. canus, L relictus, and L. ridbundus. In the nine Larus species, COI haplotypes were not grouped as distinct entities that were correctly assigned to their corresponding species, resulting in polytypic clades. These results indicate that the COI sequences need to be cautiously selected as a DNA barcode for identifying species of Korean Larus birds.

Influence of gamma rays on the cyanobacterium Synechocystis sp. PCC 6803 cells was investigated in terms of a bidirectional hydrogenase, which is encoded by hoxEFUYH genes and responsible for biohydrogen production. Irradiated cells revealed a substantial change in stoichiometry of photosystems at one day after gamma irradiation at different doses. However, as evaluated by the maximal rate of photosynthetic oxygen evolution, maximal photochemical efficiency of photosystem II, and chlorophyll content, net photosynthesis or photosynthetic capacity was not significantly different between the control and irradiated cells. Instead, transcription of hoxE, hoxH, or lexA, which encodes a subunit of bidirectional hydrogenase or the only transcriptional activator, LexA, for hox genes, was commonly enhanced in the irradiated cells. This transcriptional enhancement was more conspicuously observed immediately after gamma irradiation. In contrast, hydrogenase activities were found to somewhat lower in the irradiated cells. Therefore, we propose that transcription of hox genes should be enhanced by gamma irradiation in a LexA-mediated and possibly photosynthesis-independent manner and that this enhancement might not induce a subsequent increase in hydrogenase activities, probably due to the presence of post-transcriptional and/or post-translational regulatory mechanisms.

Objectives/Hypothesis: The aim of this study was to evaluate the relationship between the head position during sleep and the affected semicircular canal (SCC) in patients with benign paroxysmal positional vertigo (BPPV). Study Design: Prospective study at a tertiary hospital. Methods: We conducted a prospective study in patients with BPPV involving posterior or horizontal SCCs. Of a total of 425 patients diagnosed with BPPV, 83 patients showing signs of simultaneous multiple canal involvement, and those having combined otologic diseases in the same ear were excluded from the study. All patients included in the study were asked to define their preferred head-lying side at the beginning of sleep among the following choices: supine, lateral (right or left), or no predominant side. Results: Our study included 174 patients with posterior SCC BPPV (p-BPPV) and 168 patients with horizontal SCC BPPV (h-BPPV). Patients habitually adopted a lateral head position during sleep in 105 cases of p-BPPV and 109 cases of h-BPPV. Statistically significant correlation was demonstrated between the head-lying side during sleep and the affected side by BPPV (P < .01) in patients with p-BPPV as well as h-BPPV. Conclusions: There is significant correlation between the head-lying side during sleep and the side affected by BPPV in h-BPPV and p-BPPV, which may provide additional clues about the pathophysiology of BPPV. Clinically, this information may be used to provide helpful guidelines for patients with BPPV concerning their sleeping positions to prevent recurrence of BPPV. Laryngoscope, 2012

Mean platelet volume (MPV) has not yet been well-established in urinary tract infection (UTI). The purpose of this study was to evaluate the role of MPV as an acute phase reactant in children with UTI. Data from 118 young children (P = 0.001), ESR (P = 0.005), CRP (P P = 0.011) were significantly higher in the APN group than those in the lower UTI group. MPV positively correlated with PDW, CRP and negatively with platelet count. Multiple logistic regression analyses showed that CRP and MPV were independent predictive factors for APN patients. However, the area under the Receiver Operating Characteristic (ROC) curve analysis for MPV was lower than CRP. Our results suggest that MPV can be an inflammatory marker in UTI, but the predictive value of MPV was not superior to CRP in the diagnosis of APN.

Based upon the vegetation data of woody plants by plot sampling method in the natural deciduous forest of Mt. Jeombong, the study was carried out to examine importance value, rank abundance curve, and species abundance curve, and comparatively evaluate seven different species diversity indices for Log series, species richness, Margalef index, Shannon–Wiener index, Simpson index, McIntosh index, and Berger–Parker index, according to canopy layer and life form. The minimal area which meant only few more species were increased was 3.48 ha in total. The dominant species of overstory was Quercus mongolica, while Acer pseudo-sieboldianum was the dominant species of both midstory and understory. According to rank abundance curve and species abundance curve, species evenness was low. Log series and the Margalef index had a similar tendency. Also, the Shannon–Wiener index, Simpson index, and McIntosh index showed a similar tendency. However, the Berger–Parker index showed a similar trend with Log series and Margal...

The relative importance of radiation dose, storage time, and temperature in radiation processing of spinach (Spinacia oleracea L.), was evaluated in terms of the postharvest quality through a model study using leaf disks. Physiological activity and chlorophyll and carotenoid contents were measured to represent the postharvest quality (in terms of external appearance) of spinach, a leafy green vegetable. At and , the higher gamma-radiation dose caused a greater decrease in the physiological activity, depending on the storage time of 4 d. However, this decrease was not significant at and . Total chlorophyll and carotenoid contents were substantially decreased by 3 kGy at , and dose-dependently by 0.5-3 kGy at . In contrast, the proportion of lutein in total carotenoid was significantly increased in the 2-3-kGy samples only at , while that of -carotene was slightly decreased, indicating progression of leaf aging. These data suggest that the unfavorable effect of gamma irradiation on the postharvest quality of spinach could be avoided or controlled by the storage time or temperature rather than the radiation dose. The current study could be available to improve radiation processing of other leafy green vegetables.

Together with single nucleotide polymorphism (SNP), copy number variations (CNV) are recognized to be the major component of human genetic diversity and used as a genetic marker in many disease association studies. Affymetrix Genome-wide SNP 5.0 is one of the commonly used SNP array platforms for SNP-GWAS as well as CNV analysis. However, there has been no report that validated the accuracy and reproducibility of CNVs identified by Affymetrix SNP array 5.0. In this study, we compared the characteristics of CNVs from the same set of genomic DNAs detected by three different array platforms; Affymetrix SNP array 5.0, Agilent 2X244K CNV array and NimbleGen 2.1M CNV array. In our analysis, Affymetrix SNP array 5.0 seems to detect CNVs in a reliable manner, which can be applied for association studies. However, for the purpose of defining CNVs in detail, Affymetrix Genome-wide SNP 5.0 might be relatively less ideal than NimbleGen 2.1M CNV array and Agilent 2X244K CNV array, which outperform Affymetrix array for defining the small-sized single copy variants. This result will help researchers to select a suitable array platform for CNV analysis.

The natural regeneration of Fraxinus mandshurica and F. rhynchophylla was reviewed and evaluated in the natural deciduous forest of the Mt. Jumbong area on the basis of vegetation data from sample plots. The two species were largely alike in their mechanisms of both sexual and asexual reproduction. According to the ecological attributes of present and future composition ratio, inter‐species association with other species, the potentiality of shade tolerance and climax related characters, and spatial distribution pattern in mixtures with other hardwood species, F. mandshurica and F. rhynchophylla had characteristics enabling them to maintain the present level of dominance for the next succeeding generation. However, while information is still lacking about natural regeneration in the two species obtaining and applying further information, such as ecophysiological characteristics and site requirement of the species, structural attributes of composition and dynamics, and associative relations to other specie...

Copyright © 2018 Inderscience Enterprises Ltd. Background: Low-input or single-cell RNA-Seq are widely used today, but two technical questions remain: 1) in technical replicates, what proportion of noises comes from input RNA quantity rather than variation of bioinformatics tools?; 2) In single neurons, whether variation in gene expression is attributable to biological heterogeneity or just random noise? To examine the sources of variability, we have generated RNA-Seq data from low-input (10/100/1000pg) reference RNA samples and 38 single neurons from human brains. Results: For technical replicates, the quantity of input RNA is negatively correlated with expression variation. For genes in the medium- and high-expression groups, input RNA amount explains most of the variation, whereas bioinformatic pipelines explain some variation for the low-expression group. The t-distributed stochastic neighbour embedding (t-SNE) method reveals data-inherent aggregation of low-input replicate data, and suggests heterogeneity of single pyramidal neuron transcriptome. Interestingly, expression variation in single neurons is biologically relevant. Conclusions: We found that differences in bioinformatics pipelines do not present a major source of variation.

Recent discovery of the copy number variation (CNV) in normal individuals has widened our understanding of genomic variation. However, most of the reported CNVs have been identified in Caucasians, which may not be directly applicable to people of different ethnicities. To profile CNV in East-Asian population, we screened CNVs in 3578 healthy, unrelated Korean individuals, using the Affymetrix Genome-Wide Human SNP array 5.0. We identified 144,207 CNVs using a pooled data set of 100 randomly chosen Korean females as a reference. The average number of CNVs per genome was 40.3, which is higher than that of CNVs previously reported using lower resolution platforms. The median size of CNVs was 18.9 kb (range 0.2-5406 kb). Copy number losses were 4.7 times more frequent than copy number gains. CNV regions (CNVRs) were defined by merging overlapping CNVs identified in two or more samples. In total, 4003 CNVRs were defined encompassing 241.9 Mb accounting for approximately 8% of the human genome. A total of 2077 CNVRs (51.9%) were potentially novel. Known CNVRs were larger and more frequent than novel CNVRs. Sixteen percent of the CNVRs were observed inor =1% of study subjects and 24% overlapped with the OMIM genes. A total of 476 (11.9%) CNVRs were associated with segmental duplications. CNVS/CNVRs identified in this study will be valuable resources for studying human genome diversity and its association with disease.

This study examined the ecological attributes of a natural deciduous forest using a point‐centered quarter method. Seventy two points were selected randomly to investigate the vegetation. The woody species of DBH≤6 cm (first group) and DBH>6 cm (second group) were analyzed separately. The result showed that the forest had comparatively high species diversity. The first group was dominated by Lindera obtusiloba with an importance value of 24.0% and the second group was dominated by Quercus variabilis with an importance value of 41.9%. The population of Pinus koraiensis in the first group had an inverse J‐shaped density distribution along the DBH class. For the inter‐species association, Lindera obtusiloba had a significant positive association with Betula davurica, Quercus dentata and Quercus variabilis; Lindera obtusiloba had a significant negative association with Styrax obassia and Quercus mongolica; Styrax obassia had a significant negative association with Quercus variabilis and Betula davurica; and S...

Aim: Mitochondrial disorders with respiratory chain complex defect are known to show a broad spectrum of clinical phenotypes, though their contribution to renal disease has not received much attention. The aim of this study was to evaluate renal function using different markers of the glomerular filtration rate (GFR) in children with mitochondrial respiratory chain complex (MRC) defects. Methods: Twenty-two patients with MRC I defect confirmed by biochemical enzyme assays using muscle tissue, were evaluated for renal function with diethylenetriaminepentaacetic acid (DTPA) renal scintigraphy, urine creatinine clearance, serum creatinine (Scr) and cystatin C (Cys C) levels. Results: All patients showed lower levels within normal range of Scr (0.4–0.7 mg/dL, mean 0.47 mg/dL), and with no significant correlation with DTPA–GFR. Cys C showed significant correlation with DTPA–GFR (p < 0.01) providing higher diagnostic accuracy than creatinine in patients with MRC defect. Conclusion: In mitochondrial disorder with MRC defect, Scr could not fully reflect renal function due to the relatively small body mass of patients. Considering the limited clinical availability of DTPA renal scintigraphy, Cys C should be taken as the first step to evaluate GFR in mitochondrial disorders.

Background: Oral squamous cell carcinomas (OSCCs) are characterized by a high degree of local invasion and a high rate of metastases to cervical lymph nodes. Downregulation of CXCR-4 by siRNA inhibits invasion and growth of breast and colon cancer cells. However, there have been no reports on the downregulation of CXCR-4 by small interfering RNA (siRNA) in oral cancer cells. Methods: We generated two stable CXCR-4-knockdown clones (KBsi and KOSCC-25Bsi) from the KB and KOSCC-25B OSCC cell lines by lentiviral delivery. In vitro invasion and cell proliferation assays were used to investigate the effect of CXCR-4 downregulation on cell proliferation and invasiveness in KBsi and KOSCC-25Bsi. Immunohistochemistry was performed to evaluate the correlation between CXCR-4 expression and proliferation in 26 OSCC tissue samples. Results: CXCR4-knockdown OSCC cells showed reduced invasiveness. The invasiveness of KBsi decreased to 29.5% of the vector-infected controls, and KOSCC-25Bsi decreased to 38.1% of the control vector-infected cells (P

Recognizing the ecological importance of forest gap formation for forest community structure, we examined the differences in species diversity between forest gaps and closed canopy areas for trees and shrubs in three developmental stages (seedling, sapling I, and sapling II) in a typical mixed broadleaved-Korean pine forest. We randomly placed 100 sample plots ( for seedling and sapling I, and for sapling II) in forest gap and closed canopy areas of a 9 ha permanent sample plot for vegetation surveys of plants of each developmental stage in each habitat type. Even though the formation of forest gaps encouraged the occurrence of gap-dependent species and increased overall species diversity, there were no significant differences in species richness among the three developmental stages for both tree and shrub species (p>0.05). Comparing the two types of sites, statistical tests revealed no difference in species richness for trees, but highly significant differences (p0.05) for both Simpson and Shannon indices. The variance for shrub seedlings was significantly different between forest gaps and closed canopy areas, but not for sapling I and sapling II. The analysis showed that the species diversity in forest gaps was significantly different from that of closed canopy areas for seedling and sapling I (p0.05).

RE1-Silencing Transcription factor (REST) has a well-established role in regulating transcription of genes important for neuronal development. Its role in cancer, though significant, is less well understood. We show that REST downregulation in weakly invasive MCF-7 breast cancer cells converts them to a more invasive phenotype, while REST overexpression in highly invasive MDA-MB-231 cells suppresses invasiveness. Surprisingly, the mechanism responsible for these phenotypic changes does not depend directly on the transcriptional function of REST protein. Instead, it is driven by previously unstudied mid-size (30–200 nt) non-coding RNAs (ncRNAs) derived from the first exon of an alternatively spliced REST transcript: REST-003. We show that processing of REST-003 into ncRNAs is controlled by an uncharacterized serine/arginine repeat-related protein, SRRM3. SRRM3 expression may be under REST-mediated transcriptional control, as it increases following REST downregulation. The SRRM3-dependent regulation of REST-003 processing into ncRNAs has many similarities to recently described promoter-associated small RNA-like processes. Targeting ncRNAs that control invasiveness could lead to new therapeutic approaches to limit breast cancer metastasis.

Aims To determine the frequencies of the variant alleles and the genotypes of CYP2C9 in a Korean population. Methods Three hundred and fifty-eight healthy Korean subjects were studied. CYP2C9 alleles were detected by polymerase chain reaction-restriction fragment length polymorphism assays and direct sequencing assays. Results The allele frequencies were 0.934 for CYP2C9*1, 0.060 for CYP2C9*3 and 0.006 for CYP2C9*13. The CYP2C9*2,*4,*5 and *11 alleles were not detected. The frequencies of the CYP2C9*1/*1, *1/*3 and *1/*13 genotypes were 0.869, 0.120 and 0.011, respectively. Conclusion The frequency of the CYP2C9*3 allele in the Korean population studied was significantly higher than reported elsewhere, and a novel allele, CYP2C9*13, was found at a frequency of 0.006 (95% confidence interval 0, 0.012). Only three genotypes of CYP2C9, CYP2C9*1/*1,*1/*3 and *1/*13 were observed in this Korean population.

This study was conducted to estimate the biomass and nutrient distribution in understory P. koraiensis seedlings invading a mixed forest dominated by Quercus mongolica in central Korea. Total above and belowground biomass for the three overstory and understory dominant tree species were 2.70 t/ha for P. koraiensis, 210.56 t/ha for Q. mongolica, and 28.39 t/ha for Q. variabilis. P. koraiensis seedlings seemed to allocate more biomass to foliage (31.0% of total biomass) than overstory Quercus spp. (0.9%), so as to exploit the low light flux found in the shady conditions. Furthermore, the high specific leaf area of P. koraiensis seedlings indicated morphological characteristics of shade leaves in low light conditions. Total nitrogen (N) and phosphorus (P) contents for P. koraiensis seedlings and Quercus spp. were 19.6 and 1.9 kg/ha, and 94.7–626.5 and 9.4–137.6 kg/ha, respectively. Our results suggested that understory P. koraiensis seedlings exerted only a minor influence on the biomass and nutrient distrib...

This study was conducted to provide appropriate tending operation strategies for natural deciduous forests, by evaluating the stand quality, suggesting a removal plan for undesirable trees, and predicting improvement cutting practice by evaluation of tree‐form quality. The results showed that average number of trees per hectare was 804 stems, average diameter at breast height (DBH) was 22.3cm, and average height was 14.3 m. The canopy dominant species, in order of incidence, were Quercus serrata, Q. variabilis, Q. mongolica, and Fraxinus rhynchophylla. Based on the grades of five tree‐form quality factors for all trees in the study plots, we estimated the change of tree numbers, DBH, and height with the improvement cutting according to different tree quality grades. The application of the higher grade to the tending operation decreased the number of trees without significant change in DBH and height, suggesting an obvious improvement in the stand quality.

Summary Cultivated soybean (Glycine max) suffers from a narrow germplasm relative to other crop species, probably because of under-use of wild soybean (Glycine soja) as a breeding resource. Use of a single nucleotide polymorphism (SNP) genotyping array is a promising method for dissecting cultivated and wild germplasms to identify important adaptive genes through high-density genetic mapping and genome-wide association studies. Here we describe a large soybean SNP array for use in diversity analyses, linkage mapping and genome-wide association analyses. More than four million high-quality SNPs identified from high-depth genome re-sequencing of 16 soybean accessions and low-depth genome re-sequencing of 31 soybean accessions were used to select 180 961 SNPs for creation of the Axiom® SoyaSNP array. Validation analysis for a set of 222 diverse soybean lines showed that 170 223 markers were of good quality for genotyping. Phylogenetic and allele frequency analyses of the validation set data indicated that accessions showing an intermediate morphology between cultivated and wild soybeans collected in Korea were natural hybrids. More than 90 unanchored scaffolds in the current soybean reference sequence were assigned to chromosomes using this array. Finally, dense average spacing and preferential distribution of the SNPs in gene-rich chromosomal regions suggest that this array may be suitable for genome-wide association studies of soybean germplasm. Taken together, these results suggest that use of this array may be a powerful method for soybean genetic analyses relating to many aspects of soybean breeding.

In addition to single-nucleotide polymorphisms (SNP), copy number variation (CNV) is a major component of human genetic diversity. Among many whole-genome analysis platforms, SNP arrays have been commonly used for genomewide CNV discovery. Recently, a number of CNV defining algorithms from SNP genotyping data have been developed; however, due to the fundamental limitation of SNP genotyping data for the measurement of signal intensity, there are still concerns regarding the possibility of false discovery or low sensitivity for detecting CNVs. In this study, we aimed to verify the effect of combining multiple CNV calling algorithms and set up the most reliable pipeline for CNV calling with Affymetrix Genomewide SNP 5.0 data. For this purpose, we selected the 3 most commonly used algorithms for CNV segmentation from SNP genotyping data, PennCNV, QuantiSNP; and BirdSuite. After defining the CNV loci using the 3 different algorithms, we assessed how many of them overlapped with each other, and we also validated the CNVs by genomic quantitative PCR. Through this analysis, we proposed that for reliable CNV-based genomewide association study using SNP array data, CNV calls must be performed with at least 3 different algorithms and that the CNVs consistently called from more than 2 algorithms must be used for association analysis, because they are more reliable than the CNVs called from a single algorithm. Our result will be helpful to set up the CNV analysis protocols for Affymetrix Genomewide SNP 5.0 genotyping data.