Comparative single-cell transcriptomic analysis reveals differences in signaling pathways in gonadal primordial germ cells between chicken (Gallus gallus) and zebra finch (Taeniopygia guttata).

Primordial germ cells (PGCs) have been used in avian genetic resource conservation and transgenic animal production. Despite their potential applications to numerous avian taxa facing extinction due to habitat loss and degradation, research has largely focused on poultry, such as chickens, in part owing to the difficulty in obtaining intact PGCs from other species. Recently, phenotypic differences between PGCs of chicken and zebra finch, a wild bird with vocal learning, in early embryonic development have been reported. In this study, we used advanced single-cell RNA sequencing (scRNA-seq) technology to evaluate zebra finch and chicken PGCs and surrounding cells, and to identify species-specific characteristics. We constructed single-cell transcriptome landscapes of chicken gonadal PGCs for a comparison with previously reported scRNA-seq data for zebra finch. We identified interspecific differences in several signaling pathways in gonadal PGCs and somatic cells. In particular, NODAL and insulin signaling pathway activity levels were higher in zebra finch than in chickens, whereas activity levels of the downstream FGF signaling pathway, involved in the proliferation of chicken PGCs, were higher in chickens. This study is the first cross-species single-cell transcriptomic analysis targeting birds, revealing differences in germ cell development between phylogenetically distant Galliformes and Passeriformes. Our results provide a basis for understanding the reproductive physiology of avian germ cells and for utilizing PGCs in the restoration of endangered birds and the production of transgenic birds.

The influence of different hinge position on PTS during HTO: comparison between open-wedge and closed-wedge HTO.

PURPOSE: The purpose of this study was to determine the significance of hinge position through comparison between open-wedge and closed-wedge high tibial osteotomy (HTO) and to determine the ideal hinge position to minimize the effect of HTO on the posterior tibial slope (PTS) and medial proximal tibial angle (MPTA). METHODS: Procedures were performed on 32 cadaveric knees using open-wedge HTO with the standard hinge position or a low hinge position or closed-wedge HTO with the standard hinge position or a low hinge position. To define the standard hinge position in open wedge HTO, we drew a line 3-cm inferior to the medial tibial plateau toward the fibular head and located the intersection of this line with a longitudinal line 1-cm medial to fibular shaft. The low hinge position was then defined as the point 1-cm inferior to the standard position. For the standard hinge position for closed-wedge HTO, we drew a line parallel with joint line from 2-cm inferior to the lateral tibial plateau. The low hinge position was then defined as the point 1-cm inferior to the standard position. RESULTS: For the open-wedge procedure, osteotomy through the low hinge position resulted in a significantly greater PTS compared to osteotomy through the standard hinge position. MPTA was also significantly greater for the low hinge position compared to standard hinge position. In the closed-wedge HTO, neither the PTS nor MPTA was significantly different for the low and standard hinge positions. CONCLUSIONS: Hinge position significantly affects changes in the PTS and MPTA following open-wedge but not closed-wedge HTO. Understanding how to hinge position affects the PTS and MPTA is critical for surgeons performing open-wedge HTO procedures. Adopting an accurate hinge position is crucial for preventing complications, especially in open-wedge osteotomy, due to postoperative changes in the PTS and MPTA.

DMRT1 gene disruption alone induces incomplete gonad feminization in chicken.

Compared with the well-described XY sex determination system in mammals, the avian ZW sex determination system is poorly understood. Knockdown and overexpression studies identified doublesex and mab-3-related transcription factor 1 (DMRT1) as the testis-determining gene in chicken. However, the detailed effects of DMRT1 gene disruption from embryonic to adult development are not clear. Herein, we have generated DMRT1-disrupted chickens using the clustered regularly interspaced short palindromic repeats-associated protein 9 system, followed by an analysis of physiological, hormonal, and molecular changes in the genome-modified chickens. In the early stages of male chicken development, disruption of DMRT1 induced gonad feminization with extensive physiological and molecular changes; however, functional feminine reproductivity could not be implemented with disturbed hormone synthesis. Subsequent RNA-sequencing analysis of the DMRT1-disrupted chicken gonads revealed gene networks, including several novel genes linearly and non-linearly associated with DMRT1, which are involved in gonad feminization. By comparing the gonads of wild type with the genome-modified chickens, a set of genes were identified that is involved in the ZW sex determination system independent of DMRT1. Our results extend beyond the Z-dosage hypothesis to provide further information about the avian ZW sex determination system and epigenetic effects of gonad feminization.

The transcriptome of early chicken embryos reveals signaling pathways governing rapid asymmetric cellularization and lineage segregation.

The phylogenomics and comparative functional genomics of avian species were investigated in the Bird 10,000 Genomes (B10K) project because of the important evolutionary position of birds and their value as a research model. However, the systematic profiling of transcriptional changes prior to oviposition has not been investigated in avian species because of the practical difficulties in obtaining pre-oviposited eggs. In this study, a total of 137 pre-oviposited embryos were collected from hen ovaries and oviducts and subjected to RNA-sequencing analyses. Two waves of chicken zygotic genome activation (ZGA) were observed. Functionally distinct developmental programs involving Notch, MAPK, Wnt and TGFß signaling were separately detected during cleavage and area pellucida formation. Furthermore, the early stages of chicken development were compared with the human and mouse counterparts, highlighting chicken-specific signaling pathways and gradually analogous gene expression via ZGA. These findings provide a genome-wide understanding of avian embryogenesis and comparisons among amniotes.

Association between height and sleep duration in Korean adults.

The relationship between height and sleep duration is poorly understood in adults. We analysed the data from 32 698 adults collected by the 2007-2016 Korean National Health and Nutrition Examination Survey. A total of 44.4% and 9.1% participants reported short (≤6 h) and long (≥9 h) sleep duration, respectively. A shorter height was significantly associated with increased likelihood of both short and long sleep. A sex-stratified analysis revealed that the relationship between height and sleep duration was only significant in males. In conclusion, height was independently related to sleep duration in Korean men.

Hypernatremia at admission predicts poor survival in patients with terminal cancer: a retrospective cohort study.

BACKGROUND: Although palliative care providers, patients, and their families rely heavily on accurate prognostication, the prognostic value of electrolyte imbalance has received little attention. METHODS: As a retrospective review, we screened inpatients with terminal cancer admitted between January 2017 and May 2019 to a single hospice-palliative care unit. Clinical characteristics and laboratory results were obtained from medical records for multivariable Cox regression analysis of independent prognostic factors. RESULTS: Of the 487 patients who qualified, 15 (3%) were hypernatremic upon admission. The median survival time was 26 days. Parameters associated with shortened survival included male sex, advanced age (> 70 years), lung cancer, poor performance status, elevated inflammatory markers, azotemia, impaired liver function, and hypernatremia. In a multivariable Cox proportional hazards model, male sex (hazard ratio [HR] = 1.53, 95% confidence interval [CI]: 1.15-2.04), poor performance status (HR = 1.45, 95% CI: 1.09-1.94), leukocytosis (HR = 1.98, 95% CI: 1.47-2.66), hypoalbuminemia (HR = 2.06, 95% CI: 1.49-2.73), and hypernatremia (HR = 1.55, 95% CI: 1.18-2.03) emerged as significant predictors of poor prognosis. CONCLUSION: Hypernatremia may be a useful gauge of prognosis in patients with terminal cancer. Further large-scale prospective studies are needed to corroborate this finding.

BALLI: Bartlett-adjusted likelihood-based linear model approach for identifying differentially expressed genes with RNA-seq data.

BACKGROUND: Transcriptomic profiles can improve our understanding of the phenotypic molecular basis of biological research, and many statistical methods have been proposed to identify differentially expressed genes (DEGs) under two or more conditions with RNA-seq data. However, statistical analyses with RNA-seq data are often limited by small sample sizes, and global variance estimates of RNA expression levels have been utilized as prior distributions for gene-specific variance estimates, making it difficult to generalize the methods to more complicated settings. We herein proposed a Bartlett-Adjusted Likelihood-based LInear mixed model approach (BALLI) to analyze more complicated RNA-seq data. The proposed method estimates the technical and biological variances with a linear mixed-effects model, with and without adjusting small sample bias using Bartlkett's corrections. RESULTS: We conducted extensive simulations to compare the performance of BALLI with those of existing approaches (edgeR, DESeq2, and voom). Results from the simulation studies showed that BALLI correctly controlled the type-1 error rates at various nominal significance levels and produced better statistical power and precision estimates than those of other competing methods in various scenarios. Furthermore, BALLI was robust to variation of library size. It was also successfully applied to Holstein milk yield data, illustrating its practical value. CONCLUSIONS;: BALLI is statistically more efficient and valid than existing methods, and we conclude that it is useful for identifying DEGs in RNA-seq analysis.

RNA-sequencing across three matched tissues reveals shared and tissue-specific gene expression and pathway signatures of COPD.

BACKGROUND: Multiple gene expression studies have been performed separately in peripheral blood, lung, and airway tissues to study COPD. We performed RNA-sequencing gene expression profiling of large-airway epithelium, alveolar macrophage and peripheral blood samples from the same subset of COPD cases and controls from the COPDGene study who underwent bronchoscopy at a single center. Using statistical and gene set enrichment approaches, we sought to improve the understanding of COPD by studying gene sets and pathways across these tissues, beyond the individual genomic determinants. METHODS: We performed differential expression analysis using RNA-seq data obtained from 63 samples from 21 COPD cases and controls (includes four non-smokers) via the R package DESeq2. We tested associations between gene expression and variables related to lung function, smoking history, and CT scan measures of emphysema and airway disease. We examined the correlation of differential gene expression across the tissues and phenotypes, hypothesizing that this would reveal preserved and private gene expression signatures. We performed gene set enrichment analyses using curated databases and findings from prior COPD studies to provide biological and disease relevance. RESULTS: The known smoking-related genes CYP1B1 and AHRR were among the top differential expression results for smoking status in the large-airway epithelium data. We observed a significant overlap of genes primarily across large-airway and macrophage results for smoking and airway disease phenotypes. We did not observe specific genes differentially expressed in all three tissues for any of the phenotypes. However, we did observe hemostasis and immune signaling pathways in the overlaps across all three tissues for emphysema, and amyloid and telomere-related pathways for smoking. In peripheral blood, the emphysema results were enriched for B cell related genes previously identified in lung tissue studies. CONCLUSIONS: Our integrative analyses across COPD-relevant tissues and prior studies revealed shared and tissue-specific disease biology. These replicated and novel findings in the airway and peripheral blood have highlighted candidate genes and pathways for COPD pathogenesis.

Transcriptional and translational dynamics during maternal-to-zygotic transition in early chicken development.

Maternal-to-zygotic transition (MZT) is the critical process for the establishment of embryonic identity across vertebrates. During this period, the massive transcriptional activation, called zygotic genome activation (ZGA), is mediated by maternally stored factors, and maternal mRNA clearance by conserved zygotic microRNAs (miRNAs) occurs; however, the important transition in avian species was identified by morphologic perspectives only. In this study, we performed transcriptome analysis to examine the molecular transitions of intrauterine development in chickens. On the basis of coexpression analyses on RNA sequencing data, 2 waves of ZGA-mediated MZT were observed across the early embryonic stages and were associated with transcriptional and translational dynamics. Furthermore, definite transitions were observed according to the distinct developmental characteristics between cleavage and the area pellucida formation period in the functional analysis. Finally, epigenetic modification and the evolutionarily conserved miRNA expression suggest that certain MZT proceeds from Eyal-Giladi and Kochav stage VIII in early chicken development. We expect our study to provide an evolutionary link among vertebrates from the perspective of MZT regulation.-Hwang, Y. S., Seo, M., Bang, S., Kim, H., Han, J. Y. Transcriptional and translational dynamics during maternal-to-zygotic transition in early chicken development.

An evolutionarily conserved non-synonymous SNP in a leucine-rich repeat domain determines anthracnose resistance in watermelon.

KEY MESSAGE: A non-synonymous SNP of CC-NBS-LRR was firstly mapped to confer resistance to anthracnose in watermelon. Newly proposed LRR domain harboring the SNP is evolutionary conserved in the Cucurbitaceae and Fabaceae. Anthracnose disease caused by Colletotrichum devastates many plants. Despite the importance of the disease, the mechanisms of resistance against it are poorly understood. Here, we identified a non-synonymous single-nucleotide polymorphism (SNP) located in a leucine-rich repeat domain as a marker for resistance to anthracnose race 1 in watermelon, using a combination of genetic analyses. We validated this SNP in segregating populations and 59 watermelon accessions using high-resolution melting assays and Sanger sequencing. We demonstrated that the resulting arginine-to-lysine substitution is particularly conserved among the Cucurbitaceae and Fabaceae. We identified a conserved motif, IxxLPxSxxxLYNLQTLxL, found in 1007 orthologues/paralogues from 89 plant species, and discovered that residue 18 of this motif could determine resistance to disease caused by external invaders. This study provides a step forward in understanding anthracnose resistance in watermelon, as well as functional and evolutionary insight into leucine-rich repeat proteins.

Relationship between serum alkaline phosphatase level, C-reactive protein and leukocyte counts in adults aged 60 years or older.

Serum alkaline phosphatase (ALP), a useful marker of hepatobiliary or bone disorders, has been known to be associated with cardiovascular disease (CVD), which is increasingly being viewed as an inflammatory disease. C-reactive protein level and leukocyte count have also been highlighted as independent risk markers of CVD. Thus, the mechanism underlying the link between elevated ALP and CVD could be subclinical low-grade inflammation. This study aimed to examine associations of serum ALP level with inflammatory markers. This cross-sectional study included 2403 participants (1324 men and 1079 women) aged ≥60 years who participated in a health examination program. Serum ALP quartiles were categorized as follows: Q1: ≤51, Q2: 52-61, Q3: 62-74 and Q4: ≥75 U/L. The odds ratios (ORs) and 95% confidence intervals (CIs) for high CRP and leukocyte count (≥75th percentiles) were calculated after adjusting for confounding variables across serum ALP quartiles using multiple logistic regression analysis. Median CRP level and mean leukocyte count increased in accordance with serum ALP quartiles. Compared to the lowest quartile, the ORs (95% CI) of the highest quartile for high CRP and leukocyte count were 2.03 (1.50-2.76) and 1.54 (1.13-2.10) after adjusting for age, sex, body mass index, smoking status, alcohol intake, fasting plasma glucose, log-transformed triglyceride and HDL-cholesterol levels. Serum ALP level was positively and independently associated with inflammatory markers in adults aged 60 years or older.

HGTree: database of horizontally transferred genes determined by tree reconciliation.

The HGTree database provides putative genome-wide horizontal gene transfer (HGT) information for 2472 completely sequenced prokaryotic genomes. This task is accomplished by reconstructing approximate maximum likelihood phylogenetic trees for each orthologous gene and corresponding 16S rRNA reference species sets and then reconciling the two trees under parsimony framework. The tree reconciliation method is generally considered to be a reliable way to detect HGT events but its practical use has remained limited because the method is computationally intensive and conceptually challenging. In this regard, HGTree (http://hgtree.snu.ac.kr) represents a useful addition to the biological community and enables quick and easy retrieval of information for HGT-acquired genes to better understand microbial taxonomy and evolution. The database is freely available and can be easily scaled and updated to keep pace with the rapid rise in genomic information.

Adaptive Noise Reduction Algorithm to Improve R Peak Detection in ECG Measured by Capacitive ECG Sensors.

Electrocardiograms (ECGs) can be conveniently obtained using capacitive ECG sensors. However, motion noise in measured ECGs can degrade R peak detection. To reduce noise, properties of reference signal and ECG measured by the sensors are analyzed and a new method of active noise cancellation (ANC) is proposed in this study. In the proposed algorithm, the original ECG signal at QRS interval is regarded as impulsive noise because the adaptive filter updates its weight as if impulsive noise is added. As the proposed algorithm does not affect impulsive noise, the original signal is not reduced during ANC. Therefore, the proposed algorithm can conserve the power of the original signal within the QRS interval and reduce only the power of noise at other intervals. The proposed algorithm was verified through comparisons with recent research using data from both indoor and outdoor experiments. The proposed algorithm will benefit a noise reduction of noisy biomedical signal measured from sensors.

The relationship between pulmonary function and suicidal ideation in Korean adults: a nationwide survey.

Controversy surrounds the association between lung function and mental health in the general population, and previous reported results were confounded by the effect of other chronic illnesses. This study aimed to investigate whether reduced lung function was related to mental health issues, taking into consideration the relevant potential confounders. We used data from the 2008-2013 Korean National Health and Nutrition Examination Survey to examine the relationship between lung function and three mental issues (recognized stress, depressive mood, and suicidal ideation) among 22,068 Korean adults. A multiple logistic regression with adjustment for potential covariates including chronic illnesses revealed that a .5-L decrement of forced vital capacity increased the risk for suicidal ideation in both genders, but there was no significant association with recognized stress or depressive mood. We found an inverse relationship between lung function and suicidal ideation in the Korean general population.

Grating-coupled surface plasmon resonance on bulk stainless steel.

Grating-coupled surface plasmon resonance (SPR) is demonstrated with one-dimensional gratings fabricated on the surface of bulk stainless steel using imprinting combined with electrochemical etching. The extent of light coupling and the wavelengths of SPR peaks were characterized with respect to the incident angle and polarization states of the light. When the plane of incidence was orthogonal to the grating grooves, only TM polarization was absorbed at two different wavelengths. In the plane of incidence parallel to the grooves, a single resonance peak was observed only when the incident light was TE-polarized. The dependence of SPR wavelengths on the incident angle was in good agreement with theoretical consideration.

Comprehensive identification of sexually dimorphic genes in diverse cattle tissues using RNA-seq.

BACKGROUND: Molecular mechanisms associated with sexual dimorphism in cattle have not been well elucidated. Furthermore, as recent studies have implied that gene expression patterns are highly tissue specific, it is essential to investigate gene expression in a variety of tissues using RNA-seq. Here, we employed and compared two statistical methods, a simple two group test and Analysis of deviance (ANODEV), in order to investigate bovine sexually dimorphic genes in 40 RNA-seq samples distributed across two factors: sex and tissue. RESULTS: As a result, we detected 752 sexually dimorphic genes across tissues from two statistical approaches and identified strong tissue-specific patterns of gene expression. Additionally, significantly detected sex-related genes shared between two mammal species (cattle and rat) were identified using qRT-PCR. CONCLUSIONS: Results of our analyses reveal that sexual dimorphism of metabolic tissues and pituitary gland in cattle involves various biological processes. Several differentially expressed genes between sexes in cattle and rat species are shared, but show tissue-specific patterns. Finally, we concluded that two distinct statistical approaches have their advantages and disadvantages in RNA-seq studies investigating multiple tissues.

Status of dosage compensation of X chromosome in bovine genome.

Dosage compensation system with X chromosome upregulation and inactivation have evolved to overcome the genetic imbalance between sex chromosomes in both male and female of mammals. Although recent development of chromosome-wide technologies has allowed us to test X upregulation, discrete data processing and analysis methods draw disparate conclusions. A series of expression studies revealed status of dosage compensation in some species belonging to monotremes, marsupials, rodents and primates. However, X upregulation in the Artiodactyla order including cattle have not been studied yet. In this study, we surveyed the genome-wide transcriptional upregulation in X chromosome in cattle RNA-seq data using different gene filtration methods. Overall examination of RNA-seq data revealed that X chromosome in the pituitary gland expressed more genes than in other peripheral tissues, which was consistent with the previous results observed in human and mouse. When analyzed with globally expressed genes, a median X:A expression ratio was 0.94. The ratio of 1-to-1 ortholog genes between chicken and mammals, however, showed considerable reduction to 0.68. These results indicate that status of dosage compensation for cattle is not deviated from those found in rodents and primate, and this is consistent with the evolutionary history of cattle.

Characterizing Milk Production Related Genes in Holstein Using RNA-seq.

Although the chemical, physical, and nutritional properties of bovine milk have been extensively studied, only a few studies have attempted to characterize milk-synthesizing genes using RNA-seq data. RNA-seq data was collected from 21 Holstein samples, along with group information about milk production ability; milk yield; and protein, fat, and solid contents. Meta-analysis was employed in order to generally characterize genes related to milk production. In addition, we attempted to investigate the relationship between milk related traits, parity, and lactation period. We observed that milk fat is highly correlated with lactation period; this result indicates that this effect should be considered in the model in order to accurately detect milk production related genes. By employing our developed model, 271 genes were significantly (false discovery rate [FDR] adjusted p-value<0.1) detected as milk production related differentially expressed genes. Of these genes, five (albumin, nitric oxide synthase 3, RNA-binding region (RNP1, RRM) containing 3, secreted and transmembrane 1, and serine palmitoyltransferase, small subunit B) were technically validated using quantitative real-time polymerase chain reaction (qRT-PCR) in order to check the accuracy of RNA-seq analysis. Finally, 83 gene ontology biological processes including several blood vessel and mammary gland development related terms, were significantly detected using DAVID gene-set enrichment analysis. From these results, we observed that detected milk production related genes are highly enriched in the circulation system process and mammary gland related biological functions. In addition, we observed that detected genes including caveolin 1, mammary serum amyloid A3.2, lingual antimicrobial peptide, cathelicidin 4 (CATHL4), cathelicidin 6 (CATHL6) have been reported in other species as milk production related gene. For this reason, we concluded that our detected 271 genes would be strong candidates for determining milk production.

Nanofibrillar Stimulus-Responsive Cholesteric Microgels with Catalytic Properties.

We report composite stimulus-responsive cholesteric catalytically active microgels derived from filamentous supramolecular building blocks: cellulose nanocrystals (CNCs). The variation in the microgel dimensions and pitch in response to the change in ambient conditions was governed by the polymer component. The cholesteric morphology of the microgels resulted from the self-organization of CNCs in spherical confinement. The microgels exhibited excellent structural integrity and functioned as microreactors in catalytic hydrolysis reactions and in the synthesis of metal nanoparticles. Because of these collective properties, the reported microgels show much promise for application in the design of functional responsive materials.