ABSTRACT
The circadian clock is a timekeeping, homeostatic system that temporally coordinates all major cellular processes. The function of the circadian clock is compensated in the face of variable environmental conditions ranging from normal to stress-inducing conditions. Salinity is a critical environmental factor affecting plant growth, and plants have evolved the SALT OVERLY SENSITIVE (SOS) pathway to acquire halotolerance. However, the regulatory systems for clock compensation under salinity are unclear. Here, we show that the plasma membrane Na+/H+ antiporter SOS1 specifically functions as a salt-specific circadian clock regulator via GIGANTEA (GI) in Arabidopsis thaliana. SOS1 directly interacts with GI in a salt-dependent manner and stabilizes this protein to sustain a proper clock period under salinity conditions. SOS1 function in circadian clock regulation requires the salt-mediated secondary messengers cytosolic free calcium and reactive oxygen species, pointing to a distinct regulatory role for SOS1 in addition to its function as a transporter to maintain Na+ homeostasis. Our results demonstrate that SOS1 maintains homeostasis of the salt response under high or daily fluctuating salt levels. These findings highlight the genetic capacity of the circadian clock to maintain timekeeping activity over a broad range of salinity levels.
Subject(s)
Arabidopsis Proteins , Arabidopsis , Circadian Rhythm , Salt Stress , Sodium-Hydrogen Exchangers , Arabidopsis/genetics , Arabidopsis/physiology , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Protein Stability , Sodium-Hydrogen Exchangers/genetics , Sodium-Hydrogen Exchangers/metabolismABSTRACT
Perfluorooctanoic acid (PFOA), commonly found in drinking water, leads to widespread exposure through skin contact, inhalation, and ingestion, resulting in detectable levels of PFOA in the bloodstream. In this study, we found that exposure to PFOA disrupts cardiac function in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). We observed reductions in field and action potentials in hiPSC-CMs exposed to PFOA. Furthermore, PFOA demonstrated a dose-dependent inhibitory effect on various ion channels, including the calcium, sodium, and potassium channels. Additionally, we noted dose-dependent inhibition of the expression of these ion channels in hiPSC-CMs following exposure to PFOA. These findings suggest that PFOA exposure can impair cardiac ion channel function and decrease the transcription of genes associated with these channels, potentially contributing to cardiac dysfunction such as arrhythmias. Our study sheds light on the electrophysiological and epigenetic consequences of PFOA-induced cardiac dysfunction, underscoring the importance of further research on the cardiovascular effects of perfluorinated compounds (PFCs).
Subject(s)
Caprylates , Fluorocarbons , Heart Diseases , Induced Pluripotent Stem Cells , Humans , Induced Pluripotent Stem Cells/metabolism , Myocytes, Cardiac , Ion ChannelsABSTRACT
This study focuses on analysing the heights of 10,953 Korean men aged 20 to 40 years who were measured during the Joseon dynasty, the Japanese colonialisation period, and the contemporary period, the latter including both North and South Korea. This study thus provides rare long-term statistical evidence on how biological living standards have developed over several centuries, encompassing Confucianism, colonialism, capitalism, and communism. Using error bar analysis of heights for each historical sample period, this study confirms that heights rose as economic performance improved. For instance, economically poorer North Koreans were expectedly shorter, by about 6 cm, than their peers living in the developed South. Similarly, premodern inhabitants of present-day South Korea, who produced a gross domestic product (GDP) per capita below the world average, were about 4 cm shorter than contemporary South Koreans, who have a mean income above the world average. Along similar lines, North Koreans, who have a GDP per capita akin to that of the premodern Joseon dynasty, have not improved much in height. On the contrary, mean heights of North Koreans were even slightly below (by about 2.4 cm) heights of Joseon dynasty Koreans. All in all, the heights follow a U-shaped pattern across time, wherein heights were lowest during the colonial era. Heights bounced back to Joseon dynasty levels during the interwar period, a time period where South Korea benefitted from international aid, only to rise again and surpass even premodern levels under South Korea's flourishing market economy.
Subject(s)
Capitalism , Colonialism , Male , Humans , Colonialism/history , Communism , Confucianism , Republic of Korea , Socioeconomic FactorsABSTRACT
BACKGROUND: High-throughput Proteomics has been accelerated by (tandem) mass spectrometry. However, the slow speed of mass spectra analysis prevents the analysis results from being up-to-date. Tandem mass spectrometry database search requires O(|S||D|) time where S is the set of spectra and D is the set of peptides in a database. With usual values of |S| and |D|, database search is quite time consuming. Meanwhile, the database for search is usually updated every month, with 0.5-2% changes. Although the change in the database is usually very small, it may cause extensive changes in the overall analysis results because individual PSM scores such as deltaCn and E-value depend on the entire search results. Therefore, to keep the search results up-to-date, one needs to perform database search from scratch every time the database is updated, which is very inefficient. RESULTS: Thus, we present a very efficient method to keep the search results up-to-date where the results are the same as those achieved by the normal search from scratch. This method, called progressive search, runs in O(|S||ΔD|) time on average where ΔD is the difference between the old and the new databases. The experimental results show that the progressive search is up to 53.9 times faster for PSM update only and up to 16.5 times faster for both PSM and E-value update. CONCLUSIONS: Progressive search is a novel approach to efficiently obtain analysis results for updated database in tandem mass spectrometry. Compared to performing a normal search from scratch, progressive search achieves the same results much faster. Progressive search is freely available at: https://isa.hanyang.ac.kr/ProgSearch.html .
Subject(s)
Algorithms , Tandem Mass Spectrometry , Tandem Mass Spectrometry/methods , Databases, Protein , Peptides/chemistry , Proteomics/methodsABSTRACT
Density multiplication in nanopatterning is one of the most efficient techniques for increasing the resolution of the inherent patterns. Thus far, most of the density multiplication techniques integrate bottom-up (or top-down) patterning onto guide patterns prepared by the top-down approach. Although the bottom-up approach exhibits several advantages of cost-effectiveness and high resolution, very few studies have reported bottom-up patterning within a bottom-up template. In this study, the density multiplication of supramolecular cylinders into a block copolymer (BCP)-based guide lamellar pattern is demonstrated by the directed self-assembly (DSA) of a dendrimer and BCPs for the first time. Supramolecular cylinders of sub-5 nm scale are confined into trenches based on 50 and 100 nm scales of a lamellar polystyrene (PS)-poly(methyl methacrylate) (PMMA) BCP, which led to 10×-level to 20×-level density multiplication. Moreover, the orientation of the dendrimer is dependent on the dendrimer film thickness, and the corresponding mechanism is revealed. Notably, the strong guiding effect from the high-resolution guide patterns improved the ordering behavior in the highly curved pattern. Graphoepitaxy via the confinement of an ultrahigh-resolution dendrimer into the guide pattern based on BCP demonstrates promise as a density multiplication method for generating highly ordered nanostructures and complex structures.
ABSTRACT
BACKGROUND: False discovery rate (FDR) estimation is very important in proteomics. The target-decoy strategy (TDS), which is often used for FDR estimation, estimates the FDR under the assumption that when spectra are identified incorrectly, the probabilities of the spectra matching the target or decoy peptides are identical. However, no spectra matching target or decoy peptide probabilities are identical. We propose cTDS (target-decoy strategy with candidate peptides) for accurate estimation of the FDR using the probability that the spectrum is identified incorrectly as a target or decoy peptide. RESULTS: Most spectrum cases result in a probability of having the spectrum identified incorrectly as a target or decoy peptide of close to 0.5, but only about 1.14-4.85% of the total spectra have an exact probability of 0.5. We used an entrapment sequence method to demonstrate the accuracy of cTDS. For fixed FDR thresholds (1-10%), the false match rate (FMR) in cTDS is closer than the FMR in TDS. We compared the number of peptide-spectrum matches (PSMs) obtained with TDS and cTDS at a 1% FDR threshold with the HEK293 dataset. In the first and third replications, the number of PSMs obtained with cTDS for the reverse, pseudo-reverse, shuffle, and de Bruijn databases exceeded those obtained with TDS (about 0.001-0.132%), with the pseudo-shuffle database containing less compared to TDS (about 0.05-0.126%). In the second replication, the number of PSMs obtained with cTDS for all databases exceeds that obtained with TDS (about 0.013-0.274%). CONCLUSIONS: When spectra are actually identified incorrectly, most probabilities of the spectra matching a target or decoy peptide are not identical. Therefore, we propose cTDS, which estimates the FDR more accurately using the probability of the spectrum being identified incorrectly as a target or decoy peptide.
Subject(s)
Algorithms , Tandem Mass Spectrometry , Humans , Databases, Protein , HEK293 Cells , Peptides , Tandem Mass Spectrometry/methodsABSTRACT
Exponential development in artificial intelligence or deep learning technology has resulted in more trials to systematically determine the pathological diagnoses using whole slide images (WSIs) in clinical and nonclinical studies. In this study, we applied Mask Regions with Convolution Neural Network (Mask R-CNN), a deep learning model that uses instance segmentation, to detect hepatic fibrosis induced by N-nitrosodimethylamine (NDMA) in Sprague-Dawley rats. From 51 WSIs, we collected 2011 cropped images with hepatic fibrosis annotations. Training and detection of hepatic fibrosis via artificial intelligence methods was performed using Tensorflow 2.1.0, powered by an NVIDIA 2080 Ti GPU. From the test process using tile images, 95% of model accuracy was verified. In addition, we validated the model to determine whether the predictions by the trained model can reflect the scoring system by the pathologists at the WSI level. The validation was conducted by comparing the model predictions in 18 WSIs at 20× and 10× magnifications with ground truth annotations and board-certified pathologists. Predictions at 20× showed a high correlation with ground truth (R2 = 0.9660) and a good correlation with the average fibrosis rank by pathologists (R2 = 0.8887). Therefore, the Mask R-CNN algorithm is a useful tool for detecting and quantifying pathological findings in nonclinical studies.
Subject(s)
Deep Learning , Algorithms , Animals , Artificial Intelligence , Liver Cirrhosis/chemically induced , Liver Cirrhosis/diagnostic imaging , Rats , Rats, Sprague-DawleyABSTRACT
A practical scale photocatalytic air purifier equipped with a TiO2/H-ZSM-5 composite bead filter was demonstrated to be able to effectively remove indoor volatile organic compounds (VOCs) and viruses with sustainable performances under UVA-LED illumination. TiO2 hybridized with 5 wt% H-ZSM-5 zeolite significantly enhanced its photocatalytic activity for degrading VOCs including formaldehyde, acetaldehyde, and toluene, than bare TiO2. H-ZSM-5 provided strong adsorption sites for these compounds, thus accelerating their photocatalytic conversion into CO2 by adjacent TiO2 photocatalyst. Moreover, owing to its superior adsorption capacity, the composite bead filter completely prevented the emission of formaldehyde produced by photocatalytic oxidation of toluene. The sustainability of this composite bead filter for VOC removal was confirmed by regeneration and accelerated durability tests. In addition, the photocatalytic air purifier was effective in removing aerosolized viral particles of bacteriophage Phi-X 174. It was confirmed that the viruses on filter surfaces were completely inactivated by photocatalytic oxidation. TiO2/H-ZSM-5 composite beads also exhibited excellent efficacies for inactivation of pathogenic coronaviruses including SARS-CoV-2. The photocatalytic process degraded viral RNAs of SARS-CoV-2 by more than 99.999% in 1 h, eliminating the viral infectivity. Results of this study suggest that the air purifier equipped with the composite bead filter is ready for practical applications for home and hospital uses.
Subject(s)
Air Filters , COVID-19 , Volatile Organic Compounds , Zeolites , Catalysis , Humans , SARS-CoV-2 , Titanium , Virus InactivationABSTRACT
Whether emergent groups positively or negatively influence a disaster response remains inconclusive in the literature. We analyzed the effect of an emergent group on two interorganizational networks for information communication and resource coordination during a public health emergency response. Using the 2015 Middle East Respiratory Syndrome (MERS) Coronavirus in Korea as a study case, we identified an ad hoc entity that appeared in both networks. This emergent group, which consists of government officials and public health specialists, directed and coordinated organizations at the center of the response networks. We found that the emergent group positively contributed to efficient information communication but had no effect on the resource network's efficiency. Our interpretation is that the ad hoc entity was filling relational gaps in the information network, but was redundant in the resource network.
Subject(s)
Coronavirus Infections/prevention & control , Disease Outbreaks/prevention & control , Emergencies/epidemiology , Middle East Respiratory Syndrome Coronavirus , Public Health , Coronavirus Infections/epidemiology , Humans , Republic of Korea/epidemiologyABSTRACT
Arbuscular mycorrhizal (AM) symbiosis is a mutually beneficial association of plants and fungi of the subphylum Glomeromycotina. Endosymbiotic AM fungi colonize the inner cortical cells of the roots, where they form branched hyphae called arbuscules that function in nutrient exchange with the plant. To support arbuscule development and subsequent bidirectional nutrient exchange, the root cortical cells undergo substantial transcriptional reprogramming. REDUCED ARBUSCULAR MYCORRHIZA1 (RAM1), previously studied in several dicot plant species, is a major regulator of this cortical cell transcriptional program. Here, we generated ram1 mutants and RAM1 overexpressors in a monocot, Brachypodium distachyon. The AM phenotypes of two ram1 lines revealed that RAM1 is only partly required to enable arbuscule development in B. distachyon Transgenic lines constitutively overexpressing BdRAM1 showed constitutive expression of AM-inducible genes even in the shoots. Following inoculation with AM fungi, BdRAM1-overexpressing plants showed higher arbuscule densities relative to controls, indicating the potential to manipulate the relative proportion of symbiotic interfaces via modulation of RAM1 However, the overexpressors also show altered expression of hormone biosynthesis genes and aberrant growth patterns, including stunted bushy shoots and poor seed set. While these phenotypes possibly provide additional clues about the scope of influence of BdRAM1, they also indicate that directed approaches to increase the density of symbiotic interfaces will require a more focused, potentially cell type specific manipulation of transcription factor gene expression.
Subject(s)
Brachypodium/genetics , Brachypodium/microbiology , Glomeromycota/growth & development , Glomeromycota/genetics , Mycorrhizae/genetics , Plant Roots/genetics , Symbiosis/genetics , Gene Expression Regulation, Fungal , Gene Expression Regulation, Plant , Genes, Fungal , Mycorrhizae/growth & development , Phenotype , Plant Roots/growth & development , Plants, Genetically Modified , Symbiosis/physiology , Transcription FactorsABSTRACT
In plant-microbe interactions, plant sugars produced by photosynthesis are not only a carbon source for pathogens, but may also act as signals that modulate plant defense responses. Here, we report that decreasing sorbitol synthesis in apple (Malus domestica) leaves by antisense suppression of ALDOSE-6-PHOSPHATE REDUCTASE (A6PR) leads to downregulation of 56 NUCLEOTIDE BINDING/LEUCINE-RICH REPEAT (NLR) genes and converts the phenotypic response to Alternaria alternata from resistant to susceptible. We identified a resistance protein encoded by the apple MdNLR16 gene and a small protein encoded by the fungal HRIP1 gene that interact in both a yeast two-hybrid assay and a bimolecular fluorescence complementation assay. Deletion of HRIP1 in A. alternata enables gain of virulence on the wild-type control plant. Overexpression of MdNLR16 in two antisense A6PR lines increases resistance, whereas RNAi suppression of MdNLR16 in the wild-type control decreases resistance against A. alternata MdWRKY79 transcriptionally regulates MdNLR16 by binding to the promoter of MdNLR16 in response to sorbitol, and exogenous sorbitol feeding partially restores resistance of the antisense A6PR lines to A. alternata These findings indicate that sorbitol modulates resistance to A. alternata via the MdNLR16 protein that interacts with the fungal effector in a classic gene-for-gene manner in apple.
Subject(s)
Alternaria/pathogenicity , Malus/metabolism , Malus/microbiology , Plant Diseases/microbiology , Plant Proteins/metabolism , Sorbitol/pharmacology , Disease Resistance/genetics , Gene Expression Regulation, Plant/drug effects , Gene Expression Regulation, Plant/genetics , Malus/genetics , Plant Proteins/geneticsABSTRACT
BACKGROUND: The target-decoy strategy effectively estimates the false-discovery rate (FDR) by creating a decoy database with a size identical to that of the target database. Decoy databases are created by various methods, such as, the reverse, pseudo-reverse, shuffle, pseudo-shuffle, and the de Bruijn methods. FDR is sometimes over- or under-estimated depending on which decoy database is used because the ratios of redundant peptides in the target databases are different, that is, the numbers of unique (non-redundancy) peptides in the target and decoy databases differ. RESULTS: We used two protein databases (the UniProt Saccharomyces cerevisiae protein database and the UniProt human protein database) to compare the FDRs of various decoy databases. When the ratio of redundant peptides in the target database is low, the FDR is not overestimated by any decoy construction method. However, if the ratio of redundant peptides in the target database is high, the FDR is overestimated when the (pseudo) shuffle decoy database is used. Additionally, human and S. cerevisiae six frame translation databases, which are large databases, also showed outcomes similar to that from the UniProt human protein database. CONCLUSION: The FDR must be estimated using the correction factor proposed by Elias and Gygi or that by Kim et al. when (pseudo) shuffle decoy databases are used.
ABSTRACT
Large quantities of microplastics are thought to be emitted to freshwater environments via wastewater treatment plants (WWTPs). To evaluate the occurrence of microplastics in Korean WWTPs, a nationwide study was conducted for the first time in 50 representative WWTPs with large treatment capacities. Grab sampling and laboratory filtration were used for influents, whereas in situ filtration using a custom-made sampling device was used for effluents. The filtrates were pretreated using wet peroxidation and density separation prior to the identification of microplastics with a dissection microscope and Fourier-transform infrared spectroscopy. Pooled analyses of the microplastics revealed that they were predominantly fragment-shaped, and thermoplastics and synthetic fibers were the dominant microplastic materials in WWTPs. The concentration ranged from 10 to 470 L-1 in influents and 0.004 to 0.51 L-1 in effluents. The removal efficiency of microplastics during wastewater treatment was calculated to be 98.7-99.99% in 31 WWTPs. Additionally, WWTPs using advanced phosphorus removal processes exhibited higher removal efficiency than those not implementing such processes. Power-law distribution was successful in describing microplastic particle sizes down to 100 µm, although it was not applicable for smaller particles. This comprehensive monitoring study provides information on the current level and characteristics of microplastics in WWTPs in Korea.
Subject(s)
Wastewater , Water Pollutants, Chemical , Environmental Monitoring , Microplastics , Plastics , Republic of Korea , Surveys and Questionnaires , Waste Disposal, FluidABSTRACT
A skin irritation test using in vitro reconstructed human epidermis (RhE) models was established for hazard identification of irritant chemicals in accordance with UN Globally Harmonized System of Classification and Labelling of Chemicals (GHS) category. In this study, EpiDerm™ was used to assess skin irritation by oxybenzone and N,N-diethyl-m-toluamide (DEET), which are widely used sunscreen and insect repellent components, respectively. EpiDerm™ was applied with oxybenzone and DEET, combined and sequentially with each single dose. Epidermal morphology and differentiation/proliferation were examined microscopically. Oxybenzone and sequential administration groups were determined as nonirritant with cell viability >50% and the morphology was comparable to the human epidermis. Contrastingly, the DEET and coadministration groups exhibited cell viability <50% and poor epidermal morphology. Interleukin (IL)-1α release from substance-treated EpiDerm™ increased inversely to cell viability, suggesting the pro-inflammatory reaction was initiated by DEET. CK-10, E-cadherin, Ki-67, laminin, and ceramide were identified as relevant markers to assess oxybenzone- or DEET-induced epidermal injury. In conclusion, these results may indicate to be aware of the possible skin irritation by indiscriminate use of oxybenzone and DEET without animal testing.
Subject(s)
Benzophenones/toxicity , DEET/toxicity , Epidermis/drug effects , Insect Repellents/toxicity , Irritants/toxicity , Skin Irritancy Tests , Sunscreening Agents/toxicity , Cell Survival , Dermatitis, Irritant/etiology , Epidermis/pathology , HumansABSTRACT
BACKGROUND: One of the most important steps in peptide identification is to estimate the false discovery rate (FDR). The most commonly used method for estimating FDR is the target-decoy search strategy (TDS). While this method is simple and effective, it is time/space-inefficient because it searches a database that is twice as large as the original protein database. This inefficiency problem becomes more evident as protein databases get bigger and bigger. We propose a target-small decoy search strategy and present a rigorous verification that it reduces the database size and search time while retaining the accuracy of target-decoy search strategy (TDS). RESULTS: We show that peptide spectrum matches (PSMs) obtained at 1% FDR in TDS overlap ~ 99% with those in our method. (Considering that 1% FDR is used, 99% overlap means our method is very accurate.) Moreover, our method is more time/space-efficient than TDS. The search time of our method is reduced to only 1/4 of that of TDS when UniProt and its 1/8 decoy database are used. CONCLUSIONS: We demonstrate that our method is almost as accurate as TDS and more time/space-efficient than TDS. Since the efficiency of our method is more evident as the database size increases, our method is expected to be useful for identifying peptides in proteogenomics databases constructed from inflated databases using genomic data.
Subject(s)
Computational Biology/methods , Peptides/chemistry , Algorithms , Cell Line , Databases, Protein , HumansABSTRACT
BACKGROUND: Mycobacteria tuberculosis (Mtb), the causative agent of tuberculosis, is a slow-growing bacterium. Expression in Escherichia coli is a widely used method for large-scale production of diagnostic antigenic recombinant proteins. Expression of Mtb antigen in E. coli offers a rapid and, inexpensive alternative to conventional protein synthesis from Mtb. The addition of stabilizing additives during cell lysis or storage of Mtb antigenic protein plays a vital role in enhancing antigen stability. In this study, we evaluated the effects of additives on the stability of Mtb antigens expressed in E. coli. METHODS: Immunodominant Mtb antigens, i.e., CFP-10, Rv3872, TB7.7, and TB9.7, were cloned, and recombinant proteins overexpressed in E. coli were gradually degraded in a time-dependent manner by incubation at 37⯰C. Various stabilizing additives during storage or cell lysis before protein purification were investigated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot analysis. RESULTS: CFP-10 and Rv3872 were mainly expressed in soluble form. The degraded form of the expressed protein after incubation at 37⯰C was easily observed after 1 week. Increased stability was observed in a solution containing glycine for recombinant CFP-10 and Rv3872. TB9.7 was stable in a solution containing trehalose or mannitol. TB7.7 was stable in a solution containing sucrose, glycine, or polyethylene glycol. CONCLUSION: Recombinant Mtb antigen stabilization using chemical additives inhibited protein degradation, leading to increased antigen stability and purification efficiency.
Subject(s)
Antigens, Bacterial/genetics , Escherichia coli/genetics , Mycobacterium tuberculosis/genetics , Antigens, Bacterial/chemistry , Cloning, Molecular/methods , Excipients/chemistry , Gene Expression , Humans , Mycobacterium tuberculosis/chemistry , Protein Stability , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Solubility , Tuberculosis/microbiologyABSTRACT
BACKGROUND: Incidence of whooping cough is increasing in Korea. Since 2011, occurrence among adolescents and adults has risen putting vulnerable neonates at risk. National immunization guidelines now include Tdap (tetanus toxoid, reduced diphtheria toxoid, and acellular pertussis) vaccination during pregnancy and as a cocooning strategy (i.e., vaccinating adults and adolescents in contact with neonates). This study assessed post-marketing Tdap (Boostrix®, GSK, Belgium) vaccine safety in subjects ≥ 10 years. METHODS: This open, non-comparative multi-center study was conducted over six years at 10 hospitals in Korea. Subjects received Tdap in normal clinical practice according to local prescribing information. All adverse events (AEs) were recorded, classified as expected or unexpected, and severity and relationship to Tdap were assessed. RESULTS: The analysis included 672 Korean subjects (mean age, 44 years; range, 11-81), 451 were women and 211 were pregnant. Ninety subjects experienced 124 AEs (incidence 13.39%) of which six were serious AEs (SAEs) assessed as not related to vaccination, and 51 were non-SAEs related to vaccination (mostly administration site reactions). Overall 65/124 AEs were unexpected; the most common were 14 constipation, 5 dyspepsia, 4 common cold and 4 premature labor cases. One case of common cold was assessed as possibly related to vaccination. Pregnancy outcome was 'live infant, no apparent congenital anomaly' in 195 subjects (92.42%) or 'lost to follow-up' in 16 subjects. CONCLUSION: Tdap administration to Korean subjects ≥ 10 years, including pregnant women, for the prevention of diphtheria, tetanus and pertussis was shown to have a well-tolerated safety profile. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT01929291.
Subject(s)
Diphtheria-Tetanus-acellular Pertussis Vaccines/adverse effects , Product Surveillance, Postmarketing , Adolescent , Adult , Aged , Child , Diphtheria-Tetanus-acellular Pertussis Vaccines/immunology , Female , Gastrointestinal Diseases/etiology , Humans , Male , Middle Aged , Obstetric Labor, Premature/etiology , Pregnancy , Prospective Studies , Pruritus/etiology , Republic of Korea , Respiratory Tract Diseases/etiology , Tetanus/prevention & control , Whooping Cough/prevention & control , Young AdultABSTRACT
BACKGROUND: Recent advances in sequencing technology have allowed us to investigate personal genomes to find structural variations, which have been studied extensively to identify their association with the physiology of diseases such as cancer. In particular, mobile genetic elements (MGEs) are one of the major constituents of the human genomes, and cause genome instability by insertion, mutation, and rearrangement. RESULT: We have developed a new program, iMGEins, to identify such novel MGEs by using sequencing reads of individual genomes, and to explore the breakpoints with the supporting reads and MGEs detected. iMGEins is the first MGE detection program that integrates three algorithmic components: discordant read-pair mapping, split-read mapping, and insertion sequence assembly. Our evaluation results showed its outstanding performance in detecting novel MGEs from simulated genomes, as well as real personal genomes. In detail, the average recall and precision rates of iMGEins are 96.67 and 100%, respectively, which are the highest among the programs compared. In the testing with real human genomes of the NA12878 sample, iMGEins shows the highest accuracy in detecting MGEs within 20 bp proximity of the breakpoints annotated. CONCLUSION: In order to study the dynamics of MGEs in individual genomes, iMGEins was developed to accurately detect breakpoints and report inserted MGEs. Compared with other programs, iMGEins has valuable features of identifying novel MGEs and assembling the MGEs inserted.
Subject(s)
Genome, Human , High-Throughput Nucleotide Sequencing/methods , Interspersed Repetitive Sequences , Sequence Analysis, DNA/methods , Software , Algorithms , HumansABSTRACT
TiO2 nanotubes (TNT) have a highly ordered open structure that promotes the diffusion of dioxygen and substrates onto active sites and exhibit high durability against deactivation during the photocatalytic air purification. Herein, we synthesized {001} facet-exposed TiO2 nanotubes (001-TNT) using a new and simple method that can be easily scaled up, and tested them for the photocatalytic removal of volatile organic compounds (VOCs) in both a laboratory reactor and a commercial air cleaner. While the surface of TNT is mainly composed of {101} facet anatase, 001-TNT's outer surface was preferentially aligned with {001} facet anatase. The photocatalytic degradation activity of toluene on 001-TNT was at least twice as high as that of TNT. While the TNT experienced a gradual deactivation during successive cycles of photocatalytic degradation of toluene, the 001-TNT did not exhibit any sign of catalyst deactivation under the same test conditions. Under visible light irradiation, the 001-TNT showed degradation activity for acetaldehyde and formaldehyde, while the TNT did not exhibit any degradation activity for them. The 001-TNT filter was successfully scaled up and installed on a commercial air cleaner. The air cleaner equipped with the 001-TNT filters achieved an average VOCs removal efficiency of 72% (in 30 min of operation) in a 8-m3 test chamber, which satisfied the air cleaner standards protocol (Korea) to be the first photocatalytic air cleaner that passed this protocol.
Subject(s)
Nanotubes , Volatile Organic Compounds , Catalysis , Republic of Korea , Titanium , TolueneABSTRACT
Immunoglobulin G4-related disease (IgG4-RD) is a chronic, immune-mediated-, systemic disease that is characterized by IgG4 plasma cell infiltration with fibrotic changes in various organs. The most affected organs are pancreas and salivary glands. Kidney can be rarely involved, and is usually represented as a renal mass and organomegaly. Usually, elevated levels of serum IgG4 more than 135 mg/dl with organ-specific features and biopsy results showing enriched infiltration of IgG4-positive plasma cells are needed to diagnose the disease. However, we experienced two unusual cases of IgG4-RD involving kidney. IgG4-related kidney disease (IgG4-RKD) was first reported as an extra pancreatic feature of autoimmune pancreatitis(AIP) in 2004. Herein, we describe two cases of such unique presentation of IgG4RKD and a literature review focusing on clinicopathologic features of IgG4RKD. Our cases are distinct in the fact that IgG4RD invades unusual organs such as perinephric capsule or scrotum. We reported the patient who showed extinct perirenal capsule invasion with multi-organ involvement including exocrine glands in comparison to previous IgG4RKD that often involved in renal parenchyma and renal pelvis lesions. And the other patient had scrotal invasion with multifocal renal parenchymes. Referring to the features observed in these two cases, we could propose that as every organ can be related to IgG4RD, we propose clinicians to confirm the disease using imaging, serologic, and pathologic studies. We also reviewed previous reports of IgG4-RKD and summarized diverse imaging findings and pathologic features.