Search

Multi-omics integrates diverse types of biological information from genomic, proteomic, and metabolomics experiments to achieve a comprehensive understanding of complex cellular mechanisms. However, this approach is also challenging due to technical issues such as limited sample quantities, the complexity of data pre-processing, and reproducibility concerns. Furthermore, existing studies have primarily focused on technical performance assessment and the presentation of modified protocols through quantitative comparisons of the identified protein counts. Nevertheless, the specific differences in these comparisons have been minimally investigated. Here, findings obtained from various omics approaches were profiled using various extraction methods (methanol extraction, the Folch method, and Matyash methods for metabolites and lipids) and two digestion methods (filter-aided sample preparation (FASP) and suspension traps (S-Trap)) for resuspended proteins. FASP was found to be more effective for the identification of membrane-related proteins, whereas S-Trap excelled in isolating nuclear-related and RNA-processing proteins. Thus, FASP may be suitable for investigating the immune response and bacterial infection pathways, whereas S-Trap may be more effective for studies focused on the mechanisms of neurodegenerative diseases. Moreover, regarding the choice of extraction method, the single-phase method identified organic compounds and compounds related to fatty acids, whereas the two-phase extraction method identified more hydrophilic compounds such as nucleotides. Lipids with strong hydrophobicity, such as ChE and TG, were identified in the two-phase extraction results. These findings highlight that significant differences among small molecules are primarily identified due to the varying polarities of extraction solvents. These results, obtained by considering variables such as human error and batch effects in the sample preparation step, offer comprehensive and detailed results not previously provided by existing studies, thereby aiding in the selection of the most suitable pre-processing approach.

Abstract The objective of this study was to analyze the temporal and spatial characteristics of fine particulate matters by using huge hourly datasets of PM2.5, including chemical information monitored at the 6 national intensive monitoring sites (NIMSs) from 2013 to 2018 in Korea. Hourly PM2.5 raw datasets were obtained from the National Institute of Environmental Research (NIER) in Korea. Monitoring sites included urban, rural/agricultural, industrial, and marine environments. Since the PM2.5 concentration steadily decreased nationwide, each species concentration also decreased in general. One of key reasons for decreasing PM2.5 might be explained by the implementation of domestic fine dust reduction policies and external influences such as PM2.5 concentration reduction in China. It was observed that 45.0% of all datasets for 6 years were classified as good condition. The average sum of 14 elements over all sites in 2018 was calculated to be 501.5 ng/m3, and its mass ratio for PM2.5 (21.9 μg/m3) was 2.30%. The inorganic elements were generally higher in industrial/urban areas than in agricultural areas. In addition, the average TC (total carbon) over all 6 sites was 28.3% of PM2.5 with the range of 23.6% to 31.4%. The TC in small urban areas was much higher than that in marine areas or even that in large, populated urban area/industrial areas. It seemed that the latter areas were better controlled than the former area in terms of combustion activities of fossil fuels. It is suggested that these results could be play an important role as important basic data to manage ambient air quality and establish effective emission reduction strategies in each region.

Tachykinin (TK) families, including the first neuropeptide substance P, have been intensively explored in bilaterians. Knowledge of signaling of TK receptors (TKRs) has enabled the comprehension of diverse physiological processes. However, TK signaling systems are largely unknown in Lophotrochozoa. This study identified two TK precursors and two TKR isoforms in the Pacific abalone Haliotis discus hannai (Hdh), and characterized Hdh-TK signaling. Hdh-TK peptides harbored protostomian TK-specific FXGXRamide or unique YXGXRamide motifs at the C-termini. A phylogenetic analysis showed that lophotrochozoan TKRs, including Hdh-TKRs, form a monophyletic group distinct from arthropod TKRs and natalisin receptor groups. Although reporter assays demonstrated that all examined Hdh-TK peptides activate intracellular cAMP accumulation and Ca2+ mobilization in Hdh-TKR-expressing mammalian cells, Hdh-TK peptides with N-terminal aromatic residues and C-terminal FXGXRamide motifs were more active than shorter or less aromatic Hdh-TK peptides with a C-terminal YXGXRamide. In addition, we showed that ligand-stimulated Hdh-TKRs mediate ERK1/2 phosphorylation in HEK293 cells and that ERK1/2 phosphorylation is inhibited by PKA and PKC inhibitors. In three-dimensional in silico Hdh-TKR binding modeling, higher docking scores of Hdh-TK peptides were consistent with the lower EC50 values in the reporter assays. The transcripts for Hdh-TK precursors and Hdh-TKR were highly expressed in the neural ganglia, with lower expression levels in peripheral tissues. When abalone were starved for 3 weeks, Hdh-TK1 transcript levels, but not Hdh-TK2, were increased in the cerebral ganglia (CG), intestine, and hepatopancreas, contrasting with the decreased lipid content and transcript levels of sterol regulatory element-binding protein (SREBP). At 24 h post-injection in vivo, the lower dose of Hdh-TK1 mixture increased SREBP transcript levels in the CG and hepatopancreas and accumulative food consumption of abalone. Higher doses of Hdh-TK1 and Hdh-TK2 mixtures decreased the SREBP levels in the CG. When Hdh-TK2-specific siRNA was injected into abalone, intestinal SREBP levels were significantly increased, whereas administration of both Hdh-TK1 and Hdh-TK2 siRNA led to decreased SREBP expression in the CG. Collectively, our results demonstrate the first TK signaling system in gastropod mollusks and suggest a possible role for TK peptides in regulating lipid metabolism in the neural and peripheral tissues of abalone.

Abstract Background Tear deficiency due to lacrimal gland (LG) dysfunction is one of the major causes of dry eye disease (DED). Therefore, LG stem cell-based therapies have been extensively reported to regenerate injured lacrimal tissue; however, the number of stem cells in the LG tissue is low, and 2D long-term cultivation reduces the differentiation capacity of stem cells. Nevertheless, 3D LG organoids could be an alternative for a DED therapy because it is capable of prolonged growth while maintaining the characteristics of the LG tissue. Here, we report the development of LG organoids and their application as cell therapeutics. Methods Digested cells from human LG tissue were mixed with Matrigel and cultured in five different media modified from human prostate/salivary organoid culture media. After organoid formation, the growth, specific marker expression, and histological characteristics were analyzed to authenticate the formation of LG organoids. The secretory function of LG organoids was confirmed through calcium influx or proteomics analysis after pilocarpine treatment. To explore the curability of the developed organoids, mouse-derived LG organoids were fabricated and transplanted into the lacrimal tissue of a mouse model of DED. Results The histological features and specific marker expression of LG organoids were similar to those of normal LG tissue. In the pilocarpine-treated LG organoid, levels of internal Ca2+ ions and β-hexosaminidase, a lysosomal protein in tear fluid, were increased. In addition, the secreted proteins from pilocarpine-treated lacrimal organoids were identified through proteomics. More than 70% of the identified proteins were proven to exosome through gene ontology analysis. These results indicate that our developed organoid was pilocarpine reactive, demonstrating the function of LG. Additionally, we developed LG organoids from patients with Sjogren’s syndrome patients (SS) and confirmed that their histological features were similar to those of SS-derived LG tissue. Finally, we confirmed that the mouse LG organoids were well engrafted in the lacrimal tissue two weeks after transplantation. Conclusion This study demonstrates that the established LG organoids resemble the characteristics of normal LG tissue and may be used as a therapy for patients with DED.

Abstract Background Stem cell transplantation has been proposed as an alternative treatment for intractable optic nerve disorders characterized by irrecoverable loss of cells. Mesenchymal stem cells, with varying tissue regeneration and recovery capabilities, are being considered for potential cell therapies. To overcome the limitations of cell therapy, we isolated exosomes from human placenta-derived mesenchymal stem cells (hPMSCs) and investigated their therapeutic effects in R28 cells (retinal precursor cells) exposed to CoCl2. Method After 9 h of exposure to CoCl2, the hypoxic damaged R28 cells were divided into the non-treatment group (CoCl2 + R28 cells) and treatment group (CoCl2 + R28 cells treated with exosome). Immunoblot analysis was performed for Pcna, Hif-1α, Vegf, Vimentin, Thy-1, Gap43, Ermn, Neuroflament, Wnt3a, β-catenin, phospo-GSK3β, Lef-1, UBA2, Skp1, βTrcp, and ubiquitin. The proteomes of each group were analyzed by liquid chromatography/tandem mass (LC-MS/MS) spectrometry. Differentially expressed proteins (DEPs) were detected by label-free quantification, and the interactions of the proteins were examined through signal transduction pathway and gene ontology analysis. Result We observed that exosome could significantly recover proliferation damaged by CoCl2 treatment. In addition, the treatment group presented the decreased expression of Hif-1α protein (P

Pacific abalone (Haliotis discus hannai) is a commercially important mollusk; therefore, improvement of its growth performance and quality has been emphasized. During embryonic development, abalones undergo a series of distinct larval stages, including swimming veliger larvae, juveniles, and mature individuals, and their biomolecular composition varies depending on the developmental stage. Therefore, in the present study, we performed untargeted lipid profiling of abalone tissues at different developmental stages as well as the hemolymph of mature female and male abalones using ultrahigh-performance liquid chromatography-tandem mass spectrometry. These profiles can provide meaningful information to understand compositional changes in lipids through abalone metamorphosis and development. A total of 132 lipids belonging to 15 classes were identified from abalone tissues at different developmental stages. Moreover, 21 lipids belonging to 8 classes were identified from the hemolymph of mature abalones. All data were processed following strict criteria to provide accurate information. Triglycerides and phosphatidylcholines were the major lipid components identified in both tissues and hemolymph, accounting for, respectively, 27% and 15% of all lipids in tissues and, respectively, 24% and 38% of all lipids in the hemolymph. Of note, lysophosphatidylcholine was only detected in the tissues of mature abalones, paving the way for further analyses of abalone lipids based on developmental stages. The present findings offer novel insights into the lipidome of abalone tissues and hemolymph at different developmental stages, building a foundation for improving the efficiency and quality of abalone aquaculture.

IntroductionCardiovascular disease (CVD) in patients with diabetes is the leading cause of death. Finding early biomarkers for detecting asymptomatic patients with CVD can improve survival. Recently, plasma proteomics—targeted selected reaction monitoring/multiple reaction monitoring analyses (MRM)—has emerged as highly specific and sensitive tools compared with classic ELISA methods. The objective was to identify differentially regulated proteins according to the severity of the coronary artery atherosclerosis.Research design and methodsA discovery cohort, a verification cohort and a validation cohort consisted of 18, 53, and 228 subjects, respectively. The grade of coronary artery stenosis was defined as a percentage of luminal stenosis of the major coronary arteries. Participants were divided into six groups, depending on the presence of diabetes and the grade of coronary artery stenosis. Two mass spectrometric approaches were employed: (1) conventional shotgun liquid chromatography tandem mass spectrometry for a discovery and (2) quantitative MRM for verification and validation. An analysis of the covariance was used to examine the biomarkers’ predictivity beyond conventional cardiovascular risks.ResultsA total of 1349 different proteins were identified from a discovery cohort. We selected 52 proteins based on the tandem mass tag quantitative analysis then summarized as follows: chemokine (C-X-C motif) ligand 7 (CXCL7), apolipoprotein C-II (APOC2), human lipopolysaccharide-binding protein (LBP) and dedicator of cytokinesis 2 (DOCK2) in diabetes; CXCL7, APOC2, LBP, complement 4A (C4A), vitamin D-binding protein (VTDB) and laminin β1 subunit in non-diabetes. Analysis of covariance showed that APOC2, DOCK2, CXCL7 and VTDB were upregulated and C4A was downregulated in patients with diabetes showing severe coronary artery stenosis. LBP and VTDB were downregulated in patients without diabetes, showing severe coronary artery stenosis.ConclusionWe identified significant associations between circulating APOC2, C4A, CXCL7, DOCK2, LBP and VTDB levels and the degree of coronary artery stenosis using the MRM technique.

Post-mortem interval (PMI) estimation is a critical task in forensic science. In this study, we used maggots collected from pig carcasses and applied an integrated proteomics and metabolomics approach to determine potential candidate substances for the estimation of PMI. After methanol precipitation, the supernatant containing metabolites and the protein pellet were separated and subjected to metabolomic and proteomic analyses using liquid chromatography-tandem mass spectrometry (LC-MS/MS). MS/MS data were analyzed for identification and quantification using Proteome Discoverer and Compound Discoverer software. A total of 573 metabolites and more than 800 porcine proteins were identified in maggots. This is the first dataset of proteins and metabolites in maggots collected from porcine carcasses. In this study, guanosine monophosphate, xanthine, inosine, adenosine, and guanine were detected with a similar tendency to increase during early days of maggot development and then decreased gradually. We broadly profiled various biomolecules through analysis in the spot of incident. Especially, we confirmed that proteome and metabolome profiling could be performed directly and indirectly.

The haptophyte alga Emiliania huxleyi is the most abundant coccolithophore in the modern ocean and produces elaborate calcite crystals, called coccolith, in a separate intracellular compartment known as the coccolith vesicle. Despite the importance of biomineralization in coccolithophores, the molecular mechanism underlying it remains unclear. Understanding this precise machinery at the molecular level will provide the knowledge needed to enable further manipulation of biomineralization. In our previous study, altering the calcium concentration modified the calcifying ability of E. huxleyi CCMP371. Therefore in this study, we tested E. huxleyi cells acclimated to three different calcium concentrations (0, 0.1, and 10 mM). To understand the whole transcript profile at different calcium concentrations, RNA-sequencing was performed and used for de novo assembly and annotation. The differentially expressed genes (DEGs) among the three different calcium concentrations were analyzed. The functional classification by gene ontology (GO) revealed that 'intrinsic component of membrane' was the most enriched of the GO terms at the ambient calcium concentration (10 mM) compared with the limited calcium concentrations (0 and 0.1 mM). Moreover, the DEGs in those comparisons were enriched mainly in 'secondary metabolites biosynthesis, transport and catabolism' and 'signal transduction mechanisms' in the KOG clusters and 'processing in endoplasmic reticulum', and 'ABC transporters' in the KEGG pathways. Furthermore, metabolic pathways involved in protein synthesis were enriched among the differentially expressed proteins. The results of this study provide a molecular profile for understanding the expression of transcripts and proteins in E. huxleyi at different calcium concentrations, which will help to identify the detailed mechanism of its calcification.

Emiliania huxleyi is a cosmopolitan coccolithophore that plays an essential role in global carbon and sulfur cycling, and contributes to marine cloud formation and climate regulation. Previously, the proteomic profile of Emiliania huxleyi was investigated using a three-dimensional separation strategy combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS). The current study reuses the MS/MS spectra obtained, for the global discovery of post-translational modifications (PTMs) in this species without specific enrichment methods. Twenty-five different PTM types were examined using Trans-Proteomic Pipeline (Comet and PeptideProphet). Overall, 13,483 PTMs were identified in 7421 proteins. Methylation was the most frequent PTM with more than 2800 modified sites, and lysine was the most frequently modified amino acid with more than 4000 PTMs. The number of proteins identified increased by 22.5% to 18,780 after performing the PTM search. Compared to intact peptides, the intensities of some modified peptides were superior or equivalent. The intensities of some proteins increased dramatically after the PTM search. Gene ontology analysis revealed that protein persulfidation was related to photosynthesis in Emiliania huxleyi. Additionally, various membrane proteins were found to be phosphorylated. Thus, our global PTM discovery platform provides an overview of PTMs in the species and prompts further studies to uncover their biological functions. The combination of a three-dimensional separation method with global PTM search is a promising approach for the identification and discovery of PTMs in other species.

Proteomics, the large-scale study of all proteins of an organism or system, is a powerful tool for studying biological systems. It can provide a holistic view of the physiological and biochemical states of given samples through identification and quantification of large numbers of peptides and proteins. In forensic science, proteomics can be used as a confirmatory and orthogonal technique for well-built genomic analyses. Proteomics is highly valuable in cases where nucleic acids are absent or degraded, such as hair and bone samples. It can be used to identify body fluids, ethnic group, gender, individual, and estimate post-mortem interval using bone, muscle, and decomposition fluid samples. Compared to genomic analysis, proteomics can provide a better global picture of a sample. It has been used in forensic science for a wide range of sample types and applications. In this review, we briefly introduce proteomic methods, including sample preparation techniques, data acquisition using liquid chromatography-tandem mass spectrometry, and data analysis using database search, spectral library search, and de novo sequencing. We also summarize recent applications in the past decade of proteomics in forensic science with a special focus on human samples, including hair, bone, body fluids, fingernail, muscle, brain, and fingermark, and address the challenges, considerations, and future developments of forensic proteomics.

Freshwater Synechocystis sp. PCC 6803 has been considered to be a platform for the production of the next generation of biofuels and is used as a model organism in various fields. Various genomics, transcriptomics, metabolomics, and proteomics studies have been performed on this strain, whereas marine Synechocystis sp. PCC 7338 has not been widely studied despite its wide distribution. This study analyzed the proteome profiles of two Synechocystis strains using a liquid chromatography–tandem mass spectrometry-based bottom-up proteomic approach. Proteomic profiling of Synechocystis sp. PCC 7338 was performed for the first time with a data-dependent acquisition method, revealing 18,779 unique peptides and 1794 protein groups. A data-independent acquisition method was carried out for the comparative quantitation of Synechocystis sp. PCC 6803 and 7338. Among 2049 quantified proteins, 185 up- and 211 down-regulated proteins were defined in Synechocystis sp. PCC 7338. Some characteristics in the proteome of Synechocystis sp. PCC 7338 were revealed, such as its adaptation to living conditions, including the down-regulation of some photosynthesis proteins, the up-regulation of kdpB, and the use of osmolyte glycine as a substrate in C1 metabolism for the regulation of carbon flow. This study will facilitate further studies on Synechocystis 7338 to define in depth the proteomic differences between it and other Synechocystis strains.

Emiliania huxleyi is one of the most abundant marine planktons, and it has a crucial feature in the carbon cycle. However, proteomic analyses of Emiliania huxleyi have not been done extensively. In this study, a three-dimensional liquid chromatography (3D-LC) system consisting of strong cation exchange, high- and low-pH reversed-phase liquid chromatography was established for in-depth proteomic profiling of Emiliania huxleyi. From tryptic proteome digest, 70 fractions were generated and analyzed using liquid chromatography-tandem mass spectrometry. In total, more than 84,000 unique peptides and 10,000 proteins groups were identified with a false discovery rate of ≤0.01. The physicochemical properties of the identified peptides were evaluated. Using ClueGO, approximately 700 gene ontology terms and 15 pathways were defined from the identified protein groups with p-value ≤0.05, covering a wide range of biological processes, cellular components, and molecular functions. Many biological processes associated with CO2 fixation, photosynthesis, biosynthesis, and metabolic process were identified. Various molecular functions relating to protein binding and enzyme activities were also found. The 3D-LC strategy is a powerful approach for comparative proteomic studies on Emiliania huxleyi to reveal changes in its protein level and related mechanism.

The objective of this study was to analyze the temporal and spatial characteristics of fine particulate matters by using huge hourly datasets of PM2.5, including chemical information monitored at the 6 national intensive monitoring sites (NIMSs) from 2013 to 2018 in Korea. Hourly PM2.5 raw datasets were obtained from the National Institute of Environmental Research (NIER) in Korea. Monitoring sites included urban, rural/agricultural, industrial, and marine environments. Since the PM2.5 concentration steadily decreased nationwide, each species concentration also decreased in general. One of key reasons for decreasing PM2.5 might be explained by the implementation of domestic fine dust reduction policies and external influences such as PM2.5 concentration reduction in China. It was observed that 45.0% of all datasets for 6 years were classified as good condition. The average sum of 14 elements over all sites in 2018 was calculated to be 501.5 ng/m³, and its mass ratio for PM2.5 (21.9 µg/m³) was 2.30%. The inorganic elements were generally higher in industrial/urban areas than in agricultural areas. In addition, the average TC (total carbon) over all 6 sites was 28.3% of PM2.5 with the range of 23.6% to 31.4%. The TC in small urban areas was much higher than that in marine areas or even that in large, populated urban area/industrial areas. It seemed that the latter areas were better controlled than the former area in terms of combustion activities of fossil fuels. It is suggested that these results could be play an important role as important basic data to manage ambient air quality and establish effective emission reduction strategies in each region. [ABSTRACT FROM AUTHOR]

Objective: Two series of experiments were conducted to determine how the incremental levels of sodium metabisulfite (SMB)-treated fruit and vegetable discards (FVD) in diet of Hanwoo heifers and cows affect their performance and health. Methods: In Exp. 1, 36 Hanwoo heifers were stratified by age (13.3±0.83 mo) and initial body weight (305±19.7 kg), and divided randomly to one of three diets containing 0%, 10%, or 20% SMB-treated FVD (as-fed basis). The experiment lasted 110 d, including 20 d of adaptation. In Exp. 2, 24 multiparous Hanwoo cows were divided into three groups based on age (48.2±2.81 mo) and initial body condition score (2.64±0.33). Cows in each block were assigned randomly to one of three diets containing 0%, 11%, or 22% SMB-treated FVD (as-fed basis). The experiment lasted 80 d, including a 20-d adaptation period. In both experiments, SMB-treated FVD was used as a replacement for wet brewers grain in total mixed ration (TMR). Results: Growing heifers exhibited no differences in their daily feed intake (6.58±0.61 kg/d dry matter [DM]), average daily gain (0.60±0.07 kg/d), and body condition score when they consumed the incremental levels of SMB-treated FVD. Although most blood metabolites were unaffected by treatments, blood urea-N and ß-hydroxybutyrate levels decreased linearly as the SMB-treated FVD level increased in TMR. Similar to Exp. 1, minor differences were found in daily feed intake (8.27±0.72 kg DM/d) and body condition score of Hanwoo cows. Most blood metabolites remained unaffected by treatments, but blood urea-N decreased as the SMB-treated FVD level in TMR increased. Conclusion: Our findings suggest that SMB-treated FVD could be safely incorporated into the diet of Hanwoo heifers and cows, potentially improving N-use efficiency in the body while not impairing performance or health. [ABSTRACT FROM AUTHOR]

This study was conducted to evaluate and analyze fractures types in wild mammals in Korea. Wild mammals treated at 3 wildlife centers in Korea were included. Of the 63 cases included in this study, water deer was the most common species encountered with fractures. We determined 85 different fracture sites, with maximum lumber vertebral fractures followed by femoral, tibial and pelvic fractures. External skeletal fixator (ESF)-intramedullary (IM) pin (IM+ESF tie-in fixation) was the most common method applied for the surgical treatment of mammals. Lumbar vertebrae and femur were the most common bones involved. The findings of this study are expected to provide information for veterinarians regarding the frequency and characteristics of fractures in wild mammals and serve as a basic database for the types and outcomes of fractures in wild mammals. [ABSTRACT FROM AUTHOR]

The aim of the present study was to investigate the effects of tristetraprolin (TTP) on the vascular endothelial growth factor (VEGF) mRNA and protein expression levels in retinal pigment epithelial cells under hypoxic conditions, and to consider the possibility of using TTP as a novel treatment tool for neovascular age-related macular degeneration (AMD). Overexpression of TTP reduced the expression and secretion levels of VEGF in ARPE-19 cells under hypoxic conditions. TTP destabilized the VEGF mRNA by binding to adenosine and uridine-rich elements regions in its 3'-untranslated region. Furthermore, conditioned medium (CM) from TTP-overexpressing ARPE-19 cells suppressed the tube formation in human umbilical vein endothelial cells compared with hypoxic CM. These findings indicate that regulation of TTP expression may be a promising therapeutic tool for neovascular AMD, however, further research is required. [ABSTRACT FROM AUTHOR]

A slow light metamaterial based on a coupled Fabry-Pérot cavity is proposed and numerically studied using finite-difference time-domain simulations. The coupled cavity-based slow light metamaterial is composed of a periodic array of partial mirrors with low transmittance, i.e., thin metal films perforated with a subwavelength hole array. The tight-binding model is employed to investigate the transmission properties of the coupled-cavity-based metamaterial. It is shown that the group velocities of the slowly propagating modes can be controlled by adjusting the radius of holes in the mirrors. We also show that undesirable reflections at the boundaries of the finite-size metamaterial can be minimized by introducing optimized antireflection structures. [ABSTRACT FROM AUTHOR]

Background: To compare the related factors or manifestations of the two most common isolates of post-operative endophthalmitis, which were Enterococcus spp. and coagulase-negative staphylococci (CNS) in South Korea. Methods: Medical records were reviewed for cases of post-operative endophthalmitis caused by Enterococcus spp. and CNS at eight institutions between January 2004 and July 2010. Various factors including age, sex, residence, systemic diseases, smoking and drinking history, and best corrected visual acuity, and length of time between causative intraocular surgery and symptom development were compared between the two groups. Results: The total number of post-operative endophthalmitis cases was 128 and in 116 cases, microbiological culture tests from the aqueous humor or vitreous were performed. Among these cases, 67 (57.8%) were culture proven. Among these 67 cases, 19 (28.4%) were caused by Enterococcus spp., 14 (20.9%) were caused by Staphylococcus epidermidis endophthalmitis, and 5 (7.5%) were caused by other CNS spp. Age, sex, causative procedure, past medical history, social history, and laterality were not different in the two groups. Mean initial and final visual acuity were significantly worse in the Enterococcus spp. endophthalmitis group than in the CNS group (p = 0.049, 0.042, respectively). Length of time between the causative procedure and symptom development was significantly shorter in cases of Enterococcus spp. endophthalmitis (p= 0.004). Conclusions: Enterococcus spp. induce more severe and rapid-onset postoperative endophthalmitis than CNS. Infectious endophthalmitis developed within 2 days after cataract operation could be caused by Enterococcus spp. and have chance to be poor prognosis in South Korea. [ABSTRACT FROM AUTHOR]

The present study characterizes the effects of resveratrol (Res) on vascular endothelial growth factor (VEGF) secretion in retinal pigment epithelial (RPE) cells. ARPE-19 cells were treated with CoCl2, a hypoxia mimetic agent. CoCl2 treatment increased protein levels of hypoxia inducible factor-1α (HIF-1α) and CXC-chemokine receptor 4 (CXCR4), and secretion of VEGF. To confirm the effects of Res on VEGF secretion, the human umbilical vein endothelial cell tube formation assay was performed with conditioned medium from Res-treated ARPE-19 cells. The well-known antioxidant Res effectively blocked these effects and reduced phosphorylation of nuclear factor (NF)-κB, an upstream activator of CXCR4. Furthermore, Res also suppressed VEGF secretion induced by SDF-1, a ligand of CXCR4. Conditioned medium from Res-treated ARPE-19 cells clearly suppressed tube formation compared with hypoxia-treated conditioned medium. The results demonstrated that Res inhibited the hypoxia mimetic CoCl2-induced expression of VEGF in ARPE-19 cells. Res suppressed CXCR4 expression through decreased phosphorylation of NF-κB, resulting in downregulation of VEGF secretion. [ABSTRACT FROM AUTHOR]

Background: To investigate clinical features of infectious endophthalmitis over five years in a South Korean population. Methods: Medical records of consecutive patients diagnosed with infectious endophthalmitis at eight institutions located in Gyeongsangnam-do and Pusan city between January 1, 2004 and July 31, 2010 were reviewed. Results: A total of 197 patients were diagnosed and treated. An average of 30.0 infectious endophthalmitis per year was developed. The annual incidence rate of postoperative endophthalmitis during 2006 ~ 2009 was 0.037%. The ratios of male to female and right to left were 50.2%: 49.8 % and 54.8%: 43.2%, respectively. Eighth decade and spring were the peak age (36.6%) and season (32.0%) to develop the infectious endophthalmitis. The most common past history in systemic disease was hypertension (40.4%), followed by diabetes (23.4%). Cataract operation (60.4%) was the most common cause, among which most of them was uneventful phacoemulsification (95.9%). Corneal laceration (51.6%) and liver abscess (42.9%) were the most common causes of traumatic and endogenous endophthalmitis, respectively. The percentages of patients with initial and final visual acuity less than counting fingers were 62.6% and 35.2%, respectively. Treatment with vitrectomy with or without intravitreal antibiotics injection was administered to 72.6% of patients, while 17.3% received intravitreal antibiotics only. Conclusions: Our study revealed that the development of infectious endophthalmitis was related with seasonal variation and increased during our study period. Pars plana vitrectomy was preferred for the treatment of infectious endophthalmitis in South Korea. [ABSTRACT FROM AUTHOR]

The article presents a research on several benzo[c]phenanthridine alkaloids including sanguinarine, chelirubine, and macarpine in Eschscholtzia californica cell culture by using high performance liquid chromatography diode array detector (HPLC-DAD), and high performance liquid chromatography electrospray ionization tandem mass spectroscopy (HPLC-ESI-MS/MS). Topics discussed include a ternary gradient pump system, alkaloid production, and informational deducted metabolism.

Balancing the amounts of enzymes is one of the important factors to achieve optimum performance of a designed metabolic pathway. However, the random mutagenesis approach is impractical since it requires searching an unnecessarily large number of variants and often results in searching a narrow range of expression levels which are out of optimal level. Here, we developed a predictive combinatorial design method, called UTR Library Designer, which systematically searches a large combinatorial space of expression levels. It accomplishes this by designing synthetic translation initiation region of mRNAs in a predictive way based on a thermodynamic model and genetic algorithm. Using this approach, we successfully enhanced lysine and hydrogen production in Escherichia coli. Our method significantly reduced the number of variants to be explored for covering large combinatorial space and efficiently enhanced pathway efficiency, thereby facilitating future efforts in metabolic engineering and synthetic biology. [ABSTRACT FROM AUTHOR]

Angelica gigas root cultures were elicited with various elicitors, including yeast extract, chitin, methyl jasmonate, salicylic acid, and copper, with the aim of increasing the production of decursin and decursinol angelate. The treatment of A. gigas root cultures with a combination of yeast extract (2 g l−1) and copper ion (0.5 mM) at the late exponential growth phase increased decursinol angelate accumulation up to 6.86 mg l−1. The best elicitor preparation selected through in vitro experiments was also applied to roots of A. gigas whole plants grown in the field in order to investigate the potential of elicitation as a novel cultivation practice for producing medicinal herbs of improved quality. Biweekly treatments with the elicitor at 70 mg g l−1 FW roots for 10 weeks before the annual harvest resulted in an increment in both plant yields and specific productivity of decursins by 1.5- and 1.7-fold, respectively. This result implies that in vitro screening of elicitors with the ultimate aim of in planta elicitation of whole plants could be effective in terms of time and expense. The elicitation technique reported here demonstrates it potential as a strategy for improving growth and active compounds productivity of medicinal plants through short-term and pre-harvest treatment of the elicitor preparation. [ABSTRACT FROM AUTHOR]

Water network synthesis contributes to cost reduction and the conservation of water resources by reducing water consumption. A mathematical optimization model is developed in this study to synthesize an environmentally friendly water network system (WNS) by minimizing environmental impacts of a WNS. The concept of life cycle assessment (LCA) is integrated into the objective function of the model to evaluate the environmental effect scores (EESs) of principal contributors to the environmental impacts of a WNS and to optimize tradeoffs among their EESs. The mass balances are formulated from the superstructure model, and the constraints are formulated to take into account the real situation in industrial plants. A case study demonstrates the effect of the objective function on the configuration and environmental performance of a WNS and validates the mathematical optimization model. This model can be used for the design for environment (DfE) of WNSs in the context of sustainable development. [ABSTRACT FROM AUTHOR]

Production of the benzophenanthridine alkaloids in Eschscholtzia californica suspension cell cultures was optimized by adding 0.5 mg methyl jasmonate (MJ) and 0.02 mg salicylic acid (SA)/g FCW after 7 days cultivation. Sanguinarine reached 24 mg/g DCW by such treatment; 10 times higher than in control cell cultures. MJ and SA induced expression of berberine bridge enzyme and 3′-hydroxy-( S)- N-methylcoclaurine-4′- O-methyltransferase, respectively. MJ plus SA induced over-expression of both enzymes. [ABSTRACT FROM AUTHOR]

The article discusses a study which determined the economic and environmental efficiency of a water network system (WNS). Consumption of industrial and ionized water contribute to environmental management and economic costs. The study aimed to investigate the significance of WNS compared with conventional water system (CWS) using life cycle assessment (LCA) and life cycle costing (LCC) methods. It identified the factors that contribute to environmental problems and economic costs in relation to water systems. The study concluded that WNS has lower environmental burdens and economic costs compared to CWS.

Light-dependent photosynthesis of Chlorella vulgaris was investigated by using a novel photosynthesis measurement system that could cover wide ranges of incident light and cell density and reproduce accurate readings. Various photosynthesis models, which have been reported elsewhere, were classified and/or reformulated based upon the underlying hypotheses of the light dependence of the algal photosynthesis. Four types of models were derived, which contained distinct light-related variables such as the average or local photon flux density (APFD or LPFD) and the average or local photon absorption rate (APAR or LPAR). According to our experimental results, the LPFD and LPAR models could predict the experimental data more accurately although the APFD and APAR models have been widely used for the kinetic study of microalgal photosynthesis. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 83: 303–311, 2003. [ABSTRACT FROM AUTHOR]

The pathology of diabetic retinopathy includes dilatation and beading of retinal vessels, and vascular sheathing. To gain a better understanding of the molecular events leading to diabetic retinopathy, we investigated disease-specific gene responses by screening differential expression using cDNA microarray. Male Sprague-Dawley rats were intraperitoneally injected with streptozotocin (STZ, 50 mg/kg) or the control buffer and were maintained for 6 weeks. Total RNA extracted from the retinas of both groups was used for cDNA microarray analysis, Signals from all the spots representing hybridized DNA were quantified and compared between the normal and diabetic rat retinas. Among 1176 genes analyzed, the retinal expression of glucose-dependent insulinotropic polypeptide (GIP) was found to increase in STZ-induced diabetic rats compared to controls. GIP is a secreted protein, known to be released from the small intestine, which potentiates glucose-induced insulin secretion from the pancreas. However, the expression of GIP and its receptor (GIPR) has not been previously noted in the rat retina. To further validate the expression of GIP in the rat retina and to determine its possible role in the development of early diabetic retinopathy, we investigated its expression by RT-PCR, Northern blotting, and immunohistochemistry in normal and diabetic rat retinas. GIP mRNA and protein are not only expressed in the rat retina, but their levels are greater in the diabetic rat as compared to controls. And GIPR expression was also upregulated in the retinas of STZ-induced diabetic rats. We here demonstrate for the first time the expression of GIP and GIPR in the rat retina, And we also revealed some genetic events in the early stage of diabetic retinopathy including the de novo increment of GIP and GIPR expression in the retina. [ABSTRACT FROM AUTHOR]

To report acute onset lens particle glaucoma associated with a spontaneous anterior capsular dehiscence. A 66-yearold man presented with spontaneous anterior lens capsule dehiscence with an acute onset of right eye pain that was associated with white particles in the anterior chamber angle and intraocular pressure (IOP) of 55 mmHg. No trauma or other inflammatory antecedents were reported. A hypermature cataract was observed at slit lamp exam. After medical treatment without IOP control, we performed extracapsular cataract extraction and anterior vitrectomy. Anterior chamber aspirate confirmed the presence of macrophages. The postoperative IOP at one month was 16 mmHg OD without medication. Spontaneous dehiscence of the anterior lens capsule in a patient with a hypermature cataract may release lens cortical material, resulting in lens particle glaucoma. Prompt surgical removal of the lens material usually controls the high IOP, and the need for additional glaucoma surgery is not common. [ABSTRACT FROM AUTHOR]

A photonic crystal Mach–Zehnder demultiplexer (PC-MZDmux) with four output ports based on the self-collimation phenomenon in a two-dimensional (2D) PC is proposed and numerically studied using finite-difference time-domain simulations. The PC-MZDmux is composed of three Mach–Zehnder interferometers (MZIs) and each MZI consists of two 50:50 beam splitters and two perfect mirrors. Employed as the design parameters to achieve the demultiplexing functionality are the radius of phase control rods (PCRs) in the mirrors and the distance between the beam spitter and the mirror in the three MZIs. From spatial electric field distributions and transmission spectra, it is demonstrated that an incident self-collimated beam with four different frequencies can be demultiplexed to four output ports of the PC-MZDmux with proper design parameters. Our results indicate that this device design may constitute an efficient approach to light propagation manipulation and increase the application range of self-collimated beams. [ABSTRACT FROM AUTHOR]

Photonic crystal Mach–Zehnder add-drop filters (PC-MZADFs) based on the self-collimation phenomenon in a two-dimensional (2D) PC are proposed and numerically studied using finite-difference time-domain (FDTD) simulations. Each PC-MZADF is composed of a symmetric Mach–Zehnder interferometer (MZI) with an identical filter in each of its two different optical paths. Zizag-box resonators (ZBRs) and Fano resonators (FRs) are employed as the optical filters in rod-type and hole-type PCs, respectively. It is shown that self-collimated beams with the ZBR and FR resonant frequencies can be dropped or added using multiple-beam interference. We also show that the resonant frequencies of the resonators can be adjusted by varying the radii of their rods or holes. Our results indicate that this device design may constitute an efficient approach to light propagation manipulation and increase the application range of self-collimated beams. [ABSTRACT FROM AUTHOR]

AIM: To confirm the changes in proteins related with hypoxia-induced retinal cell death and to assess the effects of resveratrol (Res). METHODS: The therapeutic effect of Res was verified using an ischemic/reperfusion (I/R) model in vivo and a hypoxia modelin retinal ganglion cells (RGCs) in vitro. Death of RGCs were confirmed by TUNEL assay. Protein expression was confirmed by Western blotting and immunohistochemistry. In addition, flow cytometric analysis was used to confirm the response in the cell unit to obtain more accurate data. RESULTS: ErbB2 expression and apoptosis in the ganglion cell layer (GCL) increased after I/R injury. Treatment of Res rescued I/R-induced ganglion cell death, downregulated apoptosis and ErbB2 protein expression in the retina. In subsequent in vitro models, Res affects apoptosis by regulating the phosphorylation and expression of mouse double minute 2 homolog (MDM2), along with those of ErbB2. These results suggest that Res reverses GCL-specific apoptosis via downregulation of ErbB2 in ischemic injury. CONCLUSION: In light of Res favorable properties, it should be evaluated in the treatment of RGC death and related retinal disease characterized by ErbB2 and MDM2 expression. Therefore, Res is appropriate therapeutic agent for treating ischemic injury-related eye diseases by targeting the expression of ErbB2 and MDM2.

We present a permanent magnet–based spherical wheel motor that can be used in omnidirectional mobility applications. The proposed motor consists of a ball‐shaped rotor with a magnetic dipole and a hemispherical shell with circumferential air‐core coils attached to the outer surface acting as a stator. Based on the rotational symmetry of the rotor poles and stator coils, we are able to model the rotor poles and stator coils as dipoles. A simple physical model constructed based on a torque model enables fast numerical simulations of motor dynamics. Based on these numerical simulations, we test various control schemes that enable constant‐speed rotation along arbitrary axes with small rotational attitude error. Torque analysis reveals that the back electromotive force induced in the coils can be used to construct a control scheme that achieves the desired results. Numerical simulations of trajectories confirm that even without explicit methods for correcting the rotational attitude error, it is possible to drive the motor with a low attitude error (

We propose a substrate with high thermal conductivity, manufactured by the low‐temperature co‐fired ceramic (LTCC) multilayer circuit process technology, as a new DC/DC converter platform for power electronics applications. We compare the reliability and power conversion efficiency of a converter using the LTCC substrate with the one using a conventional printed circuit board (PCB) substrate, to demonstrate the superior characteristics of the LTCC substrates. The power conversion efficiencies of the LTCC‐ and PCB‐based synchronous buck converters are 95.5% and 94.5%, respectively, while those of nonsynchronous buck converters are 92.5% and 91.3%, respectively, at an output power of 100 W. To verify the reliability of the LTCC‐based converter, two types of tests were conducted. Storage temperature tests were conducted at −20 °C and 85 °C for 100 h each. The variation in efficiency after the tests was less than 0.3%. A working temperature test was conducted for 60 min, and the temperature of the converter was saturated at 58.2 °C without a decrease in efficiency. These results demonstrate the applicability of LTCC as a substrate for power conversion systems.

This study is to investigate the characteristic features of Acanthamoeba keratitis (AK) that differentiating it from herpetic epithelial keratitis (HEK) using anterior segment optical coherence tomography (AS-OCT). Medical records of three eyes of each AK and herpetic keratitis who had AS-OCT examination were reviewed in this study. Slit-lamp biomicroscopy and AS-OCT was performed on the initial visit and on every follow-up visits in all patients. In all three AK cases, reflective bands in the corneal stroma that correspond to the area of radial keratoneuritis were observed. The depth of the reflective bands varied in each case. After AK treatment, slit-lamp biomicroscopy confirmed that radial keratoneuritis had resolved and AS-OCT confirmed that reflective bands in the corneal stroma had also disappeared in all patients. Unlike the AS-OCT results found in AK, highly reflective HEK lesions were observed only in the subepithelial area, not in the stroma. AS-OCT seems to be helpful analyzing the specific depth of the lesion which enables to distinguish AK from HEK.

We propose a multilayered‐substrate‐based power semiconductor discrete device package for a low switching loss and high heat dissipation. To verify the proposed package, cost‐effective, low‐temperature co‐fired ceramic, multilayered substrates are used. A bare die is attached to an embedded cavity of the multilayered substrate. Because the height of the pad on the top plane of the die and the signal line on the substrate are the same, the length of the bond wires can be shortened. A large number of thermal vias with a high thermal conductivity are embedded in the multilayered substrate to increase the heat dissipation rate of the package. The packaged silicon carbide Schottky barrier diode satisfies the reliability testing of a high‐temperature storage life and temperature humidity bias. At 175 °C, the forward current is 7 A at a forward voltage of 1.13 V, and the reverse leakage current is below 100 μA up to a reverse voltage of 980 V. The measured maximum reverse current (IRM), reverse recovery time (Trr), and reverse recovery charge (Qrr) are 2.4 A, 16.6 ns, and 19.92 nC, respectively, at a reverse voltage of 300 V and di/dt equal to 300 A/μs.

In this study, magnetic steel slag biochar (MSSB) was synthesized from low-cost steel slag waste to investigate the effectiveness of steel slag biochar composite for NH4-N removal and magnetic properties in aqueous solution. The maximum adsorption capacity of NH4-N by MSSB was 4.366 mg/g according to the Langmuir model. The magnetic properties of MSSB indicated paramagnetic behavior and a saturation magnetic moment of 2.30 emu/g at 2 Tesla. The NH4-N adsorption process was well characterized by the pseudo-second order kinetic model and Temkin isotherm model. This study demonstrated the potential of magnetic biochar synthesized from steel slag waste for NH4-N removal in aqueous solution.

This study examined the feasibility of using non-sterilized swine wastewater for lipid production by an isolated microalga, Scenedesmus rubescens. Different dilution ratios using municipal wastewater as a diluent were tested to determine the suitable levels of microalgal growth in the wastewaters, its nutrient removal, and its lipid production. The highest lipid productivity (8.37 mg/L/d) and NH4+ removal (76.49%) were achieved in swine wastewater that had been diluted to 30 times using municipal wastewater. Various bacteria coexisted in the wastewaters during the cultivation of S. rubescens. These results suggest the practical feasibility of a system to produce lipids from swine wastewater by using microalgae.