Metabolomic profiles of ovariectomized mice and their associations with body composition and frailty-related parameters in postmenopausal women

BACKGROUND

Menopause, a dramatical estrogen-deficient condition, is considered the most significant milestone in women's health.

PURPOSE

To investigate the metabolite changes attributed to estrogen deficiency using random forest (RF)-based machine learning (ML) modeling strategy in ovariectomized (OVX) mice as well as determine the clinical relevance of selected metabolites in older women.

METHODS AND RESULTS

Untargeted and targeted metabolomic analyses revealed that metabolites related to TCA cycle, sphingolipids, phospholipids, fatty acids, and amino acids, were significantly changed in the plasma and/or muscle of OVX mice. Subsequent ML classifiers based on RF algorithm selected alpha-ketoglutarate (AKG), arginine, carnosine, ceramide C24, phosphatidylcholine (PC) aa C36:6, and PC ae C42:3 in plasma as well as PC aa 34:1, PC aa C34:3, PC aa C36:5, PC aa C32:1, PC aa C36:2, and sphingosine in muscle as top featured metabolites that differentiate the OVX mice from the sham-operated group. When circulating levels of AKG, arginine, and carnosine, which showed the most significant changes in OVX mice blood, were measured in postmenopausal women, higher plasma AKG levels were associated with lower bone mass, weak grip strength, poor physical performance, and increased frailty risk.

CONCLUSIONS

Metabolomics- and ML-based methods identified the key metabolites of blood and muscle that were significantly changed after ovariectomy in mice, and the clinical implication of several metabolites was investigated by looking at their correlation with body composition and frailty-related parameters in postmenopausal women. These findings provide crucial context for understanding the diverse physiological alterations caused by estrogen deficiency in women.

An extremely energetic cosmic ray observed by a surface detector array

Cosmic rays are energetic charged particles from extraterrestrial sources, with the highest-energy events thought to come from extragalactic sources. Their arrival is infrequent, so detection requires instruments with large collecting areas. In this work, we report the detection of an extremely energetic particle recorded by the surface detector array of the Telescope Array experiment. We calculate the particle's energy as [Formula: see text] (~40 joules). Its arrival direction points back to a void in the large-scale structure of the Universe. Possible explanations include a large deflection by the foreground magnetic field, an unidentified source in the local extragalactic neighborhood, or an incomplete knowledge of particle physics.

Longitudinal Analyses of Mutational Subclonal Architecture and Tumor Subtypes in Recurrent Bladder Cancer

Longitudinal tumor sequencing of recurrent bladder cancer (BC) can facilitate the investigation of BC progression-associated genomic and transcriptomic alterations. In this study, we analyzed 18 tumor specimens including distant and locoregional metastases obtained during tumor progression for five BC patients using whole-exome and transcriptome sequencing. Along with the substantial level of intratumoral mutational heterogeneity across the cases, we observed that clonal mutations were enriched with known BC driver genes and apolipoprotein B mRNA editing enzyme, catalytic polypeptide (APOBEC)-associated mutation signatures compared with subclonal mutations, suggesting the genetic makeup for BC tumorigenesis associated with APOBEC deaminase activity was accomplished early in the cancer evolution. Mutation-based phylogenetic analyses also revealed temporal dynamics of mutational clonal architectures in which the number of mutational clones varied along the BC progression and notably was often punctuated by clonal sweeps associated with chemotherapy. The bulk-level transcriptome sequencing revealed frequent subtype switching in which transcriptionally defined BC subtypes may vary during tumor progression. Longitudinal whole-exome and transcriptome sequencing of recurrent BC may advance our understanding into the BC heterogeneity in terms of somatic mutations, cell clones and transcriptome-based tumor subtypes during disease progression.

Provably Secure Mutual Authentication and Key Agreement Scheme Using PUF in Internet of Drones Deployments

Internet of Drones (IoD), designed to coordinate the access of unmanned aerial vehicles (UAVs), is a specific application of the Internet of Things (IoT). Drones are used to control airspace and offer services such as rescue, traffic surveillance, environmental monitoring, delivery and so on. However, IoD continues to suffer from privacy and security issues. Firstly, messages are transmitted over public channels in IoD environments, which compromises data security. Further, sensitive data can also be extracted from stolen mobile devices of remote users. Moreover, drones are susceptible to physical capture and manipulation by adversaries, which are called drone capture attacks. Thus, the development of a secure and lightweight authentication scheme is essential to overcoming these security vulnerabilities, even on resource-constrained drones. In 2021, Akram et al. proposed a secure and lightweight user-drone authentication scheme for drone networks. However, we discovered that Akram et al.'s scheme is susceptible to user and drone impersonation, verification table leakage, and denial of service (DoS) attacks. Furthermore, their scheme cannot provide perfect forward secrecy. To overcome the aforementioned security vulnerabilities, we propose a secure mutual authentication and key agreement scheme between user and drone pairs. The proposed scheme utilizes physical unclonable function (PUF) to give drones uniqueness and resistance against drone stolen attacks. Moreover, the proposed scheme uses a fuzzy extractor to utilize the biometrics of users as secret parameters. We analyze the security of the proposed scheme using informal security analysis, Burrows-Abadi-Needham (BAN) logic, a Real-or-Random (RoR) model, and Automated Verification of Internet Security Protocols and Applications (AVISPA) simulation. We also compared the security features and performance of the proposed scheme and the existing related schemes. Therefore, we demonstrate that the proposed scheme is suitable for IoD environments that can provide users with secure and convenient wireless communications.

Inefficient Magnetic-Field Amplification in Supersonic Laser-Plasma Turbulence

We report a laser-plasma experiment that was carried out at the LMJ-PETAL facility and realized the first magnetized, turbulent, supersonic (Ma_{turb}≈2.5) plasma with a large magnetic Reynolds number (Rm≈45) in the laboratory. Initial seed magnetic fields were amplified, but only moderately so, and did not become dynamically significant. A notable absence of magnetic energy at scales smaller than the outer scale of the turbulent cascade was also observed. Our results support the notion that moderately supersonic, low-magnetic-Prandtl-number plasma turbulence is inefficient at amplifying magnetic fields compared to its subsonic, incompressible counterpart.

Spatially distinct reprogramming of the tumor microenvironment based on tumor invasion in diffuse-type gastric cancers

PURPOSE

Histological features of diffuse-type gastric cancer (GC) indicate that the tumor microenvironment (TME) may substantially impact tumor invasiveness. However, cellular components and molecular features associated with cancer invasiveness in the TME of diffuse-type GCs are poorly understood.

EXPERIMENTAL DESIGN

We performed single-cell RNA-sequencing (scRNA-seq) using tissue samples from superficial and deep invasive layers of cancerous and paired normal tissues freshly harvested from five patients with diffuse-type GC. The scRNA-seq results were validated by immunohistochemistry and duplex in situ hybridization (ISH) in formalin-fixed paraffin-embedded tissues.

RESULTS

Seven major cell types were identified. Fibroblasts, endothelial cells, and myeloid cells were categorised as being enriched in the deep layers. Cell type-specific clustering further revealed that the superficial-to-deep layer transition is associated with enrichment in inflammatory endothelial cells and fibroblasts with upregulated CCL2 transcripts. Immunohistochemistry and duplex ISH revealed the distribution of the major cell types and CCL2-expressing endothelial cells and fibroblasts, indicating tumor invasion. Elevation of CCL2 levels along the superficial-to-deep layer axis revealed the immunosuppressive immune cell sub-types that may contribute to tumor cell aggressiveness in the deep invasive layers of diffuse-type GC. The analyses of public datasets revealed the high-level co-expression of stromal cell-specific genes and that CCL2 correlated with poor survival outcomes in GC patients.

CONCLUSIONS

This study reveals the spatial reprogramming of the TME that may underlie invasive tumor potential in diffuse-type GC. This TME profiling across tumor layers suggests new targets, such as CCL2, that can modify the TME to inhibit tumor progression in diffuse-type GC.

Exosomal miR-1305 in the oncogenic activity of hypoxic multiple myeloma cells: a biomarker for predicting prognosis

Background: Exosomes have emerged as important mediators of tumor progression, and a prognostic role for serum exosomal miRNAs has been suggested in multiple myeloma (MM). Given the association of hypoxia with tumor aggressiveness, including cancer stem cell-like phenotypes, we explored exosomal miRNAs from MM cells under hypoxic conditions and analyzed their diverse roles both in promoting oncogenic activity and in predicting prognosis.

Methods: The human MM cell line, RPMI 8226, was cultured under hypoxic conditions and their exosome production and exosomal miRNA profiles were compared with those of normoxic parental cells. The survival outcome of myeloma patients was compared using serum levels of exosomal miRNAs, and the effects of exosomal miRNAs on the target genes of MM cells and adjacent immune cells were analyzed.

Results: Increased expression of stem cell markers and exosome production were observed in hypoxic MM cells. Exosome miRNA analysis identified a higher expression of miR-1305 in exosomes isolated from hypoxic MM cells than in those of normoxic parental cells. The overall survival of patients with high exosomal miR-1305 was poorer than it was in patients with low exosomal miR-1305. In hypoxic MM cells, an increase of exosomal miR-1305 led to a decrease of cellular miR-1305 and increased expression of the miR-1305 target genes, MDM2, IGF1 and FGF2 resulted in the promotion of oncogenic activity of MM. Exosomal miR-1305 was also transferred from MM cells to macrophages, and miR-1305-transferred macrophages showed tumor-promoting, M2-macrophage phenotypes.

Conclusions: Exosome-mediated secretion of miR-1305 in MM cells promoted oncogenic activity of hypoxic MM cells and high serum levels of exosomal miR-1305.

Tumor-promoting macrophages prevail in malignant ascites of advanced gastric cancer

Gastric cancer (GC) patients develop malignant ascites as the disease progresses owing to peritoneal metastasis. GC patients with malignant ascites have a rapidly deteriorating clinical course with short survival following the onset of malignant ascites. Better optimized treatment strategies for this subset of patients are needed. To define the cellular characteristics of malignant ascites of GC, we used single-cell RNA sequencing to characterize tumor cells and tumor-associated macrophages (TAMs) from four samples of malignant ascites and one sample of cerebrospinal fluid. Reference transcriptomes for M1 and M2 macrophages were generated by in vitro differentiation of healthy blood-derived monocytes and applied to assess the inflammatory properties of TAMs. We analyzed 180 cells, including tumor cells, macrophages, and mesothelial cells. Dynamic exchange of tumor-promoting signals, including the CCL3–CCR1 or IL1B–IL1R2 interactions, suggests macrophage recruitment and anti-inflammatory tuning by tumor cells. By comparing these data with reference transcriptomes for M1-type and M2-type macrophages, we found noninflammatory characteristics in macrophages recovered from the malignant ascites of GC. Using public datasets, we demonstrated that the single-cell transcriptome-driven M2-specific signature was associated with poor prognosis in GC. Our data indicate that the anti-inflammatory characteristics of TAMs are controlled by tumor cells and present implications for treatment strategies for GC patients in which combination treatment targeting cancer cells and macrophages may have a reciprocal synergistic effect.

New strategies for treating advanced gastric cancer could emerge from insights into the interactions between white blood cells called macrophages and tumor cells in fluid known as malignant ascites that accumulates in the abdomen. Researchers in Seoul, South Korea, led by Hae-Ock Lee at The Catholic University of Korea and Woong-Yang Park at the Samsung Medical Center compared macrophages from healthy subjects with those from gastric cancer ascites. They identified molecular signaling interactions between tumor cells and macrophages that recruited macrophages into the ascites and converted them into more anti-inflammatory forms. The macrophages were then able to promote the activities of the cancer cells. The results suggest that chemicals able to inhibit or deplete proteins now identified as involved in controlling these synergistic interactions could become a new class of therapeutic agents.

Genomic, transcriptomic, and viral integration profiles associated with recurrent/metastatic progression in high-risk human papillomavirus cervical carcinomas

Acquisition of recurrent/metastatic potential by a tumor cell defines a critical step in malignant progression. However, understanding of metastatic progression at the molecular level is scarce for cervical carcinomas (CES). In this study, we performed genomic, transcriptomic, and viral profiling of five pairs of primary (CES‐P) and matched recurrent/metastatic tumors (CES‐R/M) with high risk human papillomavirus. Whole exome sequencing revealed mutation features of CES‐R/M including elevated mutation burdens and prevalent copy number alterations compared to their matched CES‐P. A relative deficit of APOBEC‐related mutation signatures accompanying the transcriptional downregulation of APOBEC3A was observed for CES‐R/M. Mutations in genes encoding epigenetic regulators were commonly observed as CES‐R/M‐specific alterations. Immunoprofiling and gene set analysis revealed CES‐Ps were enriched with transcripts representing activated anticancer immunity such as interferon‐gamma pathway, while CES‐R/M exhibited upregulation of genes involved in epithelial‐mesenchymal transition and angiogenesis. Viral capture sequencing revealed that integration sites remained enriched in viral E1 protein domain during malignant progression. Moreover, we found transcriptional upregulation of POSTN and downregulation of APOBEC3A were associated with unfavorable clinical outcomes in CES. Comprehensive genomic and transcriptomic profiling of a rare cohort including CES‐R/M identified metastases‐specific features to advance the molecular understanding into CES metastatic progression with potential clinical implications.

Alterations in the Transcriptional Programs of Myeloma Cells and the Microenvironment during Extramedullary Progression Affect Proliferation and Immune Evasion

PURPOSE

In multiple myeloma, extramedullary progression is associated with treatment resistance and a high mortality rate. To understand the molecular mechanisms controlling the devastating progression of myeloma, we applied single-cell RNA-sequencing (RNA-seq) to myeloma in the bone marrow and myelomatous pleural effusions or ascites.

EXPERIMENTAL DESIGN

Bone marrow or extramedullary myeloma samples were collected from 15 patients and subjected to single-cell RNA-seq. The single-cell transcriptome data of malignant plasma cells and the surrounding immune microenvironment were analyzed.

RESULTS

Comparisons of single-cell transcriptomes revealed the systematic activation of proliferation, antigen presentation, proteasomes, glycolysis, and oxidative phosphorylation pathways in extramedullary myeloma cells. The myeloma cells expressed multiple combinations of growth factors and receptors, suggesting autonomous and pleiotropic growth potential at the single-cell level. Comparisons of the tumor microenvironment revealed the presence of cytotoxic T lymphocytes and natural killer (NK) cells in both the bone marrow and extramedullary ascites, demonstrating a gene-expression phenotype indicative of functional compromise. In parallel, isolated myeloma cells persistently expressed class I MHC molecules and upregulated inhibitory molecules for cytotoxic T and NK cells.

CONCLUSIONS

These data suggest that myeloma cells are equipped with specialized immune evasion mechanisms in cytotoxic microenvironments. Taken together, single-cell transcriptome analysis revealed transcriptional programs associated with aggressive myeloma progression that support autonomous cell proliferation and immune evasion.

Paired whole exome and transcriptome analyses for the Immunogenomic changes during concurrent chemoradiotherapy in esophageal squamous cell carcinoma

BACKGROUND

The immunogenomic changes triggered by concurrent chemoradiation therapy (CCRT), a standard neoadjuvant treatment for locally advanced esophageal squamous cell carcinoma (ESCC), are unknown. We aimed to analyze the early immunogenomic changes in ESCC induced by CCRT and to correlate them with clinical outcomes.

METHODS

We collected biopsy samples from 40 patients with ESCC and the surgical candidates were treated with 5-fluorouracil (5-FU)/Cisplatin and concurrent radiation therapy. Endoscopic biopsy was performed before and after one treatment cycle of 5-FU/Cisplatin and 5 to 18 fractions of radiation. We analyzed immunogenomic changes using paired whole-exome sequencing (n = 29) and paired whole-transcriptome sequencing (WTS, n = 23). Multiplex immunohistochemistry (IHC) was conducted in four representative pair samples.

RESULTS

Fourteen out of 23 WTS samples (60.8%) showed increased immune scores after CCRT, as calculated by ESTIMATE. The rate of progression-free survival was higher in patients with increased immune scores compared with the remaining patients (83.1% vs. 57.1%, p = 0.25). Tumor mutation burden and neoantigen load were significantly reduced after CCRT (p < 0.001). We observed no specific correlation with non-synonymous mutations and no changes in the single-nucleotide variant spectrum after CCRT. Post-CCRT samples were enriched in gene sets related to immune signaling pathways, such as interferon gamma signaling and CD28 co-stimulation. Multiplex IHC showed an incremental trend in the proportion of CD4 positive cells in cytokeratin positive region after CCRT. However, CD8, CD20, FOXP1, PD-L1 showed no definitive trend. Proportion of immune cells calculated by CIBERSORT, showed that significant increase in neutrophils after CCRT.

CONCLUSIONS

We have comprehensively analyzed the early immunogenomic changes induced in ESCC by CCRT and correlated them with clinical outcomes. Our results provide a potential basis for combining immunotherapy with CCRT for the treatment of ESCC.

Supersonic plasma turbulence in the laboratory

The properties of supersonic, compressible plasma turbulence determine the behavior of many terrestrial and astrophysical systems. In the interstellar medium and molecular clouds, compressible turbulence plays a vital role in star formation and the evolution of our galaxy. Observations of the density and velocity power spectra in the Orion B and Perseus molecular clouds show large deviations from those predicted for incompressible turbulence. Hydrodynamic simulations attribute this to the high Mach number in the interstellar medium (ISM), although the exact details of this dependence are not well understood. Here we investigate experimentally the statistical behavior of boundary-free supersonic turbulence created by the collision of two laser-driven high-velocity turbulent plasma jets. The Mach number dependence of the slopes of the density and velocity power spectra agree with astrophysical observations, and supports the notion that the turbulence transitions from being Kolmogorov-like at low Mach number to being more Burgers-like at higher Mach numbers.

Characterisation of spatial variability in water quality in the Great Barrier Reef catchments using multivariate statistical analysis

Water quality monitoring is important to assess changes in inland and coastal water quality. The focus of this study was to improve understanding of the spatial component of spatial-temporal water quality dynamics, particularly the spatial variability in water quality and the association between this spatial variability and catchment characteristics. A dataset of nine water quality constituents collected from 32 monitoring sites over a 11-year period (2006-2016), across the Great Barrier Reef catchments (Queensland, Australia), were evaluated by multivariate techniques. Two clusters were identified, which were strongly associated with catchment characteristics. A two-step Principal Component Analysis/Factor Analysis revealed four groupings of constituents with similar spatial pattern and allowed the key catchment characteristics affecting water quality to be determined. These findings provide a more nuanced view of spatial variations in water quality compared with previous understanding and an improved basis for water quality management to protect nearshore marine ecosystem.

Biomarkers Associated with Tumor Heterogeneity in Prostate Cancer

BACKGROUND: Prostate cancers exhibit intratumor heterogeneity (ITH), like other cancer types. The ITH may affect diverse phenotypes such as treatment response, drug resistance, and clinical outcomes. It is crucial to consider ITH to understand tumorigenesis. METHODS: Genomic and transcriptomic profiles of prostate cancer patients were investigated to determine which markers are correlated with the degree of tumor heterogeneity. In addition, the correlation between the immune activity and clonality of tumors was examined. RESULTS: Tumor heterogeneity across all prostate cancer samples was variable. However, ITH events were dependent on genomic and clinical features. Interestingly, prostate-specific antigen score increased in tumors with multiple subclones, indicating high-grade tumor heterogeneity. On the other hand, CD8-positive T-cell activation decreased in highly heterogeneous tumors. Intriguingly, PTEN deletion was prominently enriched in high heterogeneity groups, with a strong association with heterozygous loss. Expression of major genes including PTEN, CDC42EP5, RNLS, GP2, NETO2, and AMPD3 was closely related to tumor heterogeneity in association with PTEN deletion. CONCLUSIONS: In prostate cancer, ITH, a potential factor affecting tumor progression, is associated with PTEN deletion and cytotoxic T cell inactivation.

Correction: The mutational landscape of ocular marginal zone lymphoma identifies frequent alterations in TNFAIP3 followed by mutations in TBL1XR1 and CREBBP

[This corrects the article DOI: 10.18632/oncotarget.14928.].

Abstract 2118: Single-cell analysis reveals dynamic interaction between myeloma and bone marrow microenvironment

Multiple myeloma (MM) is a monoclonal plasma cell (MPC) malignancy primarily propagating in the bone marrow. To understand molecular signatures of MM in association with tumor microenvironment, we performed single-cell RNA sequencing for bone marrow biopsies from seven newly diagnosed myeloma patients. Clinical parameters of 7 MM patients differed, which were recapitulated in the single-cell transcriptome analysis. In comparison to the normal bone marrow from healthy donors, patient-specific monoclonal immunoglobulin gene expression as well as high levels of plasma cell markers distinguished the MPC clusters in myeloma patients. For other cell type identification, reference transcriptome for bone marrow immune cells were utilized. Major cell populations were determined to be monocytes, T cells, B cells, and erythroid cells. T cells manifested a mature phenotype encompassing from naïve to cytotoxic effector gene expression characteristics. B cells and erythroid cell populations were in various developmental stages. Monocytes demonstrated relatively constant gene expression throughout healthy donors to myeloma patients. In more advanced tumor stages, the composition and gene expression characteristics of MPCs and bone marrow immune cells were altered. Taken together, single cell RNA sequencing reveals gene expression characteristics of both myeloma and bone marrow immune cells which provide potential therapeutic strategies targeting tumor or immune compartment.

Citation Format: Jaewoong Min, Daeun Ryu, Hae-Ock Lee, Areum Jo, Woong-Yang Park, Seok Jin Kim, Kihyun Kim. Single-cell analysis reveals dynamic interaction between myeloma and bone marrow microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2118.

Comprehensive genomic profiling of IgM multiple myeloma identifies IRF4 as a prognostic marker

Immunoglobulin M multiple myeloma (IgM MM) is an extremely rare subtype of multiple myeloma with a poor clinical outcome. In this study, bone marrow aspirates of MM patients, including two cases of IgM MM, were analyzed by whole exome sequencing and RNA sequencing. Recurrent somatic mutations in the NRAS, KRAS, CCND1, DIS3, and TP53 genes were found in IgM MM and other types of MM, in agreement with previous studies. Overall transcription profiles of IgM and other types of MM clustered together, but separate from normal blood or peripheral plasma cells. Among the differentially expressed genes in IgM MM, IRF4 was highly expressed in IgM as well as in a subset of other types of MM patients. Thus, IRF4 is an independent prognostic factor for general MM patients. Taken together, the somatic mutation and transcriptome profiles support the idea that IgM MM can be classified as an aggressive MM subtype.

Laboratory evidence of dynamo amplification of magnetic fields in a turbulent plasma

Magnetic fields are ubiquitous in the Universe. The energy density of these fields is typically comparable to the energy density of the fluid motions of the plasma in which they are embedded, making magnetic fields essential players in the dynamics of the luminous matter. The standard theoretical model for the origin of these strong magnetic fields is through the amplification of tiny seed fields via turbulent dynamo to the level consistent with current observations. However, experimental demonstration of the turbulent dynamo mechanism has remained elusive, since it requires plasma conditions that are extremely hard to re-create in terrestrial laboratories. Here we demonstrate, using laser-produced colliding plasma flows, that turbulence is indeed capable of rapidly amplifying seed fields to near equipartition with the turbulent fluid motions. These results support the notion that turbulent dynamo is a viable mechanism responsible for the observed present-day magnetization.

Prevalence and detection of low-allele-fraction variants in clinical cancer samples

Accurate detection of genomic alterations using high-throughput sequencing is an essential component of precision cancer medicine. We characterize the variant allele fractions (VAFs) of somatic single nucleotide variants and indels across 5095 clinical samples profiled using a custom panel, CancerSCAN. Our results demonstrate that a significant fraction of clinically actionable variants have low VAFs, often due to low tumor purity and treatment-induced mutations. The percentages of mutations under 5% VAF across hotspots in EGFR, KRAS, PIK3CA, and BRAF are 16%, 11%, 12%, and 10%, respectively, with 24% for EGFR T790M and 17% for PIK3CA E545. For clinical relevance, we describe two patients for whom targeted therapy achieved remission despite low VAF mutations. We also characterize the read depths necessary to achieve sensitivity and specificity comparable to current laboratory assays. These results show that capturing low VAF mutations at hotspots by sufficient sequencing coverage and carefully tuned algorithms is imperative for a clinical assay.

High-throughput sequencing is used to identify somatic variants in cancer patients. Here, the authors perform panel-based profiling of 5095 clinical samples and demonstrate that many clinically-actionable variants have low variant allele fractions, requiring assays with high detection sensitivity.

Probabilistic dietary exposure to ethyl carbamate from fermented foods and alcoholic beverages in the Korean population

The occurrence of ethyl carbamate was investigated in fermented foods and alcoholic beverages of the Korean total diet study. The concentrations of ethyl carbamate ranged from not detected to 166.5 μg kg^-1. Dietary exposure to ethyl carbamate was estimated by the probabilistic method. Estimated intakes of ethyl carbamate from foods and alcoholic beverages were 4.12 ng kg^-1 body weight (bw) per day for average consumers and 12.37 ng kg^-1 bw/day for 95th percentile high consumers. The major foods contributing to ethyl carbamate exposure were soy sauce (63%), followed by maesilju (plum liqueur, 30%), whisky (5%), and bokbunjaju (black raspberry wine, 2%). On the basis of the benchmark dose lower confidence limit 10% (BMDL₁₀) of 0.3 mg kg^-1 bw/day, margins of exposure were 128,000 for mean exposure and 40,000 for 95th percentile exposure. This indicates that the exposure of the Korean general population for ethyl carbamate is of low concern. However, careful vigilance should be continued for high consumers of fermented foods and alcoholic beverages.

Bayesian framework for parametric bivariate accelerated lifetime modeling and its application to hospital acquired infections

Infectious diseases that can be spread directly or indirectly from one person to another are caused by pathogenic microorganisms such as bacteria, viruses, parasites, or fungi. Infectious diseases remain one of the greatest threats to human health and the analysis of infectious disease data is among the most important application of statistics. In this article, we develop Bayesian methodology using parametric bivariate accelerated lifetime model to study dependency between the colonization and infection times for Acinetobacter baumannii bacteria which is leading cause of infection among the hospital infection agents. We also study their associations with covariates such as age, gender, apache score, antibiotics use 3 months before admission and invasive mechanical ventilation use. To account for singularity, we use Singular Bivariate Extreme Value distribution to model residuals in Bivariate Accelerated lifetime model under the fully Bayesian framework. We analyze a censored data related to the colonization and infection collected in five major hospitals in Turkey using our methodology. The data analysis done in this article is for illustration of our proposed method and can be applied to any situation that our model can be used.

GEPdb: a database for investigating the ternary association of genotype, gene expression and phenotype

GEPdb integrates both genome-wide association studies and expression quantitative trait loci information, the two primary sources of genome-wide mapping for genotype-phenotype and genotype-expression associations together with phenotype-associated gene lists. The GEPdb provides simultaneous interpretation of both genetic risks and potential gene regulatory pathways toward phenotypic outcome by establishing the ternary relationship of genotype-expression-phenotype (GEP). The analytic scope is further extended by linkage disequilibrium from five different populations of the international HapMap Project.

AVAILABILITY AND IMPLEMENTATION

http://ercsbweb.ewha.ac.kr/gepdb.

gsGator: an integrated web platform for cross-species gene set analysis

Background

Gene set analysis (GSA) is useful in deducing biological significance of gene lists using a priori defined gene sets such as gene ontology (GO) or pathways. Phenotypic annotation is sparse for human genes, but is far more abundant for other model organisms such as mouse, fly, and worm. Often, GSA needs to be done highly interactively by combining or modifying gene lists or inspecting gene-gene interactions in a molecular network.

Description

We developed gsGator, a web-based platform for functional interpretation of gene sets with useful features such as cross-species GSA, simultaneous analysis of multiple gene sets, and a fully integrated network viewer for visualizing both GSA results and molecular networks. An extensive set of gene annotation information is amassed including GO & pathways, genomic annotations, protein-protein interaction, transcription factor-target (TF-target), miRNA targeting, and phenotype information for various model organisms. By combining the functionalities of Set Creator, Set Operator and Network Navigator, user can perform highly flexible and interactive GSA by creating a new gene list by any combination of existing gene sets (intersection, union and difference) or expanding genes interactively along the molecular networks such as protein-protein interaction and TF-target. We also demonstrate the utility of our interactive and cross-species GSA implemented in gsGator by several usage examples for interpreting genome-wide association study (GWAS) results. gsGator is freely available at http://gsGator.ewha.ac.kr.

Conclusions

Interactive and cross-species GSA in gsGator greatly extends the scope and utility of GSA, leading to novel insights via conserved functional gene modules across different species.

MiRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting

Biogenesis and molecular function are two key subjects in the field of microRNA (miRNA) research. Deep sequencing has become the principal technique in cataloging of miRNA repertoire and generating expression profiles in an unbiased manner. Here, we describe the miRGator v3.0 update (http://mirgator.kobic.re.kr) that compiled the deep sequencing miRNA data available in public and implemented several novel tools to facilitate exploration of massive data. The miR-seq browser supports users to examine short read alignment with the secondary structure and read count information available in concurrent windows. Features such as sequence editing, sorting, ordering, import and export of user data would be of great utility for studying iso-miRs, miRNA editing and modifications. miRNA-target relation is essential for understanding miRNA function. Coexpression analysis of miRNA and target mRNAs, based on miRNA-seq and RNA-seq data from the same sample, is visualized in the heat-map and network views where users can investigate the inverse correlation of gene expression and target relations, compiled from various databases of predicted and validated targets. By keeping datasets and analytic tools up-to-date, miRGator should continue to serve as an integrated resource for biogenesis and functional investigation of miRNAs.

Effects of different extrusion conditions on the chemical and toxicological fate of fumonisin B1 in maize: a short review

Fumonisin B1 (FB1) is a common mycotoxin found in maize and maize-based food products. Although FB1 is relatively heat stable and survives most thermal processes, extrusion cooking has been shown to be effective at reducing levels of the toxin in contaminated maize. This review summarises studies on the chemical and toxicological fate of FB1 in maize extruded under different conditions. Overall, these studies indicate that stability of FB1 depends on the extrusion conditions, e.g. temperature and screw speed, and that the presence of reducing sugars augment apparent loss of the toxin. The chemical fate of FB1 was investigated by measuring FB1, hydrolysed FB1, and N-substituted FB1 compounds with a mass balance approach while the relative toxicity was determined by rat feeding trials. FB1 in contaminated grits was reduced by 21-37% and 77-87% in the absence and presence of 10% (w/w) glucose, respectively, during single-screw extrusion. Greater reductions of 64-72% and 89-94% were achieved by twin-screw extrusion. Mass balance analysis showed that most of the FB1 in grits extruded without glucose was recovered as FB1, whereas the FB1-glucose reaction product, N-(deoxy-D-fructos-1-yl)-fumonisin B1 was the prevalent form after extrusion with glucose. 23 to 38% of FB1 in extruded grits with and without added glucose was bound to component(s) of the maize grits. Only 37-46% of FB1 present in unextruded grits could be recovered as one of the fumonisin species (hydrolysed FB1, N-substituted FB1 compounds) or as matrix-bound forms in extruded grits. Reduced FB1 concentrations in extruded grits and the even lower concentrations in grits extruded with glucose resulted in a dose-dependent reduction of toxicity as shown by the less severe apoptotic lesions and sphingolipid effects that were found in the kidneys of rats. In summary, extrusion processing, especially with glucose supplementation, is potentially useful to reduce FB1 concentrations and toxicity of contaminated maize.

Construction of killer wine yeast strain

A double-stranded RNA plasmid which confers the superkiller phenotype was transferred into a wine yeast (Montrachet strain 522) and its leucine-requiring derivative (strain 694) by cytoduction, using the protoplast fusion technique. The killer wine yeast constructed completely suppressed the growth of killer-sensitive strains of Saccharomyces cerevisiae in yeast extract-peptone-glucose medium at pH 4.5, whereas the killer effect was somewhat decreased at pH 3.5. The wine yeast harboring the killer factor also inhibited the growth of killer-sensitive cells satisfactorily when it was grown in grape juice.

Natural occurrence of aflatoxins in Korean meju

Aflatoxin B1 (AFB1) was found in 35 of 60 (58.3%) meju samples with an average concentration of 7.3 ng/g by ELISA. Contamination of AFB1 was confirmed in 25 of 60 samples (41.6%) using HPLC, with an average concentration of 6.9 ng/g. Mean recoveries from meju ranged from 107% to 170% for AFB1 using ELISA at a spiking range of 1 to 50 ng/g. Over the same range, recoveries using HPLC were from 70% to 83%. The levels of AFB1 determined by ELISA and by HPLC demonstrated a close relationship between the two methods (r2 = 0.9324) employed in this study. In order to evaluate the potential health risks of AFB1 on Koreans consuming meju, we calculated the estimated probable daily intake (PDI) based on the average contamination levels and compared it with the estimated tolerable daily intake (TDI). The PDIs of AFB1 from kanjang and dwenjang were determined to be 0.04 and 0.21 ng/kg bw/day, respectively, and were higher than TDIs.

Occurrence of aflatoxin M1 in Korean dairy products determined by ELISA and HPLC

The occurrence of aflatoxin M1 (AFM1) in pasteurized milk and dairy products was investigated by using direct competitive enzyme-linked immunosorbent assay (ELISA) and high-performance liquid chromatography (HPLC). The recoveries of AFM1 from the samples spiked at levels between 5 and 500 pg/ml were 88.0-106.5% for pasteurized milk and 84.0-94.0% for yoghurt by ELISA. By HPLC, the recoveries were 103-120% for pasteurized milk and 87.0-93.0% for yoghurt. The limits of detection were found to be 2 pg/ml by ELISA and 10 pg/ml by HPLC. Among a total of 180 samples collected in Seoul, Korea, the incidence of AFM1 in pasteurized milk, infant formula, powdered milk and yoghurt was 76, 85, 75, and 83%, respectively, with a mean concentration of 18, 46, 200, and 29 pg/g, respectively, when determined by ELISA. These results obtained by ELISA were closely related to those by HPLC for AFM1 (r2 = 0.9783).

Enhanced Cloud Disruption by Magnetic Field Interaction

We present results from the first three-dimensional numerical simulations of moderately supersonic cloud motion through a tenuous, magnetized medium. We show that the interaction of the cloud with a magnetic field perpendicular to its motion has a great dynamical impact on the development of instabilities at the cloud surface. Even for initially spherical clouds, magnetic field lines become trapped in surface deformations and undergo stretching. The consequent field amplification that occurs there and, in particular, its variation across the cloud face then dramatically enhance the growth rate of Rayleigh-Taylor unstable modes, hastening the cloud disruption.

Stability of zearalenone during extrusion of corn grits

The effects of extrusion cooking on the stability of zearalenone (ZEN) in spiked (4.4 microg/g) food-grade corn grits were investigated using a twin screw extruder. A ground rice culture material containing a high level of ZEN was used to spike the corn grits. The extrusion variables were screw type (mixing and nonmixing), temperature (120, 140, and 160 degrees C), and moisture content (18, 22, and 26%). Both unextruded and extruded samples were analyzed for ZEN by high-performance liquid chromatography. Extrusion cooking of the corn grits resulted in significant reductions of ZEN in grits extruded with either mixing screws or nonmixing screws, but use of mixing screws was somewhat more effective (66 to 83%) overall than nonmixing screws (65 to 77%). Greater reduction of ZEN was observed at either 120 or 140 degrees C than at 160 degrees C. The moisture content of corn grits was not a significant factor affecting reduction of ZEN during extrusion with either mixing or nonmixing screws.

Effect of cycling temperatures on the production of deoxynivalenol and zearalenone by Fusarium graminearum NRRL 5883

The effects of three regimens of cycling incubation temperatures and incubation at constant 25 degrees C on the growth of Fusarium graminearum NRRL 5883 and production of deoxynivalenol (DON) and zearalenone (ZEN) on rice were compared. The effects of low-temperature stress were also studied by incubating rice cultures at a constant 15 degrees C for 4 weeks following incubation at constant 25 degrees C for 2 weeks. Both incubation temperature and time significantly (P < or = 0.05) affected growth of F. graminearum NRRL 5883 and production of DON and ZEN. The highest amount of free ergosterol (640 microg/g culture material) that was used as a measure of fungal growth was found in cultures incubated at temperatures cycling between 15 and 30 degrees C during a 6-week period. The highest amounts of DON (1,679 microg/g culture material) and ZEN (603 microg/g culture material) were produced in cultures incubated at a constant 25 degrees C for 2 weeks prior to incubation at a constant 15 degrees C for an additional 4 weeks. Under cycling incubation temperatures, maximum amounts of DON (850 microg/g culture material) and ZEN (98 microg/g culture material) were produced in cultures incubated at temperatures cycling between 15 and 30 degrees C for 6 weeks. Overall, there was no correlation between mold growth and production of either DON or ZEN. However, DON production and ZEN production were correlated.

Fumonisin B1 production by Fusarium moniliforme and Fusarium proliferatum as affected by cycling temperatures

The effects of temperatures cycling between 5 and 20 degrees C, 10 and 25 degrees C, and 15 and 30 degrees C on the production of fumonisin B1 (FB1) and ergosterol by Fusarium moniliforme and Fusarium proliferatum on rice was studied. Temperatures were cycled at 12-h intervals by manually moving cultures from one temperature to another. Constant temperature incubation at 25 degrees C and a low temperature stress were compared with the cycling temperature incubations. Low temperature stress was achieved by incubating rice cultures at 25 degrees C for 2 weeks followed by 15 degrees C for 4 weeks. The maximum yields of FB1 were found to be 247 microg/g by F. moniliforme at temperatures that cycled between 10 and 25 degrees C after 2 weeks and 284 microg/g by F. proliferatum when the temperatures cycled between 5 and 20 degrees C after 6 weeks. Ergosterol content of the rice cultures was also monitored. Overall, the two Fusarium species showed differences in production of FB1 and ergosterol under the various temperature treatments. The most notable differences were that the temperature treatments that stimulated greatest FB1 production were different for each species: cycling temperatures between 10 and 25 degrees C for F. moniliforme and cycling temperatures between 5 and 25 degrees C for F. proliferatum. At most temperatures, F. proliferatum produced more ergosterol than F. moniliforme. Maximum production of ergosterol by F. proliferatum occurred at 6 weeks, with temperatures that cycled between 10 and 25 degrees C, whereas F. moniliforme produced maximum amounts of ergosterol at 6 weeks, with temperatures that cycled between 15 and 30 degrees C.