Differences in endocrine and reproductive responses to substance exposure across generations: highlighting the importance of complementary findings.

This article analyzes the results from 112 Extended One-Generation Reproductive Toxicity studies. The objective was to determine if test animals show consistent endocrine and reproductive effects within the same and across different generations and life stages. The analysis, grounded in a comprehensive Binary Matrix, included 530 observed effects and 193 unique, statistically significant associations. Associations' strength was quantified using Jaccard (J) coefficients to measure effect co-occurrence in the same study. Associated effects co-occur infrequently across the whole dataset (median J = 0.231). However, specific patterns emerged: associations of same effects across generations exhibited a higher strength (median J = 0.400) compared to associations of different effects (median J = 0.222). Notably, associations with effects observed in both the parental animals of the adult first filial generation (P1) and developing second filial generations (dF2) demonstrated J coefficients (with medians ranging from 0.300 to 0.430) that were approximately twofold higher than those of other associations. Consistently, equivalent life stage associations across generations revealed statistically significant higher association strengths for the P1 and dF2 generations (medians of 0.375 and 0.333, respectively) compared to other generations (medians of 0.200 and 0.174), possibly due to longer exposure duration and altered cross-talk between pregnant P1 dam and its conceptus. Overall, it is concluded that co-occurrence of associated effects in the same study is rather infrequent and that associations with effects in P1 and dF2 are stronger than all other associations. In general, the findings underscore the importance of independently analyzing each effect per generation due to the generally low co-occurrence rates of associated effects, challenging traditional expectations of generational continuity in toxic effects.

Standard medical ethnobotany of Kohistan, North Pakistan.

BACKGROUND: This study was exclusively focused on the documentation and cross-cultural evaluation of ethnomedicinal knowledge (EMK) within the diverse linguistic groups of Kohistan situated between the Himalayan and Hindukush Mountain ranges in the north Pakistan. METHODS: Data were gathered during the field survey (May 2022 to July 2023) through group conversations, semi-structured interviews, and on-site observation. Venn diagrams were employed to illustrate the comparative assessment of EMK, and different ethnobotanical indices were utilized to examine the data. RESULTS: A total of 96 wild medicinal plant species (MPs) belonging to 74 genera and 52 botanical families were documented. The most reported MPs belong to the family Polygonaceae (11 species), followed by Asteraceae (9 species) and Lamiaceae (8 species). The ethnomedicinal uses of Leontopodium himalayanum, Pedicularis oederi, Plocama brevifolia, Polypodium sibiricum, Pteridium esculentum, Sambucus wightiana, Solanum cinereum, Teucrium royleanum, Rhodiola integrifolia, Aconitum chasmanthum were reported for the first time in this region. Among the reported taxa herbaceous species were dominated (72%), followed by trees and shrubs (17% and 10%, respectively). Digestive problems (40 taxa and 114 use reports) and skin disorders (19 taxa and 549 use reports) were the most cited disease categories, whereas M. communis, M. longifolia, Ajuga integrifolia, Ziziphus jujuba, and Clematis grata exhibited the highest percentage fidelity levels. Out of 109 documented medicinal uses, a mere 12 were shared across all linguistic groups, and Bateri emerges as a notable outlier with the highest number of medicinal uses. In addition, a significant homogeneity was noted in the reported botanical taxa (61 species) among different linguistic groups. However, since the last decade biocultural heritage of Kohistan is facing multifaceted risks that need urgent attention. CONCLUSION: Our findings could be valuable addition to the existing stock of ethnomedicinal knowledge and may provide ethnopharmacological basis to novel drug discovery for preexisting and emerging diseases prioritizing detailed phytochemical profiling and the evaluation of bioactive potential.

Visualizing set relationships: EVenn's comprehensive approach to Venn diagrams.

Venn diagrams serve as invaluable tools for visualizing set relationships due to their ease of interpretation. Widely applied across diverse disciplines such as metabolomics, genomics, transcriptomics, and proteomics, their utility is undeniable. However, the operational complexity has been compounded by the absence of standardized data formats and the need to switch between various platforms for generating different Venn diagrams. To address these challenges, we introduce the EVenn platform, a versatile tool offering a unified interface for efficient data exploration and visualization of diverse Venn diagrams. EVenn (http://www.ehbio.com/test/venn) streamlines the data upload process with a standardized format, enhancing the capabilities for multimodule analysis. This comprehensive protocol outlines various applications of EVenn, featuring representative results of multiple Venn diagrams, data uploads in the centralized data center, and step-by-step case demonstrations. Through these functionalities, EVenn emerges as a valuable and user-friendly tool for the in-depth exploration of multiomics data.

Spatial distribution dynamics for Epimedium brevicornum Maxim. from 1970 to 2020.

At different time scales, a species will experience diverse distribution changes. For Epimedium brevicornum Maxim, the phenomenon is obvious, but the understanding of the spatial dynamics of E. brevicornum under distinct time scales is poor. In this study, we modeled the potential distribution for E. brevicornum for five time scales, 1970-1979, 1980-1989, 1990-1999, 2000-2009, and 2010-2019, with different occurrence data, and the Kuenm package was used to optimize the parameter combination. Then, SDM tools and a Venn diagram were utilized to simulate the changes in highly suitable areas and spatial dynamics, respectively. Comprehensive results show that temperature seasonality (BIO4, 37.54%) has the greatest effect on the distribution of E. brevicornum, followed by minimum temperature (TMIN, 21.42%). The areas of distribution for E. brevicornum are 35.06 × 105 km2, 25.7 × 105 km2, 67.64 × 105 km2, 27.29 × 105 km2, and 9.87× 105 km2, which are mainly concentrated in Gansu, Shaanxi, Shanxi, and Henan, respectively. In addition, the largest regions for expansion, stability, and contraction under various time scales are 5.6 × 105 km2, 3.54 × 105 km2, and 3.47 × 105 km2, respectively. These changes indicate that approximately 7.96% of the regions are highly stable, and three critical counties, Wanyuan, Chenggu, and Hechuan, and Xixiang, have become significant areas for migration. Overall, our results indicate that there are different spatial distribution patterns and dynamics for E. brevicornum for different time scales. Given these results, this study also proposes comprehensive strategies for the conservation and management of E. brevicornum, which will further improve the current resource utilization status.

Essential Oil Composition of Fruits of Eight Ferulago Species Growing in Türkiye and Multivariate Statistical Analyses.

In this study, the composition of the volatile oils obtained from the fruits of 8 Ferulago species (Ferulago cassia Boiss., F. isaurica Pesmen, F. humilis Boiss., F. macrosciadia Boiss. & Balansa, F. setifolia K.Koch, F. silaifolia (Boiss.) Boiss., F. syriaca Boiss., F. trojana Akalin & Pimenov) growing naturally in Türkiye were examined by means of GC/MS and GC-FID and α-pinene was determined to be present in the fruits of four species along with other monoterpenes as major components. Principal Component Analyses (PCA) and Hierarchical Cluster Analysis (HCA) was performed, utilizing ten major components in the eight essential oils. Also, a Venn diagram was used to demonstrate chemotaxonomical variations in the composition of the essential oils of eight Ferulago species.

Flavihumibacter fluminis sp. nov., a novel thermotolerant bacterium isolated from river silt.

A yellow, Gram-stain-positive, strictly aerobic, thermotolerant, non-motile and rod-shaped bacterial strain, designated RY-1T, was isolated from a silt sample of Fuyang River, Wuqiang County, Hengshui City, Hebei Province, PR China. Cells showed oxidase- and catalase-positive activities. Growth occurred at 20-45 °C (optimum, 37 °C) and pH 6.0-8.0 (optimum, pH 7.0), and in the presence of 0-1.5 % (w/v) NaCl (optimum, 0%). A phylogenetic tree based on 16S rRNA gene sequences revealed that strain RY-1T formed a phylogenetic lineage with Flavihumibacter members within the family Chitinophagaceae. A comparison of 16S rRNA gene sequences showed that strain RY-1T was most closely related to Flavihumibacter cheonanensis WS16T (98.6 %), Flavihumibacter sediminis CJ663T (97.7 %) and Flavihumibacter solisilvae 3-3T (97.6 %). The genome size of strain RY-1T was 4.71 Mb, and the DNA G+C content was 44.3  %. The average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values between strain RY-1T and reference strains were all lower than the threshold values for species delineation. Strain RY-1T contained menaquinone-7 and iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1G as the sole respiratory isoprenoid quinone and major cellular fatty acids (≥5 %), respectively. The major polar lipids consisted of phosphatidylethanolamine, three unidentified aminolipids and four unidentified lipids. According to the results of phenotypic, phylogenetic and chemotaxonomic characteristics, strain RY-1T represents a novel species of the genus Flavihumibacter, for which the name Flavihumibacter fluminis sp. nov. is proposed. The type strain is RY-1T (=GDMCC 1.2775T=JCM 34870T).

Lysobacter selenitireducens sp. nov., isolated from river sediment.

A Gram-stain-negative, yellow-pigmented, motile, flagellated and rod-shaped bacterium, designated as 13AT, was isolated from a river sediment sample of Fuyang River in Hengshui City, Hebei Province, PR China. Strain 13AT grew at 10-37 °C (optimum, 30 °C), at pH 5.0-11.0 (optimum, pH 7.0) and at 0-7 % (w/v) NaCl concentration (optimum, 0 %). Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain 13AT belongs to the genus Lysobacter, and was most closely related to Lysobacter spongiicola DSM 21749T (97.8 %), Lysobacter concretionis DSM 16239T (97.5 %), Lysobacter daejeonensis GIM 1.690T (97.3 %) and Lysobacter arseniciresistens CGMCC 1.10752T (96.9 %). Meanwhile, the type species Lysobacter enzymogenes ATCC 29487T was selected as a reference strain (95.2 %). The genomic size of strain 13AT was 3.0 Mb and the DNA G+C content was 69.0 %. The average nucleotide identity values between strain 13AT and each of the reference type strains L. spongiicola DSM 21749T, L. concretionis DSM 16239T, L. daejeonensis GIM 1.690T, L. arseniciresistens CGMCC 1.10752T and L. enzymogenes ATCC 29487T were 75.9, 76.1, 77.7, 78.0 and 73.2 %, respectively. The digital DNA-DNA hybridization values between strain 13AT and each of the reference type strains were 21.7, 22.2, 21.9, 22.7 and 23.2 %, respectively. The average amino acid identity values between strain 13AT and each of the reference type strains were 72.5, 72.9, 72.3, 75.0 and 69.2 %, respectively. The major fatty acids were iso-C15 : 0, iso-C16 : 0 and summed feature 9 (iso-C17 : 1 ω9c and/or C16 : 0 10-methyl). The sole respiratory quinone was identified as ubiquinone-8. The polar lipid profile contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid, an unidentified lipid, four unidentified phospholipids and two unidentified glycolipids. Based on the phenotypic, physiological, phylogenetic and chemotaxonomic data, strain 13AT represents a novel species of the genus Lysobacter, for which the name Lysobacter selenitireducens sp. nov. is proposed. The type strain is 13AT (=JCM 34786T=GDMCC 1.2722T).

Accuracy and Validity of Sharma's Venn Diagram Method for Assessment of Tibial Component Rotation in Total Knee Arthroplasty.

Background: Malrotation of the tibial component in a total knee replacement leads to anterior knee pain, patella dislocations, extensor mechanism disruptions, knee stiffness and prosthesis loosening. Techniques like free-floating technique, medial 1/3 rd of the tibial tubercle, medial border of the tibial tuberosity, Akagi's line, transcondylar line of tibia, posterior condylar line of tibia, midsulcus of tibial spines, curve on curve technique have been advocated. None of these have been shown to be accurate and reproducible. We developed a novel 'Sharma's Venn Diagram' method to assess the tibial component rotation. Methods: Fifty-two consecutive knee replacements were included in a prospective observational study. The average age of the study group was 53.6 years (48-76 years) Thirty-one were females and 3 were males. The patients were followed a minimum of one years (max 2 years, average 1.8 years). 'Sharma's Venn diagram Method (C)' was compared to free-floating method (F) and post-op CT scans using Berger protocol (B). Results: Tibial rotation calculated using Sharma's Venn diagram method (C) coincided with the final component placement in 50/52 knees. The free floating method (F) coincided with method (C) in 30/52 knees with an average 4.8° external rotation in 5 knees and an average of 5.2° internal rotation in 17 knees. Bland Altman method was used to compare method (C) with Method (F), The difference was statistically significant p < 0.0001. Conclusion: Sharma's Venn diagram method is reliable, accurate and easily reproducible by any surgeon performing tkr and correlates with postoperative 2D CT-based assessment of tibial component rotation. Level II Study: Prospective observational study.

Venn Diagrams May Indicate Erroneous Statistical Reasoning in Transcriptomics.

A common application of differential expression analysis is finding genes that are differentially expressed upon treatment in only one out of several groups of samples. One of the approaches is to test for significant difference in expression between treatment and control separately in the two groups, and then select genes that show statistical significance in one group only. This approach is then often combined with a gene set enrichment analysis to find pathways and gene sets regulated by treatment in only this group. Here we show that this procedure is statistically incorrect and that the interaction between treatment and group should be tested instead. Moreover, we show that gene set enrichment analysis applied to such incorrectly defined genes group-specific genes may result in misleading artifacts. Due to the presence of false negatives, genes significant in one, but not the other group are enriched in gene sets which correspond to the overall effect of the treatment. Thus, the results appear related to the problem at hand, but do not reflect the group-specific effect of a treatment. A literature search revealed that more than a quarter of papers which used a Venn diagram to illustrate the results of separate differential analysis have also applied this incorrect reasoning.

A Cross-Cultural Analysis of Plant Resources among Five Ethnic Groups in the Western Himalayan Region of Jammu and Kashmir.

Plant resources have always been valuable in human life, and many plant species are used in medicine, food, and ritual, and resource utilization is closely related to cultural diversity. Our study was conducted from June 2019 to April 2021, during which we aimed to document the local knowledge of plant resources of five ethnic groups, i.e., the Gujjar, Bakarwal, Kashmiri, Pahari, and Dogra communities of the Jammu and Kashmir (J&K) region, Western Himalayas. Through semi-structured interviews (N = 342) and group discussions (N = 38), we collected data on the ethnobotanical uses of plant resources. The data was subjected to hierarchical cluster analysis and ordination techniques (Principal Component Analysis) via, R software of version 4.0.0. Traditional uses were classified into three groups, i.e., single-, double-, and multi-use groups. The study recorded a total of 127 plant species, belonging to 113 genera and distributed among 64 botanical families. The dominant plant families were the Asteraceae, with 8% of all species, followed by Lamiaceae (6%), Polygonaceae (5%) and Ranunculaceae (4%). The recorded plant taxa were frequently used for medicine (51.4% responses), followed by food (14.9%), and fodder (9.5%). Principal component analysis (PCA) separated three groups of provisioning services depending on plant consumption preference levels. Comparative analysis showed remarkable similarities in plant uses (food, medicinal) among the Gujjar and Bakarwal ethnic groups, as both groups share a common culture. Some plants like Azadirachta indica, Brassica campestris, Ulmus wallichiana, Amaranthus blitum, and Celtis australis were also used for magico-religious purposes. We also recorded some medicinal uses that are new to the ethnobotanical literature of the J&K Himalayas, such as for Betula utilis, Sambucus wightiana, and Dolomiaea macrocephala, in our case for example local medicinal recipe, which is derived from Dolomiaea macrocephala, often known as Nashasta, used to treat weakness, back pain, and joint pain. Similarly, we also recorded new food uses for Eremurus himalaicus. Moreover, we also observed some plants for instance, Fragaria nubicola, Betula utilis and Juniperus communis have spiritual significance (i.e., amulets and scrolls) for this part of the Himalayan region. The present study provides a useful tool for resource management and can help in developing scientifically informed strategies for the conservation of plant resources.

Relationships Between WUT (Body Weight, Urine Color, and Thirst Level) Criteria and Urine Indices of Hydration Status.

BACKGROUND: A Venn diagram consisting of percentage body mass loss, urine color, and thirst perception (weight, urine, thirst [WUT]) has been suggested as a practical method to assess hydration status. However, no study to date has examined relationships between WUT and urine hydration indices. Thus, the purpose of this study was to investigate relationships between urine specific gravity, urine osmolality, and the WUT criteria. HYPOTHESIS: Urine specific gravity and urine osmolality indicate hypohydration when the WUT criteria demonstrate hypohydration (≥2 markers). STUDY DESIGN: Laboratory cohort study. LEVEL OF EVIDENCE: Level 3. METHODS: A total of 22 women (mean ± SD; age, 20 ± 1 years; mass, 65.4 ± 12.6 kg) and 21 men (age, 21 ± 1 years; body mass, 78.7 ± 14.6 kg) participated in this study. First morning body mass, urine color, urine specific gravity, urine osmolality, and thirst level were collected for 10 consecutive days in a free-living situation. Body mass loss >1%, urine color >5, and thirst level ≥5 were used as the dehydration thresholds. The number of markers that indicated dehydration levels were counted and categorized into either 3, 2, 1, or 0 WUT markers that indicated dehydration. One-way analysis of variance with Tukey pairwise comparisons was used to assess the differences in urine specific gravity and urine osmolality between the different number of WUT markers. RESULTS: Urine specific gravity in 3 WUT markers (mean ± SD [effect size], 1.021 ± 0.007 [0.57]; P = 0.025) and 2 WUT markers (1.019 ± 0.010 [0.31]; P = 0.026) was significantly higher than 1 WUT marker (1.016 ± 0.009). Urine mosmolality in 2 WUT markers (705 ± 253 mOsmol [0.43]; P = 0.018) was significantly higher than 1 WUT (597 ± 253 mOsmol). Meeting at 3 WUT resulted in specificity of 0.956 and at 0 WUT resulted in sensitivity of 0.937 for urine osmolality>700mOsm. CONCLUSION: These results suggest that when 3 WUT markers are met, urine specific gravity and urine osmolality indicated hypohydration and 0 WUT represents a high likelihood of euhydration. 1 and 2 WUT values are indeterminate of hydration status. The WUT criterion is a useful tool to use in field settings to assess hydration status when first morning urine sample was used. CLINICAL RELEVANCE: Athletes, coaches, sports scientists, and medical professionals can use WUT criteria to monitor dehydration with reduced cost and time.

Identification of hub genes in common cancers of women in India and targeting for the search of anticancer agent from Punica granatum phytoconstituent using interaction network analysis and virtual screening.

Cancer is one of the most dreadful diseases across the globe, with the advancement in this field a great advent has been achieved in treating cancer by various therapies like chemotherapy, radiation therapy, hormone therapy, gene therapy, and many more but also the most serious concern associated with the available treatments are the toxicities or the side effects linked to them, apart from this the treatment of many malignancies are still not available, because of these such issues, tremendous research is still going on in the whole world to find a better and more potent treatment option for cancer. Cancer develops due to the synergistic effects of both genetic and epigenetic factors. The mutations that change the normal functioning of the genes are responsible for cancer. Various genes are associated with cancers; many genes are commonly found to be mutated in diverse cancer types. In the present work, the genetic co-relation among the top five common cancers in Indian women has tried to be established, after that the identification of the hub gene was carried out with the use of CytoHubba module of Cytoscape. The hub gene product signaling pathway was then targeted for molecular docking with phytoconstituents of Punica granatum while the stability of the docked protein and ligand complex was validated through Molecular Dynamics Simulation.Communicated by Ramaswamy H. Sarma.

Using Venn Diagrams to Evaluate Digital Contact Tracing: Panel Survey Analysis.

BACKGROUND: Mitigation of the spread of infection relies on targeted approaches aimed at preventing nonhousehold interactions. Contact tracing in the form of digital proximity tracing apps has been widely adopted in multiple countries due to its perceived added benefits of tracing speed and breadth in comparison to traditional manual contact tracing. Assessments of user responses to exposure notifications through a guided approach can provide insights into the effect of digital proximity tracing app use on managing the spread of SARS-CoV-2. OBJECTIVE: The aim of this study was to demonstrate the use of Venn diagrams to investigate the contributions of digital proximity tracing app exposure notifications and subsequent mitigative actions in curbing the spread of SARS-CoV-2 in Switzerland. METHODS: We assessed data from 4 survey waves (December 2020 to March 2021) from a nationwide panel study (COVID-19 Social Monitor) of Swiss residents who were (1) nonusers of the SwissCovid app, (2) users of the SwissCovid app, or (3) users of the SwissCovid app who received exposure notifications. A Venn diagram approach was applied to describe the overlap or nonoverlap of these subpopulations and to assess digital proximity tracing app use and its associated key performance indicators, including actions taken to prevent SARS-CoV-2 transmission. RESULTS: We included 12,525 assessments from 2403 participants, of whom 50.9% (1222/2403) reported not using the SwissCovid digital proximity tracing app, 49.1% (1181/2403) reported using the SwissCovid digital proximity tracing app and 2.5% (29/1181) of the digital proximity tracing app users reported having received an exposure notification. Most digital proximity tracing app users (75.9%, 22/29) revealed taking at least one recommended action after receiving an exposure notification, such as seeking SARS-CoV-2 testing (17/29, 58.6%) or calling a federal information hotline (7/29, 24.1%). An assessment of key indicators of mitigative actions through a Venn diagram approach reveals that 30% of digital proximity tracing app users (95% CI 11.9%-54.3%) also tested positive for SARS-CoV-2 after having received exposure notifications, which is more than 3 times that of digital proximity tracing app users who did not receive exposure notifications (8%, 95% CI 5%-11.9%). CONCLUSIONS: Responses in the form of mitigative actions taken by 3 out of 4 individuals who received exposure notifications reveal a possible contribution of digital proximity tracing apps in mitigating the spread of SARS-CoV-2. The application of a Venn diagram approach demonstrates its value as a foundation for researchers and health authorities to assess population-level digital proximity tracing app effectiveness by providing an intuitive approach for calculating key performance indicators.

Oak Species Quercus robur L. and Quercus petraea Liebl. Identification Based on UHPLC-HRMS/MS Molecular Networks.

Two species of oak are dominant in French forests: pedunculate oak (Quercus robur L.) and sessile oak (Quercus petraea Liebl.). Their differentiation is not straightforward but is essential to better understand their respective molecular content in order to better valorize them. Thus, to improve oak species identification, an untargeted UHPLC-HRMS/MS method associated with a two-step data treatment was developed to analyze a wide range of specialized metabolites enabling the comparison of both species of oak extracts. Pooled extracts from sessile and pedunculate oaks, composed of extracts from several trees of pure species from various origins, were compared using first the Venn diagram, as a quick way to get an initial idea of how close the extracts are, and then using a molecular network to visualize, on the one hand, the ions shared between the two species and, on the other hand, the compounds specific to one species. The molecular network showed that the two species shared common clusters mainly representative of tannins derivatives and that each species has specific molecules with similar fragmentation patterns, associated in specific clusters. This methodology was then applied to compare these two pooled extracts to unknown individuals in order to determine the species. The Venn diagram allowed for the quick presumption of the species of the individual and then the species could be assigned more precisely with the molecular network, at the level of specific clusters. This method, developed for the first time, has several interests. First, it makes it possible to discriminate the species and to correctly assign the species of unknown samples. Moreover, it gave an overview of the metabolite composition of each sample to better target oak tree utilization and valorization.

ggVennDiagram: An Intuitive, Easy-to-Use, and Highly Customizable R Package to Generate Venn Diagram.

Venn diagrams are widely used diagrams to show the set relationships in biomedical studies. In this study, we developed ggVennDiagram, an R package that could automatically generate high-quality Venn diagrams with two to seven sets. The ggVennDiagram is built based on ggplot2, and it integrates the advantages of existing packages, such as venn, RVenn, VennDiagram, and sf. Satisfactory results can be obtained with minimal configurations. Furthermore, we designed comprehensive objects to store the entire data of the Venn diagram, which allowed free access to both intersection values and Venn plot sub-elements, such as set label/edge and region label/filling. Therefore, high customization of every Venn plot sub-element can be fulfilled without increasing the cost of learning when the user is familiar with ggplot2 methods. To date, ggVennDiagram has been cited in more than 10 publications, and its source code repository has been starred by more than 140 GitHub users, suggesting a great potential in applications. The package is an open-source software released under the GPL-3 license, and it is freely available through CRAN (https://cran.r-project.org/package=ggVennDiagram).

Volatile profiles of two genotype Agaricus bisporus species at different growth stages.

The compositions of volatile compounds in fresh mushrooms varied with their genotype species, maturity and growth conditions. This study aimed to identify volatile compounds in five growth stages of two genotype (A15 and W192) Agaricus bisporus species and used mathematical analysis to explain result. A total of 67 different compounds were identified by HS-SPME-GC-MS. Nine key-aroma substances including alcohols, ketones and aldehydes were found by Venn diagram and odor activity values. This improved method can be quickly analyzed the different samples characteristic volatile compounds without time consuming through quantifications. The sum of aroma compounds concentration was highest in the seedling stage (0.5-1.5 cm) and decreased with growth. Meanwhile, benzene acetaldehyde and 3-octanone as dominate parts of overall-aroma maybe affected by benzaldehyde and 3-nonanon during the mushroom growth. Since the harvest stage (3-5 cm). The mushroom flavor of A15 is more abundant than that of W192, therefore, A15 is more suitable for industrial production.

Quantitative Cell Subset Analysis Using Antibody Microarrays.

The expression patterns of surface antigens are associated with the differentiation status and functional characteristics of mammalian cells. To analyze the surface antigen expression pattern in a high-throughput manner, antibody microarrays have been developed by several groups, including ours. This analysis can be performed using cell-binding assays on microarrays; moreover, this approach has advantages over conventional flow cytometry (FCM). Unlike FCM, the microarray-based method cannot evaluate the concurrent expression of more than two surface antigens on a single cell, and therefore, it cannot be used for cell subset analysis. To overcome this drawback, we prepared an antibody microarray with spots presenting co-immobilized multiple antibodies together with spots presenting each antibody separately. The co-immobilized spots are expected to be reactive for every surface antigen specific to the co-immobilized antibodies. In addition, the concept of an algebra of sets is incorporated into the derivation of quantitative data regarding cell subsets. Here, taking cell subsets with respect to two surface antigens as the simplest example, antibody microarrays were prepared and initially subjected to validation studies to verify the accuracy of cell-binding assays. Quantitative subset analysis was performed using antibody microarrays prepared using the anti-CD13 and anti-CD49f antibodies. For model populations that consisted of discrete subsets, THP-1, HL-60, CCRF-CEM, and Ramos cell lines were used because they were found by FCM to have a singular phenotype, that is, CD13+CD49f+, CD13+CD49f-, CD13-CD49f+, and CD13-CD49f-, respectively. Five populations were prepared by mixing these cells at various ratios and analyzed for their subsets using microarrays. The results showed that the experimentally determined abundance ratios of the four model subsets were in good agreement with the predetermined abundance ratios, which provided the proof of principle for the new method in the quantitative subset analysis.

Neuronal Development-Related miRNAs as Biomarkers for Alzheimer's Disease, Depression, Schizophrenia and Ionizing Radiation Exposure.

Radiation exposure may induce Alzheimer's disease (AD), depression or schizophrenia. A number of experimental and clinical studies suggest the involvement of miRNA in the development of these diseases, and also in the neuropathological changes after brain radiation exposure. The current literature review indicated the involvement of 65 miRNAs in neuronal development in the brain. In the brain tissue, blood, or cerebral spinal fluid (CSF), 11, 55, or 28 miRNAs are involved in the development of AD respectively, 89, 50, 19 miRNAs in depression, and 102, 35, 8 miRNAs in schizophrenia. We compared miRNAs regulating neuronal development to those involved in the genesis of AD, depression and schizophrenia and also those driving radiation-induced brain neuropathological changes by reviewing the available data. We found that 3, 11, or 8 neuronal developmentrelated miRNAs from the brain tissue, 13, 16 or 14 miRNAs from the blood of patient with AD, depression and schizophrenia respectively were also involved in radiation-induced brain pathological changes, suggesting a possibly specific involvement of these miRNAs in radiation-induced development of AD, depression and schizophrenia respectively. On the other hand, we noted that radiationinduced changes of two miRNAs, i.e., miR-132, miR-29 in the brain tissue, three miRNAs, i.e., miR- 29c-5p, miR-106b-5p, miR-34a-5p in the blood were also involved in the development of AD, depression and schizophrenia, thereby suggesting that these miRNAs may be involved in the common brain neuropathological changes, such as impairment of neurogenesis and reduced learning memory ability observed in these three diseases and also after radiation exposure.

FunRich enables enrichment analysis of OMICs datasets.

High-throughput methods to profile the genome, transcriptome, proteome and metabolome of various systems has become a routine in multiple research laboratories around the world. Hence, to analyse and interpret these heterogenous datasets user-friendly bioinformatics tools are needed. Here, we discuss FunRich tool that enables biologists to perform functional enrichment analysis on the generated datasets. Users can perform enrichment analysis with a variety of background databases and have complete control in updating or modifying the content in most of the databases. Specifically, users can download and update the background database from UniProt at any time thereby allowing a robust background database that can support annotations from >18 taxonomies. Users can create customizable Venn diagrams, pie charts, bar graphs and heatmaps of publication quality for their datasets using FunRich (http://www.funrich.org). Overall, FunRich tool is user-friendly and enables users to perform various analysis on their datasets with minimal or no aid from bioinformaticians.

Roseomonas selenitidurans sp. nov., isolated from urban soil, and emended description of Roseomonas frigidaquae.

An aerobic, non-motile, Gram-stain-negative, pink, convex, coccobacilli-shaped, mesophilic bacterium, designated strain BU-1T, was isolated from an urban soil sample from Zibo city, Shandong province, PR China. The strain grew at 20-37 °C (optimum, 30 °C), pH 5-10 (optimum, pH 7) and growth occurred with 0-2 % (w/v) NaCl (optimally with 0.5 %). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that BU-1T was closely related to members of the genus Roseomonas and had highest 16S rRNA gene sequence similarities with Roseomonas frigidaquae JCM 15073T (97.8 %), Roseomonas tokyonensis JCM 14634T (96.9 %), Roseomonas stagni JCM 15034T (96.5 %), and Roseomonas riguiloci JCM 17520T (95.9 %). BU-1T also formed a subcluster with R. frigidaquae JCM 15073T and R. stagni JCM 15034T in phylogenetic trees based on genomic sequences. The genome size of BU-1T was 5.79 Mb and the DNA G+C content was 71.7 %. ANI, dDDH and AAI values between BU-1T and R. frigidaquae JCM 15073T were 84.0, 27.2 and 86.7 %, respectively. Furthermore, the genome of BU-1T contained 5446 predicted protein coding genes and 4945 (90.8%) of them had classifiable functions. BU-1T contained Q-10 as the main ubiquinone. The predominant fatty acids (>10 %) were summed feature 3, summed feature 8 and C16:0. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and five unidentified aminolipids. Combined data from phenotypic, phylogenetic and chemotaxonomic studies indicated that strain BU-1T is a representative of a novel species of the genus Roseomonas. Since strain BU-1T can reduce highly toxic selenite [Se(IV)] to low toxicity elemental selenium [Se(0)], the name Roseomonas selenitidurans sp. nov. is proposed. The type strain is BU-1T (=KACC 21750T =GDMCC 1.1776T).