Characterizing the microbial communities inhabiting specimens is one of the primary objectives of microbiome studies. A short-read sequencing platform for reading partial regions of the 16S rRNA gene ...is most commonly used by reducing the cost burden of next-generation sequencing (NGS), but misclassification at the species level due to its length being too short to consider sequence similarity remains a challenge. Loop Genomics recently proposed a new 16S full-length-based synthetic long-read sequencing technology (sFL16S). We compared a 16S full-length-based synthetic long-read (sFL16S) and V3-V4 short-read (V3V4) methods using 24 human GUT microbiota samples. Our comparison analyses of sFL16S and V3V4 sequencing data showed that they were highly similar at all classification resolutions except the species level. At the species level, we confirmed that sFL16S showed better resolutions than V3V4 in analyses of alpha-diversity, relative abundance frequency and identification accuracy. Furthermore, we demonstrated that sFL16S could overcome the microbial misidentification caused by different sequence similarity in each 16S variable region through comparison the identification accuracy of Bifidobacterium, Bacteroides, and Alistipes strains classified from both methods. Therefore, this study suggests that the new sFL16S method is a suitable tool to overcome the weakness of the V3V4 method.
The recurrent neural network (RNN) model, which is a deep-learning network that can memorize past information, is used in this paper to memorize continuous movements in indoor positioning to reduce ...positioning error. To use an RNN model in Wi-Fi-fingerprint based indoor positioning, data set must be sequential. However, Wi-Fi fingerprinting only saves the received signal strength indicator for a location, so it cannot be used as RNN data. For this reason, we propose a movement path data generation technique that generates data for an RNN model for sequential positioning from Wi-Fi fingerprint data. Movement path data can be generated by creating an adjacency list for Wi-Fi fingerprint location points. However, creating an adjacency matrix for all location points requires a large amount of computation. This problem is solved by dividing indoor environment by K-means clustering and creating a cluster transition matrix based on the center of each cluster.
Colorectal cancer is driven by the accumulation of driver mutations, but the contributions of specific mutations to different steps in malignant progression are not fully understood. In this study, ...we generated mouse models harboring different combinations of key colorectal cancer driver mutations (
) in intestinal epithelial cells to comprehensively investigate their roles in the development of primary tumors and metastases.
mutation caused intestinal adenomas and combination with
mutation or
deletion induced submucosal invasion. The addition of
mutation yielded epithelial-mesenchymal transition (EMT)-like morphology and lymph vessel intravasation of the invasive tumors. In contrast, combinations of
with
and
mutation were insufficient for submucosal invasion, but still induced EMT-like histology. Studies using tumor-derived organoids showed that
was critical for liver metastasis following splenic transplantation, when this mutation was combined with either
plus
or
deletion, with the highest incidence of metastasis displayed by tumors with a
genotype. RNA sequencing analysis of tumor organoids defined distinct gene expression profiles characteristic for the respective combinations of driver mutations, with upregulated genes in
tumors found to be similarly upregulated in specimens of human metastatic colorectal cancer. Our results show how activation of Wnt and Kras with suppression of TGFβ signaling in intestinal epithelial cells is sufficient for colorectal cancer metastasis, with possible implications for the development of metastasis prevention strategies.
These findings illuminate how key driver mutations in colon cancer cooperate to drive the development of metastatic disease, with potential implications for the development of suitable prevention strategies.
.
Recently, various application fields utilizing Wi-Fi fingerprint data have been under research. However, fingerprint data collected from a specific location does not include relevant information, ...such as continuity. Therefore, most indoor positioning technologies predict the user’s location based on location signals collected at specific points within the indoor space, without taking into account the user’s movements. Hence, there is a need for technology that improves the accuracy of indoor positioning while moving. This paper proposes a technique to generate movement path data by applying the concepts of “BB” and “Grid Cell” from computer vision to Wi-Fi fingerprint data. This approach represents data points as bounding boxes (BBs), then establishes grid cells and clusters of these BBs to generate adjacency information. Subsequently, movement path data are created based on this information. We utilized the movement path information generated from the dataset as training data for machine learning and introduced an enhanced indoor positioning technology. First, the experiments in this paper assessed the performance of the proposed technology based on the number of paths in the LSTM model. Second, the performance of clustering methods was compared through experiments. Finally, we evaluated the performance of various machine learning models. The experimental results confirmed a maximum accuracy of 94.48% when determining the location based on route information. Clustering performance improved accuracy by up to 3%. In comparative experiments with machine learning models, accuracy improved by up to 2.8%.
•First draft genome of the popular shiitake mushroom, Lentinula edodes B17.•The genome consists of 46.1Mb genome comprising 13,028 predicted gene models.•Genes predicted to encode amino acids ...metabolisms, lignocellulolytic enzymes and 1,3-beta-glucanases.
Lentinula edodes, the popular shiitake mushroom, is one of the most important cultivated edible mushrooms. It is used as a food and for medicinal purposes. Here, we present the 46.1Mb draft genome of L. edodes, comprising 13,028 predicted gene models. The genome assembly consists of 31 scaffolds. Gene annotation provides key information about various signaling pathways and secondary metabolites. This genomic information should help establish the molecular genetic markers for MAS/MAB and increase our understanding of the genome structure and function.
Lentinula edodes is one of the most popular edible mushroom species in the world and contains useful medicinal components, such as lentinan. The light-induced formation of brown film on the ...vegetative mycelial tissues of L. edodes is an important process for ensuring the quantity and quality of this edible mushroom. To understand the molecular mechanisms underlying this critical developmental process in L. edodes, we characterized the morphological phenotypic changes in a strain, Chamaram, associated with abnormal brown film formation and compared its genome-wide transcriptional features.
In the present study, we performed genome-wide transcriptome analyses of different vegetative mycelium growth phenotypes, namely, early white, normal brown, and defective dark yellow partial brown films phenotypes which were exposed to different light conditions. The analysis revealed the identification of clusters of genes specific to the light-induced brown film phenotypes. These genes were significantly associated with light sensing via photoreceptors such as FMN- and FAD-bindings, signal transduction by kinases and GPCRs, melanogenesis via activation of tyrosinases, and cell wall degradation by glucanases, chitinases, and laccases, which suggests these processes are involved in the formation of mycelial browning in L. edodes. Interestingly, hydrophobin genes such as SC1 and SC3 exhibited divergent expression levels in the normal and abnormal brown mycelial films, indicating the ability of these genes to act in fruiting body initiation and formation of dikaryotic mycelia. Furthermore, we identified the up-regulation of glycoside hydrolase domain-containing genes in the normal brown film but not in the abnormal film phenotype, suggesting that cell wall degradation in the normal brown film phenotype is crucial in the developmental processes related to the initiation and formation of fruiting bodies.
This study systematically analysed the expression patterns of light-induced browning-related genes in L. edodes. Our findings provide information for further investigations of browning formation mechanisms in L. edodes and a foundation for future L. edodes breeding.
The use of alternative biocides has increased due to their economic and ecological relevance. Although data regarding the toxicity of commercial alternative biocides in marine organisms are ...accumulating, little is known about their toxic pathways or mechanisms. To compare the toxic effects of commercial alternative biocides on non-target pelagic fish (flounder) embryos, we investigated the adverse effects of developmental malformation and transcriptional changes. Three biocides including Diuron, Irgarol 1051® and Sea-Nine 211® produced a largely overlapping suite of developmental malformations, including tail-fin fold defects and dorsal body axis curvature. In our test, the potencies of these biocides were ranked in the following order with respect to malformation and mortalities: Sea-Nine 211® > Irgarol 1051® > Diuron. Consistent with the toxicity rankings, the expression of genes related to heart formation was greater in embryonic flounder exposed to Sea-Nine 211® than in those exposed to Irgarol 1051® or Diuron, while expression of genes related to fin malformation was greater in the Irgarol 1051® exposure group. In analyses of differential gene expression (DEG) profiles (fold change of genes with a cutoff P < 0.05) by high-throughput sequencing (RNA-seq), genes associated with nervous system development, transmembrane transport activity, and muscle cell development were significantly changed commonly. Embryos exposed to Diuron showed changes related to cellular protein localization, whereas genes associated with immune system processes were up-regulated significantly in embryos exposed to Irgarol 1051®. Genes related to actin filament organization and embryonic morphogenesis were up-regulated in embryos exposed to Sea-Nine 211®. Overall, our study provides a better understanding of the overlapping and unique developmental toxic effects of three commercial booster biocides through transcriptomic analyses in a non-target species, embryonic flounder.
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•Developmental defects of the most commercially used booster biocides were investigated on non-target marine species.•Sea-Nine 211® was most developmental toxic biocides among three biocides regarding malformation and mortalities analysis.•Three biocides were produced common toxic effects associated with nervous system development.•Genes related to immune system processes were variated in embryos exposed to Irgarol 1051®.•Genes related to embryonic morphogenesis were up-regulated in embryos exposed to Sea-Nine 211.
Most pollen analysis in Korea has focused on the Holocene Epoch, because pre-last glacial maximum terrestrial archives suitable for palynological study in the Korean Peninsula are limited. Thus, to ...verify the responses of vegetation to climate changes over the orbital timescales, analysis of pollen in marine sediments is needed. Here, we present the pollen record of hemipelagic sediments of core DD09-ST21 obtained from the northern Ulleung Basin in the East Sea. The palynofloral assemblages were dominated by warm temperate broadleaved trees and boreal conifers during interglacial and glacial periods, respectively. We also demonstrated that bisaccate pollen and herbaceous pollen in the palynological sequence can be used as indicators of the variation in the East Asian winter monsoon (EAWM) intensity during the last glacial period and freshwater inflow into the East Sea, respectively. During glacial periods, the EAWM intensified in response to weakening of the summer insolation at 60° N, while freshwater influx into the East Sea decreased due to a decrease in precipitation.
•Paleovegetation changes in the East Sea during the last glacial period were reconstructed.•Changes of herbaceous pollen abundance correspond with fluctuations of freshwater inflow into the East Sea.•Bisaccate pollen was used as an indicator of East Asian winter monsoon intensity.
Plants memorize previous pathogen attacks and are "primed" to produce a faster and stronger defense response, which is critical for defense against pathogens. In plants, cytosines in transposons and ...gene bodies are reported to be frequently methylated. Demethylation of transposons can affect disease resistance by regulating the transcription of nearby genes during defense response, but the role of gene body methylation (GBM) in defense responses remains unclear.
Here, we find that loss of the chromatin remodeler decrease in DNA methylation 1 (ddm1) synergistically enhances resistance to a biotrophic pathogen under mild chemical priming. DDM1 mediates gene body methylation at a subset of stress-responsive genes with distinct chromatin properties from conventional gene body methylated genes. Decreased gene body methylation in loss of ddm1 mutant is associated with hyperactivation of these gene body methylated genes. Knockout of glyoxysomal protein kinase 1 (gpk1), a hypomethylated gene in ddm1 loss-of-function mutant, impairs priming of defense response to pathogen infection in Arabidopsis. We also find that DDM1-mediated gene body methylation is prone to epigenetic variation among natural Arabidopsis populations, and GPK1 expression is hyperactivated in natural variants with demethylated GPK1.
Based on our collective results, we propose that DDM1-mediated GBM provides a possible regulatory axis for plants to modulate the inducibility of the immune response.
Schisandra chinensis, an ancient member of the most basal angiosperm lineage which is known as the ANITA, is a fruit-bearing vine with the pharmacological effects of a multidrug system, such as ...antioxidant, anti-inflammatory, cardioprotective, neuroprotective, anti-osteoporosis effects. Its major bioactive compound is represented by lignans such as schisandrin. Molecular characterization of lignan biosynthesis in S. chinensis is of great importance for improving the production of this class of active compound. However, the biosynthetic mechanism of schisandrin remains largely unknown.
To understand the potential key catalytic steps and their regulation of schisandrin biosynthesis, we generated genome-wide transcriptome data from three different tissues of S. chinensis cultivar Cheongsoon, including leaf, root, and fruit, via long- and short-read sequencing technologies. A total of 132,856 assembled transcripts were generated with an average length of 1.9 kb and high assembly completeness. Overall, our data presented effective, accurate gene annotation in the prediction of functional pathways. In particular, the annotation revealed the abundance of transcripts related to phenylpropanoid biosynthesis. Remarkably, transcriptome profiling during fruit development of S. chinensis cultivar Cheongsoon revealed that the phenylpropanoid biosynthetic pathway, specific to coniferyl alcohol biosynthesis, showed a tendency to be upregulated at the postfruit development stage. Further the analysis also revealed that the pathway forms a transcriptional network with fruit ripening-related genes, especially the ABA signaling-related pathway. Finally, candidate unigenes homologous to isoeugenol synthase 1 (IGS1) and dirigent-like protein (DIR), which are subsequently activated by phenylpropanoid biosynthesis and thus catalyze key upstream steps in schisandrin biosynthesis, were identified. Their expression was increased at the postfruit development stage, suggesting that they may be involved in the regulation of schisandrin biosynthesis in S. chinensis.
Our results provide new insights into the production and accumulation of schisandrin in S. chinensis berries and will be utilized as a valuable transcriptomic resource for improving the schisandrin content.
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