Genome assembly and visualization of aggressive wheat blast strain 16MoT01

Wheat blast, a highly destructive fungal disease caused by pathotype Magnaporthe oryzae Triticum, can cause up to 100% yield loss in wheat fields under optimal pathogen conditions. Until 2016, the disease had been confined to South America, but recent outbreaks of the disease in Asia and Africa threaten the global wheat supply. This study aims to characterize the genome structure of strain 16MoT01, which has proven to be particularly aggressive even towards wheat genotypes that have previously been resistant to blast. Genomic DNA from 16MoT01 was sequenced using Oxford Nanopore long read sequencing, assembled with Canu, and polished using Illumina reads, resulting in a finished chromosome-level assembly consisting of seven core-chromosomes, a mini-chromosome, and a mitochondrial genome. When compared to the reference genome of strain B71, the core-chromosomes show high similarity and the mini-chromosome shows a high level of divergence. The presence of mini-chromosomes will be confirmed through contour-clamped electric field (CHEF) gel electrophoresis. The CHEF protocol was developed using genomic DNA from a rice blast fungus. This assembly provides another reference genome and potential insights into what makes this strain so aggressive

Multipath trapping dynamics of nanoparticles towards an integrated waveguide with a high index contrast

Optical trapping and manipulation of nanoparticles in integrated photonics devices have recently received increasingly more attention and greatly facilitated the advances in lab-on-chip technologies. In this work, by solving motion equation numerically, we study the trapping dynamics of a nanoparticle near a high-index-contrast slot waveguide, under the influence of water flow perpendicular to the waveguide. It is shown that a nanoparticle can go along different paths before it gets trapped, strongly depending on its initial position relative to the integrated waveguide. Due to localized optical field enhancement on waveguide sidewalls, there are multiple trapping positions, with a critical area where particle trapping and transport are unstable. As the water velocity increases, the effective trapping range shrinks, but with a rate that is smaller than the increasing of water velocity. Finally, the trapping range is shown to decrease for smaller slot width that is below 100 nm, even though smaller slot width generates stronger local optical force

Influencing factors of different development stages of green food industry: a system dynamic model

The green food industry is important for China because it bears the additional expectation of promoting the rural economy Heilongjiang Province is a representative example, which is one of the main production bases of green food With this in mind, this paper takes Heilongjiang Province as an example to research the main influencing factor of the green food industry This article uses system dynamics methods to construct research models and uses mathematical models to calculate the industry lifecycle. Different from previous studies, this paper provides the life cycle of the industry and discusses the effects of influencing factors during the different periods The main conclusion includes: The stage before 2011 is the termination period, the stage from 2011 to 2019 is the growth period, and the stage after 2019 is the property period By the final time of the simulation, there are no signs of filtering; The enterprise scale is the main influencing factor that can make positive effects on the output value of the green food industry from the growth period, and others have no objective impact from beginning to end; Undesirably high level of financial investment will execute a negative effect for industrial development in the property period, at least in terms of output value

Chromosome-level genome assembly of a regenerable maize inbred line A188

Background: The maize inbred line A188 is an attractive model for elucidation of gene function and improvement due to its high embryogenic capacity and many contrasting traits to the first maize reference genome, B73, and other elite lines. The lack of a genome assembly of A188 limits its use as a model for functional studies. Results: Here, we present a chromosome-level genome assembly of A188 using long reads and optical maps. Comparison of A188 with B73 using both whole-genome alignments and read depths from sequencing reads identify approximately 1.1 Gb of syntenic sequences as well as extensive structural variation, including a 1.8-Mb duplication containing the Gametophyte factor1 locus for unilateral cross-incompatibility, and six inversions of 0.7 Mb or greater. Increased copy number of carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. High ccd1 expression in seeds together with low expression of yellow endosperm 1 (y1) reduces carotenoid accumulation, accounting for the white seed phenotype of A188. Furthermore, transcriptome and epigenome analyses reveal enhanced expression of defense pathways and altered DNA methylation patterns of the embryonic callus. Conclusions: The A188 genome assembly provides a high-resolution sequence for a complex genome species and a foundational resource for analyses of genome variation and gene function in maize. The genome, in comparison to B73, contains extensive intra-species structural variations and other genetic differences. Expression and network analyses identify discrete profiles for embryonic callus and other tissues

Aqueous extract of Amydrium sinense (Engl.) H. Li alleviates hepatic fibrosis by suppressing hepatic stellate cell activation through inhibiting Stat3 signaling

Background: The present study aimed to investigate the protective effect of the water extract of Amydrium sinense (Engl.) H. Li (ASWE) against hepatic fibrosis (HF) and clarify the underlying mechanism.Methods: The chemical components of ASWE were analysed by a Q-Orbitrap high-resolution mass spectrometer. In our study, an in vivo hepatic fibrosis mouse model was established via an intraperitoneal injection of olive oil containing 20% CCl4. In vitro experiments were conducted using a hepatic stellate cell line (HSC-T6) and RAW 264.7 cell line. A CCK-8 assay was performed to assess the cell viability of HSC-T6 and RAW264.7 cells treated with ASWE. Immunofluorescence staining was used to examine the intracellular localization of signal transducer and activator of transcription 3 (Stat3). Stat3 was overexpressed to analyse the role of Stat3 in the effect of ASWE on HF.Results: Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that candidate targets of ASWE, associated with protective effects against hepatic fibrosis, were related to inflammation response. ASWE ameliorated CCl4-induced liver pathological damage and reduced the liver index and alanine transaminase (ALT) and aspartate transaminase (AST) levels. ASWE also decreased the serum levels of collagen Ⅰ (Col Ⅰ) and hydroxyproline (Hyp) in CCl4-treated mice. In addition, the expression of fibrosis markers, including α-SMA protein and Acta2, Col1a1, and Col3a1 mRNA, was downregulated by ASWE treatment in vivo. The expression of these fibrosis markers was also decreased by treatment with ASWE in HSC-T6 cells. Moreover, ASWE decreased the expression of inflammatory markers, including the Tnf-α, Il6 and Il1β, in RAW264.7 cells. ASWE decreased the phosphorylation of Stat3 and total Stat3 expression and reduced the mRNA expression of the Stat3 gene in vivo and in vitro. ASWE also inhibited the nuclear shuttling of Stat3. Overexpression of Stat3 weakened the therapeutic effect of ASWE and accelerated the progression of HF.Conclusion: The results show that ASWE protects against CCl4-induced liver injury by suppressing fibrosis, inflammation, HSC activation and the Stat3 signaling pathway, which might lead to a new approach for preventing HF

Yao medicine Amydrium hainanense suppresses hepatic fibrosis by repressing hepatic stellate cell activation via STAT3 signaling

Ethnopharmacological relevance: Hepatic fibrosis (HF) occurs in response to chronic liver injury and may easily develop into irreversible liver cirrhosis or even liver cancer. Amydrium hainanense water extract (AHWE) is a water-soluble component extracted from the Yao medicine Amydrium hainanense (H.Li, Y.Shiao & S.L.Tseng) H.Li, which is commonly used for treating inflammatory diseases in folk. Previous evidence suggested that AHWE significantly inhibited hepatic stellate cell activation. However, little is known regarding the therapeutic effect of AHWE in HF and its underlying action mechanism.Objective: Investigation of the therapeutic effect of AHWE in HF and its underlying mechanism.Methods: The therapeutic effect of AHWE was tested in vivo using an HF mouse model via an intraperitoneal injection of carbon tetrachloride (CCl4). Histological evaluation of liver injury and fibrosis were tested by H&E staining and Masson’s trichrome staining. Serum levels of ALT, AST, collagen type I (Col I), and hydroxyproline (HYP) were measured. The mRNA expression of liver fibrotic and inflammatory genes were tested, and the protein levels of alpha smooth muscle actin (α-SMA) and signal transducers and activators of transcription 3 (STAT3) were analyzed. The in vitro experiments were conducted using HSC-T6 and RAW264.7 cell lines.Results: Treatment with AHWE significantly reversed histopathological liver damage and liver function abnormalities in CCl4 mouse model. Also, the serum levels of ALT, AST, Col I, and HYP in CCl4-induced HF mice were improved in AHWE treatment. Further, AHWE showed a remarkable inhibitory effect on the expression of fibrosis markers (Acta2, Col1a1, and Col3a1) and inflammatory factors (Stat3, Tnfa, Il6, and Il1b) induced by CCl4. The results of in vitro experiments were consistent with those obtained in vivo. In addition, it is shown that STAT3 signaling was involved in the anti-fibrotic effects of AHWE as evidenced by STAT3 overexpression.Conclusion: The present study proposed a novel ethnomedicine for HF and suggested the underlying role of STAT3 signaling pathway regulation in this anti-fibrotic effect of the proposed medicine. These findings would serve as solid scientific evidence in support of the development of AHWE as a novel alternative or complementary therapy for HF prevention and treatment

Prognostic and therapeutic implications of iron-related cell death pathways in acute myeloid leukemia

Acute myeloid leukemia (AML) is a blood cancer that is diverse in terms of its molecular abnormalities and clinical outcomes. Iron homeostasis and cell death pathways play crucial roles in cancer pathogenesis, including AML. The objective of this study was to examine the clinical significance of genes involved in iron-related cell death and apoptotic pathways in AML, with the intention of providing insights that could have prognostic implications and facilitate the development of targeted therapeutic interventions. Gene expression profiles, clinical information, and molecular alterations were integrated from multiple datasets, including TCGA-LAML and GSE71014. Our analysis identified specific molecular subtypes of acute myeloid leukemia (AML) displaying varying outcomes, patterns of immune cell infiltration, and profiles of drug sensitivity for targeted therapies based on the expression of genes involved in iron-related apoptotic and cell death pathways. We further developed a risk model based on four genes, which demonstrated promising prognostic value in both the training and validation cohorts, indicating the potential of this model for clinical decision-making and risk stratification in AML. Subsequently, Western blot analysis showed that the expression levels of C-Myc and CyclinD1 were significantly reduced after CD4 expression levels were knocked down. The findings underscore the potential of iron-related cell death pathways as prognostic biomarkers and therapeutic targets in AML, paving the way for further research aimed at understanding the molecular mechanisms underlying the correlation between iron balance, apoptosis regulation, and immune modulation in the bone marrow microenvironment

Towards on-chip spectroscopy based on a single microresonator

Frequency comb generation in the mid-infrared (mid-IR)region is attractive recently. Here, we propose the Ge-on-Si microresonator for power-efficient frequency comb generation in the mid-IR. An octave-spanning comb can be obtained with power reduced to 190 mW. The robustness of the frequency comb generation with localized spectral loss is also analyzed. Based on the analysis, we propose a novel architecture of on-chip spectroscopy systems in the mid-IR