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"Yong Min"
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حان الآن الوقت للنوم : (عادات النوم لدى الحيونات)
يعرض هذا الكتاب \"حان الآن الوقت للنوم عادات النوم لدى الحيونات\" تأليف يون-شيل هور أوقات وأماكن وكيفية النوم لدى المخلوقات الحية على الأرض بجوها ويابستها وبحارها ويبين ردود الفعل في حال تعرض هذه المخلوقات للخطر أثناء اليقظة والنوم ووأيضا يبين أهمية النوم بالنسبة للمخلوقات كافة والبحث عن حلول إبداعية كيف يستخلص من مشكلاته.
BOOK
New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication
Background
Transposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and leucine-rich-repeat proteins (NLRs), the major disease-resistance gene families, has been unexplored in plants.
Results
We report two high-quality de novo genomes (
Capsicum baccatum
and
C. chinense
) and an improved reference genome (
C. annuum
) for peppers. Dynamic genome rearrangements involving translocations among chromosomes 3, 5, and 9 were detected in comparison between
C. baccatum
and the two other peppers. The amplification of
athila
LTR-retrotransposons, members of the
gypsy
superfamily, led to genome expansion in
C. baccatum
. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs are abundant across the angiosperms and, in most cases, are lineage-specific.
Conclusions
Our study reveals that retroduplication has played key roles for the massive emergence of NLR genes including functional disease-resistance genes in pepper plants.
Journal Article
Polyunsaturated fatty acid biosynthesis pathway determines ferroptosis sensitivity in gastric cancer
Ferroptosis is an iron-dependent regulated necrosis mediated by lipid peroxidation. Cancer cells survive under metabolic stress conditions by altering lipid metabolism, which may alter their sensitivity to ferroptosis. However, the association between lipid metabolism and ferroptosis is not completely understood. In this study, we found that the expression of elongation of very longchain fatty acid protein 5 (ELOVL5) and fatty acid desaturase 1 (FADS1) is up-regulated in mesenchymal-type gastric cancer cells (GCs), leading to ferroptosis sensitization. In contrast, these enzymes are silenced by DNA methylation in intestinal-type GCs, rendering cells resistant to ferroptosis. Lipid profiling and isotope tracing analyses revealed that intestinal-type GCs are unable to generate arachidonic acid (AA) and adrenic acid (AdA) from linoleic acid. AA supplementation of intestinal-type GCs restores their sensitivity to ferroptosis. Based on these data, the polyunsaturated fatty acid (PUFA) biosynthesis pathway plays an essential role in ferroptosis; thus, this pathway potentially represents a marker for predicting the efficacy of ferroptosis-mediated cancer therapy.
Journal Article
Deconvolution of diffuse gastric cancer and the suppression of CD34 on the BALB/c nude mice model
Background
Gastric cancer is a considerable burden for worldwide patients. And diffuse gastric cancer is the most insidious subgroup with poor survival. The phenotypic characterization of the diffuse gastric cancer cell line can be useful for gastric cancer researchers. In this article, we aimed to characterize the diffuse gastric cancer cells with MRI and transcriptomic data. We hypothesized that gene expression pattern is associated with the phenotype of the cells and that the heterogeneous enhancement pattern and the high tumorigenicity of SNU484 can be modulated by the perturbation of the highly expressed gene.
Methods
We evaluated the 9.4 T magnetic resonance imaging and transcriptomic data of the orthotopic mice models from diffuse gastric cancer cells such as SNU484, Hs746T, SNU668, and KATO III. We included MKN74 as an intestinal cancer control cell. After comprehensive analysis integrating MRI and transcriptomic data, we selected CD34 and validated the effect by shRNA in the BALB/c nude mice models.
Results
SNU484, SNU668, Hs746T, and MKN74 formed orthotopic tumors by the 5 weeks after cell injection. The diffuse phenotype was found in the SNU484 and Hs746T. SNU484 was the only tumor showing the heterogeneous enhancement pattern on T2 images with a high level of CD34 expression. Knockdown of CD34 decreased the round-void shape in the H&E staining (
P
= 0.028), the heterogeneous T2 enhancement, and orthotopic tumorigenicity (100% vs 66.7%). The RNAseq showed that the suppressed CD34 is associated with the downregulated gene-sets of the extracellular matrix remodeling.
Conclusion
Suppression of CD34 in the human-originated gastric cancer cell suggests that it is important for the round-void histologic shape, heterogeneous enhancement pattern on MRI, and the growth of gastric cancer cell line.
Journal Article
Redox-inactive metal ions modulate the reactivity and oxygen release of mononuclear non-haem iron(III)–peroxo complexes
Redox-inactive metal ions that function as Lewis acids play pivotal roles in modulating the reactivity of oxygen-containing metal complexes and metalloenzymes, such as the oxygen-evolving complex in photosystem II and its small-molecule mimics. Here we report the synthesis and characterization of non-haem iron(
III
)–peroxo complexes that bind redox-inactive metal ions, (TMC)Fe
III
–(μ,η
2
:η
2
-O
2
)–M
n
+
(M
n
+
= Sr
2+
, Ca
2+
, Zn
2+
, Lu
3+
, Y
3+
and Sc
3+
; TMC, 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane). We demonstrate that the Ca
2+
and Sr
2+
complexes showed similar electrochemical properties and reactivities in one-electron oxidation or reduction reactions. However, the properties and reactivities of complexes formed with stronger Lewis acidities were found to be markedly different. Complexes that contain Ca
2+
or Sr
2+
ions were oxidized by an electron acceptor to release O
2
, whereas the release of O
2
did not occur for complexes that bind stronger Lewis acids. We discuss these results in the light of the functional role of the Ca
2+
ion in the oxidation of water to dioxygen by the oxygen-evolving complex.
Non-haem iron(
III
)-peroxo complexes that bind redox-inactive metal ions are synthesized to investigate the role of the Ca
2+
ion in the oxidation of water to dioxygen in photosystem II. The electrochemical properties and reactions of these compounds with an electron donor and an acceptor are found to be markedly dependent on the Lewis acidity of redox-inactive metal ions.
Journal Article
Pan-cancer analysis of somatic mutations and transcriptomes reveals common functional gene clusters shared by multiple cancer types
To discover functional gene clusters across cancers, we performed a systematic pan-cancer analysis of 33 cancer types. We identified genes that were associated with somatic mutations and were the cores of a co-expression network. We found that multiple cancer types have relatively exclusive hub genes individually; however, the hub genes cooperate with each other based on their functional relationship. When we built a protein-protein interaction network of hub genes and found nine functional gene clusters across cancer types, the gene clusters divided not only the region of the network map, but also the function of the network by their distinct roles related to the development and progression of cancer. This functional relationship between the clusters and cancers was underpinned by the high expression of module genes and enrichment of programmed cell death, and known candidate cancer genes. In addition to protein-coding hub genes, non-coding hub genes had a possible relationship with cancer. Overall, our approach of investigating cancer genes enabled finding pan-cancer hub genes and common functional gene clusters shared by multiple cancer types based on the expression status of the primary tumour and the functional relationship of genes in the biological network.
Journal Article
Mechanism of Cisplatin-Induced Cytotoxicity Is Correlated to Impaired Metabolism Due to Mitochondrial ROS Generation
The chemotherapeutic use of cisplatin is limited by its severe side effects. In this study, by conducting different omics data analyses, we demonstrated that cisplatin induces cell death in a proximal tubular cell line by suppressing glycolysis- and tricarboxylic acid (TCA)/mitochondria-related genes. Furthermore, analysis of the urine from cisplatin-treated rats revealed the lower expression levels of enzymes involved in glycolysis, TCA cycle, and genes related to mitochondrial stability and confirmed the cisplatin-related metabolic abnormalities. Additionally, an increase in the level of p53, which directly inhibits glycolysis, has been observed. Inhibition of p53 restored glycolysis and significantly reduced the rate of cell death at 24 h and 48 h due to p53 inhibition. The foremost reason of cisplatin-related cytotoxicity has been correlated to the generation of mitochondrial reactive oxygen species (ROS) that influence multiple pathways. Abnormalities in these pathways resulted in the collapse of mitochondrial energy production, which in turn sensitized the cells to death. The quenching of ROS led to the amelioration of the affected pathways. Considering these observations, it can be concluded that there is a significant correlation between cisplatin and metabolic dysfunctions involving mROS as the major player.
Journal Article
Optimal Design of PMSM Based on Automated Finite Element Analysis and Metamodeling
To obtain accurate optimal design results in electric machines, the finite element analysis (FEA) technique should be used; however, it is time-consuming. In addition, when the design of experiments (DOE) is conducted in the optimal design process, mechanical design, analysis, and post process must be performed for each design point, which requires a significant amount of design cost and time. This study proposes an automated DOE procedure through linkage between an FEA program and optimal design program to perform DOE easily and accurately. Parametric modeling was developed for the FEA model for automation, the files required for automation were generated using the macro function, and the interface between the FEA and optimal design program was established. Shape optimization was performed on permanent magnet synchronous motors (PMSMs) for small electric vehicles to maximize torque while maintaining efficiency, torque ripple, and total harmonic distortion of the back EMF using the built-in automation program. Fifty FEAs were performed for the experimental points selected by optimal Latin hypercube design and their results were analyzed by screening. Eleven metamodels were created for each output variable using the DOE results and root mean squared error tests were conducted to evaluate the predictive performance of the metamodels. The optimization design based on metamodels was conducted using the hybrid metaheuristic algorithm to determine the global optimum. The optimum design results showed that the average torque was improved by 2.5% in comparison to the initial model, while satisfying all constraints. Finally, the optimal design results were verified by FEA. Consequently, it was found that the proposed optimal design method can be useful for improving the performance of PMSM as well as reducing design cost and time.
Journal Article
Construction of deep learning-based disease detection model in plants
Accurately detecting disease occurrences of crops in early stage is essential for quality and yield of crops through the decision of an appropriate treatments. However, detection of disease needs specialized knowledge and long-term experiences in plant pathology. Thus, an automated system for disease detecting in crops will play an important role in agriculture by constructing early detection system of disease. To develop this system, construction of a stepwise disease detection model using images of diseased-healthy plant pairs and a CNN algorithm consisting of five pre-trained models. The disease detection model consists of three step classification models, crop classification, disease detection, and disease classification. The ‘unknown’ is added into categories to generalize the model for wide application. In the validation test, the disease detection model classified crops and disease types with high accuracy (97.09%). The low accuracy of non-model crops was improved by adding these crops to the training dataset implicating expendability of the model. Our model has the potential to apply to smart farming of Solanaceae crops and will be widely used by adding more various crops as training dataset.
Journal Article