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Oryza CLIMtools:A genome–environment association resource reveals adaptive roles for heterotrimeric G proteins in the regulation of rice agronomic traits

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Plant Communications 2024年第4期5卷 145-165页

作者： Angel Ferrero-Serrano David Chakravorty Kobie J.Kirven Sarah M.Assmann Biology Department Pennsylvania State University208 Mueller LaboratoryUniversity ParkPA 16802USA Intercollege Graduate Degree Program in Bioinformatics and Genomics Pennsylvania State University208 Mueller LaboratoryUniversity ParkPA 16802USA

Modern crop varieties display a degree of mismatch between their current distributions and the suitability of the local climate for their *** address this issue,we present Oryza CLIMtools(https://***/CLIMtools/oryza_v1.0/),thefirst resource for pan-genome prediction of climate-associated genetic variants in a crop *** CLIMtools consists of interactive web-based databases that enable the user to(1)explore the local environments of traditional rice varieties(landraces)in South-East Asia and(2)investigate the environment by genome associations for 658 Indica and 283 Japonica rice landrace accessions collected from georeferenced local environments and included in the 3K Rice Ge-nomes *** demonstrate the value of these resources by identifying an interplay betweenflowering time and temperature in the local environment that is facilitated by adaptive natural variation in OsHD2 and disrupted by a natural variant in *** quantitative trait locus analysis has suggested the impor-tance of heterotrimeric G proteins in the control of agronomic ***,we analyzed the climate associations of natural variants in the different heterotrimeric G protein *** identified a coordi-nated role of G proteins in adaptation to the prevailing potential evapotranspiration gradient and revealed their regulation of key agronomic traits,including plant height and seed and panicle *** conclude by highlighting the prospect of targeting heterotrimeric G proteins to produce climate-resilient crops.

关键词： Oryza sativa rice G by E adaptation flowering time GWAS OsHD2 OsSOC1 heterotrimeric G pro-tein OsRGA1 d1 OsGS3 OsDEP1 OsGGC2

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Dual-targeting compounds possessing enhanced anticancer activity via microtubule disruption and histone deacetylase inhibition

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European Journal of Medicinal Chemistry 2024年 265卷 116042页

作者： Tseng, Yu-Wei Yang, Tsung-Jung Hsu, Yuan-Ling Liu, Jyung-Hurng Tseng, Yin-Chen Hsu, Tse-Wei Lu, Yueh Pan, Szu-Hua Cheng, Ting-Jen Rachel Fang, Jim-Min Department of Chemistry National Taiwan University Taipei 106 Taiwan Graduate Institute of Medical Genomics and Proteomics College of Medicine National Taiwan University Taipei 100 Taiwan Graduate Institute of Genomics and Bioinformatics College of Life Sciences National Chung Hsing University Taichung 40227 Taiwan The Genomics Research Center Academia Sinica Taipei 115 Taiwan Doctoral Degree Program of Translational Medicine National Taiwan University Taipei 100 Taiwan Genome and Systems Biology Degree Program National Taiwan University and Academia Sinica Taipei 100 Taiwan

Dual-targeting anticancer agents 4–29 are designed by combining the structural features of purine-type microtubule-disrupting compounds and HDAC inhibitors. A library of the conjugate compounds connected by appropriate linkers was synthesized and found to possess HDACs inhibitory activity and render microtubule fragmentation by activating katanin, a microtubule-severing protein. Among various zinc-binding groups, hydroxamic acid shows the highest inhibitory activity of Class I HDACs, which was also reconfirmed by three-dimensional quantitative structure-activity relationship (3D-QSAR) pharmacophore prediction. The purine–hydroxamate conjugates exhibit enhanced cytotoxicity against MDA-MB231 breast cancer cells, H1975 lung cancer cells, and various clinical isolated non-small-cell lung cancer cells with different epidermal growth factor receptor (EGFR) status. Pyridyl substituents could be used to replace the C2 and N9 phenyl moieties in the purine-type scaffold, which can help to improve the solubility under physiological conditions, thus increasing cytotoxicity. In mice treated with the purine–hydroxamate conjugates, the tumor growth rate was significantly reduced without causing toxic effects. Our study demonstrates the potential of the dual-targeting purine–hydroxamate compounds for cancer monotherapy. © 2023 Elsevier Masson SAS

关键词： Breast cancer Histidine deacetylase Hydroxamate Katanin Lung cancer Microtubule Purine-type conjugate

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Targeting protein-protein interaction interfaces with antiviral N protein inhibitor in SARS-CoV-2

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Biophysical Journal 2024年第4期123卷 478-488页

作者： Hong, Jhen-Yi Lin, Shih-Chao Kehn-Hall, Kylene Zhang, Kai-Min Luo, Shun-Yuan Wu, Hung-Yi Chang, Sui-Yuan Hou, Ming-Hon Institute of Genomics and Bioinformatics and Department of Life Sciences National Chung Hsing University Taichung Taiwan Bachelor Degree Program in Marine Biotechnology College of Life Sciences National Taiwan Ocean University Keelung Taiwan Department of Biomedical Sciences and Pathobiology Virginia-Maryland College of Veterinary Medicine Virginia Polytechnic Institute and State University Blacksburg VA United States Center for Emerging Zoonotic and Arthropod-borne Pathogens Virginia Polytechnic Institute and State University Blacksburg VA United States Department of Chemistry National Chung Hsing University Taichung Taiwan Graduate Institute of Veterinary Pathobiology College of Veterinary Medicine National Chung Hsing University. Taichung Taiwan Department of Clinical Laboratory Sciences and Medical Biotechnology College of Medicine National Taiwan University Taipei Taiwan PhD Program in Medical Biotechnology National Chung Hsing University Taichung Taiwan Biotechnology Center National Chung Hsing University Taichung Taiwan

Coronaviruses not only pose significant global public health threats but also cause extensive damage to livestock-based industries. Previous studies have shown that 5-benzyloxygramine (P3) targets the Middle East respiratory syndrome coronavirus (MERS-CoV) nucleocapsid (N) protein N-terminal domain (N-NTD), inducing non-native protein-protein interactions (PPIs) that impair N protein function. Moreover, P3 exhibits broad-spectrum antiviral activity against CoVs. The sequence similarity of N proteins is relatively low among CoVs, further exhibiting notable variations in the hydrophobic residue responsible for non-native PPIs in the N-NTD. Therefore, to ascertain the mechanism by which P3 demonstrates broad-spectrum anti-CoV activity, we determined the crystal structure of the SARS-CoV-2 N-NTD:P3 complex. We found that P3 was positioned in the dimeric N-NTD via hydrophobic contacts. Compared with the interfaces in MERS-CoV N-NTD, P3 had a reversed orientation in SARS-CoV-2 N-NTD. The Phe residue in the MERS-CoV N-NTD:P3 complex stabilized both P3 moieties. However, in the SARS-CoV-2 N-NTD:P3 complex, the Ile residue formed only one interaction with the P3 benzene ring. Moreover, the pocket in the SARS-CoV-2 N-NTD:P3 complex was more hydrophobic, favoring the insertion of the P3 benzene ring into the complex. Nevertheless, hydrophobic interactions remained the primary stabilizing force in both complexes. These findings suggested that despite the differences in the sequence, P3 can accommodate a hydrophobic pocket in N-NTD to mediate a non-native PPI, enabling its effectiveness against various CoVs. © 2024 Biophysical Society

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Using ensemble learning and hierarchical strategy to predict the outcomes of ESWL for upper ureteral stone treatment

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Computers in Biology and Medicine 2024年 179卷 108904-108904页

作者： Chen, Chi-Wei Liu, Wayne-Young Huang, Lan-Ying Chu, Yen-Wei Graduate Degree Program of Smart Healthcare & Bioinformatics I-Shou University Kaohsiung City Taiwan Department of Biomedical Engineering I-Shou University Kaohsiung City Taiwan Doctoral Program in Medical Biotechnology National Chung Hsing University Taichung City Taiwan Department of Urology Jen-Ai Hospital Taichung City Taiwan Graduate Institute of Genomics and Bioinformatics National Chung Hsing University Taichung City Taiwan Institute of Molecular Biology National Chung Hsing University Taichung City Taiwan Agricultural Biotechnology Center National Chung Hsing University Taichung City Taiwan Rong Hsing Research Center for Translational Medicine Taichung City Taiwan Ph. D Program in Medical Biotechnology National Chung Hsing University Taichung City Taiwan Taichung402 Taiwan

Urinary tract stones are a common and frequently recurring medical issue. Accurately predicting the success rate after surgery can help avoid ineffective medical procedures and reduce unnecessary healthcare costs. This study collected data from patients with upper ureter stones who underwent extracorporeal shock wave lithotripsy, including cases of successful as well as unsuccessful stone removal after the first and second lithotripsy procedures, and constructed prediction systems for the outcomes of the first and second lithotripsy procedures. Features were extracted from three categories of information: patient characteristics, stone characteristics, and extracorporeal shock wave lithotripsy machine data, and additional features were created using Feature Creation. Finally, the impact of features on the models was analyzed using six methods to calculate feature importance. Our prediction model for the first lithotripsy, selected from among 43 methods and seven ensemble learning techniques, achieves an AUC of 0.91. For the second lithotripsy, the AUC reaches 0.76. The results indicate that the detailed and binary information provided by patients regarding their history of stone experiences contributes differently to the predictive accuracy of the first and second lithotripsy procedures. The prediction tool is available at https://***/ks. © 2024

关键词： Machine learning

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Comparing the prediction performance of machine learning and deep learning methods for 3c-like protease cleavage sites 23

Comparing the prediction performance of machine learning and...

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7th International Conference on Medical and Health Informatics, ICMHI 2023

作者： Huang, Lan-Ying Chen, Chi-Wei Chang, Kai-Po Chu, Yen-Wei Medical Biotechnology National Chung Hsing University Taichung402 Taiwan Department of Pathology School of Medicine China Medical University Taichung402 Taiwan Department of Pathology China Medical University Hospital Taichung402 Taiwan Graduate Degree Program of Smart Healthcare and Bioinformatics I-Shou University Kaohsiung82445 Taiwan Department of Biomedical Engineering I-Shou University Kaohsiung82445 Taiwan Institute of Genomics and Bioinformatics National Chung Hsing University Taichung402 Taiwan Institute of Molecular Biology National Chung Hsing University Taichung402 Taiwan Agricultural Biotechnology Center National Chung Hsing University Taichung402 Taiwan Biotechnology Center National Chung Hsing University Taichung402 Taiwan Translational Medicine National Chung Hsing University Taichung402 Taiwan Rong Hsing Research Center for Translational Medicine National Chung Hsing University Taichung402 Taiwan Taichung402 Taiwan

ISBN: (纸本)9798400700712

The impact of COVID-19 on the human body after infection requires further investigation. The protease carried by the virus may interact with cellular proteins, thereby affecting the regulatory pathways. Machine learning can provide predictive information to aid the research design in such studies. This study examined the effectiveness of different encoding methods for training models using traditional machine learning and deep learning methods. Using the advantages of deep learning methods for high-dimensional data analysis, amino acid properties were extracted and classified. Viral polyprotein data were used as the training set and human protein substrates were collected from the literature as the independent test set. In the one-dimensional convolutional neural network model, the accuracy of the independent test set was the highest, at 0.832. © 2023 ACM.

关键词： Coronavirus

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A solanum lycopersicum solanum pimpinellifolium linkage map of tomato displaying genomic locations of R-genes, RGAs, and candidate resistance/defense-response ESTs

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International Journal of Plant genomics 2008年第1期2008卷 926090页

作者： Foolad, Majid R. Sharma, Arun Zhang, Liping Nio-Liu, David Ashrafi, Hamid Institute for Plant Genomics and Biotechnology Texas AandM University College Station TX 77843 United States Nephrology Division Department of Medicine Baylor College of Medicine Houston TX 77030 United States Monsanto Canada Inc. MB R3Y 1P6 3-75 Scurfield Boulevard Winnipeg Canada Department of Plant Sciences University of California-Davis Davis CA 95616 One Shields Avenue United States Department of Horticulture Intercollege Graduate Degree Program in Genetics Pennsylvania State University University Park PA 16802 United States

We have identified an accession (LA2093) within the tomato wild species Solanum pimpinellifolium with many desirable characteristics, including biotic and abiotic stress tolerance and good fruit quality. To utilize the full genetic potential of LA2093 in tomato breeding, we have developed a linkage map based on an F 2 population of a cross between LA2093 and a tomato breeding line, using 115 RFLP, 94 EST, and 41 RGA markers. The map spanned 1002.4cM of the 12 tomato chromosomes with an average marker distance of 4.0cM. The length of the map and linear order of the markers were in good agreement with the published maps of tomato. The ESTs were chosen based on their sequence similarities with known resistance or defense-response genes, signal-transduction factors, transcriptional regulators, and genes encoding pathogenesis-related proteins. Locations of several ESTs and RGAs coincided with locations of several known tomato resistance genes and quantitative resistance loci (QRLs), suggesting that candidate-gene approach may be effective in identifying and mapping new R genes. This map will be useful for marker-assisted exploitation of desirable traits in LA2093 and other S. pimpinellifolium accessions, and possibly for utilization of genetic variation within S. lycopersicum.

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Method: Isolation of Epithelial Cell RNA from Frozen Jejunum Segments While Minimizing Smooth Muscle Cell RNA Contamination

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Current Developments in Nutrition 2020年第SUPPL 2期4卷 4141182-4141182页

作者： Ye, Shumao Matthan, Nirupa Lamon-Fava, Stefania Solano-Aguilar, Gloria Turner, Jerrold Wang, Xiang-Dong Walker, Maura Chai, Zhi Lakshman, Sukla Urban Jr., Joseph Lichtenstein, Alice Cardiovascular Nutrition Laboratory Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University USDA ARS Beltsville Human Nutrition Research Center Diet Genomics and Immunology Laboratory Laboratory of Mucosal Barrier Pathobiology Department of Pathology Brigham and Woman's Hospital and Harvard Medical School Nutrition and Cancer Laboratory Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University Section of Preventive Medicine and Epidemiology Boston University School of Medicine Intercollege Graduate Degree Program in Physiology and Department of Nutritional Science Pennsylvania State University

AbstractObjectivesHigh RNA quality is a prerequisite for accurate PCR and sequencing results. Dissecting a specific tissue fraction from frozen samples while maintaining RNA quality is challenging. Starting with frozen pig jejunum segments, we describe a novel method to isolate epithelial cell RNA while minimizing contamination with smooth muscle cell RNA. MethodsJejunum tissue segments from Ossabaw pigs ( N = 30) were snap-frozen in liquid nitrogen upon harvest from a diet-statin study and stored at –80°C. At the time of RNA isolation samples were incubated in prechilled RNA later-ICE at –20°C for 24 hours, opened longitudinally, and epithelium cleanly separated from the muscle layer using a scalpel and tweezers. Total RNA was extracted from the epithelium using TRI-reagent. RNA Quality Indicator (RQI) of total RNA was measured using Experion RNA StdSens Analysis kit. RNA-sequencing was performed on Illumina NextSeq 500 platform. Raw sequencing data were aligned to the domestic pig ( sus scrofa 11.1) reference genome and applied to subsequent analyses. xCell, a gene signature-based tool trained by thousands of single cell types from various sources, was used to estimate enrichment of epithelial cells (target) and smooth muscle cells (contamination) across samples. A Student t-test was used to compare the enrichment scores of these two cell types between the current method and a traditional method (small jejunal pieces collected at necropsy and stored frozen until RNA isolation). ResultsRQI ranged from 8.6 to 9.7, above the standard for RNA sequencing (RQI > 8). The enrichment score of epithelial cells was significantly higher in the current method (mean = 0.030, SD = 0.006) compared to the traditional method (mean = 0.016, SD = 0.013) ( P < 0.0001). The enrichment score of smooth muscle cells was significantly lower in the current method (mean = 0.043, SD = 0.035) compared to the traditional method (mean = 0.13, SD = 0.093) ( P < 0.0001). ConclusionsThe current met

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Western Versus Heart Healthy Dietary Pattern Alters Genes Expression Associated with Lipid Metabolism, Interferon Signaling and Inflammation in Jejunum of Ossabaw Pigs

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Current Developments in Nutrition 2020年第SUPPL 2期4卷 4140577-4140577页

AbstractObjectivesA gastrointestinal tract (GI) that allows for bacterial translocation has been associated with enhanced systemic inflammation and may play a critical role in the development of coronary artery disease (CAD). Diet quality and statin therapy are established modulators of CAD, but their effect in GI health is relatively unexplored. Jejunal mucosa gene expression was compared in Ossabaw pigs fed a heart healthy-type diet (HHD) and Western-type diet (WD), with and without statin therapy. MethodsPigs ( N = 32) were randomized into 4 groups and fed isocalorically for 6 months: WD (high in saturated fat, refined carbohydrate, cholesterol, and low in fiber) or HHD (high in unsaturated fat, whole grains, fruits and vegetables, fiber, supplemented with fish oil, and low in cholesterol), with or without statin therapy. RNA sequencing was conducted in isolated jejunal mucosa at the end of the study. Principal component analysis, hierarchical clustering and xCell analysis were used to cross-check and ensure consistent sampling. Two-factor edgeR analysis and Ingenuity Pathway Analysis were used to identify genes, pathways, and biological functions altered by diet and/or statin. Independent of groups, Spearman’s correlation coefficients were calculated to identify associations between genes of interest and atherosclerotic lesion severity in the coronary arteries or cardiometabolic risk factors (serum triglyceride, LDL, HDL, TNF-α, hsCRP). ResultsHHD and WD resulted in differential expression of genes related to lipid metabolism ( SCD, FADS1, SQLE) in the jejunal mucosa. The expression of these genes was associated with atherosclerotic lesion severity and serum lipoprotein concentrations. Higher interferon signaling and inflammation were observed in pigs fed WD versus HHD. In the jejunal mucosa, 7 genes related to inflammation were significantly associated with serum TNF-α and/or hsCRP concentrations. There was no significant effect of statin on gene expression, no

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