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Genome-wide association studies identify loci controlling specialized seed metabolites in Arabidopsis
No full textPlants synthesize specialized metabolites to facilitate environmental and ecological interactions. During evolution, plants diversified in their potential to synthesize these metabolites. Quantitative differences in metabolite levels of natural Arabidopsis (Arabidopsis thaliana) accessions can be employed to unravel the genetic basis for metabolic traits using genome-wide association studies (GWAS). Here, we performed metabolic GWAS on seeds of a panel of 315 A. thaliana natural accessions, including the reference genotypes C24 and Col-0, for polar and semi-polar seed metabolites using untargeted ultra-performance liquid chromatography-mass spectrometry. As a complementary approach, we performed quantitative trait locus (QTL) mapping of near-isogenic introgression lines between C24 and Col-0 for specific seed specialized metabolites. Besides common QTL between seeds and leaves, GWAS revealed seed-specific QTL for specialized metabolites, indicating differences in the genetic architecture of seeds and leaves. In seeds, aliphatic methylsulfinylalkyl and methylthioalkyl glucosinolates associated with the ALKENYL HYDROXYALKYL PRODUCING loci (GS-ALK and GS-OHP) on chromosome 4 containing alkenyl hydroxyalkyl producing 2 (AOP2) and 3 (AOP3) or with the GS-ELONG locus on chromosome 5 containing methylthioalkyl malate synthase (MAM1) and MAM3. We detected two unknown sulfur-containing compounds that were also mapped to these loci. In GWAS, some of the annotated flavonoids (kaempferol 3-O-rhamnoside-7-O-rhamnoside, quercetin 3-O-rhamnoside-7-O-rhamnoside) were mapped to transparent testa 7 (AT5G07990), encoding a cytochrome P450 75B1 monooxygenase. Three additional mass signals corresponding to quercetin-containing flavonols were mapped to UGT78D2 (AT5G17050). The association of the loci and associating metabolic features were functionally verified in knockdown mutant lines. By performing GWAS and QTL mapping, we were able to leverage variation of natural populations and parental lines to study seed specialized metabolism. The GWAS data set generated here is a high-quality resource that can be investigated in further studies.journal articl
A Proteorhodopsin-Related Photosensor Expands the Repertoire of Structural Motifs Employed by Sensory Rhodopsins
No full textMicrobial rhodopsins are light-activated retinal-binding membrane proteins that perform a variety of ion transport and photosensory functions. They display several cases of convergent evolution where the same function is present in unrelated or very distant protein groups. Here we report another possible case of such convergent evolution, describing the biophysical properties of a new group of sensory rhodopsins. The first representative of this group was identified in 2004 but none of the members had been expressed and characterized. The well-studied haloarchaeal sensory rhodopsins interacting with methyl-accepting Htr transducers are close relatives of the halobacterial proton pump bacteriorhodopsin. In contrast, the sensory rhodopsins we describe here are relatives of proteobacterial proton pumps, proteorhodopsins, but appear to interact with Htr-like transducers likewise, even though they do not conserve the residues important for the interaction of haloarchaeal sensory rhodopsins with their transducers. The new sensory rhodopsins display many unusual amino acid residues, including those around the retinal chromophore; most strikingly, a tyrosine in place of a carboxyl counterion of the retinal Schiff base on helix C. To characterize their unique sequence motifs, we augment the spectroscopy and biochemistry data by structural modeling of the wild-type and three mutants. Taken together, the experimental data, bioinformatics sequence analyses, and structural modeling suggest that the tyrosine/aspartate complex counterion contributes to a complex water-mediated hydrogen-bonding network that couples the protonated retinal Schiff base to an extracellular carboxylic dyad.journal articl
Investigating the Effects of Pruning Vision-Transformer's White Patches on Document-Related Tasks
Get PDF奈良先端科学技術大学院大学修士(工学)master thesi
Development of Machine Learning-Based Web System for Estimating Pleural Effusion Using Multi-Frequency Bioelectrical Impedance Analyses
No full textBackground: Transthoracic impedance values have not been widely used to measure extravascular pulmonary water content due to accuracy and complexity concerns. Our aim was to develop a foundational model for a novel system aiming to non-invasively estimate the intrathoracic condition of heart failure patients. Methods: We employed multi-frequency bioelectrical impedance analysis to simultaneously measure multiple frequencies, collecting electrical, physical, and hematological data from 63 hospitalized heart failure patients and 82 healthy volunteers. Measurements were taken upon admission and after treatment, and longitudinal analysis was conducted. Results: Using a light gradient boosting machine, and a decision tree-based machine learning method, we developed an intrathoracic estimation model based on electrical measurements and clinical findings. Out of the 286 features collected, the model utilized 16 features. Notably, the developed model demonstrated high accuracy in discriminating patients with pleural effusion, achieving an area under the receiver characteristic curves (AUC) of 0.905 (95% CI: 0.87020130.792, and p < 0.0001). Conclusions: Our findings indicate the potential of machine learning and transthoracic impedance measurements for estimating pleural effusion. By incorporating noninvasive and easily obtainable clinical and laboratory findings, this approach offers an effective means of assessing intrathoracic conditions.journal articl
NAISTSOCRR at the NTCIR-17 MedNLP-SC Radiology Report Subtask
No full textThis paper describes how we tackled the Medical Natural Language Processing for Radiology Report TNM staging (RR-TNM) Subtask as participants of NTCIR17. The RR-TNM Subtask is a MedNLP-SC original task to classify radiology reports under multiple criteria. We introduced three different methods based on pre-trained language models (PLMs), including a medical-specific model. Notably, our combination approach, utilizing JMedRoBERTa (manbyo-wordpiece) for label T, Tohoku-BERT-v3 for label N, and UTH-BERT for label M, achieved an accuracy of 0.3704 on the test data. This performance was the highest among all participants, emphasizing the effectiveness of our strategy.conference pape
Thermoresponsive star-shaped polymer with heteroarm type with methacrylates: preparation by living radical polymerization method and its topological effect
Get PDFWe first designed the thermoresponsive star-shaped polymer with heteroarm structure based on methacrylates by living radical polymerization with Ru catalyst. The lowest critical solution temperature (LCST) of the heteroarm polymer was controlled within the range 262006:2006:$200617 and LCST of 35 °C, and poly(methyl methacrylate) (PMMA), and possessed approximately six arms of P(DEGMA-stat-TEGMA) and approximately two arms of PMMA. This heteroarm star-shaped polymer was insoluble in water. However, the star-shaped polymer-coated surface showed thermoresponsivity, in which the contact angle of the captive bubble changed from 131 ± 0.6° at 20 °C to 126 ± 1.9° at 40 °C. This result indicates that such heteroarm star-shaped polymers can be promising materials for constructing thermoresponsive surfaces using simple coating methods.journal articl
Particles and film preparation of ester-free type poly(trimethylene carbonate) derivatives bearing aromatic groups initiated with hydrophilic initiators
Get PDFAs our previous reports of facile synthetic ester-free type trimethylene carbonate-aromatic derivatives, we were herein prepared a series of particles and thin films of poly(trimethylene carbonate) (PTMC) bearing diphenyl-, bis-phenyl, and trityl pendants. The hydrophilic groups were featured at chain end while the side chain was introduced several hydrophobic aromatic groups as well as typical ester-free PTMC. Approaching the particle formation, oligo ethylene glycol was selected as hydrophilic initiator due to the high mobility, and biocompatibility. The synthetic PTMC particles were fabricated via self-organized precipitation method, its structural properties, morphologies, and surface behaviors were systematically explored. To examine the impact of structure, we investigated the degradation study of PTMC-trityl film coating which was enabled to convey a deceleration in enzymatic system.journal articl
Synthesis of ester-free poly(trimethylene carbonate) bearing cinnamyl moiety for antibacterial biomaterials applications
Get PDFAntimicrobial biocompatible polymers have highly desirable materials in medical technology to prevent any healthcare-associated infections from the in-dwelling on medical device that could pose a risk to patients, and this is gaining attention particularly in the context of the current COVID-19 pandemic. In this study, ester free type of poly(trimethylene carbonate) (PTMC) derivatives containing cinnamyl group has been synthesized. Also, several of alcohol-based initiators; benzyl alcohol, 2,2-dimethyl-1-propanol, 4-(2-hydroxyethoxy) benzaldehyde and 2-(p-tolyloxy)ethan-1-ol and polymer structure has been designed and analyzed its molecular weight on thermal and physical properties effect. The homopolymers and copolymers of PTMC derivatives with cinnamyl group had achieved with molecular weight up to 7400 05A9C respectively. Different types of essential oil, which is thymol and carvacrol, have been incorporated with cinnamyl PTMC had resulted the suppression of E.coli and S.aureus growth. The results showed a promising of introduction of cinnamyl derivatives into ester free-type of PTMC derivatives, as well as create more alcohol-initiators for polymerization of trimethylene carbonate, for more advanced development in the future.journal articl
Learning Boltzmann Machines using Quantum-assisted Monte Carlo
Get PDF奈良先端科学技術大学院大学修士(工学)master thesi
