scholarly journals Fine-Tuning of the Grain Size by Alternative Splicing of GS3 in Rice

Rice ◽  
2022 ◽  
Vol 15 (1) ◽  
Author(s):  
Lei Liu ◽  
Ying Zhou ◽  
Feng Mao ◽  
Yujuan Gu ◽  
Ziwei Tang ◽  
...  
Keyword(s):  
Grain Size ◽  
Alternative Splicing ◽  
Fine Tuning ◽  
General Mechanism ◽  
Transcriptional Level ◽  
Negative Effects ◽  
Size Regulation ◽  
Multiple Signaling ◽  
Fine Tune ◽  
Translational Level

AbstractGrain size is subtly regulated by multiple signaling pathways in rice. Alternative splicing is a general mechanism that regulates gene expression at the post-transcriptional level. However, to our knowledge, the molecular mechanism underlying grain size regulation by alternative splicing is largely unknown. GS3, the first identified QTL for grain size in rice, is regulated at the transcriptional and post-translational level. In this study, we identified that GS3 is subject to alternative splicing. GS3.1 and GS3.2, two dominant isoforms, accounts for about 50% and 40% of total transcripts, respectively. GS3.1 encodes the full-length protein, while GS3.2 generated a truncated proteins only containing OSR domain due to a 14 bp intronic sequence retention. Genetic analysis revealed that GS3.1 overexpressors decreased grain size, but GS3.2 showed no significant effect on grain size. Furthermore, we demonstrated that GS3.2 disrupts GS3.1 signaling by competitive occupation of RGB1. Therefore, we draw a conclusion that the alternative splicing of GS3 decreases the amount of GS3.1 and GS3.2 disrupts the GS3.1 signaling to inhibit the negative effects of GS3.1 to fine-tune grain size. Moreover, the mechanism is conserved in cereals rather than in Cruciferae, which is associated with its effects on grain size. The results provide a novel, conserved and important mechanism underlying grain size regulation at the post-transcriptional level in cereals.

Fine-tuning of the Grain Size by Alternative Splicing of GS3 in Rice

2021 ◽  
Author(s):  
Lei Liu ◽  
Ying Zhou ◽  
Feng Mao ◽  
Yujuan Gu ◽  
Ziwei Tang ◽  
...  
Keyword(s):  
Grain Size ◽  
Alternative Splicing ◽  
Fine Tuning ◽  
General Mechanism ◽  
Transcriptional Level ◽  
Negative Effects ◽  
Size Regulation ◽  
Multiple Signaling ◽  
Fine Tune ◽  
Translational Level

Abstract Grain size is subtly regulated by multiple signaling pathways in rice. Alternative splicing is a general mechanism that regulates gene expression at the post-transcriptional level. However, to our knowledge, the molecular mechanism underlying grain size regulation by alternative splicing is largely unknown. GS3, the first identified QTL for grain size in rice, is regulated at the transcriptional and post-translational level. In this study, we identified that GS3 is subject to alternative splicing. GS3.1 and GS3.2, two dominant isoforms, accounts for about 50% and 40% of total transcripts, respectively. GS3.1 encodes the full-length protein, while GS3.2 generated a truncated proteins only containing OSR domain due to a 14 bp intronic sequence retention. Genetic analysis revealed that GS3.1 overexpressors decreased grain size, but GS3.2 showed no significant effect on grain size. Furthermore, we demonstrated that GS3.2 disrupts GS3.1 signaling by competitive occupation of RGB1. Therefore, we draw a conclusion that the alternative splicing of GS3 decreases the amount of GS3.1 and GS3.2 disrupts the GS3.1 signaling to inhibit the negative effects of GS3.1 to fine-tune grain size. Moreover, the mechanism is conserved in cereals rather than in Cruciferae, which is associated with its effects on grain size. The results provide a novel, conserved and important mechanism underlying grain size regulation at the post-transcriptional level in cereals.

Fine-Tuning Electronic Properties of Luminescent Pt(II) Complexes via Vertex-Differentiated Coordination of Sterically Invariant Carborane-Based Ligands

2018 ◽  
Author(s):  
Kent O. Kirlikovali ◽  
Jonathan C. Axtell ◽  
Kierstyn Anderson ◽  
Peter I. Djurovich ◽  
Arnold L. Rheingold ◽  
...  
Keyword(s):  
Coordination Chemistry ◽  
Metal Complexes ◽  
Electronic Properties ◽  
Fine Tuning ◽  
Fine Tune

We report the synthesis of two isomeric Pt(II) complexes ligated by doubly deprotonated 1,1′-bis(<i>o</i>-carborane) (<b>bc</b>). This work provides a potential route to fine-tune the electronic properties of luminescent metal complexes by virtue of vertex-differentiated coordination chemistry of carborane-based ligands.

scholarly journals Fine-tuning of a generative neural network for designing multi-target compounds

2021 ◽  
Author(s):  
Thomas Blaschke ◽  
Jürgen Bajorath
Keyword(s):  
Neural Network ◽  
Small Molecules ◽  
De Novo ◽  
Pharmaceutical Research ◽  
Generative Models ◽  
Fine Tuning ◽  
Data Sets ◽  
Single Target ◽  
Fine Tune ◽  
Target Activity

AbstractExploring the origin of multi-target activity of small molecules and designing new multi-target compounds are highly topical issues in pharmaceutical research. We have investigated the ability of a generative neural network to create multi-target compounds. Data sets of experimentally confirmed multi-target, single-target, and consistently inactive compounds were extracted from public screening data considering positive and negative assay results. These data sets were used to fine-tune the REINVENT generative model via transfer learning to systematically recognize multi-target compounds, distinguish them from single-target or inactive compounds, and construct new multi-target compounds. During fine-tuning, the model showed a clear tendency to increasingly generate multi-target compounds and structural analogs. Our findings indicate that generative models can be adopted for de novo multi-target compound design.

scholarly journals Scanning electron microscope fine tuning using four-bar piezoelectric actuated mechanism

2018 ◽  
Vol 69 (1) ◽  
pp. 24-31
Author(s):  
Khaled S. Hatamleh ◽  
Qais A. Khasawneh ◽  
Adnan Al-Ghasem ◽  
Mohammad A. Jaradat ◽  
Laith Sawaqed ◽  
...  
Keyword(s):  
Electron Microscope ◽  
Scanning Electron Microscope ◽  
Inverse Kinematic ◽  
Fine Tuning ◽  
Electron Microscopes ◽  
Tuning Strategy ◽  
Scanning Electron Microscopes ◽  
Fine Tune ◽  
Kinematic Solution ◽  
Scanning Electron

Abstract Scanning Electron Microscopes are extensively used for accurate micro/nano images exploring. Several strategies have been proposed to fine tune those microscopes in the past few years. This work presents a new fine tuning strategy of a scanning electron microscope sample table using four bar piezoelectric actuated mechanisms. The introduced paper presents an algorithm to find all possible inverse kinematics solutions of the proposed mechanism. In addition, another algorithm is presented to search for the optimal inverse kinematic solution. Both algorithms are used simultaneously by means of a simulation study to fine tune a scanning electron microscope sample table through a pre-specified circular or linear path of motion. Results of the study shows that, proposed algorithms were able to minimize the power required to drive the piezoelectric actuated mechanism by a ratio of 97.5% for all simulated paths of motion when compared to general non-optimized solution.

Methylation of the nuclear poly(A)-binding protein by type I protein arginine methyltransferases – how and why

2013 ◽  
Vol 394 (8) ◽  
pp. 1029-1043 ◽  
Author(s):  
Elmar Wahle ◽  
Bodo Moritz
Keyword(s):  
Active Sites ◽  
Binding Protein ◽  
Arginine Methylation ◽  
Fine Tuning ◽  
General Mechanism ◽  
Type I ◽  
Protein Arginine Methyltransferases ◽  
Low Protein ◽  
Backbone Conformation ◽  
Arginine Residues

Abstract Asymmetric dimethylation of arginine side chains in proteins is a frequent posttranslational modification, catalyzed by type I protein arginine methyltransferases (PRMTs). This article summarizes what is known about this modification in the nuclear poly(A)-binding protein (PABPN1). PABPN1 contains 13 dimethylated arginine residues in its C-terminal domain. Three enzymes, PRMT1, 3, and 6, can methylate PABPN1. Although 26 methyl groups are transferred to one PABPN1 molecule, the PRMTs do so in a distributive reaction, i.e., only a single methyl group is transferred per binding event. As PRMTs form dimers, with the active sites accessible from a small central cavity, backbone conformation around the methyl-accepting arginine is an important determinant of substrate specificity. Neither the association of PABPN1 with poly(A) nor its role in poly(A) tail synthesis is affected by arginine methylation. At least at low protein concentration, methylation does not affect the protein’s tendency to oligomerize. The dimethylarginine residues of PABPN1 are located in the binding site for its nuclear import receptor, transportin. Arginine methylation weakens this interaction about 10-fold. Very recent evidence suggests that arginine methylation as a way of fine-tuning the interactions between transportin and its cargo may be a general mechanism.

scholarly journals Multipotent Genetic Suppression of Retrotransposon-Induced Mutations by Nxf1 through Fine-Tuning of Alternative Splicing

PLoS Genetics ◽  
2009 ◽  
Vol 5 (5) ◽  
pp. e1000484 ◽  
Author(s):  
Dorothy Concepcion ◽  
Lisbeth Flores-García ◽  
Bruce A. Hamilton
Keyword(s):  
Alternative Splicing ◽  
Fine Tuning ◽  
Induced Mutations ◽  
Genetic Suppression

A Study of the Influence of Data Complexity and Similarity on Soft Biometrics Classification Performance in a Transfer Learning Scenario

2021 ◽  
Vol 18 (2) ◽  
pp. 56-65
Author(s):  
Marcelo Romero ◽  
◽  
Matheus Gutoski ◽  
Leandro Takeshi Hattori ◽  
Manassés Ribeiro ◽  
...  
Keyword(s):  
Transfer Learning ◽  
Classification Performance ◽  
Fine Tuning ◽  
Similarity Metrics ◽  
Soft Biometrics ◽  
Final Layer ◽  
The One ◽  
Fully Connected ◽  
The Relationship ◽  
Fine Tune

Transfer learning is a paradigm that consists in training and testing classifiers with datasets drawn from distinct distributions. This technique allows to solve a particular problem using a model that was trained for another purpose. In the recent years, this practice has become very popular due to the increase of public available pre-trained models that can be fine-tuned to be applied in different scenarios. However, the relationship between the datasets used for training the model and the test data is usually not addressed, specially where the fine-tuning process is done only for the fully connected layers of a Convolutional Neural Network with pre-trained weights. This work presents a study regarding the relationship between the datasets used in a transfer learning process in terms of the performance achieved by models complexities and similarities. For this purpose, we fine-tune the final layer of Convolutional Neural Networks with pre-trained weights using diverse soft biometrics datasets. An evaluation of the performances of the models, when tested with datasets that are different from the one used for training the model, is presented. Complexity and similarity metrics are also used to perform the evaluation.

scholarly journals Human microRNAs in host–parasite interaction: a review

3 Biotech ◽  
2020 ◽  
Vol 10 (12) ◽  
Author(s):  
Sujay Paul ◽  
Luis M. Ruiz-Manriquez ◽  
Francisco I. Serrano-Cano ◽  
Carolina Estrada-Meza ◽  
Karla A. Solorio-Diaz ◽  
...  
Keyword(s):  
Noncoding Rna ◽  
Fine Tuning ◽  
Transcriptional Level ◽  
Response Modulation ◽  
Rna Molecules ◽  
Small Noncoding Rna ◽  
Diagnosis And Prognosis ◽  
Cell Proliferation And Differentiation ◽  
Host Parasite ◽  
The Impact

AbstractMicroRNAs (miRNAs) are a group of small noncoding RNA molecules with significant capacity to regulate the gene expression at the post-transcriptional level in a sequence-specific manner either through translation repression or mRNA degradation triggering a fine-tuning biological impact. They have been implicated in several processes, including cell growth and development, signal transduction, cell proliferation and differentiation, metabolism, apoptosis, inflammation, and immune response modulation. However, over the last few years, extensive studies have shown the relevance of miRNAs in human pathophysiology. Common human parasitic diseases, such as Malaria, Leishmaniasis, Amoebiasis, Chagas disease, Schistosomiasis, Toxoplasmosis, Cryptosporidiosis, Clonorchiasis, and Echinococcosis are the leading cause of death worldwide. Thus, identifying and characterizing parasite-specific miRNAs and their host targets, as well as host-related miRNAs, are important for a deeper understanding of the pathophysiology of parasite-specific diseases at the molecular level. In this review, we have demonstrated the impact of human microRNAs during host−parasite interaction as well as their potential to be used for diagnosis and prognosis purposes.

scholarly journals A Novel AdpA Homologue Negatively Regulates Morphological Differentiation inStreptomyces xiamenensis318

2019 ◽  
Vol 85 (7) ◽  
Author(s):  
Xu-Liang Bu ◽  
Jing-Yi Weng ◽  
Bei-Bei He ◽  
Min-Juan Xu ◽  
Jun Xu
Keyword(s):  
Cell Growth ◽  
Secondary Metabolism ◽  
Gene Cluster ◽  
Morphological Differentiation ◽  
Gene Clusters ◽  
Transcriptional Level ◽  
Negative Effects ◽  
Promoter Regions ◽  
Content Type ◽  
Enhanced Production

ABSTRACTThe pleiotropic transcriptional regulator AdpA positively controls morphological differentiation and regulates secondary metabolism in mostStreptomycesspecies.Streptomyces xiamenensis318 has a linear chromosome 5.96 Mb in size. How AdpA affects secondary metabolism and morphological differentiation in such a naturally minimized genomic background is unknown. Here, we demonstrated that AdpASx, an AdpA orthologue inS. xiamenensis, negatively regulates cell growth and sporulation and bidirectionally regulates the biosynthesis of xiamenmycin and polycyclic tetramate macrolactams (PTMs) inS. xiamenensis318. Overexpression of theadpASxgene inS. xiamenensis318 had negative effects on morphological differentiation and resulted in reduced transcription of putativessgA,ftsZ,ftsH,amfC,whiB,wblA1,wblA2,wblE, and a gene encoding sporulation-associated protein (sxim_29740), whereas the transcription of putativebldDandbldAgenes was upregulated. Overexpression ofadpASxled to significantly enhanced production of xiamenmycin but had detrimental effects on the production of PTMs. As expected, the transcriptional level of theximgene cluster was upregulated, whereas the PTM gene cluster was downregulated. Moreover, AdpASxnegatively regulated the transcription of its own gene. Electrophoretic mobility shift assays revealed that AdpASxcan bind the promoter regions of structural genes of both theximand PTM gene clusters as well as to the promoter regions of genes potentially involved in the cell growth and differentiation ofS. xiamenensis318. We report that an AdpA homologue has negative effects on morphological differentiation inS. xiamenensis318, a finding confirmed when AdpASxwas introduced into the heterologous hostStreptomyces lividansTK24.IMPORTANCEAdpA is a key regulator of secondary metabolism and morphological differentiation inStreptomycesspecies. However, AdpA had not been reported to negatively regulate morphological differentiation. Here, we characterized the regulatory role of AdpASxinStreptomyces xiamenensis318, which has a naturally streamlined genome. In this strain, AdpASxnegatively regulated cell growth and morphological differentiation by directly controlling genes associated with these functions. AdpASxalso bidirectionally controlled the biosynthesis of xiamenmycin and PTMs by directly regulating their gene clusters rather than through other regulators. Our findings provide additional evidence for the versatility of AdpA in regulating morphological differentiation and secondary metabolism inStreptomyces.

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