Mutation of OsCAX1a Results in Panicle Degeneration in Rice

2021 ◽  
Author(s):  
Quan Gan ◽  
Fengshun Song ◽  
Cuixiang Lin ◽  
Dahu Ni
Keyword(s):  
Protein Sequence ◽  
Essential Role ◽  
Cereal Crops ◽  
View Point ◽  
Mutation Site ◽  
Protein Sequence Alignment ◽  
Qrt Pcr ◽  
Panicle Development ◽  
Motif Identification ◽  
First Time

Abstract Background: Rice is one of the most common cereal crops in China. Increasing the yield of rice has always been a primary purpose of rice breeding. However, panicle degeneration in rice, a complex characteristic regulated by many genes and commonly encountered in rice production, seriously reduces the yield. Findings: In this study, we obtained a new apical panicle degeneration mutant named ym48, which exhibits a serious degeneration rate and reduced grain yield in rice. After fine mapping, the OsCAX1a gene responsible for Ca2+ selection and transportation was identified. In the ym48 mutant of the OsCAX1a gene, a A to G substitution was noted at the 190th nucleotide, and the corresponding 64th amino acid was changed from threonine to alanine. Also, the tolerance from Ca2+ stress was damaged due to the mutation. Phylogenetics, protein sequence alignment and motif identification of CAX family members in Arabidopsis and rice indicated that this mutation site was highly conserved and might play an essential role in Ca2+ transportation. Moreover, the OsCAX1a expression pattern was analyzed in rice. qRT-PCR and GUS (β-glucuronidase) staining experiments showed that OsCAX1a was highly expressed in roots, stems and panicles and that its expression increased with panicle development. Conclusions: These results demonstrated that OsCAX1a played an essential role in the regulation of panicle development for the first time and mutation of OsCAX1a would generate the panicle degeneration in rice. This study provided a new view point to explore the mechanism of panicle development and degeneration in rice.

scholarly journals Cytotoxic Effect of RecombinantMycobacterium tuberculosisCFP-10/ESAT-6 Protein on the Crucial Pathways of WI-38 Cells

2009 ◽  
Vol 2009 ◽  
pp. 1-10 ◽  
Author(s):  
Kun-Nan Tsai ◽  
Err-Cheng Chan ◽  
Tsung-Yeh Tsai ◽  
Kuei-Tien Chen ◽  
Chun-Yu Chen ◽  
...  
Keyword(s):  
Focal Adhesion ◽  
Microarray Data ◽  
Cytotoxic Effect ◽  
Time Course ◽  
Essential Role ◽  
Topological Properties ◽  
Regulatory Effect ◽  
Qrt Pcr ◽  
Focal Adhesion Pathway ◽  
Pathway Databases

To unravel the cytotoxic effect of the recombinant CFP-10/ESAT-6 protein (rCFES) on WI-38 cells, an integrative analysis approach, combining time-course microarray data and annotated pathway databases, was proposed with the emphasis on identifying the potentially crucial pathways. The potentially crucial pathways were selected based on a composite criterion characterizing the average significance and topological properties of important genes. The analysis results suggested that the regulatory effect of rCFES was at least involved in cell proliferation, cell motility, cell survival, and metabolisms of WI-38 cells. The survivability of WI-38 cells, in particular, was significantly decreased to 62% with 12.5 μMrCFES. Furthermore, the focal adhesion pathway was identified as the potentially most-crucial pathway and 58 of 65 important genes in this pathway were downregulated by rCFES treatment. Using qRT-PCR, we have confirmed the changes in the expression levels of LAMA4, PIK3R3, BIRC3, and NFKBIA, suggesting that these proteins may play an essential role in the cytotoxic process in the rCFES-treated WI-38 cells.

scholarly journals 902. A Randomized, Double-Blind, Placebo-Controlled Study to Evaluate the Efficacy of a Single Immunization of Ad26.RSV.preF against RSV Infection in a Viral Challenge Model in Healthy Adults

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S27-S28 ◽  
Author(s):  
John DeVincenzo ◽  
Efi Gymnopoulou ◽  
Els De Paepe ◽  
Bryan Murray ◽  
Arangassery Rosemary Bastian ◽  
...  
Keyword(s):  
Disease Severity ◽  
Healthy Adults ◽  
Controlled Study ◽  
Clinical Strain ◽  
Double Blind ◽  
Double Blind Placebo ◽  
Qrt Pcr ◽  
Rsv Infection ◽  
First Time ◽  
Over Time

Abstract Background Despite the high disease burden of RSV in older adults and children, there is currently no approved vaccine. Ad26.RSV.preF, an experimental RSV vaccine, has demonstrated immunogenicity and tolerability in first-in-human clinical studies. The aim of this study was to assess the potential of the Ad26.RSV.preF vaccine to protect against RSV infection and disease in an established RSV human challenge model, used for the first time to evaluate a vaccine. Methods We conducted a randomized, double-blind, placebo-controlled, human challenge study (NCT03334695). Healthy adults received 1 × 1011 vp Ad26.RSV.preF vaccine (active) or placebo (pbo) intramuscularly. After 28 days, volunteers were challenged intranasally with a low-passage clinical strain of RSV-A (0.8 mL of Memphis 37b) and then quarantined for 12 days. Nasal washes were collected twice daily throughout quarantine, starting 2 days post-challenge (viral load [VL] by qRT-PCR and quantitative cultures). Disease severity was recorded thrice daily using symptom diary cards. Results Fifty-three volunteers (active, n = 27; pbo, n = 26) were challenged with RSV-A. Quantitative viral assessments were consistently lower in active than pbo. The primary endpoint of the study was met: the area under the curve (AUC) for RSV VL over time (via qRT-PCR) was significantly lower in active pbo (P = 0.012). Median peak VL was lower for active (0 log10 copies/mL) than pbo (5.4 log10 copies/mL). Median AUC for RSV VL over time (quantitative culture) was lower for active than pbo (0 vs. 109, P = 0.002). Disease severity was lower for active than pbo, with a median AUC total symptom score of 35 (active) vs. 167 (pbo) (P = 0.002). Overall, RSV infection (defined by qRT-PCR alone or combined with symptoms) and disease severity over time were lower in active vs. pbo. Conclusion RSV infections, VL, and RSV disease severity were consistently lower in healthy adults receiving Ad26.RSV.preF vs. placebo, demonstrating promising protection from RSV infection and disease. This was the first time that antiviral prevention was observed against RSV after active immunization. Ad26.RSV.preF warrants further evaluation in field trials for efficacy against natural RSV infections in populations considered at risk of severe RSV disease. Disclosures All Authors: No reported Disclosures.

scholarly journals Analysis of Structures and Epitopes of Surface Antigen Glycoproteins Expressed in Bradyzoites ofToxoplasma gondii

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Hua Cong ◽  
Min Zhang ◽  
Qingli Zhang ◽  
Jing Gong ◽  
Haizi Cong ◽  
...  
Keyword(s):  
Immune Response ◽  
Toxoplasma Gondii ◽  
Immune Responses ◽  
Surface Antigen ◽  
Protein Sequence ◽  
Protozoan Parasite ◽  
3D Models ◽  
Chronic Infections ◽  
Homologous Proteins ◽  
Protein Sequence Alignment

Toxoplasma gondiiis a protozoan parasite capable of infecting humans and animals. Surface antigen glycoproteins, SAG2C, -2D, -2X, and -2Y, are expressed on the surface of bradyzoites. These antigens have been shown to protect bradyzoites against immune responses during chronic infections. We studied structures of SAG2C, -2D, -2X, and -2Y proteins using bioinformatics methods. The protein sequence alignment was performed by T-Coffee method. Secondary structural and functional domains were predicted using software PSIPRED v3.0 and SMART software, and 3D models of proteins were constructed and compared using the I-TASSER server, VMD, and SWISS-spdbv. Our results showed that SAG2C, -2D, -2X, and -2Y are highly homologous proteins. They share the same conserved peptides and HLA-I restricted epitopes. The similarity in structure and domains indicated putative common functions that might stimulate similar immune response in hosts. The conserved peptides and HLA-restricted epitopes could provide important insights on vaccine study and the diagnosis of this disease.

scholarly journals AlphaFold at CASP13

2019 ◽  
Vol 35 (22) ◽  
pp. 4862-4865 ◽  
Author(s):  
Mohammed AlQuraishi
Keyword(s):  
Protein Structure ◽  
Protein Sequence ◽  
Structure Prediction ◽  
Computational Prediction ◽  
Data Bank ◽  
Academic Community ◽  
Physical Contact ◽  
Evolutionary Analysis ◽  
History Of ◽  
First Time

Abstract Summary: Computational prediction of protein structure from sequence is broadly viewed as a foundational problem of biochemistry and one of the most difficult challenges in bioinformatics. Once every two years the Critical Assessment of protein Structure Prediction (CASP) experiments are held to assess the state of the art in the field in a blind fashion, by presenting predictor groups with protein sequences whose structures have been solved but have not yet been made publicly available. The first CASP was organized in 1994, and the latest, CASP13, took place last December, when for the first time the industrial laboratory DeepMind entered the competition. DeepMind's entry, AlphaFold, placed first in the Free Modeling (FM) category, which assesses methods on their ability to predict novel protein folds (the Zhang group placed first in the Template-Based Modeling (TBM) category, which assess methods on predicting proteins whose folds are related to ones already in the Protein Data Bank.) DeepMind's success generated significant public interest. Their approach builds on two ideas developed in the academic community during the preceding decade: (i) the use of co-evolutionary analysis to map residue co-variation in protein sequence to physical contact in protein structure, and (ii) the application of deep neural networks to robustly identify patterns in protein sequence and co-evolutionary couplings and convert them into contact maps. In this Letter, we contextualize the significance of DeepMind's entry within the broader history of CASP, relate AlphaFold's methodological advances to prior work, and speculate on the future of this important problem.

scholarly journals Perennial Ryegrass Contains Gluten-Like Proteins That Could Contaminate Cereal Crops

2021 ◽  
Vol 8 ◽  
Author(s):  
Sophia Escobar-Correas ◽  
James A. Broadbent ◽  
Alicja Andraszek ◽  
Sally Stockwell ◽  
Crispin A. Howitt ◽  
...  
Keyword(s):  
Multiple Reaction Monitoring ◽  
Wheat Gluten ◽  
Shotgun Proteomics ◽  
Cereal Crops ◽  
Wheat Cultivars ◽  
Liquid Chromatography Mass Spectrometry ◽  
Free Products ◽  
Poaceae Family ◽  
Gliadin Peptides ◽  
First Time

Background: To ensure safe consumption of gluten-free products, there is a need to understand all sources of unintentional contamination with gluten in the food chain. In this study, ryegrass (Lolium perenne), a common weed infesting cereal crop, is analysed as a potential source of gluten-like peptide contamination.Materials and Methods: Ten ryegrass cultivars were analysed using shotgun proteomics for the presence of proteins from the prolamin superfamily. A relative quantitative assay was developed to detect ryegrass gluten-like peptides in comparison with those found in 10 common wheat cultivars.Results: A total of 19 protein accessions were found across 10 cultivars of ryegrass for the protein families of PF00234-Tryp_alpha_amyl, PF13016-Gliadin, and PF03157-Glutenin_HMW. Protein and peptide homology searches revealed that gliadin-like peptides were similar to avenin and gamma-gliadin peptides. A total of 20 peptides, characteristic of prolamin superfamily proteins, were selected for liquid chromatography mass spectrometry (LC-MS) with multiple reaction monitoring (MRM). Only two of the monitored peptides were detected with high abundance in wheat, and all others were detected in ryegrass. Glutenin and alpha-amylase/trypsin inhibitor peptides were reported for the first time in ryegrass and were noted to be conserved across the Poaceae family.Conclusion: A suite of gluten-like peptides were identified using proteomics that showed consistent abundance across ryegrass cultivars but were not detected in wheat cultivars. These peptides will be useful for differentiating wheat gluten contamination from ryegrass gluten contamination.

Codon usage and protein sequence pattern dependency in different organisms: A Bioinformatics approach

2015 ◽  
Vol 13 (02) ◽  
pp. 1550002
Author(s):  
Mohammad-Hadi Foroughmand-Araabi ◽  
Bahram Goliaei ◽  
Kasra Alishahi ◽  
Mehdi Sadeghi ◽  
Sama Goliaei
Keyword(s):  
Gene Regulation ◽  
Codon Usage ◽  
Protein Sequence ◽  
Multinomial Logistic Regression ◽  
Translation Efficiency ◽  
Translation Rate ◽  
Protein Levels ◽  
Synonymous Codons ◽  
First Time

Although it is known that synonymous codons are not chosen randomly, the role of the codon usage in gene regulation is not clearly understood, yet. Researchers have investigated the relation between the codon usage and various properties, such as gene regulation, translation rate, translation efficiency, mRNA stability, splicing, and protein domains. Recently, a universal codon usage based mechanism for gene regulation is proposed. We studied the role of protein sequence patterns on the codons usage by related genes. Considering a subsequence of a protein that matches to a pattern or motif, we showed that, parts of the genes, which are translated to this subsequence, use specific ratios of synonymous codons. Also, we built a multinomial logistic regression statistical model for codon usage, which considers the effect of patterns on codon usage. This model justifies the observed codon usage preference better than the classic organism dependent codon usage. Our results showed that the codon usage plays a role in controlling protein levels, for genes that participate in a specific biological function. This is the first time that this phenomenon is reported.

scholarly journals Effect of trans-chalcone on hepatic IL-8 through the regulation of miR-451 in male rats

2018 ◽  
Vol 52 (1) ◽  
pp. 1-5 ◽  
Author(s):  
Elham Karimi-Sales ◽  
Sajad Jeddi ◽  
Arshad Ghaffari-Nasab ◽  
Mina Salimi ◽  
Mohammad Reza Alipour
Keyword(s):  
Serum Level ◽  
Proinflammatory Cytokines ◽  
Serum Levels ◽  
Male Rats ◽  
Positive Effects ◽  
Qrt Pcr ◽  
Group Control ◽  
First Time ◽  
Hepatic Level

Abstract Objective. Trans-chalcone is a chalcone with hepatoprotective and anti-inflammatory effects. However, the mechanism of these positive effects, especially on miR-451 as an inflammatory regulator, is poorly understood. In this regard, this microRNA (miRNA) acts by inhibition of hepatic interleukin-8 (IL-8) production in the liver which is one of the main proinflammatory cytokines. Th is study for the first time examined the effect of trans-chalcone on miR-451/IL-8 pathway. Methods. In present study, 21 male rats were randomly divided into 3 groups (n=7 per each group): control which received solvent (NS), groups 2 (N2T) and 3 (N6T), which received transchalcone for 2 and 6 weeks, respectively. Hepatic level of miR-451 was measured by qRT-PCR. Serum levels of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) as well as hepatic level of IL-8 protein were measured. Results. Trans-chalcone decreased hepatic level of IL-8 protein and serum level of ALT aft er 2 weeks of treatment without significant change in hepatic miR-451. Moreover, it increased hepatic level of miR-451 and reduced hepatic IL-8 as well as AST and ALT aft er 6 weeks. Conclusion. Based on the results of present study, miR-451/IL-8 pathway is a possible mechanism for hepatoprotective action of trans-chalcone in long-term.

slimb coordinates wg and dpp expression in the dorsal-ventral and anterior-posterior axes during limb development

Development ◽  
1998 ◽  
Vol 125 (17) ◽  
pp. 3411-3416 ◽  
Author(s):  
N.A. Theodosiou ◽  
S. Zhang ◽  
W.Y. Wang ◽  
T. Xu
Keyword(s):  
Genetic Analysis ◽  
Limb Development ◽  
Imaginal Disc ◽  
Essential Role ◽  
Present Evidence ◽  
First Time ◽  
Anterior Posterior

In the Drosophila leg disc, wingless (wg) and decapentaplegic (dpp) are expressed in a ventral-anterior and dorsal-anterior stripe of cells, respectively. This pattern of expression is essential for proper limb development. While the Hedgehog (Hh) pathway regulates dpp and wg expression in the anterior-posterior (A/P) axis, mechanisms specifying their expression in the dorsal-ventral (D/V) axis are not well understood. We present evidence that slimb mutant clones in the disc deregulate wg and dpp expression in the D/V axis. This suggests for the first time that their expression in the D/V axis is actively regulated during imaginal disc development. Furthermore, slimb is unique in that it also deregulates wg and dpp in the A/P axis. The misexpression phenotypes of slimb- clones indicate that the regulation of wg and dpp expression is coordinated in both axes, and that slimb plays an essential role in integrating A/P and D/V signals for proper patterning during development. Our genetic analysis further reveals that slimb intersects the A/P pathway upstream of smoothened (smo).

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