scholarly journals A novel WD40-repeat protein involved in formation of epidermal bladder cells in the halophyte quinoa

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Tomohiro Imamura ◽  
Yasuo Yasui ◽  
Hironori Koga ◽  
Hiroki Takagi ◽  
Akira Abe ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Shoot Apex ◽  
In Silico ◽  
Genetic Basis ◽  
Wd40 Repeat ◽  
Shoot Apices ◽  
Saline Tolerance ◽  
Trichome Formation ◽  
Bladder Cells ◽  
And Function

AbstractHalophytes are plants that grow in high-salt environments and form characteristic epidermal bladder cells (EBCs) that are important for saline tolerance. To date, however, little has been revealed about the formation of these structures. To determine the genetic basis for their formation, we applied ethylmethanesulfonate mutagenesis and obtained two mutants with reduced levels of EBCs (rebc) and abnormal chloroplasts. In silico subtraction experiments revealed that the rebc phenotype was caused by mutation of REBC, which encodes a WD40 protein that localizes to the nucleus and chloroplasts. Phylogenetic and transformant analyses revealed that the REBC protein differs from TTG1, a WD40 protein involved in trichome formation. Furthermore, rebc mutants displayed damage to their shoot apices under abiotic stress, suggesting that EBCs may protect the shoot apex from such stress. These findings will help clarify the mechanisms underlying EBC formation and function.

scholarly journals Meta-QTL analysis and identification of candidate genes for quality, abiotic and biotic stress in durum wheat

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jose Miguel Soriano ◽  
Pasqualina Colasuonno ◽  
Ilaria Marcotuli ◽  
Agata Gadaleta
Keyword(s):  
Molecular Markers ◽  
Abiotic Stress ◽  
Durum Wheat ◽  
Candidate Genes ◽  
Biotic Stress ◽  
Qtl Analysis ◽  
Complex Traits ◽  
Genetic Basis ◽  
Agronomic Traits ◽  
Plant Performance

AbstractThe genetic improvement of durum wheat and enhancement of plant performance often depend on the identification of stable quantitative trait loci (QTL) and closely linked molecular markers. This is essential for better understanding the genetic basis of important agronomic traits and identifying an effective method for improving selection efficiency in breeding programmes. Meta-QTL analysis is a useful approach for dissecting the genetic basis of complex traits, providing broader allelic coverage and higher mapping resolution for the identification of putative molecular markers to be used in marker-assisted selection. In the present study, extensive QTL meta-analysis was conducted on 45 traits of durum wheat, including quality and biotic and abiotic stress-related traits. A total of 368 QTL distributed on all 14 chromosomes of genomes A and B were projected: 171 corresponded to quality-related traits, 127 to abiotic stress and 71 to biotic stress, of which 318 were grouped in 85 meta-QTL (MQTL), 24 remained as single QTL and 26 were not assigned to any MQTL. The number of MQTL per chromosome ranged from 4 in chromosomes 1A and 6A to 9 in chromosome 7B; chromosomes 3A and 7A showed the highest number of individual QTL (4), and chromosome 7B the highest number of undefined QTL (4). The recently published genome sequence of durum wheat was used to search for candidate genes within the MQTL peaks. This work will facilitate cloning and pyramiding of QTL to develop new cultivars with specific quantitative traits and speed up breeding programs.

scholarly journals Genetic basis for glandular trichome formation in cotton

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Dan Ma ◽  
Yan Hu ◽  
Changqing Yang ◽  
Bingliang Liu ◽  
Lei Fang ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Glandular Trichome ◽  
Trichome Formation

In Silico Identification of Novel Acute Myeloid Leukemia Associated Missense SNPs in Human CEBPA Gene

2020 ◽  
pp. 10-24
Keyword(s):  
Acute Myeloid Leukemia ◽  
In Silico ◽  
Myeloid Leukemia ◽  
Gene Interaction ◽  
Nucleotide Polymorphisms ◽  
Future Perspectives ◽  
Single Nucleotide ◽  
In Silico Identification ◽  
And Function ◽  
Acute Myeloid

Single nucleotide polymorphisms (SNPs) in CEBPA gene have been found to be associated with cancer especially Acute Myeloid Leukemia (AML). Therefore, the identification of functional and structural polymorphisms in CEBPA is important to study and discover therapeutics targets and potential malfunctioning. For this purpose, several bioinformatics tools were used for the identification of disease-associated nsSNPs, which might be vital for the structure and function of CEBPA, making them extremely important. In silico tools used in this study included SIFT, PROVEAN, PolyPhen2, SNP&GO and PhD-SNP, followed by ConSurf and I-Mutant. Protein 3D modelling was carried out using I-TASSER and MODELLER v9.22, while GeneMANIA and string were used for the prediction of gene-gene interaction in this regard. From our study, we found that the L345P, R333C, R339Q, V328G, R327W, L317Q, N292S, E284A, R156W, Y108N and F82L mutations were the most crucial SNPs. Additionally, the gene-gene interaction showed the genes having correlation with CEBPA’s co-expressions and importance in several pathways. In future, these 11 mutations should be investigated while studying diseases related to CEBPA, especially for AML. Being the first of its kind, future perspectives are proposed in this study, which will help in precision medicine. Animal models are of great significance in finding out CEBPA effects in disease.

Cloning, characterization and in silico studies on abiotic stress responsive Hsp17.9 from Prosopis cineraria

2018 ◽  
Vol 23 (4) ◽  
pp. 731-740 ◽  
Author(s):  
Amritpal Kaur ◽  
Harinder Vishwakarma ◽  
Albert Maibam ◽  
Jasdeep Chatrath Padaria
Keyword(s):  
Abiotic Stress ◽  
In Silico ◽  
Prosopis Cineraria ◽  
In Silico Studies

scholarly journals Structure and function insights garnered from in silico modeling of the thrombospondin type-1 domain-containing 7A antigen

2018 ◽  
Vol 87 (2) ◽  
pp. 136-145 ◽  
Author(s):  
Shana V. Stoddard ◽  
Colin L. Welsh ◽  
Maggie M. Palopoli ◽  
Serena D. Stoddard ◽  
Mounika P. Aramandla ◽  
...  
Keyword(s):  
In Silico ◽  
Structure And Function ◽  
In Silico Modeling ◽  
And Function

In silico study of the structure and function of Streptococcus mutans plasmidic proteins

2017 ◽  
Vol 13 (2) ◽  
Author(s):  
Silvia Caprari ◽  
Giovanni Minervini ◽  
Valentina Brandi ◽  
Fabio Polticelli
Keyword(s):  
Streptococcus Mutans ◽  
In Silico ◽  
Structure And Function ◽  
Positive Bacterium ◽  
Gram Positive ◽  
In Silico Study ◽  
And Function

AbstractThe Gram-positive bacterium

scholarly journals The riddle of phyllotaxis: exquisite control of divergence angle

2016 ◽  
Vol 85 (4) ◽  
Author(s):  
Takuya Okabe
Keyword(s):  
Plant Species ◽  
Shoot Apex ◽  
Evidence Base ◽  
Divergence Angle ◽  
Shoot Apices ◽  
Essential Point

Phyllotaxis studies published in German in the 1930s have reported intriguing regularity in the arrangement of incipient leaves on shoot apices of a wide variety of plant species. However, these studies have received little attention today, even though they provide a crucial evidence base for understanding this mathematical phenomena. Here I recapitulate the essential point by means of illustrative examples. It is emphasized that accurate control of apical divergence angle is at the heart of the numerical riddle of spiral phyllotaxis. The accurate patterning at the shoot apex has an unexpected evolutionary benefit of being optimally adaptive in the subsequent events of phyllotactic change to occur on an elongating shoot.

scholarly journals In silico promoter and expression analyses of rice Auxin Binding Protein 57 (ABP57)

2021 ◽  
Vol 8 (3) ◽  
pp. 741-748
Author(s):  
Farah Afiqah Baharuddin ◽  
Zhan Xuan Khong ◽  
Zamri Zainal ◽  
Noor Liyana Sukiran
Keyword(s):  
Abiotic Stress ◽  
In Silico ◽  
Binding Protein ◽  
Transcript Level ◽  
Regulatory Elements ◽  
Biochemical Properties ◽  
Auxin Receptor ◽  
Reverse Transcription Pcr ◽  
Auxin Binding ◽  
Auxin Binding Protein

Auxin Binding Protein 57 (ABP57) is one of the molecular components involved in rice response to abiotic stress. The ABP57 gene encodes an auxin receptor which functions in activating the plasma membrane H+-ATPase. Biochemical properties of ABP57 have been characterized; however, the function of ABP57, particularly on stress and hormone responses is still limited. This study was conducted to understand the regulation of ABP57 expression under abiotic stress. Thus, in silico identification of cis-acting regulatory elements (CAREs) in the promoter region of ABP57 was performed. Several motifs and transcription factor binding site (TFBS) that are involved in abiotic stress such as ABRE, DRE, AP2/EREBP, WRKY and NAC were identified. Next, expression analysis of ABP57 under drought, salt, auxin (IAA) and abscisic acid (ABA) was conducted by reverse transcription-PCR (RT-PCR) to verify the effect of these treatments on ABP57 transcript level. ABP57 was expressed at different levels in the shoot and root under drought conditions, and its expression was increased under IAA and ABA treatments. Moreover, our results showed that ABP57 expression in the root was more responsive to drought, auxin and ABA treatments compared to its transcript in the shoot. This finding suggests that ABP57 is a drought-responsive gene and possibly regulated by IAA and ABA.

scholarly journals Novel deleterious nsSNPs within MEFV gene that could be used as Diagnostic Markers to Predict Hereditary Familial Mediterranean Fever: Using bioinformatics analysis

2018 ◽  
Author(s):  
Mujahed I. Mustafa ◽  
Tebyan A Abdelhameed ◽  
Fatima A. Abdelrhman ◽  
Soada Ahmed Osman ◽  
Mohamed A. Hassan
Keyword(s):  
Familial Mediterranean Fever ◽  
In Silico ◽  
Mediterranean Basin ◽  
Mefv Gene ◽  
Structure And Function ◽  
Diagnostic Markers ◽  
Novel Mutations ◽  
Bioinformatics Tools ◽  
Mediterranean Fever ◽  
And Function

AbstractBackgroundFamilial Mediterranean Fever (FMF) is the most common auto inflammatory disease (AID) affecting mainly the ethnic groups originating from Mediterranean basin, we aimed to identify the pathogenic SNPs in MEFV by computational analysis software.MethodsWe carried out in silico prediction of structural effect of each SNP using different bioinformatics tools to predict substitution influence on protein structure and function.Result23 novel mutations out of 857 nsSNPs that are found to be deleterious effect on the MEFV structure and function.ConclusionThis is the first in silico analysis in MEFV gene to prioritize SNPs for further genetic mapping studies. After using multiple bioinformatics tools to compare and rely on the results predicted, we found 23 novel mutations that may cause FMF disease and it could be used as diagnostic markers for Mediterranean basin populations.

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