Comprehensive In Silico Analysis and Transcriptional Profiles Highlight the Importance of Mitochondrial Dicarboxylate Carriers (DICs) on Hypoxia Response in Both Arabidopsis thaliana and Eucalyptus grandis

Plant dicarboxylate carriers (DICs) transport a wide range of dicarboxylates across the mitochondrial inner membrane. The Arabidopsis thalianaDIC family is composed of three genes (AtDIC1, 2 and 3), whereas two genes (EgDIC1 and EgDIC2) have been retrieved in Eucalyptus grandis. Here, by combining in silico and in planta analyses, we provide evidence that DICs are partially redundant, important in plant adaptation to environmental stresses and part of a low-oxygen response in both species. AtDIC1 and AtDIC2 are present in most plant species and have very similar gene structure, developmental expression patterns and absolute expression across natural Arabidopsis accessions. In contrast, AtDIC3 seems to be an early genome acquisition found in Brassicaceae and shows relatively low (or no) expression across these accessions. In silico analysis revealed that both AtDICs and EgDICs are highly responsive to stresses, especially to cold and submergence, while their promoters are enriched for stress-responsive transcription factors binding sites. The expression of AtDIC1 and AtDIC2 is highly correlated across natural accessions and in response to stresses, while no correlation was found for AtDIC3. Gene ontology enrichment analysis suggests a role for AtDIC1 and AtDIC2 in response to hypoxia, and for AtDIC3 in phosphate starvation. Accordingly, the investigated genes are induced by submergence stress in A. thaliana and E. grandis while AtDIC2 overexpression improved seedling survival to submergence. Interestingly, the induction of AtDIC1 and AtDIC2 is abrogated in the erfVII mutant that is devoid of plant oxygen sensing, suggesting that these genes are part of a conserved hypoxia response in Arabidopsis.

Download Full-text

IN SILICO ANALYSIS OF GENE EXPRESSION PATTERNS DURING EARLY DEVELOPMENT OF XENOPUS LAEVIS

Biocomputing 2000 ◽

10.1142/9789814447331_0042 ◽

1999 ◽

Author(s):

N. POLLET ◽

H. A. SCHMIDT ◽

V. GAWANTKA ◽

C. NIEHRS ◽

M. VINGRON

Keyword(s):

Gene Expression ◽

Xenopus Laevis ◽

Early Development ◽

In Silico ◽

Expression Patterns ◽

In Silico Analysis ◽

Gene Expression Patterns ◽

Silico Analysis

Download Full-text

In Silico Analysis of Laccifer Lacca as a Potential Therapeutic Agent for Cervical, Breast and Lung Cancers

Journal of Drug Delivery and Therapeutics ◽

10.22270/jddt.v11i3.4802 ◽

2021 ◽

Vol 11 (3) ◽

pp. 79-85

Author(s):

Ashish Kumar ◽

Neeraj Kumar ◽

Balwan Singh

Keyword(s):

Nitric Oxide ◽

Molecular Docking ◽

In Silico ◽

A549 Cells ◽

In Silico Analysis ◽

Wide Range ◽

Anticancer Therapeutics ◽

Anti Inflammatory ◽

Silico Analysis

Laccifer lacca has generally been used as pigmenting, coloring agent and dying in chemical industry. Although, it has wide range of industrial applications, but inappropriately, due to lesser availability of data, it has been ignored. Keeping in mind, the wide application of Laccifer lacca, we tried to report the in-silico anti-cancer effects. The experimental techniques used to determine the structure was X-RAY diffraction. The reported resolution of this entry is 2.80 Å. Percentile scores (ranging between 0-100) for global authentication metrics of the record. In silico have a good pool to explore various parameters in molecular docking. We have performed in silico analysis of the active components of Laccifer lacca against the cervical, breast and lung cancer proteins and also found that lac extract enhances the production of anti-inflammatory markers and the increase is significant when compared to the standard vinblastine. It has been demonstrated by Lala and colleagues that a short lived molecule nitric oxide can result in the progression of human tumours. Therefore, the prominent antioxidant activity of phytochemical that can act as inhibitors of nitric oxide production can act as anticancer therapeutics. Both methanolic and aqueous extract shows significant anticancer effect on the hela, MCF-7 & A549 cells suggesting them as potential anticancer therapeutics for future. Keywords: Laccifer lacca, In-vitro & In-silico analysis, Carcinogenesis, Anti-inflammatory, Molecular Docking.

Download Full-text

The Expression Patterns of BECN1, LAMP2, and PINK1 Genes in Colorectal Cancer Are Potentially Regulated by Micrornas and CpG Islands: An In Silico Study

Journal of Clinical Medicine ◽

10.3390/jcm9124020 ◽

2020 ◽

Vol 9 (12) ◽

pp. 4020

Author(s):

Martyna Bednarczyk ◽

Edyta Fatyga ◽

Sylwia Dzięgielewska-Gęsiak ◽

Dariusz Waniczek ◽

Beniamin Grabarek ◽

...

Keyword(s):

Colorectal Cancer ◽

In Silico ◽

Expression Patterns ◽

Cpg Islands ◽

In Silico Analysis ◽

Epigenetic Changes ◽

Grid Infrastructure ◽

In Silico Study ◽

Silico Analysis

Background: Autophagy plays a dual role of tumor suppression and tumor promotion in colorectal cancer. The study aimed to find those microRNAs (miRNAs) important in BECN1, LAMP2, and PINK1 regulation and to determine the possible role of the epigenetic changes in examined colorectal cancer using an in silico approach. Methods: A total of 44 pairs of surgically removed tumors at clinical stages I‒IV and healthy samples (marginal tissues) from patients’ guts were analyzed. Analysis of the obtained results was conducted using the PL-Grid Infrastructure and Statistica 12.0 program. The miRNAs and CpG islands were estimated using the microrna.org database and MethPrimer program. Results: The autophagy-related genes were shown to be able to be regulated by miRNAs (BECN1—49 mRNA, LAMP2—62 mRNA, PINK1—6 mRNA). It was observed that promotion regions containing at least one CpG region were present in the sequence of each gene. Conclusions: The in silico analysis performed allowed us to determine the possible role of epigenetic mechanisms of regulation gene expression, which may be an interesting therapeutic target in the treatment of colorectal cancer.

Download Full-text

In silico analysis and developmental expression of ubiquitin-conjugating enzymes in Schistosoma mansoni

Parasitology Research ◽

10.1007/s00436-015-4362-x ◽

2015 ◽

Vol 114 (5) ◽

pp. 1769-1777 ◽

Cited By ~ 3

Author(s):

Marcela P. Costa ◽

Victor F. Oliveira ◽

Roberta V. Pereira ◽

Fabiano C. P. de Abreu ◽

Liana K. Jannotti-Passos ◽

...

Keyword(s):

Schistosoma Mansoni ◽

In Silico ◽

In Silico Analysis ◽

Developmental Expression ◽

Conjugating Enzymes ◽

Ubiquitin Conjugating Enzymes ◽

Silico Analysis

Download Full-text

In Vitro Phenotypic Activity and In Silico Analysis of Natural Products from Brazilian Biodiversity on Trypanosoma cruzi

Molecules ◽

10.3390/molecules26185676 ◽

2021 ◽

Vol 26 (18) ◽

pp. 5676

Author(s):

Raiza B. Peres ◽

Ludmila F. de A. Fiuza ◽

Patrícia B. da Silva ◽

Marcos M. Batista ◽

Flávia da C. Camillo ◽

...

Keyword(s):

Natural Products ◽

Trypanosoma Cruzi ◽

In Silico ◽

In Silico Analysis ◽

Mammalian Host ◽

Reference Drug ◽

Wide Range ◽

Pure Compounds ◽

Silico Analysis

Chagas disease (CD) affects more than 6 million people worldwide. The available treatment is far from ideal, creating a demand for new alternative therapies. Botanical diversity provides a wide range of novel potential therapeutic scaffolds. Presently, our aim was to evaluate the mammalian host toxicity and anti-Trypanosoma cruzi activity of botanic natural products including extracts, fractions and purified compounds obtained from Brazilian flora. In this study, 36 samples of extracts and fractions and eight pure compounds obtained from seven plant species were evaluated. The fraction dichloromethane from Aureliana fasciculata var. fasciculata (AFfPD) and the crude extract of Piper tectoniifolium (PTFrE) showed promising trypanosomicidal activity. AFfPD and PTFrE presented EC50 values 10.7 ± 2.8 μg/mL and 12.85 ± 1.52 μg/mL against intracellular forms (Tulahuen strain), respectively. Additionally, both were active upon bloodstream trypomastigotes (Y strain), exhibiting EC50 2.2 ± 1.0 μg/mL and 38.8 ± 2.1 μg/mL for AFfPD and PTFrE, respectively. Importantly, AFfPD is about five-fold more potent than Benznidazole (Bz), the reference drug for CD, also reaching lower EC90 value (7.92 ± 2.2 μg/mL) as compared to Bz (23.3 ± 0.6 μg/mL). Besides, anti-parasitic effect of eight purified botanic substances was also investigated. Aurelianolide A and B (compounds 1 and 2) from A. fasciculata and compound 8 from P. tuberculatum displayed the best trypanosomicidal effect. Compounds 1, 2 and 8 showed EC50 of 4.6 ± 1.3 μM, 1.6 ± 0.4 μM and 8.1 ± 0.9 μM, respectively against intracellular forms. In addition, in silico analysis of these three biomolecules was performed to predict parameters of absorption, distribution, metabolism and excretion. The studied compounds presented similar ADMET profile as Bz, without presenting mutagenicity and hepatotoxicity aspects as predicted for Bz. Our findings indicate that these natural products have promising anti-T. cruzi effect and may represent new scaffolds for future lead optimization.

Download Full-text

Molecular modeling of the interaction of the dihydroquercetin and its metabolites with cyclooxygenase-2

Bulletin of Siberian Medicine ◽

10.20538/1682-0363-2019-3-101-106 ◽

2019 ◽

Vol 18 (3) ◽

pp. 101-106 ◽

Cited By ~ 2

Author(s):

R. P. Terekhov ◽

I. A. Selivanova

Keyword(s):

Molecular Modeling ◽

In Silico ◽

In Silico Analysis ◽

Cyclooxygenase 2 ◽

Protein Data Bank Code ◽

Antiinflammatory Drugs ◽

Study Objective ◽

Wide Range ◽

Cox 2 ◽

Silico Analysis

Background. Dihydroquercetin (DHQ) is a natural flavonoid. It has a wide range of pharmacological effects, which includes anti-inflammatory activity. There is a gap in our knowledge about the biochemical mechanisms of the therapeutic potency implementation of this compound. This fact slows down the process of the drug development using DHQ. Molecular modeling is designed to further translate the research from the fundamental experimentation to the real clinical practice. Purpose. The study objective was to estimate DHQ as a cyclooxygenase-2 (COX-2) inhibitor by using in silico analysis.Materials and methods. The information about the COX-2 structure was obtained from the Protein Data Bank (code 5KIR). The 3D-models of DHQ were generated by using the ChemBioDraw Ultra software. Docking was carried out in the GOLD program after the corresponding validation of molecular modeling algorithms based on experimental data of X-ray diffraction analysis.Results. The design of this study is based on the rational selecting of the virtual ligand structures. It gives an opportunity to optimize the quantum-mechanical calculation. By using in silico analysis, it was shown that DHQ and some of its metabolites demonstrate ability of binding to SER353, SER530, and ARG513 of COX-2 at the catalytic site.Conclusion. Important α-amino acids for intermolecular interaction of DHQ and its metabolites with COX-2 were determined during this study. Our data can be used for the development of new antiinflammatory drugs on the base of DHQ.

Download Full-text

Comparative in Silico Analysis of Ferric Reduction Oxidase (FRO) Genes Expression Patterns in Response to Abiotic Stresses, Metal and Hormone Applications

Molecules ◽

10.3390/molecules23051163 ◽

2018 ◽

Vol 23 (5) ◽

pp. 1163 ◽

Cited By ~ 6

Author(s):

Izhar Muhammad ◽

Xiu-Qing Jing ◽

Abdullah Shalmani ◽

Muhammad Ali ◽

Shi Yi ◽

...

Keyword(s):

In Silico ◽

Abiotic Stresses ◽

Expression Patterns ◽

In Silico Analysis ◽

Genes Expression ◽

Silico Analysis

Download Full-text

In Silico Analysis of Extended-Spectrum β-Lactamases in Bacteria

Antibiotics ◽

10.3390/antibiotics10070812 ◽

2021 ◽

Vol 10 (7) ◽

pp. 812

Author(s):

Patrik Mlynarcik ◽

Hana Chudobova ◽

Veronika Zdarska ◽

Milan Kolar

Keyword(s):

In Silico ◽

Phylogenetic Trees ◽

Bacterial Resistance ◽

Public Health Problem ◽

In Silico Analysis ◽

Amino Acid Sequences ◽

Extended Spectrum ◽

Wide Range ◽

Phosphoethanolamine Transferases ◽

Silico Analysis

The growing bacterial resistance to available β-lactam antibiotics is a very serious public health problem, especially due to the production of a wide range of β-lactamases. At present, clinically important bacteria are increasingly acquiring new elements of resistance to carbapenems and polymyxins, including extended-spectrum β-lactamases (ESBLs), carbapenemases and phosphoethanolamine transferases of the MCR type. These bacterial enzymes limit therapeutic options in human and veterinary medicine. It must be emphasized that there is a real risk of losing the ability to treat serious and life-threatening infections. The present study aimed to design specific oligonucleotides for rapid PCR detection of ESBL-encoding genes and in silico analysis of selected ESBL enzymes. A total of 58 primers were designed to detect 49 types of different ESBL genes. After comparing the amino acid sequences of ESBLs (CTX-M, SHV and TEM), phylogenetic trees were created based on the presence of conserved amino acids and homologous motifs. This study indicates that the proposed primers should be able to specifically detect more than 99.8% of all described ESBL enzymes. The results suggest that the in silico tested primers could be used for PCR to detect the presence of ESBL genes in various bacteria, as well as to monitor their spread.

Download Full-text

Comparative gene-based in silico analysis of transcriptomes in different bovine tissues and (or) organs

Genome ◽

10.1139/g04-084 ◽

2004 ◽

Vol 47 (6) ◽

pp. 1164-1172 ◽

Cited By ~ 2

Author(s):

Zhihua Jiang ◽

Xiao-Lin Wu ◽

Matthew D Garcia ◽

Kirsten B Griffin ◽

Jennifer J Michal ◽

...

Keyword(s):

Expressed Sequence Tags ◽

In Silico ◽

Expression Patterns ◽

In Silico Analysis ◽

Orthologous Genes ◽

Functional Relations ◽

Human Genes ◽

Expressed Sequence ◽

Silico Analysis ◽

Tissue Library

A gene-based approach was used to annotate 322 168 cattle expressed sequence tags (ESTs) based on human genes in order to census the transcriptomes, analyze their expression similarities, and identify genes preferentially expressed in different bovine tissues and (or) organs. Of the 34 157 human coding genes used in a standalone BLAST search, 14 928 could be matched with provisional orthologous sequences in a total of 230 135 bovine ESTs. The remaining 92 033 bovine ESTs were estimated to represent an additional 5970 genes in cattle. On average, ~8600 genes were estimated to be expressed in a single tissue and (or) organ and 13 000 in a pooled tissue library. On the basis of the estimated numbers of genes, no more than 3% of genes would be missed when ~34 000 ESTs were sequenced from a single tissue and (or) organ library and ~40 000 ESTs from a pooled source, respectively. Cluster analyses of the gene expression patterns among 12 single tissues and (or) organs in cattle revealed that their expression similarities would depend on physiological functions. In addition, a total of 1502 genes were identified as preferentially expressed genes in these 12 single tissues and (or) organs with LOD (logarithm of the odds, base 10) ≥ 3.0. Therefore, our study provides some insights for further investigating the developmental and functional relations of various tissues and organs in mammals.Key words: cattle, expressed sequence tags (ESTs), orthologous genes, comparative gene-based approach, in silico census, tissue/organs, transcriptomes.

Download Full-text