MUNEEBA MALIK¹, MAMOONA MAQBOOL², TOOBA NISAR³, TAZEEM AKHTER⁴, JAVED AHMED UJAN^5,6, ALANOOD S. ALGARNI⁷, FAKHRIA A. AL JOUFI⁸, SULTAN SHAFI K. ALANAZI⁹, MOHAMMAD HADI ALMOTARED¹⁰, MOUNIR M. SALEM BEKHIT¹¹, MUHAMMAD JAMIL^12,*

Oncology Research, Vol.31, No.6, pp. 899-916, 2023, DOI:10.32604/or.2023.030760 - 15 September 2023

Abstract The low survival rate of Kidney renal clear cell carcinoma (KIRC) patients is largely attributed to cisplatin resistance. Rather than focusing solely on individual proteins, exploring protein-protein interactions could offer greater insight into drug resistance. To this end, a series of in silico and in vitro experiments were conducted to identify hub genes in the intricate network of cisplatin resistance-related genes in KIRC chemotherapy. The genes involved in cisplatin resistance across KIRC were retrieved from the National Center for Biotechnology Information (NCBI) database using search terms as “Kidney renal clear cell carcinoma” and “Cisplatin resistance”. The genes… More >

Mehdi Hassan^1,2, Safdar Ali³, Jin Young Kim^2,*, Muhammad Sanaullah⁴, Hani Alquhayz⁵, Khushbakht Safdar⁶

CMC-Computers, Materials & Continua, Vol.76, No.2, pp. 1643-1663, 2023, DOI:10.32604/cmc.2023.038578 - 30 August 2023

Abstract Breast cancer resistance protein (BCRP) is an important resistance protein that significantly impacts anticancer drug discovery, treatment, and rehabilitation. Early identification of BCRP substrates is quite a challenging task. This study aims to predict early substrate structure, which can help to optimize anticancer drug development and clinical diagnosis. For this study, a novel intelligent approach-based methodology is developed by modifying the ResNet101 model using transfer learning (TL) for automatic deep feature (DF) extraction followed by classification with linear discriminant analysis algorithm (TLRNDF-LDA). This study utilized structural fingerprints, which are exploited by DF contrary to conventional More >

Hafiza Arooj Razzaq¹, Siddra Ijaz^1,*, Imran Ul Haq², Faisal Saeed Awan¹

Phyton-International Journal of Experimental Botany, Vol.92, No.8, pp. 2451-2460, 2023, DOI:10.32604/phyton.2023.030501 - 25 June 2023

Abstract The imperative aspect of the CRISPR/Cas9 system is a short stretch of 20 nucleotides of gRNA that control the overall specificity. Due to the small size, the chance of its multiple occurrences in the genome increases; however, a few mismatches are tolerated by the Cas9 endonuclease activity. An accurate and careful in silico-based off-target prediction while target selection is preferred to address the issue. These predictions are based on a comprehensive set of selectable parameters. Therefore, we investigated the possible off-target prediction and their screening in StERF3 gene-edited potato plants while developing StERF3-loss-of-function mutants using CRISPR/Cas9 More >

SEUNGHYUN AHN¹, JUNG-YEON LEE¹, JIHA SUNG^1,2, HYUN JOO KIM³, SEYEON PARK^1,2,*

BIOCELL, Vol.47, No.7, pp. 1661-1673, 2023, DOI:10.32604/biocell.2023.027984 - 21 June 2023

Abstract Background: Although the GABAA receptor (GABAAR) has been proposed as the main action site for sevoflurane, isoflurane, halothane, enflurane, propofol, and benzodiazepines (BZDs), binding of these anesthetics with high-resolution structures of the GABAAR have been rarely examined by comparative docking analyses. Moreover, various combinations of ligands on more GABAARs with various subtypes need to be analyzed to understand the elaborate action mechanism of GABAARs better because some GABAA ligands showed specificity toward the distinct subtypes of the GABAAR. Methods: We performed in silico docking analysis to compare the binding modes of sevoflurane, isoflurane, halothane, enflurane, propofol,… More >

Oliver Tusevski^1,*, Marija Todorovska¹, Jasmina Petreska Stanoeva², Marina Stefova², Sonja Gadzovska Simic¹

Phyton-International Journal of Experimental Botany, Vol.92, No.3, pp. 921-941, 2023, DOI:10.32604/phyton.2023.024995 - 29 November 2022

Abstract Three Hypericum perforatum hairy root lines (HR B, HR F and HR H) along with non-transformed roots were analyzed for phenolic compounds composition and in vitro enzyme inhibitory properties. In silico molecular modeling was performed to predict the interactions of the most representative phenolic compounds in HR clones with enzymes related to depression, neurodegeneration and diabetes. Chromatographic analyses revealed that HR clones represent an efficient source of quinic acid and hydroxybenzoic acids, epicatechin and procyanidin derivatives, quercetin and kaempferol glycosides, as well numerous xanthones. In vitro antidepressant activity of HR extracts through monoamine oxidase A (MAO-A) inhibition was attributed… More >

Rachele Allena^1,*, Denis Aubry²

Molecular & Cellular Biomechanics, Vol.19, No.1, pp. 1-16, 2022, DOI:10.32604/mcb.2022.018958 - 12 January 2022

Abstract Cells adapt to their environment and stimuli of different origin. During confined migration through sub-cellular and sub-nuclear pores, they can undergo large strains and the nucleus, the most voluminous and the stiffest organelle, plays a critical role. Recently, patterned microfluidic devices have been employed to analyze the cell mechanical behavior and the nucleus self-deformations. In this paper, we present an in silico model to simulate the interactions between the cell and the underneath microstructured substrate under the effect of the sole gravity. The model lays on mechanical features only and it has the potential to assess… More >

KATARINA BARALIć^1,*, KATARINA ŽIVANčEVIć¹, DRAGICA BoŽIĆ¹, DANYEL JENNEN², ALEKSANDRA BUHA DJORDJEVIC¹, EVICA ANTONIJEVIć MILJAKOVIć¹, DANIJELA ĐUKIć-ĆOSIć¹

BIOCELL, Vol.46, No.2, pp. 519-533, 2022, DOI:10.32604/biocell.2022.018271 - 20 October 2021

Abstract This in silico toxicogenomic study aims to explore the relationship between phthalates and bisphenol A (BPA) co-exposure and obesity, as well as its comorbid conditions, in order to construct a possible set of genomic biomarkers. The Comparative Toxicogenomics Database (CTD; http://ctd.mdibl.org) was used as the main data mining tool, along with GeneMania (https://genemania.org), ToppGene Suite (https://toppgene.cchmc.org) and DisGeNET (http://www.disgenet.org). Among the phthalates, bis(2-ethylhexyl) phthalate (DEHP) and dibutyl phthalate (DBP) were chosen as the most frequently curated phthalates in CTD, which also share similar mechanisms of toxicity. DEHP, DBP and BPA interacted with 84, 90 and 194… More >

JIAYU ZHANG^1,2,3,#, RUOYAN CAO^1,2,3,#, JIANMIN PENG^1,2,3, QINCHAO HU^1,2,3, JUAN XIA^1,2,3,*, BIN CHENG^1,2,3,*

BIOCELL, Vol.46, No.1, pp. 111-125, 2022, DOI:10.32604/biocell.2022.016612 - 28 September 2021

Abstract Metabolic reprogramming and immunologic suppression are two critical characteristics promoting the progression of head and neck squamous cell carcinoma (HNSCC). The integrative analysis of all the metabolism-related genes (MRGs) in HNSCC is lacking and the interaction between the metabolism and the immune characteristics also requires more exploration to uncover the potential mechanisms. Therefore, this study was designed to establish a prognostic signature based on all the MRGs in HNSCC. Genes of HNSCC samples were available from the TCGA and GEO databases while the MRGs were retrieved from a previous study. Ultimately 4 prognostic MRGs were… More >

DANIEL WAI-HUNG HO^1,2,#, XUEYING LYU^1,2,#, IRENE OI-LIN NG^1,2,*

BIOCELL, Vol.45, No.6, pp. 1495-1500, 2021, DOI:10.32604/biocell.2021.017227 - 01 September 2021

Abstract Oncovirus infection is crucial in human malignancies. Certain oncoviruses can lead to structural variations in the human genome known as viral genomic integration, which can contribute to tumorigenesis. Existing viral integration detection tools differ in their underlying algorithms pinpointing different aspects or features of viral integration phenomenon. We discuss about major procedures in performing viral integration detection. More importantly, we provide a technical update on Virus-Clip to facilitate its usage on the latest human genome builds (hg19 and hg38) and the adoption of multi-thread mode for faster initial read alignment. By comparing the execution of More >

CÜNEYT UÇARLI^*

BIOCELL, Vol.45, No.6, pp. 1673-1685, 2021, DOI:10.32604/biocell.2021.016316 - 01 September 2021

Abstract RAV (Related to ABI3/VP1) transcription factors are unique members of the AP2-ERF superfamily with AP2 and B3 domains and play important roles in the regulation of seed germination, plant growth, and stress response. In the study, 7 RAV genes, named HvRAVs, were identified in barley based on the available genome sequences. While five of the seven HvRAVs were located on chromosome 3, HvRAV5 and HvRAV7 were located on chromosome 1 and 4, respectively. Six of the predicted HvRAVs were intron-less, except HvRAV2, which had one intron. HvRAV proteins have shown basic, instable, and hydrophilic properties. The AP2 domain specific… More >