فهرست مطالب

Molecular Biology Research Communications
Volume:12 Issue: 3, Sep 2023

  • تاریخ انتشار: 1402/06/10
  • تعداد عناوین: 4
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  • Romina Mashayekh-Poul, Maryam Azimzadeh-Irani *, Seyedeh Zeinab Masoomi-Nomandan Pages 95-107
    The human epidermal growth factor receptor (EGFR/ErbB) family consists of four members (ErbB1-4) and belongs to the superfamily of receptor tyrosine kinases (RTKs). The ErbB family members participate in multiple cellular pathways and are the key players in several cancers (brain, breast, lung etc.). Activation of these family members depends on their extracellular domains forming back-to-back hetero/homo dimers. Moreover, dimers are glycosylated, which is a crucial post-translational modification that affects the conformation and function of the protein. Here, molecular modeling and molecular docking are used to comprehensively investigate the dimerization mechanism in glycosylated back-to-back active dimer formation in the entire ErbB receptors for the first time. Results showed that 21 out of 37 clusters of active back-to-back dimers formed by all family members are through heterodimerization. Including; ErbB1-ErbB3/ErbB4, ErbB2-ErbB3/ErbB4 and ErbB3-ErbB4. Ranking ErbB2-ErbB3 as the most stabilized back-to-back dimeric construct. While glycan arrangements favor both homo/hetero dimerization at the dimeric interfaces, it promotes heterodimerization by stabilizing and packing the ligand binding sites of EGFR and ErbB2 respectively. These findings pave the path to future heterodimeric interface/glycan targeting rational anti-cancer drug designs for ErbB receptors.
    Keywords: ErbB receptors, Dimerization, Back-to-back dimer, Molecular modeling
  • Serbulent Yiğit, Selim Kul, Recai Aci *, Adem Keskin, Tuğçe Tuygun, Esra Duman Pages 109-115
    In this study, the relationship between RORA 23bp indel genotype and allele frequency with twin pregnancy, fertility, live weight and milk yield in 106 female Akkaraman ewes raised in Elazığ province was investigated. In the study conducted in Elâzığ province, 10ml milk was collected from 106 Akkaraman sheep and DNA was extracted from these milk. In RORA 23bp indel genotype frequency, DD genotype was found more than ID and II genotypes and RORA 23bp indel ın allele frequency, the D allele was found to be higher than the I allele. In both the first and second parity, the twinning rate was found to be lower.  In both the first and second parity, the twinning rate was higher in the DD genotype, and it was observed that this genotype promınated mıddle lıvestock weıght and mılk yıeld. According to the results of our study, mutations in the RORA gene, which is a gene affecting reproductive efficiency in sheep, do not have a positive effect on fertility and twinning rate in Akkaraman sheep. To sum, this study provided theoretical references for the comprehensively research of the function of RORA gene and the breeding of Akkaraman  Sheep. The 23-bp indel variants can be considered as molecular markers for litter size of sheep for marker-assisted selection breeding.
    Keywords: Sheep, RORA, Insertion, deletion (Indel), Mmutation, Litter size
  • Nour Samman, Hassan Mohabatkar *, Parisa Rabiei Pages 117-126
    Phospholipases, as important lipolytic enzymes, have diverse industrial applications. Regarding the stability of extremophilic archaea’s proteins in harsh conditions, analyses of unusual features of their proteins are significantly important for their utilization. This research was accomplished to in silico study of archaeal phospholipases’ properties and to develop a pioneering method for distinguishing these enzymes from other archaeal enzymes via machine learning algorithms and Chou’s pseudo-amino acid composition concept. The non-redundant sequences of archaeal phospholipases were collected. BioSeq-Analysis sever was used with Support Vector Machine (SVM), Random Forests (RF), Covariance Discrimination (CD), and Optimized Evidence-Theoretic K-nearest Neighbor (OET-KNN) as powerful machine learnings algorithms. Also, different Chou’s pseudo-amino acid composition modes were performed and then, 5-fold cross-validation was applied to the sequences. Based on our results, the OET-KNN predictor, with 96% accuracy, yields the best performance in SC-PseAAC mode by 5-fold cross-validation. This predictor also achieved very high values of specificity (95%), sensitivity (96%), Matthews’s correlation coefficient (0.92), and accuracy (96%). The present investigation yielded a robust anticipatory model for the archaeal phospholipase prediction utilizing the tenets PseAAC and OET-KNN machine learning algorithm.
    Keywords: Archaea, Phospholipases, Machine learning, Chou’s PseAAC
  • Masoud Jabraili, Solmaz Moniri-Javadhesari *, Nasser Pouladi, MohammadAli Hosseinpour-Feizi Pages 127-131

    Thyroid cancer is the most common malignancy of the endocrine system. LncRNAs play critical role in various cellular processes and are associated with several diseases. CCAT2 is a lncRNA molecule overexpressed in thyroid cancer. Single nucleotide polymorphisms in CCAT2 gene can cause changes in the structure and function of CCAT2 transcripts and susceptibility to several diseases. This study aimed to evaluate the association of rs6983267 in CCAT2 gene with thyroid cancer susceptibility in the Azeri population of Iran. In this "case-control" study, genomic DNA was extracted from peripheral blood of 102 individuals affected by thyroid cancer and 103 healthy individuals as controls. Genotyping was performed using TETRA-ARMS polymerase chain reaction. Statistical analysis showed no significant association between genotypes and/or alleles with the occurrence of thyroid cancer in the studied population, patients' gender, and tumor type. Nevertheless, we found that the allelic and genotypic distribution of this SNP was associated with the size of thyroid tumors in patients. It is assumed that investigating more individuals from both case and control group may further determine the genotypic and allelic frequencies of this SNP locus in Iranian-Azeri population.

    Keywords: Thyroid cancer, Polymorphism, rs6983267, lncRNA, CCAT2