The role of S477N mutation in the molecular behavior of SARS-CoV-2 spike protein: An in-silico perspective

The attachment of SARA-CoV-2 happens between ACE2 and the receptor binding domain (RBD) on the spike protein. Mutations in this domain can affect the binding affinity of the spike protein for ACE2. S477N, one of the most common mutations reported in the recent variants, is located in the RBD. Today's computational approaches in biology, especially during the SARS-CoV-2 pandemic, assist researchers in predicting a protein's behavior in contact with other proteins in more detail. In this study, we investigated the interactions of the S477N-hACE2 in silico to find the impact of this mutation on its binding affinity for ACE2 and immunity responses using dynamics simulation, protein–protein docking, and immunoinformatics methods. Our computational analysis revealed an increased binding affinity of N477 for ACE2. Four new hydrogen and hydrophobic bonds in the mutant RBD-ACE2 were formed (with S19 and Q24 of ACE2), which do not exist in the wild type. Also, the protein spike structure in this mutation was associated with an increase in stabilization and a decrease in its fluctuations at the atomic level. N477 mutation can be considered as the cause of increased escape from the immune system through MHC-II.     

Functional Significance of K+ Channel β-Subunit KCNE3 in Auditory Neurons

The KCNE3 β-subunit interacts with and regulates the voltage-dependent gating, kinetics, and pharmacology of a variety of Kv channels in neurons. Because a single neuron may express multiple KCNE3 partners, it is impossible to predict the overall functional relevance of the single transmembrane domain peptide on the pore-forming K⁺ channel subunits with which it associates. In the inner ear, the role of KCNE3 is undefined, despite its association with Meniere disease and tinnitus. To gain insights on the functional significance of KCNE3 in auditory neurons, we examined the properties of spiral ganglion neurons (SGNs) in Kcne3 null mutant neurons relative to their age-matched controls. We demonstrate that null deletion of Kcne3 abolishes characteristic wide variations in the resting membrane potentials of SGNs and yields age-dependent alterations in action potential and firing properties of neurons along the contour of the cochlear axis, in comparison with age-matched wild-type neurons. The properties of basal SGNs were markedly altered in Kcne3^−/− mice compared with the wild-type controls; these include reduced action potential latency, amplitude, and increased firing frequency. Analyses of the underlying conductance demonstrate that null mutation of Kcne3 results in enhanced outward K⁺ currents, which is sufficient to explain the ensuing membrane potential changes. Additionally, we have demonstrated that KCNE3 may regulate the activity of Kv4.2 channels in SGNs. Finally, there were developmentally mediated compensatory changes that occurred such that, by 8 weeks after birth, the electrical properties of the null mutant neurons were virtually indistinguishable from the wild-type neurons, suggesting that ion channel remodeling in auditory neurons progresses beyond hearing onset.     

Autosomal recessive mental retardation: homozygosity mapping identifies 27 single linkage intervals, at least 14 novel loci and several mutation hotspots

Mental retardation (MR) has a worldwide prevalence of around 2% and is a frequent cause of severe disability. Significant excess of MR in the progeny of consanguineous matings as well as functional considerations suggest that autosomal recessive forms of MR (ARMR) must be relatively common. To shed more light on the causes of autosomal recessive MR (ARMR), we have set out in 2003 to perform systematic clinical studies and autozygosity mapping in large consanguineous Iranian families with non-syndromic ARMR (NS-ARMR). As previously reported (Najmabadi et al. in Hum Genet 121:43-48, 2007), this led us to the identification of 12 novel ARMR loci, 8 of which had a significant LOD score (OMIM: MRT5-12). In the meantime, we and others have found causative gene defects in two of these intervals. Moreover, as reported here, tripling the size of our cohort has enabled us to identify 27 additional unrelated families with NS-ARMR and single-linkage intervals; 14 of these define novel loci for non-syndromic ARMR. Altogether, 13 out of 39 single linkage intervals observed in our cohort were found to cluster at 6 different loci on chromosomes, i.e., 1p34, 4q27, 5p15, 9q34, 11p11-q13 and 19q13, respectively. Five of these clusters consist of two significantly overlapping linkage intervals, and on chr 1p34, three single linkage intervals coincide, including the previously described MRT12 locus. The probability for this distribution to be due to chance is only 1.14 × 10(-5), as shown by Monte Carlo simulation. Thus, in contrast to our previous conclusions, these novel data indicate that common molecular causes of NS-ARMR do exist, and in the Iranian population, the most frequent ones may well account for several percent of the patients. These findings will be instrumental in the identification of the underlying genes.     

Expression analysis of circulating plasma long noncoding RNAs in colorectal cancer: The relevance of lncRNAs ATB and CCAT1 as potential clinical hallmarks

Long noncoding RNAs (lncRNAs) have been demonstrated to regulate a variety of cell processes and involve in the development and progression of colorectal cancer (CRC). Recently, the circulating lncRNAs have emerged as minimally invasive biomarkers for cancer diagnosis and prognosis. We aimed to examine the plasma expression level of long noncoding RNAs lnc-ATB, lnc-CCAT1, and lnc-OCC-1 in CRC patients and evaluate the clinical values. A total of 74 pretreatment CRC and 74 healthy blood biopsies were subjected to differentially evaluate the expression levels of three lncRNAs (OCC-1, CCAT1, and ATB). Briefly, after plasma separation and total RNA extraction, RNAs were reversely transcribed to complementary DNA followed by amplification using a quantitative real-time polymerase chain reaction technique for lncRNA expression analysis. The results showed that the expression levels of lnc-ATB (p < 0.001) and CCAT1 (p = 0.024), but not OCC-1 (p = 0.24), were significantly upregulated in the CRC compared with the healthy group. The calculated AUC of ROC was 0.78 (95% confidence interval [CI]: 0.811–0.94) for lnc-ATB and 0.64 (95% CI: 0.811–0.94) for CCAT1, which were indicative of a high discriminatory power (p < 0.001). The highest accuracy for lncRNA-ATB was obtained at a cutoff point of 2.5, which corresponded to sensitivity and specificity of 82% and 75%, respectively. Our results suggested a significant accuracy of lncRNA-ATB and lncRNA-CCAT1 in distinguishing CRC patients from healthy individuals.     

A radiobiological comparison of hypo-fractionation versus conventional fractionation for breast cancer 3D-conformal radiation therapy

BackgroundThe present research was aimed to compare the toxicity and effectiveness of conventional fractionated radiotherapy versus hypo-fractionated radiotherapy in breast cancer utilizing a radiobiological model.Materials and methodsThirty-five left-sided breast cancer patients without involvement of the supraclavicular and axillary lymph nodes (with the nodal stage of N0) that had been treated with conventional or hypo-fractionated were incorporated in this study. A radiobiological model was performed to foretell normal tissue complication probability (NTCP) and tumor control probability (TCP).ResultsThe data represented that TCP values for conventional and hypo-fractionated regimens were 99.16 ± 0.09 and 95.96 ± 0.48, respectively (p = 0.00). Moreover, the NTCP values of the lung for conventional and hypo-fractionated treatment were 0.024 versus 0.13 (p = 0.035), respectively. Also, NTCP values of the heart were equal to zero for both regimens.ConclusionIn summary, hypo-fractionated regimens had comparable efficacy to conventional fraction radiation therapy in the case of dosimetry parameters for patients who had left breast cancer. But, utilizing the radiobiological model, conventional fractionated regimens presented better results compared to hypo-fractionated regimens.     

Targeted disruption of tyrosylprotein sulfotransferase-2, an enzyme that catalyzes post-translational protein tyrosine O-sulfation, causes male infertility

Tyrosine O-sulfation is a post-translational modification mediated by one of two Golgi tyrosylprotein sulfotransferases (TPST-1 and -2) expressed in all mammalian cells. Tyrosine sulfation plays an important role in the function of some known TPST substrates by enhancing protein-protein interactions. To explore the role of these enzymes in vivo and gain insight into other potential TPST substrates, TPST-2-deficient mice were generated by targeted disruption of the Tpst2 gene. Tpst2(+/-) mice appear normal and, when interbred, yield litters of normal size with a Mendelian distribution of the targeted mutation. Tpst2(-/-) mice have moderately delayed growth but appear healthy and attain normal body weight by 10 weeks of age. In contrast to Tpst1(-/-) males that have normal fertility, Tpst2(-/-) males are infertile. Tpst2(-/-) sperm are normal in number, morphology, and motility in normal media and appear to capacitate and undergo acrosomal exocytosis normally. However, they are severely defective in their motility in viscous media and in their ability to fertilize zona pellucida-intact eggs. Adhesion of Tpst2(-/-) sperm to the egg plasma membrane is reduced compared with wild type sperm, but sperm-egg fusion is similar or even increased. These data strongly suggest that tyrosine sulfation of unidentified substrate(s) play a crucial role in these processes and document for the first time the critical importance of post-translational tyrosine sulfation in male fertility.     

Short-term effect of weight loss through restrictive bariatric surgery on serum levels of vaspin in morbidly obese subjects

The aims of this study were to evaluate the short-term effects of laparoscopic restrictive bariatric surgery (LRBS) on plasma levels of vaspin and the potential associations of changes in vaspin levels with changes in anthropometric indices, insulin-resistance and dietary intake. Thirty, severely obese subjects (21 female; mean age, 32.5 years) with a mean body mass index (BMI) of 44.1 ± 4.9 kg/m(2) underwent LRBS. Measurements of anthropometric indices, dietary intakes, physical activity and plasma vaspin concentrations were performed prior to, and six weeks after LRBS. Insulin-sensitivity was estimated using the homeostasis model assessment of insulin-resistance (HOMA-IR). Six weeks after LRBS, BMI decreased to a mean of 38.4 ± 4.9 kg/m(2). Significant reductions were also observed in waist circumference (WC), daily intakes of calorie, fat and protein, and plasma concentrations of triglyceride. No significant change was observed in fasting levels of insulin, blood sugar or HOMA-IR. Vaspin decreased significantly (0.26 ± 0.17 vs 0.36 ± 0.20, p=0.048) following surgery. While the percentage change of vaspin was not correlated with percent changes in anthropometric indices and HOMA-IR, it correlated positively with the percentage change in intake of calories, fat and protein: this correlation remained significant even after adjustment for sex and changes in WC and HOMA-IR. Our study suggests that LRBS decreases the serum vaspin concentrations in parallel with the restriction of dietary intake. Furthermore, decreased levels of vaspin early after LRBS seem more likely to result from decreased dietary intake rather than weight-loss-induced insulin sensitivity improvement.