Biology subjects

Hassan, S. S.

Publications and source records attributed to Hassan, S. S..

31 records · Page 2Linked to original sources

bioRxiv2020

Possible transmission flow of SARS-CoV-2 based on ACE2 features

Angiotensin-converting enzyme 2 (ACE2) is the cellular receptor for the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that is engendering the severe coronavirus disease 2019 (COVID-19) pandemic. The spike (S) protein receptor-binding domain (RBD) of SARS-CoV-2 binds to the three sub-domains viz. amino acids (aa) 22-42, aa 79-84, and aa 330-393 of ACE2 on human cells to initiate entry. It was reported earlier that the receptor utilization capacity of ACE2 proteins from different species, such as cats, chimpanzees, dogs, and cattle, are different. A comprehensive analysis of ACE2 receptors of nineteen species was carried out in this study, and the findings propose a possible SARS-CoV-2 transmission flow across these nineteen species.

bioinformatics↗

bioRxiv2020

Notable sequence homology of the ORF10 protein introspects the architecture of SARS-COV-2

The global public health is endangered due to COVID-19 pandemic, which is caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Despite having similar pathology to MERS and SARS-CoV, the infection fatality rate of SARS-CoV-2 is likely lower than 1%. SARS-CoV-2 has been reported to be uniquely characterized by the accessory protein ORF10, which contains eleven cytotoxic T lymphocyte (CTL) epitopes of nine amino acids length each, across various human leukocyte antigen (HLA) subtypes. In this study, all missense mutations found in sequence databases were examined across twnety-two unique SARS-CoV-2 ORF10 variants that could possibly alter viral pathogenicity. Some of these mutations decrease the stability of ORF10, e.g. I4L and V6I were found in the MoRF region of ORF10 which may also possibly contribute to Intrinsic protein disorder. Furthermore, a physicochemical and structural comparative analysis was carried out on SARS-CoV-2 and Pangolin-CoV ORF10 proteins, which share 97.37% amino acid homology. The high degree of physicochemical and structural similarity of ORF10 proteins of SARS-CoV-2 and Pangolin-CoV open questions about the architecture of SARS-CoV-2 due to the disagreement of these two ORF10 proteins over their sub-structure (loop/coil region), solubility, antigenicity and change from the strand to coil at amino acid position 26, where tyrosine is present. Altogether, SARS-CoV-2 ORF10 is a promising pharmaceutical target and a protein which should be monitored for changes which correlate to change pathogenesis and clinical course of COVID-19 infection.

bioinformatics↗

bioRxiv2020

A unique view of SARS-CoV-2 through the lens of ORF8 protein

Immune evasion is one of the unique characteristics of COVID-19 attributed to the ORF8 protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This protein is involved in modulating the host adaptive immunity through downregulating MHC (Major Histocompatibility Complex) molecules and innate immune responses by surpassing the interferon mediated antiviral response of the host. To understand the immune perspective of the host with respect to the ORF8 protein, a comprehensive study of the ORF8 protein as well as mutations possessed by it, is performed. Chemical and structural properties of ORF8 proteins from different hosts, that is human, bat and pangolin, suggests that the ORF8 of SARS-CoV-2 and Bat RaTG13-CoV are very much closer related than that of Pangolin-CoV. Eighty-seven mutations across unique variants of ORF8 (SARS-CoV-2) are grouped into four classes based on their predicted effects. Based on geolocations and timescale of collection, a possible flow of mutations was built. Furthermore, conclusive flows of amalgamation of mutations were endorsed upon sequence similarity and amino acid conservation phylogenies. Therefore, this study seeks to highlight the uniqueness of rapid evolving SARS-CoV-2 through the ORF8.

molecular biology↗

bioRxiv2020

Pathogenetic Perspective of Missense Mutations of ORF3a Protein of SARS-CoV2

One of the most important proteins for COVID-19 pathogenesis in SARS-CoV2 is the ORF3a protein which is the largest accessory protein among others accessory proteins coded by coronavirus genome. The major roles of the protein include virulence, infectivity, ion channel activity, morphogenesis and virus release. The coronavirus, SARS-CoV2 is continuously evolving naturally and thereby the encoded proteins are also mutating rapidly. Therefore, critical study of mutations in ORF3a is certainty important from the pathogenetic perspective. Here, a sum of 175 various non-synonymous mutations in the ORF3a protein of SARS-CoV2 are identified and their corresponding effects in structural stability and functions of the protein ORF3a are studied. Broadly three different classes of mutations, such as neutral, disease and mixed (neutral and disease) type mutations were observed. Consecutive mutations in some ORF3a proteins are established based on timeline of detection of mutations. Considering the amino acid compositions over the ORF3a primary protein sequences, twenty clusters are detected based on K-means clustering method. Our findings on 175 novel mutations of ORF3a proteins will extend our knowledge of ORF3a, a vital accessory protein in SARS-CoV2, which would assist to enlighten on the pathogenicity of this life-threatening COVID-19.

genomics↗

bioRxiv2020

Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birth

Identification of pregnancies at risk of preterm birth (PTB), the leading cause of newborn deaths, remains challenging given the syndromic nature of the disease. We report a longitudinal multi-omics study coupled with a DREAM challenge to develop predictive models of PTB. We found that whole blood gene expression predicts ultrasound-based gestational ages in normal and complicated pregnancies (r=0.83), as well as the delivery date in normal pregnancies (r=0.86), with an accuracy comparable to ultrasound. However, unlike the latter, transcriptomic data collected at <37 weeks of gestation predicted the delivery date of one third of spontaneous (sPTB) cases within 2 weeks of the actual date. Based on samples collected before 33 weeks in asymptomatic women we found expression changes preceding preterm prelabor rupture of the membranes that were consistent across time points and cohorts, involving, among others, leukocyte-mediated immunity. Plasma proteomic random forests predicted sPTB with higher accuracy and earlier in pregnancy than whole blood transcriptomic models (e.g. AUROC=0.76 vs. AUROC=0.6 at 27-33 weeks of gestation).

bioinformatics↗

bioRxiv2020

Molecular conservation and Differential mutation on ORF3a gene in Indian SARS-CoV2 genomes

A global emergency due to the COVID-19 pandemic demands various studies related to genes and genomes of the SARS-CoV2. Among other important proteins, the role of accessory proteins are of immense importance in replication, regulation of infections of the coronavirus in the hosts. The largest accessory proteins in the SARS-CoV2 genome is ORF3a which modulates the host response to the virus infection and consequently it plays an important role in pathogenesis. In this study, an attempt is made to decipher the conservation of nucleotides, dimers, codons and amino acids in the ORF3a genes across thirty two genomes of Indian patients. ORF3a gene possesses single and double point mutations in Indian SARS-CoV2 genomes suggesting the change of SARS-CoV2s virulence property in Indian patients. We find that the parental origin of the ORF3a gene over the genomes of SARS-CoV2 and Pangolin-CoV is same from the phylogenetic analysis based on conservations of nucleotides and so on. This study highlights the accumulation of mutation on ORF3a in Indian SARS-CoV2 genomes which may provide the designing therapeutic approach against SARS-CoV2.

genomics↗

bioRxiv2020

On spatial molecular arrangements of SARS-CoV2 genomes of Indian patients

A pandemic caused by the SARS-CoV2 is being experienced by the whole world since December, 2019. A thorough understanding beyond just sequential similarities among the protein coding genes of SARS-CoV2 is important in order to differentiate or relate to the other known CoVs of the same genus. In this study, we compare three genomes namely MT012098 (India-Kerala), MT050493 (India-Kerala), MT358637 (India-Gujrat) from India with NC_045512 (China-Wuhan) to view the spatial as well as molecular arrangements of nucleotide bases of all the genes embedded in these four genomes. Based on different features extracted for each gene embedded in these genomes, corresponding phylogenetic relationships have been built up. Differences in phylogenetic tree arrangement with individual gene suggest that three genomes of Indian origin have come from three different origins or the evolution of viral genome is very fast process. This study would also help to understand the virulence factors, disease pathogenicity, origin and transmission of the SARS-CoV2.

bioinformatics↗

bioRxiv2019

Single Cell Transcriptional Signatures of the Human Placenta in Term and Preterm Parturition

More than 135 million births occur each year; yet, the molecular underpinnings of human parturition in gestational tissues, and in particular the placenta, are still poorly understood. The placenta is a complex heterogeneous organ including cells of both maternal and fetal origin, and insults that disrupt the maternal-fetal dialogue could result in adverse pregnancy outcomes such as preterm birth. There is limited knowledge of the cell type composition and transcriptional activity of the placenta and its compartments during physiologic and pathologic parturition. To fill this knowledge gap, we used scRNA-seq to profile the placental villous tree, basal plate, and chorioamniotic membranes of women with or without labor at term and those with preterm labor. Significant differences in cell type composition and transcriptional profiles were found among placental compartments and across study groups. For the first time, two cell types were identified: 1) lymphatic endothelial decidual cells in the chorioamniotic membranes, and 2) non-proliferative interstitial cytotrophoblasts in the placental villi. Maternal macrophages from the chorioamniotic membranes displayed the largest differences in gene expression (e.g. NFKB1) in both processes of labor; yet, specific gene expression changes were also detected in preterm labor. Importantly, several placental scRNA-seq transcriptional signatures were modulated with advancing gestation in the maternal circulation, and specific immune cell type signatures were increased with labor at term (NK-cell and activated T-cell) and with preterm labor (macrophage, monocyte, and activated T-cell). Herein, we provide a catalogue of cell types and transcriptional profiles in the human placenta, shedding light on the molecular underpinnings and non-invasive prediction of the physiologic and pathologic parturition.\n\nOne sentence summaryThe common molecular pathway of parturition for both term and preterm spontaneous labor is characterized using single cell gene expression analysis of the human placenta.

genomics↗

bioRxiv2019

Functional activity of antisera against recombinant Zika virus envelope protein subunits expressed in Escherichia coli

The global Zika virus (ZIKV) outbreak across continents has been drawing research attentions to researchers and healthcare professionals. It highlights the urgent development of ZIKV vaccines that offer rapid, precise and specific protection to those living in the high-risk regions - the tropical and subtropical regions. As a public health priority, there is a progressive development in the discovery of vaccine candidates and design in recent years. Many efforts have been placed in the in vitro development of ZIKV subunits as the vaccine candidate in various protein expression systems, including bacteria, yeast, plant cells, insect cells and mammalian cells. However, due to the lack of knowledge on humoral and cellular immune responses against virus vaccines, a commercialised vaccine against Dengue virus (DENV) has been suspended due to a health scare in Philippines. Moreover, the closely-related DENV and ZIKV has indicated serological cross-reactivity between both viruses. This has led to greater attentions to precautions needed during the design of ZIKV and DENV vaccines. In this study, we pre-selected, synthesised and expressed the domain III of ZIKV envelope protein (namely rEDIII) based on a previously-established report (GenBank: AMC13911.1). The characteristics of purified ZIKV rEDIII was tested using SDS-PAGE, Western blotting and LC-MS/MS. Since the ZIKV rEDIII has been well reported as a potential protein candidate in ZIKV vaccine development, we assessed the possible outcome of preexisting immunity against the rEDIII proteins by conducting dot-blotting assays using mice antisera pre-immunised with ZIKV particles (ZIKV strain: MRS_OPY_Martinique_PaRi_2015, GenBank: KU647676). Surprisingly, the antisera was able to recognise the rEDIII of a different ZIKV strain (GenBank: AMC13911.1). Despite its great antigenicity in eliciting humoral and cellular immunity against ZIKV infection, our finding calls for greater attention to evaluate the details of ZIKV rEDIII as a stand-alone vaccine candidate.

molecular biology↗

bioRxiv2018

Dynamics of the Previte-Hoffman food web modelwith small immigrations

The ecological dynamics of prey-predator systems are extensively studied over a century. Previte and Hoffman introduced a three species(predator-prey with an omnivore) model in 2013. We demonstrate the asymptotic stability of the Previte and Hoffman modified model adding with small immigration into the prey or predator or omnivore population. A comparison of dynamics is also drawn with immigration and without immigration. It is worth noting that the qualitative dynamics is unchanged among the immigration system over the classical Previte-Hoffman system.

ecology↗

bioRxiv2018

The variations of human miRNAs and Ising like base pairing models

miRNAs are small about 22-base pair long, RNA molecules are of extreme biological importance. Like other longer RNA molecules, messages in miRNAs are encoded by the permutations of only four nucleotide bases represented by A, U, C and G. However, just like words in any language, not all combination of these alphabets make a meaningful word. In fact, we find that the distributions of nucleotides bases in human miRNAs show significant deviation from randomness. First, a miRNA sequence containing four bases are mapped into a binary string with three kinds of classifications according to their chemical properties. Then, we propose a simple nearest neighbor model (Ising model) to understand the statistical variations in human miRNAs.

bioinformatics↗

bioRxiv2017

Distribution of Purines and Pyrimidines over miRNAs of Human, Gorilla and Chimpanzee

Meaningful words in English need vowels to break up the sounds that consonants make. The Nature has encoded her messages in RNA molecules using only four alphabets A, U, C and G in which the nine member double-ring bases (adenine (A) and Guanine (G)) are purines, while the six member single-ring bases (cytosine (C) and uracil (U)) are pyrimidines. Four bases A, U, C and G of RNA sequences are divided into three kinds of classifications according to their chemical properties. One of the three classifications, the purine-pyrimidine class is important. In understanding the distribution (organization) of purines and pyrimidines over some of the non-coding regions of RNA, all miRNAs from three species of Family Hominidae (namely human, gorilla and chimpanzee) are considered. The distribution of purines and pyrimidines over miRNA shows deviation from randomness. Based on the quantitative metrics (fractal dimension, Hurst exponent, Hamming distance, distance pattern of purine-pyrimidine, purine-pyrimidine frequency distribution and Shannon entropy) five different clusters have been made. It is identified that there exists only one miRNA in human hsa-miR-6124 which is purely made of purine bases only.\n\nAMS Subject Classification: 92B05 & 92B15

bioinformatics↗

bioRxiv2017

Computational Complex Predator-Prey Dynamics

Two species predator-prey with stage structure of mature and immature mathematical models are studied over the last few decades. Xin-an Zhang et al studied a mathematical model with stage structure of two species in 2010. In this article, an attempt has been made to comprehend the coupled predator-prey dynamics with mature-immature stage structure and compare the dynamics with the existing model. The present model studied by Xin-an Zhang et al is purely realistic with assumptions of positive parameters. From the mathematical curiosity, we wonder to investigate the same with complex parameters and compared with the foreseen results. In addition, the present model is slightly modified to see some new dynamics of some additional fixed point including the previous fixed points.

ecology↗