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Hassan, S. S.

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

At least 19 recordsLinked to original sources

Quantitative Deciphering of Mammalian Histamine Receptors through Mathematical Genomics

Histamine receptors (HRH1-HRH4) are G-protein coupled receptors (GPCRs) that mediate essential physiological functions, including neurotransmission, gastric acid secretion, immune regulation, and presynaptic autoregulation. Despite their importance, systematic comparative analyses across mammalian histamine receptor sequences remain scarce. In this study, we performed a comprehensive evaluation of HRH1-HRH4 across multiple mammalian species, integrating sequence homology, invariant residue mapping, amino acid substitutions, compositional frequencies, Shannon entropy, polystring distributions, intrinsic disorder profiling, and phylogenetic clustering. HRH2 and HRH1 were highly conserved among primates, HRH3 showed strong cohesion within rodents, while HRH4 exhibited pronounced divergence consistent with immune-related specialization. Invariant residues localized to transmembrane helices and activation motifs (D107, W428/Y431, NPxxY), underscoring strict evolutionary constraints on ligand binding, receptor stability, and G-protein coupling. Substitutions were confined to non-essential lipid-facing and loop regions, predominantly conservative in nature, enabling diversification without disrupting the GPCR fold. Amino acid frequency and entropy analyses revealed hydrophobic dominance with subtype-specific enrichment of polar residues, while disorder profiling identified HRH1 as the most dynamic and HRH2 as the most structurally constrained. Polystring analysis highlighted conserved motifs (WWW, PP) alongside subtype- and species-specific repeats, reflecting evolutionary strategies balancing receptor stability with adaptive flexibility. Phylogenetic clustering confirmed subtype-specific cohesion, with HRH3 and HRH4 forming compact clades, HRH1 showing moderate dispersion, and HRH2 forming the most isolated cluster. Collectively, these findings demonstrate that mammalian histamine receptor evolution is governed by conserved biophysical cores and selective variability, offering insights into structural conservation, functional diversification, and translational relevance for drug design and model selection.

bioinformatics↗

CpG-induced regions associated compositional stratification of human essential proteins through mathematical genomics

CpG islands are genomic regions enriched in cytosine-phosphate-guanine dinucleotides, typically associated with gene promoters and regulatory elements. While their role in transcriptional regulation is well established, their influence on protein sequence composition remains underexplored. In this study, 3,222 essential proteins from Homo sapiens were analyzed to investigate the impact of CpG island architecture on amino acid usage, sequence complexity, and chromosomal distribution. Codons containing both cytosine and guanine were mapped to five CpG-induced amino acids, and their relative abundance was quantified across proteins. CpG-induced regions were identified using a sliding window approach, and metrics such as average CpG density, longest CpG-induced region length, and sequence coverage were computed. Motif composition within these regions was characterized using polarity and charge-based indices. Clustering revealed consistent bipartite subgroup structures, indicating compositional stratification among essential proteins. Shannon entropy quantified compositional complexity, revealing a significant shift between clusters (p = 5. x 50 10-145). Cluster 1 proteins showed lower entropy and greater heterogeneity, whereas Cluster 2 showed higher entropy and tighter distributions, indicating distinct regimes of variability. Additionally, we examined CpG island overlap within coding exons of essential genes and found that CpG-depleted proteins are predominantly encoded by genes with minimal CGI coverage, whereas CpG-induced proteins span both low- and high-overlap classes. CGI-associated CpGs were consistently enriched toward the 5' end of essential genes, indicating a positional bias in CpG distribution. These findings establish a quantitative framework linking CpG island distribution to proteomic architecture and offer a scalable strategy for motif annotation, epigenetic modeling, and functional stratification. Future applications include predictive modeling of protein function, disease association, and regulatory dynamics.

genomics↗

A Mathematical Genomics Perspective on the Moonlighting Role of Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH)

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a well-conserved enzyme across Archaea, Bacteria, and Eukarya, known not only for its canonical role in glycolysis, but also for diverse moonlighting functions including transcription regulation, host-pathogen interactions, and immune modulation. Studying GAPDH quantitatively is crucial for understanding how subtle variations at the sequence and structural levels drive such functional diversity across evolutionary lineages. In this study, 165 GAPDH protein sequences from 158 organisms were analyzed to uncover conserved and divergent features underlying multifunctionality. While core catalytic residues were strongly preserved, selective enrichment of small non-polar residues such as valine and alanine suggested a structural basis for flexibility and adaptive potential. The balanced distribution of order- and disorder-promoting residues and the avoidance of long homopolymeric stretches indicated evolutionary selection for both structural coherence and local flexibility. Spatial distribution of amino acids in GAPDH sequences revealed low fractal variance across sequences, with moderate differences in residue clustering patterns pointing to localized adaptations without compromising overall organization. These findings demonstrate that GAPDH multifunctionality is encoded through compositional signatures and conserved spatial architecture, allowing the coexistence of metabolic stability and regulatory plasticity. The results have broad implications for understanding protein evolution, structural adaptability in extreme environments, and functional versatility in pathogenic contexts. This study establishes GAPDH as a model for exploring principles of protein moonlighting and highlights the potential of quantitative compositional analysis in uncovering hidden functional layers.

genomics↗

Proximal relationships of moonlighting Proteins in Escherichia coli: a mathematical genomic perspective

Moonlighting proteins in Escherichia coli (E.coli) perform multiple independent functions without altering their primary amino acid sequence, challenging the "one gene-one enzyme" hypothesis. Bacterial proteins serve various functions, including host cell adhesion, extracellular matrix interaction, and immune modulation, while also supporting essential physiological processes within the bacteria. Identifying these proteins in pathogens and tracking their genetic changes is crucial for understanding bacterial survival and virulence. A quantitative understanding of these proteins is pivotal as it enables the identification of specific patterns and relationships between amino acid composition, protein stability, and functional versatility. This study quantitatively analyzes fifty E. coli moonlighting proteins, focusing on their structural and functional features. Key findings include variability in amino acid composition, with alanine predominating, and a preference for non-polar residues, which may enhance protein stability. Quantitative features analyses identified seven distinct proximal sets, reflecting the proteins spatial arrangements of amino acids, structural diversity, and functional roles in processes such as metabolism, stress response, and gene regulation. These results deepen our understanding of the multifunctionality of E. coli moonlighting proteins, indicating their adaptability and implications for bacterial survival and pathogenicity.

genomics↗

Cultivation and molecular characterization of Foley catheterized urine, clean catch urine, and vaginal swabs from pregnant women prior to delivery

The bladder and urine have historically been considered sterile, especially in the context of clinical assessment. Yet, enhanced culture techniques and advances in DNA sequencing surveys have revealed a low microbial biomass microbiota in the bladders of most healthy individuals. Yet very few studies have investigated the urinary microbiota of pregnant women, who are at increased risk of urinary tract infections (UTIs) that can lead to pregnancy complications such as spontaneous preterm birth. To better understand the potential role of a bladder microbiota during pregnancy, we characterized the urinary microbiota of 25 pregnant women (delivering at or beyond 36 weeks gestation) by comparing the bacterial profiles of their paired catheter urine, clean catch urine, and vaginal swabs through both cultivation and molecular microbiological survey methods. For culture, three bacterial taxa were detected in at least 20% of all urine samples (Lactobacillus species, coagulase negative Staphylococcus species, and Ureaplasma urealyticum). All three taxa were detected less frequently in Foley catheter urine than in clean catch urine. Ureaplasma urealyticum was the most frequently recovered bacterium in Foley catheter urine (13/25 women). It was also identified as being more relatively abundant in Foley catheter urine than in the vagina through 16S rRNA gene surveys. Other lower abundance Gram-positive anaerobic cocci (i.e., Finegoldia and Anaerococcus) were also more relatively abundant in Foley catheter urine than clean catch urine or vaginal swabs. However, all sample types had high relative abundances of Lactobacillus and Gardnerella species. Overall, this suggests that, although vaginal microbiota contamination cannot be completely avoided, Foley catheterized urine is effective at characterizing the low abundance bladder microbiota, including Ureaplasma, Finegoldia, and Anaerococcus species. This warrants their further consideration as commensal members of the bladder microbiome during pregnancy.

microbiology↗

Methuselah Proteins in Longevity: Unraveling Their Impact Through Mathematical Genomics

This study provides a quantitative and comprehensive analysis of 18 Methuselah (mth) protein variants from fruit flies, focusing on their evolutionary relationships, structural features, and functional roles in aging and longevity. Phylogenetic analysis identified two major clades of mth proteins, with the first clade indicating conserved functions across Drosophila species and the second clade reflecting gene duplication and diversification. The study found five distinct functional subclasses of mth proteins through amino acid frequency and poly-string analyses, linked to their structural diversity and role in longevity. Structural topology and post-translational modifications reveal similarities with G-protein-coupled receptors (GPCRs), suggesting that mth proteins are crucial for signal transduction and cellular health. Variability in propeptide cleavage sites and intrinsic protein disorder further highlight adaptive roles in signaling. The findings underscore the importance of a quantitative and comprehensive approach to studying Methuselah genes, offering insights into their functional versatility and evolutionary dynamics. This enhanced quantitative understanding contributes to advancing research on aging and longevity.

genomics↗

Molecular Genomic Insights into Melanoma Associated Proteins PRAME and BAP1

BackgroundMelanoma, a worldwide widespread skin cancer with over 325,000 yearly incidences, demands a thorough understanding of its molecular components to create effective therapeutics. This study looks at the PRAME (cutaneous melanoma-associated antigen) and BAP1 (gene controlling gene-environment interactions) proteins, which are important in melanoma development and are important for understanding the molecular landscape of melanoma. IntroductionWhile playing a crucial role in melanoma, the structural and functional characteristics of PRAME and BAP1 remain unidentified. This work tries to unravel their complexities by investigating conserved residues, sequence invariance, and other molecular characteristics that contribute to their importance in melanoma. Promising therapeutic targets for melanoma therapy are identified by analyzing these proteins at the molecular level. MethodsThe study makes extensive use of bioinformatics methods to analyze PRAME and BAP1, including sequence conservation, inherent disorder, polyglutamic acid presence, and polarity alterations. Established approaches are used to investigate residue changes and their effects on protein folding, aggregation, and interactions. ResultsPRAME and BAP1 conserved residues highlight their critical roles in protein function and interaction. Sequence invariance indicates the possibility of functional relevance and evolutionary conservation. In intrinsically disordered proteins (IDPRs), PRAME has enhanced intrinsic disorder and flexibility, whereas BAP1 has changed disorder-promoting residue sequences. Polyglutamic acid strings are found in both proteins, emphasizing their modulatory involvement in protein interactions. Protein folding and aggregation are influenced by polarity shifts, with a balanced distribution of acidic and basic residues preserving native structures. The ratios and distributions of amino acids, particularly neutral residues, have a profound influence on interactions and gene dysregulation. ConclusionPRAME and BAP1 structural and functional understanding pave the way for diagnostic and tailored treatment options in melanoma. Differences in residue alterations, polarity distributions, and amino acid ratios provide intriguing drug design options. This research contributes to a better knowledge of melanoma-associated two proteins, opening the path for novel diagnostic and therapy techniques in skin cancer and beyond.

bioinformatics↗

Unveiling the Genetic Tapestry: Rare Disease Genomics of Spinal Muscular Atrophy and Phenylketonuria Proteins

Rare diseases, defined by their low prevalence, present significant challenges, including delayed detection, expensive treatments, and limited research. This study delves into the genetic basis of two noteworthy rare diseases in Saudi Arabia: Phenylketonuria (PKU) and Spinal Muscular Atrophy (SMA). PKU, resulting from mutations in the phenylalanine hydroxylase (PAH) gene, exhibits geographical variability and impacts intellectual abilities. SMA, characterized by motor neuron loss, is linked to mutations in the survival of motor neuron 1 (SMN1) gene. Recognizing the importance of unveiling signature genomics in rare diseases, we conducted a quantitative study on PAH and SMN1 proteins of multiple organisms by employing various quantitative techniques to assess genetic variations. The derived signature-genomics contributes to a deeper understanding of these critical genes, paving the way for enhanced diagnostics and treatments for disorders associated with PAH and SMN1.

genomics↗

The Distal-Proximal Relationships Among the Human Moonlighting Proteins: Evolutionary hotspots and Darwinian checkpoints

Moonlighting proteins, known for their ability to perform multiple, often unrelated functions within a single polypeptide chain, challenge the traditional "one gene, one protein, one function" paradigm. As organisms evolved, their genomes remained relatively stable in size, but the introduction of post-translational modifications and sub-strategies like protein promiscuity and intrinsic disorder enabled multifunctionality. Enzymes, in particular, exemplify this phenomenon, engaging in unrelated processes alongside their primary catalytic roles. This study employs a systematic, quantitative informatics approach to shed light on human moonlighting protein sequences. Phylogenetic analyses of human moonlighting proteins are presented, elucidating the distal-proximal relationships among these proteins based on sequence-derived quantitative features. The findings unveil the captivating world of human moonlighting proteins, urging further investigations in the emerging field of moonlighting proteomics, with the potential for significant contributions to our understanding of multifunctional proteins and their roles in diverse cellular processes and diseases.

genomics↗

SARS-CoV-2 NSP14 governs mutational instability and assists in making new SARS-CoV-2 variants

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the rapidly evolving RNA virus behind the COVID-19 pandemic, has spawned numerous variants since its 2019 emergence. The multifunctional NSP14 enzyme, possessing exonuclease and mRNA capping capabilities, serves as a key player. Notably, single and co-occurring mutations within NSP14 significantly influence replication fidelity and drive variant diversification. This study comprehensively examines 120 co-mutations, 68 unique mutations, and 160 conserved residues across NSP14 homologs, shedding light on their implications for phylogenetic patterns, pathogenicity, and residue interactions. Quantitative physicochemical analysis categorizes 3953 NSP14 variants into three clusters, revealing genetic diversity. This research underscores the dynamic nature of SARS-CoV-2 evolution, primarily governed by NSP14 mutations. Understanding these genetic dynamics provides valuable insights for therapeutic and vaccine development.

bioinformatics↗

Biology of Coital Behavior: Looking Through the Lens of Mathematical Genomics

Research has shown that genetics and epigenetics regulate mating behavior across multiple species. Previous studies have generally focused on the signaling pathways involved and spatial distribution of the associated receptors. However a thorough quantitative characterization of the receptors involved may offer deeper insight into mating behavioral patterns. Here oxytocin, arginine-vasopressin 1a, dopamine 1, and dopamine 2 receptors were investigated across 76 vertebrate species. The receptor sequences were characterized by polarity-based randomness, amino acid frequency-based Shannon entropy and Shannon sequence variability, intrinsic protein disorder, binding affinity, stability and pathogenicity of homology-based SNPs, structural and physicochemical features. Hierarchical clustering of species was derived based on structural and physicochemical features of the four receptor sequences separately, which eventually led to proximal relationships among 29 species. Humans were found to be significantly distant phylogenetically from the prairie voles, a representative of monogamous species based on coital behavior. Furthermore, the mouse (polygamous), the prairie deer mouse (polygamous), and the prairie vole (monogamous) although being proximally related (based on quantitative genomics of receptors), differed in their coital behavioral pattern, mostly, due to behavioral epigenetic regulations. This study adds a perspective that receptor genomics does not directly translate to behavioral patterns.

genomics↗

Nanopore sequencing of antibiotic-resistant Klebsiella pneumoniae JRCGR1 isolate from Pakistan and country scale pan-genomics

Klebsiella pneumoniae is a gram-negative, encapsulated, non-motile bacterium that can cause damage to human lungs. Antibiotic resistance of this strain requires constant monitoring and for this purpose, Oxford nanopore mediated whole genome sequencing was done for a strain acquired from the pleural fluid of a diabetic patient suffering from chronic kidney disease. A genome of 5.98 MB was obtained, with 8,869 CDSs and 110 RNAs. Around 96 proteins were seen as involved in virulence, disease or defense, while 25 antibiotic resistance genes were identified. Pan-genome was inferred as open, with 12,857 and 1,303 CDSs forming respective accessory and core genome of antibiotic resistant Pakistani strains (n=168) of this species. Apart from notable antimicrobial resistance genes like beta-lactamases, a gene conferring resistance to colistin was also mined. To the best of our knowledge, this is first report of nanopore mediated long read sequencing of a hypermucoviscous virulent K. pneumoniae from Pakistan.

genomics↗

Possible Functional Proximity of Various Organisms Based on Taste Receptors Genomics

Taste is one of the essential senses in providing the organism a faithful representation of the external world. Taste perception is responsible for basic food and drink appraisal and bestows the organism with valuable discriminatory power. Umami and sweet are "good" tastes that promote consumption of nutritive food, whereas bitter and sour are "bad" tastes that alert the organism to toxins and low pH, promoting rejection of foods containing harmful substances. Not every animal has the same sense of taste as humans. Variation in the taste receptor genes contributes to inter and intra organism differences of taste (sweet/bitter) sensation and preferences. Therefore a deeper understanding was needed to comprehend taste perception by various vertebrates and accordingly elucidate a possible proximity among them. In this study, a total 20 Type-1 (sweet) and 189 Type-2 (bitter) taste receptor complete-amino acid sequences were taken from the 20 vertebrate organisms (18 mammalian, 1 aves, and 1 amphibian). Among 10 primates, 8 including humans were very close based on genomics of taste receptors and rodent organisms viz. the rat and mouse were away from them. This investigation throws light on the similitude and dissimilitude of perception of sweet and bitter taste among 20 different organisms, steered by quantitative analysis of their genomic data. Furthermore, it enlightened that ligand binding affinity of sweet/bitter taste molecules in the taste receptors of any proximal pair of organisms would be similar.

genomics↗

SARS-CoV-2 variants show a gradual declining pathogenicity and pro-inflammatory cytokine stimulation and an increasing antigenic and anti-inflammatory cytokine induction

Hyper-transmissibility with decreased disease severity are typical characteristics of Omicron variant. To understand this phenomenon, we used various bioinformatics approaches to analyze randomly selected genome sequences (one each) of the Gamma, Delta, and Omicron variants submitted to NCBI from 15 to 31 December 2021. We show that: (i) Pathogenicity of SARS-CoV-2 variants decreases in the order: Wuhan > Gamma > Delta > Omicron; however, the antigenic property follows the order: Omicron > Gamma > Wuhan > Delta. (ii) Omicron Spike RBD has lower pathogenicity but higher antigenicity than other variants. (iii) Decreased disease severity by Omicron variant may be due to its decreased pro-inflammatory and IL-6 stimulation and increased IFN-{gamma} and IL-4 induction efficacy. (iv) Mutations in N protein are associated with decreased IL-6 induction and human DDX21-mediated increased IL-4 production in Omicron. (v) Due to mutations, the stability of S, M, N, and E proteins decreases in the order: Omicron > Gamma > Delta > Wuhan. (vi) Stronger Spike RBD-hACE2 binding in Omicron is associated with increased transmissibility. However, the lowest stability of the Omicron Spike protein makes Spike RBD-hACE2 interaction weak for systemic infection and for causing severe disease. Finally (vii), the highest instability of Omicron E protein may also be associated with decreased viral maturation and low viral load leading to less severe disease and faster recovery. Our method may be used for other similar viruses, and these findings will contribute to the understanding of the dynamics of SARS-CoV-2 variants and the management of emerging variants.

bioinformatics↗

An Issue of Concern: Unique Truncated ORF8 Protein Variants of SARS-CoV-2

Open reading frame 8 (ORF8) protein is one of the most evolving accessory proteins in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19). It was previously reported that the ORF8 protein inhibits presentation of viral antigens by the major histocompatibility complex class I (MHC-I) and interacts with host factors involved in pulmonary inflammation. The ORF8 protein assists SARS-CoV-2 to evade immunity and replication. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein defines the B.1.1.7 lineage of SARS-CoV-2, which is engendering the second wave of COVID-19. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) due to the Q27STOP mutations were identified among 49055 available B.1.1.7 SARS-CoV-2 sequences. The results show that only one of the 47 T-ORF8 variants spread to over 57 geo-locations in North America, and other continents which includes Africa, Asia, Europe and South America. Based on various quantitative features such as amino acid homology, polar/non-polar sequence homology, Shannon entropy conservation, and other physicochemical properties of all specific 47 T-ORF8 protein variants, a collection of nine possible T-ORF8 unique variants were defined. The question of whether T-ORF8 variants work similarly to ORF8 has yet to be investigated. A positive response to the question could exacerbate future COVID-19 waves, necessitating severe containment measures.

bioinformatics↗

Implications Derived from S-Protein Variants of SARS-CoV-2 from Six Continents

Spike (S) proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are critical determinants of the infectivity and antigenicity of the virus. Several mutations in the spike protein of SARS-CoV-2 have already been detected, and their effect in immune system evasion and enhanced transmission as a cause of increased morbidity and mortality are being investigated. From pathogenic and epidemiological perspectives, spike proteins are of prime interest to researchers. This study focused on the unique variants of S proteins from six continents Asia, Africa, Europe, Oceania, South America, and North America. In comparison to the other five continents, Africa (29.065%) had the highest percentage of unique S proteins. Notably, only North America had 87% (14046) of the total (16143) specific S proteins available in the NCBI database(across all continents). Based on the amino acid frequency distributions in the S protein variants from all the continents, the phylogenetic relationship implies that unique S proteins from North America were significantly different from those of the other five continents. Overtime, the unique variants originating from North America are most likely to spread to the other geographic locations through international travel or naturally by emerging mutations. Hence it is suggested that restriction of international travel should be considered, and massive vaccination as an utmost measure to combat the spread of COVID-19 pandemic. It is also further suggested that the efficacy of existing vaccines and future vaccine development must be reviewed with careful scrutiny, and if needed, further re-engineered based on requirements dictated by new emerging S protein variants.

bioinformatics↗

Clade GR and Clade GH Isolates in Asia Show Highest Amount of SNPs

Clades are monophyletic groups composed of a common ancestor and all its lineal descendants. As the propensity of virulence of a disease depends upon the type of clade the virus belongs to and it causes different fatality rates of disease in different countries, so the clade-wise analysis of SARS-CoV-2 isolates collected from different countries can illuminate the actual evolutionary relationships between them. In this study, 1566 SARS-CoV-2 genome sequences across ten Asian countries are collected, clustered, and characterized based on the clade they belong to. The isolates are compared to the Wuhan reference sequence (Accession no:MN996528.1) to identify the mutations that occurred at different protein regions. Structural changes in amino acids due to mutations lead to functional instability of the proteins. Detailed clade-wise functional assessments are carried out to quantify the stability and vulnerability of the mutations occurring in SARS-CoV-2 genomes which can shade light on personalized prevention and treatment of the disease and encourage towards the invention of clade-specific vaccines.

systems biology↗

Variability of Accessory Proteins Rules the SARS-CoV-2 Pathogenicity

The coronavirus disease 2019 (COVID-19) is caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) which is pandemic with an estimated fatality rate less than 1% is ongoing. SARS-CoV-2 accessory proteins ORF3a, ORF6, ORF7a, ORF7b, ORF8, and ORF10 with putative functions to manipulate host immune mechanisms such as interferons, immune signaling receptor NLRP3 (NOD-, LRR-, and pyrin domain-containing 3) inflammasome, inflammatory cytokines such as interleukin 1{beta} (IL-1{beta}) are critical in COVID-19 pathology. Outspread variations of each of the six accessory proteins of all complete proteomes (available as of October 26, 2020, in the National Center for Biotechnology Information depository) of SARS-CoV-2, were observed across six continents. Across all continents, the decreasing order of percentage of unique variations in the accessory proteins was found to be ORF3a>ORF8>ORF7a>ORF6>ORF10>ORF7b. The highest and lowest unique variations of ORF3a were observed in South America and Oceania, respectively. This finding suggests that the wide variations of accessory proteins seem to govern the pathogenicity of SARS-CoV-2, and consequently, certain propositions and recommendations can be made in the public interest.

bioinformatics↗