Current Trends in OMICS <p style="text-align: justify;">Current Trends in OMICS (CTO) is a biannual open-access, double-blind peer-reviewed international journal. The journal is interested to publish high-quality original research articles dealing with all the aspects of multi-OMICS studies in Biology and Medicine. The articles reflecting different ethical and legal effects of various scientific and technological developments and the use of different Bioinformatics tools to analyze the experimental data in different OMICS technologies are also welcomed.</p> Knowledge and Research Support Services, University of Management and Technology, Lahore, Pakistan en-US Current Trends in OMICS 2790-8283 <p>Author(s) retain copyright and grant the journal right of first publication with the work simultaneously licensed under a <a href="">Creative Commons Attribution (CC-BY) 4.0 License</a> that allows others to share the work with an acknowledgment of the work’s authorship and initial publication in this journal.</p> Current Situation of Breast Cancer in Pakistan and the Dire Need of Early Diagnosis <p>Globocan statistics underscore Pakistan’s noticeable position in terms of the breast cancer burden, highlighting a concerning and escalating trajectory in its daily progression. Breast cancer stands as the most predominant and fatal malignancy in Pakistan, reporting 25,928 cases in the year 2020, accounting for 14% of all cancer diagnosis. The country is reported to have the maximum incidence and mortality rates in Asia, a dire result of the lack of national cancer registry. Late diagnosis, often determined by sociocultural factors, considerably contributes to the high mortality rate. Several risk factors, such as reproductive factors, age, dietary habits, further complicate the situation. Moreover, economic obstacles deter many from receiving the required treatment. The current review features the dire need for inclusive policies and improved affordability to battle breast cancer’s escalating influence in Pakistan.</p> Najeeb Ullah Khan Bibi Maryam Khan Imad Azam Atif Hayat Copyright (c) 2024 Dr. Najeeb Ullah Khan, Imad Azam, Atif Hayat 2024-03-20 2024-03-20 4 2 01 20 10.32350/cto.42.01 Diversity Analysis of Catechol 2, 3-dioxygenase in POPs Metabolizing Bacteria using In-silico Approach <p>The persistent nature of persistent organic pollutants (POPs), lipophilicity, and volatility has resulted in their high concentration, not only in environmental resources but also in living organisms. Their complete removal is possible only by mineralization using enzyme-based strategies. Catechol 2, 3-dioxygenase is reportedly involved in the degradation of a wide variety of POPs. This study was designed to determine the diversity of this enzyme among highly efficient bioremediating bacteria. Seven bacteria belonging to genera acinetobacter, pseudomonas, burkholderia, stutzerimonas, and paraburkholderia were targeted. Sequences of the enzyme were retrieved from Uniprot database and analyzed via ProtParam, CELLU, and SOPMA tools and AlphaFold database. The enzyme was found to be cytoplasmic. The physicochemical properties of the enzyme were recorded as pI 4.75 – 5.50, aliphatic index (73.41 – 88.55), instability index (24.98 – 43.37), and GRAVY (-0.209 – 0.511). The secondary structure attributes were recorded to be α-helix (30.13 – 37.30), extended strand (18.27 – 21.54), β-turn (5.14 – 6.95), and random coil (38.33 – 42.95). All the proteins showed complex folding except in Pseudomonas sp strain EST1001. These properties may be exploited during the selection, purification, manipulation, and cloning of the enzyme for efficient bioremediation.</p> Fatima Muccee Copyright (c) 2023 Fatima Muccee 2023-12-20 2023-12-20 4 2 10.32350/cto.41.03 Reducing Multidrug-Resistant (MDR) Klebsiella pneumoniae via the Efficient Use of Bacteriophages ZI3 and HI3 <p><em>Klebsiella pneumoniae</em> is a common cause of multidrug-resistant (MDR) pneumonia, bacteremia, urinary tract infections (UTIs), and other systemic infections. <em>K. pneumoniae </em>is the third most common pathogen in blood cultures from sepsis patients. It can cause severe epidemic and endemic nosocomial infections. Antibiotic treatment of <em>K. pneumoniae </em>infections is getting increasingly challenging due to the development of antimicrobial resistance among pathogens. Hence, a new alternative strategy is required to treat such infections. Bacteriophages are the most prevalent biological entity on the planet with an estimated 10<sup>31</sup> particles. As obligatory intracellular parasites, they infect bacterial cells. They have a high host specificity and can replicate and lyse bacterial cells. In this research, two novel indigenous bacteriophages against <em>K. pneumoniae </em>strain kp8890 were isolated, characterized, and labeled as ZI3 and HI3. Both these phages were found to have a specific host range for <em>K. pneumoniae. </em>HI3 was able to lyse 7 out of 10 different <em>K. pneumoniae </em>clinical isolates, while ZI3 was able to lyse 5 out of 10 isolates, although it could not infect bacteria from other species. The isolated phages showed viability up&nbsp;to 50°C and pH ranging from 3 to 9. HI3 inhibited bacterial growth for 18 hours. Whereas, ZI3 showed an excellent bacterial reduction ability by inhibiting and decreasing the number of initial bacterial inoculum for 24 hours of observation. Keeping in view the excellent bacterial growth reduction, phage titer, pH and thermal stability, and host range, it is suggested that both bacteriophages, that is, ZI3 and HI3 can be potential phage therapy candidates after necessary animal modeling and clinical trials in the future.</p> Zia Ullah Iqbal Ahmad Alvi Zeeshan Niaz Iftikhar Ullah Atta Ullah Shafiq Ur Rehman Copyright (c) 2023 Zia Ullah, Iqbal Ahmad Alvi, Zeeshan Niaz, Iftikhar Ullah, Atta Ullah, Shafiq Ur Rehman 2023-12-20 2023-12-20 4 2 17 35 10.32350/cto.41.02 Detection of DNA Damage in Fish using Comet Assay <p>Heavy metals have an enduring presence, risky characteristics, and the propensity to accumulate in the environment. This is why heavy metal toxics are widely acknowledged as harmful environmental pollutants. Heavy metals damage both aquatic and terrestrial ecosystems, posing a major risk to the environment and human health. Four freshwater fish species namely <em>Labeo rohita, Catla catla, Hypophthalmichthys molitrix, and Ctenopharyngodon idella</em> were the focus of this investigation. This study investigated the potential genotoxic effects of lead (Pb), copper (Cu), and cadmium (Cd) on the above fish species through the application of comet assay test. The fish were exposed to these metals at four distinct concentrations (19%, 24%, 31%, and 50% of the LC<sub>50</sub>) over the course of 40 days. All four fish species were exposed to metals to varying degrees, according to the genetic damage index, cumulative tail length of comets, and the proportion of damaged cells. In contrast to <em>Catla catla, Hypophthalmichthys molitrix </em>had the highest prevalence of DNA damage. The current study suggests that the presence of these particular metals in Pakistan's aquatic ecosystems may have an adverse effect on the DNA of the country's fish species. Metals cause damage to DNA in fibroblast cells through distinct mechanisms when present in water, air, and soil. Comet assay test has a remarkable sensitivity that helps to identify extremely low amounts of DNA damage. Out of the four fish species, <em>Ctenopharyngodon idella</em> showed higher levels of damaged cells, a higher genetic damage index, and a cumulative comet tail length as compared to others. All four fish species experienced a significant increase in DNA damage, genetic damage index, and comet tail length at 50% concentration of metals LC<sub>50.</sub></p> Ahmad Manan Mustafa Chatha Saima Naz Syeda Saira Iqbal Azka Kiran Maria Lateef Unab Zahra Fatima Yasmin Nimra Amjad Ammara Javaid Copyright (c) 2023 Ahmad Manan Mustafa Chatha, Saima Naz, Syeda Saira Iqbal, Azka Kiran, Maria Lateef, Unab Zahra, Fatima Yasmin, Nimra Amjad, Ammara Javaid 2023-11-02 2023-11-02 4 2 01 16 10.32350/cto.41.01 Antioxidant and Antimicrobial Activity of Cuscuta reflexa ROXB. and Few Members of Family Convolvulaceae <p>Antioxidant activity of 12 species, of which one was <em>Cuscuta reflexa </em>Roxb. which belongs to the family of <em>Cuscutaceae </em>as well as 11 of <em>Convolvulaceae</em>, collected from district Bhimber, Mirpur and Kotli were measured by using ABTS, DPPH and FRAP assay. The total phenol and flavonoid contents of the whole plant of all the selected species were investigated. <em>Ipomoea eriocarpa </em>showed a comparatively higher amount of total polyphenols (0.98 ± 0.073 mg/gdw). The maximum DPPH value was shown by <em>Ipomoea carnea </em>Jacq (5.6%) and the minimum value was shown by <em>Convolvulus arvensis </em>L. extracts (3.0 %). ABTS was the highest by <em>Convolvulus prostrastus</em> and the lowest by <em>Ipomoea carnea.</em> In FRAP assay, the highest value was 2.75 by <em>Ipomoea hederacia </em>and the lowest value was 0.31 by <em>I. arachnosperma</em> Welw. The antifungal and antibacterial activity of the methanolic extracts of the whole plant of all the selected species was carried out by using both bacterial and fungal strains. Two gram positive bacteria namely <em>Staphylococcus aureus </em>and<em> Bacillus subtilis, </em>two gram negative bacteria namely <em>E. coli</em> and<em> Pseudomonas aeruginosa,</em> two fungal strains of <em>Aspergillus niger </em>and <em>Aspergillus oryzae</em> were used to carry out antimicrobial activity. For the comparison of inhibition zones showed by plant extracts against bacterial and fungal strains. Erythromycin, tetracycline and cefoparazone were used as standard for bacterial strains. Moreover, fungivine and Terbinafine were used as standard antibiotics against fungal strains. Among fungal strains, the highest zone of inhibition was shown by <em>Cuscuta reflexa </em>Roxb<em>. </em>extract against <em>Aspergillus niger, </em>that is 5.55±0.3, while the lowest zone of inhibition, that is, 0.60±0.28mm was shown by <em>Evolvulus alsinoides</em> (L.) extract against <em>Aspergillus oryzae</em>. Plants from the <em>Convolvulaceae</em> family have had frequent traditional uses for different therapeutic purposes. Furthermore, all plants selected for this study showed strong antimicrobial, antifungal, and antioxidant activity. Their further detailed phytochemical studies can help to develop plant-based therapeutic agents</p> Qumqum Noshad Muhammad Ajaib Aysha Kiran Copyright (c) 2023 Qumqum Noshad, Muhammad Ajaib, Aysha Kiran 2023-08-25 2023-08-25 4 2 01 14 10.32350/cto.32.01 MicroRNAs: An Overview of their Discovery, Biogenesis, Computational Prediction, and Potential Clinical Applications <p>The invention of next generation technologies which are aimed to resolve human health issues is gaining importance. Micro-RNAs (miRNAs) analysis is are an important discovery in the field of molecular biology. miRNAs are small endogenous RNAs which are involved in the regulation of post-transcriptional genes expression. They have been identified in different organisms, such as viruses, plants, human beings, and animals by using computational analysis tools. miRNAs are best predicted by next generation sequencing. They play a role as potential biomarkers in developmental processes. They are important therapeutic agents which play their role in diseases, such as cardiovascular, autoimmune, cancer, and neural degenerative diseases. The current study aimed to explore miRNAs and their clinical applications. For this purpose, miRNAs were analyzed as therapeutic agents and molecular biomarkers.</p> Iqra Kainat Sara Khan Anam Zahra Misbah Saleem Copyright (c) 2023 Iqra Kainat, Sara Khan, Anam Zahra, Misbah Saleem 2023-08-25 2023-08-25 4 2 15 32 10.32350/cto.32.02 Effect of CYP2C9 rs2860905 Polymorphism on the Efficacy of Losartan in Pakistani Hypertensive Patients <p>Hypertension is a multifactorial disease characterized by high blood pressure in blood vessels. It is caused by the dysregulation of renin angiotensin aldosterone system (RAAS). It is a major risk factor for other metabolic diseases including cardiovascular diseases, diabetes, and others. Various RAAS targeting drugs such as losartan are prescribed as the first line therapy to treat hypertension. However, their efficacy varies among individuals owing to genetic variations in drug binding substrates or drug metabolizing enzymes, which convert the prodrug to active drug. CYP2C9 gene encodes for an enzyme which metabolizes losartan. Various studies have concluded that genetic variations in CYP2C9 affect the response of losartan due to the variation in its metabolism. Thus, the current study aimed to check the effect of CYP2C9 rs2860905 G&gt;A polymorphism on the efficacy of losartan. For this purpose, a total of 48 subjects were selected and genotyped for rs2860905 polymorphism using in-house developed tetra-ARMS-PCR. The subjects were divided into responding (n=34) and non-responding (n=14) groups on the basis of their blood pressure after treatment with losartan. Statistical analysis demonstrated that rs2860905 GG genotype was more prevalent in the responding group as compared to the non-responding group (50% vs. 36%). Multinomial regression analysis showed that the carriers of GA or AA genotype did not respond to losartan treatment efficiently as compared to those of GG genotype. However, these results could not achieve statistical significance. To conclude, CYP2C9 rs2860905 G&gt;A polymorphism does not affect the efficacy of losartan in Pakistani hypertensive subjects.</p> Qurat Ul Ain Haider Hafsa Saeed Wajiha Ikram Usama Ikram Misbah Hussain Copyright (c) 2023 Qurat Ul Ain Haider, Hafsa Saeed , Wajiha Ikram, Usama Ikram, Misbah Hussain 2023-08-25 2023-08-25 4 2 64 77 10.32350/cto.32.05 Identification and Analysis of Hub Genes and Biological Pathways Involved in Alzheimer’s Disease (AD) Using Transcriptomics Dataset <p>Alzheimer’s disease (AD) is an irreversible and progressive neurodegenerative disorder. The brain mechanisms involved in this disease remain largely unknown. Hence, this study used the integrated bioinformatics approach to analyze a high throughput sequencing dataset (GSE162873) in order to identify the potential biomarkers involved in the pathophysiology of this disease. DESeq2 package was used for the identification of differentially expressed genes (DEGs) from both healthy and diseased patients. DAVID, a web-based bioinformatics resource, was used to perform functional enrichment analysis. StringApp plugin in Cytoscape was utilized to construct the protein-protein interaction (PPI) networks, whereas hub genes were identified through <em>cytoHubba</em>. MCODE was used to perform module analysis, ClueGO to evaluate the KEGG pathways enriched in modules, and miRNet platform for the interaction analysis of miRNAs and hub genes. Drug-genes interaction analysis was performed using DGIdb resource to find out the related drugs. A total of 652 DEGs were screened which were significantly enriched in GO terms. KEGG pathways analysis showed that PI3K-Akt signaling, hippo signaling, MAPK signaling, TGF-beta signaling, and sphingolipid signaling were significantly enriched pathways. A total of 12 hub genes were found to be significantly interacting with miR-603, miR-10b-5p, miR-124-3p, and miR-1-3p, and some FDA approved drugs. The current study provided an insight into the molecular mechanisms of AD and identified some potential biomarker genes, their pathways, miRNAs, and drugs which might be useful for diagnostic and therapeutic purposes.</p> Humaira Amin Asghar Shabbir Khuram Shahzad Copyright (c) 2023 Humaira Amin, Asghar Shabbir, Khuram Shahzad 2023-08-25 2023-08-25 4 2 42 63 10.32350/cto.32.04 Genetic Correlation of Conformation Traits with Semen Traits in Chinese Holstein Bulls: A Preliminary Investigation <p>The current study conducted a preliminary investigation of genetic correlations in Chinese Holstein bulls to improve their semen quantity and quality by indirect selection of conformation traits. The results of seven semen traits and nine conformation traits showed that the heritability estimates of semen traits ranged from 0.24 (post-thaw motility) to 0.63 (volume per ejaculation), while the conformation traits ranged from 0.29 (pin width) to 0.80 (withers height). Phenotypic correlation between scrotal circumference (SC) and semen concentration per ejaculation (SCPE), SC and total number of sperm per ejaculation (TNS), and SC and total number of motile sperm per ejaculation (TNMS) was 0.22, 0.25, and 0.24, respectively. Genetic correlation between SC and SCPE, SC and TNS, and SC and TNMS was 0.41, 0.40, and 0.38, respectively. To summarize, moderate or high heritability of semen traits indicated that genetic improvement of semen quality by selection is feasible, where SC could be a useful trait for indirect selection or as correlated information to improve semen quantity and production.</p> Jian Yang Xiao Wang Jie Xue Yundong Gao Jianbin Li Copyright (c) 2023 Xiao Wang 2023-08-25 2023-08-25 4 2 33 41 10.32350/cto.32.03 Current State of Artificial Intelligence (AI) in Oncology: A Review <p>Artificial intelligence (AI) has made significant strides in recent years toward resolving a wide range of biological issues, including a number of occurrences connected to cancer. Deep learning is an adaptable sector of AI that enables the automatic extraction of features. It is increasingly being used in various fields of cancer research, both scientific and clinical. In this study, several current applications of AI in oncology, including the situations in which deep learning has effectively addressed intractable disputes, are discussed. This study also discusses the challenges that need to be surmounted before such an application of AI may be implemented more broadly. Similarly, it brings to light resources and data sets that can assist in maximizing the potential of AI. Essential insights in oncology may be generated based on the development of novel methodologies and uses of AI, making it possible for substantial changes to be made to clinical practice.</p> Aqib Ali Samreen Naeem Sania Anam Muhammad Munawar Ahmed Copyright (c) 2023 Samreen Naeem 2023-06-15 2023-06-15 4 2 01 17 10.32350/cto.31.01 In Silico Analysis to Predict the Pathogenic Variants of CANT1 Gene Causing Desbuquios Dysplasia (DBQD) Type 1 <p>Desbuquois dysplasia (DBQD) is an autosomal recessive chondrodysplasia that belongs to the multiple dislocation group and causes parental and afterbirth growth retardation, hand and proximal femur abnormalities, joint laxity, and scoliosis. Several missense and splice site mutations in <em>CANT1</em> gene are linked with the development of DBQD. <em>In silico</em> approaches can predict the pathogenic variations causing hereditary diseases. Hence, in the current study, <em>in silico</em> analysis was used to forecast the variants of <em>CANT1</em> gene that harm the functionality of calcium-dependent nucleotidase. A total of 281 variants with uncertain significance, retrieved from the <em>gnomAD</em>, dbSNP, ClinVar, and Variation Viewer databases, were analyzed using CADD, Meta SNP, CAPiCE, and Condel to predict 61 highly pathogenic variants. Stability change predicting computational tools were applied to filter 19 highly pathogenic amino acid variants that impact protein dynamics via sample conformation or during vibrational entropy. UCSF Chimera was used for interactive visualization and analysis of unwanted interaction among 5 variants in the molecular structure of the protein. Ligand binding computational tools were used to interpret the protein-ligand interactions. A total of three (3) post-translational modification sites were also predictably disrupted by 16 variants. Spice and HSF 3.1 tools were applied to 95 variants to check their disease-causing potential. The variants of the gene were analyzed using computational tools based on different algorithms. The most damaging variants of <em>CANT1</em> gene that can affect the functionality and stability of the protein were predicted. It was determined that an extensive <em>in silico</em> analysis can determine the likely pathogenic variations for further <em>in vitro</em> experimental analysis.</p> Zainab Asif Mirza Ayman Naeem Aamna Syed Rana Muhammad Mateen Muhammad Irfan Fareed Dr. Mureed Husaain Copyright (c) 2023 Dr. Mureed Husaain 2023-06-15 2023-06-15 4 2 18 38 10.32350/cto.31.02 Morphological and Genetic Identification of Head Taunsa Barrage Fish Species <p>The current study aims to construct a thorough barcoding reference database of fishes in the Head Taunsa Barrage and assess the usefulness of employing the COI gene for fish species identification. A total of 15 genera, 10 families, and 7 orders of fish were used to collect a total of 19 mitochondrial COI barcode sequences. These sequences had an average length of 800 base pairs. Within species, genera, families, orders, and classes, the average Kimura two-parameter (K2P) distances were 0.97%, 0.99%, 1.23%, and 1.26%, respectively. According to their taxonomic classification, species were commonly clustered in the K2P neighbor-joining trees based on the sequence. DNA barcoding was employed in this study to identify species with a high degree of accuracy. Moreover, it was concluded that COI sequencing can be used to recognize fish species.</p> Dr. Saima Naz Ahmad Manan Mustafa Chatha Urooj Nazir Syeda Saira Iqbal Durali DANABAS Copyright (c) 2023 Dr. Saima Naz, Ahmad Manan Mustafa Chatha, Durali DANABAS , Urooj Nazir , Saba Iqbal 2023-06-15 2023-06-15 4 2 39 59 10.32350/cto.31.03 Development of T-ARMS-PCR to Detect MYBPC3 Gene Variation in Hypertrophic Cardiomyopathy (HCM) Patients <p>Hypertrophic cardiomyopathy (HCM) is a common and complex, genetically inherited, cardiovascular disorder. It is typically inherited in an autosomal dominant manner with variable penetrance and mutable expression. Mutations in MYBPC3 gene is one of the genetic causes of HCM. Only 0.2% of general population suffers from HCM. The MYBPC3 gene provides instructions for making cardiac myosin binding protein C, which is imperative for the maintenance and regulation of normal cardiac functions. This study aims to explore the reported SNP rs1052373 from exon 30 of MYBPC3 gene in the population of Punjab, Pakistan. The reported SNP rs1052373 was analysed using Tetra Amplification Refractory Mutation System Polymerase Chain Reaction (T-ARMS-PCR) to find the allelic frequency in the selected population. T-ARMS-PCR is a cost effective, flexible, rapid, and accurate tool for genotyping.&nbsp; The specific sequences of MYBPC3 gene from exons 30 and 31 and introns 29, 30, and 31 were retrieved from NCBI (<a href=""></a>). A tetra primer designing tool known as Primer 1 ( was used to design the primers for the targeted region of MYBPC3 gene. In this study, the genotyping of previously reported SNP rs1052373 showed variation in the disease group, giving CC, CT, and TT genotypes with the frequency of 0.04. The genotyping analysis of rs1052373 showed that the allelic frequency of homozygous condition T/T was 0.02 and the allelic frequency of heterozygous condition C/T was 0.02 in disease group as compared to the control group. In the latter, the homozygous T/T and heterozygous C/T genotypes were not observed in any individuals. All the individuals in control group carried homozygous C/C genotype. While, the frequency of homozygous C/C genotype was 0.96 in disease group. The findings of this study would help to find novel molecular markers for HCM diagnosis.</p> Haleema Sadia Waqas Ahmed Khan Misbah Hussain Iqra Murtza Copyright (c) 2023 waqas khan 2023-06-15 2023-06-15 4 2 60 72 10.32350/cto.31.04 Phenotypic and Genotypic Detection of Virulence Factors Affecting Proteus mirabilis Clinical Isolates <p>The current study attempts the phenotypic and molecular detection of the virulence factors of <em>Proteus mirabilis</em> clinical isolates. A total of 600 urine samples were collected from urinary tract-infected patients at Khyber Teaching Hospital, Peshawar, Pakistan. <em>P. mirabilis</em> isolates were identified through different biochemical tests. Virulence factors including urease production, biofilm formation, and swarming phenomenon were determined by using different markers (ureC1, rsbA, and luxS genes), identified via the polymerase chain reaction (PCR) technique. Out of the selected samples, 95 samples (15.83%) were identified as <em>P. mirabilis</em>. The molecular study showed that all isolates (100%) possessed the ureC gene. Whereas, 90.52% and 92.63% of the isolates gave positive results for biofilm formation (rsbA gene) and swarming phenomenon (luxS gene), respectively. The phenotypic and molecular study of <em>P. mirabilis</em> virulence factors provides a better understanding of how <em>P. mirabilis</em> infection spreads. The results could be used for prevention and improvements in its clinical treatment.</p> Fawad Hayat Muddasir Khan Muhammad Umair Sajeela Akbar Rida Javed Syed Hussain Shah Copyright (c) 2023 Fawad Hayat, MUDDASIR KHAN, Sajeela Akbar, Rida Javed, Syed Hussain Shah 2023-06-15 2023-06-15 4 2 73 85 10.32350/cto.31.05 Current Antibiotics Resistance Patterns of Salmonella typhi in District Peshawar, Khyber Pakhtunkhwa, Pakistan <p><em>Salmonella infection is most common in developing countries. In the current study, the prevalence and resistance pattern of Salmonella typhi from April, 2021 to March, 2022 in District Peshawar, Pakistan was identified/traced. Out of a total of 210 patients, 89 (43%) were found positive for S. typhi. Of these, 47 (52.8%) were men and 42 (47.2%) were women. The current study was conducted in four different sessions. It showed that nalidixic acid is the leading resistant drug. No significant differences were observed in antibiotics resistance with respect to age and gender (p≥0.05). To conclude, highly observed prevalence of S. typhi is a serious health concern. It was also concluded that season has no effect on the resistance pattern</em></p> Salman Ahmad Muhammad Salman Muhammad Arshid Malik Muhammad Umair Parsa Rehman Muddasir Khan Copyright (c) 2022 Salman Ahmad, Muhammad Salman, Muhammad Arshid Malik, Muhammad Umair 2023-02-21 2023-02-21 4 2 67 78 10.32350/cto.22.05 Molecular Identification of I-2 Gene, a Fusarium Wilt Resistant Marker in Selected Varieties of Tomato <p><em>Fusarium wilt is a well-known disease of tomatoes all over the world. The use of resistant varieties is the most efficient approach to control this disease. The current study was carried out to investigate the presence of marker gene(s) resistant to Fusarium wilt in tomato germplasm. This research subsequently sets out which one of the resistant varieties is suitable to be used to contain the disease. Thirteen varieties namely Pusa ruby, Pant bahar, Punjab chhahara, Arka alak, Arak abha, Ratan, CLN-2116-B, CLN-1767-238-2Y, CLSN-2123-A, CLN-1621-E, CLN-1621-T, CLN-1621-L, and CLN-2026-C were screened for the presence of I-2 resistance gene, a marker known to confer resistance to the race 2 of F. oxysporum f. sp. Lycopersici, using PCR-based molecular identification. Two varieties namely Arak abha and Ratan were tested positive for the presence of I-2 against race 2 of the pathogen.</em></p> Tariq Mahmood Nobia Aziz Inam Ullah Azizuddin Fida M. Abbasi Hamid Ali Hussain Shah Copyright (c) 2022 Tariq Mahmood, Nobia Aziz, Inamullah, Azizuddin, Fida M. Abbasi, Hamid Ali, Hussain Shah 2023-02-21 2023-02-21 4 2 25 35 10.32350/cto.22.02 Comparative Analysis of Methicillin-resistant Staphylococcus aureus through Whole Genome Sequencing (WGS) in the Largest Tertiary Care Hospital in Peshawar, Pakistan <p><em>Methicillin-resistant Staphylococcus aureus (MRSA) is a globally disseminated antibiotic-resistant pathogen that causes mild to severe infections. The population structure of MRSA is highly clonal. Individual genetic clones harbor specific plasmids and determinants for antibiotic resistance and virulence. Therefore, whole genome sequencing (WGS) of five MRSA isolates of the predominant genetic lineage was performed to gain insight into the most prevalent endemic strains. Sequencing libraries were arranged in accordance with the Nextera XT DNA Library Prep Guide (Illumina). WGS was performed on Illumina NextSeq 500 platform with 2×151bp using a NextSeq Mid-Output Kit. The sequenced genome was characterized for spa type, MLST type, SCCmec type, plasmid, antibiotic resistance gene, and virulence gene. This characterization was performed by publicly available bioinformatics tools, available on the website of the Center for Genomic Epidemiology. All the isolates were characterized as ST8/t064-SCCmecIVa (2B) clones of MRSA. A total number of 13 resistance genes, 11 virulence genes, and 6 types of plasmids were identified in the sequenced isolates of MRSA. Furthermore, the sequenced isolates showed a similar pattern of distribution for antibiotic resistance genes and virulence genes. WGS revealed that the isolates were genetically closely related and showed a similar pattern of distribution for different genetic markers. Therefore, these strains could be an accidental case cluster or cluster of an outbreak.&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;</em></p> Aman Ullah Muhammad Arif Khan Saira Ikram Ullah Tanveer Tara Daud Ahmad Muhammad Asif Zeb Copyright (c) 2022 Aman Ullah, Muhammad Arif Khan, Saira, Ikram Ullah, Tanveer Tara, Daud Ahmad, Muhammad Asif Zeb 2022-12-28 2022-12-28 4 2 56 66 10.32350/cto.22.04 In Silico Analysis of Functional SNPs in Human CRB2 GENE Associated with Focal Segmental Glomerulosclerosis <p><em>The CRB2 gene contributes to the onset hereditary focal segmental glomerulosclerosis, which damages the kidney, particularly the glomerulus, and results in chronic kidney failure. The pathogenicity of CRB2 non-synonymous single nucleotide polymorphisms (nsSNPs) was predicted in this work using a variety of bioinformatics techniques for mutation analysis. For this purpose, 1201 nsSNPs from dbSNP-NCBI were retrieved for the analysis, and 20 were predicted deleterious. The 20 missense variants are G349D, C629S, R534W, G178D, C620Y, C620S, R628C, R633G, R633W, E643A, T841M, R960S, R960C, P1064T, P1064S, N800K, G1088D, T1187P, R1249Q, and R1249P. &nbsp;SIFT, PROVEAN, Mutation Assessor, and PANTHER, four sequence homology-based approaches, suggested that one variation, R960S, was benign and that 19 SNPs were deleterious. Six supervised-based approaches, including SNAP2, MutPred2, SuSPect, PhD-SNP, SNPs&amp;Go, and PMut, predicted 14 SNPs as detrimental in all six applied methods. Hence, 13 variations were identified harmful by one structure-based technique, Poly-Phen, and two consensus-based methods, Meta-SNP and Predict-SNP. The CRB2 protein's mutant and wild-type structures were predicted using a laser. Following PyMol 5 structural analysis, the mutations rs879255250 cysteine at 620 changes to tyrosine, variation rs879255250 glycine at 178 changes to aspartate, and variant rs1322315181 glycine at 178 changes to sspartate arginine changes to proline at position 1249, and cysteine changes to serine at position 620, with variants rs147412276 and rs868484209. Proline at position 1064 alterations to serine were expected to be extremely harmful and resulted in structural changes in the protein, which may be candidates for the FSGS etiology. These CBR2 nsSNPs may, thus, be the possibilities for diagnostic genetic screening and therapeutic molecular targeting.</em></p> Imran Sattar Hajira Maqbool Muhammad Shahbaz Aslam Iram Gull Imran Tipu Mishel Zainab Copyright (c) 2022 Imran Sattar, Hajira Maqbool, Dr. Muhammad Shahbaz Aslam, Dr. Iram Gull, Dr. Imran Tipu, Mishel Zainab 2022-12-28 2022-12-28 4 2 36 55 10.32350/cto.22.03 Genetic Identification and Phylogenetic Relationship of Fish Species at Panjnad, Abbasia, and Abu Dahbi Canals (Punjab, Pakistan) Based on Mitochondrial COI Sequences <p><em>Fish is an extremely nutritious food abundant in important minerals, vitamin D, proteins, and omega-3 fatty acids. Mislabeling of fish products is a major problem in the fish industry. It affects market prices and causes price fluctuations. Phylogenetic analysis of nucleotide sequences could be used to verify the identity of misidentified fish species. In this study, five species (Cirrhinus mrigala, Hypophthalmichthys molitrix, Actinopterygii sp. [OC218 and OC21] and Mastacembelus armatus) were identified based on their phylogenetic analysis using the Cytochrome C Oxidase 1 (COI) gene amplified through PCR. The average product size was 658 base pairs. The comparison of obtained sequences was implemented through the National Center for Biotechnology Information (NCBI) database and Basic Local Alignment Search Tool (BLAST). The most similar sequences were downloaded for comparison with the obtained sequencing results. By using Molecular Evolutionary Genetics Analysis (MEGA X) the rate of different transitional substitutions was determined to be 11.33, while the rate of transversional substitutions was determined as 6.83. Transition/Transversion bias was 0.83. Kimura 2-parameter (K2p) model was used for the estimation of this substitution pattern. Since most freshwater fish species belonged to the same order or family, phylogenetic tree analysis indicated that they should be grouped together. By using the InterPro data that provides functional analysis of protein sequences by categorizing them into families, the activity and regulatory pathways of COI gene were identified to show its activity on protein level, especially for performing some important physiological functions. Each species of fish can be identified based on their speciation, nodes position, and distance from their parent nodes. Based on the closest phylogenetic relations, a DNA sequence-based study was developed for the accurate identification of fish species.</em></p> Saima Naz Ahmad Manan Mustafa Chatha Durali Danabas Naila Kousar Naeem Mehmood Ashraf Copyright (c) 2022 Dr. Saima Naz, Ahmad Manan Mustafa Chatha, Durali DANABAS3, , Naila Kouser, Naeem Mehmood Ashraf 2022-12-28 2022-12-28 4 2 1 24 10.32350/cto.22.01 Interpretations of Heamatological Parameters in COVID-19 Patients with Diabetic Mellitus Comorbidity <p><em>Coronaviruses (CoVs) can infect a wide range of wild and domestic hosts including animals, avian, mammals, rodents, and human beings. COVID infection has already been reported in whales, bats, mice, birds, and giraffes,s and infection to domestic and life stock cause heavy losses to the economy. These viruses cause mild to severe respiratory, enteric, and systemic infections. Worldwide 525,268,297 (May 19, 2022) individuals have been infected since the first case of COVID-19 was reported in Wuhan China with 6,295,402 deaths (May 19, 2022). In Pakistan, a total of 1,529,560 cases of COVID-19 have been reported with 30,379 deaths (May 19, 2022). Province wise data reported 577,201 cases in Sindh, 219,616 in KPK, 506,865 in Punjab, 135,312 in Islamabad, 35,494 in Baluchistan, and 43,324/11,748 in AJK/GB. This study evaluated the hematological parameters in diabetic patients affected by COVID-19. This cross-sectional retrospective study was conducted at the Department of Pathology, Aziz Bhatti Shaheed Hospital, Gujrat, Pakistan. Data were collected from a total of 111 patients of COVID-19 with DM comorbidities and analyzed for the comparison of Leukocytes parameters, platelets count, Red Blood Cell (RBC) counts, and their indices Packed Cell Volume (PCV), Mean Corpuscular Volume (MCV), Mean Corpuscular Hemoglobin (MCH) and Mean Corpuscular Hemoglobin Concentration (MCHC)] with their reference values. The mean RBC count was 4.45 with SD (±0.84). The data also showed the mean of Hemoglobin (Hb) level as 12.45 g/dl (SD ±3.01), PCV as 36.06 (SD ±9.16), MCV as 81.86 (SD ±7.32), MCH as 29.05 (SD ±6.27), and MCHC as 32.61 (SD ±3.65). A comparison was also made between male and female COVID-19-enrolled patients for hematological associated changes in DM. The frequency distribution of leukocytes and </em><em>thrombocytes showed lymphocytosis and thrombocytopenia. &nbsp;It was Concluded that hematological parameters are important in monitoring disease severity, progression, and management in COVID-19 patients with diabetes comorbidity.</em></p> <p><em>&nbsp;</em></p> Zia-ur-Rehman Farooqi Nimra Shaheen Umair Waqas Abid Ali Waqar Mehmood Dar Copyright (c) 2022 Dr. Zia Farooqi, Nimra Shaheen, Umair Waqas, Abid Ali, Waqar Mehmood Dar 2022-06-30 2022-06-30 4 2 89 98 10.32350/cto.21.05