Current Trends in OMICS

Anophthalmia and Microphthalmia in Pakistan: Current Genetic Insights and Future Perspectives

Usman Hameed, Ammara Saleem, Memoona Idrees, Muhammad Ansar — Tue, 15 Apr 2025 00:00:00 +0000

Anophthalmia and microphthalmia (A/M) are genetic disorders characterized by the absence or reduced size of the ocular globe, as compared to the globe size of the normal population. These disorders can be inherited in both autosomal recessive and dominant patterns. Certain genes have been reported to contribute significantly to the emergence of diseased phenotypes. Mutation in Forkhead Box E3 gene has been reported in different studies involving the Pakistani population, where the pattern of inheritance is autosomal recessive. Moreover, ALDH1A3 and VSX2 have been associated as well with severe phenotypes of A/M. SOX2 has been reported in the cases of de novo mutations and syndromic microphthalmia. The current review summarizes the most recurrent mutations in these genes in patients suffering from A/M in Pakistan. It showcases the importance of variant studies and how the demographic location of individuals may make them susceptible to a particular type of mutation. It also compares mutation profiles between the Pakistani population and global cohorts, emphasizing the impact of consanguineous marriages on the high prevalence of these conditions in the country. More studies may prove helpful in formulating a diagnostic kit for this disease so that a genotype-phenotype correlation can be established.

Characterization of Nicotine Degradation Associated Proteins in Paenarthrobacter nicotinovorans: An In-Silico Analysis

Fatima Muccee — Wed, 05 Mar 2025 00:00:00 +0000

Use of nicotine degrading bacteria (NDB) to degrade nicotine from tobacco waste contaminated soil is emerging as the most promising strategy. In the current study, three nicotine degradation associated proteins from NDB Paenarthrobacter nicotinovorans i. e., nicotine dehydrogenase (ndhA), 6-hydroxypseudooxynicotine dehydrogenase (kdhL), and nicotine blue oxidoreductase (nboR) were characterized. For this purpose, coding sequences (CDS) were retrieved from Uniprot database. These sequences were then subjected to analysis via PROTPARAM tool, Multiple Em for Motif Elicitation (MEME) suite, SOPMA, SwissModel, Transmembrane Topology Prediction and Classification (TMHMM), and Peptide cutter software. Characterization revealed values of alpha helix, extended strands, and random coil ranging between (29-44%), (14.49-21.08%), and (40.99-53.65%), respectively. Instability index, aliphatic index, and grand average of hydropathy (GRAVY) were observed as 26.76-44%, 91.06-101.32%, and -0.176- 0.091%, respectively. All the proteins exhibited highly complex 3D configuration and multiple number of conserved protein motifs. The number of cleavage sites analyzed for nghA, kdhL, and nboR was 515, 1313, and 313, respectively. The characteristics explored in the current study might be used to modify these proteins in order to maximize nicotine removal from environmental sources.

Pathogenicity Prediction of Potential Variants in TULP1 Gene causing Hereditary RP: An In-silico Approach

Faryal Sadiq — Mon, 16 Dec 2024 07:43:45 +0000

Retinitis Pigmentosa (RP) is a term used to describe a group of eye disorders related to retina damage. Due to the formation of bone spicules inside the retina of the affected individuals, patients suffer from poor eye vision or complete blindness, rarely. The reason of the disease could be genetic defects or environmental factors, for instance comorbidity, light exposure, and ethnicity. Tubby-like protein (TULP1) is expressed in the retina of the eye, specifically inside rod and cone cells, and mutations inside the gene can cause changes in structure and function of photoreceptor cells. The current study may provide new insights to understand the genetic variations found in TULP1 gene from the genomic to proteomic level, thus predicting the highly pathogenic variations causing RP. Different bioinformatic tools employing different algorithms were used to score the pathogenic variants, hence cross validating the results. Twenty (20) pathogenic missense variants which can destroy the protein structure as discussed in the study, thirteen (13) splice site variants, and lastly, nine (9) frameshift, seven (7) stop-gained variants were concluded as highly pathogenic for the candidate gene.

Decoding Breast Cancer Progression: Influence of miR-155-3p as Modulator of Molecular Signaling Pathways and Genetic Targets

Fri, 15 Nov 2024 00:00:00 +0000

Breast cancer is an eminent cause of fatality in women, worldwide. It is predominantly propelled by aberrant gene expression. A pivotal element in this mechanism is the disrupted regulation of microRNAs, particularly miR-155-3p. This investigation delves into the impact of miR-155-3p in breast cancer by employing advance methodologies, such as KEGG, DIANA, and Reactome Database, in order to unveil its genetic targets and molecular repercussions. It identifies six genes targeted and downregulated by miR-155-3p in breast cancer cells. This downregulation disrupts multiple vital biological pathways, including MAPK, AKT, STAT3, NFkB, and NOTCH signaling. These pathways play a crucial role in cellular processes, such as angiogenesis, apoptosis, DNA damage response, cell cycle control, and oncogene expression. Modifying these pathways by miR-155-3p underscores its substantial influence on the progression of breast cancer. The findings exemplify that the upregulation of miR-155-3p is a major contributing factor in the advancement of breast cancer. This upregulation initiates a series of molecular events that intensify the disease. Comprehending this mechanism is imperative for the development of targeted therapies. The implications of this research extend beyond the scientific community, presenting the potential for groundbreaking clinical applications. Furthermore, it establishes that miR-155-3p can be used as a diagnostic marker for breast cancer. This could significantly transform the landscape of breast cancer management, instilling hope both for improved outcomes and preventive strategies.

Morphological and Genetic Identification of Fish Species of River Ravi, Pakistan

Ayesha Eeman, Saima Naz, Ahmad Manan Mustafa Chatha, Syeda Saira Iqbal — Sun, 10 Nov 2024 00:00:00 +0000

DNA barcoding is a method that examines a specific part of the mitochondrial genome known as the cytochrome c oxidase subunit I (COI) gene, for species identification and biodiversity studies. The current study assessed the effectiveness of using the COI gene for the identification of fish species by constructing a phylogenetic tree with the help of a reference database of fish from the Head Balloki, River Ravi, Pakistan. A total of 15 fish species were analyzed with a 685-base pair (bp) segment of the mitochondrial COI gene sequenced (or "barcoded") for each species. These species represented 15 genera, 10 families, and 6 orders. On average, the sequences were 630 base pairs long. In terms of base composition, the average T content was the highest, while the average G content was the lowest. The AT content (54.1%) was higher than the GC content (45.9%). An analysis of nucleotide pair frequencies across the dataset revealed that out of 685 sites, 385 (56.20%) were conserved within the sequence. Of the 685 sites, 294 sites (42.92%) were variable and 226 (33%) were parsimony informative, while 66 of 685 sites (9.64%) were singletons. In the dataset, transitional pairings (si= 64) were more common than trans-versional pairings (sv = 57), with a si/sv (R) ratio of 1.1. On average, there were 483 pairs where the nucleotides were the same (ii). The average frequencies of nucleotide bases in these sequences were as follows: T (28.8%), C (28.1%), A (25.3%), and G (17.8%). The average Kimura two-parameter (K2P) distances within species, families, and orders were 0.24±0.01%, 0.24±0.02%, and 0.24±0.01%, respectively. Although, each species has a distinct cox1 sequence, various species might occasionally have similar haplotypes. In order to investigate evolutionary links, the maximum likelihood analysis approach was merged with the barcode-based method. In line with the taxonomy categories, the phylogenetic tree generated various groupings that were verified. The current study showed that cox1 sequencing, or DNA barcoding, is a useful method to accurately identify fish species based on both genetic and morphological characteristics.

Evolutionary Dynamics of Polintons: A Rarely Investigated Superfamily of DNA Transposons

Muhammad Umair Khan, Faisal Nouroz, Amina Waheed, Shumaila Noreen — Thu, 10 Oct 2024 00:00:00 +0000

Polintons, also known as ‘Maverick’ is a rarely investigated superfamily of DNA transposons. Although, discovered in recent decades, these elements are now found in several eukaryotic genomes due to the advancements and expansions in genome sequencing projects. The current study was conducted to investigate the evolutionary genomics and distribution of Polintons in various genomes. Approximately, 102 Polinton elements from various species were collected from Repbase – GIRI database. They have shown a high structural diversity and ranged in sizes from 03 to 42kb. The phylogenetic relationship and evolutionary history of the Polinton superfamily was investigated using bioinformatics software. Phylogenetic trees were created based on two major protein coding domains, such as RVE integrase and DNA POL B. In both cases, the sequences were clustered in 2 clades, several sub-clades, and groups with variable number of elements in each group. The cladograms represented the extensive genetic diversity and evolutionary history of these elements and allowed to observe the intricate branching patterns and relationships within the Polinton superfamily. The cladogram provides a roadmap to explore the relationships and dynamics of the Polinton superfamily in detail. The current study aimed to enhance the understanding of evolutionary dynamics of Polintons found in different organisms.

Current Situation of Breast Cancer in Pakistan and the Dire Need of Early Diagnosis

Najeeb Ullah Khan, Bibi Maryam Khan, Imad Azam, Atif Hayat — Wed, 20 Mar 2024 00:00:00 +0000

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.

Detection of Single Nucleotide Polymorphism (SNP) rs2235371 of IRF6 Gene in Patients with Non-Syndromic Cleft Lip and Palate

Kifayat Ullah, Tooba Komal, Ghafran Ali — Tue, 05 Mar 2024 00:00:00 +0000

The orofacial clefts are the most common structural birth defects among newborn babies. They consist of two groups, namely Cleft Palate (CP) and Cleft Lip (CL). Infants born with clefts have considerable problems during communication, swallowing, and face certain challenges due to facial deformity. These problems remain throughout the life if not treated and entail long-lasting effects on the health and social life of an individual. Untreated infants need special care as they have higher morbidity and mortality rates. The primary objective of this study is to detect the Single Nucleotide Polymorphism (SNP) rs2235371 within the IRF6 gene and assess its potential association in patients diagnosed with Non-Syndromic Cleft Lip/Palate (NSCL/P). The participants were selected through a non-probability sampling technique, specifically the purposive sampling method. In accordance with this approach, a total of 50 patients afflicted with NSCL/P, representing both the genders, were sampled. Furthermore, to establish a comparative baseline, an additional 50 healthy individuals were also recruited to serve as the control group. After taking their informed consent, blood was collected in EDTA vials. PCR (Polymerase Chain Reaction) and RFLP were performed on each sample to find SNP. After sample collection, processing, and analysis, SPSS (20.00 version) was used to analyze all previously generated data. After sample analysis, 72% of CL/P (cleft lip and palate) patients were found to have SNP with or without a family history. The association of SNP rs2235371 with disease was measured by applying chi-square. The results provided no evidence of the association between given SNP and disease. As compared to previous research, this study showed a low frequency of SNP rs2235371 in patients with NSCL/P. To get a better understanding of the association of SNP rs2235371 with NSCL/P, large-scale research with an increased sample size should be conducted.

Coronavirus Epidemiology, Diagnosis, and Vaccination Statistics in Pakistan, China, and India: A Brief Review

Tue, 05 Mar 2024 00:00:00 +0000

The global population has witnessed significant disruptions towards healthcare systems due to the Coronavirus pandemic. The World Health Organization (WHO) has designated it as a global health concern. Certain viruses within the Coronaviridae family predominantly inflict damage upon the respiratory system. The symptoms of infection may vary in severity, ranging from mild to severe, and in certain cases, can even lead to fatality. The most commonly observed symptoms include pyrexia, dyspnea, rigours, and gastrointestinal disturbances. Presently, COVID-19 stands as the prevailing subject of investigation within the academic community. The objective of the current study was to consolidate the present comprehensive material in a single source, hence enhancing the fundamental comprehension necessary for subsequent research endeavors.

Unveiling the Secrets of Obesity with Machine Learning (ML) Techniques/Algorithms

Abdur Rauf, Muhammad Ammar, Mahnoor Azhar, Nasreen Noor, Syeda Marriam Bakhtiar — Sun, 03 Mar 2024 00:00:00 +0000

Obesity is the most significant health threat all over the world as it is considered the mother of all diseases. Recent decades have witnessed an extensive shift towards sedentary lifestyles including adaptation to luxury modes of transportation, processed food, lack of physical activities, and prolonged screen times. The trend of using cars and motorcycles to travel even short distances has emerged as a critical component in Pakistan's obesity pandemic. Whenever the causes of obesity are discussed, the focus remains always on processed food and genetic factors. This study is an effort to exploit a machine-learning-based pathway to predict the major causes of obesity using machine learning (ML) algorithms. For this research, a dataset of 2,111 instances of various age groups and lifestyles was employed. For analysis, three efficient ML algorithms known as k-nearest neighbor (k-NN or KNN), support vector machine (SVM), and decision tree (DT) were utilized. It was observed that the excessive use of personal transport and comparatively limited availability and use of public transport has been a significant cause of obesity in Class II and III obese individuals. From the experimental results, strong association rules with minimum confidence value of 25% and maximum support value of 80% were obtained. Also, DT with random forest technique was found to have the highest accuracy of 90.36%, with the recall factor value of 98.73%. This signifies the fact that sedentary lifestyle and mode of transportation have a significant impact on rising obesity level.

Diversity Analysis of Catechol 2, 3-dioxygenase in POPs Metabolizing Bacteria using In-silico Approach

Fatima Muccee — Tue, 26 Dec 2023 00:00:00 +0000

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.

Reducing Multidrug-Resistant (MDR) Klebsiella pneumoniae via the Efficient Use of Bacteriophages ZI3 and HI3

Wed, 20 Dec 2023 00:00:00 +0000

Klebsiella pneumoniae is a common cause of multidrug-resistant (MDR) pneumonia, bacteremia, urinary tract infections (UTIs), and other systemic infections. K. pneumoniae is the third most common pathogen in blood cultures from sepsis patients. It can cause severe epidemic and endemic nosocomial infections. Antibiotic treatment of K. pneumoniae 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 10³¹ 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 K. pneumoniae strain kp8890 were isolated, characterized, and labeled as ZI3 and HI3. Both these phages were found to have a specific host range for K. pneumoniae. HI3 was able to lyse 7 out of 10 different K. pneumoniae 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 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.

Detection of DNA Damage in Fish using Comet Assay

Thu, 02 Nov 2023 00:00:00 +0000

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 Labeo rohita, Catla catla, Hypophthalmichthys molitrix, and Ctenopharyngodon idella 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 LC₅₀) 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 Catla catla, Hypophthalmichthys molitrix 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, Ctenopharyngodon idella 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_50.

Antioxidant and Antimicrobial Activity of Cuscuta reflexa ROXB. and Few Members of Family Convolvulaceae

Qumqum Noshad, Muhammad Ajaib, Aysha Kiran — Fri, 25 Aug 2023 00:00:00 +0000

Antioxidant activity of 12 species, of which one was Cuscuta reflexa Roxb. which belongs to the family of Cuscutaceae as well as 11 of Convolvulaceae, 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. Ipomoea eriocarpa showed a comparatively higher amount of total polyphenols (0.98 ± 0.073 mg/gdw). The maximum DPPH value was shown by Ipomoea carnea Jacq (5.6%) and the minimum value was shown by Convolvulus arvensis L. extracts (3.0 %). ABTS was the highest by Convolvulus prostrastus and the lowest by Ipomoea carnea. In FRAP assay, the highest value was 2.75 by Ipomoea hederacia and the lowest value was 0.31 by I. arachnosperma 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 Staphylococcus aureus and Bacillus subtilis, two gram negative bacteria namely E. coli and Pseudomonas aeruginosa, two fungal strains of Aspergillus niger and Aspergillus oryzae 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 Cuscuta reflexa Roxb. extract against Aspergillus niger, that is 5.55±0.3, while the lowest zone of inhibition, that is, 0.60±0.28mm was shown by Evolvulus alsinoides (L.) extract against Aspergillus oryzae. Plants from the Convolvulaceae 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

MicroRNAs: An Overview of their Discovery, Biogenesis, Computational Prediction, and Potential Clinical Applications

Iqra Kainat, Sara Khan, Anam Zahra, Misbah Saleem — Fri, 25 Aug 2023 00:00:00 +0000

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.

Effect of CYP2C9 rs2860905 Polymorphism on the Efficacy of Losartan in Pakistani Hypertensive Patients

Qurat Ul Ain Haider, Hafsa Saeed , Wajiha Ikram, Usama Ikram, Misbah Hussain — Fri, 25 Aug 2023 00:00:00 +0000

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>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>A polymorphism does not affect the efficacy of losartan in Pakistani hypertensive subjects.

Identification and Analysis of Hub Genes and Biological Pathways Involved in Alzheimer’s Disease (AD) Using Transcriptomics Dataset

Humaira Amin, Asghar Shabbir, Khuram Shahzad — Fri, 25 Aug 2023 00:00:00 +0000

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 cytoHubba. 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.

Genetic Correlation of Conformation Traits with Semen Traits in Chinese Holstein Bulls: A Preliminary Investigation

Jian Yang, Xiao Wang, Jie Xue, Yundong Gao, Jianbin Li — Fri, 25 Aug 2023 00:00:00 +0000

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.

Current State of Artificial Intelligence (AI) in Oncology: A Review

Aqib Ali, Samreen Naeem, Sania Anam, Muhammad Munawar Ahmed — Thu, 15 Jun 2023 00:00:00 +0000

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.

In Silico Analysis to Predict the Pathogenic Variants of CANT1 Gene Causing Desbuquios Dysplasia (DBQD) Type 1

Thu, 15 Jun 2023 00:00:00 +0000

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 CANT1 gene are linked with the development of DBQD. In silico approaches can predict the pathogenic variations causing hereditary diseases. Hence, in the current study, in silico analysis was used to forecast the variants of CANT1 gene that harm the functionality of calcium-dependent nucleotidase. A total of 281 variants with uncertain significance, retrieved from the gnomAD, 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 CANT1 gene that can affect the functionality and stability of the protein were predicted. It was determined that an extensive in silico analysis can determine the likely pathogenic variations for further in vitro experimental analysis.