BioScientific Review

In Silico Characterization of Hypothetical Protein AZJ53_10480 in Streptococcus pneumoniae

Nimra Hanif — 2024-09-23

Background. Streptococcus pneumoniae is a major human pathogen responsible for serious infections such as pneumonia. Despite extensive research, many proteins in S. pneumoniae, including hypothetical proteins, remain uncharacterized, limiting the understanding of the bacterium's pathogenic mechanisms.

Methods. This study utilizes in silico tools to characterize the hypothetical protein AZJ53_10480 from S. pneumoniae. Sequence alignment and phylogenetic analysis were conducted using BLASTp and ClustalW, while PSIPRED and I-TASSER predicted the protein’s secondary and tertiary structures. Molecular docking studies were performed with AutoDock Vina to assess potential interactions with the antiviral drug sofosbuvir

Results. The in silico analysis revealed that the hypothetical protein AZJ53_10480 shares structural and functional similarities with viral capsid proteins of the hepatitis C virus. The protein was found to have a mixed localization, suggesting potential multifunctionality within the bacterial cell. Molecular docking studies indicated a strong binding affinity between AZJ53_10480 and sofosbuvir, suggesting that this protein could be a potential target for therapeutic intervention.

Conclusion. This study highlights structural properties and functional roles of hypothetical protein AZJ53_10480 in S. pneumoniae of . The findings suggest that AZJ53_10480 may play a role in the pathogenicity of this bacterium and could serve as a novel target for therapeutic development. Further experimental studies are needed to validate these findings and explore the protein's potential as a drug target.

Highlights

In silico analysis reveals structural similarities between the hypothetical protein AZJ53_10480 and viral capsid proteins.
Docking studies suggest AZJ53_10480 as a potential target for antiviral drugs like sofosbuvir.
The study provides new insights into the possible pathogenic role of hypothetical proteins in Streptococcus pneumoniae.

Isolation and Characterization of Vermamoeba vermiformis from Swimming Pools in Lahore, Pakistan

Muhammad Tariq Zahid — 2024-10-11

Background. Free-living amoebae (FLA) are common in aquatic environments and their interaction with humans can lead to significant public health risks. Many of these amoebae are opportunistic pathogens, causing infrequent yet severe diseases. Vermamoeba vermiformis, a widely distributed FLA, has been associated with keratitis infection, often in conjunction with Acanthamoeba. Furthermore, V. vermiformis can serve as a host for pathogenic bacteria, such as Legionella pneumophila and Stenotrophomonas maltophilia, amplifying potential health risks. This study aimed to investigate the presence of FLA in three (3) swimming pools situated in Lahore, Pakistan.

Methodology. A total of eighteen (18) water samples were collected from the swimming pools and filtered using 0.45μm cellulose acetate filter papers. The filter papers were carefully placed upside down on non-nutrient agar (NNA) plates seeded with heat-attenuated E. coli. A pure culture of FLA was obtained through repeated subculturing on NNA plates seeded with E. coli, ensuring the results' reliability and validity.

Results. Samples from all three (3) pools exhibited the presence of FLA. The isolated FLA was identified as V. vermiformis based on its morphological appearance under the light microscope, and molecular characterization was performed using the SSU rRNA gene sequence. The trophozoites of V. vermiformis were elongated and cylindrical, with a single pseudopodium, giving them a limax shape. The cysts of V. vermiformis had a double-walled oval and round structure. A clear hyaloplasm was observed at the anterior end of the pseudopodia of actively moving V. vermiformis under a light microscope.

Conclusion. SSU rRNA, gene-based, molecular characterization confirmed isolated FLA as a local isolate of V. vermiformis. Phylogenetic analysis indicated its close homology with Echinamoeba. The presence of V. vermiformis in swimming pool water poses a potential threat to human health, as it is an opportunistic pathogen and a well-known host of different pathogenic bacteria.

Prevalence, In Silico Analysis and Possible Molecular Drug Therapy for Specific Meningitis Types

Beenish Khanzada — 2024-11-08

Background. Meningitis is the inflammation of the membranes surrounding the brain and spinal cord. This study was designed to determine the prevalence of meningitis along with the docking of bacterial proteins with drugs used to treat meningitis.

Methodology. A cross-sectional study was conducted including 100 febrile seizure children admitted to the hospitals of Hyderabad, Pakistan. Demographic data was recorded via a questionnaire. Cerebrospinal fluid (CSF) and blood were analyzed clinically. Molecular docking via PyRx―a virtual screening tool―was performed and Chi-square test was applied to interpret the data.

Results. Out of the 100 patients included in the study, 32 had been diagnosed with meningitis, 53 were suspected patients, and 15 were patients of encephalitis. Among diagnosed meningitis patients, 47% had bacterial meningitis, 16% had viral meningitis, while only 9% had TBM. Moreover, 28% of patients were partially treated with a mortality rate of 18%. Low glucose levels, high protein levels, and high neutrophil count were found in cerebrospinal fluid (CSF). The majority of patients were vaccinated (48%). Meningitis was more frequent among infant children and the results were statistically significant (p-value = 0.01). Molecular docking revealed that ceftriaxone had the greatest affinity for bacterial proteins, while Haemophilus influenza Hia Adhesin (3syj) and Pneumolysin (5aoe) had the lowest Kd values of -9 and -8.6, respectively.

Conclusion. Bacterial meningitis was found to be the most prevalent type with 32% prevalence. Ceftriaxone could be the drug of choice if meningitis is caused by 3syj or 5aoe. However, either vancomycin or meropenem may be preferred over ceftriaxone if meningitis is caused by 1p4t (Neisserial surface protein A).

Investigating the Anti-Tubercular Potential of Novel Non-Antibiotic Agents against Drug-Resistant Mycobacterium Tuberculosis

Muhammad Fayaz Khan — 2024-11-04

Background. The ever-increasing prevalence of multidrug-resistant Mycobacterium tuberculosis (MDR-TB) presents an alarming challenge to existing tuberculosis (TB) treatment stratgies. Hence, the current study explores the potential of dihydroergotamine and abiraterone acetate, two non-antibiotic compounds, as innovative anti-tubercular agents.

Methods. In silico analyses were conducted to identify potential drug targets for dihydroergotamine and abiraterone acetate. Subsequently, these compounds were evaluated for their bactericidal efficacy against both the reference H37Rv strain and an MDR-TB strain of M. tuberculosis in vitro. A range of drug concentrations were tested to determine their inhibitory effects.

Results. Both dihydroergotamine and abiraterone acetate exhibited substantial inhibitory activity against M. tuberculosis. Dihydroergotamine demonstrated efficacy at higher concentrations (128 µg and 256 µg), while abiraterone acetate exhibited potency at lower concentrations (64 µg, 128 µg, and 256 µg). The observed dose-dependent inhibitory effect emphasizes the importance of optimizing drug concentrations in anti-tubercular therapy.

Conclusion. Both compounds act as potential anti-tubercular agents by effectively inhibiting the growth of M. tuberculosis, with abiraterone acetate demonstrating greater potency at lower concentrations. These findings suggest both compounds may be promising candidates for further research and development as potential treatments for tuberculosis.

Efficacy of Charcoal and Water Based Formulations of Bacillus subtilis to Promote the Growth of Triticum aestivum (L.)

Shafqat Nawaz — 2024-11-16

Background. Plant growth-promoting rhizobacteria (PGPR) are used with different carrier materials that provide habitat and nutrients to the bacteria. Charcoal is an important carrier material which also acts as the source of carbon for microorganisms.

Objective. This study aims to analyze the effects of charcoal and water-based formulations of Bacillus subtilis on the growth parameters of wheat plant, namely Triticum aestivum L.

Methodology. Five strains of B. subtilis were selected including Z-12, Z-16, Z-24, Z-44, and Z-66. The cellular morphology of the strains was examined by performing Gram and endospore staining. For their further characterization, several biochemical tests were performed. Strains were evaluated for auxin production by growing them in Luria-Bertani (LB) broth, supplemented with 0, 400, and 800 μg/ml concentrations of L-tryptophan. Charcoal and water-based formulations of single and mixed cultures, namely C1 (Z-12, Z-44, Z-66), C2 (Z-12, Z-16, Z-24), and C3 (Z-16, Z-44, Z-66) were applied to soil and seeds, respectively. Multiple growth parameters were examined under laboratory and natural conditions including root length, shoot length, fresh weight, dry weight, tillers, spike length, and seed weight.

Results. Colorimetric analyses revealed strains Z-44 and Z-66 as more active in auxin production. Under laboratory conditions (water-based), mixed culture C1 showed maximum improvement in all parameters. Among water-based formulations, mixed cultures C1 and C3 successfully exhibited maximum growth under natural conditions. Among charcoal-based formulations, strains Z-12 and Z-24 recorded maximum improvement in seed weight and spikelet count at the final harvesting stage.

Conclusion. The study concluded that both types of PGPR formulations significantly enhanced the growth parameters of wheat.

Potential Benefits of Pomegranate as an Additive in Fish Diet and Fish Products: A Review

Meerub Sarfraz — 2024-11-16

Pomegranate (Punica granatum), commonly known as “Anar”, is an ancient fruit. It is preferably consumed due to its pleasing taste and high nutritious value along with some other associated health benefits. These benefits are not only meant for human beings, however, also for the fish. In recent times, scientific interest in pomegranate and its consumption has increased due to its numerous health benefits. Therefore, the current study aimed to review the most recent literature on different properties of the pomegranate. These properties include antimicrobial and antioxidant activities, its effect on hematological and growth parameters along with the role of pomegranate as a preservative in fish and fish products. The current study evaluated previously conducted studies to determine the effect of pomegranate on different systems of fish. Results showed that the intake of pomegranate effectively increased the growth of juvenile fish and dietary value of fish, boosted the hematological and immune responses, as well as feed efficiency and antioxidant activity. Moreover, it also showed antioxidant properties and proved effective for the preservation of fish fillets by reducing lipid oxidation, chemical degradation, and microbial growth in stored fish. Therefore, the incorporation of pomegranate in fish food has numerous applications. However, additional research is required to ascertain the safe limits.