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Fulltext Diversity pattern of Plasmodium knowlesi merozoite surface protein 4 (MSP4) in natural population of Malaysia

Ahmed MA, Saif A, Quan FS

PLoS One, 2019;14(11):e0224743.
PMID: 31751362 DOI: 10.1371/journal.pone.0224743

Human infections due to the monkey malaria parasite Plasmodium knowlesi are increasingly being reported from Malaysia. The parasite causes high parasitaemia, severe and fatal malaria in humans thus there is a need for urgent measures for its control. The MSP4 is a potential vaccine candidate, which is well studied in Plasmodium falciparum and Plasmodium vivax; however, no study has been conducted in the orthologous gene of P. knowlesi. In this study, we investigated the level of polymorphisms, haplotypes, natural selection and population structure of full-length pkmsp4 in 32 clinical samples from Malaysian Borneo along with 4 lab-adapted strains. We found low levels of polymorphism across the gene with exon I showing higher diversity than the exon II. The C- terminal epidermal growth factor (EGF) domains and GPI-anchored region within exon II were mostly conserved with only 2 non-synonymous substitutions. Although 21 amino acid haplotypes were found, the frequency of mutation at the majority of the polymorphic positions was low. We found evidence of negative selection at the exon II of the gene indicating existence of functional constraints. Phylogenetic haplotype network analysis identified shared haplotypes and indicated geographical clustering of samples originating from Peninsular Malaysia and Malaysian Borneo. High population differentiation values were observed within parasite populations originating from Malaysian Borneo (Kapit, Sarikei and Betong) and laboratory-adapted strains obtained from Peninsular Malaysia and Philippines indicating distinct population structure. This is the first study to genetically characterize the full-length msp4 gene from clinical isolates of P. knowlesi from Malaysia and thus would be very useful for future rational vaccine studies. Further studies with higher number of samples and functional characterization of the protein will be necessary.
Fulltext Moving object detection using dynamic motion modelling from UAV aerial images

Saif AF, Prabuwono AS, Mahayuddin ZR

ScientificWorldJournal, 2014;2014:890619.
PMID: 24892103 DOI: 10.1155/2014/890619

Motion analysis based moving object detection from UAV aerial image is still an unsolved issue due to inconsideration of proper motion estimation. Existing moving object detection approaches from UAV aerial images did not deal with motion based pixel intensity measurement to detect moving object robustly. Besides current research on moving object detection from UAV aerial images mostly depends on either frame difference or segmentation approach separately. There are two main purposes for this research: firstly to develop a new motion model called DMM (dynamic motion model) and secondly to apply the proposed segmentation approach SUED (segmentation using edge based dilation) using frame difference embedded together with DMM model. The proposed DMM model provides effective search windows based on the highest pixel intensity to segment only specific area for moving object rather than searching the whole area of the frame using SUED. At each stage of the proposed scheme, experimental fusion of the DMM and SUED produces extracted moving objects faithfully. Experimental result reveals that the proposed DMM and SUED have successfully demonstrated the validity of the proposed methodology.
Fulltext Moment feature based fast feature extraction algorithm for moving object detection using aerial images

Saif AF, Prabuwono AS, Mahayuddin ZR

PLoS One, 2015;10(6):e0126212.
PMID: 26030818 DOI: 10.1371/journal.pone.0126212

Fast and computationally less complex feature extraction for moving object detection using aerial images from unmanned aerial vehicles (UAVs) remains as an elusive goal in the field of computer vision research. The types of features used in current studies concerning moving object detection are typically chosen based on improving detection rate rather than on providing fast and computationally less complex feature extraction methods. Because moving object detection using aerial images from UAVs involves motion as seen from a certain altitude, effective and fast feature extraction is a vital issue for optimum detection performance. This research proposes a two-layer bucket approach based on a new feature extraction algorithm referred to as the moment-based feature extraction algorithm (MFEA). Because a moment represents the coherent intensity of pixels and motion estimation is a motion pixel intensity measurement, this research used this relation to develop the proposed algorithm. The experimental results reveal the successful performance of the proposed MFEA algorithm and the proposed methodology.
Fulltext Public Knowledge and Adherence to Hand Hygienic Guidelines for the Prevention of SARS-CoV-2 Transmission: A Cross-sectional Survey from Pakistan

Yaseen MO, Saif A, Khan TM, Yaseen M

Disaster Med Public Health Prep, 2022 Oct;16(5):1922-1928.
PMID: 33762050 DOI: 10.1017/dmp.2021.92

OBJECTIVE: Good hand hygienic practices are considered an important factor to curb the transmission and emergence of SARS-CoV -2. Various studies, conducted previously during the outbreaks of SARS-CoV and MERS-CoV, have ascertained the effectiveness of adopting good hand hygienic practices to curb the emergence of these viruses. This study aims to explore public hand hygienic practices during the peak pandemic period.
METHOD: A descriptive cross-sectional study was conducted among the general population of Pakistan to investigate the knowledge and perception about hand hygiene, self-reported hand hygiene practices, adherence to hand hygienic guidelines, and barriers to optimal hand hygiene. Kruskal-Wallis test, Mann-Whitney U test, and Regression model were used for statistical analysis.
RESULTS: There was a significant difference in area-based knowledge (P = 0.026), beliefs (P = 0.027), and practices (P = 0.002) regarding hand hygiene. The results of regression analysis revealed that people in urban areas were more likely to have better knowledge (β = 0.108, CI = 0.076 - 0.05, P = 0.008) and better adherence (β = 0.115, CI = 0.514 - 2.68, P = 0.004) to hand hygienic practices.
CONCLUSION: Advertisements on television and other electronic media with appealing slogans could be effective in making people more compliant to optimal hand hygienic practices.
Fulltext The antioxidant activity, preliminary phytochemical screening of Zingiber zerumbet and antimicrobial efficacy against selective endodontic bacteria

Assiry AA, Ahmed N, Almuaddi A, Saif A, Alshahrani MA, Mohamed RN, et al.

Food Sci Nutr, 2023 Aug;11(8):4853-4860.
PMID: 37576053 DOI: 10.1002/fsn3.3462

Antibiotic resistance is rising across the world. For a very long time, bitter ginger (Zingiber zerumbet) has been used as one of the most popular herbal remedies to treat a wide range of common diseases. Ginger has been shown to have antioxidant and antibacterial activity. It has various bioactive chemicals that might be utilized as an alternative treatment option for many infectious diseases. The present study aimed to examine the biochemical profile of ginger, antioxidant, and antibacterial activity against selective endodontic microbes. Antioxidant was measured using DPPH and antibacterial activity was performed using disk diffusion tests. Streptococcus mutants, Enterococcus faecalis, Staphylococcus spp., and Lactobacillus spp. were tested for antibacterial activity. Before evaluating the dried extracts, all solvents were eliminated using rotary evaporation. The obtained IC50 value revealed that ethanol extract had the greatest antioxidant activity. Concerning each bacterium, the plant extracts demonstrated considerable antibacterial activity (p = .001). Ethanol extracts showed the strongest antibacterial activity against the studied microorganisms. This study highlights that the Zingiber zerumbet (Z. zerumbet) is a strong antibacterial herb against multidrug-resistant (MDR) gram-positive bacteria. It may also be employed as a possible natural antioxidant source.
Fulltext Identification, Mapping, and Genetic Diversity of Novel Conserved Cross-Species Epitopes of RhopH2 in Plasmodium knowlesi With Plasmodium vivax

Ahmed MA, Deshmukh GY, Zaidi RH, Saif A, Alshahrani MA, Wazid SW, et al.

Front Cell Infect Microbiol, 2021;11:810398.
PMID: 35096656 DOI: 10.3389/fcimb.2021.810398

Malaria is a major public health concern, and any tangible intervention during the pre-elimination phase can result in a significant reduction in infection rates. Recent studies have reported that antigens producing cross-protective immunity can play an important role as vaccines and halt malaria transmission in different endemic regions. In this study, we studied the genetic diversity, natural selection, and discovered novel conserved epitopes of a high molecular weight rhoptry protein 2 (RhopH2) in clinical samples of Plasmodium knowlesi and Plasmodium vivax cross-protective domains, which has been proven to produce cross-protective immunity in both species. We found low levels of nucleotide diversity (P. knowlesi; π ~ 0.0093, SNPs = 49 and P. vivax π ~ 0.0014, SNPs = 23) in P. knowlesi (n = 40) and P. vivax (n = 65) samples in the PkRhopH2 cross-protective domain. Strong purifying selection was observed for both species (P. knowlesi; dS - dN = 2.41, p < 0.009, P. vivax; dS - dN = 1.58, p < 0.050). In silico epitope prediction in P. knowlesi identified 10 potential epitopes, of which 7 epitopes were 100% conserved within clinical samples. Of these epitopes, an epitope with 10 amino acids (QNSKHFKKEK) was found to be fully conserved within all P. knowlesi and P. vivax clinical samples and 80%-90% conservation within simian malaria ortholog species, i.e., P. coatneyi and P. cynomolgi. Phylogenetic analysis of the PkRhopH2 cross-protective domain showed geographical clustering, and three subpopulations of P. knowlesi were identified of which two subpopulations originated from Sarawak, Malaysian Borneo, and one comprised only the laboratory lines from Peninsular Malaysia. This study suggests that RhopH2 could be an excellent target for cross-protective vaccine development with potential for outwitting strain as well as species-specific immunity. However, more detailed studies on genetic diversity using more clinical samples from both species as well as the functional role of antibodies specific to the novel conserved epitope identified in this study can be explored for protection against infection.
Fulltext In Silico Analysis Reveals High Levels of Genetic Diversity of Plasmodium knowlesi Cell Traversal Protein for Ookinetes and Sporozoites (PkCelTOS) in Clinical Samples

Ahmed MA, Baruah P, Saif A, Han JH, Al-Zharani M, Wazid SW, et al.

Trop Med Infect Dis, 2023 Jul 26;8(8).
PMID: 37624318 DOI: 10.3390/tropicalmed8080380

The cell-traversal protein for ookinetes and sporozoites (CelTOS), expressed on the surface of ookinetes and sporozoitesin Plasmodium species, is a promising malaria vaccine candidate. CelTOS is essential for parasite invasion into mosquito midgut and human hepatocytes, thereby contributing to malaria transmission and disease pathogenesis. This study explores the genetic diversity, polymorphisms, haplotypes, natural selection, phylogenetic analysis, and epitope prediction in the full-length Plasmodium knowlesi CelTOS gene in clinical samples from Sarawak, Malaysian Borneo, and long-term laboratory strains from Peninsular Malaysia and the Philippines. Our analysis revealed a high level of genetic variation in the PkCelTOS gene, with a nucleotide diversity of π ~ 0.021, which was skewed towards the 3' end of the gene. This level of diversity is double that observed in PfCelTOS and 20 times that observed in PvCelTOS from worldwide clinical samples. Tests of natural selection revealed evidence for positive selection within clinical samples. Phylogenetic analysis of the amino acid sequence of PkCelTOS revealed the presence of two distinct groups, although no geographical clustering was observed. Epitope prediction analysis identified two potential epitopes (96AQLKATA102 and 124TIKPPRIKED133) using the IEDB server and one epitope (125IKPPRIKED133) by Bcepred server on the C' terminal region of PkCelTOS protein. Both the servers predicted a common epitope region of nine amino acid length (IKPPRIKED) peptide, which can be studied in the future as a potential candidate for vaccine development. These findings shed light on the genetic diversity, polymorphism, haplotypes, and natural selection within PkCelTOS in clinical samples and provide insights about its future prospects as a potential candidate for P. knowlesi malaria vaccine development.