Biology subjects

Musa, A.

Publications and source records attributed to Musa, A..

11 recordsLinked to original sources

bioRxiv2026

CCL19-CCR7 mediated recruitment of T cells is associated with the leishmanin skin test in individuals with prior exposure to Leishmania parasites

A delayed-type hypersensitivity (DTH) response induced by the intradermal inoculation of leishmanin antigens is used to detect prior exposure to the protozoan parasite Leishmania. Leishmanin antigen preparations are an important tool in disease surveillance studies in endemic areas. Commercial scale leishmanin antigens are being developed for wider deployment in assessing vaccine efficacy and latent infections in the field. Previous studies with leishmanin induced DTH response were limited to analysis of PBMCs. To investigate the mediators of DTH response, we performed spatial transcriptomic analysis of the DTH skin biopsies obtained from a Leishmania endemic foci. Compared to healthy skin biopsy, macrophages and T cells, and IL-16 and TNF that attract CD4+ T cells, were elevated in Langerhans cells in the DTH biopsies. Both IFN-{gamma} and its receptors were similarly elevated in the DTH biopsies. Chemokines CCL2, CCL5, CCL8 and CCL19, and the corresponding receptors were elevated in DTH biopsies, with CCL19-CCR7 as the most salient interaction in our Cellchat analysis. These data reveal biomarkers of DTH response following leishmanin inoculation and enable appropriate formulation and reintroduction of leishmanin skin test antigens for disease surveillance.

immunology↗

bioRxiv2025

Genome analysis of Lactobacillus plantarum and Lactobacillus brevis isolated from traditionally fermented Ethiopian kocho and their probiotic properties

Probiotics are essential for promoting health, with lactic acid bacteria (LAB) from traditional fermented foods like Ethiopian kocho offering valuable benefits. The objective of this study was to systematically analyse the genomic characteristics, bacteriocin production, and probiotic potential of LAB strains isolated from fermented Ethiopian kocho. The research involved isolating LAB from kocho, assessing their tolerance to acid and bile salts, evaluating antimicrobial activity, determining antibiotic susceptibility, and conducting whole-genome sequencing (WGS) to investigate genetic relatedness. Out of 150 LAB isolates, 7 (4.67%) exhibited remarkable acid tolerance, surviving at rates between 50.52-74.05% and 33.33-62.40% after 3 and 6 hours of exposure to pH 2, respectively. These seven acid-tolerant isolates also demonstrated exceptional resistance to 0.3% bile salt, maintaining survival rates ranging from 88.96% to 98.10% over 24 hours. In addition, the isolates displayed inhibitory effects against several important foodborne pathogenic bacteria, underscoring their potential as natural antimicrobial agents. Antibiotic susceptibility testing revealed that all isolates were susceptible to ampicillin, tetracycline, and erythromycin, whereas the most potent isolates exhibited significant resistance to kanamycin. Notably, four of the seven isolates showed resistance to streptomycin, while the remaining three were sensitive. The WGS analysis revealed that the isolates belonged to the Lactobacillus genus, including six Lactobacillus plantarum strains and one Lactobacillus brevis strain. Genomic analysis using the Bayesian Analysis of Gene Essentiality (BAGEL) tool predicted the presence of two class II bacteriocins across all seven strains, further supporting their potential as functional probiotic candidates. Overall, our findings highlight the probiotic potential of the seven Lactobacillus strains, demonstrating their acid and bile salt tolerance, antimicrobial properties, and genetic predisposition for bacteriocin production.

microbiology↗

bioRxiv2025

Validation of diverse and previously untraceable Sendai virus copyback viral genomes by Direct RNA Sequencing

Copyback viral genomes (cbVGs) are truncated viral genomes with complementary ends produced when the viral negative-sense RNA virus polymerase detaches from the replication template and resumes elongation from the nascent strand. Despite advances in methods to identify cbVGs based on the site of polymerase break and rejoin, PCR-based tools cannot provide full length sequences of most cbVGs and/or can introduce errors and artifacts during cbVG amplification. These limitations have painted a limited picture of the diverse population of cbVGs generated during infection. To improve our ability to obtain native full-length sequences of cbVGs, we optimized Direct RNA Sequencing (DRS) as a fast and simple tool to sequence full-length cbVGs and designed a BLAST-based analysis approach to identify cbVGs from long-read sequencing data. We analyzed the DRS outputs of multiple Sendai virus stocks to highlight both the utility and limitations of this tool. We found that to capture the dominant 546 nucleotide cbVG produced by Sendai virus strain Cantell, the length of complementarity between the virus trailer and the DRS oligonucleotide should optimally be increased to up to 32 nucleotides. We also demonstrate comparable quality of cbVG sequences by DRS from as little RNA as 17.6ng from the media fraction or 50ng of from the cellular fraction of cells infected with SeV, in contrast to the recommended 1000ng. Importantly, we validated different cbVG species from two recombinant Sendai virus stocks, including for the first time cbVGs whose break positions occurred at or near position one in the reference genome. ImportanceMost viruses of the order Mononegavirales has been demonstrated to naturally generate copyback viral genomes. These genomes are critical determinants of infection outcomes; they interfere with standard virus replication by competing for viral resources, activate antiviral responses, and inhibit protein translation. Despite their critical roles in infection, current tools to study copyback viral genomes rely either on preexisting knowledge of the sequence of a target RNA or require reverse-transcription and amplification of the target RNA, biasing toward short cbVGs and introducing relatively high rates of errors. Our lab has long advocated for RNA virologists to sequence their stocks to assess the role cbVGs may have in their infections. Toward this effort, we detail the optimization of Direct RNA Sequencing to sequence full-length cbVGs while maintaining the integrity of the native cbVG RNA and present the Long-Read cbVG Analysis (LoCA; https://github.com/lopezlab-washu/LOCA.git) script as a highly accessible BLAST-based tool for cbVG detection.

microbiology↗

bioRxiv2024

Plasmo3Net: A Convolutional Neural Network-Based Algorithm for Detecting Malaria Parasites in Thin Blood Smear Images

Early diagnosis of malaria is crucial for effective control and elimination efforts. Microscopy is a reliable field-adaptable malaria diagnostic method. However, microscopy results are only as good as the quality of slides and images obtained from thick and thin smears. In this study, we developed deep learning algorithms to identify malaria-infected red blood cells (RBCs) in thin blood smears. Three algorithms were developed based on a convolutional neural network (CNN). The CNN was trained on 15,060 images and evaluated using 4,000 images. After a series of fine-tuning and hyperparameter optimization experiments, we selected the top-performing algorithm, which was named Plasmo3Net. The Plasmo3Net architecture was made up of 13 layers: three convolutional, three max-pooling, one flatten, four dropouts, and two fully connected layers, to obtain an accuracy of 99.3%, precision of 99.1%, recall of 99.6%, and F1 score of 99.3%. The maximum training accuracy of 99.5% and validation accuracy of 97.7% were obtained during the learning phase. Four pre-trained deep learning models (InceptionV3, VGG16, ResNet50, and ALexNet) were selected and trained alongside our model as baseline techniques for comparison due to their performance in malaria parasite identification. The topmost transfer learning model was the ResNet50 with 97.9% accuracy, 97.6% precision, 98.3 % recall, and 97.9% F1 score. The accuracy of the Plasmo3Net in malaria parasite identification highlights its potential for automated malaria diagnosis in the future. With additional validation using more extensive and diverse datasets, Plasmo3Net could evolve into a diagnostic workflow suitable for field applications.

bioinformatics↗

bioRxiv2024

Identification of distinct genotypes in circulating RSV A strains based on variants on the virus replication-associated genes

Respiratory syncytial virus is a common cause of respiratory infection that often leads to hospitalization of infected younger children and older adults. RSV is classified into two strains, A and B, each with several subgroups or genotypes. One issue with the definition of these subgroups is the lack of a unified method of identification or genotyping. We propose that genotyping strategies based on the genes coding for replication-associated proteins could provide critical information on the replication capacity of the distinct subgroup, while clearly distinguishing genotypes. Here, we analyzed the virus replication-associated genes N, P, M2, and L from de novo assembled RSV A sequences obtained from 31 newly sequenced samples from hospitalized patients in Philadelphia and 78 additional publicly available sequences from different geographic locations within the US. In-depth analysis and annotation of the protein variants in L and the other replication-associated proteins N, P, M2-1, and M2-2 identified the polymerase protein L as a robust target for genotyping RSV subgroups. Importantly, our analysis revealed non-synonymous variations in L that were consistently accompanied by conserved changes in its co-factor P or the M2-2 protein, suggesting associations and interactions between specific domains of these proteins. These results highlight L as an alternative to other RSV genotyping targets and demonstrate the value of in-depth analyses and annotations of RSV sequences as it can serve as a foundation for subsequent in vitro and clinical studies on the efficiency of the polymerase and fitness of different virus isolates. IMPORTANCEGiven the historical heterogeneity of Respiratory Syncytial Virus (RSV) and the disease it causes, there is a need to understand the circulating RSV strains each season. This requires an informative and consensus method of genotype definition. Here, we carried out a variant analysis that shows a pattern of specific variations among the replication-associated genes of RSV A across different seasons. Interestingly, these variation patterns point to previously defined interactions of domains within these genes, suggesting co-variation in the replication-associated genes. Our results also suggest a genotyping strategy that can prove to be particularly important in understanding the genotype-phenotype correlation in the era of RSV vaccination, where selective pressure on the virus to evolve is anticipated. More importantly, the categorization of RSV strains based on these patterns may prove to be of prognostic value.

microbiology↗

bioRxiv2022

Valproic acid exposure alters social visual lateralization and asymmetric gene expression in zebrafish larvae

Cerebral asymmetry is critical for typical brain function and development, at the same time altered brain lateralization seems to be associated with neuropsychiatric disorders. In autism spectrum disorders (ASD) studies have suggested reduced functional and structural cerebral asymmetry, reporting changes in asymmetric activation of brain structures involved in language and social processing, and increased prevalence of left-handedness. Zebrafish are increasingly emerging as model species to study brain lateralization, using asymmetric development of the habenula, a phylogenetically old brain structure associated with social and emotional processing, to investigate the relationship between brain asymmetry and social behavior. We exposed 5-hour post-fertilization zebrafish embryos to valproic acid (VPA), a compound used to model the core signs of ASD in many vertebrate species, and assessed social interaction, visual lateralization and gene expression in the thalamus and the telencephalon. VPA-exposed zebrafish exhibit social deficits and a deconstruction of social visual laterality to the mirror. We also observe changes in the asymmetric expression of the epithalamic marker leftover and in telencephalic gene expression in adult zebrafish. Our data indicate that VPA exposure neutralizes the animals visual field bias, with a complete loss of the left-eye use bias in front of their own mirror image, and alters brain asymmetric gene expression, opening new perspectives to investigate brain lateralization and its link to atypical social cognitive development, considering zebrafish as an animal model for the autistic syndrome.

neuroscience↗

bioRxiv2022

Toxicological study on methanol root bark extract of Acacia sieberiana (Fabaceae) in Wistar rats

BackgroundThe plant Acacia sieberiana belongs to the family Fabaceae. It has been used in ethnomedical practice to manage bleeding, rheumatism, pain, pyrexia, kidney diseases, gastrointestinal problems, parasitic and infectious diseases, hepatitis, cough, epilepsy, mouth ulcer and many more. Phytochemical compounds such as ellagic acid, quercetin, isoferulic acid, gallic acid, kaempferol, luteolin, apigenin, glucoside dihydroacacipetalin, acacipetalin and many others were isolated from Acacia sieberiana. Previous pharmacological investigations have reported that the plant has anticancer, antimicrobial, antidiarrhoeal and antitrypanosomal effects. Despite the therapeutic properties of this plant, no safety information is available in the literature. Hence, this work intends to investigate the sub-acute toxicity effects of Acacia sieberiana root bark extract (ASE). The phytochemical and oral median lethal dose (LD50) evaluations on the ASE were done in line with the standard protocols. The sub-acute toxic effects of the ASE (250, 750, and 1,500 mg/kg) were investigated following administration of the ASE daily for 28-consecutive days based on the Organization of Economic Cooperation and Development (OECD) 407 protocols in rats. The weekly body weights were monitored and the rats were euthanized on the 29th day. The blood samples from the animals were obtained for biochemical and haematological determinations. The liver, kidney, lung and heart were removed for histological investigations. ResultsThe ASE revealed triterpenes, tannins, saponins, cardiac glycosides, flavonoids, and alkaloids. The oral LD50 values was >5,000 mg/kg. The ASE remarkably (p<0.05) declined the body weight of the rats in consideration to the control categories. There was also a remarkable (p<0.05) elevation in ALP, urea and lymphocytes. The cardiac histology revealed no abnormalities. However, the liver produced dose-dependent hepatocellular necrosis and vacuolations. Besides, lymphocyte hyperplasia and glomerular necrosis were observed in the kidneys and alveolar congestion in the lungs. ConclusionsThe ASE is relatively non-toxic on acute administration. In contrast, it could pose slight hepatic and renal toxicity on sub-acute administration.

pharmacology and toxicology↗

bioRxiv2022

Acacia sieberiana (Fabaceae) Attenuates Paracetamol and Bile Duct Ligation-Induced Hepatotoxicity via Modulation of Biochemical and Oxidative Stress Biomarkers

BackgroundThe plant Acacia sieberiana (Fabaceae) is traditionally used to manage hepatitis. This research work aims to investigate the hepatoprotective effectiveness of root bark extract of Acacia sieberiana (ASE) against paracetamol (PCM) and bile duct ligation (BDL)-induced hepatotoxicity. The phytochemical and median lethal dose (LD50) investigations were conducted. The rats were pre-treated with the ASE (250, 750, 1,500 mg/kg) once daily via oral route for 7 consecutive days. On the 8th day, liver injury was initiated by PCM administration (2g/kg). Similarly, in the BDL-induced liver injury, the animals were administered ASE (125, 250 and 380 mg/kg) intraperitoneally for 7 consecutive days. After 24 hours, blood samples and hepatic tissues were obtained for biochemical and histopathological investigations. ResultsPhytocomponents determination revealed glycosides, triterpenes, glycosides, saponins, tannins, flavonoids and alkaloids. The oral and intraperitoneal LD50 values of the ASE were >5,000 and 1,300 mg/kg, respectively. The ASE efficiently (p<0.05) decreased the alanine transaminase (ALT) and aspartate transaminase (AST) levels and elevated the albumin and total protein (TP) levels. The direct bilirubin effectively (p<0.05) decreased at 750 mg/kg. Besides, the extract efficiently elevated the glutathione peroxidase (GPx), superoxide dismutase (SOD), and catalase (CAT) in relation to the PCM hepatotoxic group. Also, the malondialdehyde (MDA) concentration was reduced by the ASE. Meanwhile, in the BDL- induced liver injury, the ASE remarkably (p<0.05) declined the AST, ALP, bilirubin and MDA. Besides, there was effective (p<0.05) elevation in SOD, GPx and CAT in the ASE-treated groups. The morphology of liver tissue was preserved at 125 and 250 mg/kg ASE groups from BDL-induced necrosis and vascular congestion. ConclusionThe study shows that the ASE has hepatoprotective actions against liver damage by possible modulation of biochemical and oxidative stress biomarkers

pharmacology and toxicology↗

bioRxiv2022

Molecular docking, simulation and binding free energy analysis of small molecules as PfHT1 inhibitors

Malaria chemotherapy has been plagued by parasite resistance. Novel drugs must be continually explored for malaria treatment. Plasmodium falciparum requires host glucose for survival and proliferation. Protein involved in hexose permeation, P. falciparum hexose transporter 1 (PfHT1) is a potential drug target. We performed high throughput virtual screening of 21,352 small-molecule compounds against PfHT1. The stability of the lead compound complexes was evaluated via molecular dynamics (MD) simulation for 100 nanoseconds. We also investigated the pharmacodynamic, pharmacokinetic and physiological characteristics of the compounds in accordance with Lipinksi rules for drug-likeness to bind and inhibit PfHT1. Molecular docking and free binding energy analyses were carried out using Molecular Mechanics with Generalised Born and Surface Area (MMGBSA) solvation to determine the selectivity of the hit compounds for PfHT1 over the human glucose transporter (hGLUT1) orthologue. Five important compounds were identified: Hyperoside (CID5281643); avicularin (CID5490064); sylibin (CID5213); harpagoside (CID5481542) and quercetagetin (CID5281680). The compounds formed intermolecular interaction with the binding pocket of the target via conserved amino acid residues (Val314, Gly183, Thr49, Asn52, Gly183, Ser315, Ser317, and Asn48). The MMGBSA analysis of the complexes yielded high free binding energies. Four (CID5281643, CID5490064, CID5213, and CID5481542) of the identified compounds were found to be stable within the PfHT1 binding pocket throughout the 100 nanoseconds simulation run time. The four compounds demonstrated higher affinity for PfHT1 than the human major glucose transporter (hGLUT1). This investigation demonstrates the inhibition potential of sylibin, hyperoside, harpagoside, and avicularin against PfHT1 receptor. Robust preclinical investigations are required to validate the chemotherapeutic properties of the identified compounds.

bioinformatics↗

bioRxiv2020

Novel algorithms for PFGE bacterial typing: Number of co-migrated DNA fragments, linking PFGE to WGS results and computer simulations for evaluation of PulseNet international typing protocols

BackgroundStandard protocols for Pulsed-field gel electrophoresis (PFGE) were adopted and being used in a global scale for surveillance of many bacterial food-borne diseases. Matched PFGE bands are considered regardless of co-migration of different DNA fragments. Molecular epidemiology is turning toward whole genome sequencing (WGS). Although, WGS results can be digested In-silico, PFGE and WGS data are being compared separately. We describe a new image analysis algorithm that enables identification of how many DNA fragments co-migrate during PFGE. We built a database that compare described PFGE results to in-silico obtained digestion models (from WGS). Reliability of the method was assessed in-silico using novel computer simulation approach. From WGS, 1,816 digestion model (DMs) were obtained as recommended by PulseNet international. Simulation codes were designed to predict PFGE profiles when DMs are separated at 5% PFGE resolution in addition to expected co-migration levels. ResultsPFGE simulation has shown that about 35% of DNA fragments co-migrate at 5% PFGE resolution. Similar result was obtained when wet-lab PFGE profiles were analyzed using image analysis algorithm mentioned earlier. When image analysis results were compared to DMs, results returned by geltowgs.uofk.edu database revealed reasonable relatedness to DMs. In terms of number of PFGE typable DNA fragments, 45,517 were typable (representing 46.54% out of 97,801). Previously mentioned typable fragments (in terms of typable sizes) comprised 91.24% of the sum of nucleotides of all chromosomes tested (7.24 billion bp). However, significant variations were shown within and between different digestion protocols. ConclusionsIdentification of co-migration levels will reveal the third dimension of PFGE profiles. This will provide a better way for evaluating isolate relationships. Linking old PFGE results to WGS by means of simulation demonstrated here will provide a chance to link millions of PFGE epidemiological data accumulated during the last 24 years to the new WGS era. Evaluation of population dynamics of pathogenic bacteria will be deeper through space and time. Selection of restriction enzymes for PFGE typing will have a powerful in-silico evaluation tool.

microbiology↗

bioRxiv2020

A Second Generation Leishmanization Vaccine with a Markerless Attenuated Leishmania major Strain using CRISPR gene editing

Leishmaniasis is a debilitating and often fatal neglected tropical disease caused by Leishmania protozoa transmitted by infected sand flies. Vaccination through leishmanization with live Leishmania major has been used successfully but is no longer practiced because it resulted in unacceptable skin lesions. A second generation leishmanization is described here using a CRISPR genome edited L. major strain (LmCen-/-). Notably, LmCen-/- is the first genetically engineered gene deleted Leishmania strain that is antibiotic resistant marker free and does not have any off-target mutations. Mice immunized with LmCen-/- had virtually no visible lesions following challenge with L. major-infected sand flies while non-immunized animals developed large and progressive lesions with a 2-log fold higher parasite burden. LmCen-/- immunization showed protection and an immune response comparable to leishmanization. LmCen-/- is safe since it was unable to cause disease even in immunocompromised mice, induces robust host protection against vector sand fly challenge and because it is marker free, can be advanced to human vaccine trials.

microbiology↗