Biology subjects

Ahmed, S. A.

Publications and source records attributed to Ahmed, S. A..

7 recordsLinked to original sources

bioRxiv2025

Psychedelics Relax Priors and Reshape Orbitofrontal Dynamics

Psychedelics such as psilocybin and ketamine are gaining attention as rapid-acting treatments for psychiatric disorders, yet the mechanisms by which they alter cognition remain unclear. A key hypothesis--the REBUS model--proposes that psychedelics relax high-level priors, allowing bottom-up sensory information to exert greater influence over perception and behavior. Here, we test this model in mice performing a free-response perceptual decision-making task that disambiguates prior-driven and sensory-driven decision strategies. Acute administration of psilocybin or ketamine significantly slowed decision times and improved accuracy. Behavioral modeling that combined drift diffusion and GLM-HMM frameworks revealed that these changes were mediated by increased decision thresholds and a marked shift into sensory-engaged cognitive states. Whole-brain c-Fos mapping identified a distributed decision-making network, with psychedelics selectively modulating cortical and subcortical nodes. Calcium imaging in the orbitofrontal cortex (OFC)--a key region for integrating priors and sensory inputs--revealed preserved decision-related selectivity under psychedelics, while exhibiting reduced neuronal correlations--population-level signatures of weakened top-down influence and relaxed priors. Together, these results provide circuit-level support for the REBUS model, showing that psychedelics reconfigure brain-wide and local dynamics to promote more deliberate, flexible, and sensory-driven decision policies.

neuroscience↗

bioRxiv2025

A Novel Sarocladium spinificis Strain Suppresses Coccidioides posadasii Growth: Morphological and Genetic Perspectives

Sarocladium is a diverse fungal genus with implications in both plant and human diseases, exhibiting roles in pathogenicity, endophytism, and biocontrol. This study characterizes two Sarocladium spinificis strains, CA16 (CBS 144516) and CA18 (CBS 144517), isolated from patients initially suspected of having coccidioidomycosis. Morphological, phylogenetic, and genomic analyses confirmed their classification within the Sarocladium genus, closely related to S. spinificis. Both strains exhibited growth at 24{degrees}C and 37{degrees}C, with distinct morphological features. Comparative genomic analysis identified unique orthologous clusters and functional gene families associated with adaptability and potential pathogenicity. Notably, these strains demonstrated enhanced production of secreted proteins, CAZymes, and peptidases, highlighting metabolic versatility. Co-cultivation experiments revealed that S. spinificis strains CA16 and CA18 inhibited the growth of Coccidioides posadasii, suggesting competitive interactions and potential antifungal properties. These findings underscore the ecological and clinical significance of S. spinificis and its impact on microbial communities, advancing our understanding of its diversity, pathogenic potential, and antifungal capabilities. ImportanceAccurate identification and characterization of emerging fungal pathogens are essential for improving diagnosis and treatment. Sarocladium spinificis, though not widely recognized as a human pathogen, exhibits traits suggesting a potential role in opportunistic infections. This study provides the first detailed morphological, phylogenetic, and genomic characterization of clinical S. spinificis isolates, highlighting its ability to survive at body temperature and its antifungal resistance. Additionally, we demonstrate that these strains inhibit Coccidioides posadasii, the agent of Valley fever, suggesting ecological competition or antifungal properties. These findings contribute to understanding fungal interactions in clinical and environmental settings, with implications for fungal pathogenesis and antifungal strategies. By uncovering new aspects of S. spinificis biology, this work expands knowledge of Sarocladium species in human health and lays the foundation for future research on its ecological role, pathogenic potential, and therapeutic applications.

microbiology↗

bioRxiv2024

Computational Models of Age-Associated Cognitive Slowing

BackgroundCognitive slowing accompanies normal aging, yet understanding of the mechanisms of slowing is limited at the network and neuronal level. Relating the pathophysiological factors responsible for cognitive slowing, and interpreting its relationship to working memory, requires multiscale computer modeling. ObjectiveThe aim of this research is to explore multiple mechanisms of cognitive slowing using computational modeling of the cortex to link neuronal activity with cognitive content. MethodWe developed multiscale computer models of a simple cognitive task - Condition 1 of the Stroop recognition task - using the Nengo system, a cognitive simulation environment with a semantic pointer architecture developed to model cognitive tasks using spiking neural networks. We explored how changes associated with aging such as increased input noise, axonal loss, neuronal loss, and feedback would affect the function of the models. ResultsAxonal loss and increased input noise produced profound slowing. High levels of neuronal loss severely impaired memory and paradoxically decreased slowing via the ability to respond more quickly by "releasing" a prior memory. Increased feedback improved memory at the cost of increased slowing. ConclusionOur simulations suggest that significant slowing could be caused by white matter loss (axonal loss) or input signal degradation (which could be caused by visual or other afferent system worsening). As neuronal loss markedly decreased the duration of working memory, we propose that physiological feedback is increased to preserve working memory at the cost of further cognitive slowing.

neuroscience↗

bioRxiv2024

Description of new micro-colonial fungi species Neophaeococcomyces mojavensis, Coniosporium tulheliwenetii, and Taxawa tesnikishii cultured from biological soil crusts

Black yeasts and relatives comprise Micro-Colonial Fungi (MCFs) which are slow-growing stress-tolerant micro-eukaryotes that specialize in extreme environments. MCFs are paraphyletic and found in the Orders Chaetothyriales (Eurotiomycetes) and Dothideales (Dothidiomycetes). We have isolated and described three new MCFs species from desert biological soil crusts (BSCs) collected from two arid land regions: Joshua Tree National Park (Mojave Desert) and UC Natural Reserve at Boyd Deep Canyon (confluence of Mojave and Sonoran Deserts). BSCs are composite assemblages of cyanobacteria, eukaryotic algae, fungi, lichens, and bryophytes embedded into the surface of desert soils, providing a protective buffer against the harsh desert environment. Our work focused on one type of desert BSC, the cyanolichen crust dominated by Collema sp. Using culture-dependent protocols, three MCFs were axenically isolated from their respective samples along with the extracted DNA. Their genomes were sequenced using Illumina and Nanopore, and finally assembled and annotated using hybrid assembly approaches and established bioinformatics pipelines to conduct final taxonomic phylogenetic analysis and placement. The three species described here are unique specimen from desert BSCs, here we introduce, Neophaeococcomyces mojavensis (Chaetothyriales), Cladosporium tulheliwenetii (Dothideales), and Taxawa tesnikishii (Dothideales).

microbiology↗

bioRxiv2024

The fine-tuning of synapse development by oxidative stress and autophagy requires presynaptic ATM kinase

Two processes held in delicate balance during the fine tuning of synapse development are oxidative stress and autophagy: each can promote synapse expansion yet in excess are toxic. How this balance is maintained is not fully understood. While ataxia-telangiectasia mutated (ATM) is recognized as a key regulator of the DNA damage response, there is increasing evidence of a neuronal-specific role for this ubiquitous kinase and deficiency causes early-onset neurodegeneration. We report a requirement for presynaptic Drosophila ATM (dATM) in neurodevelopment that is independent of its functions in the DNA damage response. Reduction of presynaptic dATM expression causes hypersensitivity to raised oxidative stress and a failure to induce autophagy which leaves mitochondria in excess in neurons. We demonstrate that presynaptic dATM coordinates autophagy through the conserved ATM-AMPK axis. Similarly to mammalian ATM, neuronal dATM is predominantly cytosolic and forms synaptic foci. dATM also colocalizes with autophagosomes. We propose a model wherein dATM responds to increased reactive oxygen species resulting from heightened neuronal activity by activating autophagy to induce synaptic growth, while protecting the neuron from excitotoxicity and oxidative stress.

developmental biology↗

bioRxiv2021

Antibiotic Susceptibility Profile of Campylobacter Spp from Poultry

Campylobacteriosis is found among the four important worldwide food borne pathogens. In intensive poultry rearing systems in Sudan the use of oral antibiotics is essential to preserve health. Accordingly, there is a high threat for the thermophilic Campylobacter spp inhabitant in the intestinal tract of food animals to develop resistance to commonly used antibiotics. Contamination of broiler meat with pathogenic strains of resistant Campylobacter could, therefore, result in a form of campylobacteriosis in humans that is difficult to treat. To the best of our knowledge, there are no data available relating antibiotic resistant against these bacteria in poultry in Sudan, hence the aim of this study was to determine the antimicrobial susceptibility profile of thermophilic Campylobacter spp. isolated from broiler in Khartoum by disk diffusion. Sensitivity of fourteen isolates against seven antibiotics namely Neomycin, Nitrofurantoin, Nalidixic acid, Gentamycin, Streptomycin, Tetracycline and Erythromycin were studied. The result showed that Nitrofurantoin was found as highly sensitive (64.3%). It was also observed that Erythromycin, Gentamycin, Streptomycin and Neomycin verified the following resistant against isolates recovered 92.9%, 71.4%, 71.4%, 64.3% respectively. Multidrug resistant against five, four, three and two antibiotics was also reported. It was concluded that poultry meat in Khartoum could complicate the antimicrobial therapy in human as multidrug resistant of campylobacter was detected.

microbiology↗

bioRxiv2021

Redox Nanomedicine Cures Chronic Kidney Disease (CKD) by Mitochondrial Reconditioning

Targeting reactive oxygen species (ROS) while maintaining cellular redox signaling is crucial in the development of redox medicine for the therapeutic benefit as the origin of several prevailing diseases including chronic kidney disease (CKD) is linked to ROS imbalance and associated mitochondrial dysfunction. Here, we have shown that an indigenously developed nanomedicine comprising of Mn3O4 nanoparticles duly functionalized by biocompatible ligand citrate (C-Mn3O4 NPs) can maintain cellular redox balance in an animal model. We developed a cisplatin-induced CKD model in C57BL/6j mice where severe mitochondrial dysfunction resulting in oxidative distress lead to the pathogenesis. Four weeks of treatment with C-Mn3O4 NPs restored renal function, preserved normal kidney architecture, ameliorated overexpression of pro-inflammatory cytokines, and arrested glomerulosclerosis and interstitial fibrosis in CKD mice. A detailed study involving human embryonic kidney (HEK 293) cells and isolated mitochondria from experimental animals revealed that the molecular mechanism behind the pharmacological action of the nanomedicine involves protection of structural and functional integrity of mitochondria from oxidative damage, the subsequent reduction in intracellular ROS, and maintenance of cellular redox homeostasis. To the best of our knowledge, such studies that efficiently treated a multifaceted disease like CKD using a biocompatible redox nanomedicine are sparse in the literature. Successful clinical translation of this nanomedicine may open a new avenue in redox-mediated therapeutics of several other diseases (e.g., diabetic nephropathy, neurodegeneration, and cardiovascular disease) where oxidative distress plays a central role in pathogenesis.

pharmacology and toxicology↗