Tham, C. | Search bioRxiv

bioRxiv2024

Activation mapping in multi-center rat sensory-evoked functional MRI datasets using a unified pipeline.

Functional Magnetic Resonance Imaging (fMRI) in rodents is pivotal for understanding the mechanisms underlying Blood Oxygen Level-Dependent (BOLD) signals and phenotyping animal models of disorders, amongst other applications. Despite its growing use, comparing rodent fMRI results across different research sites remains challenging due to variations in experimental protocols. Here, we aggregated and analyzed 22 sensory-evoked rat fMRI datasets from 12 imaging centers, totaling scans from 220 rats, to assess the consistency of results across diverse protocols. We applied a standardized preprocessing pipeline and evaluated the impact of different hemodynamic response function models on group and individual level activity patterns. Our analysis revealed inter-dataset variability attributed to differences in experimental design, anesthesia protocols, and imaging parameters. We identified robust activation clusters in all (22/22) datasets. The comparison between stock human models implemented in software and rat-specific models showed significant variations in the resulting statistical maps. Our findings emphasize the necessity for standardized protocols and collaborative efforts to improve the reproducibility and reliability of rodent fMRI studies. We provide open access to all datasets and analysis code to foster transparency and further research in the field.

neuroscience↗

bioRxiv2024

Microbial Analysis and Sanitization of Hydroponic Farming Facilities in Singapore

This study performed microbial analysis of nutrient film technique (NFT) hydroponic systems at three indoor farms in Singapore. To justify the necessity to sanitize the hydroponic systems, strong biofilm-forming bacteria were isolated from the facility and investigated with their influence on Salmonella colonizing on polyvinyl chloride (PVC) coupons in hydroponic nutrient solutions. Last, sanitization solutions were evaluated with both laboratory-scale and field-scale tests. As a result, the microbiome composition in NFT systems was found to be highly farm-specific. Strong biofilm formers Corynebacterium tuberculostearicum C2 and Pseudoxanthomonas mexicana C3 were found to facilitate the attachment and colonization of Salmonella on PVC coupons. When forming dual-species biofilms, the presence of C2 and C3 also significantly promoted the growth of Salmonella (P < 0.05). Sodium hypochlorite (NaOCl) exhibited superior efficacy in biofilm removal compared to hydrogen peroxide (H2O2) and sodium percarbonate (SPC). NaOCl at 50 ppm reduced C2 and C3 counts to < 1 log CFU/cm2 within 12 h, whereas neither 3% H2O2 nor 1% SPC achieved such an effect. In operational hydroponic systems, the concentration of NaOCl needed to achieve biofilm elimination increased to 500 ppm, likely due to the presence of organic matter accumulated during the crop cultivation and the higher persistence of the naturally formed multispecies biofilms. The sanitization (500 ppm NaOCl for 12 h) did not impede subsequent plant growth but chlorination by-product chlorate was detected with high levels from the hydroponic solution and plants in the sanitized systems without rinsing. IMPORTANCEThis studys significance lies first in its elucidation of the necessity to sanitize the hydroponic farming systems. The microbiome in hydroponic systems, although most of the times non-pathogenic, might serve as a hotbed for pathogens colonization and thus pose a higher risk for food safety. We thus explored sanitization solutions with both laboratory-scale and field-scale tests. Of the three tested sanitizers, NaOCl was the most effective and economical option, whereas one must note the vital importance of rinsing the hydroponic systems after sanitization with NaOCl.

microbiology↗