Biology subjects

Youssef, A.

Publications and source records attributed to Youssef, A..

3 recordsLinked to original sources

bioRxiv2022

Quantifying the Effect of an Acute Stressor in Laying Hens using Thermographic Imaging and Vocalizations

The laying hen sector has multiple issues concerning the animals welfare. One crucial factor negatively impacts chicken welfare is stress. The conventional way of measuring and assessing chicken stress is time-consuming and subjective to the assessor. On the other hand, sensing and sensor technologies can be used to obtain objective, continuous and non-invasive/contactless measures of animal behavioural and physiological welfare indicators. The present study aims to investigate the use of thermographic imaging and microphones (sound) in obtaining objective indicators for acute stress in laying hens. During this study, 40 laying hens were stressed by opening an umbrella as a stressor starting from one day age until nine-weeks old. The birds were stressed every other day. Another 12 birds were housed in another cage. These birds were not stressed and served as a control group. The surface temperatures of the birds comb and beak decreased (1{degrees}C and 2.5{degrees}C respectively) in response to the applied stressor. This effect was only seen in the treatment group and not in the control birds. The number of vocalisations the birds produced significantly decreased shortly after stress. The number of calls in the stressed group decreased from 39.5 to 12.1 calls/minute, where the control group decreased from 27.8 to 22.5 calls/minute. It was hypothesized that the number of vocalisations would increase after stress. This difference could be due to the daily behavioural rhythm performed by the birds. The birds might naturally produce more calls at certain hours of the day because of certain behaviours they perform. Three different neural network algorithms were employed to differentiate between the vocalisation of stressed and the control group. This was done by converting the audio files to images and feeding them to the pretrained convolutional neural networks (CNN). The Resnet CNN had the highest categorising accuracy with an overall accuracy of 86 percent. The changes in surface temperature of the beak, comb, eye, and head, as well as the results from the audio analysis could serve as potential indicator for acute stress in laying hens. Future research is warranted to validate the methodologies and findings under different environmental conditions and stressors.

bioengineering↗

bioRxiv2021

A multi-tiered map of EMT defines major transition points and identifies vulnerabilities

Epithelial to mesenchymal transition (EMT) is a complex cellular program proceeding through a hybrid E/M state linked to cancer-associated stemness, migration and chemoresistance. Deeper molecular understanding of this dynamic physiological landscape is needed to define events which regulate the transition and entry into and exit from the E/M state. Here, we quantified >60,000 molecules across ten time points and twelve omic layers in human mammary epithelial cells undergoing TGF{beta}-induced EMT. Deep proteomic profiles of whole cells, nuclei, extracellular vesicles, secretome, membrane and phosphoproteome defined state-specific signatures and major transition points. Parallel metabolomics showed metabolic reprogramming preceded changes in other layers, while single-cell RNA sequencing identified transcription factors controlling entry into E/M. Covariance analysis exposed unexpected discordance between the molecular layers. Integrative causal modeling revealed co-dependencies governing entry into E/M that were verified experimentally using combinatorial inhibition. Overall, this dataset provides an unprecedented resource on TGF{beta} signaling, EMT and cancer.

systems biology↗

bioRxiv2021

Comparative investigation of the Diabetic foot ulcer microbiome

BackgroundMany factors may affect wound healing in Diabetic foot ulcer, namely, microbial density, microorganisms, microbial synergy, the host immune response, and infected tissue quality. MethodologyThis study used a cross-sectional design. We assessed 38 Subjects with DFUs, 23 neuroischaimic, and 15 neuropathic, for microbiota colonizing the DFU utilizing traditional cultures and 16S gene sequencing methods. All the relevant clinical factors were collected. Wound swabs were collected for both traditional microbiological analysis, direct swab (DSM), and cultured (CM) microbiome analysis. DNA isolation, and 16SrRNA hypervariable regions were amplified. Bioinformatics analysis was performed using IonReporter Software, statistical analysis, and diversity indices were computed with vegan R-package. ResultsThe traditional microbiological method was able to detect a maximum of one or two pathogens, and, in some cases, no pathogen was detected. The total number of the observed species was 176. The number of identified species was higher in the cultured microbiome (155) than the direct swab microbiome (136). Diversity analysis indicated that biological diversity is higher in the cultured microbiome compared with the DSM. The Shannon H index was 2.75 for the cultured microbiome and 2.63 for DSM. We observed some differences in the major bacterial taxa amongst neuroischaimic and neuropathic DFU microbiomes. ConclusionsCultured microbiome is superior to both the traditional method and direct swab microbiome. The Neuroischaimic group showed higher values for the tested diversity indices than the Neuroischaimic group. Neither Cluster Analysis nor Principal Component Analysis showed apparent clustering amongst the two types of ulcers.

microbiology↗