PseAAC2Vec protein encoding for TCR protein sequence classification.

The classification and prediction of T-cell receptors (TCRs) protein sequences are of significant interest in understanding the immune system and developing personalized immunotherapies. In this study, we propose a novel approach using Pseudo Amino Acid Composition (PseAAC) protein encoding for accurate TCR protein sequence classification. The PseAAC2Vec encoding method captures the physicochemical properties of amino acids and their local sequence information, enabling the representation of protein sequences as fixed-length feature vectors. By incorporating physicochemical properties such as hydrophobicity, polarity, charge, molecular weight, and solvent accessibility, PseAAC2Vec provides a comprehensive and informative characterization of TCR protein sequences. To evaluate the effectiveness of the proposed PseAAC2Vec encoding approach, we assembled a large dataset of TCR protein sequences with annotated classes. We applied the PseAAC2Vec encoding scheme to each sequence and generated feature vectors based on a specified window size. Subsequently, we employed state-of-the-art machine learning algorithms, such as support vector machines (SVM) and random forests (RF), to classify the TCR protein sequences. Experimental results on the benchmark dataset demonstrated the superior performance of the PseAAC2Vec-based approach compared to existing methods. The PseAAC2Vec encoding effectively captures the discriminative patterns in TCR protein sequences, leading to improved classification accuracy and robustness. Furthermore, the encoding scheme showed promising results across different window sizes, indicating its adaptability to varying sequence contexts.

Molecular identification and cross-immunogenic study on two field isolates of Mycoplasma synoviae isolated from broilers in five districts of Khyber Pakhtunkhwa.

Background: Mycoplasma synoviae (MS) is an important poultry pathogen causing heavy economic losses Worldwide. Subclinical persistence of this pathogen is the major issue to control its prevalence. Aim: This study aimed to determine the molecular and cross-immunogenicity of MS among broilers in five Districts of Khyber Pakhtunkhwa (KP). Methods: This study was conducted by collecting 434 specimen samples from 40 broiler farms and desi poultry in five districts of KP. Specimen samples from the broiler birds (n = 150), broiler farm environment (n = 264), and desi poultry birds (n = 20) were aseptically collected and serially passaged in Modified Frey's broth. The homologous and heterologous antibody reactions were studied in rabbits. Before inoculation into rabbits, the MS isolates were inactivated by formalin and adjuvanted with Montanide. Results: The overall turbidity prevalence in Frey's broth was observed as 109/434 (25.11%) samples, and these turbidity-positive samples were shifted on Frey's agar. After the appearance of classic fried egg colonies, the Biochemical confirmation was supported by the production of catalase and phosphatase, reduction of tetrazolium, film and spot assay, and fermentation of glucose for species differentiation in avian mycoplasma. The MS prevalence percentage was recorded as 2% (9/434) through biochemical tests. The PCR results showed 0.5% MS prevalence with two field isolates (named MS-1 and MS-2). Both MS-1 and MS-2 field isolates showed similar values (42.2) of homologous geometric mean titer (GMT). While the heterologous GMT for MS-1 serum against MS-2 isolate was lower (27.9) as compared to MS-2 serum against MS1 isolate (38.9). No titer was detected in the control group (Group-III). Conclusion: In conclusion, the results indicated the existence of MS in broiler birds and high homologous titers recorded between field isolates, which is a perpetual menace to poultry.