Large-scale comparative genomics to refine the organization of the global population structure.

The White-Kauffmann-Le Minor (WKL) scheme is the most widely used typing scheme for reporting the disease prevalence of the enteric pathogen. With the advent of whole-genome sequencing (WGS), methods have increasingly replaced traditional serotyping due to reproducibility, speed and coverage. However, despite integrating genomic-based typing by serotyping tools such as SISTR, serotyping in certain contexts remains ambiguous and insufficiently informative.

Phylogenetic analysis of porcine circovirus 3 circulating in Canadian pigs.

Introduction: Porcine circovirus 3 (PCV3) has been detected in pigs worldwide and associated with several clinical signs.

Methods: To investigate the genetic diversity of PCV3 strains circulating in Canada, 44 PCV3 positive samples from Saskatchewan (2/44), Manitoba (2/44), Quebec (4/44), Alberta (11/44) and Ontario (25/44) submitted to diagnostic laboratories in Canada between 2019 and 2021 were sequenced and analyzed.

Results: Phylogenetic analysis of capsid genes showed that all of the 44 Canadian strains classified into PCV3a and segregated into seven lineages with common amino acid changes observed at A24V, R27K, N56D, T77S, Q98R, L150I (F) and R168K positions.

Experiment level curation of transcriptional regulatory interactions in neurodevelopment.

To facilitate the development of large-scale transcriptional regulatory networks (TRNs) that may enable in-silico analyses of disease mechanisms, a reliable catalogue of experimentally verified direct transcriptional regulatory interactions (DTRIs) is needed for training and validation. There has been a long history of using low-throughput experiments to validate single DTRIs. Therefore, we reason that a reliable set of DTRIs could be produced by curating the published literature for such evidence.

Systematic evaluation of isoform function in literature reports of alternative splicing.

Background: Although most genes in mammalian genomes have multiple isoforms, an ongoing debate is whether these isoforms are all functional as well as the extent to which they increase the functional repertoire of the genome. To ground this debate in data, it would be helpful to have a corpus of experimentally-verified cases of genes which have functionally distinct splice isoforms (FDSIs).

Results: We established a curation framework for evaluating experimental evidence of FDSIs, and analyzed over 700 human and mouse genes, strongly biased towards genes that are prominent in the alternative splicing literature.

PCR Amplification Strategies Towards Full-length HIV-1 Genome Sequencing.

The advent of next-generation sequencing has enabled greater resolution of viral diversity and improved feasibility of full viral genome sequencing allowing routine HIV-1 full genome sequencing in both research and diagnostic settings. Regardless of the sequencing platform selected, successful PCR amplification of the HIV-1 genome is essential for sequencing template preparation. As such, full HIV-1 genome amplification is a crucial step in dictating the successful and reliable sequencing downstream.

Expression of human leukocyte antigen G is associated with prognosis in nasopharyngeal carcinoma.

Human leukocyte antigen G (HLA-G) has multiple immune regulatory functions including the induction of immune tolerance in malignancies. The roles of HLA-G have not been investigated in nasopharyngeal carcinoma (NPC). This study is aimed to evaluate the role of HLA-G as prognostic factor for NPC patients as well as its role in the immune regulation.

Expression of heat shock protein 70 in nasopharyngeal carcinomas: different expression patterns correlate with distinct clinical prognosis.

Background: Heat shock protein 70, a stress protein, has been implicated in tumor progression. However, its role in nasopharyngeal carcinoma (NPC) progression has not yet been clearly investigated.

Methods: Immunohistochemistry (IHC) was employed to examine the expression patterns of Hsp70, human leukocyte antigen -A (HLA-A) in NPC tissue samples.

Face recognition using dual-tree complex wavelet features.

We propose a novel facial representation based on the dual-tree complex wavelet transform for face recognition. It is effective and efficient to represent the geometrical structures in facial image with low redundancy. Moreover, we experimentally verify that the proposed method is more powerful to extract facial features robust against the variations of shift and illumination than the discrete wavelet transform and Gabor wavelet transform.