Biology subjects
Publications and source records attributed to Velasquez, C..
Withdrawal StatementThe authors have withdrawn this pre-print manuscript because of some inadvertent errors and inconclusive data discovered upon further review. Therefore, the authors do not wish this work to be cited as reference for research and review articles from other research groups. If you have any questions, please contact the corresponding author.
Due to technical and computational limitations, original attempts to compare humans to other non-human primates (NHP) were restricted to specific gene and protein comparisons. With the advances in supercomputing and whole genome sequencing technology, these studies can be revisited to explore entire genomes unbiasedly. A novel alignment-dependent homology algorithm that utilizes a linear search-based approach to find segments of homolog sequences based on a given length of word size, ranging from 32 bp to 1000 bp, was used to perform whole genome comparisons. These sequences were then compared over each chromosome of both the target and control species. Chromosome similarities between Pan paniscus and Homo sapiens varied greatly across various chromosomes. At 32-bp granularity, chromosome 3 showed the highest similarity (91.96%), while chromosome 5 showed the lowest similarity (59.66%). Overall, this indicates that while there are significant similarities in the anatomical structures, physiological structures, and protein similarities, there are significant differences in the genomic code between the two species. Additionally, not all sequences are conserved equally, underscoring the need to study the role that gene duplications, transpositions, and horizontal gene transfer may play in species divergence.
Alopecia areata is an autoimmune disorder affecting approximately 2% of the global population, characterized by immune-mediated disruption of hair follicle immune privilege and unpredictable hair loss. While CD4 and CD8 T cells are established drivers of pathogenesis, the roles of other immune cell populations remain incompletely defined. Here, we reaffirm the pathogenic role of CD8 T cells and identify a contribution of epidermal {gamma}{delta} T cells and macrophages to alopecia areata. Using publicly available single-cell RNA sequencing (scRNAseq) data from the skin of C3H/HeJ mice with alopecia areata, we demonstrate that epidermal {gamma}{delta} T cells upregulate genes associated with immune homeostasis, proliferation, and inflammation, including BST2, an interferon-stimulated antiviral protein. In vivo, epidermal {gamma}{delta} T cells and keratinocytes are increased in number, with BST2 expression enriched around hair follicles. BST2 is also expressed on CD8 T cells actively producing IFN-{gamma} and on CD11b+ macrophages with signatures of antiviral and complement system pathways. In human alopecia areata skin, BST2 expression is elevated in alopecia areata and downregulated following treatment with the JAK inhibitor tofacitinib. Together, these findings position BST2 as a marker of interferon-driven immune activation and highlight epidermal {gamma}{delta} T cells as a contributor to alopecia areata pathogenesis.
Here we describe the metagenome composition, community functional annotation, and diversity of prokaryotic microbial species derived from calcareous stromatolite formations discovered in the dry stream bed of the open-canopy, ephemeral San Felipe Creek in the Anza Borrego Desert. In this environment, resident microbes must be able to adapt to the harsh conditions of extreme heat, high UV light, desiccation and fluctuating solubilization/precipitation and hydration/evaporation. Metagenomic analysis revealed a community capable of carrying out complete nitrogen fixation and assimilatory nitrate reduction, forming biofilms and quorum sensing, and potentially forming thick-walled akinetes as desiccation-resistant stages. Nitrogen cycling is likely to play a fundamental role in mediating both the structure of the stromatolite microbial community and the mineral precipitation/dissolution. The viruses present in the stromatolites, particularly Nodularia and Mycobacterium phages are also likely to impact community population dynamics and activity. Stromatolite community members possess different morphological and physiological strategies to cope with desiccation stress. Metagenomic signatures were found for scytonemin, carotenoids, synthesis of potential microsporine-like amino acids; genes involved in microalgal desiccation tolerance, including those encoding aquaporins, chaperones, antioxidants; and enzymes responsible for the synthesis of trehalose, sucrose, and polyamines. The stromatolite ecosystem provides a diverse array of microniches where different functional guilds can develop complex metabolite exchange with the substrate supporting their life in extreme conditions. Metagenome analyses revealed several genes that might enable a specialized and unique group of endolithic cyanobacteria including Chroococcidiopsis, Hyella, Myxosarcina, and Pleurocapsa to derive metals and important nutrients from rocks, being potentially destructive for the calcareous formations. Our study revealed environmental adaptations of freshwater microbial communities in desert stream stromatolites which may provide valuable insights into Precambrian paleoenvironments, which are little known.