Biodiversity Informatics
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Leucism in an East Asian Bullfrog (Hoplobatrachus chinensis) tadpole from Ba Den Mountain, Vietnam
Get PDFTwo new prey items for Baird\u27s Patch-nosed Snake (Salvadora bairdi Jan 1860), in west-central Puebla, Mexico.
Get PDFBeyond the ordinary: Thanatosis during shedding in Daboia russelii (Shaw and Nodder 1797) and a predator-prey interaction of Fowlea piscator (Schneider 1799), Hoplobatrachus tigerinus (Daudin 1803), and Lissemys punctata (Lacépède 1788) in Gandhinagar, Gujarat.
Get PDFVector meson production using the Balitsky-Kovchegov equation including the dipole orientation
Get PDFIn this proceedings a solution of the target-rapidity Balitsky-Kovchegov (BK) equation is presented considering the complete impact-parameter dependence, including the orientation of the dipole with respect to the impact-parameter vector. The target-rapidity formulation of the BK equation introduces non-locality in rapidity. Three different prescriptions are considered to take into account the rapidities preceding the initial condition. The solutions are used to compute the structure functions of the proton and the diffractive photo- and electro-production of off protons. The predictions agree well with HERA data, confirming that the target-rapidity Balitsky-Kovchegov equation with the full impact-parameter dependence is a viable tool to study the small Bjorken- limit of perturbative QCD at current facilities like RHIC and LHC as well as in future colliders like the EIC
Recent results on ultra-peripheral collisions with the ALICE experiment
Get PDFRecent measurements of J/ψ photoproduction based on data from ultra-peripheral Pb–Pb and p–Pb collisions recorded by the ALICE experiment during Run 2 of the LHC are presented. Photoproduction, as a photon-induced process, is sensitive to the structure of hadrons, and the results are of great importance for a better understanding of how gluon saturation and nuclear shadowing function in high-energy quantum chromodynamics. The energy evolution of coherent J/ψ photoproduction has been measured, indicating a strong suppression of nuclear gluon densities at high energies. The energy dependence has also been measured for exclusive and dissociative J/ψ production off the proton. The average distribution of nuclear gluon matter in the transverse plane, along with its fluctuations, has been studied for the first time using measurements of the dependence of coherent and incoherent J/ψ photoproduction on the transferred momentum t. Lastly, the data from coherent photoproduction of J/ψ in Pb–Pb ultra-peripheral collisions have been found to be compatible with a transverse polarization
Delineating the roles of HOXB13 X285K variant in prostate cancer
Get PDFHOXB13 X285K is a frameshift mutant due to the deletion of one nucleotide, c.853delT, within the HOXB13 stop codon, resulting in an extension of HOXB13 protein by 96 amino acids on the C terminus. It was found primarily in men of West African ancestry and associated with early-onset prostate cancer (PCa) and more advanced stage. Whether and how X285K contributes to PCa progression remains largely unknown. Here, we established isogenic 22Rv1 cell lines with heterozygous wildtype/X285K HOXB13, which recapitulates the genotypes of X285K in PCa patients. In addition, using the unique C-terminal region as an antigen, we developed an antibody that specifically recognizes the HOXB13 X285K protein. Lastly, we demonstrated that X285K retained the function of HOXB13 in suppressing target genes, such as FASN and PSA. In summary, our data suggest that the isogenic cell lines and the antibody generated in this study will be useful for a comprehensive investigation of X285K function in PCa
CRISPR-Cas12: A Versatile Tool for Genome Editing and Beyond
Get PDFCRISPR-Cas systems are emerging gene editing toolkits that have been used for the manipulation of DNA and RNA, among which CRISPR-Cas12 demonstrates superior properties in terms of target DNA engineering in vivo compared to CRISPR-Cas9 as well as nucleic acid detection compared to CRISPR-Cas13. A comprehensive understanding of the mechanisms and emerging applications of CRISPR-Cas12-based technologies is critical for maximizing their benefits across various fields, including basic science, medicine, and food safety. In this study, we review the molecular features of both natural and engineered CRISPR-Cas12 compared to CRISPR-Cas9 and CRISPR-Cas13, and we provide an overview of established CRISPR-Cas12-based genome editing and diagnostic platforms. Furthermore, we discuss the advantages, challenges, and prospects for future directions of CRISPR-Cas12 in gene editing and nucleic acid detection
Long-Read Sequencing Outperforms Short-Read Sequencing in Detecting Most Structural Variations
Get PDFStructural variations (SV) are common in the cancer genome and play critical roles in regulating tumorigenesis. In the past decades, many SVs have been detected through analyses of whole-genome sequencing (WGS) data generated mainly by Illumina paired-end short-read sequencing (SRS). Recent advances in long-read sequencing (LRS) techniques provide exciting opportunities for SV detection. However, a comprehensive analysis of the pros and cons of LRS and SRS in detecting SVs in a cancer genome is still lacking. Here, we performed WGS of the LNCaP prostate cancer cell line through LRS using the Oxford Nanopore Technology and called main SVs, which were compared to those derived from publicly available LNCaP SRS data. Strikingly, LRS is superior in detecting insertions of all sizes and deletions of <1000 bp long, whereas SRS is very useful in capturing long deletions, taking advantage of its paired-end reads. LRS identified more precise breakpoints of detected SVs. In addition, we found that SRS called many duplications and inversions, most of which were not confirmed by LRS, likely due to ambiguity in SRS read alignment to repetitive regions, leading to errors in SV calling. In conclusion, LRS outperformed SRS in detecting most SVs, except deletions longer than LRS read lengths. Our study highlights the advantages of LRS in resolving complex genomic rearrangements and underscores its potential for improving SV detection in cancer genomics