More Like this

1. Deviance as an historical artefact: a scoping review of psychological studies of body modification

   https://doi.org/10.1057/s41599-023-01511-6  

   Owens, Rebecca; Filoromo, Steven J.; Landgraf, Lauren A.; Lynn, Christopher D.; Smetana, Michael R. (December 2023, Humanities and Social Sciences Communications)

   Abstract Body modification is a blanket term for tattooing, piercing, scarring, cutting, and other forms of bodily alteration generally associated with fashion, identity, or cultural markings. Body modifications like tattooing and piercing have become so common in industrialised regions of the world that what were once viewed as marks of abnormality are now considered normal. However, the psychological motivations for body modification practices are still being investigated regarding deviance or risky behaviours, contributing to a sense in the academic literature that body modifications are both normal and deviant. We explored this inconsistency by conducting a scoping review of the psychological literature on body modifications under the assumption that the psychological and psychiatric disciplines set the standard for related research. We searched for articles in available online databases and retained those published in psychology journals or interdisciplinary journals where at least one author is affiliated with a Psychology or Psychiatry programme ( N  = 94). We coded and tabulated the articles thematically, identifying five categories and ten subcategories. The most common category frames body modifications in general terms of risk, but other categories include health, identity, credibility/employability, and fashion/attractiveness. Trends in psychology studies seem to follow the shifting emphasis in the discipline from a clinical orientation regarding normality and abnormality to more complex social psychological approaches. 

   more » « less
2. Protein-derived cofactors: chemical innovations expanding enzyme catalysis

   https://doi.org/10.1039/d4cs00981a  

   Graciano, Angelica; Liu, Aimin (March 2025, Chemical Society Reviews)

   Goss, Rebecca (Ed.)

   Protein-derived cofactors, formed through posttranslational modification of a single amino acid or covalent crosslinking of amino acid side chains, represent a rapidly expanding class of catalytic moieties that redefine enzyme functionality. Once considered rare, these cofactors are recognized across all domains of life, with their repertoire growing from 17 to 38 types in two decades in our survey. Their biosynthesis proceeds via diverse pathways, including oxidation, metal-assisted rearrangements, and enzymatic modifications, yielding intricate motifs that underpin distinctive catalytic strategies. These cofactors span paramagnetic and non-radical states, including both mono-radical and crosslinked radical forms, sometimes accompanied by additional modifications. While their discovery has accelerated, mechanistic understanding lags, as conventional mutagenesis disrupts cofactor assembly. Emerging approaches, such as site-specific incorporation of non-canonical amino acids, now enable precise interrogation of cofactor biogenesis and function, offering a viable and increasingly rigorous means to gain mechanistic insights. Beyond redox chemistry and electron transfer, these cofactors confer enzymes with expanded functionalities. Recent studies have unveiled new paradigms, such as long-range remote catalysis and redox-regulated crosslinks as molecular switches. Advances in structural biology, mass spectrometry, and biophysical spectroscopy continue to elucidate their mechanisms. Moreover, synthetic biology and biomimetic chemistry are increasingly leveraging these natural designs to engineer enzyme-inspired catalysts. This review integrates recent advances in cofactor biogenesis, reactivity, metabolic regulation, and synthetic applications, highlighting the expanding chemical landscape and growing diversity of protein-derived cofactors and their far-reaching implications for enzymology, biocatalysis, and biotechnology. 

   more » « less
3. Sulfur Modification in Natural RNA and Therapeutic Oligonucleotides

   https://doi.org/10.1039/D1CB00038A  

   Zheng, Ya Ying; Wu, Ying; Begley, Thomas; Sheng, Jia (January 2021, RSC Chemical Biology)

   null (Ed.)

   Sulfur modifications have been discovered on both DNA and RNA. Sulfur substitution of oxygen atoms at nucleobase or backbone locations in the nucleic acid framework led to a wide variety of sulfur-modified nucleosides and nucleotides. While the discovery, regulation and functions of DNA phosphorothioate (PS) modification, where one of the non-bridging oxygen atoms is replaced by sulfur on the DNA backbone, are important topics, this review focuses on the sulfur modification in natural cellular RNAs and therapeutic nucleic acids. The sulfur modifications on RNAs exhibit diversity in terms of modification locations and cellular functions, but the various sulfur modifications share common biosynthetic strategies across RNA species, cell types and all domains of life. The first section reviews the post-transcriptional sulfur modifications on nucleobase with emphasis on thiouridine on tRNA and phosphorothioate modification on RNA backbones, as well as the functions of the sulfur modifications on different species of cellular RNAs. The second section reviews the biosynthesis of different types of sulfur modifications and summarizes the general strategy for the biosynthesis of sulfur-containing RNA residues. One of the main goals of investigating the sulfur modifications is to enrich the genomic drug development pipeline and enhance our understandings of the rapidly growing nucleic acid-based gene therapy. The last section of the review focuses on the current drug development strategies employing sulfur substitution of oxygen atoms in therapeutic RNAs. 

   more » « less
4. Two-dimensional identification and localization of isomers in crystallin peptides using TWIM-MS

   https://doi.org/10.1039/D0AN01036G  

   Wu, Hoi-Ting; Julian, Ryan R. (January 2020, The Analyst)

   Recent studies have illuminated connections between spontaneous chemical reactions that cause isomerization at specific protein residues and various age-related diseases including cataracts and Alzheimer's. These discoveries provide impetus for better analytical methods to detect and characterize isomerization in proteins, which will enable a more complete understanding of the underlying relationship between these modifications and biology. Herein we employ a two-dimensional approach for identification of peptides isomers that also includes pinpointing of the modified residue. Collision-induced dissociation is used to fragment ions in the first dimension, followed by separation of the fragments with travelling-wave ion mobility. By comparing data obtained from both isomers, differences in either fragment-ion intensities or arrival-time distributions can be used to identify isomeric forms and the specific site of modification within the peptides. Synthetic peptide standards with sequences derived from long-lived proteins in the eye lens and isomerization at serine, aspartic acid, and glutamic acid were examined. Although both dimensions are capable of isomer identification, ion mobility is much better at determining the site of modification. In general, separation of isomeric forms by ion mobility is possible but does not follow predictable trends dictated by sequence or fragment-ion length. In most cases, however, the site of isomerization can be precisely determined. 

   more » « less
5. Combining Nanopore direct RNA sequencing with genetics and mass spectrometry for analysis of T-loop base modifications across 42 yeast tRNA isoacceptors

   https://doi.org/10.1093/nar/gkae796  

   Shaw, Ethan A.; Thomas, Niki K.; Jones, Joshua D.; Abu-Shumays, Robin L.; Vaaler, Abigail L.; Akeson, Mark; Koutmou, Kristin S.; Jain, Miten; Garcia, David M. (September 2024, Nucleic Acids Research)

   Abstract Transfer RNAs (tRNAs) contain dozens of chemical modifications. These modifications are critical for maintaining tRNA tertiary structure and optimizing protein synthesis. Here we advance the use of Nanopore direct RNA-sequencing (DRS) to investigate the synergy between modifications that are known to stabilize tRNA structure. We sequenced the 42 cytosolic tRNA isoacceptors from wild-type yeast and five tRNA-modifying enzyme knockout mutants. These data permitted comprehensive analysis of three neighboring and conserved modifications in T-loops: 5-methyluridine (m5U54), pseudouridine (Ψ55), and 1-methyladenosine (m1A58). Our results were validated using direct measurements of chemical modifications by mass spectrometry. We observed concerted T-loop modification circuits—the potent influence of Ψ55 for subsequent m1A58 modification on more tRNA isoacceptors than previously observed. Growing cells under nutrient depleted conditions also revealed a novel condition-specific increase in m1A58 modification on some tRNAs. A global and isoacceptor-specific classification strategy was developed to predict the status of T-loop modifications from a user-input tRNA DRS dataset, applicable to other conditions and tRNAs in other organisms. These advancements demonstrate how orthogonal technologies combined with genetics enable precise detection of modification landscapes of individual, full-length tRNAs, at transcriptome-scale. 

   more » « less