PLOS Biology: New Articles

1. Disruption of HaVipR1 confers Vip3Aa resistance in the moth crop pest <i>Helicoverpa armigera</i>

   by Andreas Bachler, Amanda Padovan, Craig J. Anderson, Yiyun Wei, Yidong Wu, Stephen Pearce, Sharon Downes, Bill James, Ashley E. Tessnow, Gregory A. Sword, Michelle Williams, Wee Tek Tay, Karl H. J. Gordon, Tom K. Walsh

   The global reliance on Bacillus thuringiensis (Bt) proteins for controlling lepidopteran pests in cotton, corn, and soybean crops underscores the critical need to understand resistance mechanisms. Vip3Aa, one of the most widely deployed and currently effective Bt proteins in genetically modified crops, plays a pivotal role in pest management. This study investigates the molecular basis of Vip3Aa resistance in Australian Helicoverpa armigera through genetic crosses, and integrated genomic and transcriptomic analyses. We identified a previously uncharacterized gene, LOC110373801 (designated HaVipR1), as potentially important in Vip3Aa resistance in two field-derived resistant lines. Functional validation using CRISPR/Cas9 knockout in susceptible lines confirmed the gene’s role in conferring high-level resistance to Vip3Aa. Despite extensive laboratory selection of Vip3Aa-resistant colonies in Lepidoptera, the biochemical mechanisms underlying resistance have remained elusive. Our research identifies HaVipR1 as a potential contributor to resistance, adding to our understanding of how insects may develop resistance to this important Bt protein. The identification of HaVipR1 contributes to our understanding of potential resistance mechanisms and may inform future resistance management strategies. Future work should explore the biochemical pathways influenced by HaVipR1 and assess its interactions with other resistance mechanisms. The approach utilized here underscores the value of field-derived resistant lines for understanding resistance in agricultural pests and highlights the need for targeted approaches to manage resistance sustainably.
2. qByte: An open-source isothermal fluorimeter for democratizing analysis of nucleic acids, proteins and cells

   by Francisco J. Quero, Guy Aidelberg, Hortense Vielfaure, Yann Huon de Kermadec, Severine Cazaux, Amir Pandi, Ana Pascual-Garrigos, Anibal Arce, Samuel Sakyi, Urs Gaudenz, Fernan Federici, Jennifer C. Molloy, Ariel B. Lindner

   Access to affordable and reliable scientific instrumentation remains a significant barrier to the democratization of healthcare and scientific research. In the field of biotechnology, in particular, the complexity, cost, and infrastructure requirements of many instruments continue to limit their accessibility, especially in resource-limited environments. Despite the recent increase in the development of open-source tools, driven by advances in digital fabrication and electronic prototyping, few of these projects have reached large-scale implementation or validation in real-world settings. Here, we present qByte, an open-source, 8-tube isothermal fluorimeter designed to overcome these barriers by offering a cost-effective ($60) yet production-ready solution. qByte leverages standard digital manufacturing and Printed Circuit Board (PCB) assembly techniques and is designed to be portable, making it ideal for both laboratory and field use. The device has been benchmarked against commercial real-time thermocyclers and spectrophotometers, showing comparable results across four key applications: nucleic acid amplification and detection, including the on-site diagnosis of human parasites in Ghana, analysis of protein activity and stability, genetic construct characterization, and bacterial viability tests. Taken together, our results proved qByte as flexible and reliable equipment for a variety of biological tests and applications, while its affordability and open-source design simplify further development and allow adaptation to the needs of future users.
3. The m⁵C reader Ybx1 regulates embryonic cortical neurogenesis by promoting progenitor cell cycle progression

   by Jian Zhang, Pengfei Che, Zhuoxuan Yang, Pingrui Zhang, Yuxuan Shui, Xibin Lu, Jiuzhou Xu, Yuanchu She, Yanbo Zhang, Jun Yu, Sheng-Jian Ji

   The reversible epitranscriptomic mark, 5-methylcytosine (m⁵C) modification, is implicated in numerous cellular processes, but its role in neural development remains largely unexplored. In this study, we discovered high expression of the m⁵C reader Ybx1 in the developing mouse cortex. To elucidate its role in cortical development, Ybx1 was ablated in embryonic cortical neural stem cells (NSCs). Interestingly, conditional knockout (cKO) of Ybx1 led to perinatal mortality in mice, along with abnormal cortical development. Cortical progenitor cells lacking Ybx1 exhibited impaired proliferation and differentiation. Multi-omics analysis identified the target mRNAs of Ybx1, which encode the key cell cycle regulatory proteins converging on cyclin D2 (Ccnd2). Ybx1 was found to regulate the stability of its target transcripts. Both knockdown and overexpression of Ybx1 targets via in utero electroporation confirmed that they mediated Ybx1 regulation of proliferation and differentiation of neural precursor cells. Further analysis showed that the G1 to S phase transition in cortical progenitor cells is delayed in the Ybx1 cKO. This study highlights the crucial function of the m⁵C reader protein Ybx1 in promoting cell cycle progression of the embryonic cortical progenitors, essential for proper cortical development.
4. An animal toxin-antidote system kills cells by creating a novel cation channel

   by Lews Caro, Aguan D. Wei, Christopher A. Thomas, Galen Posch, Ahmet Uremis, Michaela C. Franzi, Sarah J. Abell, Andrew H. Laszlo, Jens H. Gundlach, Jan-Marino Ramirez, Michael Ailion

   Toxin-antidote systems are selfish genetic elements composed of a linked toxin and antidote. The peel-1 zeel-1 toxin-antidote system in C. elegans consists of a transmembrane toxin protein PEEL-1 which acts cell autonomously to kill cells. Here we investigate the molecular mechanism of PEEL-1 toxicity. We find that PEEL-1 requires a small membrane protein, PMPL-1, for toxicity. Together, PEEL-1 and PMPL-1 are sufficient for toxicity in a heterologous system, HEK293T cells, and cause cell swelling and increased cell permeability to monovalent cations. Using purified proteins, we show that PEEL-1 and PMPL-1 allow ion flux through lipid bilayers and generate currents which resemble ion channel gating. Our work suggests that PEEL-1 kills cells by co-opting PMPL-1 and creating a cation channel.
5. Rhythm profiling using COFE reveals multi-omic circadian rhythms in human cancers in vivo

   by Bharath Ananthasubramaniam, Ramji Venkataramanan

   The study of ubiquitous circadian rhythms in human physiology requires regular measurements across time. Repeated sampling of the different internal tissues that house circadian clocks is both practically and ethically infeasible. Here, we present a novel unsupervised machine learning approach (COFE) that can use single high-throughput omics samples (without time labels) from individuals to reconstruct circadian rhythms across cohorts. COFE can simultaneously assign time labels to samples and identify rhythmic data features used for temporal reconstruction, while also detecting invalid orderings. With COFE, we discovered widespread de novo circadian gene expression rhythms in 11 different human adenocarcinomas using data from The Cancer Genome Atlas (TCGA) database. The arrangement of peak times of core clock gene expression was conserved across cancers and resembled a healthy functional clock except for the mistiming of a few key genes. Moreover, rhythms in the transcriptome were strongly associated with the cancer-relevant proteome. The rhythmic genes and proteins common to all cancers were involved in metabolism and the cell cycle. Although these rhythms were synchronized with the cell cycle in many cancers, they were uncoupled with clocks in healthy matched tissue. The targets of most of FDA-approved and potential anti-cancer drugs were rhythmic in tumor tissue with different amplitudes and peak times. These findings emphasize the utility of considering “time" in cancer therapy, and suggest a focus on clocks in healthy tissue rather than free-running clocks in cancer tissue. Our approach thus creates new opportunities to repurpose data without time labels to study circadian rhythms.