Biology subjects

Yen, J.

Publications and source records attributed to Yen, J..

5 recordsLinked to original sources

bioRxiv2024

The response of multi-disease and insect-resistant tomato lines to the accumulation of TYLCV, a whitefly-transmitted virus

Tomato (Solanum lycopersicum) is a major vegetable crop grown worldwide for its culinary versatility and nutritional richness. The whitefly-transmitted Tomato yellow leaf curl virus (TYLCV) poses a significant threat to its cultivation. The management strategies for this disease include controlling the virus and/or the vector. The multi-disease and insect-resistant lines developed by the World Vegetable Centre (WorldVeg) contain Ty-1/Ty-3 genes for virus resistance and WF2-10 and WF3-09 genes for whitefly resistance. This study evaluates the efficacy of suppressing virus accumulation in multi-disease and insect-resistant tomato lines compared to Ty-resistant or whitefly-resistant lines and a susceptible check. Preference bioassays, controlled inoculation with viruliferous whiteflies, and acylsugar quantification revealed that multi-disease and insect-resistant lines, developed at WorldVeg, had significantly higher acylsugar concentration and were less preferred by the whitefly adults for settling and whiteflies had high adult mortality. The multi-disease and insect-resistant lines also showed less severe disease symptoms and reduced virus accumulation over time when compared to Ty-resistant, whitefly-resistant, and susceptible check. The findings reveal that the multi-disease and insect-resistant lines are superior in mitigating the threat posed by TYLCV compared to TYLCV-resistant lines. These results underscore the potential of combined virus and vector resistance in tomatoes as a key element of Integrated Pest Management strategies against whitefly-transmitted TYLCV, offering a sustainable solution for safeguarding tomato production.

plant biology↗

bioRxiv2021

Introduction bias: Imbalance in species introductions may obscure the identification of traits associated with invasiveness

1The introduction stage is usually overlooked in trait-based studies of invasiveness, implicitly assuming that species introductions are random. However, human activities promote the movement of specific types of species. Thus, species deliberately introduced for distinct purposes (e.g. gardening, forestry) or as contaminants of human commodities (e.g. stowaway) will likely show particular traits. If species with certain traits have been preferentially introduced (i.e. introduction bias), some traits may have been mistakenly linked to species invasion abilities due to their influence on introduction probability. In this work, we propose a theoretical framework with different scenarios of introduction bias. The introduction scenarios are: (1) Random introduction, independent from traits; (2) Biologically biased introduction, following the worldwide distribution of the trait; and (3) Human biased introduction, following a theoretical introduction pathway that favours the introduction of species with high values of the trait. We evaluate how the introduced trait distributions in these scenarios may affect trait distributions in naturalized and invasive species pools under different hypothesized associations between traits and the probabilities of naturalization and invasion. The aim of this work is to identify situations where ignoring introduction bias may lead to spurious correlations being found between species traits and species ability to become naturalized or invasive. Our framework strongly points to the need to evaluate the traits of species that have become naturalized or invasive along with the traits of species that have failed to do so in order to unravel any existing introduction bias that may confound the correlation between species traits and invasion success. Overlooking a possible introduction bias may lead to the overestimation of the correlation between the trait and the species invasion ability, especially in cases when the pool of introduced species shows extreme values of the trait distribution (as compared to a random introduction). Trait-based studies that deserve special attention to avoid undesired effects of introduction bias on their findings are: those that investigate naturalization using only the pool of naturalized species, and those studies that examine invasiveness by comparing invasive species with native species.

ecology↗

bioRxiv2021

Robust RNA editing via recruitment of endogenous ADARs using circular guide RNAs

Akin to short-hairpin RNAs and antisense oligonucleotides which efficaciously recruit endogenous cellular machinery such as Argonaute and RNase H to enable targeted RNA knockdown, simple long antisense guide RNAs (1) can recruit endogenous adenosine deaminases acting on RNA (ADARs) to enable programmable A-to-I RNA editing, without requiring co-delivery of any exogenous proteins. This approach is highly specific, however the efficiency is typically lower than observed with enzyme overexpression. Conjecturing this was due in part to the short half-life and residence times of guide RNAs, here we engineer highly stable circular ADAR recruiting guide RNAs (cadRNAs), which can be delivered not only by genetically encoding on DNA vectors, but also via transfection of RNA molecules transcribed in vitro. Using these cadRNAs, we observed robust RNA editing across multiple sites and cell lines, in both untranslated and coding regions of RNAs, vastly improved efficiency and durability of RNA editing, and high transcriptome-wide specificity. High transcript-level specificity was achieved by further engineering to reduce bystander editing. Additionally, in vivo delivery of cadRNAs via adeno-associated viruses (AAVs) enabled robust 38% RNA editing of the mPCSK9 transcript in C57BL/6J mice livers, and 12% UAG-to-UGG RNA correction of the amber nonsense mutation in the IDUA-W392X mouse model of mucopolysaccharidosis type I-Hurler (MPS I-H) syndrome. Taken together, cadRNAs enable efficacious programmable RNA editing with application across diverse protein modulation and gene therapeutic settings.

bioengineering↗

bioRxiv2020

Directed Evolution of Adenine Base Editors with Increased Activity and Therapeutic Application

The foundational adenine base editors (e.g. ABE7.10) enable programmable C*G to T*A point mutations but editing efficiencies can be low at challenging loci in primary human cells. Here we further evolve ABE7.10 using a library of adenosine deaminase variants to create ABE8s. At NGG PAM sites, ABE8s result in [~]1.5x higher editing at protospacer positions A5-A7 and [~]3.2x higher editing at positions A3-A4 and A8-A10 compared with ABE7.10. Non-NGG PAM variants have a [~]4.2-fold overall higher on-target editing efficiency than ABE7.10. In human CD34+ cells, ABE8 can recreate a natural allele at the promoter of the {gamma}-globin genes HBG1 and HBG2, with up to 60% efficiency, causing persistence of fetal hemoglobin. In primary human T cells, ABE8s achieve 98-99% target modification which is maintained when multiplexed across three loci. Delivered as mRNA, ABE8s induce no significant levels of sgRNA-independent off-target adenine deamination in genomic DNA and very low levels of adenine deamination in cellular mRNA.

genomics↗

bioRxiv2019

Understanding patterns of abiotic and biotic stress resilience to unleash the potential of crop wild relatives for climate-smart legume breeding

Although new varieties are urgently needed for climate-smart legume production, legume breeding lags behind with cereals and underutilizes wild relatives. This paper provides insights in patterns of abiotic and biotic stress resilience of legume crops and wild relatives to enhance the use and conservation of these genetic resources for climate-smart legume breeding. We focus on Vigna, a pantropical genus with more than 88 taxa including important crops such as cowpea and mung bean. Sources of pest and disease resistance occur in more than 50 percent of the Vigna taxa, which were screened while sources of abiotic stress resilience occur in less than 20 percent of the taxa, which were screened. This difference suggests that Vigna taxa co-evolve with pests and diseases while taxa are more conservative to adapt to climatic changes and salinization. Twenty-two Vigna taxa are poorly conserved in genebanks or not at all. This germplasm is not available for legume breeding and requires urgent germplasm collecting before these taxa extirpate on farm and in the wild. Vigna taxa, which tolerate heat and drought stress are rare compared with taxa, which escape these stresses or tolerate salinity. These rare Vigna taxa should be prioritized for conservation and screening for multifunctional traits of combined abiotic and biotic stress resilience. The high presence of salinity tolerance compared with drought stress tolerance, suggests that Vigna taxa are good at developing salt-tolerant traits compared with drought-tolerant traits. Vigna taxa are therefore of high value for legume production in areas that suffer from salinization.

plant biology↗