Biology subjects

Guzman, F.

Publications and source records attributed to Guzman, F..

3 recordsLinked to original sources

bioRxiv2026

A standard area diagram for potato common scab: comparable performance of image- and object-based validation

Potato common scab (Streptomyces sp.) is an economically important disease that reduces the quality and market value of tubers. A key aspect in developing management strategies involves accurately quantifying the disease. Due to the three-dimensional nature of the tuber and the heterogeneous distribution of lesions across its surface, visual estimates of severity can be challenging. Therefore, the objectives of this study were to develop and validate a standard area diagram (SAD) for estimating common scab severity on potato tubers and to compare validation outcomes obtained using real tubers and digital images. A SAD comprising six severity levels (from 1.3 to 66.8%) was developed based on image analysis of naturally infected tubers. Validation was conducted using two complementary approaches in which inexperienced raters evaluated either real potato tubers or digital images of the same tubers under unaided and aided conditions. Accuracy, bias components, and inter-rater reliability were quantified using absolute error metrics, Lins concordance correlation coefficient, intraclass correlation coefficients, and overall concordance correlation coefficients. Use of the SAD significantly improved accuracy, reduced systematic bias, and increased inter-rater reliability across both validation approaches. No significant differences were detected between assessments conducted on real tubers and images, although image-based evaluations showed a slight, non-significant tendency toward reduced scale and location bias under aided conditions. These results demonstrate that a dimension-aware SAD integrating information across the full tuber surface enhances the reliability and reproducibility of visual severity assessments and supports the use of image-based evaluations for training, large-scale surveys, and remote or collaborative applications involving three-dimensional plant organs.

plant biology↗

bioRxiv2023

Histone variant H2B.Z acetylation is necessary for maintenance of Toxoplasma gondii biological fitness

Through regulation of DNA packaging, histone proteins are fundamental to a wide array of biological processes. A variety of post-translational modifications (PTMs), including acetylation, constitute a proposed histone code that is interpreted by "reader" proteins to modulate chromatin structure. Canonical histones can be replaced with variant versions that add an additional layer of regulatory complexity. The protozoan parasite Toxoplasma gondii is unique among eukaryotes in possessing a novel variant of H2B designated H2B.Z. The combination of PTMs and the use of histone variants is important for gene regulation in T. gondii, offering new targets for drug development. In this work, T. gondii parasites were generated in which the 5 N-terminal acetylatable lysines in H2B.Z were mutated to either alanine (c-Myc-A) or arginine (c-Myc-R). c-Myc-A mutant only displayed a mild effect in its ability to kill mice. c-Myc-R mutant presented an impaired ability to grow and an increase in differentiation to latent bradyzoites. This mutant line was also more sensitive to DNA damage, displayed no virulence in mice, and provided protective immunity against future infection. While nucleosome composition was unaltered, key genes were abnormally expressed during in vitro bradyzoite differentiation. Our results show that the N-terminal positive charge patch of H2B.Z is important for these procceses. Pull down assays with acetylated N-terminal H2B.Z peptide and unacetylated one retrieved common and differential interactors. Acetylated peptide pulled down proteins associated with chromosome maintenance/segregation and cell cycle, opening the question of a possible link between H2B.Z acetylation status and mitosis.

cell biology↗

bioRxiv2021

Decentralizing cell-free RNA sensing with the use of low-cost cell extracts

Cell-free gene expression systems have emerged as a promising platform for field-deployed biosensing and diagnostics. When combined with programmable toehold switch-based RNA sensors, these systems can be used to detect arbitrary RNAs and freeze-dried for room temperature transport to the point-of-need. These sensors, however, have been implemented using reconstituted PURE cell-free protein expression systems that are difficult to source in the Global South due to their high commercial cost and cold-chain shipping requirements. Here, we describe the implementation of RNA toehold switch-based sensors using E. coli cell lysate-based cell-free protein expression systems, which can be produced locally and reduce the cost of sensors by two orders of magnitude. We then demonstrate that these in-house cell lysates provide sensor performance comparable to commercial PURE cell-free systems. We further optimize use of these lysates with a CRISPRi strategy to enhance the stability of linear DNAs, enabling the direct use of PCR products for fast screening of new designs. As a proof-of-concept, we develop novel toehold sensors for the plant pathogen Potato Virus Y (PVY), which dramatically reduces the yield of this important staple crop. The local implementation of low-cost cell-free toehold sensors could enable biosensing capacity at the regional level and lead to more decentralized models for global surveillance of infectious disease.

bioengineering↗