Biology subjects

Mejia, L.

Publications and source records attributed to Mejia, L..

6 recordsLinked to original sources

bioRxiv2026

Preclinical validation of AAV9-TECPR2 gene therapy in a novel knock-in model of TECPR2-related disorder

TECPR2-related disorder is a rare, autosomal recessive neurodevelopmental and neurodegenerative disease characterized by early-onset motor dysfunction, sensory- and autonomic neuropathy, and progressive neurological decline with early mortality. Currently, there are no effective treatments for individuals affected by this debilitating condition. To advance our understanding of disease mechanisms and explore therapeutic strategies, we developed and then characterized a knock-in (KI) mouse model carrying the human TECPR2 c.1319delC frameshift mutation. TECPR2-KI mice exhibit a subset of disease-relevant phenotypes, most prominently abnormal gait, along with reduced body weight and altered tactile sensitivity. We additionally observe a reduction in acoustic startle responses, consistent with dysfunction of brainstem-associated sensorimotor pathways. Histopathological analyses reveal progressive accumulation of axonal spheroids in the dorsal column nuclei, together with abnormalities in autophagy-related markers, features previously reported in individuals with TECPR2-related disorder. To assess the therapeutic potential of gene replacement, we delivered TECPR2 via intracisternal infusion of AAV9/TECPR2 in neonatal KI mice. Gene therapy restored mechanosensory function, normalized gait and startle responses, maintain autophagic homeostasis, and partially reduced axonal pathology. These findings demonstrate that TECPR2-associated deficits are not only replicable in this new mouse model but are also amenable to postnatal intervention. Our study introduces a genetically accurate murine model of TECPR2 deficiency, identifies brainstem-associated phenotypes, and provides preliminary evidence supporting the feasibility of AAV9-mediated TECPR2 gene delivery, establishing a foundation for future translational research in a currently untreatable disease. One-Sentence Key MessageTECPR2 deficiency disrupts brainstem sensory-motor circuits, impairing autophagy and tactile, gait, and startle function and is prevented by neonatal AAV9.

neuroscience↗

bioRxiv2025

Exploring prophages in Salmonella enterica: an in-silico approach

Prophages play a crucial role in shaping host physiology, influencing traits such as virulence and antimicrobial resistance. In Salmonella enterica, prophages can constitute up to 30% of the accessory genome, contributing significantly to its genetic diversity and adaptability. In this study, we employed an in-silico approach to identify prophages within S. enterica genomes obtained poultry and clinical isolates. A total of 151 S. enterica sequences were assembled using SPAdes and subsequently quality-filtered with Abyss and BUSCO. Prophage sequences were detected using Phigaro and CheckV, followed by quality assessment with PHASTEST. The identification was performed using a custom database comprising 60 S. enterica prophages from previous studies. Comparative genomics, including gene annotation and recombination detection, were performed on representative prophages. Virulence genes were identified using VFDB and VirulenceFinder databases. Lastly, phylogenetic analysis of the prophages was carried out based on terminase and integrase sequences. We obtained 142 S. enterica genomes to analyze their prophage content. Peduovirus pro483 was highly prevalent among S. Infantis isolates and carried two cargo proteins: an Imma/Irre metalloendopeptidase and a fimbrial protein. In contrast, a related S. Enteritidis isolate also harboring Peduovirus pro483 carried a different set of cargo genes--HEPN-MAE-28990 and a cytosine-specific methyltransferase--suggesting horizontal transfer or a recent phage acquisition event. Enterobacteria phage ST104, found in S. Typhimurium, exhibited nearly complete identity to its reference and encoded superinfection exclusion proteins (SieA, SieB), enhancing phage resistance. Phylogenetic analyses supported their classification and revealed distinct evolutionary relationships tied to host serovar and environment. To our knowledge, this is the first study to describe prophage diversity in S. enterica strains isolated from Ecuadorian poultry farms, providing insights into their potential role in strain adaptation and public health relevance.

microbiology↗

bioRxiv2023

The Auxin Response Factor ARF27 is required for maize root morphogenesis

Crop root systems are central to nutrition acquisition and water usage. Root hairs and lateral roots contribute to fine-scale patterning of root systems and can offer many advantages for improving root function without drastically impacting overall system architecture. Key genetic regulators underpinning root hair morphogenesis have been well characterized in the model plant Arabidopsis but are less understood in maize. Here, we identify a novel determinant of root hair morphogenesis and auxin responses in maize, AUXIN RESPONSE FACTOR27 (ARF27), using both reverse and quantitative genetic approaches. ARF27 is enriched in maize primary root tissues at both the transcript and protein level. Loss of ARF27 leads to short primary roots and reduced root hair formation, while lateral root density is unaltered. In arf27 roots, auxin-responsive gene expression is dysregulated, which is consistent with the predicted function of this transcription factor. Moreover, a genome wide association study (GWAS) to uncover genetic determinants of auxin-dependent root traits identified ARF27 as a candidate gene. Furthermore, auxin hypersensitive maize genotypes exhibit altered crown root length and surface area in field-grown plants. A gene regulatory network (GRN) was reconstructed and an ARF27 subnetwork was integrated with DAP-seq and GWAS data to identify ARF27 target genes. The ARF27 GRN includes known maize root development genes, such as ROOTLESS CONCERNING CROWN ROOTS (RTCS), ROOTHAIRLESS 3 (RTH3) and RTH6. Altogether this work identifies a novel genetic driver of auxin-mediated root morphogenesis in maize that can inform agricultural strategies for improved crop performance.

plant biology↗

bioRxiv2023

GAUT10 is required for Arabidopsis root cell differentiation and elongation

O_LICell wall properties of the root apical meristem (RAM) are poorly understood compared to the elongation and maturation zones of the developing root. GAUT10 is a pectin biosynthesizing enzyme that is post-transcriptionally regulated by auxin that influences Arabidopsis RAM size in a sucrose-dependent manner. C_LIO_LIUsing live-cell microscopy, we have determined the short root phenotype of the gaut10 loss of function allele is due to a reduction in both RAM cell number and epidermal cell elongation. In addition, the absence of GAUT10 leads to a reduction in lateral root cap and epidermal cell marker line expression, indicating root cell differentiation defects in this mutant. C_LIO_LIGAUT10 is required for normal pectin and hemicellulose composition in primary Arabidopsis roots. Loss of GAUT10 leads to a reduction in galacturonic acid and xylose in primary cell walls and alters the presence of rhamnogalacturonan (RG) I and homogalacturonan (HG) polymers in the root. C_LIO_LIAuxin mediated gene expression and metabolism is altered in gaut10 roots, suggesting that cell wall composition may influence auxin pathways. C_LI

plant biology↗

bioRxiv2021

slim shady is a novel allele of PHYTOCHROMEB present in the T-DNA line SALK_015201

Auxin is a hormone that is required for hypocotyl elongation during seedling development. In response to auxin rapid changes in transcript and protein abundance occur in hypocotyls and some auxin responsive gene expression is linked to hypocotyl growth. To functionally validate proteomic studies, a reverse genetics screen was performed on mutants in auxin-regulated proteins to identify novel regulators of plant growth. This uncovered a long hypocotyl mutant, which we called slim shady, in an annotated insertion line in IMMUNOREGULATORY RNA-BINDING PROTEIN (IRR). Overexpression of the IRR gene failed to rescue the slim shady phenotype and characterization of a second T-DNA allele of IRR found that it had a wild-type hypocotyl length. The slim shady mutant has an elevated expression of numerous genes associated with the brassinosteroid-auxin-phytochrome (BAP) regulatory module compared to wild-type, including transcription factors that regulate brassinosteroid, auxin and phytochrome pathways. Additionally, slim shady seedlings fail to exhibit a strong transcriptional response to auxin. Using whole genome sequence and transcriptomics data for SALK_015201C we determined that a novel single nucleotide polymorphism in PHYTOCHROME B was responsible for the slim shady phenotype. This is predicted to convert induce a frameshift and premature stop codon at leucine 1125, within the histidine kinase-related domain of the carboxy terminus of PHYB, which is required for phytochrome signaling and function. Genetic complementation analyses with phyb-9 confirmed that slim shady is a mutant allele of PHYB. This study advances our understanding of the molecular mechanisms in seedling development, by furthering our understanding of how light signaling is linked to auxin dependent cell elongation. Furthermore, this study highlights the importance of confirming the genetic identity of research material before attributing phenotypes to known mutations sourced from T-DNA stocks.

plant biology↗

bioRxiv2020

One is not enough: on the effects of reference genome for the mapping and subsequent analyses of short-reads

Mapping of high-throughput sequencing (HTS) reads to a single arbitrary reference genome is a frequently used approach in microbial genomics. However, the choice of a reference may represent a source of errors that may affect subsequent analyses such as the detection of single nucleotide polymorphisms (SNPs) and phylogenetic inference. In this work, we evaluated the effect of reference choice on short-read sequence data from five clinically and epidemiologically relevant bacteria (Klebsiella pneumoniae, Legionella pneumophila, Neisseria gonorrhoeae, Pseudomonas aeruginosa and Serratia marcescens). Publicly available whole-genome assemblies encompassing the genomic diversity of these species were selected as reference sequences, and read alignment statistics, SNP calling, recombination rates, dN/dS ratios, and phylogenetic trees were evaluated depending on the mapping reference. The choice of different reference genomes proved to have an impact on almost all the parameters considered in the five species. In addition, these biases had potential epidemiological implications such as including/excluding isolates of particular clades and the estimation of genetic distances. These findings suggest that the single reference approach might introduce systematic errors during mapping that affect subsequent analyses, particularly for data sets with isolates from genetically diverse backgrounds. In any case, exploring the effects of different references on the final conclusions is highly recommended. Author summaryMapping consists in the alignment of reads (i.e., DNA fragments) obtained through high-throughput genome sequencing to a previously assembled reference sequence. It is a common practice in genomic studies to use a single reference for mapping, usually the reference genome of a species --a high-quality assembly. However, the selection of an optimal reference is hindered by intrinsic intra-species genetic variability, particularly in bacteria. Biases/errors due to reference choice for mapping in bacteria have been identified. These are mainly originated in alignment errors due to genetic differences between the reference genome and the read sequences. Eventually, they could lead to misidentification of variants and biased reconstruction of phylogenetic trees (which reflect ancestry between different bacterial lineages). However, a systematic work on the effects of reference choice in different bacterial species is still missing, particularly regarding its impact on phylogenies. This work intended to fill that gap. The impact of reference choice has proved to be pervasive in the five bacterial species that we have studied and, in some cases, alterations in phylogenetic trees could lead to incorrect epidemiological inferences. Hence, the use of different reference genomes may be prescriptive to assess the potential biases of mapping.

genomics↗