Biology subjects

Eastman, G.

Publications and source records attributed to Eastman, G..

6 recordsLinked to original sources

bioRxiv2026

Exploring the potential role of the TETRATRICOPEPTIDE THIOREDOXIN-LIKE gene family in nitrogen-fixing and water-restricted soybean plants

The TETRATRICOPEPTIDE THIOREDOXIN-LIKE (TTL) proteins are a plant-specific family proposed to function as peripheral membrane proteins that contribute to abiotic stress tolerance in Arabidopsis, likely by maintaining cell wall integrity through brassinosteroid signaling. Previously, we identified a TTL gene that was differentially regulated at the translational level in nitrogen-fixing soybean plants under water deficit (WD) conditions. This finding prompted the characterization of the soybean TTL gene family. Using the Glycine max v4.0 proteome, we identified ten TTL homologs (GmTTL1-GmTTL10), which are unevenly distributed across five chromosomes. Phylogenetic and structural analyses grouped these genes into three clades and revealed a highly conserved exon-intron organization. Likewise, GmTTL proteins display a conserved number and arrangement of TPR and TRXL motifs. To gain insights into their potential biological functions, we integrated co-expression and differential expression analyses. This approach identified a co-expression module enriched for translationally downregulated genes related to the Gene Ontology terms "cellular anatomical entity", "membrane", "cell periphery", "cell wall modification", "nitrate assimilation", and "cell wall organization or biogenesis". Protein-protein interaction network analysis of this specific subset of genes uncovered a novel GmTTL connection with two nitrate reductase enzymes in nitrogen-fixing plants subjected to WD, potentially linking the TTL gene family to new functions or roles. This study provides a framework for future functional studies of GmTTL proteins and their contribution to abiotic stress adaptation in soybean. Key MessageThis work presents the first functional characterization of TTLs proteins in legume species and highlights key processes that may link the TTL gene family to new functions or roles.

Plant Biology↗

bioRxiv2025

The use of Benzonase to produce ribosome footprints simplifies translational levels quantification by Ribo-seq

Gene expression quantification through genomics methods is crucial for understanding diverse biological contexts. Among these methods, ribosome profiling (Ribo-seq) stands out as a valuable tool for uncovering post-transcriptional gene expression regulation by providing a comprehensive view of the translatome. While current protocols are time-intensive with limited variations, we introduced the use of the Benzonase enzyme to generate ribosome footprints from a polysome-enriched fraction that exhibit expected characteristics in size, transcriptome mapping, and periodicity. Comparing translatome from Benzonase- and RNAse I-derived footprints reveals minimal differences underscoring Benzonases potential to streamline the protocol, reducing time, cost and bias. We further demonstrate Ribo-seq application in primary neuronal cultures, using Benzonase to digest the post-mitochondrial supernatant, thereby bypassing the labor-intensive ribosome/polysome purification step. The introduction of such protocol variations for Ribo-seq, especially for challenging low-input samples, offers a significant advancement of this resource for the community. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/642103v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@b5e325org.highwire.dtl.DTLVardef@153ccf9org.highwire.dtl.DTLVardef@b5f123org.highwire.dtl.DTLVardef@ea6bab_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2024

Water deficit response in nodulated soybean roots: a comprehensive transcriptome and translatome network analysis

Soybean establishes a mutualistic interaction with nitrogen-fixing rhizobacteria, acquiring most of its nitrogen requirements through symbiotic nitrogen fixation. This crop is susceptible to water deficit; evidence suggests that its nodulation status--whether it is nodulated or not-- can influence how it responds to water deficit. The translational control step of gene expression has proven relevant in plants subjected to water deficit. Here, we analyzed soybean roots differential responses to water deficit at transcriptional, translational, and mixed (transcriptional + translational) levels. Thus, the transcriptome and translatome of four combined-treated soybean roots were analyzed. We found hormone metabolism-related genes among the differentially expressed genes (DEGs) at the translatome level in nodulated and water-restricted plants. Also, weighted gene co-expression network analysis followed by differential expression analysis identified gene modules associated with nodulation and water deficit conditions. Protein-protein interaction network analysis was performed for subsets of mixed DEGs of the modules associated with the plant responses to nodulation, water deficit, or their combination. Our research reveals that the stand-out processes and pathways in the before-mentioned plant responses partially differ; terms related to glutathione metabolism and hormone signal transduction (2C protein phosphatases) were associated with the response to water deficit, terms related to transmembrane transport, response to abscisic acid, pigment metabolic process were associated with the response to nodulation plus water deficit. Still, two processes were common: galactose metabolism and branched-chain amino acid catabolism. A comprehensive analysis of these processes could lead to identifying new sources of tolerance to drought in soybean.

plant biology↗

bioRxiv2023

Cannabidiol prevents the locomotor sensitization induced by cocaine and caffeine and upregulates genes of extracellular matrix and anti-inflammatory pathways in the nucleus accumbens: a transcriptome-wide analysis

Cannabidiol (CBD), a non-psychotomimetic phytocannabinoid found in the Cannabis plant, has emerged as a potential therapeutic agent for psychostimulant use disorders. In recent work, we demonstrated that CBD is able to attenuate the expression of locomotor sensitization and the enhanced metabolic activity in the nucleus accumbens (NAc) generated by the combination of cocaine and caffeine. CDB interacts directly or indirectly with several molecular targets, so the underlying mechanisms of its beneficial effects are hard to determine. Here we used high-throughput RNA-sequencing in mices NAc after a sensitization protocol with combined cocaine plus caffeine and a CBD pre-treatment, to identify the major pathways and genes involved in CBD attenuating behavioral effects. Results indicated that CBD pretreatment consistently reduced both the acquisition and expression of cocaine and caffeine locomotor sensitization. The transcriptome analysis revealed that CBD pre-treatment enriched genes and functional association between proteins mainly related to extracellular matrix (ECM) organization and cell interactions in the NAc. Moreover, the neuroinflammation and BDNF signaling pathways were also influenced by CBD. Some specially enriched genes such as Tnc were identified as interesting specific candidates for follow-up studies. These findings provide valuable and novel insights into molecular mechanisms of CBD putatively associated with a protective effect on psychostimulant actions. A better understanding of the therapeutic targets of CBD can open new avenues for psychostimulant use disorder treatment strategies.

neuroscience↗

bioRxiv2023

Structural and functional damage to neuronal nuclei caused by extracellular tau oligomers

INTRODUCTIONNeuronal nuclei are normally smoothly surfaced. In Alzheimers disease (AD) and other tauopathies, though, they often develop invaginations. We investigated mechanisms and functional consequences of neuronal nuclear invagination in tauopathies. METHODSNuclear invagination was assayed by immunofluorescence in brain, and in cultured neurons before and after extracellular tau oligomers (xcTauO) exposure. Nucleocytoplasmic transport was assayed in cultured neurons. Gene expression was investigated using nanoString nCounter technology and qRT-PCR. RESULTSInvaginated nuclei were twice as abundant in human AD as in cognitively normal adults, and were increased in mouse neurodegeneration models. In cultured neurons, nuclear invagination was induced by xcTauOs by an intracellular tau-dependent mechanism. xcTauOs impaired nucleocytoplasmic transport, increased histone H3 trimethylation at lysine 9 and altered gene expression, especially by increasing tau mRNA. DISCUSSIONxcTauOs may be a primary cause of nuclear invagination in vivo, and by extension, impair nucleocytoplasmic transport and induce pathogenic gene expression changes.

neuroscience↗

bioRxiv2021

Transcriptional and translational regulation of pathogenesis in Alzheimer's disease model mice

BackgroundDefining the cellular mechanisms that drive Alzheimers disease (AD) pathogenesis and progression will be aided by studies defining how gene expression patterns change during pre-symptomatic AD and the ensuing periods of steadily declining cognition. Previous studies have emphasized changes in transcriptional regulation, but not translational regulation, leaving the ultimate results of gene expression alterations relatively unexplored in the context of AD. ObjectiveTo identify genes whose expression might be regulated at the transcriptional, and especially at the translational levels in AD, we analyzed gene expression in cerebral cortex of two AD model mouse strains, CVN (APPSwDI;NOS2-/-) and Tg2576 (APPSw), and their companion wild type (WT) strains at 6 months of age by tandem RNA-Seq and Ribo-Seq (ribosome profiling). MethodsIdentical starting pools of bulk RNA were used for RNA-Seq and Ribo-Seq. Differential gene expression analysis was performed at the transcriptional and translational levels separately, and also at the translational efficiency level. Regulated genes were functionally evaluated by gene ontology tools. ResultsCompared to WT mice, AD model mice had similar levels of transcriptional regulation, but displayed differences in translational regulation. A specific microglial signature associated with early stages of A{beta} accumulation was up-regulated at both transcriptome and translatome levels in CVN mice. Although the two mice strains did not share many regulated genes, they showed common regulated pathways related to APP metabolism associated with neurotoxicity and neuroprotection. ConclusionThis work represents the first genome-wide study of brain translational regulation in animal models of AD, and provides evidence of a tight and early translational regulation of gene expression controlling the balance between neuroprotective and neurodegenerative processes in brain.

neuroscience↗