Leaf bleaching is associated with extensive transcriptional reprogramming in avocado trees with sunblotch disease.

The acclimating mechanisms of Nannochloropsis sp. In response to long-term high CO2 stress-the important role of active cytoplasmic pH regulation.

Camellia sinensis (L.) O. Kuntze exhibits severely restricted growth at low temperatures, resulting in reduced tea leaf yield and quality. BRI1-EMS-suppressor (BES) transcription factors, as key components of the brassinosteroids (BR) signaling pathway, are highly homologous to BZR and jointly regulate plants' adaptation to environmental stress. In this study, the CsBES1-14 gene was successfully cloned and identified from the transcriptome database of tea plant. Biochemical analyses identified CsBES1-14 as a nuclear localized transcriptional activator, and BR and low temperature induced its expression. Arabidopsis thaliana plants overexpressing CsBES1-14 exhibited increased chilling tolerance by promoting root growth and increasing the expression of cold responsive genes. Conversely, the suppression of CsBES1-14 through virus-induced gene silencing (VIGS) in tea plant notably impaired cold tolerance. Transcription Factor-centered Yeast One-Hybrid screening identified CsCOR413 as a downstream target, and electrophoretic mobility shift assays confirmed the direct binding of CsBES1-14 to specific cis-elements in the CsCOR413 promoter. Exogenous application of brassinazole (BRZ) and VIGS silencing experiments verified that the ICE-CBF cold response pathway could regulate the low-temperature-regulated protein CsCOR413. In summary, these findings elucidate that CsCOR413 expression is modulated not only by the classic ICE-CBF signaling pathway but also directly regulated by CsBES1-14. These findings outline the key components of the cold resistance network in tea plant and provide novel molecular targets for genetic improvement strategies in perennial crops.

Histone acetyltransferases and N-terminal acetyltransferases orchestrate development and metamorphosis in the yellow fever mosquito, Aedes aegypti.

Root nodules host nitrogen-fixing bacteria and likely evolved through modifications of the lateral root program. Members of the NOOT-BOP-COCH-LIKE transcriptional coregulator family suppress root identity in nodules and plant hormones play key roles in nodule organogenesis, but the interaction between these pathways is unclear. In this study, we investigate how COCH regulates nodule identity through crosstalk with plant hormones, using the Pisum sativum cochleata (Pscoch) mutant - which forms root-nodule hybrids - in combination with hormone biosensors, double mutants, hormone quantification, and RNA-seq analysis. We found that COCH suppresses cytokinin levels and response during nodule formation. By contrast, PsCOCH promotes auxin accumulation and precise auxin response patterning in nodules. Mutant coch developing nodules have gene expression profiles more similar to that of root primordia, with increased expression of defence and auxin response genes and reduced expression of cytokinin biosynthesis genes compared to wild-type. We found gibberellin is unlikely to act downstream of PsCOCH. Constitutive expression of PsCOCH also produces root-nodule hybrids and we found intriguing links between the autoregulation of nodulation pathway and PsCOCH. We show that PsCOCH is required for spatial tight regulation of auxin and cytokinin during nodule organogenesis and identify key hormone and signalling genes that act downstream of COCH.

Metatranscriptomic analysis of lanthanum driven multi-element metabolic regulation in a rare earth tolerant microbial consortium.

In silico prediction of gallic acid binding to Zika virus NS3/RdRp proteins and in vitro confirmation of its antiviral activity.

Tissue engineering can be accomplished in a plethora of ways, ranging from direct deposition of cells onto scaffolds and chips to contactless volumetric printing of 3D structures. Recent studies have examined the feasibility of using acoustic manipulation of cells in vitro and in situ, although these studies have not yet identified the critical quality requirements to create complex tissues. To this end, we present a methodology for generating and evaluating acoustically patterned 3D vascular tissue for biomedical studies. Over a period of 7 days, tissues were able to generate self-assembling vasculature, deposit a self-secreted extracellular matrix network, and demonstrate changes in angiogenic gene expression in response to acoustic patterning. These behaviors demonstrated a positive correlation between the quality of alignment and associated vascular structure following acoustic manipulation, suggesting a relationship between patterning and tissue development. These findings identify necessary requirements for creating self-assembling vasculature in vitro, accounting for biological and physical parameters.

DNA-binding transcriptional regulators control gene expression in response to environmental cues. A subset of these proteins, called transmembrane transcriptional regulators (TTRs), directly bind DNA to regulate transcription while remaining anchored in the cytoplasmic membrane. Prior work has shown that in the presence of the polysaccharide chitin, two TTRs, TfoS and ChiS, coordinate to induce the expression of TfoR, a small RNA that is critical for natural transformation in Vibrio cholerae. Specifically, it was shown that ChiS recruits the PtfoR locus to the membrane, thereby allowing subsequent activation of this promoter by TfoS. However, it was also shown that increasing TfoS protein levels bypasses this coordination, allowing TfoS to activate the promoter independently. It therefore remains unclear which molecular mechanisms drive the requirement for ChiS under native conditions. Here, we show that ChiS binds PtfoR with a higher affinity than TfoS. We hypothesized that the low affinity of TfoS for PtfoR helps reinforce its dependence on ChiS for activation. To test this, we isolated a mutant allele of the TfoS DNA-binding domain with higher affinity for PtfoR. We show that this high-affinity TfoS allele promotes ChiS-independent activation of PtfoR and dysregulates chitin-dependent phenotypes in V. cholerae. These results demonstrate that the relative DNA-binding affinity of these TTRs facilitates their coordination, which is necessary for optimal V. cholerae fitness on chitin.IMPORTANCEDNA-binding transmembrane transcriptional regulators (TTRs) are critical for some bacterial species to properly sense and respond to their environments. Recent work highlights that pairs of TTRs can coordinate their activities to regulate gene expression, allowing them to sensitively control behaviors like virulence and horizontal gene transfer. However, the mechanisms that enable this coordination remain poorly understood. Here, we show that the relative DNA-binding affinity of paired TTRs is a critical feature that can drive their coordination.

Doxorubicin (DOX) is an effective anticancer drug; however, it can cause cardiotoxicity by inducing DNA double-strand breaks in cardiomyocytes. Cardiotoxicity can manifest immediately or years following treatment. Most human in vitro models of DOX-induced cardiotoxicity (DIC) focus on the acute effects of DOX treatment. To understand the long-term effects, we profiled the global gene expression response to DOX exposure over time. We treated iPSC-derived cardiomyocytes from six individuals with DOX for 24 h and assayed responses after 0, 24, and 144 h of recovery. DNA damage, determined by γH2AX expression, is induced following DOX treatment and is resolved by the final recovery timepoint. We identified both acute and chronic gene expression response signatures. The chronic signature, representing 501 genes, is enriched for p53 target genes, DNA damage response (DDR) genes, and senescence-associated genes compared to acute response genes. p53 target genes are persistently activated, and DDR genes are progressively downregulated over time. Our results suggest an altered cell state following repair of double-strand breaks that is distinct from preexposed cells. Doxorubicin response genes with persistent changes in expression can be applied to the design of toxicity biomarkers or therapeutic targets.

Microbial small RNAs (sRNAs) can regulate human genes. Higher plasma concentrations of microbial tRNA-derived RNA-1 (tDR-1) were previously associated with lower rheumatoid arthritis (RA) disease activity. This study examined whether tDR-1 concentrations differ in anti-cyclic citrullinated peptide-3 positive (CCP3+) at-risk individuals (ARI) based on who later develops clinical RA and discriminate later conversion status beyond established risk factors, and whether tDR-1 has in vitro effects. Plasma tDR-1 concentrations were measured in CCP3+ ARI. Group differences in log-transformed tDR-1 were assessed by lognormal Welch's t-test and logistic regression. Area under the receiver operating characteristic curve (AUROC) was used to evaluate discriminatory ability. Human THP-1 monocyte-derived macrophages were treated with tDR-1 versus scramble control and gene expression was assessed by NanoString Immunology panel. Among 60 CCP3+ ARI, 25 later developed clinical RA ("converters") over a mean of 2.2 years, while 35 did not ("non-converters") over a mean of 5.3 years. Baseline plasma tDR-1 concentrations were significantly higher (5.4-fold) in non-converters versus converters, even after adjustment for additional RA risk factors (shared epitope, smoking, rheumatoid factor) (P=5.1x10-4). The AUROC improved from 0.722 for these risk factors alone to 0.902 with the addition of tDR-1 (P=0.003). In vitro, tDR-1 significantly downregulated many type 1 interferon response genes in THP-1 cells. Higher plasma tDR-1 concentrations were associated with non-conversion to clinical RA in CCP3+ ARI. tDR-1's reducing type 1 interferon response gene expression suggests a potential mechanism by which microbes, and tDR-1, could affect RA development.

Land plants demonstrate high tolerance to acute ionizing radiation compared to other metazoans. However, few studies have analyzed plant gene expression in response to low-dose ionizing radiation. The present study performed two different sets of transcriptomic analysis of acutely exposed potato plants to 0.5-5Gy of gamma radiation. In the first experiment, a total of 4,955 genes were differentially expressed in treated versus control plants. Among them, the gene expression of thirty-five genes were proportionally increased in a dose dependent manner. GO terms of these genes was enriched in DNA repair and metabolism related gene categories. Treatments caused no observable phenotypic effect until six weeks post-treatment, when apical growth aberrations led to an increase in lateral branching that corresponded with the total dose of gamma radiation. A second experiment analyzed the effect of shorter-duration exposures over the same dose range. While the shorter-duration exposures led to increased differentially expressed genes, thirty-one out of thirty-five genes identified in the first analysis were consistently expressed in this experiment. Also, the gene expression of these gene groups was reduced to baseline levels after recovery, indicating these genes are specific responsive genes against IR stress. Taken together, we identified DNA repair and metabolism related genes that were expressed at ~ 1Gy of gamma radiation. These findings are important for future biotechnological studies to improve stress tolerance in plants, as well as, in the design of advanced potato phytosensors to report gamma radiation injuries.

Understanding what shapes variation in organisms' capacity to utilize novel resources is essential to predicting how species will respond to environmental change. For herbivores, exposure to toxic phytochemicals in novel plants may limit persistence in new habitats. We investigated the behavioral, physiological, genetic, and microbial consequences of diet switching in two closely related species of rodent herbivores that each consume differentially toxic plants in their native habitat, and that maintain different dietary strategies (i.e., relative dietary specialist versus relative generalist). In reciprocal laboratory feeding trials, we exposed wild-caught woodrats (genus Neotoma) to toxins characteristic of either familiar or novel plant secondary compounds. We measured changes in food and water intake, locomotor activity, gut microbial composition, and gene expression across the digestive tract following feeding trials. The dietary generalist responded minimally, but the specialist responded strongly when exposed to the novel diet. This response included behavioral and genetic components including increased water intake, reduction in locomotor activity, increased differential expression of detoxification genes, and a greater shift in gut microbial composition. The dietary specialist exhibited a strong response to diet switching that corresponded with ecologically relevant shifts in behavior and physiology that would have negative fitness consequences. Although the dietary specialist had a strong genetic and microbial response to novel plant secondary compounds, this response would likely be insufficient to overcome the immediate challenge of exposure to novel dietary toxins in the wild. Our results underscore the link between feeding strategy and the capacity to shift to novel dietary resources in response to environmental change.

Group A Streptococcus (GAS) causes millions of infections annually, including a recent global surge in invasive disease. To survive in the human host, GAS must rapidly reprogram virulence gene expression in response to host-derived stresses. This study characterizes two conserved transcriptional regulators, SpxA1 and SpxA2, that govern this response through interaction with RNA polymerase to indirectly influence the DNA-binding activity of downstream transcription factors. We show that SpxA2, activated by a cell envelope stress-sensing system responding to human antimicrobial peptides, reshapes the binding of the master virulence regulator CovR in a promoter-specific manner, coupling cell envelope stress sensing to virulence gene regulation. The stoichiometric balance between SpxA1 and SpxA2 functions as a regulatory rheostat calibrating overall virulence gene regulatory tone, providing a framework for understanding how RNA polymerase-interacting regulators coordinate stress responses and virulence gene control across Gram-positive bacterial pathogens.

Spatial transcriptomic techniques provide a wealth of information useful in guiding drug development, while three-dimensional (3D) cell cultures have demonstrated power in accelerating drug approvals. However, techniques for robust spatial analysis of 3D cultures are limited. Here, we present a transfection-based method for constructing cellular spheroids through a layer-by-layer approach, in which DNA barcodes encode the spatial positioning of cells. Our technique facilitates multiplex single-cell RNA sequencing, providing spatial maps of gene expression and drug response, while correlative imaging reveals the locations of barcoded cell populations and quantifies local tissue elasticity. We show that model HeLa 3D spheroids display heterogeneous responses to drugs, which may arise through diffusion gradients of the drug, or from differences in metabolism, nutrient supply, and cellular stressors. The ability to create spatially encoded cellular assemblies may help to reveal spatial variation in gene expression within 3D culture models.

Bacterial small non-coding RNAs (sRNAs) play critical roles in virulence, stress adaptation, and host-pathogen interactions. Transcriptomic analyses during infection can help reveal pathogen-derived sRNAs required for pathogenesis, providing valuable insights for the development of novel therapeutic strategies. However, the low abundance of pathogen biomass within the host tissues poses a significant challenge for such analyses. We employed two-step cell disruption to enrich Staphylococcus aureus cells from infected mouse organs and conducted RNA-seq analysis to examine staphylococcal sRNAs expressed during infection. qRT-PCR was used to confirm the gene expression. A knockout mutant of highly expressed sRNA, RsaC, was generated, and RNA-seq under in vivo as well as in vitro aerobic and anaerobic conditions were compared between the wild-type and ΔrsaC strains. Virulence of S. aureus was assessed using both mouse and silkworm survival assays. We identified RsaC as one of the most highly expressed sRNAs in mouse organ with consistent increment over time post-infection. Through gene disruption and complementation, we demonstrated that RsaC is an independent virulence determinant required for full pathogenicity of S. aureus in a murine infection model. Besides, rsaC influenced gene expression in response to oxygen availability and host-associated stress. Further analysis revealed that mutation of two genes downregulated in ΔrsaC in vivo, NWMN_RS03420 (sodium: proton antiporter) and NWMN_RS12015 (hypothetical protein), reduced S. aureus virulence in a silkworm model. These findings identify RsaC as a novel independent virulence determinant that supports S. aureus adaptation within the host.

Bacterial ribonucleases regulate gene expression in response to environmental stress and host interactions. In Staphylococcus aureus, the hibernation-promoting factor (Hpf) induces the formation of RNase R-resistant 100S ribosomes. We previously showed that the bifunctional 3’−5’ exoribonuclease YhaM cleaves the hpf transcript, reducing Hpf synthesis and leading to ribosome degradation. No atomic structure of any YhaM homolog bound to its substrate is available and biological investigations of YhaM remain limited. Here we find that deletion of yhaM attenuates S. aureus virulence in a Galleria mellonella infection model. We further determined electron cryomicroscopy structures of YhaM-RNA complexes. YhaM adopts a hexameric complex arranged in a ring, with its N-terminal oligonucleotide/oligosaccharide-binding (OB) domains positioned on both sides of the ring while the catalytic histidine/aspartate-rich (HD) domain active sites are buried within the interior. The OB-1” domain recognizes the hpf hairpin by the formation of complementary minor groove interactions. Structures of YhaM bound to a single-stranded RNA reveal how the 3’ ends of two RNAs are positioned within the catalytic HD domain poised for catalysis. RNA binding by two YhaM OB domains is mediated through engagement of both the backbones and nucleobases of the RNA substrate, where stacking of aromatic residues and nucleobases likely contributes to substrate recognition. Although six YhaM active sites are present, only two engage in RNA cleavage and further point to the importance of the remaining YhaM monomers as structural scaffolds for guiding RNA to the active site. In summary, these findings provide insights into the unique assembly of an understudied bacterial RNase.

Selenium biofortification in soybean is one approach to addressing widespread selenium deficiency in human populations, yet the temporal dynamics of gene expression and antioxidant responses following selenium enrichment remain poorly characterized. Here, we examined the physiological and transcriptional responses of the HK88 soybean variety to selenium-enriched nutrient solution treatment, with seedlings sampled at 1, 24, and 48 h post-treatment. Total tissue selenium rose from 0.01 mg/kg at 1 h to 0.33 mg/kg at 48 h, with parallel increases in both inorganic and organic fractions, consistent with active biotransformation, though this interpretation remains to be confirmed experimentally. Antioxidant responses followed a distinct temporal pattern: superoxide dismutase (SOD) and peroxidase (POD) activities were initially lower in treated plants at 1 h relative to controls but were elevated at 24 and 48 h, while catalase (CAT) activity remained comparatively low across all time points. Malondialdehyde (MDA) levels were lower in selenium-treated plants at 1 h, suggesting early membrane stabilization, though this difference was no longer apparent by 48 h. RNA sequencing of 18 libraries identified 6,793 differentially expressed genes (DEGs) at 1 h, peaking at 13,196 (approximately 18% of the 72,513 annotated genes) at 24 h, then declining to 8,996 at 48 h. A Venn diagram analysis identified 565 DEGs shared across all three time points, comprising 196 consistently up-regulated and 369 consistently down-regulated genes. Up-regulated genes were enriched for nucleotide transmembrane transport functions, including ATP, ADP, and purine transport, with associated ABC transporter activity. Down-regulated genes were predominantly associated with primary carbon metabolism, including monosaccharide biosynthesis, gluconeogenesis, and the Calvin cycle. Gene Set Variation Analysis (GSVA) indicated positive enrichment scores for nucleotide transport pathways at 24 and 48 h in treated plants, contrasting with negative scores in controls. Mantel tests revealed significant associations between gene set activity profiles and measured physiological traits, particularly for gene sets related to molecular function and selenium accumulation. These findings suggest that selenium biofortification in HK88 is associated with a coordinated metabolic shift, in which primary carbon fixation is reduced while nucleotide transport capacity is enhanced, supporting antioxidant defense during selenium assimilation.

DNA methylation is an epigenetic modification that regulates gene expression in response to environmental exposures. We measured differential DNA methylation levels in blood before after general anesthesia and surgery in participants with and without postoperative delirium (POD) and postoperative neurocognitive disorder (PNCD). Blood sampling, delirium assessment and cognitive testing were prospectively performed at baseline before non-cardiac, non-neurologic surgery, and at 24 hours (24h) and 6 weeks (6wk) thereafter in 94 participants comprising 13 with POD and 81 without POD, and 40 with PNCD and 54 without PNCD 6wk after surgery who were matched for age and sex in the INTUIT and MADCO cohorts. DNA methylation was assessed using the Illumina Infinium MethylationEPIC Beadchip. 132 differentially methylated positions (DMPs) annotated to 198 differentially methylated genes (DMGs) were identified in 94 participants 24h after surgery compared to baseline with a local false discovery rate (LFDR) <0.05 including CHRNB1 , LGALS1 , SMAD4 , RYR2 , CHST11 , CDC25B , OBSCN , ABHD16A . No DMPs were identified between samples collected at baseline compared to 6wk after surgery. In baseline samples, 8 DMPs annotated to 12 DMGs were identified between participants who did and did not develop POD including MBTD1, BID, PPAN, ANGPTL6, PHF21B, and RBM5 . In 24h samples, 87 DMPs annotated to 91 DMGs were identified between participants with and without POD including CLEC19A, FILIP1, ERICH1, PSENEN, SLC6A3, and TMEM196. In 6wk samples, 1 DMP annotated to FILIP1 and LOC124901509 in participants with and without POD. No DMPs in baseline, 24h or 6wk blood samples were identified between patients with and without PNCD at 6k after surgery. Differential DNA methylation levels are present throughout the genome 24h after anesthesia and surgery. Differential DNA methylation levels before surgery and at 24h after surgery distinguishes patients with and without POD. Differential DNA methylation levels were not identified between baseline and 6wk after surgery in the entire cohort, or between patients with and without PNCD at 6 weeks.

BackgroundBrassica rapa is an oilseed crop used for vegetable oil production, with applications in both human consumption and industrial purposes. RNAi-guided gene families play crucial roles in plant growth and development by regulating gene expression in response to various pathogens and abiotic stressors. However, these gene families in this species have not yet been studied in detail. Therefore, this research aims to explore the major RNAi genes, including their characterization and underlying functions for crop improvement.ResultsOur analysis identified 4 BrDCL, 13 BrAGO, and 6 BrRDR genes from the Brassica rapa genome. Phylogenetic analysis revealed that the identified genes were evolutionarily related to the RNAi genes in Arabidopsis. The domain, exon-intron, and motif structures of genes and proteins were very similar to those of A. thaliana. Moreover, sequence logo and relative frequency analysis showed that lysine (K), serine(S), valine (V), leucine (L), and glutamic acid (E) were highly significant (p < 0.01) amino acids in motifs. The genes were distributed across the 10 chromosomes, and segmental duplication was observed in BrAGO1 and BrAGO4. GO analysis showed that genes were involved in important biological processes such as defense response to virus (p < 0.01), post-transcriptional gene silencing (p < 0.01), etc., and molecular pathways, for example, RNA polymerase activity (p < 0.01), siRNA binding(p < 0.01), etc. The largest number of genes was associated with the nucleus, chloroplast, and cytosol. Trans-regulatory analysis showed that the top-ranked TF families accounted for 393 (78%) of 502 regulators, including Dof 115 (23%), bZIP 58(11.55%), C2H2 49(9.76%), ERF 30(6%), BBR-BPC 29(5.77%), MICK-MADS 23(4.58%), MYB, TCP, and WRKY each 23 (4.58%), with AP2 regulating 21(4.18%) TFs. Gene-TF network analysis showed that eight key TF families were highly connected to RNAi genes. The associated cis-acting elements were classified as hormone, light, and various stress-responsive. 10 key RNAi genes interacted with most of the TFs, comprising 302 TFs (~61%), among which BrAGO1a (48 TFs~10%) and BrAGO1b (40 TFs~8%) were influential. Expression analysis demonstrated that most genes showed expression in the root, seeds, flowers, leaves of seedlings, silique, and seed coats.ConclusionOverall results would provide valuable resources for improving stress-tolerant transgenic lines by initiating knockdown of negative regulators of stress responses, increasing defense-related gene expression, or generating host-induced gene-silencing molecules that target pathogens and pests. Also, by manipulating BrRNAi genes, one can significantly improve crop traits such as disease resistance, abiotic stress tolerance, and crop yield with quality in B. rapa.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12863-026-01441-7.