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At least 19 recordsLinked to original sources

PubMed1977

Improved staining boxes for fast, uniform staining of ultrathin sections on grids.

A standard LKB (LKB-Produkter Ab. S-161, 25 Brommma 1, Sweden) grid storage box is converted into several grid staining boxes by sawing the body of the box into segments along rows of its grid storage cavities. The staining boxes can be cut out to any required size or shape. The polymethyacrylate storage box cover is discarded. Covers for the staining boxes are cut from thin sheet vinyl, which is more chemically resistant than polymethyacrylate. Corresponding 2 mm diameter holes are drilled through the vinyl covers and the bottoms of the grid storage cavities of the staining boxes to convert the storage cavities into staining chambers. For staining, the covers are tied to the boxes with sewing thread and the assembled units are put into vials. The separate staining chambers prevent intermingling of and mechanical damage to grids during the staining procedure. Ultrathin sections are more cleanly and uniformly stained in bulk by the use of these staining boxes than they are when stained individually by a standard method.

Cytological Techniques↗

PubMed2025

Transposable Elements Drive Regulatory and Functional Innovation of F-box Genes.

Protein domains of transposable elements (TEs) and viruses increase the protein diversity of host genomes by recombining with other protein domains. By screening 10 million eukaryotic proteins, we identified several domains that define multicopy gene families and frequently co-occur with TE/viral domains. Among these, a Tc1/Mariner transposase helix-turn-helix (HTH) domain was captured by F-box genes in the Caenorhabditis genus, creating a new class of F-box genes. For specific members of this class, like fbxa-215, we found that the HTH domain is required for diverse processes including germ granule localization, fertility, and thermotolerance. Furthermore, we provide evidence that Heat Shock Factor 1 (HSF-1) mediates the transcriptional integration of fbxa-215 into the heat shock response by binding to Helitron TEs directly upstream of the fbxa-215 locus. The interactome of HTH-bearing F-box factors suggests roles in post-translational regulation and proteostasis, consistent with established functions of F-box proteins. Based on AlphaFold2 multimer proteome-wide screens, we propose that the HTH domain may diversify the repertoire of protein substrates that F-box factors regulate post-translationally. We also describe an independent capture of a TE domain by F-box genes in zebrafish. In conclusion, we identify two independent TE domain captures by F-box genes in eukaryotes and provide insights into how these novel proteins are integrated within host gene regulatory networks.

Animals↗

PubMed2026

Genome-wide characterization of MADS-box genes and their roles in axillary bud development in tobacco.

A total of 118 NtMADS-box genes were identified in tobacco, revealing their potential roles in axillary bud development. Preliminary overexpression analysis indicated that NtMADS91 promotes axillary bud development. MADS-box transcription factors are core regulators of plant development, but their functions in axillary bud development in Nicotiana tabacum L. have not been systematically elucidated. In this study, 118 NtMADS-box genes were identified from the tobacco genome. Phylogenetic analysis classified them into type I (comprising the Mα and Mγ subfamilies) and type II (comprising the MIKC* and MIKCC clades). Promoter analysis revealed that cis-acting elements were predominantly associated with light and hormone responses. RNA-seq analysis of axillary buds after topping identified 60 differentially expressed NtMADS-box genes, from which 12 candidate genes with significant expression changes were selected. Tissue-specific qRT-PCR revealed that seven of these genes were preferentially expressed in axillary buds, with members of the SOC1 and SVP subfamilies accounting for the majority. Exogenous application of abscisic acid and the strigolactone analog GR24 significantly suppressed the expression of most candidate genes, including NtMADS91. The preliminary overexpression analysis suggested that NtMADS91 may promote axillary bud growth, increasing both the number and length of axillary buds. This study lays a foundation for future dissection of the regulatory mechanisms of the NtMADS-box gene family in axillary bud development and provides promising candidate genes for research related to tobacco axillary bud development.

Nicotiana↗

PubMed2025

Genome-wide identification and expression profiling of the MADS-box gene family in Lavandula angustifolia.

BACKGROUND: MADS-box genes encode transcription factors critical for plant development, particularly floral organogenesis, flowering time regulation, and adaptation to environmental stresses. Among these, the MIKCC-type genes are pivotal regulators in floral developmental processes. Although the evolutionary diversification and functional dynamics of MADS-box genes have been extensively characterized in model plants such as Arabidopsis thaliana and Oryza sativa, their evolutionary relationships and functional profiles in Lavandula angustifolia, an economically significant aromatic plant, remain poorly understood. RESULTS: Genome-wide analysis identified 173 MADS-box genes in L. angustifolia, categorized into type I (Mα: 26; Mβ: 0; Mγ: 10) and type II (MIKCC: 125; MIKC*: 12) based on phylogenetic comparisons with A. thaliana. The MIKCC subgroup was further subdivided into 12 subclasses, including genes central to the ABCDE model of floral organ specification. Structural analyses revealed distinct conserved motifs and exon-intron configurations specific to each subgroup, indicative of functional divergence. Synteny analysis demonstrated Whole Genome Duplication (WGD) and segmental duplications as major contributors to MIKCC gene family expansion, notably among genes linked to floral organ development. Expression profiling via RNA-seq and quantitative real-time PCR (qPCR) showed type II MADS-box genes exhibited higher expression levels with pronounced tissue-specific and developmental stage-specific expression patterns compared to type I genes. Many type II genes displayed significant associations with floral organogenesis, floral transition, and abiotic stress responses, underscoring their essential roles in reproductive development and environmental adaptability in L. angustifolia. CONCLUSIONS: The identification and comprehensive characterization of 173 MADS-box genes in L. angustifolia highlight the significant expansion of the MIKCC subgroup driven primarily by WGD and segmental duplications. The distinct structural features and specific expression patterns observed provide insights into the functional divergence and complexity of these genes, particularly regarding floral organogenesis and adaptation to environmental stress. This study establishes a robust molecular basis for further functional analysis and genetic improvement of aromatic plants.

MADS Domain Proteins↗

PubMed2026

Comparative transcriptomics reveals hormone signaling and MADS-box genes in divergent development of inflorescences and tendrils in grapevine lateral shoots.

Hormone signaling and MADS-box genes regulate grapevine tendril and inflorescence growth divergence, offering molecular insights for managing tendril growth. Grapevine (Vitis vinifera L.) tendrils and inflorescences are homologous organs; however, their divergent development has important agronomic consequences because excessive tendril growth increases vineyard management costs. To explore the regulatory mechanisms, we compared the inflorescence-prone cultivar 'Einset Seedless' (ENT) with the tendril-prone cultivar 'Pinot Noir' (PN) using anatomical observation, transcriptome analysis of specific tendril nodes, and functional characterization of MADS-box genes. ENT exhibited a higher flowering rate at tendril nodes 1-4 than PN. Transcriptome profiling of specific tendril nodes uncovered 549 differentially expressed genes (DEGs) through an intersection/exclusion strategy, with Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment indicating that hormone and mitogen-activated protein kinase (MAPK) signaling were the primary candidates driving the divergence. To assess the spatiotemporal dynamics of these DEGs, we performed Mfuzz clustering, which revealed that multiple expression trajectories were highly consistent with the flowering gradient across different ENT and PN nodes. Plant hormone signal transduction was the predominantly enriched pathway across all dynamic clusters, highlighting the centrality of phytohormones in this process. Guided by this transcriptional evidence, we measured endogenous zeatin and gibberellin (GA₃) contents in the nodal tissues. Remarkably, the zeatin-to-GA₃ ratio not only paralleled the flowering gradient but also correlated with the cluster expression trajectories, providing physiological evidence for a cytokinin-gibberellin interaction model governing organ divergence. Additionally, we analyzed the differentially expressed transcription factors among the DEGs and identified a MADS-box gene, FRUITFULL-LIKE (VvFUL-L), which was markedly upregulated in PN tendrils. Heterologous overexpression of VvFUL-L in arabidopsis promoted early flowering and reduced inflorescence branching, suggesting its potential role in regulating lateral meristem development and affecting tendril formation. Collectively, these findings establish that Hormone Signaling, particularly cytokinin-GA crosstalk, and MADS-box regulators, such as VvFUL-L, are key regulators of inflorescence versus tendril growth in grapevines, providing a basis for future molecular and breeding studies.

Vitis↗

PubMed2004

The proneural proteins Atonal and Scute regulate neural target genes through different E-box binding sites.

For a particular functional family of basic helix-loop-helix (bHLH) transcription factors, there is ample evidence that different factors regulate different target genes but little idea of how these different target genes are distinguished. We investigated the contribution of DNA binding site differences to the specificities of two functionally related proneural bHLH transcription factors required for the genesis of Drosophila sense organ precursors (Atonal and Scute). We show that the proneural target gene, Bearded, is regulated by both Scute and Atonal via distinct E-box consensus binding sites. By comparing with other Ato-dependent enhancer sequences, we define an Ato-specific binding consensus that differs from the previously defined Scute-specific E-box consensus, thereby defining distinct E(Ato) and E(Sc) sites. These E-box variants are crucial for function. First, tandem repeats of 20-bp sequences containing E(Ato) and E(Sc) sites are sufficient to confer Atonal- and Scute-specific expression patterns, respectively, on a reporter gene in vivo. Second, interchanging E(Ato) and E(Sc) sites within enhancers almost abolishes enhancer activity. While the latter finding shows that enhancer context is also important in defining how proneural proteins interact with these sites, it is clear that differential utilization of DNA binding sites underlies proneural protein specificity.

3' Flanking Region↗

PubMed2025

Effect of Chang'an decoction on ulcerative colitis by regulating T helper 17 cells and regulatory T cellsRab27 in the p53/high mobility group box 1 pathway.

OBJECTIVE: To explore the effect of Chang'an decoction (, CAD) of ameliorating the immune imbalances in ulcerative colitis (UC) by regulating Rab27 in the P53/high mobility group box 1 pathway. METHODS: The functions and important signaling pathways of the Rab27- and UC-related genes were analyzed viathe use of microarray data from the gene expression omnibus database, gene ontology database, Kyoto encyclopedia of genes and genomes database and gene set enrichment analysis. Dextran sulfate sodium salt-induced colitis mouse model was used to verify the bioinformatics results. Colon length, body weight, and disease activity index were measured. Hematoxylin and eosin staining was applied to validate the histopathology. Tight junction proteins were detected by immunohistochemistry. The proportions of T helper 17 cells (Th17) and regulatory T cells (Treg) in mesenteric lymph nodes were measured viaflow cytometry. Proinflammatory cytokines like interleukin (IL) 17 (IL-17), IL-21 and IL-22 and anti-inflammatory cytokines like transforming growth factor β and IL-10 in the serum and colon of mice were detected by enzyme-linked immunosorbent assay and quantitative real-time polymerase chain reaction, respectively. The expression levels of high mobility group box 1 (HMGB1), P53 and phospho- P53 (P-P53) in colonic tissues were detected by immunofluorescence and Western blotting. RESULTS: Bioinformatics analysis revealed that compared with normal tissues, the expression of Rab27 was significantly increased in UC tissues. Receiver operating characteristic curve showed that Rab27 has the potential to be used as a biomarker for the diagnosis of disease activity. Enrichment analysis showed that UC and Rab27 were mainly associated with small molecule transport, nutrient metabolism, transmembrane transport and the downstream pathway of P53. According to animal experiments, the expression of Rab27 was increased in UC tissues, which aggravated the colonic pathological damage, activated the expression of HMGB1, and also leaded to the imbalance of Th17 and Treg cells. After CAD intervention, Rab27 overexpression, weight loss, colon shortening, and pathological damage were substantial reduced, the expression of tight junction proteins, zona occludens 1 and Occludin were increased. The effect of CAD at high-dose was more obvious. In addition, CAD upgraded the number of Treg cells and the production of TGF-β and IL-10, while decreasing the number of Th17 cells and the expression of inflammatory cytokines (IL-17, IL-21, and IL-22). Moreover, colon inflammation was alleviated by CAD, as indicated by the regulation of HMGB1 and P-P53 expression. CONCLUSION: The expression of Rab27, HMGB1 and P-P53 could be decreased by CAD, and the balance of Th17 and Treg cells as well as their related cytokines could be regulated by CAD.

Animals↗

PubMed1979

[Manipulation box to measure the motor performance involving the distal musculature of the arm in primates (author's transl)].

For studies of motor performance in the baboon, regarding precise finger movements, a new latch-box was developed. The device was designed so as to involve mainly the distal musculature of the arm. Handling the different knobs or latches which open the compartments of the box had to be performed in a given motor sequence. Monkeys were trained to use two fingers of the hand: thumb and index. Data are presented which show that, after exclusion of a central nervous structure, it is possible to differentiate the performance obtained with the device described above that obtained in a pointing task, mainly involving the proximal musculature.

Animals↗

PubMed2026

Genomic diversity, antimicrobial resistance, and virulence-associated characteristics of Escherichia coli recovered from poultry hatchery-box material.

Hatcheries are early points of exposure of newly hatched chicks to Escherichia coli from eggshell debris, dust, meconium, and the hatchery environment. This study used descriptive genomic surveillance to characterize population structure, antimicrobial resistance, virulence-associated genes, plasmid replicons, and genetic relatedness in a purposively selected collection of E. coli recovered from hatchery-box material in a Czech commercial poultry hatchery. From 83 samples collected between 2019 and 2023, 409 isolates were recovered. Following within-sample reduction based on antimicrobial susceptibility profiles and PCR screening for selected APEC-associated virulence genes, 91 isolates enriched for cefotaxime-medium recovery or APEC-associated gene profiles were selected for Illumina whole-genome sequencing. The sequenced collection comprised 35 sequence types across nine phylogenetic groups or clades; phylogroup B1 (59/91) and ST162 (28/91) predominated. ColV-associated markers were detected in 88 isolates, acquired resistance genes in 61, and a multidrug-resistant phenotype in 31. Seventeen isolates were resistant to ceftazidime; eight carried ESBL or plasmid-mediated AmpC determinants, while eight additional isolates had the chromosomal ampC promoter substitution C-42T as the only identified determinant associated with this phenotype. Closely related isolates, including ST131, ST162, and ST675, were recovered from different samples or parent-farm groups within restricted sampling periods. These findings document genomically diverse, resistance- and virulence-associated E. coli in hatchery-box material and identify genetically related isolates that warrant investigation through structured longitudinal sampling. Because sampling was unequal and isolates were purposively selected, the findings do not provide prevalence estimates or demonstrate source, transmission, persistence, or pathogenicity.

APEC-associated virulence genes↗

PubMed2026

Plant U-box E3 ligases: Versatile regulators of environmental stress adaptation and ABA signaling.

Ubiquitination is a reversible post-translational modification that orchestrates a wide spectrum of fundamental processes throughout the plant life cycle. Executed by a hierarchical E1-E2-E3 cascades, this modification tags targets with ubiquitin to modulate their turnover, activity, or subcellular compartmentalization. Among the diverse E3 ligase families, plant U-box (PUB) proteins stand out as a prominent class that determines substrate selection and has emerged as a focal point of stress biology. In this review, we first delineate the structural features of PUB proteins, highlighting their conserved domains and associated regulatory motifs. We then systematically dissect their multifaceted functions in abiotic stress adaptation, encompassing drought, salinity, extreme temperatures, oxidative stress, heavy metal toxicity, with particular emphasis on their integration with ABA signaling networks. We further outline critical knowledge gaps and propose future strategies to decode the regulatory architecture of PUBs. Collectively, this review provides a theoretical foundation and new insights for facilitating the genetic improvement of crop resilience in the face of continuously intensifying environmental stresses through the manipulation of PUB-mediated ubiquitination networks.

ABA signaling↗

PubMed2025

Oncogenic DEAD-box ATPase DDX41 establishes transcript ensembles via CLK3-dependent and -independent mechanisms.

Post-transcriptional diversification of RNA transcripts mediated by complex processing machinery, including DEAD-box ATPases, establishes and maintains cellular phenotypes. For example, DDX41 controls RNA splicing, innate immune signaling, and genome stability. Although heterozygous DDX41 germline genetic variation occurs in familial myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML), the DDX41 contributions to splicing globally, biological processes, and pathogenic mechanisms are incompletely defined. Using a genetic rescue system with Ddx41+/- myeloid progenitors, we established global wildtype DDX41 and pathogenic variant mechanisms. Differing from pathogenic variants of other RNA splicing regulators, DDX41 deficiency compromised multiple splicing steps. DDX41-regulated transcripts encoded factors controlling RNA splicing, including Cdc2-like kinase 3 (CLK3). DDX41 regulated Clk3 transcripts, and elevated CLK3 during myeloid differentiation. Loss-of-function analysis revealed DDX41-regulated splicing commonly, but not always, required CLK3. Thus, through a mechanism utilizing a splicing factor kinase that itself is DDX41-regulated, DDX41 establishes transcript ensembles in myeloid progenitors.

DEAD-box RNA Helicases↗

PubMed1976

Euflavine: effect on brain heavy metal content and staining pattern, and on shuttle box behavior in goldfish.

Goldfish were exposed to euflavine in doses of 7-100 mg/l for 1h-14 days. The treatment resulted in a reduced stainability of the brain with the Timm histochemical procedure for "heavy metals". In contrast, analysis by flameless atomic absorption spectrophotometry showed no significant changes in the concentrations of zinc and of copper after euflavine treatment. In the shuttle box a significant increase in general activity was found. These results, compared to earlier work with other chelating agents, indicate that such drugs do not have a uniform effect on behavior, and that they do not cause a true depletion of heavy metals in the brain.

Acridines↗

PubMed2026

Evolutionary architecture and lineage-specific diversification of Forkhead box transcription factors in Perna viridis.

The Forkhead box (Fox) transcription factors are evolutionarily conserved regulators of development, cell cycle, and apoptosis across metazoans. This study provides the first comprehensive genome-wide analysis of the Fox gene family in the Asian green mussel (Perna viridis). We identified 28 Fox genes distributed across 10 chromosomes. Comparative analysis reveals the absence of the FoxI, FoxQ1, FoxR and FoxS subfamily, consistent with other bivalves and indicative of lineage-specific gene loss during molluscan evolution. Notably, gene duplications in the FoxAB, FoxD, FoxH, FoxN1-4, FoxQ2 and FoxQD subfamilies may reflect functional diversification associated with environmental adaptation. Exon-intron structural variability, including intron loss in several paralogues, suggests structural diversification and potential regulatory variation. Phylogenetic reconstruction confirmed the monophyly of core Fox classes while highlighting divergent expansion patterns in lophotrochozoans. Selection analyses showed strong purifying selection across duplicated Fox paralogs, supporting functional conservation after lineage-specific expansion. Gene Ontology enrichment linked Fox genes to stress response, apoptosis, and transcriptional regulation. By integrating phylogenetic, structural, and transcriptomic analyses, this study provides a genomic framework for understanding Fox gene organisation, evolution, and tissue-associated expression patterns in Perna viridis and establishes a comparative resource for future functional studies in bivalves.

Animals↗

PubMed2026

A wild soybean MADS-box gene GsAGL62 improves seed weight by enhancing cytokinin signaling and cell proliferation.

Soybean seed weight is a key yield determinant, but the transcriptional mechanisms connecting hormone signaling to seed growth are poorly understood. Here, we identify GsAGL62, a wild soybean MADS-box transcription factor located within a previously mapped hundred-seed weight (HSW) locus and a domestication-associated selective sweep. Functional analyses show that overexpression of GsAGL62 in cultivated soybean significantly increases HSW, whereas ethyl methanesulfonate (EMS)-induced gmagl62 mutants reduce it. Integrated transcriptomic and metabolomic analyses reveal that GsAGL62 enhances cytokinin accumulation and signaling cytokinin-associated responses, accompanied by increased expression of genes involved in cell proliferation. Mechanistically, GsAGL62 directly binds to the promoter of the conserved growth inhibitor GmATPK2 and represses its transcription. Consistently, independent EMS-induced gmatpk2 mutants exhibit increased seed weight, supporting GmATPK2 as a downstream negative regulator of seed growth. Population genetic analyses further reveal strong differentiation of GsAGL62 promoter haplotypes during soybean domestication and improvement. These haplotypes show differential promoter activities and are associated with distinct agronomic performance, suggesting that cis-regulatory variation at GsAGL62 contributes to its selection during soybean improvement. Collectively, our findings establish a regulatory module linking GsAGL62 to cytokinin-associated responses, cell proliferation, and seed growth, and highlight GsAGL62 as a potential target for soybean yield improvement.

Cell proliferation↗

PubMed1975

Hormonal dissociation of limbic lesion effects on shuttle box avoidance in rats.

Rats with septal or hippocampal lesions, relative to normal rats, showed facilitated acquisition of a shuttle box avoidance response. The rats with septal lesions were also highly resistant to extinction compared with normal rats. When the same lesion effects were examined in hypophysectiomized rats, the animals with septal lesions continued to show facilitated performance, and those rats with hippocampal lesions performed no differently than nonoperated control animals. These findings are consistent with the hypothesis that the facilitated avoidance performance found in rats with hippocampal lesions is attributable to lesion-induced changes in hypophyseal activity, but similar changes induced by septal lesions are not.

Acoustic Stimulation↗

PubMed2016

Expanding the amino acid repertoire of ribosomal polypeptide synthesis via the artificial division of codon boxes.

In ribosomal polypeptide synthesis the library of amino acid building blocks is limited by the manner in which codons are used. Of the proteinogenic amino acids, 18 are coded for by multiple codons and therefore many of the 61 sense codons can be considered redundant. Here we report a method to reduce the redundancy of codons by artificially dividing codon boxes to create vacant codons that can then be reassigned to non-proteinogenic amino acids and thereby expand the library of genetically encoded amino acids. To achieve this, we reconstituted a cell-free translation system with 32 in vitro transcripts of transfer RNASNN (tRNASNN) (S = G or C), assigning the initiator and 20 elongator amino acids. Reassignment of three redundant codons was achieved by replacing redundant tRNASNNs with tRNASNNs pre-charged with non-proteinogenic amino acids. As a demonstration, we expressed a 32-mer linear peptide that consists of 20 proteinogenic and three non-proteinogenic amino acids, and a 14-mer macrocyclic peptide that contains more than four non-proteinogenic amino acids.

Amino Acid Sequence↗

PubMed2026

Telomere-to-telomere genome of Phoebe chekiangensis reveals that age-dependent CHG hypomethylation promotes floral transition via MADS-box gene activation.

Phoebe species are renowned for their highly valuable 'golden thread' timber; however, their protracted juvenile phase presents a significant obstacle to mechanistic investigations of floral induction. Phoebe chekiangensis, a rare early-flowering representative within this genus, provides a unique model system for dissecting the vegetative-to-reproductive phase transition. Nevertheless, the absence of a high-quality reference genome has severely hindered molecular insights into its developmental regulation. Here, we present the first telomere-to-telomere (T2T) genome assembly for P. chekiangensis, comprising two completely gap-free haplotypes with contig N50 values exceeding 65 Mb, base-level quality scores >36, and Long Terminal Repeat Assembly Index scores surpassing the gold standard threshold of 20. Approximately 29 000 genes were annotated per haplotype, supported by a BUSCO completeness score of >97%. Age-resolved transcriptomic landscapes identified two MADS-box transcription factors, PcMADS5 (AP1-like) and PcMADS19.1 (SOC1-like), as core activators of the floral transition. Both genes triggered precocious flowering when ectopically expressed in Arabidopsis thaliana. Whole-genome bisulfite sequencing revealed a progressive, age-dependent decline in CHG (where H is A, C, or T) DNA methylation, which was particularly pronounced at the PcMADS19.1 locus. Notably, DML1/2, which mediate active DNA demethylation, were coordinately upregulated during the onset of reproductive growth. Chemical demethylation using 5-azacytidine further diminished CHG methylation and selectively enhanced PcMADS19.1 expression, confirming a causal relationship between CHG hypomethylation and transcriptional activation. This work delivers the first chromosome-scale T2T genome within the genus Phoebe and uncovers CHG demethylation as a previously unrecognized epigenetic switch governing reproductive competence in woody perennials.

Journal Article↗

PubMed1977

View box exercises for teaching problem solving in radiology.

An organized radiologic problem-solving system is presented for developing improved view box exercises for students and residents. It is based on six components: (1) problem sensing, (2) problem hypothesizing, (3) problem searching and definition, (4) problem identification, (5) resolution, and (6) verification. Since all examinations by the practicing radiologist involve these components, worthwhile simulated clinical management games should also incorporate them. A simulated radiologic exercise should be a valid measurement of the resident's ability to manage a wide range of clinical situations and techniques and should improve problem-solving strategies. Use of simulated clinical cases eliminates risk to patients during the educational process.

Audiovisual Aids↗