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PubMed1977

Quadratic analyses of reciprocal crosses.

Three different models, a two-way factorial model for familiarity, an orthogonalizing transform of this model to a diallel model, and a bio model more representative of the biological situation, are interrelated in terms of their components of variance and covariance. It is clarified that there are five components that can be reckoned with in the analysis of reciprocal crosses, including distinct maternal and paternal variances. Estimation of the components and tests of hypotheses concerning them are outlined for two types of mating designs with reciprocals. One deisgn involves a factorial mating design between two distinct sets of parents or parental lines and the other a diallel of all crosses from a single set of parents or parental lines. Both designs provide the same types of information and similar tests of hypotheses. At least some parts of the analyses corresponding to the factorial model are required to separate the maternal and paternal variances. A least squares partitioning of the sums of squares according to the diallel model, but with expectations expressed in terms of the bio model, provides most of the tests of hypotheses of interest. Worked examples are given.

Crosses, Genetic↗
PubMed2025

Deep learning guided programmable design of Escherichia coli core promoters from sequence architecture to strength control.

Core promoters are essential regulatory elements that control transcription initiation, but accurately predicting and designing their strength remains challenging due to complex sequence-function relationships and the limited generalizability of existing AI-based approaches. To address this, we developed a modular platform integrating rational library design, predictive modelling, and generative optimization into a closed-loop workflow for end-to-end core promoter engineering. Conserved and spacer region of core promoters exert distinct effects on transcriptional strength, with the former driving large-scale variation and the latter enabling finer gradation. Based on this insight, Mutation-Barcoding-Reverse Sequencing approach was used and constructed a synthetic promoter library comprising 112 955 variants with minimal redundancy and a 16 226-fold expression range. A Transformer-based model trained on this dataset achieved a Pearson correlation of 0.87 with experimentally measured promoter strengths. When combined with a conditional diffusion model, the system enabled de novo generation of promoter sequences with defined strengths, achieving a design-to-measurement correlation of 0.95 and maintaining high accuracy (R = 0.93) across varied sequence contexts. The designed promoters consistently preserved their intended strength gradients, demonstrating robust plug-and-play functionality. This work establishes a scalable and extensible platform (www.yudenglab.com) for deep learning-guided programmable design of Escherichia coli core promoters, enabling precise transcriptional control.

Promoter Regions, Genetic↗
PubMed1976

[Analysis of muscle electrical activity during indirect rhythmic stimulation].

A mathematical model of transformation of the electrical signals in the peripheral neuromuscular junction, and a method of analysing the experimental data obtained in experiments on the muscle and muscle fibers of rat diaphragm in indirect rhythmic stimulation is described. The parameters characterizing the muscle by frequency potentiation and depression properties were determined as a result of the EMG analysis.

Animals↗
PubMed2026

Epigenetic Reprogramming and Zygotic Genome Activation in Human Preimplantation Development: Mechanisms, Models, and Translational Prospects.

PURPOSE: Early human embryogenesis unfolds through a tightly coupled sequence of events-clearance of maternal transcripts, remodeling of parental chromatin, zygotic genome activation (ZGA), lineage segregation, implantation, and post-implantation patterning-accompanied by epigenetic reprogramming, including X-chromosome dosage compensation around the time of implantation. This review aims to synthesize recent advances in understanding this developmental program and to consider their implications for reproductive medicine. METHODS: I review recent literature on human early embryogenesis, with particular emphasis on findings enabled by single-cell genomics and stem-cell-based embryo modeling, and integrate these insights to identify human-specific features of early development. RESULTS: These approaches have made previously inaccessible aspects of human early embryogenesis experimentally tractable, revealing molecular and epigenetic features that distinguish human development from that of model organisms, including species-specific dynamics of ZGA, maternal transcript clearance, chromatin reprogramming, and X-chromosome dosage compensation. CONCLUSIONS: Advances in single-cell genomics and embryo modeling are transforming our understanding of human early embryogenesis. Building on these insights, while recognizing their current limitations, I propose a vision for improving reproductive medicine, including the potential for next-generation embryo selection strategies.

Journal Article↗
PubMed1979

Professionalism: rise and fall.

Historically, the early professionalization movements in medicine and the law appear as organizational projects which aspire to monopolize income and opportunities in markets of services or labor and to monopolize status and work privileges in occupational hierarchies. Their central task is to standardize training and link it to actual or potential markets of labor or services, a linkage that is structurally effected in the modern university. The second wave of professionalization has different protagonists than the older "market professions": placed in a different structural situation, the bureaucratic professions transform the model of profession (which they adopt as a strategy of collective ascension) into an ideology. The import of the ideology of professionalism is examined in relation to two issues: the relationships between professional occupations and bureaucratic organizations; and the position of professional occupations within the larger structure of inequality. Analysis of the first point requires consideration of the distinctions between professional occupations in the public and private sectors, the use of professional knowledge and the image of profession in bureaucratic organizations, and the specific characteristics of professions that produce their own knowledge. In the discussion of the second point, professional occupations and their ideology are examined in relation to other occupations and to the possibilities of political awareness generated by uncertain professional statuses.

Certification↗
PubMed2026

Establishment of an efficient Agrobacterium-mediated genetic transformation protocol for Saccharum officinarum using Black Cheribon as a model genotype.

Efficient Agrobacterium-mediated transformation (AMT) is vital for the biotechnological improvement of sugarcane (Saccharum spp.). Saccharum officinarum is the main ancestor of all modern cultivars, yet little research has been conducted on its AMT system. In this work, an efficient AMT protocol for S. officinarum was developed, with Black Cheribon as the model genotype owing to its superior tissue culture performance and regeneration capacity. The optimized agro-infection protocol comprised the following main parameters: concentration of acetosyringone (AS) in Agrobacterium culture, concentration of AS for infection, Agrobacterium concentration at OD600 = 0.4, infection time of 30 minutes, vacuum infiltration time of 10 minutes and co-cultivation time of 3 days. To further improve transformation efficiency, 0.5 mg/L thidiazuron and 200 mg/L citric acid were added to the regeneration medium, which enhanced the regeneration of shoots. A modified stage-dependent selection strategy (FlexII) was established by using glufosinate-ammonium at concentrations of 2.0, 1.0, and 0.75 mg/L in the callus proliferation, shoot regeneration, and rooting stages, respectively. This strategy was more successful than the minimum inhibitory concentration-based strategy in S. officinarum transformation. The optimized protocol further boosted the transformation efficiency of Black Cheribon from 1.12% to 7.17%. The resulting transgenic lines were confirmed by PCR amplification of T-DNA regions and immunochromatographic detection of Bar protein expression in primary transformants, respectively. These results provide a sound technical foundation for the functional genomics and biotechnological optimization of S. officinarum germplasm, and may serve as a reference for future transformation studies in other sugarcane germplasm.

Agrobacterium↗
PubMed1979

Transformation and relational-structure schemes for visual pattern recognition. Two models tested experimentally with rotated random-dot patterns.

Two models for visual pattern recognition are described; the one based on application of internal compensatory transformations to pattern representations, the other based on encoding of patterns in terms of local features and spatial relations between these local features. These transformations and relational-structure models are each endowed with the same experimentally observed invariance properties, which include independence to pattern translation and pattern jitter, and, depending on the particular versions of the models, independence to pattern reflection and inversion (180 degrees rotation). Each model is tested by comparing the predicted recognition performance with experimentally determined recognition performance using as stimuli random-dot patterns that were variously rotated in the plane. The level of visual recognition of such patterns is known to depend strongly on rotation angle. It is shown that the relational-structure model equipped with an invariance to pattern inversion gives responses which are in close agreement with the experimental data over all pattern rotation angles. In contrast, the transformation model equipped with the same invariances gives poor agreement to the experimental data. Some implications of these results are considered.

Field Dependence-Independence↗
PubMed1979

Mathematical models and the statistical analyses of cell transformation experiments.

Statistical methods are developed and applied to the fitting of the one-hit curves to chemically induced transformations in Syrian hamster colonies. Data from several experiments in two laboratories are shown to fit the model well at all but the highest doses of benzo(a)pyrene. The ratio of the estimated parameters of the one-hit curves ("transformicities") is proposed as a measure of the enhancement by X-irradiation. Statistical tests for possible nonrandom variation among dishes are developed for the situation where a sample of dishes is used to estimate the total number of surviving cells. The methods of fitting and estimation are also extended to this case. Further analyses exclude selection as an explanation for the observed increase in transformation frequency with increased carcinogen concentration. The reproducibility of the fit of the one-hit model and the radiation enhancement measures is ascribed to the uniqueness of this in vitro system in which the direct target cell-insult interaction is not modulated by host intervention.

Animals↗
PubMedDate not supplied

[Energy transformation in mechanoreceptors].

The values of relative threshold deformations and of the mechanosensitivity coefficent are evaluated for some mechanoreceptors. The thermodynamical model of energy transformation in a primary act of mechanoreception is presented, the values of mechanical elastic energy stored in the membrane are calculated. The model of the mechanosensitive center as the ion-selective channel, changing dimensions of its protein part due to closing and opening of the channel is shown to give satisfactory values of the free energy change of the system at the threshold stimulus.

Animals↗
PubMed1978

Human placental cells transformed by tsA mutants of simian virus 40: a model system for the study of placental functions.

Human placental cells were transformed with wild-type simian virus 40 (SV40) and temperature-sensitive SV40 mutants of the A and B classes. Four criteria for transformation were used: decreased generation time, increased saturation density, increased efficiency of growth on plastic, and ability to overgrow a nontransformed monolayer. Cell lines transformed by tsA mutants lost the transformed phenotype at the restrictive temperature (40 degrees); therefore, the A function of SV40 is required for the maintenance of the transformed phenotype activity, an inhibition of human chorionic gonadotropin synthesis, and an increase in thymidine kinase activity were seen when human placental cells transformed by wild-type or tsB mutants of SV40 were grown at 33 degrees or 40 degrees and when tsA transformants were grown at 33 degrees. When tsA transformants were grown at 40 degrees, alkaline phosphatase activity and human chorionic gonadotropin synthesis were greatly stimulated and thymidine kinase activity was greatly reduced, approximating their levels in the placenta.

Alkaline Phosphatase↗
PubMed2025

Naturally competent bacteria and their genetic parasites-a battle for control over horizontal gene transfer?

Host-mediated natural competence for transformation of DNA and mobile genetic element (MGE)-driven conjugation and transduction are key modes of horizontal gene transfer. While these mechanisms are traditionally believed to shape bacterial evolution by enabling the acquisition of new genetic traits, numerous studies have elucidated an antagonistic relationship between natural transformation and MGEs. A new role of natural transformation as a chromosome-curing mechanism has now been proposed. Experimental data, along with mathematical models, suggest that transformation can eliminate deleterious MGEs. Supporting this hypothesis, MGEs have been shown to use various mechanisms to decrease or block transformability, such as disrupting competence genes, regulating the development of competence, hindering DNA uptake machinery, producing DNases that target the exogenous (transforming) DNA, and causing lysis of competent cells. A few examples of synergistic relationships between natural transformation and MGEs have also been reported, with natural transformation facilitating MGE transfer and phages enhancing transformation by supplying extracellular DNA through lysis and promoting competence via kin discrimination. Given the complexity of the relationships between natural transformation and MGEs, the balance between antagonism and synergy likely depends on specific selection pressures in a given context. The evidence collected here indicates a continuous conflict over horizontal gene transfer in bacteria, with semiautonomous MGEs attempting to disrupt host-controlled DNA acquisition, while host competence mechanisms work to resist MGE interference.

Gene Transfer, Horizontal↗
PubMed2025

Dual genetic loci and flavonoid metabolism orchestrate fruiting body coloration in Flammulina filiformis: a multi-omic roadmap for fungal pigmentation.

BACKGROUND: The fruiting bodies of macrofungi exhibit diverse coloration, traditionally attributed to melanin and carotenoid biosynthesis. This study is the first to reveal that flavonoids, rather than these classical pigments, are the predominant contributors to yellow pigmentation in the Flammulina filiformis. OBJECTIVE: To uncover the genetic basis and key regulatory genes involved in pigment formation in F. filiformis fruiting bodies, and to establish a model framework for studying color genetics in macrofungi. METHODS: Metabolomic profiling was conducted on yellow and white F. filiformis fruiting bodies to identify key pigment components. A segregating population was constructed, followed by integrated multi-omics analyses-including bulk segregant analysis (BSA), genome-wide association study (GWAS), and transcriptomics-to map regulatory loci and candidate genes. Functional roles were validated via genetic transformation and protein structural modeling. RESULTS: Flavonoid accumulation was identified as the biochemical hallmark of pigmented fruiting bodies. Genetic analysis revealed a dual regulatory mechanism: a qualitative locus governing pigmentation presence and a quantitative trait determining color intensity. Combined BSA and GWAS pinpointed a major locus, Ffcrs, within a recombination-suppressed region. Transcriptomic analysis identified two key regulators, Ffakr (a transcriptional activator) and Ffpal (encoding phenylalanine ammonia-lyase). Functional verification via transformation, structural modeling, and metabolite profiling in transgenic lines confirmed their essential roles in flavonoid biosynthesis and pigmentation. CONCLUSION: This study uncovers a flavonoid-based pigmentation mechanism in F. filiformis and elucidates a complex genetic architecture shaped by both qualitative and quantitative loci, providing a new paradigm for understanding pigment formation in macrofungi. The identified regulatory factors establish a molecular foundation for the precise manipulation of economically important pigmentation traits in edible mushroom.

Flavonoids↗
PubMed2026

AI-driven diagnostic and prognostic models for metabolic dysfunction-associated steatotic liver disease: insights from clinical, imaging, and multi-omics studies-a scoping review.

Metabolic dysfunction-associated steatotic liver disease (MASLD), formerly known as non-alcoholic fatty liver disease (NAFLD), is the most common chronic liver disease around the world, affecting 33.6% of the adult population (95% CI: 28.1%-39.5%; I 2 = 99.9%), or roughly one in three. The extent of the liver damage is variable, from simple steatosis to metabolic dysfunction-associated steatohepatitis (MASH, formerly NASH), cirrhosis and hepatocellular carcinoma (HCC). Early diagnosis is essential to prevent serious liver damage. Traditional diagnostic techniques such as liver biopsy, imaging, and biomarker testing are all invasive, costly, reduced sensitive to early-stage disease, and they also have variability among observers. Modern diagnostic and prognostic approaches based on the principles of Artificial Intelligence (AI) and specifically on machine learning (ML) and deep learning (DL) have enabled multimodal approaches integrating clinical, imaging and molecular data. This scoping review conducted per PRISMA-ScR guidelines, synthesizes findings from 73 studies (search window 2020-2026) across three dimensions: clinical data driven models, imaging-based classifiers (ultrasound, CT and MRI), and multi-omics (genomics, transcriptomics and proteomics) techniques. Moreover, emergence of models such as U-Net and LiverNet 2.x, classification models like DeepLiverNet and BiLSTM models, as well as transformer frameworks and the identification of biomarkers models are also described. This study also investigates challenges such as data heterogeneity, data interpretability, fairness and real-world clinical application. Finally, important areas of research opportunities and future directions are highlighted to present a developing clinically applicable, explainable and ethical AI solutions to manage MASLD.

MASLD↗