Binarization of gene expression data is a critical prerequisite for the synthesis of Boolean gene regulatory network (GRN) models from omics datasets. In practice, thresholding methods remain the dominant approach, yet they oversimplify the underlying biology by ignoring gene-specific functional roles and failing on sparse or single-snapshot data. To overcome these limitations, we propose Bi4Back, a novel regulation-based binarization algorithm that combines thresholding with iterative forward and backward Boolean propagation guided by a known signed regulatory graph - supplied as a required input rather than inferred - and corrects inconsistencies through a dedicated detection step. Bi4Back thus infers the binary states of genes given a network, not the network itself. The algorithm operates on as few as a single steady-state measurement and infers missing or uncertain binary states in a biologically consistent manner. Validation against ODE simulations of artificial and established Boolean GRNs spanning stable equilibria, oscillatory regimes, and continuous time-series trajectories shows exact agreement with the threshold-defined ground truth on stable artificial networks, near-exact agreement (dissimilarity distance down to d=1/11, reaching exact agreement at fully converged snapshots) on established models that converge to equilibrium, and graceful, phase- and topology-dependent degradation under oscillatory dynamics. The algorithm exhibits good robustness to up to ±50% multiplicative measurement noise, with dissimilarity distances remaining close to or better than the noise-free baseline, while performance under missing data depends critically on the topological centrality of unmeasured genes-a finding that yields a clear experimental design principle: measurement completeness for hub genes outweighs precision for peripheral ones. Robustness testing over 100,000 parameter-randomized simulations confirms reliability across diverse biological conditions. Scalability analysis across networks of 10 to 100 genes confirms computation times under 2 seconds throughout. Implementations in R and Mathematica are publicly available.

The assessment of aberrant transcription events in rare disease patients holds great promise for enhancing the prioritization of causative genes-a strategy already widely adopted in clinical settings to improve diagnostic accuracy. Nevertheless, the accurate identification of causal genes remains a substantial challenge.

Mammalian placentation represents one of the most striking evolutionary innovations among vertebrates, and accumulating evidence indicates that virus-derived genes-particularly the metavirus-derived PEG10 and PEG11/RTL1-have played indispensable but distinct roles: PEG10 in the emergence of therian viviparity and PEG11/RTL1 in the subsequent differentiation between marsupial and eutherian placental types. Notably, the metavirus-derived SIRH/RTL gene group, which includes PEG10 and PEG11/RTL1, exhibits unique and diverse functions not only in placenta development but also within microglia of the brain. Because microglia originate from yolk sac progenitors, these findings suggest that extraembryonic tissues such as the placenta and yolk sac provided permissive environments that enabled the retention, expression and functional domestication of virus-derived sequences. Once the placenta itself was established through viral gene integration, it may in turn have acted as a powerful driver of eutherian evolution through recurrent acquisition and co-option of additional virus-derived genes-a process we refer to as "placenta-driven evolution." This perspective offers a unified framework in which viral gene acquisition is viewed as a key driver of genomic innovation, tightly intertwined with the emergence of viviparity, subsequent divergence at the marsupial-eutherian split, and continued diversification of placental structure and function across eutherian lineages.

The myoblast-to-adipocyte trans-differentiation model is crucial for studying the regulatory mechanisms underlying ectopic fat deposition and cell fate determination. However, the comprehensive dynamics of chromatin accessibility and interactions during this process remain largely unexplored. To address this, we performed an integrative analysis of bulk and single-cell multi-omics data (ATAC-seq, RNA-seq), and Hi-C data on an adipogenesis model in C2C12 myoblasts. Our findings revealed significant reprogramming of chromatin accessibility driven by adipogenic lineage-specific transcription factors (TFs), particularly Cebps and Stats, during trans-differentiation. Notably, 63.46% of the distal open chromatin regions with increased accessibility were shared between myogenesis and adipogenesis. Further joint analysis with Hi-C data suggests that these pre-established enhancers in myoblasts undergo a "regulatory redirection," shifting their influence from myogenic to adipogenic genes-a phenomenon we termed "enhancer snatch." This model was validated by knocking out a "snatched" enhancer (Enhancer-R/L), which was found to be a critical regulator of both Rbl1 and Lbp expression. Overall, our study uncovers a mechanism that pre-established enhancers in original cell lineage are predominantly utilized by lineage-specific TFs during chromatin reprogramming, thereby altering cell's differentiation trajectory.

The tephritid stem gall fly, Procecidochares utilis Stone (Diptera: Trypetidae), serves as an effective biocontrol agent against the invasive plant Eupatorium adenophorum (syn. Ageratina adenophorum) by inducing galls through larval saliva secretions, thereby inhibiting the growth of E. adenophorum. Despite this, the genetic basis of gall induction by P. utilis remains unexplored. This study generated a chromosome-level genome of P. utilis, totaling 467.64 Mb with a scaffold N50 of 74.29 Mb, organized into six pseudochromosomes. Comparative genomic analysis revealed a significant expansion of apolipoprotein D (ApoD) genes-a novel finding among gall-forming insects. Salivary gland transcriptomics identified 124 putative secreted proteins, with ApoD expansions exhibiting predominant expression. Among 29 identified ApoD genes in the P. utilis genome, 24 formed a species-specific clade, predominantly expressed in larvae and salivary glands. Notably, 21 of these genes were associated with salivary gland secretion. PuApoD311, uniquely expressed in P. utilis larvae and salivary glands, was successfully recombinantly produced in Sf9 cells using the baculovirus system. Injection of recombinant PuApoD311 into E. adenophorum resulted in the formation of "gall-like structures, characterized by analogous lateral root proliferation" structures, and elevated zeatin levels, indicating its pivotal role in gall formation. These findings contribute to our comprehension of salivary gland protein evolution in P. utilis and the molecular mechanisms governing gall induction by this biocontrol agent.

Bacterial membrane vesicles (MVs) are critical mediators of virulence factor delivery and intercellular communication, yet the mechanisms by which hosts detect and respond to these vesicles remain poorly characterized. Through transcriptional profiling, we found that MVs derived from the non-lethal pathogenic Erwinia carotovora carotovora 15 (Ecc15) robustly induce reactive oxygen species (ROS) production and systemically upregulate Jon genes-a family of immune-related genes-in the Drosophila intestine 24 h post-infection. Strikingly, these effects contrast with transcriptional changes observed upon gut-specific overexpression of CRTC, the coactivator of the conserved transcription factor cAMP response element-binding protein (CREB). Intriguingly, ingestion of OMVs from Ecc15 or from the Gram-positive bacterium Lactobacillus plantarum (L.plantarum) significantly suppresses CREB activity in enterocytes (ECs). Fractionation experiments revealed that proteinaceous components within bacterial MVs inhibited CREB activity by reducing apical Ca2+ levels in ECs. Mechanistically, the CRTC/CREB cascade promoted gut microbial load by transcriptionally repressing PGRP-SC2-dependent amidase activity, a pathway independent of the canonical Relish/Imd signaling axis. Furthermore, OMVs from E. coli (BL21) also potently suppressed expression of pro-inflammatory factors, such as IL-6 and CXCL10 in NIH3T3 by blocking the activity of CREB. Collectively, these findings demonstrated that CREB play a conserved role on sense bacterial MVs and trigger anti-infection defenses in both Drosophila and mammalian systems, unveiling a novel paradigm in host-microbe communication.

Infections caused by Staphylococcus aureus (S. aureus) in patients undergoing mastectomy followed by breast reconstruction present significant therapeutic challenges. Studies suggest that S. aureus may be transmitted from nasal carriage, potentially leading to postoperative infections. However, knowledge regarding the potential pathogenicity of S. aureus nasal carriage strains in women undergoing breast reconstruction in Poland remains limited. This study aimed to characterize S. aureus isolates obtained from screening nasal swabs.

Although it is generally believed that large DNA viruses capture genes by horizontal gene transfer (HGT), the detailed manner of such transfer has not been fully elucidated. Here, we searched for genes in the coleopteran entomopoxvirus (EV) Anomala cuprea entomopoxvirus (ACEV) that might have been gained by ACEV by HGT. We classified the potential source organisms for HGT into three categories: the host A. cuprea; other organisms, including viruses unrelated to EVs; and organisms with uncertain host attribution. Of the open reading frames (ORFs) of the ACEV genome, 2.1 % were suggested to have been gained from the host by ACEV or its recent ancestor via HGT; 8.7 % were possibly from organisms other than the host, and 3.7 % were possibly from the third category of organisms via HGT. The analysis showed that ACEV contains some interesting ORFs obtained by HGT, including a large ATP-binding cassette protein (ABC transporter) ORF and a tenascin ORF (IDs ACV025 and ACV123, respectively). We then performed a detailed analysis of the HGT of the ACEV large ABC transporter ORF-the largest of the ACEV ORFs. mRNA sequences obtained by RNA-seq from fat bodies-sites of ACEV replication-and midgut tissues-sites of initial infection-of the virus's host A. cuprea larvae were subjected to BLAST analysis. One type of ABC transporter ORF from the fat bodies and two types from the midgut tissues, one of which was identical to that in the fat bodies, had the greatest identity to the ABC transporter ORF of ACEV. The two types from the host had high levels of identity to each other (approximately 95 % nucleotide sequence identity), strongly suggesting that the host ABC transporter group consisting of the two types was the origin of ACV025. We then determined the sequence (12,381 bp) containing a full-length gene of the A. cuprea ABC transporter. It turned out to be a transcription template for the abovementioned mRNA found in both tissues. In addition, we determined a large part (ca. 6.9 kb) of the template sequence for the mRNA found only in the midgut tissues. The results showed that the ACEV ABC transporter ORF is missing parts corresponding to introns of the host ABC transporter genes, indicating that the ORF was likely acquired by HGT in the form of mRNA. The presence of definite duplicated sequences adjacent to the ACEV ABC transporter genes-a sign of LINE-1 retrotransposon-mediated HGT-was not observed. An approximately 2-month ACV025 transcription experiment suggested that the transporter sequence is presumed to be continuously functional. The amino acid sequence of ACV025 suggests that its product might function in the regulation of phosphatide in the host-cell membranes.

Purpose: Breastfeeding is associated with numerous short- and long-term neonatal and maternal health benefits. Specifically, in BRCA1/2 female carriers, breastfeeding has been shown to reduce the considerably increased risks of breast and ovarian cancer. Nevertheless, there is paucity of data referring to the recommended postpartum surveillance of BRCA1/2 carriers. The purpose of this study was to evaluate the recommendations of health professionals regarding breastfeeding in BRCA carriers. Methods: This cross-sectional survey was conducted using an anonymous questionnaire distributed through the "Good BRCA Genes-a support and information group for BRCA carriers" association. The questionnaire included Likert scale and open-ended questions, aimed to evaluate the performance of health professionals at various aspects of the recommended follow-up. Results: Of the 388 participants, 233 (60.0%) expressed dissatisfaction with explanations provided by health professionals regarding pregnancy and breastfeeding. Women reporting dissatisfaction with explanations were younger (36.8 ± 7.0 years) compared to those satisfied with the explanations (38.8 ± 7.6 years, p = 0.0081). No significant differences were noted between women satisfied and those dissatisfied with the explanations in terms of age of genetic diagnosis, origin, religion, geographic location, and the rates of personal or familial cancer history. Of the 175 responses to an open question "please describe the reasons for unsatisfactory explanation," 76.6% stated they received no explanation on the subject, whereas 5.4% described minimal explanation or conflicting recommendations. Surprisingly, 4.7% recalled being advised to avoid, stop, or limit breastfeeding. Discussion: The results of this survey emphasize the lack of knowledge of health professionals on the issue of breastfeeding in BRCA carriers. As genetic variants in these genes involve significant proportion of the population (up to 2.5% in Ashkenazi Jewish population), raising the awareness of health care personnel to the benefits of breastfeeding in these women seems prudent.

The article presents the latest data on pathological changes after cerebral ischemia caused by cardiac arrest. The data include amyloid accumulation, tau protein modification, neurodegenerative and cognitive changes, and gene and protein changes associated with Alzheimer's disease. We present the latest data on the dysregulation of genes related to the metabolism of the amyloid protein precursor, tau protein, autophagy, mitophagy, apoptosis, and amyloid and tau protein transport genes. We report that neuronal death after cerebral ischemia due to cardiac arrest may be dependent and independent of caspase. Moreover, neuronal death dependent on amyloid and modified tau protein has been demonstrated. Finally, the results clearly indicate that changes in the expression of the presented genes play an important role in acute and secondary brain damage and the development of post-ischemic brain neurodegeneration with the Alzheimer's disease phenotype. The data indicate that the above genes may be a potential therapeutic target for brain therapy after ischemia due to cardiac arrest. Overall, the studies show that the genes studied represent attractive targets for the development of new therapies to minimize ischemic brain injury and neurological dysfunction. Additionally, amyloid-related genes expression and tau protein gene modification after cerebral ischemia due to cardiac arrest are useful in identifying ischemic mechanisms associated with Alzheimer's disease. Cardiac arrest illustrates the progressive, time- and area-specific development of neuropathology in the brain with the expression of genes responsible for the processing of amyloid protein precursor and the occurrence of tau protein and symptoms of dementia such as those occurring in patients with Alzheimer's disease. By carefully examining the common genetic processes involved in these two diseases, these data may help unravel phenomena associated with the development of Alzheimer's disease and neurodegeneration after cerebral ischemia and may lead future research on Alzheimer's disease or cerebral ischemia in new directions.

The patient reported here underwent hematopoietic stem cell transplantation (HSCT) due to chronic granulomatous disease (CGD) caused by biallelic mutations of the NCF1 gene. Two years later, he developed AML, which was unexpected and was recognized via sex-mismatched chromosomes as deriving from the donor cells; the patient was male, and the donor was his sister. Donor cell leukemia (DCL) is very rare, and it had never been reported in patients with CGD after HSCT. In the subsequent ten years, the AML relapsed three times and the patient underwent chemotherapy and three further HSCTs; donors were the same sister from the first HSCT, an unrelated donor, and his mother. The patient died during the third relapse. The DCL was characterized since onset by an acquired translocation between chromosomes 9 and 11, with a molecular rearrangement between the MLL and MLLT3 genes-a quite frequent cause of AML. In all of the relapses, the malignant clone had XX sex chromosomes and this rearrangement, thus indicating that it was always the original clone derived from the transplanted sister's cells. It exhibited the ability to remain quiescent in the BM during repeated chemotherapy courses, remission periods and HSCT. The leukemic clone then acquired different additional anomalies during the ten years of follow-up, with cytogenetic results characterized both by anomalies frequent in AML and by different, non-recurrent changes. This type of cytogenetic course is uncommon in AML.

The Open Genes database was created to enhance and simplify the search for potential aging therapy targets. We collected data on 2402 genes associated with aging and developed convenient tools for searching and comparing gene features. A comprehensive description of genes has been provided, including lifespan-extending interventions, age-related changes, longevity associations, gene evolution, associations with diseases and hallmarks of aging, and functions of gene products. For each experiment, we presented the necessary structured data for evaluating the experiment's quality and interpreting the study's findings. Our goal was to stay objective and precise while connecting a particular gene to human aging. We distinguished six types of studies and 12 criteria for adding genes to our database. Genes were classified according to the confidence level of the link between the gene and aging. All the data collected in a database are provided both by an API and a user interface. The database is publicly available on a website at https://open-genes.org/.

Nematomorpha (hairworms) is a phylum of parasitic ecdysozoans, best known for infecting arthropods and guiding their hosts toward water, where the parasite can complete its life cycle. Over 350 species of nematomorphs have been described, yet molecular data for the group remain scarce. The few available mitochondrial genomes of nematomorphs are enriched with long inverted repeats, which are embedded in the coding sequences of their genes-a remarkably unusual feature exclusive to this phylum. Here, we obtain and annotate the repeats in the mitochondrial genome of another nematomorph species-Parachordodes pustulosus. Using genomic and transcriptomic libraries, we investigate the impact of inverted repeats on the read coverage of the mitochondrial genome. Pronounced drops in the read coverage coincide with regions containing long inverted repeats, denoting the 'blind spots' of short-fragment sequencing libraries. Phylogenetic inference with the novel data reveals multiple disagreements between the traditional system of Nematomorpha and molecular data, rendering several genera paraphyletic, including Parachordodes.

A Lactobacillus delbrueckii ssp. lactis strain named A4, isolated from the gut of an Armenian honeybee, was subjected to a probiogenomic characterization because of its unusual origin. A whole-genome sequencing was performed, and the bioinformatic analysis of its genome revealed a reduction in the genome size and the number of the genes-a process typical for the adaptation to endosymbiotic conditions. Further analysis of the genome revealed that Lactobacillus delbrueckii ssp. lactis strain named A4 could play the role of a probiotic endosymbiont because of the presence of intact genetic sequences determining antioxidant properties, exopolysaccharides synthesis, adhesion properties, and biofilm formation, as well as an antagonistic activity against some pathogens which is not due to pH or bacteriocins production. Additionally, the genomic analysis revealed significant potential for stress tolerance, such as extreme pH, osmotic stress, and high temperature. To our knowledge, this is the first report of a potentially endosymbiotic Lactobacillus delbrueckii ssp. lactis strain adapted to and playing beneficial roles for its host.

The need for sensitive monitoring of minimal/measurable residual disease (MRD) in multiple myeloma emerged as novel therapies led to deeper responses. Moreover, the potential benefits of blood-based analyses, the so-called liquid biopsy is prompting more and more studies to assess its feasibility. Considering these recent demands, we aimed to optimize a highly sensitive molecular system based on the rearranged immunoglobulin (Ig) genes to monitor MRD from peripheral blood. We analyzed a small group of myeloma patients with the high-risk t(4;14) translocation, using next-generation sequencing of Ig genes and droplet digital PCR of patient-specific Ig heavy chain (IgH) sequences. Moreover, well established monitoring methods such as multiparametric flow cytometry and RT-qPCR of the fusion transcript IgH::MMSET (IgH and multiple myeloma SET domain-containing protein) were utilized to evaluate the feasibility of these novel molecular tools. Serum measurements of M-protein and free light chains together with the clinical assessment by the treating physician served as routine clinical data. We found significant correlation between our molecular data and clinical parameters, using Spearman correlations. While the comparisons of the Ig-based methods and the other monitoring methods (flow cytometry, qPCR) were not statistically evaluable, we found common trends in their target detection. Regarding longitudinal disease monitoring, the applied methods yielded complementary information thus increasing the reliability of MRD evaluation. We also detected indications of early relapse before clinical signs, although this implication needs further verification in a larger patient cohort.