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Satellite DNAs in Drosophila koepferae (repleta group) reveal patterns of origin, chromosomal organization, transcription, and turnover in the buzzatii cluster.

Satellite DNAs (satDNAs) are non-coding tandem repeats that can comprise more than 20% of eukaryotic genomes. They contribute to structural and regulatory processes in the genome and often evolve rapidly, shaping early stages of genetic differentiation between populations and species. Although Drosophila has long served as a model for studying satDNA biology, little is known about satDNAs in non-model Drosophila species, particularly within the repleta group, one of the most species-rich lineages in the genus. To reduce such bias, several studies have focused on the buzzatii cluster (repleta group). However, D. koepferae remained the only species lacking comprehensive satDNA data, limiting comparative analyses. Here, we used publicly available genomic sequencing data from two D. koepferae populations (Argentina and Bolivia) to characterize their satDNA content. Both populations share the same set of five satDNAs (CDSTR8, CDSTR138, CDSTR230, DBC-150 and CDSTR177), which together account for ~ 0,9% of the genomic DNA. We show that CDSTR177 originated through amplification of an internal segment of the Galileo transposable element, an event restricted to D. koepferae. All satDNAs localize to heterochromatic regions, with CDSTR138 most likely associated to the centromeres of most chromosomes. Transcripts from all satDNAs were detected, although at low levels. Our results provide new insights into the origin, genomic contribution, expression and evolution of satDNAs in the buzzatii cluster, support incipient differentiation between Argentinean and Bolivian populations of D. koepferae and contribute to clarifying the phylogenetic position of this species within the buzzatii cluster.

Animals↗

Urban stormwater infrastructure as a microplastic superhighway: a critical review of transport dynamics, modelling, and mitigation across pavements and drainage networks.

This review examines the transport, fate, modelling, and mitigation of Microplastics (MPs) in urban stormwater infrastructure, with emphasis on pavements, runoff pathways, micro-drainage, and macro-drainage systems. Following a systematic review approach, more than 1000 records were screened and approximately 50 core studies were retained when they addressed urban stormwater or drainage-related MP transport with adequate methodological reporting; marine-only studies and biological-effect studies without direct relevance to transport processes were excluded. The evidence shows that stormwater systems function not merely as passive conduits but as dynamic reactive transport systems with temporary storage, where particle mobilisation, sedimentation, resuspension, and temporary retention regulate MP export. Road surfaces, especially high-traffic areas, are major reservoirs of tyre wear, road-marking, atmospheric, and litter-derived particles that are rapidly mobilised during rainfall. Conventional grab sampling may underestimate MP loads, which in some cases exceed treated wastewater effluent loads by up to six-fold. Drainage structures such as manholes can immobilise up to 17.3% of near-neutrally buoyant particles, while biofouling and aggregation may shift buoyant polymers from wash-load to bedload. Mitigation systems, including permeable pavements, bioretention, wetlands, and technical inserts, can achieve high removal of coarse MPs, but performance declines for fine particles below 100 µm. The review highlights the need for standardised flow-proportional sampling, physically informed modelling, and treatment-train strategies targeting both surface sources and in-network storage.

Microplastics↗

Signal recognition particle 14 binds to importin α in Plasmodium falciparum.

BACKGROUND: The eukaryotic signal recognition particle (SRP) consists of six proteins and one SRP RNA. This ribonucleoprotein complex assembles inside the nucleus. Nucleocytoplasmic transport is an essential process for the biogenesis of signal recognition particles (SRPs) as well as for the survival of a cell. There are studies on cells that indicate the import receptor is responsible for import of SRP proteins into nucleus, but there is a lack of evidence that SRP proteins directly bind with import receptors. METHODS AND RESULTS: Coding sequences of SRP 14 and importin α were amplified from synthesized cDNA and genomic DNA, respectively, of Plasmodium falciparum cultivated in vitro culture. The amplified products were cloned and expressed in E. coli, followed by purification. A binding study was conducted on glutathione-agarose as well as in a 96-well plate format at different concentrations of SRP 14 with immobilized importin α. CONCLUSION: This is the first report of direct binding between importin α and a eukaryotic signal recognition particle 14 (SRP 14). A cost-effective 96-well plate-based assay has also been developed to study the binding of cargoes of importin α.

Plasmodium falciparum↗

Saliva-based RT-LAMP assays support heat shock protein 70 as a promising transcript marker for estrus identification in buffaloes.

Buffaloes do not exhibit overt estrus signs particularly during summer, leading to a significant economic loss to farmers. Previous studies have identified several candidate transcripts (HSP70, TIMP1, TLR4 and HSD17B1), abundant in buffalo saliva during estrus stage. However, there is no widely applicable technology for estrus detection targeting these transcripts. Therefore, the present study aimed to develop reverse transcription loop mediated isothermal amplification (RT-LAMP) assays for these candidate transcripts using buffalo saliva. Saliva samples were collected from 10 cyclic buffaloes and RT-LAMP assays were optimized for salivary RNA as well as direct saliva. Among the four candidate transcripts, HSP70 showed a statistically significant colour change (p-value = 0.0191) at the estrus stage compared to the diestrus stage. This abundance of HSP70 was also supported in large simulated population datasets (10,000 animals) generated using R. Further, the RT-LAMP assays were tested using direct saliva without RNA isolation, and the colour change in the samples during estrus suggested the feasibility of estrus identification using direct saliva, overcoming the tedious step of RNA isolation. The detection of HSP70 using either direct saliva or salivary RNA indicated its potential as a marker for estrus identification. Similarly, TLR4 appeared to be another potential biomarker for RT-LAMP reaction using direct saliva, but it needs further validation in both RNA and direct saliva samples. Overall, the proof-of-concept on RT-LAMP assays optimized for salivary transcripts in the present study would be useful for estrus identification in tropical production systems following further validation on a larger sample size.

Animals↗

APOL1 kidney disease: a critical narrative review of molecular mechanisms, clinical heterogeneity, and the emerging therapeutic landscape.

BACKGROUND: The G1 and G2 variants of the APOL1 gene represent significant genetic risk factors for APOL1 kidney disease and contribute substantially to the excess burden of renal disease observed in individuals of African ancestry. Importantly, both variants exhibit incomplete penetrance, with only approximately 15-20% of high-risk genotype carriers ultimately developing overt nephropathy. OBJECTIVE: To provide a critically appraised, clinically oriented narrative synthesis of APOL1 kidney disease that (i) assigns an explicit certainty rating to each major mechanistic and clinical claim, (ii) identifies where published estimates diverge, where associations remain contested, and where conclusions have been overstated in the secondary literature, and (iii) aligns terminology, testing guidance and therapeutic expectations with the conclusions of the 2025 KDIGO Controversies Conference and with clinical trial data available to August 2026. METHODS: This literature narrative review was performed using a literature search of PubMed and Scopus focusing on APOL1-related nephropathy. Mainly studies published from 2010 to 2026 were considered; however, some selected historical papers from 2005 to 2010 were used for better understanding of the underlying mechanisms and history. Used search terms were "APOL1," "APOL1 risk variants," "chronic kidney disease," AMPLITUDE trial, MZE829, HORIZON trial, "focal segmental glomerulosclerosis," "HIV-associated nephropathy," "podocyte injury," "inaxaplin," "VX-147," KDIGO 2025, and "antisense oligonucleotides." Trial status and topline results for agents in development were additionally verified against ClinicalTrials.gov registrations and sponsor disclosures. The literature search was last updated on 10 August 2026. The inclusion criteria of the study were peer-reviewed original articles, genome-wide association studies, randomised controlled trials, translational studies, mechanistic investigations, and high-quality review articles published in the English language. Exclusion criteria included conference abstracts without peer review, duplicate papers, non-English publications with unreliable translation, and case reports with no relevance to the underlying mechanisms. More attention was paid to studies focusing on molecular pathogenesis of APOL1 nephropathy, second-hit pathophysiology, genotypes/phenotypes, and new therapies (e.g. inhibitors such as Inaxaplin). The review method and design have been prepared according to SANRA (Scale for the Assessment of Narrative Review Articles) criteria. Among eligible articles, priority was given to studies with larger sample sizes, more recent publication dates, higher-impact peer-reviewed journals, and direct clinical or mechanistic relevance to APOL1-associated nephropathy; where multiple studies addressed the same question, the most methodologically rigorous and most recent source was preferentially cited. To move beyond description, each principal claim carried forward into this review was assigned a qualitative certainty rating (high, moderate, low or very low) on the basis of study design, consistency across independent cohorts, directness of the evidence to human disease, and precision of the estimate. These ratings, together with the study design that would be required to resolve each remaining uncertainty, are presented in Table 5. This grading represents a structured judgement by the authors and is not a formal GRADE assessment. RESULTS: Pathogenic actions of APOL1 risk alleles depend on toxic gain-of-function activities that result from the disruption of ion channels. Mitochondrial dysfunction, endoplasmic reticulum stress, and inflammasome activation play roles as secondary downstream modulators of podocyte damage. The existence of incomplete penetrance and lack of symptoms in people with high-risk alleles highlights the need for secondary triggers, including environmental, infectious, and inflammatory factors, for disease onset and progression. High-risk APOL1 genotypes increase the likelihood of rapidly progressing kidney diseases like FSGS, which amplify susceptibility in HIVAN when accompanied by secondary causes like HIV infection. Management is mainly through renin-angiotensin antagonists, but recent treatments include antisense oligonucleotides, immunomodulators, and small molecule inhibitors like inaxaplin. Although promising, inaxaplin (VX-147) showed a ~47% reduction in urine protein/creatinine ratio (UPCR) in Phase 2a trial; however, these findings are based on a relatively small sample size, an open-label study design, and short-term follow-up, and therefore require confirmation in ongoing Phase 3 studies. As this is a narrative review rather than a primary study, no new patient-level data are reported. Across the studies synthesised, high-risk APOL1 genotypes were consistently associated with podocyte injury and with a faster decline in kidney function than low-risk genotypes; however, the magnitude of this association varied substantially with how cohorts were ascertained. The association is robust and reproducible for focal segmental glomerulosclerosis, HIV-associated nephropathy, and hypertension-attributed kidney failure, and remains inconsistent for diabetic kidney disease. Therapeutic development has accelerated, but the supporting clinical evidence remains early phase. Inaxaplin (VX-147) reduced the urine protein-to-creatinine ratio by approximately 47.6% at week 13 in a 16-participant, single-group, open-label Phase 2a study, and is now being evaluated in the randomised, double-blind, placebo-controlled Phase 2/3 AMPLITUDE trial (NCT05312879), whose pre-specified week 48 interim analysis is anticipated in early 2027. MZE829, an orally administered APOL1 inhibitor, produced a mean 35.6% reduction in the urine albumin-to-creatinine ratio at 12 weeks in the Phase 2 HORIZON study; because HORIZON was a small, open-label, single-arm basket study (15 participants enrolled, 12 evaluable) whose primary endpoints were safety and tolerability, this reduction is neither placebo adjusted nor the result of a formal test of efficacy. To date, no APOL1-targeted agent has demonstrated benefit on a hard kidney endpoint. CONCLUSION: APOL1 is the clearest current example of a genetically defined, mechanism-targetable kidney disease, but its evidence base is uneven. The genetic association is firmly established; whereas much of the mechanistic literature derives from overexpression systems, several downstream pathways remain contested, and every APOL1-targeted therapy is so far supported only by short-term, surrogate-endpoint data. The principal unresolved issues are the determinants of incomplete penetrance, the absence of a validated progression biomarker and of any model reproducing the common slowly progressive phenotype, and the long-term efficacy and safety of APOL1-directed therapy. Genotype-guided risk stratification is therefore best regarded as clinically reasonable but not yet proven, and routine population-level screening is not currently supported.

AMPLITUDE trial↗

Multi-omics analysis reveals Protein Kinase A-associated regulatory remodeling during adaptation of Trichoderma reesei to lignocellulosic substrate.

The filamentous fungus Trichoderma reesei is a major industrial source of holocellulolytic enzymes, and its response to complex carbon sources is regulated by nutrient-sensing mechanisms, including the cyclic adenosine monophosphate (cAMP)-protein kinase A (PKA) signaling pathway. Here, we integrated transcriptomics, quantitative proteomics, and phosphoproteomics to analyze PKAc1-associated responses in the parental strain QM9414 and a Δpkac1 strain cultivated under glucose or sugarcane bagasse conditions. Deletion of pkac1 was associated with altered growth-related phenotypes and reduced extracellular activities of selected biomass-depolymerizing enzymes. Multi-omics profiling revealed condition-dependent changes affecting subsets of carbohydrate-active enzymes (CAZymes) genes and proteins, nutrient transporters, stress-associated proteins, and regulatory factors. Phosphoproteomics identified phosphorylation-state changes associated with pkac1 deletion, including reduced phosphorylation at sites enriched for the PKA consensus motif. In silico peptide docking was used to prioritize candidate PKAc1-associated substrates for future validation, including a Sec 7-derived peptide with favorable docking behavior relative to the control peptide. Together, these data support a working model in which PKAc1 contributes to regulatory and phosphorylation-state remodeling during adaptation to sugarcane bagasse, with effects on the magnitude and/or timing of selected CAZyme-related outputs in T. reesei.

Trichoderma↗

Recombinant bovine chymosin expression in microalgae Chlamydomonas reinhardtii chloroplast: A step towards algal biomanufacturing of dairy enzymes.

Chymosin is the major proteolytic enzyme for cheese manufacture, where it plays an important role in the co-precipitation of milk casein. Traditional extraction of chymosin from the abomasum of young ruminants is associated with high limitations, including low yield, high production cost, and ethical issues of animal slaughter. In this study, we report on a recombinant strategy towards the production of bioactive Bos taurus chymosin in the chloroplasts of the microalga Chlamydomonas reinhardtii. The cym gene encoding preprocymosin was inserted into the chloroplast genome by the glass bead-mediated DNA transformation procedure. Successful integration and expression of the transgene were confirmed by spot test analysis, polymerase chain reaction (PCR), western blot, and enzyme-linked immunosorbent assay (ELISA). The functional activities of the recombinant enzyme were checked by the standard milk clotting assay. The engineered microalgal strains produced chymosin with an average concentration of 90 mg/kg fresh weight, i.e., 1.6% of the total soluble protein. These results show that chloroplast-engineered C. reinhardtii is a promising, sustainable, and animal-free platform for the efficient production of the industrially relevant chymosin.

Animals↗

Safety profiles of CAR-T cell therapy in systematic autoimmune diseases: a systematic review and analysis.

BACKGROUND: Chimeric antigen receptors (CARs)-T cell therapy is emerging as a potent approach for autoimmune diseases. However, its application in autoimmune conditions remains limited, and safety outcomes observed in malignancies can't reliably serve as a reference. Therefore, it's necessary to summarize the safety profiles in autoimmune diseases to provide evidence for future expanding trials. METHODS: A systematic review was conducted to analyze the CAR-T therapy safety in rheumatic diseases via database searches up to December 2025. Studies reporting safety data were included, while abstracts, reviews, and cases with malignancies were excluded. Factors associated with cytokine release syndrome (CRS) were analyzed using Firth's penalized logistic regression. RESULTS: This study included 38 studies, involving a total of 115 patients with autoimmune disease. Severe adverse events were rare. CRS and immune effector cell-associated neurotoxicity syndrome (ICANS) occurred in 70.4% and 4.3% of patients, respectively. Most CRS were low-grade. Multivariate analysis identified BCMA-targeted therapy and allogeneic CAR-T products may as independent factors associated with a reduced risk of CRS. Transient hematologic toxicity and hypogammaglobulinemia were frequently reported, with infections occurring in nearly half of the patients. However, prolonged cytopenia and severe infection were infrequent. CONCLUSION: Based on the current available evidence, CAR-T therapy appears to have a generally manageable safety profile in autoimmune diseases, supporting its potential as a promising treatment option for patients with relapsed or refractory autoimmune diseases. However, these findings remain preliminary, and further expanded studies are warranted in the future to provide higher-level evidence.

Humans↗

Genome-wide characterization of the tomato PERK gene family and its expression profiling under abiotic stresses.

UNLABELLED: This study presents the first systematic genome-wide characterization of the proline-rich extensin-like receptor kinases (PERK) gene family in tomato (Solanum lycopersicum) and their transcriptional responses under abiotic stresses. Using the latest SL4.0/ITAG4.0 genome assembly, we identified six SlPERK genes, all harboring the conserved Ser/Thr protein kinase domain. Evolutionary and structural analyses revealed strong purifying selection (Ka/Ks&#x2009;<&#x2009;1), distinct exon-intron organizations, and the presence of stress- and hormone-responsive cis-regulatory elements in their promoters. Furthermore, post-transcriptional regulation by 57 miRNAs and complex protein-protein interaction networks were predicted. To validate their stress-responsive roles, two tomato cultivars (GMOTL-1 and Roma) were subjected to cold, heat, and salinity treatments. Quantitative RT-PCR analysis revealed cultivar-specific expression dynamics: SlPERK4 exhibited strong transient induction under cold and heat stress, while SlPERK6 was highly responsive to salinity. Notably, the GMOTL-1 cultivar displayed significantly higher and broader stress-responsive expression profiles compared to Roma, indicating a potential role of these SlPERK genes in cultivar-specific stress tolerance. These findings provide a comprehensive genomic resource and establish a critical foundation for the functional validation and molecular breeding for stress-resilience tomato cultivars. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s13205-026-05044-y.

Abiotic stress↗

Modeling meningioma in vitro in the omics era.

Meningioma biology has been substantially clarified by recent omics-based studies, which have identified recurrent mutations, copy-number alterations, and distinct molecular subgroups. However, although these approaches have provided a valuable framework, they are inherently limited in their ability to establish direct causal relationships. The mechanistic studies are therefore indispensable for translating these molecular observations into biological understanding. Nevertheless, the mechanistic literature has often evolved in a fragmented manner, with individual pathways and model systems studied in relative isolation from the broader multi-omic landscape. In this review, we synthesize these complementary bodies of work into an integrated framework and outline a clear roadmap for future studies. We first review the historical development of established meningioma cell lines, their current molecular characterization, and the recent emergence of 3D models and organoids. Intrinsic challenges in modeling meningioma in vitro are discussed, including the difficulty of establishing immortalized cell lines from predominantly benign tumors, genetic alterations introduced during immortalization, and drift under culture conditions that differ substantially from those of the parental tumors. Next, insights from functional studies centered on these models are integrated within the molecular framework established by large-scale omics analyses. To avoid fragmentation and overemphasis on isolated findings, prior studies are organized into six categories based on major signaling pathways: Hippo, PI3K/Akt/mTOR, MAPK, Wnt/&#x3b2;-catenin, FOXM1, and Notch. Finally, lessons from other cancer models, including experimental approaches to chromosome-scale genomic disturbances, are considered to provide a more integrated view of meningioma biology and to highlight directions for future research.

Meningioma↗

Prevalence and pattern of psychological symptoms in form of dental fear and anxiety in children and adolescents with traumatic dental injuries: a systematic review.

BACKGROUND/AIMS: This systematic review aimed to evaluate the level and pattern of dental fear and anxiety (DFA) amongst children and adolescents with traumatic dental injuries (TDI) and, where available, to compare these outcomes with non-traumatised controls. METHODS: An a priori protocol was developed and registered in PROSPERO (CRD420261329946). A comprehensive literature search was conducted in PubMed, EMBASE, Web of Science, and Scopus on 3 March 2026, with additional grey literature, citation, and reference searching. No language or time restrictions were applied. Observational clinical studies assessing DFA in individuals with TDI using validated tools were included. Two reviewers independently screened studies, extracted data, and assessed risk of bias using the Joanna Briggs Institute checklist. Certainty of evidence was evaluated using the GRADE approach. RESULTS: A total of 2885 records were identified, of which 4 cross-sectional studies met the inclusion criteria after screening. Studies were conducted in Croatia and Kosovo and included paediatric populations. Sample sizes ranged from 147 to 505 participants. Different validated scales (CFSS-DS, CDAS, S-DAI) were used to assess DFA. Overall, children with TDI demonstrated predominantly low levels of dental fear and anxiety across assessment tools. However, findings were inconsistent, with some studies reporting lower or similar anxiety levels in TDI patients compared to controls. Risk of bias was moderate or high in three of the four studies, and the overall certainty of evidence was rated as low to very low due to methodological limitations, heterogeneity, and imprecision. CONCLUSION: The limited available evidence suggests that children and adolescents with TDI do not consistently present with higher levels of dental fear and anxiety than non-traumatised controls. These findings indicate that TDI does not inherently cause DFA, underscoring the critical role of empathetic behaviour support in mitigating post-traumatic dental fear. However, the evidence is based on a small number of regionally concentrated cross-sectional studies with low to very low certainty. Future prospective studies using standardised TDI classifications, validated DFA instruments, and clearly defined assessment time points are needed.

Dental anxiety↗

Hope is linked with more favorable tumor molecular signatures in serous ovarian cancer.

INTRODUCTION: Hope has been associated with improved quality of life and lower mortality in cancer, but the underlying biological mechanisms are poorly characterized. We previously reported that hope was associated with less inflammation and more normalized diurnal cortisol pre-treatment among women with ovarian cancer. We also reported associations of socio-environmental factors with pro-metastatic processes. Here, we used genome-wide transcriptional profiling to quantify associations between hope and tumor molecular signatures reflecting invasiveness, inflammation, and cellular immunity. METHOD: Participants were 74 women with serous ovarian cancer who provided demographic information and completed surveys pre-surgery. Hope was assessed using a face-valid item from the Center for Epidemiological Studies Depression Scale (CES-D). Depression was assessed using the full CES-D without the hope item. Illumina HT12 microarrays were used to assay tumor RNA, and associations between hope and tumor gene expression were quantified, adjusting for depression, age, BMI, grade, and stage. RESULTS: Adjusting for covariates, hope was associated with multiple favorable differences in RNA expression, including lower levels of mesenchymal differentiation (p&#x202f;=&#x202f;0.008) and pro-inflammatory gene regulation (NF-&#x3ba;B: p&#x202f;<&#x202f;0.001; IRF1: p&#x202f;=&#x202f;0.024; STAT: p&#x202f;=&#x202f;0.018), elevated epithelial differentiation (p&#x202f;=&#x202f;0.011), and elevated activity of the IRF7 transcription factor which promotes cellular immunity (p&#x202f;=&#x202f;0.016). CONCLUSIONS: These data suggest that hope is associated with an ovarian tumor gene expression profile characterized by reduced epithelial-mesenchymal transition (EMT) and inflammatory activity, and increased activity of a transcription factor promoting cellular immunity. These findings highlight potential biological implications of a resilience factor such as hope, but need replication with more robust assessments of hope.

Epithelial mesenchymal transition↗

Robust error-minimization in the genetic code across physicochemical metrics and variant codes: A graph-theoretic analysis in GF(2)6.

The standard genetic code reduces the impact of point mutations, but the robustness of this property across physicochemical metrics, naturally occurring variant codes, and codon-reassignment mechanisms remains incompletely quantified. Embedding the 64 codons in GF(2)6 represents the hypercube Q6 as a coordinate-dependent subgraph of the encoding-independent single-nucleotide mutation graph H(3,4), and enables continuous &#x3c1;-interpolation between the two. Under a quartet-pattern shuffle null (n=10,000), the standard code is significantly low-cost across four established, code-independent physicochemical distance metrics with partially overlapping content (Grant ham p=0.0062; Miyata p<0.001; Woese polar requirement p=0.003; Kyte-Doolittle hydropathy p=0.001), and the signal strengthens monotonically as &#x3c1; moves Q6&#x2192;H(3,4). A structure-aware sensitivity analysis under the alignment-derived ProtSub matrix (Jia & Jernigan 2021) yields the most extreme percentile of any measure tested (p=0.0004; all five p-values pass Bonferroni at &#x3b1;=0.05). Across the 27 NCBI translation tables, near-optimality is preserved: 11 of 12 informative-distance variants retain top-5% placement after BH-FDR correction. Natural codon reassignments avoid disrupting codon-family connectivity: under the encoding-independent H(3,4) adjacency, observed events are topology-breaking at relative risk 0.32 versus the candidate landscape (permutation p&#x2264;10-4). The H(3,4) result is stable by construction; the Q6 decomposition is representation-specific and fails to show depletion under 8 of 24 base-to-bit encodings, so we report H(3,4) as the primary test and Q6 as a sensitivity. Event-level conditional-logit modelling shows that topology avoidance and local physicochemical cost provide complementary, only weakly correlated signal (rs=0.15), and that topology adds explanatory value beyond physicochemistry under both Q6 and encoding-independent H(3,4) adjacency. Retrospective reanalysis of nine genome-recoding datasets is consistent with codon-family topology operating as an evolutionary-trajectory constraint distinct from acute engineering fitness. The contribution is the second axis: code evolution is jointly constrained by physicochemical smoothness and codon-family topological integrity, and these two constraints are partly independent.

Codon reassignment↗

Real-world clinical utility of exome sequencing in pediatric drug-resistant epilepsy: Experience from a tertiary center in Thailand.

BACKGROUND: Genomic testing has increasingly contributed to the diagnosis and management of pediatric drug-resistant epilepsy (DRE), particularly in patients with suspected genetic etiologies. This study evaluated the diagnostic yield and real- world clinical utility of whole-exome sequencing (WES) in children with DRE. METHODS: Children with DRE and seizure onset before 15&#xa0;years of age were enrolled between January 2020 and December 2023. Clinical data, including demographics, seizure characteristics, developmental history, electroencephalography (EEG), brain magnetic resonance imaging (MRI), and prior investigations, were reviewed. WES was performed in all probands and, when available, their parents. Variants were interpreted according to standard guidelines. Clinical utility and 1-year seizure and developmental outcomes were assessed from follow-up records. RESULTS: Fifty-six patients (23 males, 33 females) were included. The median age at seizure onset was 1&#xa0;year (interquartile range [IQR] 0.3-4&#xa0;years), and 96.4% had developmental comorbidities. Pathogenic or likely pathogenic variants were identified in 39% (22/56), with the highest diagnostic yield in children with seizure onset before 3&#xa0;years of age. Channelopathies accounted for most genetically solved cases (68%), predominantly involving sodium channel genes. Genetic diagnoses provided clinical utility in 73% (16/22) of solved cases by guiding treatment and precision management. At 1-year follow-up, genetically solved patients showed more favorable seizure and developmental outcomes than those with genetically unsolved patients. CONCLUSION: WES achieved a 39% diagnostic yield and substantial clinical utility in pediatric DRE, particularly in early-onset and channelopathy-related disorders. These findings support early molecular diagnosis to facilitate genotype-informed management in appropriately selected children. However, the more favorable developmental and seizure outcomes observed in genetically solved patients should be interpreted with caution, as they may have been influenced by multiple factors beyond genetic diagnosis. In resource-limited settings, careful clinical phenotyping remains essential for treatment decisions and for prioritizing children for genomic testing.

Clinical utility↗

Targeting TP53 in triple-negative breast cancer: Molecular pathogenesis, therapeutic implications, and emerging pharmacological strategies.

Triple-negative breast cancer (TNBC) remains a highly aggressive and therapeutically challenging subtype, defined by the absence of oestrogen, progesterone, and HER2 expression. Tumour Protein 53 (TP53) mutations represent the most frequent genetic alteration, occurring in over 80% of cases and driving tumour initiation, progression, and therapeutic resistance. Mutant p53 proteins not only lose canonical tumour-suppressive functions but also often acquire gain-of-function (GOF) oncogenic properties that promote metastasis, genomic instability, and resistance to mechanisms like ferroptosis. This review examines the biological role of TP53 in TNBC pathogenesis and evaluates emerging pharmacological strategies aimed at targeting these vulnerabilities. Key approaches include the pharmacological reactivation of mutant p53 using small molecules such as APR-246, COTI-2, and the mutation-specific reactivator rezatapopt (PC14586), which has shown significant clinical tumour reduction in Y220C-mutant patients. Other strategies involve targeted protein degradation, the exploitation of synthetic lethal interactions (e.g., Chk1 or Aurora kinase B inhibition), and the use of natural products like cryptolepine or piperine derivatives. Recent clinical evidence further highlights the potential of combining epigenetic agents like decitabine with chemotherapy in TP53-mutant populations. Integrating TP53 mutation status into biomarker-driven treatment paradigms is a pivotal step toward achieving precision oncology and improving clinical outcomes for patients with TNBC.

Precision oncology↗

Comparative genomics and adult-female transcriptomics prioritize physiological candidate pathways in the aquatic acentropine moth Paracymoriza distinctalis.

Freshwater-associated life histories are rare in Lepidoptera, and the physiological systems accompanying them remain poorly resolved. We integrated adult-female whole-body RNA-seq from Paracymoriza distinctalis (n&#xa0;=&#xa0;3) and three terrestrial crambids (n&#xa0;=&#xa0;3, 3, and 2) with focused comparative genomics to prioritize testable candidate pathways. Adult-female expression-biased genes were enriched for muscle contraction and myofibril assembly, carbohydrate and nucleotide-related metabolism, response to stimulus, and regulation of signal transduction. Protein-interaction analysis further identified coherent modules associated with RNA processing, carbon metabolism, the citrate cycle, and RAF/MAPK signaling. At the genome level, P. distinctalis retained broad macrosynteny with two crambid relatives, whereas putative lineage-biased genes were enriched for vitelline membrane formation, embryonic development, apoptosis, cytoskeletal organization, and transferase activity. Because the transcriptomes were obtained from whole adult females, these patterns may reflect locomotor, reproductive, metabolic, and tissue-composition differences and should not be interpreted as direct mechanisms of larval aquatic adaptation. Together, the results identify a concise set of adult-stage physiological candidates for stage-resolved, tissue-specific, and functional validation.

Acentropinae↗

Antibacterial and preventive effects of Terminalia chebula Retz. aqueous extract and methyl gallate in American shad Alosa sapidissima (Wilson, 1981) against Aeromonas hydrophila YML1.

American shad, Alosa sapidissima (Wilson, 1981), is an economically important emerging species in recirculating aquaculture systems and photovoltaic aquaculture. However, Aeromonas hydrophila poses a threat to the healthy development of its aquaculture industry. This study investigated the effects of 95.5&#xa0;mg&#xb7;L-1 aqueous extract from Terminalia chebula Retz. and 318.3&#xa0;mg&#xb7;L-1 methyl gallate (Experiment I) and methyl gallate at 31.8-127.3&#xa0;mg&#xb7;L-1 (Experiment II) together with A. hydrophila YML1 challage groups (1.0&#xa0;&#xd7;&#xa0;107 and 1.58&#xa0;&#xd7;&#xa0;105&#xa0;CFU&#xb7;mL-1 in Experiments I and II) on liver morphology, hepatic enzyme profiles, and transcriptional responses in American shad. Results for Experiment I showed after high-dose pathogen infection, vacuolar degeneration and inflammatory cell infiltration were observed. In addition, caspase-3, tumor necrosis factor &#x3b1; (TNF-&#x3b1;), and malondialdehyde (MDA) contents increased significantly, and the steroid biosynthesis pathway was significantly enriched via the transcriptional analysis. However, inflammation and apoptosis remained evident after high-dose A. hydrophila YML1 infection. After treatment with 95.5&#xa0;mg&#xb7;L-1&#xa0;T. chebula Retz. extract, triphosphopyridine nucleotide (NADPH), Fructose-1,6-bisphosphatase (FBP), and phospho fructo kinase 1 (PFK) levels decreased significantly. After treatment with 318.3&#xa0;mg&#xb7;L-1 methyl gallate, nicotinamide adenine dinucleotide (NADH), NADPH, PFK, caspase-3, TNF-&#x3b1;, and MDA contents decreased significantly. For Experiment II, caspase-3 and TNF-&#x3b1; also decreased in the 31.8&#xa0;mg&#xb7;L-1 group at 24-96&#xa0;h and in the 127.3&#xa0;mg&#xb7;L-1 group at 96&#xa0;h. The peroxisome proliferator-activated receptor (PPAR) signaling pathway and fatty acid metabolism were also significantly enriched after methyl gallate treatment.Different expression genes (DEGs) in the cytokine-cytokine receptor interaction pathway showed a time- and dose-dependent pattern. At 48&#xa0;h, the MAPK signaling pathway and apoptosis were enriched in the 95.5&#xa0;mg&#xb7;L-1 group, whereas at 96&#xa0;h the PPAR-MAPK (mitogen-activated protein kinase) signaling pathway was enriched, with downregulation of fabp7b, soat2, cpt1ab2, and pparg. These changes were associated with inflammatory cell infiltration and increased MDA contents. Enhanced fatty acid degradation, possibly via cpt2, together with reduced fatty acid transporter transcription, may have alleviated liver injury in shad.

American shad↗

FANCM is required for the PAX3::FOXO1-driven oncogenic program in rhabdomyosarcoma.

Many cancers are driven by mutationally altered transcription factors (TFs) that rewire cells to an oncogenic state. Cells must activate specific mechanisms to tolerate the burden of oncogenic TF activity. To define such mechanisms, we focused on a canonical oncogenic fusion protein-driven cancer, alveolar rhabdomyosarcoma (ARMS), where the PAX3::FOXO1 fusion protein hyperactivates and mislocalizes PAX3 and FOXO1 TF functions. Employing sequential functional genomic CRISPR-Cas9 screens, we identified FANCM, a DNA translocase in the Fanconi anemia pathway, as a selective dependency in PAX3::FOXO1+ ARMS. FANCM loss reduces fusion protein levels, induces myogenic differentiation, and disrupts the PAX3::FOXO1 transcriptional program, thereby halting oncogenic proliferation. Mechanistically, FANCM depletion exacerbates replication stress (RS) and DNA damage signaling, with chromatin-associated RS enriched at PAX3::FOXO1 target gene loci, resulting in selective downregulation of the oncogenic program. CRISPR exon-tiling screens prioritized FANCM's helicase and DNA-binding domains as essential for this dependency, linking FANCM-mediated replication fork binding to sustained oncogenesis.

ARMS↗