Abstract: Due to its molecular structure we find a specific reaction mechanism of ozone in biological systems, which requires low doses. By contrast to disinfection, where ozone is added over a certain period of time (ct concept) until disinfection becomes effective, we must pay particular attention to concentrations and dosages so as not to increase oxidative stress in patients, e.g., those with chronic inflammatory diseases and high oxidative stress. Here we start with a deeper insight into the effect of ozone on Red Bood Cells (RBC) and the glutathione system which can be blocked at higher concentrations if needed, such as is the case in reducing the plasmodium falciparum growth. At low ozone concentrations, the RBC metabolism is activated, 2,3-diphosphoglycerate (2.3-DPG) increases and oxygen is easily released from hemoglobin, which is helpful in diabetes and sporting activities. In mononuclear cells low dose ozone acts as a redox bioregulator, e.g., by downregulating proinflammatory cytokines and oxidative stress.

Abstract: Glycine N-methyltransferase (GNMT), a S-adenosylmethionine (SAM)-dependent methyltransferase, is primarily expressed in the liver and plays a key role in regulating liver metabolism and protecting against liver injury. Several studies have shown that deficiency or downregulation of GNMT is strongly associated with the pathogenesis of hepatocellular carcinoma (HCC), highlighting its critical role as a tumor suppressor. Other studies have shown that GNMT is also strongly correlated with the pathogenesis of metabolic dysfunction-associated fatty liver disease (MAFLD). Although many factors regulate GNMT expression, recent studies have identified microRNAs (miRNAs), such as miR-873-5p and miR-224, as key post-transcriptional regulators that directly target GNMT mRNA and suppress its expression in HCC and MAFLD. This review provides an overview of GNMT’s role in liver physiology and how its dysregulation contributes to the progression of HCC and MAFLD, with a focus on the regulation of GNMT by miR-873-5p and miR-224. We also highlight the potential of these two miRNAs as biomarkers and therapeutic targets for HCC and MAFLD, discussing emerging strategies such as antisense-based inhibition, gene therapy, and small-molecule inducers aimed at restoring GNMT expression.

Abstract: During aging, bone marrow stromal (a.k.a. mesenchymal stem) cells (BMSC) shift their lineage commitment away from osteogenesis and towards adipogenesis, resulting in bone loss and marrow fat accumulation. We previously reported that during osteogenesis, BMSCs activate mitochondrial oxidative phosphorylation (OXPHOS) by downregulating cyclophilin D (CypD) expression and, consequently, mitochondrial permeability transition pore (MPTP) activity. We also reported that in contrast, during adipogenesis, BMSCs upregulate CypD/MPTP, activate glycolysis, and inhibit OXPHOS. To further study the role of CypD/MPTP in BMSC bioenergetics and adipogenesis and bone marrow fat accumulation, we used CypD/MPTP loss-of-function (LOF) or gain-of-function (GOF) models in osteoadipoprogenitors in vitro and in vivo. We found that CypD/MPTP LOF impairs while GOF enhances adipogenesis in vitro and in ectopic bone grafts in vivo. In addition, bioenergetic profiling and metabolomics analyses show evidence of corresponding metabolic reprogramming in CypD/MPTP LOF and GOF cells. In summary, our study demonstrated the role of CypD/MPTP activity during BMSC adipogenesis, facilitating the understanding of stem cell fate determination and molecular mechanism of age-related bone loss as well as bone marrow fat accumulation.

Abstract: Background: n-3 Docosapentaenoic acid (DPA; 22:5 n-3) is increasingly viewed as a distinct long-chain omega-3 fatty acid with biological activities that are not fully captured by EPA or DHA. However, progress remains limited by restricted access to high-purity DPA: most commercial sources contain DPA as a minor component, and published isolation strategies often yield only enriched mixtures or require multi-step workflows that are difficult to scale in standard laboratories. Objectives: To establish a robust, laboratory-accessible purification workflow to obtain DPA ethyl ester at high purity while preserving oxidative quality. Methods: Candidate lipid sources were screened to select an optimal DPA-containing feedstock. Oils were stabilized with antioxidants and pre-fractionated by cold crystallization (−20 °C) to reduce saturated lipids and oxidation by-products. Preparative separation used a stacked C18 flash system (15 μm + 45 μm in series) operated isocratically (methanol/water 92:8, v/v) at 120 mL/min. Fractions were analyzed by GC and iteratively reinjected to progressively enrich the DPA window. Solvent was recovered by distillation and reused. Results: Omegavie® 4020EE (6.6% DPA) was identified as the best starting material. Pretreatment eliminated detectable TBARS-derived malondialdehyde. The isocratic purification-loop strategy produced tens of grams of DPA ethyl ester at >98% purity (GC–FID) with high overall recovery (~90%) and >90% solvent recycling. Identity and purity were confirmed by GC–MS and ^1H NMR, and oxidation indices remained low (peroxide value < 0.2 meq/kg; p-anisidine < 3). Conclusions: This scalable, solvent-conscious protocol enables reliable access to high-purity DPA and should be adaptable to other low-abundance polyunsaturated fatty acids.

Abstract:

For a long time, glycolysis and mitochondrial oxidative phosphorylation were opposed to each other. Glycolysis work when there is a lack of oxygen, the mitochondria supply ATP in oxygen environment. In recent decades, it has been discovered that glycolysis in vivo works always and the final product is lactate. Lactate can accumulate and is the transport form for pyruvate. In this review, we look at how obligate lactate formation during glycolysis affects the tricarboxylic acid (TCA) cycle and mitochondrial respiration. We conclude that fatty acid β-oxidation is a prerequisite for obligate lactate formation during glycolysis, which in turn promotes and enhances the anaplerotic functions of the TCA cycle. In this way, a supply of two types of substrates for mitochondria is formed: fatty acids as the basic energy substrates, and lactate as an emergency substrate for the heart, skeletal muscles, and brain. High steady-state levels of lactate and ATP, supported by β-oxidation, stimulate gluconeogenesis and thus supporting the lactate cycle. It is concluded that mitochondrial fatty acids β-oxidation and glycolysis constitute a single interdependent system of energy metabolism of the human body.

Abstract: Galectin-3 (Gal-3) is a β-galactoside-binding lectin implicated in metabolic inflammation, cardiovascular and renal dysfunction, neurodegenerative disorders, and obesity-related pathologies. Although Gal-3 is recognized as a clinically relevant biomarker, the mechanisms controlling its tissue expression and circulating abundance remain poorly defined. O-GlcNAcase (Oga; encoded by Mgea5), the enzyme that removes O-linked β-N-acetylglucosamine (O-GlcNAc) from proteins, regulates nutrient-sensitive signaling and transcriptional processes that overlap with Gal-3 associated disease pathways. To investigate the relationship between metabolic status and Gal-3 expression, male mice were fed a high fat diet (HFD) for eight weeks to induce obesity. HFD-fed mice exhibited significant increases in body weight and fasting and fed blood glucose levels compared with lean controls, confirming metabolic dysregulation. ELISA revealed approximately threefold higher serum and plasma Gal-3 concentrations in obese mice, indicating enhanced Gal-3 production in diet-induced obesity. To determine whether Oga regulates Gal-3 expression, Oga wild-type (WT), heterozygous (HET), and knockout (KO) mice were analyzed. Circulating Gal-3 protein levels were significantly reduced in Oga KO mice, with intermediate levels in Oga HET animals. RT-qPCR revealed genotype-dependent modulation of Gal-3 (Lgals3) mRNA expression across multiple tissues, demonstrating tissue-specific regulation by Oga. These findings establish Oga as a critical regulator of Gal-3 expression and systemic abundance. The data reveal a mechanistic link between O-GlcNAc signaling and lectin-mediated metabolic inflammation, suggesting that Oga activity influences Gal-3 homeostasis and may affect its interpretation as a biomarker in metabolic disease.

Abstract:

The Warburg effect, classically defined as the preferential use of glycolysis by cancer cells in the presence of oxygen, has been a central concept in cancer biology since a long time. Otto Warburg had originally proposed that defective mitochondrial respiration was the primary cause of aerobic glycolysis in cancer cells. While this hypothesis profoundly influenced early cancer metabolism research, it has now become increasingly clear that this interpretation has gaping. Advances in biochemistry, molecular biology and metabolomics demonstrate that mitochondria in many cancers are functional and play essential roles in biosynthesis, signaling and energy production. Aerobic glycolysis in cancer cells is now recognized as an adaptive metabolic strategy that supports rapid proliferation by providing metabolic intermediates, maintaining redox balance, and enabling cellular signaling rather than maximizing ATP yield. This review discusses the Warburg effect through the lens of modern cancer metabolism. It contrasts classical misconceptions with current evidences, discusses key regulatory pathways like HIF-1α, PI3K/Akt/mTOR, c-Myc and PKM2, and examine the central role of lactate as both a metabolic fuel and a signaling molecule. It further explores metabolic heterogeneity, the reverse Warburg effect, immune–metabolic interactions, and the relevance of oxidative phosphorylation in cancer. Finally, some unresolved questions are highlighted that is critical for future understanding of cancer metabolism.

Abstract: MicroRNAs (miRNAs) are small non-coding RNAs that play central roles in post-transcriptional gene regulation and cellular homeostasis maintenance. Dysregula-tion of miRNA expression is increasingly recognized as a key contributor to tissue injury during the acute phase and to disease progression in the chronic phase. Chronic kidney disease (CKD) commonly progresses and ultimately leads to kidney failure through interstitial fibrosis, which is the final common pathway of CKD progression. Interstitial fibrosis is driven not only by fibroblast activation but also by a phenotypic transition of injured tubular epithelial cells, infiltrating macrophages, and peritubular capillary cells. These multifaceted cellular pathways induce and exacerbate interstitial fibrosis, and several miRNAs have been identified as important regulators of these pathways. In addition to fibrotic pathophysiological features, disease-specific dysregulation of miRNAs has been increasingly detected in various causes of CKD, including diabetic kidney disease, chronic glomerulonephritis, and nephrosclerosis. In this review, we provide an integrated overview of miRNA-mediated regulation in CKD, with particular emphasis on cell lineage functions within fibrotic pathways and disease-specific roles. Finally, we discuss the emerging potential of miRNAs as biomarkers and therapeutic targets for CKD and highlight future research directions.

Abstract: The spontaneous emergence of macroscopic dissipative structures in systems driven by generalized chemical potentials is well-established in non-equilibrium thermodynamics. Some examples are, hurricanes, Bénard cells, reaction-diffusion patterns, and atmospheric/oceanic currents. Less recognized, however, are microscopic dissipative structures that form when the driving potential excites internal molecular degrees of freedom (electronic states and nuclear coordinates), typically via high-energy photons. The thermodynamic dissipation theory for the origin of life posits that the core biomolecules of all three domains of life originated as self-organized molecular dissipative structures—chromophores or pigments—that proliferated across the Archean ocean surface to absorb and dissipate the intense “soft” UV-C (205–280 nm) and UV-B (280–315 nm) solar flux into heat. Thermodynamic coupling to ancillary antenna and surface-anchoring molecules subsequently increased photon dissipation and enabled more complex dissipative processes, including modern photosynthesis, to dissipate lower-energy but higher-flux UV-A and visible light. Further thermodynamic coupling to abiotic geophysical cycles (e.g., diurnal, water cycles, winds, and ocean currents) ultimately produced today’s biosphere, efficiently dissipating the full incident solar spectrum well into the infrared. This paper details three examples of molecular dissipative structuring (nucleotides, fatty acids, pigments) and argues that dissipative structuring, rather than natural selection, is the fundamental creative force in biology at all levels of hierarchy.

Abstract: Background/Objectives: Dysregulation of purinergic signaling influences tumor progression and immune evasion in hepatocellular carcinoma (HCC). We aimed to characterize the transcriptional landscape of this system, identify prognostic markers, and investigate how the tumor microenvironment modulates pharmacological response to combined sorafenib and doxazosin in 3D spheroid models. Methods: We integrated RNA-seq data from the TCGA-LIHC to identify differentially expressed genes, pathway enrichment, gene co-expression networks, prognostic associations, and machine learning-based biomarker selection. Modulation of key targets was assessed in HepG2 and HepG2/LX-2 spheroids treated with sorafenib and doxazosin using qPCR and flow cytometry. Results: Transcriptomics revealed dysregulation and network fragmentation, where high expression of ADA, NT5E, and ADORA1 correlated with poor overall survival. In 3D models, co-treatment significantly downregulated NT5E and ADORA1 mRNA expression, while ADORA2A was specifically reduced in the co-culture setting. For ADA, effect size analysis revealed a large magnitude of inhibition in HepG2 spheroids. Although flow cytometry showed high CD73 protein expression remained stable across treatments in co-culture, the combination therapy successfully overcame stromal protection, significantly increasing apoptosis (active caspase-3) in both mono- and co-culture spheroids compared to vehicle and monotherapy. Conclusions: We identified a purinergic prognostic signature in HCC and demonstrated that the combination therapy of sorafenib and doxazosin targets the adenosine-generating axis and specific receptors. We show that the stromal microenvironment sustains CD73 protein expression even under transcriptional inhibition, highlighting the critical role of 3D co-culture models in deciphering therapeutic resistance mechanisms.

Abstract: Copper-organic compounds are being investigated as antitumor candidates. Besides their efficacy as cytotoxic agents alone, the oxidative potential of electrochemical Cu2+-to-Cu1+ transition emerges as an attractive approach for elimination of tumor cells otherwise resistant to chemotherapy. To minimize side effects of the potent oxidative burst upon Cu(II) reduction, the metal cations should be delivered to the tumor site. Taking advantage of the ability of bisphosphonates to accumulate in the bone, we synthesized Cu(II) complexes of zoledronic acid (ZA), an FDA-approved drug for prevention of bone destruction. New CuZA complexes obtained upon precipitation of ZA and different copper salts were structurally identical, consisting of two organic moieties coordinated by three metal cations. Combined treatment with water-soluble formulations of CuZA and cysteine triggered rapid death in human cell lines. This effect was achievable with non-toxic concentrations of CuZA and cysteine alone. Importantly, the K562 chronic myelogenous leukemia cells that demonstrated an attenuated response to the 3d generation Bcr-Abl tyrosine kinase inhibitor in the medium conditioned by bone marrow-derived fibroblasts, were readily killed by CuZA-cysteine combination. Thus, oxidative burst upon metal reduction in CuZA complexes emerges as a promising method of eradication of tumor cells in the bone microenvironment.

Abstract: Objectives To summarize evidence on the role of nutrition in regulating tissue crosstalk and to identify key knowledge gaps relevant to metabolic health and disease. Background Tissues continuously communicate to maintain metabolic balance. This inter-organ communication, referred to as tissue crosstalk, enables organs such as the liver, adipose tissue, skeletal muscle, gut, and immune system to coordinate responses to nutritional and environmental signals. Disruption of these pathways is increasingly recognized as a central feature of metabolic disorders, including obesity, type 2 diabetes, and non-alcoholic fatty liver disease. Nutrition plays a critical role in shaping tissue crosstalk beyond its role as a source of energy and building blocks. Dietary signals transmitted through hormones, cytokines, metabolites, and other mediators are strongly influenced by macronutrient quality and food matrix characteristics, thereby modifying metabolic and inflammatory signaling across organs. Methods This narrative review synthesizes evidence from human and experimental studies examining how nutrition regulates tissue crosstalk, with emphasis on macronutrient quality and gut microbiota–mediated mechanisms. Results The gut microbiota represents a key link between diet and systemic metabolic regulation. Dietary patterns influence microbial composition and activity, leading to the production of metabolites such as short-chain fatty acids, bile acid derivatives, and tryptophan-related2compounds. These microbial products act as signaling molecules that affect distant tissues and support coordinated metabolic responses. Evidence suggests that whole foods and food matrices may modulate these interactions more effectively than isolated nutrients or supplements. Conclusion Macronutrient quality and diet–microbiota interactions emerge as central regulators of inter- organ communication. Important gaps remain regarding the context-dependent effects of dietary protein quality and the influence of plant-based dietary patterns under conditions of positive energy balance. Addressing these gaps may help inform nutritional strategies aimed at supporting metabolic health beyond weight loss alone.

Abstract: Cancer remains one of the most significant health challenges facing humanity today. Extensive oncological research has demonstrated that cancer progression is not solely driven by malignant cells but also by the tumor microenvironment (TME), which plays a crucial role in tumor development, immune evasion and metastasis. As a result, the TME has emerged as a promising therapeutic target. Nanotechnology has revolutionized cancer diagnosis and treatment, with metallic nanoparticles (mNPs) being extensively studied. However, their effects on the TME remain poorly understood. While some molecular pathways through which mNPs influence the TME have been identified, these findings likely represent only a small fraction of the underlying mechanisms, as analyzed in this review. Furthermore, a major challenge in studying these interactions is the lack of physiologically relevant models, as currently available cell culture and in vivo systems often fail to accurately replicate the complex and dynamic interactions of the TME. These limitations underscore the urgent need for more comprehensive research to establish the TME as a viable therapeutic target for treatment strategies involving NPs. Specifically, a deeper understanding of how mNPs interact with the TME at multiple levels, including immune modulations, stromal remodeling and metabolic reprogramming, is essential toward optimizing the therapeutic potential of mNPs in cancer care.

Abstract: Glutathione-S-Transferase T1 (GSTT1) and M1 (GSTM1) are key enzymes involved in phase II detoxification. Null genotypes resulting from gene deletions lead to a complete loss of enzymatic activity, reducing the capacity to metabolize xenobiotics and increasing the risk of adverse effects. Although genotype frequencies vary across ethnic groups, data from non-European populations, particularly Andean populations, remain limited. In this cross-sectional study, the frequency of GSTM1 and GSTT1 null genotypes was determined in 206 individuals from Cusco and Junín. Genotyping was performed by PCR using genomic DNA extracted from peripheral blood. The frequency of the GSTM1 null genotype was 49.51%, whereas that of GSTT1 was 25.24%. Combined genotype analysis showed that 63.11% of participants carried at least one null genotype and 11.65% carried both null variants. No significant differences were observed between Cusco and Junín. Compared with previously reported data, these frequencies were similar to those observed in Peruvian coastal and several South American populations. At the intercontinental level, frequencies were comparable to Europe, the Middle East, and Asia, but differed from Sub-Saharan Africa and Native American populations. This first molecular characterization of GSTM1 and GSTT1 null genotypes in Andean populations provides a baseline for pharmacogenetics and precision medicine research in high-altitude settings.

Abstract:

This study aimed to evaluate FOXC1-mediated regulatory mechanisms on gene and protein expression profiles in primary human limbal epithelial cells (pLECs), via siRNA knockdown; under basal and lipopolysaccharide (LPS) and interleukin-1β (IL-1β) induced inflammatory conditions. Gene expression was analysed for markers related to inflammation (CCL2, IL-6, IL-8, TNF-α, TGF-β), epithelial differentiation (KRT3, KRT12, KRT13, PAX6, FOXC1), cell proliferation and remodelling (FOSL2, MKi67, MMP2, VEGFA) and retinoic acid metabolism (ALDH3A1, CRABP2, CYP1B1, FABP5, RDH10, RBP1, STRA6). FOXC1 siRNA silencing in human pLECs significantly altered mRNA expression across multiple functional pathways, including inflammatory signaling (CCL2, IL-6, IL-8, IL-1α, VEGFA; p≤0.030), epithelial differentiation (KRT12, KRT13, PAX6; p≤0.045), cell proliferation and stress response (FOSL2, MKi67, VEGFA; p≤0.048) and retinoic acid metabolism (ALDH3A1, CRABP2, CYP1B1, FABP5, RDH10, STRA6; p≤0.037). Corresponding protein levels, evaluated by Western blotting and ELISA, were significantly modulated for the FABP5–CRABP2 axis, IL-6, IL-8, IL-1α, KRT12, KRT13, TGF-β, and RDH10 under different treatment conditions; (p≤0.045). FOXC1 maintains an anti-inflammatory, immune-quiescent state and coordinates TGF-β–mediated signaling, keratin expression, and retinoic acid metabolism to preserve corneal epithelial identity and homeostasis. Disruption of FOXC1 expression perturbs these pathways, potentially predisposing the ocular surface to fibrosis, lineage instability, and impaired regenerative capacity.

Abstract: Polyglutamine expansion in Ataxin-2 (ATXN2) is responsible for rare, dominantly in-herited Spinocerebellar Ataxia type 2 (SCA2). Together with its paralog Ataxin-2-like (ATXN2L), both proteins received much interest since deletion of their yeast and fly orthologs alleviates TDP-43-triggered neurotoxicity in Amyotrophic Lateral Sclerosis models. Their typical structure across evolution combines LSm with LSm-Associated Domains and a PAM2 motif. To understand the physiological regulation and functions of Ataxin-2 homologs, the phylogenesis of sequences was analyzed. Human ATXN2 harbors multiple alternative start codons, e.g. from an intrinsically disordered se-quence (IDR) present since armadillo, or from the polyQ sequence that arose since amphibians, or from the LSm domain since primitive eukaryotes. Multiple smaller isoforms also exist across the C-terminus. Therapeutic knockdown of polyQ expansions in human ATXN2 should selectively target exon 1B. PolyQ repeats developed repeat-edly, usually framed and often interrupted by (poly)Pro, originally near PAM2. The LSmAD sequence appeared in algae as the characteristic Ataxin-2 feature with strong conservation. Frequently, Ataxin-2 has added domains, likely due to transcriptional readthrough of neighbor genes during cell stress. These chimerisms show enrichment of rRNA processing; nutrient store mobilization; membrane strengthening via lipid, protein, and glycosylated components; and cell protrusions. Thus, any mutation of Ataxin-2 has complex effects, also affecting membrane resilience.

Abstract: This paper does not present new experimental data, but it offers unique insights into the replication mechanism and DNA topology based on ambidextrous double helix model. Analysis of positively and negatively supercoiled plasmids revealed that the differences between them could be reasonably explained by the ambidextrous double helix model, but not by the classical double helix model. The superhelical structure of DNA has been understood and explained in an unprecedented way, which may help us better unravel the mysteries of nature. Acquiring knowledge is important, but finding the right way of thinking that breaks with tradition and inspires new ideas is even more crucial.

Abstract: The Mediator complex is a central regulator of eukaryotic transcription, functioning as a dynamic molecular bridge between gene-specific transcription factors and RNA polymerase II (Pol II). Although decades of research have established its modular architecture and fundamental role in transcriptional control, recent advances have significantly expanded our understanding of its structural conformations, subunit-specific functions, and links to human disease. This review provides a comprehensive overview of the Mediator complex, highlighting key structural and functional discoveries from the past decade and synthesizing its diverse roles in transcriptional regulation. We further discuss emerging concepts and future directions for therapeutically targeting Mediator, particularly in cancer. Together, these insights position the Mediator complex as a highly conserved yet adaptable, signal-responsive regulatory hub with broad implications for both normal physiology and disease pathogenesis.

Abstract: Sports science is rapidly changing with new discoveries in molecular biology and artificial intelligence. Modern “omics” tools, such as genomics, proteomics, and metabolomics along with AI-based analytics, help us understand how a child’s body builds muscle, responds to training, and recovers after exercise. These technologies also help identify factors that may increase the risk of injury. Simple genetic tests, including variations like ACE I/D and ACTN3 R577X, provide insights into traits linked to endurance, strength, and muscle performance. Protein and metabolite testing, supported by AI models, can reveal how efficiently the body uses energy or repairs tissues after activity. This review article provides the most recent and up-to-date knowledge regarding modern technologies used for performance enhancement. These scientific tools are not meant to label or limit children. Instead, they help parents and coaches understand each child’s individual needs and support healthier training decisions. AI-driven interpretations can guide choices about training intensity, rest, recovery, and nutrition in a safe and personalized manner. Overall, this paper offers practical guidance for using molecular and AI-driven sportomics responsibly. Our goal is to empower parents and coaches with informed, balanced, and child-centric strategies for enhancing performance.

Abstract: Recombinogenic DNA damage can initiate chromosomal rearrangements that can alter gene expression or accelerate cancer progression in higher eukaryotes. Thus, there is a critical need to identify genes that suppress chromosomal rearrangements and environmental exposures that promote genetic instability. Cell cycle checkpoints modulate the cell cycle so that DNA repair occurs before the replication or segregation of damaged chromosomes. Saccharomyces cerevisiae (budding yeast) RAD9 was the first cell cycle checkpoint gene identified, which initiated intensive research studies into the mechanisms of checkpoint activation and the phenotypes of checkpoint mutants. The budding yeast Rad9 protein serves as both an adaptor and scaffold that facilitates downstream effector activation to orchestrate a DNA damage response at multiple stages of the cell cycle, which facilitate double-strand break (DSB) repair by sister chromatid recombination. However, the role of RAD9 in homologous recombination and in suppressing gross chromosomal rearrangements (GCRs) is not completely understood. In this review we discuss how RAD9 can promote genome instability resulting from aberrant DNA replication intermediates, while suppressing DSB-associated rearrangements. We also discuss possible mechanisms accounting for the synergistic increase in genomic instability in double mutants defective in both RAD9 and recombinational repair. We emphasize that while there is an overlap between checkpoint and recombinational repair pathways, RAD9 and checkpoint pathways can function independently to suppress chromosomal instability. These studies thus elucidate checkpoint mechanisms that control homologous recombination between repeated sequences.