Processing of DNA Polymerase-Blocking Lesions during Genome Replication Is Spatially and Temporally Segregated from Replication Forks.

Tracing DNA repair factors by fluorescence microscopy provides valuable information about how DNA damage processing is orchestrated within cells. Most repair pathways involve single-stranded DNA (ssDNA), making replication protein A (RPA) a hallmark of DNA damage and replication stress. RPA foci emerging during S phase in response to tolerable loads of polymerase-blocking lesions are generally thought to indicate stalled replication intermediates. We now report that in budding yeast they predominantly form far away from sites of ongoing replication, and they do not overlap with any of the repair centers associated with collapsed replication forks or double-strand breaks. Instead, they represent sites of postreplicative DNA damage bypass involving translesion synthesis and homologous recombination. We propose that most RPA and recombination foci induced by polymerase-blocking lesions in the replication template are clusters of repair tracts arising from replication centers by polymerase re-priming and subsequent expansion of daughter-strand gaps over the course of S phase.

EXO1 and DNA2-mediated ssDNA gap expansion is essential for ATR activation and to maintain viability in BRCA1-deficient cells.

DNA replication faces challenges from DNA lesions originated from endogenous or exogenous sources of stress, leading to the accumulation of single-stranded DNA (ssDNA) that triggers the activation of the ATR checkpoint response. To complete genome replication in the presence of damaged DNA, cells employ DNA damage tolerance mechanisms that operate not only at stalled replication forks but also at ssDNA gaps originated by repriming of DNA synthesis downstream of lesions. Here, we demonstrate that human cells accumulate post-replicative ssDNA gaps following replicative stress induction. These gaps, initiated by PrimPol repriming and expanded by the long-range resection factors EXO1 and DNA2, constitute the principal origin of the ssDNA signal responsible for ATR activation upon replication stress, in contrast to stalled forks. Strikingly, the loss of EXO1 or DNA2 results in synthetic lethality when combined with BRCA1 deficiency, but not BRCA2. This phenomenon aligns with the observation that BRCA1 alone contributes to the expansion of ssDNA gaps. Remarkably, BRCA1-deficient cells become addicted to the overexpression of EXO1, DNA2 or BLM. This dependence on long-range resection unveils a new vulnerability of BRCA1-mutant tumors, shedding light on potential therapeutic targets for these cancers.

Non-recombinogenic roles for Rad52 in translesion synthesis during DNA damage tolerance.

DNA damage tolerance relies on homologous recombination (HR) and translesion synthesis (TLS) mechanisms to fill in the ssDNA gaps generated during passing of the replication fork over DNA lesions in the template. Whereas TLS requires specialized polymerases able to incorporate a dNTP opposite the lesion and is error-prone, HR uses the sister chromatid and is mostly error-free. We report that the HR protein Rad52-but not Rad51 and Rad57-acts in concert with the TLS machinery (Rad6/Rad18-mediated PCNA ubiquitylation and polymerases Rev1/Pol ζ) to repair MMS and UV light-induced ssDNA gaps through a non-recombinogenic mechanism, as inferred from the different phenotypes displayed in the absence of Rad52 and Rad54 (essential for MMS- and UV-induced HR); accordingly, Rad52 is required for efficient DNA damage-induced mutagenesis. In addition, Rad52, Rad51, and Rad57, but not Rad54, facilitate Rad6/Rad18 binding to chromatin and subsequent DNA damage-induced PCNA ubiquitylation. Therefore, Rad52 facilitates the tolerance process not only by HR but also by TLS through Rad51/Rad57-dependent and -independent processes, providing a novel role for the recombination proteins in maintaining genome integrity.

Objective Evaluation of Laparoscopic Experience Based on Muscle Electromyography and Accelerometry Performing Circular Pattern Cutting Tasks: A Pilot Study.

Purpose.The aim of this work is to present a new physical laparoscopy simulator with an electromyography (EMG)/accelerometry-based muscle activity recording system, EvalLap EMG-ACC, and perform objective evaluation of laparoscopic skills based on the quantification of muscle activity of participants with different levels of laparoscopic experience. Methods. EMG and ACC signals were obtained from 14 participants (6 experts, 8 medical students) performing circular pattern cutting tasks using a laparoscopic box trainer with the Trigno (Delsys Inc, Natick, MA) portable wireless system of 16 wireless sensors. Sensors were placed on the proximal and distal muscles of the upper extremities. Seven evaluation metrics were proposed and compared between skilled and novice surgeons. Results. The proximal and distal arm muscles (trapezius, deltoids, biceps, and forearms) were most active while executing laparoscopic tasks. Laparoscopic experience was associated with differences in EMG amplitude (Aavg), muscle activity (iEMG), hand acceleration (iACH), user movement (iAC), and muscle fatigue. For the cutting task, the deltoid, bicep, forearm EMG amplitude, and user movement significantly differed between experience groups. Conclusion. This pilot study demonstrates that different muscle groups are preferentially activated during laparoscopic tasks depending on the level of surgical experience. Expert surgeons showed less muscle activity compared with novices. EvalLap EMG-ACC represents a promising means to distinguish surgeons with basic cutting skills from those who have not yet developed these skills.

Spatial separation between replisome- and template-induced replication stress signaling.

Polymerase-blocking DNA lesions are thought to elicit a checkpoint response via accumulation of single-stranded DNA at stalled replication forks. However, as an alternative to persistent fork stalling, re-priming downstream of lesions can give rise to daughter-strand gaps behind replication forks. We show here that the processing of such structures by an exonuclease, Exo1, is required for timely checkpoint activation, which in turn prevents further gap erosion in S phase. This Rad9-dependent mechanism of damage signaling is distinct from the Mrc1-dependent, fork-associated response to replication stress induced by conditions such as nucleotide depletion or replisome-inherent problems, but reminiscent of replication-independent checkpoint activation by single-stranded DNA Our results indicate that while replisome stalling triggers a checkpoint response directly at the stalled replication fork, the response to replication stress elicited by polymerase-blocking lesions mainly emanates from Exo1-processed, postreplicative daughter-strand gaps, thus offering a mechanistic explanation for the dichotomy between replisome- versus template-induced checkpoint signaling.

Human TREX1 Repairs 3'-End DNA Lesions in Vitro.

Human three-prime repair exonuclease 1 (TREX1) is the major 3' to 5' exonuclease that functions to deplete the cytosolic DNA to prevent the autoimmune response. TREX1 is upregulated and translocates from cytoplasm to the nucleus in response to genotoxic stress, but the function of nuclear TREX1 is not well understood. Herein, we wish to report our in vitro finding that TREX1 efficiently excises 3'-phospho-α,ß-unsaturated aldehyde and 3'-deoxyribose phosphate that are commonly produced as base excision repair intermediates and also from the nonenzymatic strand incision at abasic sites.

Humoral and Cellular Responses to mRNA-1273 and BNT162b2 SARS-CoV-2 Vaccines Administered to Hemodialysis Patients.

RATIONALE & OBJECTIVE: Patients with kidney failure who are receiving maintenance dialysis have a higher risk of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and worse clinical outcomes after coronavirus disease 2019 (COVID-19) than the general population. Therefore, immunization against SARS-CoV-2 with effective vaccines is an important component of health-maintenance strategies for these patients. This study evaluated the humoral and cellular responses to messenger RNA (mRNA) SARS-CoV-2 vaccines in this population. STUDY DESIGN: Observational prospective multicenter cohort study. SETTING & PARTICIPANTS: 205 patients treated at 3 dialysis units at the Hospital Clínic of Barcelona (Spain) were vaccinated from February 3 to April 4, 2021, and followed until April 23, 2021. EXPOSURE: Immunization with either the mRNA-1273 (Moderna) or BNT162b2 (Pfizer-BioNTech) SARS-CoV-2 mRNA vaccine. OUTCOME: Seroconversion, defined as the detection of IgG antibodies to the receptor-binding domain of the S1 spike antigen of SARS-CoV-2 (anti-S1-RBD IgG), and the identification of activated CD4+T cells 3 weeks after completing vaccination. Anti-S1-RBD IgG levels were also analyzed as a secondary outcome. ANALYTICAL APPROACH: Univariate and multivariable logistic and multiple linear regression models were used to evaluate the associations between vaccination and study outcomes. RESULTS: We found that 97.7% of 175 vaccinated patients who were seronegative at baseline developed a response (humoral, cellular, or both); 95.4% of these patients seroconverted, while 62% of those tested for cellular immunity had a positive response. Greater age and immunosuppressive treatment were associated with lower antibody levels. LIMITATIONS: Mandatory vaccine administration by health authorities. Anti-S1-RBD IgG levels were reported up to 150U/mL and cellular immune responses were characterized qualitatively. Antibody assay and cellular response assessment may not be comparable with previously published laboratory approaches. CONCLUSIONS: Immunization with mRNA vaccines generated a humoral and cellular immune response in a high proportion of patients with kidney failure receiving maintenance dialysis. These findings as well as the high risk of infection and poor clinical outcomes among these patients make their vaccination a health priority.

The helicase Pif1 functions in the template switching pathway of DNA damage bypass.

Replication of damaged DNA is challenging because lesions in the replication template frequently interfere with an orderly progression of the replisome. In this situation, complete duplication of the genome is ensured by the action of DNA damage bypass pathways effecting either translesion synthesis by specialized, damage-tolerant DNA polymerases or a recombination-like mechanism called template switching (TS). Here we report that budding yeast Pif1, a helicase known to be involved in the resolution of complex DNA structures as well as the maturation of Okazaki fragments during replication, contributes to DNA damage bypass. We show that Pif1 expands regions of single-stranded DNA, so-called daughter-strand gaps, left behind the replication fork as a consequence of replisome re-priming. This function requires interaction with the replication clamp, proliferating cell nuclear antigen, facilitating its recruitment to damage sites, and complements the activity of an exonuclease, Exo1, in the processing of post-replicative daughter-strand gaps in preparation for TS. Our results thus reveal a novel function of a conserved DNA helicase that is known as a key player in genome maintenance.

Vancomycin hemodialysis: Clearance differences between high-flux hemodialysis and on-line hemodiafiltration.

The aim of this study was to analyze the differences between vancomycin clearance (Kd) with high-flux hemodialysis (HFHD) and on-line hemodiafiltration (OL-HDF). The OL-HDF therapy combined the diffusion and convective transport of solutes. To compare the Kd, a vancomycin loading dose of 1 g was administered intravenously post-dialysis to 11 chronic and anuric (<100 mL/24 h) hemodialysis patients, undergoing HFHD and post-dilutional OL-HDF in consecutive therapies. Additional doses of 0.5 g were administered after 45 minutes at the end of each dialysis therapy during antibiotic treatment. Blood samples were drawn from arterial and venous lines at the start of hemodialysis sessions and at the first, second, third, and fourth hours. Additional samples were drawn at 15, 30, and 45 minutes after the end of dialysis therapy. Vancomycin plasma concentration, blood urea nitrogen (BUN), creatinine, and ß2 -microglobulin were measured. The patients' hydration status was evaluated by bioimpedance analysis. The mean of vancomycin dialyzer clearance (Kddc ) calculated was 110.8 ± 15 mL/min with HFHD and 146.8 ± 13.8 mL/min with OL-HDF (P = 0.025). Significant differences were also obtained for ß2 -microglobulin clearance, Kddc 72.6 ± 15.4 mL/min with HFHD and 113.4 ± 24.2 mL/min with OL-HDF (P = 0.012), whereas no differences were found for BUN or creatinine. Additionally, to analyze differences between HFHD and OL-HDF, a variable volume dual pool mathematical model was developed to estimate the body clearance (Kdbc ), extraction mass (Me ), and inter-compartment mass-transfer coefficient (K12 ) of each molecule. A higher vancomycin Kddc with OL-HDF produced by convection improved removal of antibiotic; this can compromise achieving a therapeutic concentration target. We recommended evaluating increased loading doses of vancomycin and avoiding administration during OL-HDF to assure adequate treatment.

Role for RNA:DNA hybrids in origin-independent replication priming in a eukaryotic system.

DNA replication initiates at defined replication origins along eukaryotic chromosomes, ensuring complete genome duplication within a single S-phase. A key feature of replication origins is their ability to control the onset of DNA synthesis mediated by DNA polymerase-α and its intrinsic RNA primase activity. Here, we describe a novel origin-independent replication process that is mediated by transcription. RNA polymerase I transcription constraints lead to persistent RNA:DNA hybrids (R-loops) that prime replication in the ribosomal DNA locus. Our results suggest that eukaryotic genomes have developed tools to prevent R-loop-mediated replication events that potentially contribute to copy number variation, particularly relevant to carcinogenesis.

Manganese redistribution by calcium-stimulated vesicle trafficking bypasses the need for P-type ATPase function.

Regulation of intracellular ion homeostasis is essential for eukaryotic cell physiology. An example is provided by loss of ATP2C1 function, which leads to skin ulceration, improper keratinocyte adhesion, and cancer formation in Hailey-Hailey patients. The yeast ATP2C1 orthologue PMR1 codes for a Mn(2+)/Ca(2+) transporter that is crucial for cis-Golgi manganese supply. Here, we present evidence that calcium overcomes the lack of Pmr1 through vesicle trafficking-stimulated manganese delivery and requires the endoplasmic reticulum Mn(2+) transporter Spf1 and the late endosome/trans-Golgi Nramp metal transporter Smf2. Smf2 co-localizes with the putative Mn(2+) transporter Atx2, and ATX2 overexpression counteracts the beneficial impact of calcium treatment. Our findings suggest that vesicle trafficking promotes organelle-specific ion interchange and cytoplasmic metal detoxification independent of calcineurin signaling or metal transporter re-localization. Our study identifies an alternative mode for cis-Golgi manganese supply in yeast and provides new perspectives for Hailey-Hailey disease treatment.

[Reproduction of Saccodon dariensis (Teleostei: Parodontidae) in Guatapé River tributaries, Magdalena River basin, Colombia]. / Reproducción de Saccodon dariensis (Teleostei: Parodontidae) en afluentes del río Guatapé, cuenca del río Magdalena, Colombia.

The Andean mountain region of Colombia has a high diversity of fish, with high number of endemic species. To promote their protection and conservation, the knowledge of their general and reproductive biology is necessary. With this aim, the reproductive biology of Saccodon dariensis, in the Peñoles and El Cardal creeks, Guatape River mid-basin, Magdalena River Basin, was studied, to determine reproductive differences between individuals with different oral polymorphism (morpho I vs. morpho IV, according to Roberts, 1974), and to define a possible spatial or temporal reproductive isolation. Ten field samplings were carried out between October 2007 and February 2012, in periods of rain (October and November 2007, May 2008 and November 2011), dry (January and March 2010, February 2012), transition from rain to dry (June 2011) and transition from dry to rain (March 2008 and September 2011). Samples were caught using electrofishing equipment and cast nets (10 mm between knots). A total of 468 specimens were analyzed, 268 of which were females and 200 males. The average catch size for the total number of individuals studied was 109.6 mm SL (65.5-174.0 mm), with 108.0 mm SL for females (67.7-174.0) and 111.9 mm SL (65.5-149.4) for males. Females predominated in the catches, and the sex ratio of 1.0:1.34 significantly deviated from the theoretical distribution 1:1. Similarly, morpho IV predominated in the catches, and morphs ratio was 1.00:1.48. Based on the monthly evolution of the gonadosomatic index (GSI) and the proportion of mature specimens, the spawning season occurs during periods of transition from dry to rainy season when water level begins to raise. The lowest values of the condition factor that match the maximum values of GSI, indicates that this species accumulated body energy reserves that are used during the gonadal maturation and spawning. The mean size at sexual maturity (L50) was 88.8 mm SL in females and 109.3 mm SL in males. The fecundity of S. dariensis fluctuated between 1 137 and 39 303 (mean = 8 309, SD = 9 021) and the relative fecundity between 144 and 1 131 oocytes/g of total weight (mean = 439 ± 212). The diameter of the oocytes was 0.54 mm (SD = 0.07). Different development in oocytes was not observed, suggesting massive spawning. The coexistence of the two morphs, external fertilization and simultaneous occurrence of reproductive peaks found in this study did not provide support for a possible spatial or temporal reproductive isolation of morphotypes.

Using yeast to model calcium-related diseases: example of the Hailey-Hailey disease.

Cross-complementation studies offer the possibility to overcome limitations imposed by the inherent complexity of multicellular organisms in the study of human diseases, by taking advantage of simpler model organisms like the budding yeast Saccharomyces cerevisiae. This review deals with, (1) the use of S. cerevisiae as a model organism to study human diseases, (2) yeast-based screening systems for the detection of disease modifiers, (3) Hailey-Hailey as an example of a calcium-related disease, and (4) the presentation of a yeast-based model to search for chemical modifiers of Hailey-Hailey disease. The preliminary experimental data presented and discussed here show that it is possible to use yeast as a model system for Hailey-Hailey disease and suggest that in all likelihood, yeast has the potential to reveal candidate drugs for the treatment of this disorder. This article is part of a Special Issue entitled: Calcium signaling in health and disease. Guest Editors: Geert Bultynck, Jacques Haiech, Claus W. Heizmann, Joachim Krebs, and Marc Moreau.

Mathematical Modeling of Different Molecule Removal on On-Line Haemodiafiltration: Influence of Dialysis Duration and Infusion Flow.

BACKGROUND: In a previous study on a nocturnal, every-other-day online haemodiafiltration scheme, different removal patterns were observed for urea, creatinine, ß2-​microglobulin, myoglobin and prolactin. The aim of this study was to evaluate the influence of dialysis duration and infusion flow (Qi) on the removal of different molecular weight (MW) solutes, and to quantify the effect of the different treatments on the kinetics of the solutes by using a classical two-compartment model. METHODS: This prospective, in-center study was carried out in 10 patients on a nocturnal, every-other-day online post-dilution haemodiafiltration program. Each patient received four dialysis sessions with different conditions, two 4-h sessions (with infusion flows of 50 or 100 ml/min) and two 8-h sessions (with infusion flows of 50 or 100 ml/min). To analyze the solute kinetics, blood samples were obtained hourly during the dialysis treatments and in the first 3 h post-dialysis. RESULTS: Removal patterns differed in the molecules studied, which were quantified by means of the two-compartment mathematical model. The main results show the impact of dialysis duration on the removal of low molecular weight molecules (urea and creatinine), while the impact of Qi is clearly shown for high molecular weight molecules (myoglobin and prolactin). For middle molecular weight solutes, such as ß2-microglobulin, both factors (duration and Qi) enhance the removal efficiency of the dialyzer. CONCLUSIONS: Our study evaluates experimentally and mathematically how treatment time and infusion flow affect the filtration of solutes of different MW during post-dilution haemodiafiltration. The results provided by the present study should help physicians to select and individualise the most appropriate schedules to deliver an optimum diffusive and convective dialysis dose for each patient.

BRCA1/BARD1 ubiquitinates PCNA in unperturbed conditions to promote continuous DNA synthesis.

Deficiencies in the BRCA1 tumor suppressor gene are the main cause of hereditary breast and ovarian cancer. BRCA1 is involved in the Homologous Recombination DNA repair pathway and, together with BARD1, forms a heterodimer with ubiquitin E3 activity. The relevance of the BRCA1/BARD1 ubiquitin E3 activity for tumor suppression and DNA repair remains controversial. Here, we observe that the BRCA1/BARD1 ubiquitin E3 activity is not required for Homologous Recombination or resistance to Olaparib. Using TULIP2 methodology, which enables the direct identification of E3-specific ubiquitination substrates, we identify substrates for BRCA1/BARD1. We find that PCNA is ubiquitinated by BRCA1/BARD1 in unperturbed conditions independently of RAD18. PCNA ubiquitination by BRCA1/BARD1 avoids the formation of ssDNA gaps during DNA replication and promotes continuous DNA synthesis. These results provide additional insight about the importance of BRCA1/BARD1 E3 activity in Homologous Recombination.

Impaired manganese metabolism causes mitotic misregulation.

Manganese is an essential trace element, whose intracellular levels need to be carefully regulated. Mn(2+) acts as a cofactor for many enzymes and excess of Mn(2+) is toxic. Alterations in Mn(2+) homeostasis affect metabolic functions and mutations in the human Mn(2+)/Ca(2+) transporter ATP2C1 have been linked to Hailey-Hailey disease. By deletion of the yeast orthologue PMR1 we have studied the impact of Mn(2+) on cell cycle progression and show that an excess of cytosolic Mn(2+) alters S-phase transit, induces transcriptional up-regulation of cell cycle regulators, bypasses the need for S-phase cell cycle checkpoints and predisposes to genomic instability. On the other hand, we find that depletion of the Golgi Mn(2+) pool requires a functional morphology checkpoint to avoid the formation of polyploid cells.

[Diversity of birds in the Agricultural Center Cotové, Santa Fe de Antioquia, Colombia]. / Diversidad de aves en el Centro Agropecuario Cotové, Santa Fe de Antioquia, Colombia.

Fragmentation of natural habitats is a central concern of biodiversity conservation and is considered a significant factor contributing to species loss and populations decline. We studied this in Cotové Agricultural Center in the municipality of Santa Fe de Antioquia (Colombia),where the conversion of natural forests to different land use systems, has limited the amount of available habitat. With the aim to describe the effect of habitat loss on bird presence in five land uses (fruiting trees, silvopastoral systems, secondary forest, pasture low density of trees and grass cutting) in this area, we studied bird diversity using two methods: fixed point counts and mist nets to analyze the influence of land use in the composition, richness and abundance of birds present were studied. A total of 6633 individuals of 101 species were observed of which 11 species were migratory. The insectivorous and frugivorous foraging guilds were better represented. The Shannon index indicated the highest values of alpha diversity for the silvopastoral system, and the fruit with the lowest. The grazing and silvopastoral land systems shared more species with low tree density. The importance of the environmental heterogeneity found is highlighted as a positive factor for bird species richness, mostly of low and middle habitat specificity, and preferably from edge habitats and open areas. In order to preserve natural regeneration and connectivity between different land use types, and to promote stability of bird species populations, some management actions should be implemented in the area.