MaterniCode: New Bioinformatic Pipeline to Detect Fetal Aneuploidies and Rearrangements Using Next-Generation Sequencing.

Objective: The present study is aimed at introducing and evaluating MaterniCode, a state-of-the-art bioinformatic pipeline for noninvasive prenatal testing (NIPT) that leverages the Ion Torrent semiconductor sequencing platform. The initiative strives to revolutionize prenatal diagnostics by offering a rapid and cost-effective method without sacrificing accuracy. Methods: Two distinct bioinformatic strategies were employed for fetal sex determination, one of which achieved 100% accuracy. We analyzed 1225 maternal blood samples for fetal aneuploidies, benchmarking against the industry standard Illumina VeriSeq™ NIPT Solution v2. The capability of MaterniCode to detect and characterize complex chromosomal anomalies was also assessed. Results: MaterniCode achieved near-perfect accuracy in fetal sex determination through chromosome Y (chrY )-specific gene analysis, whereas the alternative method, employing the ratio of high-quality mapped reads on chrY relative to all reads, delivered 100% accuracy. For fetal aneuploidy detection, both the integrated WisecondorX and NIPTeR algorithms demonstrated a 100% sensitivity and specificity rate, consistent with Illumina VeriSeq™ NIPT Solution v2. The pipeline also successfully identified and precisely mapped significant chromosomal abnormalities, exemplified by a 2.4 Mb deletion on chromosome 13 and a 3 Mb duplication on chromosome 2. Conclusion: MaterniCode has proven to be an innovative and highly efficient tool in the domain of NIPT, demonstrating excellent sensitivity and specificity. Its robust capability to effectively detect a wide range of complex chromosomal aberrations, including rare and subtle variations, positions it as a promising and valuable addition to prenatal diagnostic technologies. This enhancement to diagnostic precision significantly aids clinicians in making informed decisions during pregnancy management.

SARS-CoV-2 rapidly evolves lineage-specific phenotypic differences when passaged repeatedly in immune-naïve mice.

The persistence of SARS-CoV-2 despite the development of vaccines and a degree of herd immunity is partly due to viral evolution reducing vaccine and treatment efficacy. Serial infections of wild-type (WT) SARS-CoV-2 in Balb/c mice yield mouse-adapted strains with greater infectivity and mortality. We investigate if passaging unmodified B.1.351 (Beta) and B.1.617.2 (Delta) 20 times in K18-ACE2 mice, expressing the human ACE2 receptor, in a BSL-3 laboratory without selective pressures, drives human health-relevant evolution and if evolution is lineage-dependent. Late-passage virus causes more severe disease, at organism and lung tissue scales, with late-passage Delta demonstrating antibody resistance and interferon suppression. This resistance co-occurs with a de novo spike S371F mutation, linked with both traits. S371F, an Omicron-characteristic mutation, is co-inherited at times with spike E1182G per Nanopore sequencing, existing in different within-sample viral variants at others. Both S371F and E1182G are linked to mammalian GOLGA7 and ZDHHC5 interactions, which mediate viral-cell entry and antiviral response. This study demonstrates SARS-CoV-2's tendency to evolve with phenotypic consequences, its evolution varying by lineage, and suggests non-dominant quasi-species contribution.

Incorporating the pedigree information in multi-environment trial analyses for improving common vetch.

Common vetch is one of the most profitable forage legumes due to its versatility in end-use which includes grain, hay, green manure, and silage. Furthermore, common vetch is one of the best crops to rotate with cereals as it can increase soil fertility which results in higher yield in cereal crops. The National Vetch Breeding Program located in South Australia is focused on developing new vetch varieties with higher grain and dry matter yields, better resistance to major diseases, and wider adaptability to Australian cropping environments. As part of this program, a study was conducted with 35 field trials from 2015 to 2021 in South Australia, Western Australia, Victoria, and New South Wales with the objective of determining the best parents for future crosses and the vetch lines with highest commercial value in terms of grain yield production. A total of 392 varieties were evaluated. The individual field trials were combined in a multi-environment trial data, where each trial is identified as an environment. Multiplicative mixed models were used to analyze the data and a factor analytic approach to model the genetic by environment interaction effects. The pedigree of the lines was then assembled and incorporated into the analysis. This approach allowed to partition the total effects into additive and non-additive components. The total and additive genetic effects were inspected across and within environments for broad and specific selections of the lines with the best commercial value and the best parents. Summary measures of overall performance and stability were used to aid with selection of parents. To the best of our knowledge, this is the first study which used the pedigree information to breed common vetch. In this paper, the application of this statistical methodology has been successfully implemented with the inclusion of the pedigree improving the fit of the models to the data with most of the total genetic variation explained by the additive heritable component. The results of this study have shown the importance of including the pedigree information for common vetch breeding programs and have improved the ability of breeders to select superior commercial lines and parents.

Colocalization of expression transcripts with COVID-19 outcomes is rare across cell states, cell types and organs.

Identifying causal genes at GWAS loci can help pinpoint targets for therapeutic interventions. Expression studies can disentangle such loci but signals from expression quantitative trait loci (eQTLs) often fail to colocalize-which means that the genetic control of measured expression is not shared with the genetic control of disease risk. This may be because gene expression is measured in the wrong cell type, physiological state, or organ. We tested whether Mendelian randomization (MR) could identify genes at loci influencing COVID-19 outcomes and whether the colocalization of genetic control of expression and COVID-19 outcomes was influenced by cell type, cell stimulation, and organ. We conducted MR of cis-eQTLs from single cell (scRNA-seq) and bulk RNA sequencing. We then tested variables that could influence colocalization, including cell type, cell stimulation, RNA sequencing modality, organ, symptoms of COVID-19, and SARS-CoV-2 status among individuals with symptoms of COVID-19. The outcomes used to test colocalization were COVID-19 severity and susceptibility as assessed in the Host Genetics Initiative release 7. Most transcripts identified using MR did not colocalize when tested across cell types, cell state and in different organs. Most that did colocalize likely represented false positives due to linkage disequilibrium. In general, colocalization was highly variable and at times inconsistent for the same transcript across cell type, cell stimulation and organ. While we identified factors that influenced colocalization for select transcripts, identifying 33 that mediate COVID-19 outcomes, our study suggests that colocalization of expression with COVID-19 outcomes is partially due to noisy signals even after following quality control and sensitivity testing. These findings illustrate the present difficulty of linking expression transcripts to disease outcomes and the need for skepticism when observing eQTL MR results, even accounting for cell types, stimulation state and different organs.

Proteome-wide Mendelian randomization implicates nephronectin as an actionable mediator of the effect of obesity on COVID-19 severity.

Obesity is a major risk factor for Coronavirus disease (COVID-19) severity; however, the mechanisms underlying this relationship are not fully understood. As obesity influences the plasma proteome, we sought to identify circulating proteins mediating the effects of obesity on COVID-19 severity in humans. Here, we screened 4,907 plasma proteins to identify proteins influenced by body mass index using Mendelian randomization. This yielded 1,216 proteins, whose effect on COVID-19 severity was assessed, again using Mendelian randomization. We found that an s.d. increase in nephronectin (NPNT) was associated with increased odds of critically ill COVID-19 (OR = 1.71, P = 1.63 × 10-10). The effect was driven by an NPNT splice isoform. Mediation analyses supported NPNT as a mediator. In single-cell RNA-sequencing, NPNT was expressed in alveolar cells and fibroblasts of the lung in individuals who died of COVID-19. Finally, decreasing body fat mass and increasing fat-free mass were found to lower NPNT levels. These findings provide actionable insights into how obesity influences COVID-19 severity.

Genomic atlas of the plasma metabolome prioritizes metabolites implicated in human diseases.

Metabolic processes can influence disease risk and provide therapeutic targets. By conducting genome-wide association studies of 1,091 blood metabolites and 309 metabolite ratios, we identified associations with 690 metabolites at 248 loci and associations with 143 metabolite ratios at 69 loci. Integrating metabolite-gene and gene expression information identified 94 effector genes for 109 metabolites and 48 metabolite ratios. Using Mendelian randomization (MR), we identified 22 metabolites and 20 metabolite ratios having estimated causal effect on 12 traits and diseases, including orotate for estimated bone mineral density, α-hydroxyisovalerate for body mass index and ergothioneine for inflammatory bowel disease and asthma. We further measured the orotate level in a separate cohort and demonstrated that, consistent with MR, orotate levels were positively associated with incident hip fractures. This study provides a valuable resource describing the genetic architecture of metabolites and delivers insights into their roles in common diseases, thereby offering opportunities for therapeutic targets.

Assessing cellular internalization and endosomal escape abilities of novel BUFII-Graphene oxide nanobioconjugates.

Cell-penetrating agents based on functionalized nanoplatforms have emerged as a promising approach for developing more efficient and multifunctional delivery vehicles for treating various complex diseases that require reaching different intracellular compartments. Our previous work has shown that achieving full cellular coverage and high endosomal escape rates is possible by interfacing magnetite nanoparticles with potent translocating peptides such as Buforin II (BUF-II). In this work, we extended such an approach to two graphene oxide (GO)-based nanoplatforms functionalized with different surface chemistries to which the peptide molecules were successfully conjugated. The developed nanobioconjugates were characterized via spectroscopic (FTIR, Raman), thermogravimetric, and microscopic (SEM, TEM, and AFM) techniques. Moreover, biocompatibility was assessed via standardized hemocompatibility and cytotoxicity assays in two cell lines. Finally, cell internalization and coverage and endosomal escape abilities were estimated with the aid of confocal microscopy analysis of colocalization of the nanobioconjugates with Lysotracker Green®. Our findings showed coverage values that approached 100% for both cell lines, high biocompatibility, and endosomal escape levels ranging from 30 to 45% and 12-24% for Vero and THP-1 cell lines. This work provides the first routes toward developing the next-generation, carbon-based, cell-penetrating nanovehicles to deliver therapeutic agents. Further studies will be focused on elucidating the intracellular trafficking pathways of the nanobioconjugates to reach different cellular compartments.

Alternative splicing in the lung influences COVID-19 severity and respiratory diseases.

Hospital admission for COVID-19 remains common despite the successful development of vaccines and treatments. Thus, there is an ongoing need to identify targets for new COVID-19 therapies. Alternative splicing is an essential mechanism for generating functional diversity in protein isoforms and influences immune response to infection. However, the causal role of alternative splicing in COVID-19 severity and its potential therapeutic relevance is not fully understood. In this study, we evaluated the causal role of alternative splicing in COVID-19 severity and susceptibility using Mendelian randomization (MR). To do so, we performed two-sample MR to assess whether cis-sQTLs spanning 8,172 gene splicing in 5,295 genes were associated with COVID-19 outcomes in the COVID-19 Host Genetics Initiative, including up to 158,840 COVID-19 cases and 2,782,977 population controls. We identified that alternative splicing in lungs, rather than total RNA expression of OAS1, ATP11A, DPP9 and NPNT, was associated with COVID-19 severity. MUC1 splicing was associated with COVID-19 susceptibility. Further colocalization analyses supported a shared genetic mechanism between COVID-19 severity with idiopathic pulmonary fibrosis at ATP11A and DPP9 loci, and with chronic obstructive lung diseases at NPNT. We lastly showed that ATP11A, DPP9, NPNT, and MUC1 were highly expressed in lung alveolar epithelial cells, both in COVID-19 uninfected and infected samples. Taken together, these findings clarify the importance of alternative splicing of proteins in the lung for COVID-19 and other respiratory diseases, providing isoform-based targets for drug discovery.

Proteome-wide Mendelian randomization implicates nephronectin as an actionable mediator of the effect of obesity on COVID-19 severity

Obesity is a major risk factor for COVID-19 severity; however, the underlying mechanism is not fully understood. Considering that obesity influences the human plasma proteome, we sought to identify circulating proteins mediating the effects of obesity on COVID-19 severity. We first screened 4,907 plasma proteins to identify proteins influenced by body mass index (BMI) using Mendelian randomization (MR). This yielded 1,216 proteins, whose effects on COVID-19 severity were assessed, again using MR. This two-step approach identified nephronectin (NPNT), for which a one standard deviation increase was associated with severe COVID-19 (odds ratio = 1.71, 95% CI: 1.45-2.02, P = 1.63 x 10-10). Colocalization analyses indicated that an NPNT splice isoform drove this effect. Overall, NPNT mediates 3.7% of the total effect of BMI on severe COVID-19. Finally, we found that decreasing body fat mass and increasing fat-free mass can lower NPNT levels and thus may improve COVID-19 outcomes. These findings provide actionable insights into how obesity influences COVID-19 severity.

Treatment with type-i collagen scaffolds in patients with venous ulcers. case report

ABSTRACT Introduction: Chronic venous insufficiency affects about 5% of the global adult population. Venous leg ulcers are one of the most frequent complications of this pathology, with a global prevalence of 2%. This disease affects both the quality of life of patients and, due to the high cost of the treatment, the health system. Compressive therapy and moist wound healing have been the gold standard treatment. However, when complications occur, they may not be effective. Case report: This is the case of a 66-year-old female patient with venous ulcers on her lower limbs and symptoms of fever and local pain that did not respond to conventional therapies. The patient was treated with a new dermal substitute made of an acellular type-I collagen membrane, which promotes the closure of the ulcer by stimulating the replacement of injured tissue with tissue similar to the healthy one. The condition of the patient improved at 16 weeks, and after 8 months of treatment there was no recurrence of the lesions. Conclusions: Acellular type-I collagen membrane developed by the Tissue Engineering Working Group of the Department of Pharmacy of the Universidad Nacional de Colombia is effective in treating venous ulcers of the lower limbs. Its low cost facilitates the access of the whole population to therapies based on its application.

RESUMEN Introducción. La insuficiencia venosa crónica afecta alrededor del 5% de la población adulta en el mundo; una de sus mayores complicaciones son las úlceras en miembros inferiores, las cuales tienen una prevalencia mundial del 2%. Las úlceras afectan la calidad de vida de los pacientes e impactan al sistema de salud debido a los altos costos de atención que genera. El tratamiento de referencia es la terapia compresiva y la cura húmeda de las heridas, sin embargo estas intervenciones pueden no ser efectivas cuando las lesiones se complican. Presentación del caso. Paciente femenina de 66 años con úlceras venosas en miembros inferiores acompañadas de fiebre y dolor local que no respondían a las terapias convencionales. La paciente fue tratada con un nuevo sustituto dérmico basado en una membrana acelular de colágeno tipo I que contribuye al cierre de la úlcera al estimular el remplazo del tejido lesionado por tejido similar al sano, con lo cual tuvo mejoría a las 16 semanas; después de 8 meses de terminado el tratamiento no se presentó recurrencia de las lesiones. Conclusiones. La membrana acelular de colágeno tipo I desarrollada por el Grupo de Trabajo en Ingeniería de Tejidos del Departamento de Farmacia de la Universidad Nacional de Colombia es efectiva en el tratamiento de úlceras venosas en miembros inferiores y su bajo costo facilita el acceso de toda la población a terapias basadas en su aplicación.

CgSTE11 mediates cross tolerance to multiple environmental stressors in Candida glabrata.

Candida glabrata is a human commensal and an opportunistic human fungal pathogen. It is more closely related to the model yeast Saccharomyces cerevisiae than other Candida spp. Compared with S. cerevisiae, C. glabrata exhibits higher innate tolerance to various environmental stressors, including hyperthermal stress. Here we investigate the molecular mechanisms of C. glabrata adaptation to heat stress via adaptive laboratory evolution. We show that all parallel evolved populations readily adapt to hyperthermal challenge (from 47 °C to 50 °C) and exhibit convergence in evolved phenotypes with extensive cross-tolerance to various other environmental stressors such as oxidants, acids, and alcohols. Genome resequencing identified fixation of mutations in CgSTE11 in all parallel evolved populations. The CgSTE11 homolog in S. cerevisiae plays crucial roles in various mitogen-activated protein kinase (MAPK) signaling pathways, but its role is less understood in C. glabrata. Subsequent verification confirmed that CgSTE11 is important in hyperthermal tolerance and the observed extensive cross-tolerance to other environmental stressors. These results support the hypothesis that CgSTE11 mediates cross-talks between MAPK signaling pathways in C. glabrata in response to environmental challenges.

Coronary artery treatment with a urea-based paclitaxel-coated balloon: the European-wide FALCON all-comers DCB Registry (FALCON Registry).

AIMS: The aim of this study was to investigate the use of a drug-coated balloon (DCB) in daily clinical practice and provide further evidence on the safety and efficacy of paclitaxel-coated balloon treatment using urea as an inert excipient. METHODS AND RESULTS: Between December 2013 and December 2015, 757 patients treated for coronary lesions with the IN.PACT Falcon balloon were enrolled in this prospective real-world all-comers registry. The primary outcome was the clinically driven target lesion revascularisation (TLR) rate at 12 months. The secondary outcome was major adverse cardiac events (MACE) defined as cardiac death, myocardial infarction, TLR and target vessel revascularisation (TVR). Out of 805 lesions, 43.1% were de novo, and 53.2% drug-eluting stent (DES) or bare metal stent (BMS) in-stent restenosis (ISR). TLR at 12 months was 6.2% and TVR 8.3%. MACE occurred in 9.7% of patients with a composite of cardiac death in 0.8% and myocardial infarction in 2.7% plus TLR/TVR. Subgroup analysis confirmed a TLR rate of 7.5% for ISR (2.1% BMS and 9.5% DES) and 4.9% for de novo lesions. CONCLUSIONS: The IN.PACT Falcon urea-based paclitaxel-coated balloon is safe and efficient in de novo and ISR lesions with low rates of TLR/TVR. The high proportion of treatment of de novo lesions indicates that a DCB-only strategy is nowadays common.

Stability of Signaling Pathways during Aging-A Boolean Network Approach.

Biological pathways are thought to be robust against a variety of internal and external perturbations. Fail-safe mechanisms allow for compensation of perturbations to maintain the characteristic function of a pathway. Pathways can undergo changes during aging, which may lead to changes in their stability. Less stable or less robust pathways may be consequential to or increase the susceptibility of the development of diseases. Among others, NF- κ B signaling is a crucial pathway in the process of aging. The NF- κ B system is involved in the immune response and dealing with various internal and external stresses. Boolean networks as models of biological pathways allow for simulation of signaling behavior. They can help to identify which proposed mechanisms are biologically representative and which ones function but do not mirror physical processes-for instance, changes of signaling pathways during the aging process. Boolean networks can be inferred from time-series of gene expression data. This allows us to get insights into the changes of behavior of pathways such as NF- κ B signaling in aged organisms in comparison to young ones.

Intermediate CD14++CD16+ monocytes decline after transcatheter aortic valve replacement and correlate with functional capacity and left ventricular systolic function.

BACKGROUND: Transcatheter aortic valve replacement (TAVR) is the method of choice for patients with severe aortic valve stenosis, who are ineligible or at high risk for surgery. Though TAVR leads to a significant reduction in mortality, a notable amount of patients are re-hospitalized early after TAVR. Parameters or biomarkers predicting outcome are therefore needed to identify patients who benefit most. Specific monocyte subsets have been associated with cardiovascular diseases and were shown to possess prognostic value. METHODS: Peripheral blood was drawn before and after transfemoral TAVR with the self-expanding CoreValve, Boston Lotus or the balloon-expanding Edwards Sapien prosthesis. Classical (CD14++CD16-), intermediate (CD14++CD16+) and non-classical (CD14+CD16++) monocyte subsets were determined by flow cytometry. Transthoracic echocardiography was performed before, early after as well as 3 months after the TAVR procedure. RESULTS: No significant differences in the absolute monocyte counts were found after TAVR. A significant decline in the intermediate monocyte population was though observed early after TAVR (pre 4.01±0.38%, post 2.803±0.34%, p≤0.05). Creatinine levels stayed stable after TAVR procedure and intermediate monocytes were associated with worse renal function. Monocyte decline was not related to changes in CRP-, noradrenaline, cortisol or aldosterone-levels. The amount of intermediate monocytes correlated with worse cardiac function and predicted the possibility to reach an improvement in NYHA functional class at 3 months after TAVR. CONCLUSIONS: A significant decline of intermediate monocytes occurs shortly after TAVR. High levels of intermediate monocytes were associated with worse cardiac function and predicted poor functional capacity, hinting at a possible prognostic value.

Impact of Preprocedural Left Ventricular Ejection Fraction on 1-Year Outcomes After MitraClip Implantation (from the ACCESS-EU Phase I, a Prospective, Multicenter, Nonrandomized Postapproval Study of the MitraClip Therapy in Europe).

This report describes the 12-month outcomes of the a prospective, multicenter, nonrandomized post-approval study of the MitraClip therapy in Europe (ACCESS-EU postapproval study of MitraClip therapy) with respect to preprocedural left ventricular ejection fraction (LVEF). Transcatheter deployment of the MitraClip device may be considered for patients who are not suitable for conventional surgery. A total of 567 patients with significant mitral regurgitation (MR) underwent MitraClip therapy. Of those, 393 had functional MR (FMR) and were subdivided by preprocedural LVEF (A: 10% to 20%, B: >20% to 30%, C: >30% to 40%, D: >40%). Procedural safety and efficacy and treatment outcomes including MR grade, New York Heart Association (NYHA) functional class, 6-minute walk test, and the Minnesota Living with Heart Failure Questionnaire were analyzed at baseline, 30 days, and 12 months. Baseline mean logistic EuroSCORE was 25 ± 19; 87% of patients were in NYHA classes III or IV (A: 96%, B: 83%, C: 90%, D: 86%). There was no incidence of death or stroke intraprocedurally. Eleven patients died within 30 days with no differences among subgroups. Kaplan-Meier survival at 12 months was 81.8% (A: 71%, B: 79%, C: 87%, D: 86%). There was a significant improvement in MR severity at 30 days and 12 months (p <0.0001). At 12 months, all subgroups experienced similar improvements in NYHA class, 6-minute walk test, and Minnesota Living with Heart Failure Questionnaire. This real-world registry reports promising results of MitraClip therapy in patients with FMR. In conclusion, the low rates of hospital mortality and adverse events in patients with FMR-even in patients with severely reduced LVEF-provide additional evidence of substantial benefits after MitraClip implantation.

Plan de atención integral de enfermería para el cuidado de personas con úlceras por presión / Integral plan nursing care of people with pressure ulcers

Antecedentes. Las úlceras por presión son un problema de salud pública que afecta al paciente, su familia y el sistema de salud; provocan sufrimiento que afecta su calidad de vida. El tratamiento genera altos costos para la institución y aumenta la carga de trabajo en el equipo de salud. Las intervenciones de enfermería para planear el cuidado eficaz, oportuno e individualizado en personas con úlceras por presión se basan en valoración integral de la persona, actividades de prevención, diagnóstico, tratamiento y rehabilitación con el uso de taxonomías NANDA-NIC-NOC, que permiten responder cuestionamientos sobre la seguridad, eficiencia y costo-efectividad del cuidado de enfermería. Objetivo. Proponer un plan de atención de enfermería integral para las personas con úlceras por presión. Material y Métodos. Revisión sistemática de literatura científica de los últimos 5 años en las bases de datos Medline, CINAHL, LILACS, FECYT, Embase y SciELO. Resultados. Construcción de un plan de atención de enfermería flexible basado en evidencia científica, resultado de los hallazgos de la revisión sistemática, que oriente la toma de decisiones en el cuidado integral de las personas con Úlceras por Presión y contribuya a la calidad de los servicios de salud mejorando la Calidad de Vida relacionada con la Salud. Conclusiones. Es preciso brindar un cuidado integral basado en evidencia científica conducente a establecer medidas preventivas que guíe la intervención de enfermería eficaz e individualizada garante de la limitación del daño y la rehabilitación oportuna de las personas con Úlceras por Presión, aportando al desarrollo y visibilidad disciplinar.

Background. Pressure Ulcers are a public health problem that affects the patient, their family and the health care system; causing suffering to affect their quality of life. The treatment results in high costs for the institution and increases the workload on the health care team. Nursing interventions to plan effective, timely and individualized care in people with pressure ulcers, are based on integral evaluation of the person, prevention, diagnosis, treatment and rehabilitation taxonomies using NANDA-NIC-NOC, the let them answer questions about the safety, efficiency and cost-effectiveness of nursing practice. Objectives. Propose a plan of integral nursing care for people with pressure ulcers. Material and methods. Systematic review of scientific literature of the last 5 years in the Medline, CINAHL, LILACS, FECYT, Embase y SciELO. Results. Building a flexible plan of nursing care based on scientific evidence, resulting from the findings of the systematic review, to guide decision making in the integral care of people with pressure ulcers and contributes to the quality of health services improving the quality of life related to health. Conclusions. It is necessary to provide integral care based on scientific evidence conducive to establish preventive measures to guide effective nursing intervention and individualized guarantor of damage limitation and timely rehabilitation of persons with Pressure Ulcers, contributing to the development and visibility discipline.

Biological effects and equivalent doses in radiotherapy: A software solution.

BACKGROUND: The limits of TDF (time, dose, and fractionation) and linear quadratic models have been known for a long time. Medical physicists and physicians are required to provide fast and reliable interpretations regarding delivered doses or any future prescriptions relating to treatment changes. AIM: We, therefore, propose a calculation interface under the GNU license to be used for equivalent doses, biological doses, and normal tumor complication probability (Lyman model). MATERIALS AND METHODS: THE METHODOLOGY USED DRAWS FROM SEVERAL SOURCES: the linear-quadratic-linear model of Astrahan, the repopulation effects of Dale, and the prediction of multi-fractionated treatments of Thames. RESULTS AND CONCLUSIONS: The results are obtained from an algorithm that minimizes an ad-hoc cost function, and then compared to an equivalent dose computed using standard calculators in seven French radiotherapy centers.

Cysteine coordination of Pb(II) is involved in the PbrR-dependent activation of the lead-resistance promoter, PpbrA, from Cupriavidus metallidurans CH34.

BACKGROUND: The pbr resistance operon from Cupriavidus metallidurans CH34 plasmid pMOL30 confers resistance to Pb(II) salts, and is regulated by the Pb(II) responsive regulator PbrR, which is a MerR family activator. In other metal sensing MerR family regulators, such as MerR, CueR, and ZntR the cognate regulator binds to a promoter with an unusually long spacer between the -35 and -10 sequences, and activates transcription of resistance genes as a consequence of binding the appropriate metal. Cysteine residues in these regulators are essential for metal ion coordination and activation of expression from their cognate promoter. In this study we investigated the interaction of PbrR with the promoter for the structural pbr resistance genes, PpbrA, effects on transcriptional activation of altering the DNA sequence of PpbrA, and effects on Pb(II)-induced activation of PpbrA when cysteine residues in PbrR were mutated to serine. RESULTS: Gel retardation and footprinting assays using purified PbrR show that it binds to, and protects from DNase I digestion, the PpbrA promoter, which has a 19 bp spacer between its -35 and -10 sites. Using ß-galactosidase assays in C. metallidurans, we show that when PpbrA is changed to an 18 bp spacer, there is an increase in transcriptional activation both in the presence and absence of Pb(II) salts up to a maximum induction equivalent to that seen in the fully-induced wild-type promoter. Changes to the -10 sequence of PpbrA from TTAAAT to the consensus E. coli -10 sequence (TATAAT) increased transcriptional activation from PpbrA, whilst changing the -10 sequence to that of the Tn501 mer promoter (TAAGGT) also increased the transcriptional response, but only in the presence of Pb(II). Individual PbrR mutants C14S, C55S, C79S, C114S, C123S, C132S and C134S, and a double mutant C132S/C134S, were tested for Pb(II) response from PpbrA, using ß-galactosidase assays in C. metallidurans. The PbrR C14S, C79S, C134S, and C132S/C134S mutants were defective in Pb(II)-induced activation of PpbrA. CONCLUSIONS: These data show that the metal-dependent activation of PbrR occurs by a similar mechanism to that of MerR, but that metal ion coordination is through cysteines which differ from those seen in other MerR family regulators, and that the DNA sequence of the -10 promoter affects expression levels of the lead resistance genes.

Transcriptional activation of MerR family promoters in Cupriavidus metallidurans CH34.

Metal responsive MerR family transcriptional regulators are widespread in bacteria and activate the transcription of genes involved in metal ion detoxification, efflux, or homeostasis, in response to the presence of cognate metal species in the cytoplasm. MerR family regulators recognize and bind to dyad symmetrical DNA sequences in specific promoters that have a spacer region between the -35 and -10 sequences which is longer than the canonical 16-18 bp spacer for other sigma(70)-dependent promoters. In this study we report beta-galactosidase assays of MerR family-regulated gene expression in the multiple metal resistant bacterium Cupriavidus metallidurans. A series of pMU2385 reporter plasmid derivatives containing cloned MerR family-activated promoters were used to determine metal ion-induced responses from different MerR family regulated promoters, as well as regulators cloned with the cognate promoter into pMU2385. Mercuric ion-responsive MerR and lead ion-responsive PbrR activity was confirmed using this assay system as well as MerR family activator activity on heterologous promoters PcopA, PcadA, and Pzcc from Escherichia coli, Pseudomonas aeruginosa and Bordetella pertussis, respectively. In C. metallidurans CH34, transcription from these promoters was activated by MerR family regulators encoded on the chromosome or megaplasmids in response to copper (PcopA), and lead (PcadA and PzccA), showing that MerR family activators in C. metallidurans can act on MerR family promoters from other organisms, which have sequence differences to the predicted C. metallidurans promoters.

Mercury resistance determinants related to Tn21, Tn1696, and Tn5053 in enterobacteria from the preantibiotic era.

Three mer transposons from the Murray collection of preantibiotic enterobacteria show >99% sequence identity to current isolates. Tn5073 is most closely related to Tn5036 and Tn1696, and Tn5074 is most closely related to Tn5053. Tn5075 is most closely related to Tn21 but lacks integron In2 and is flanked by insertion elements.