Activity of DNA polymerase κ across the genome in human fibroblasts.

DNA polymerase κ (Polκ) is a specialized polymerase that has multiple cellular roles such as translesion DNA synthesis, replication of repetitive sequences, and nucleotide excision repair. We have developed a method for capturing DNA synthesized by Polκ utilizing a Polκ-specific substrate, N2-(4-ethynylbenzyl)-2'-deoxyguanosine (EBndG). After shearing of the DNA into 200 to 500 bp lengths, the EBndG-containing DNA was covalently bound to biotin using the Cu(I)-catalyzed alkyne-azide cycloaddition reaction and isolated with streptavidin beads. Isolated DNA was then ligated to adaptors, followed by PCR amplification and next-generation sequencing to generate genome-wide repair maps. We have termed this method polymerase κ sequencing. Here, we present the human genome maps for Polκ activity in an undamaged cell line. We found that Polκ activity was enhanced in GC-rich regions, euchromatin regions, the promoter of genes, and in DNA that is replicated early in the S phase.

Multi-focused laboratory experiments based on Quorum Sensing and Quorum Quenching for acquiring Microbial Physiology concepts.

After a time away from the classrooms and laboratories due to the global pandemic, the return to teaching activities during the semester represented a challenge to both teachers and students. Our particular situation in a Microbial Physiology course was the necessity of imparting in shorter time, laboratory practices that usually take longer. This article describes a 2-week-long laboratory exercise that covers several concepts in an interrelated way: conjugation as a gene transfer mechanism, regulation of microbial physiology, production of secondary metabolites, degradation of macromolecules, and biofilm formation. Utilizing a Quorum Quenching (QQ) strategy, the Quorum Sensing (QS) system of Pseudomonas aeruginosa is first attenuated. Then, phenotypes regulated by QS are evidenced. QS is a regulatory mechanism of microbial physiology that relies on signal molecules. QS is related in P. aeruginosa to several virulence factors, some of which are exploited in the laboratory practices presented in this work. QQ is a phenomenon by which QS is interrupted or attenuated. We utilized a QQ approach based on the enzymatic degradation of the P. aeruginosa QS signals to evidence QS-regulated traits that are relevant to our Microbial Physiology course. Results obtained with the same test performed by a random group of students before and after the activities show the positive effectiveness of the approach presented in this work.

Psychometric properties and invariance of an English self-efficacy scale for university students in Peru.

Background: English is a global language used to communicate with members of the international community. Self-efficacy in learning English is an important factor that is influenced by perceived importance, interest, and beliefs about the ability to successfully perform tasks in English. Objective: The aim is to develop and validate a measurement instrument to assess English self-efficacy. Methods: A total of 453 students from different Peruvian universities participated, with ages ranging from 18 to 60 years (M = 23; SD = 6.18). Statistical techniques for latent variables were used and recommendations for educational and psychological tests were followed in its construction. The sample was divided into two groups to perform exploratory factor analysis (EFA) and confirmatory factor analysis (CFA). Results: The English Self-Efficacy Scale (ESS-P) is representative and relevant in terms of its item content (Aiken's V > 0.70). Its internal structure is organized into three first order factors and a second order factor that are consistent with the theoretical proposal and was confirmed through CFA with excellent goodness-of-fit indices (χ2 = 1184.9, gl = 626, CFI = 0.92, TLI = 0.92, RMSEA = 0.06 y SRMR = 0.04). It also has adequate internal consistency in its three factors (Reading α/ω = 0.96), Oral Communication (α/ω = 0.95), and Writing (α/ω = 0.97) and the whole scale (α/ω = 0.98), is invariant with respect to sex, and has a conceptual relationship with variables such as academic self-efficacy and exam anxiety. Conclusion: The ESS-P is a measurement instrument with evidence of validity, factorial invariance, and good reliability of its scores. Therefore, it can be used in future studies in the academic context.

Vinasse as a substrate for inoculant culture and soil fertigation: Advancing the circular and green economy.

Vinasse is a by-product with a key role in circular economy. In this work, we analyze sugarcane vinasse as culture medium for obtaining single and mixed inoculants. Trichoderma harzianum MT2 was cultured in single and sequential co-culture with Pseudomonas capeferrum WCS358 or Rhizobium sp. N21.2. Fungal biomass in single culture was more than three folds higher in vinasse than in a standard medium, and was higher in co-culture with Rhizobium sp. N21.2 than with P. capeferrum WCS358. Bacterial growths in vinasse, in particular P. capeferrum WCS358, were improved in co-culture with T. harzianum MT2. Residual vinasses, obtained after microbial growth, presented almost neutral pH and lower conductivities and toxicity than raw vinasse. Fertigation with residual vinasses modifies characteristics of soil evidenced in the total N, cation exchange capacity, urease and acid phosphatase, and microbial metabolic diversity, in comparison to raw vinasse. In general, soil fertigation with residual vinasse from co-culture with P. capeferrum WCS358 is more similar to irrigation with water. Treatment evaluation indicates that vinasse is suitable for the production of mixed inoculants containing T. harzianum. The co-culture with P. capeferrum WCS358 improves the characteristics of the residual vinasse allowing a fertigation with less detrimental effect in soil in comparison to Rhizobium sp. N21.2. Obtaining valuable biomass of single or mixed inoculants in vinasse with lower ecological impact is relevant for the circular and green economy.

Complement inhibitors for kidney disease.

A refined understanding of the role of complement in the pathogenesis of glomerular and other kidney diseases has, over the past two decades, been matched by the development of novel, complement-targeting therapies. As we increasingly recognize the important role that complement activation across all three pathways-classical, lectin and alternative-plays in glomerular lesions both rare (e.g. C3 glomerulopathy) and common (e.g. immunoglobulin A nephropathy), we can identify avenues for precise, targeted approaches to modifying the natural history of these kidney diseases. In this review, we survey the evidence on using complement inhibition from the earliest, small-scale studies focusing on C5-targeting agents to more recent, large, multicenter, randomized trials utilizing complement blockade higher up in the complement pathway at the level of C3. We conclude by examining where the field of complement targeting therapy may be headed in light of these studies.

Feasibility of a Peer Mentor Training Program for Patients Receiving Hemodialysis: An Educational Program Evaluation.

Rationale and Objective: The 'PEER-HD' multicenter study tests the effectiveness of peer mentorship to reduce hospitalizations in patients receiving maintenance hemodialysis. In this study, we describe the feasibility, efficacy, and acceptability of the mentor training program. Study Design: Educational program evaluation including the following aspects: (1) description of training content, (2) quantitative analysis of feasibility and acceptability of the program, and (3) quantitative pre-post analysis of efficacy of the training to impart knowledge and self-efficacy. Setting and Participants: Data were collected using baseline clinical and sociodemographic questionnaires from mentor participants enrolled in Bronx, NY, and Nashville, TN, themselves receiving maintenance hemodialysis. Analytical Approach: The outcome variables were the following: (1) feasibility measured by training module attendance and completion, (2) efficacy of the program to impart knowledge and self-efficacy measured by kidney knowledge and self-efficacy surveys, and (3) acceptability as measured by an 11-item survey of trainer performance and module content. Results: The PEER-HD training program included 4 2-hour modules that covered topics including dialysis-specific knowledge and mentorship skills. Of the 16 mentor participants, 14 completed the training program. There was complete attendance to all training modules, though some patients required flexibility in scheduling and format. Performance on posttraining quizzes was consistent with high knowledge (mean scores ranged from 82.0%-90.0% correct). Mean dialysis-specific knowledge scores trended higher post training than at baseline though this difference was not statistically significant (90.0% vs 78.1%; P = 0.1). No change in mean self-efficacy scores was demonstrated from before to after training, among mentor participants (P = 0.2). Program evaluation assessments of acceptability were favorable [mean of all patient scores (0-4) within each module ranged from 3.43-3.93]. Limitations: Small sample size. Conclusions: The PEER-HD mentor training program required accommodation to patients' schedules but was feasible. Participants rated the program favorably, and although the comparison of performance on knowledge assessments post- and pre-program showed uptake of knowledge, this was not statistically significant.

Modulation of quorum sensing activity by copper sulfate, potassium dichromate, and cadmium chloride in biosensor strains.

Beyond their biological roles, metals have a strong impact on the environment. It has been reported that metals are also inhibitory of Quorum Sensing (QS) mechanisms, ones of the best characterized signaling systems in bacteria and fungi. We analyzed the effect of CuSO4, CdCl2, and K2Cr2O7, on QS systems sharing or differing in the bacterial host or the QS signal. The results in this study show that CuSO4 can not only be inhibitory, but also stimulatory of QS activity: at 0.2 mM increased six fold the activity in Chromobacterium subtsugae CV026. This behavior is related to the concentration of the metal and the particular QS system: E. coli MT102 (pJBA132) was no affected, but CuSO4 decreased the QS activity of Pseudomonas putida F117 (pKR-C12) to half its control values. K2Cr2O7 increased four and three folds the QS activities of E. coli MT102 (pJBA132) and P. putida F117 (pAS-C8), respectively, but without effect when combined with CuSO4 or CdCl2. CdCl2 only showed a positive effect in CV026 when combined with CuSO4. Results suggest that factors related with the culture conditions impact on the influence of the metals, and reinforce the importance of the environment in the modulation of QS activity.

Anemia Management in the Cancer Patient With CKD and End-Stage Kidney Disease.

Anemia is a common medical problem among patients with cancer and chronic kidney disease (CKD). Although anemia in patients with CKD is often treated with iron and erythropoietin-stimulating agents, there are controversies with regard to the use of erythropoietin-stimulating agents in cancer patients. In this article, we review the treatment of anemia in patients with cancer and CKD, in addition to summarizing the current guidelines in treatment of anemia in these patients.

Utility of EST-SNP Markers for Improving Management and Use of Olive Genetic Resources: A Case Study at the Worldwide Olive Germplasm Bank of Córdoba.

Olive, the emblematic Mediterranean fruit crop, owns a great varietal diversity, which is maintained in ex situ field collections, such as the World Olive Germplasm Bank of Córdoba (WOGBC), Spain. Accurate identification of WOGBC, one of the world's largest collections, is essential for efficient management and use of olive germplasm. The present study is the first report of the use of a core set of 96 EST-SNP markers for the fingerprinting of 1273 accessions from 29 countries, including both field and new acquired accessions. The EST-SNP fingerprinting made possible the accurate identification of 668 different genotypes, including 148 detected among the new acquired accessions. Despite the overall high genetic diversity found at WOGBC, the EST-SNPs also revealed the presence of remarkable redundant germplasm mostly represented by synonymy cases within and between countries. This finding, together with the presence of homonymy cases, may reflect a continuous interchange of olive cultivars, as well as a common and general approach for their naming. The structure analysis revealed a certain geographic clustering of the analysed germplasm. The EST-SNP panel under study provides a powerful and accurate genotyping tool, allowing for the foundation of a common strategy for efficient safeguarding and management of olive genetic resources.

How Temperatures May Affect the Synthesis of Fatty Acids during Olive Fruit Ripening: Genes at Work in the Field.

A major concern for olive cultivation in many extra-Mediterranean regions is the adaptation of recently introduced cultivars to environmental conditions different from those prevailing in the original area, such as the Mediterranean basin. Some of these cultivars can easily adapt their physiological and biochemical parameters in new agro-environments, whereas others show unbalanced values of oleic acid content. The objective of this study was to evaluate the effects of the thermal regime during oil synthesis on the expression of fatty acid desaturase genes and on the unsaturated fatty acid contents at the field level. Two cultivars (Arbequina and Coratina) were included in the analysis over a wide latitudinal gradient in Argentina. The results suggest that the thermal regime exerts a regulatory effect at the transcriptional level on both OeSAD2 and OeFAD2-2 genes and that this regulation is cultivar-dependent. It was also observed that the accumulated thermal time affects gene expression and the contents of oleic and linoleic acids in cv. Arbequina more than in Coratina. The fatty acid composition of cv. Arbequina is more influenced by the temperature regime than Coratina, suggesting its greater plasticity. Overall, findings from this study may drive future strategies for olive spreading towards areas with different or extreme thermal regimes serve as guidance for the evaluation olive varietal patrimony.

Insight in the quorum sensing-driven lifestyle of the non-pathogenic Agrobacterium tumefaciens 6N2 and the interactions with the yeast Meyerozyma guilliermondii.

Agrobacterium tumefaciens is considered a prominent phytopathogen, though most isolates are nonpathogenic. Agrobacteria can inhabit plant tissues interacting with other microorganisms. Yeasts are likewise part of these communities. We analyzed the quorum sensing (QS) systems of A. tumefaciens strain 6N2, and its relevance for the interaction with the yeast Meyerozyma guilliermondii, both sugarcane endophytes. We show that strain 6N2 is nonpathogenic, produces OHC8-HSL, OHC10-HSL, OC12-HSL and OHC12-HSL as QS signals, and possesses a complex QS architecture, with one truncated, two complete systems, and three additional QS-signal receptors. A proteomic approach showed differences in QS-regulated proteins between pure (64 proteins) and dual (33 proteins) cultures. Seven proteins were consistently regulated by quorum sensing in pure and dual cultures. M. guilliermondii proteins influenced by QS activity were also evaluated. Several up- and down- regulated proteins differed depending on the bacterial QS. These results show the QS regulation in the bacteria-yeast interactions.

Stability of the Salmonella Typhimurium rcsC11 mutant under different stress conditions.

The virulence genes of Salmonella are modulated during infection by several regulatory systems, and the RcsCDB system is one of the most important of these. The S. Typhimurium EG14873 (rcsC11) strain harbours the rcsC11 point mutation, displaying a constitutive activation of this system, which is characterized by mucoid colonies and attenuated virulence phenotypes. In this work, the stability of the rcsC11 mutation was analysed under stress conditions. Under acid and anaerobic stresses, we observed the appearance of small and non-mucoid colonies of the rcsC11 strain. The sequencing of the rcsC gene from these colonies showed that the mutation is conserved. Moreover, we found that small colonies were also generated when the wild-type strain grew in acid and anaerobic conditions. It is worth noting that the transition from normal to atypical colonies of both strains only took place after several days of incubation and was not observed during eukaryotic cell infection. Therefore, the appearance of these atypical colonies is a characteristic feature of S. Typhimurium strains under stressful situations and does not involve a reversion of the rcsC11 allele and nor does it imply any risk to mammalian cells. Therefore, we propose that the S. Typhimurium rcsC11 strain is a good candidate for the development of attenuated vaccines.

Plasticity of fruit and oil traits in olive among different environments.

Olive is a long-living perennial species with a wide geographical distribution, showing a large genetic and phenotypic variation in its growing area. There is an urgent need to uncover how olive phenotypic traits and plasticity can change regardless of the genetic background. A two-year study was conducted, based on the analysis of fruit and oil traits of 113 cultivars from five germplasm collections established in Mediterranean Basin countries and Argentina. Fruit and oil traits plasticity, broad-sense heritability and genotype by environment interaction were estimated. From variance and heritability analyses, it was shown that fruit fresh weight was mainly under genetic control, whereas oleic/(palmitic + linoleic) acids ratio was regulated by the environment and genotype by environment interaction had the major effect on oil content. Among the studied cultivars, different level of stability was observed, which allowed ranking the cultivars based on their plasticity for oil traits. High thermal amplitude, the difference of low and high year values of temperature, negatively affected the oil content and the oleic acid percentage. Information derived from this work will help to direct the selection of cultivars with the highest global fitness averaged over the environments rather than the highest fitness in each environment separately.

Rapunzel syndrome with double simultaneous trichobezoar in a teenager: Clinical Case Report. / Síndrome de Rapunzel con doble tricobezoar simultáneo en una adolescente: Reporte de caso.

Resumen: Introduction: Trichobezoars are an intraluminal accumulation of ingested hair. The Rapunzel syndrome refers to the presence of gastric trichobezoars which extend to the small intestine together with trichotillomania and trichophagia, that occur predominantly in psychiatric patients of pediatric age. OBJECTIVE: To analyze the clinical course and resolution of this syndrome in a case report. Likewise, we provide information about the family environment and psycho-emotional context of the patients and help the reader identify similar circumstances in their clinical practice. CASE REPORT: Female 14-year-old patient with history of trichotillomania and trichophagia of two years of evolution, who consulted for epigastric pain associated with weight loss, nausea, and postprandial fullness. During the physical examination, the patient was found to have bald patches in the scalp along with a palpable mass that seemed to be confined to the gastric limits. Imaging studies revealed gastric occupation due to a bezoar formation. The patient was treated surgically with laparotomy and gastrostomy, and two simultaneous trichobezoars were removed from the patient´s stomach and duodenum, the patient also underwent psycho-emotional professional counseling. CONCLUSION: Rapunzel´s syndrome, far for being a merely surgical entity, also requires psychoemotional assessment to prevent it recurrence and limit its severity.

Síndrome de Rapunzel con doble tricobezoar simultáneo en una adolescente: Reporte de caso / Rapunzel syndrome with double simultaneous trichobezoar in a teenager: Clinical Case Report

Resumen: Introducción: Los tricobezoares son acúmulos intraluminales de cabello ingerido. El síndrome de Rapunzel hace referencia a la presencia de los tricobezoares gástricos que se extienden al intestino delgado, sumados a la tricotilomanía y tricofagia, los cuales ocurren preferentemente en pacientes psiquiátricos en edad pediátrica. Objetivo: Analizar la aparición y manejo de este síndrome, propor cionando de igual manera datos acerca del entorno familiar y psicoemocional para que, por medio del análisis de los mismos, en un futuro se pueda identificar el riesgo en pacientes con circunstancias similares. Caso clínico: Paciente femenina de 14 años con antecedentes de tricotilomanía y tricofagia de dos años de evolución, que consultó por cuadro de dolor epigástrico asociado a sensación de plenitud posprandial, náuseas y pérdida de peso. Al examen destacaban áreas alopécicas en el cuero cabelludo y a la palpación abdominal se identificó un plastrón cuyo contorno parecía corresponder a los límites gástricos. En los estudios de imágenes se encontró una ocupación gástrica por bezoar. Con la laparotomía más gastrostomía se identificaron dos tricobezoares simultáneos en estómago y duodeno, que fueron resueltos quirúrgicamente y la paciente fue manejada con abordaje psicoemocional. Conclusión: El síndrome de Rapunzel, lejos de ser meramente una entidad quirúrgica, requiere un apoyo psicoemocional para prevenir su recurrencia y limitar su severidad.

Resumen: Introduction: Trichobezoars are an intraluminal accumulation of ingested hair. The Rapunzel syndrome refers to the presence of gastric trichobezoars which extend to the small intestine together with trichotillomania and trichophagia, that occur predominantly in psychiatric patients of pediatric age. Objective: To analyze the clinical course and resolution of this syndrome in a case report. Likewise, we provide information about the family environment and psycho-emotional context of the patients and help the reader identify similar circumstances in their clinical practice. Case report: Female 14-year-old patient with history of trichotillomania and trichophagia of two years of evolution, who consulted for epigastric pain associated with weight loss, nausea, and postprandial fullness. During the physical examination, the patient was found to have bald patches in the scalp along with a palpable mass that seemed to be confined to the gastric limits. Imaging studies revealed gastric occupation due to a bezoar formation. The patient was treated surgically with laparotomy and gastrostomy, and two simultaneous trichobezoars were removed from the patient´s stomach and duodenum, the patient also underwent psycho-emotional professional counseling. Conclusion: Rapunzel´s syndrome, far for being a merely surgical entity, also requires psychoemotional assessment to prevent it recurrence and limit its severity.

Olive Cultivation in the Southern Hemisphere: Flowering, Water Requirements and Oil Quality Responses to New Crop Environments.

Olive (Olea europaea L.) is a crop well adapted to the environmental conditions prevailing in the Mediterranean Basin. Nevertheless, the increasing international demand for olive oil and table olives in the last two decades has led to expansion of olive cultivation in some countries of the southern hemisphere, notably in Argentina, Chile, Perú and Australia. While the percentage of world production represented by these countries is still low, many of the new production regions do not have typical Mediterranean climates, and some are located at subtropical latitudes where there is relatively little information about crop function. Thus, the primary objective of this review was to assess recently published scientific literature on olive cultivation in these new crop environments. The review focuses on three main aspects: (a) chilling requirements for flowering, (b) water requirements and irrigation management, and (c) environmental effects on fruit oil concentration and quality. In many arid and semiarid regions of South America, temperatures are high and rainfall is low in the winter and early spring months compared to conditions in much of the Mediterranean Basin. High temperatures have often been found to have detrimental effects on olive flowering in many olive cultivars that have been introduced to South America, and a better understanding of chilling requirements is needed. Lack of rainfall in the winter and spring also has resulted in an urgent need to evaluate water requirements from the flower differentiation period in the winter to early fruit bearing. Additionally, in some olive growing areas of South America and Australia, high early season temperatures affect the timing of phenological events such that the onset of oil synthesis occurs sooner than in the Mediterranean Basin with most oil accumulation taking place in the summer when temperatures are very high. Increasing mean daily temperatures have been demonstrated to decrease fruit oil concentration (%) and negatively affect some aspects of oil quality based on both correlative field studies and manipulative experiments. From a practical standpoint, current findings could be used as approximate tools to determine whether the temperature conditions in a proposed new growing region are appropriate for achieving sustainable oil productivity and quality.

Colorectal Cancer Survival Disparities among Puerto Rican Hispanics: A Comparison to Racial/Ethnic Groups in the United States.

PURPOSE: Ethnic/racial disparities in colorectal cancer (CRC) survival have been well documented. However, there is limited information regarding CRC survival among Hispanic subgroups. This study reports the 5-year relative survival of Puerto Rican Hispanic (PRH) CRC patients and the relative risk of death compared to other racial/ethnic groups in the US. METHODS: CRC incidence data from subjects ≥50 years was obtained from the Puerto Rico Central Cancer Registry and the Surveillance, Epidemiology and End Results (SEER) database from January 1, 2001 to December 31, 2003. Relative survival rates were calculated using the life tables from the population of PR and SEER. A Poisson regression model was used to assess relative risk of death by stage, sex, and age. RESULTS: A total of 76,444 subjects with incident CRC were analyzed (non-Hispanic White (NHW) n=59,686; non-Hispanic black (NHB) n=7,700; US Hispanics (USH) n=5,699; PRH n=3,359). Overall and stage-specific five-year survival rates differed by race/ethnicity. When comparing PRH to the other racial/ethnic groups, PRH had the lowest survival rates in regional cancers and were the only racial/ethnic group where a marked 5-year survival advantage was observed among females (66.0%) compared to males (60.3%). A comparable and significantly higher relative risk of death of CRC was observed for PRH and NHB compared to NHW. CONCLUSIONS: Our findings establish baseline CRC survival data for PRH living in Puerto Rico. The gender and racial/ethnic disparities observed in PRH compared to US mainland racial/ethnic groups warrant further investigation of the risk factors affecting this Hispanic subgroup.

Variability in almond oil chemical traits from traditional cultivars and native genetic resources from Argentina.

Almond (Prunus dulcis (Miller) D.A. Webb) genetic resources (Marcona, Guara, Non Pareil, IXL, AI, Martinelli C, Emilito INTA, Cáceres Clara Chica, Javier INTA) were studied during two consecutive crop years in order to evaluate variations in kernel oil yield and composition, and oil oxidative parameters. Total oil, oleic acid, α-tocopherol and squalene contents were found to range between 48.0% and 57.5%, 65% and 77.5%, 370 and 675 µg/g oil, and 37.9 and 114.2 µg/g oil, respectively. The genotype was the main variability source for all these chemical traits. The α-tocopherol content seems to be the most important contributor to both the radical scavenging capacity and the oxidative stability of almond oils analysed. Results obtained from the local genotypes namely Martinelli C, Emilito INTA and Javier INTA may be of interest for almond breeding focused to improve kernel oil yield and composition.

The RcsCDB regulatory system plays a crucial role in the protection of Salmonella enterica serovar Typhimurium against oxidative stress.

Dps, the most abundant protein during the stationary growth phase, in Salmonella enterica is required for resistance to reactive oxygen species produced by the host during infection. It has been reported that in Salmonella dps expression is controlled by RpoS and Fur proteins. However, the regulation and function of Dps remain to be resolved. In the present work we demonstrate that activation of the complex RcsCDB regulatory system increases dps expression during exponential growth of Salmonella. In addition, we show that such dps upregulation produces high levels of H2O2 resistance. This phenotype allows the bacteria to avoid reactive oxygen species killing at early stages of growth, thus protecting its genetic material.