Safety and Effectiveness of Probiotics in Preterm Infants with Necrotizing Enterocolitis.

Although necrotizing enterocolitis is a leading cause of morbidity and mortality among preterm infants, its underlying pathophysiology is not fully understood. Gut dysbiosis, an imbalance between commensal and pathogenic microbes, in the preterm infant is likely a major contributor to the development of necrotizing enterocolitis. In this review, we will discuss the increasing use of probiotics in the NICU, an intervention aimed to mitigate alterations in the gut microbiome. We will review the existing evidence regarding the safety and effectiveness of probiotics, and their potential to reduce rates of necrotizing enterocolitis in preterm infants.

Safety and Effectiveness of Probiotics in Preterm Infants with Necrotizing Enterocolitis.

Although necrotizing enterocolitis is a leading cause of morbidity and mortality among preterm infants, its underlying pathophysiology is not fully understood. Gut dysbiosis, an imbalance between commensal and pathogenic microbes, in the preterm infant is likely a major contributor to the development of necrotizing enterocolitis. In this review, we will discuss the increasing use of probiotics in the NICU, an intervention aimed to mitigate alterations in the gut microbiome. We will review the existing evidence regarding the safety and effectiveness of probiotics, and their potential to reduce rates of necrotizing enterocolitis in preterm infants.

Large-scale meta-genome-wide association study reveals common genetic factors linked to radiation-induced acute toxicities across cancer types.

BACKGROUND: This study was designed to identify common genetic susceptibility and shared genetic variants associated with acute radiation-induced toxicity across 4 cancer types (prostate, head and neck, breast, and lung). METHODS: A genome-wide association study meta-analysis was performed using 19 cohorts totaling 12 042 patients. Acute standardized total average toxicity (STATacute) was modelled using a generalized linear regression model for additive effect of genetic variants, adjusted for demographic and clinical covariates (rSTATacute). Linkage disequilibrium score regression estimated shared single-nucleotide variation (SNV-formerly SNP)-based heritability of rSTATacute in all patients and for each cancer type. RESULTS: Shared SNV-based heritability of STATacute among all cancer types was estimated at 10% (SE = 0.02) and was higher for prostate (17%, SE = 0.07), head and neck (27%, SE = 0.09), and breast (16%, SE = 0.09) cancers. We identified 130 suggestive associated SNVs with rSTATacute (5.0 × 10‒8 < P < 1.0 × 10‒5) across 25 genomic regions. rs142667902 showed the strongest association (effect allele A; effect size ‒0.17; P = 1.7 × 10‒7), which is located near DPPA4, encoding a protein involved in pluripotency in stem cells, which are essential for repair of radiation-induced tissue injury. Gene-set enrichment analysis identified 'RNA splicing via endonucleolytic cleavage and ligation' (P = 5.1 × 10‒6, P = .079 corrected) as the top gene set associated with rSTATacute among all patients. In silico gene expression analysis showed that the genes associated with rSTATacute were statistically significantly up-regulated in skin (not sun exposed P = .004 corrected; sun exposed P = .026 corrected). CONCLUSIONS: There is shared SNV-based heritability for acute radiation-induced toxicity across and within individual cancer sites. Future meta-genome-wide association studies among large radiation therapy patient cohorts are worthwhile to identify the common causal variants for acute radiotoxicity across cancer types.

Effect of Honey, Coenzyme Q10, and ß-Carotene/α-Tocopherol as Novel Additives in Rabbit-Sperm Cryopreservation Extender.

The effectiveness of rabbit-sperm cryopreservation is still below average compared to other domestic species. After the sperm cryopreservation process, post-thawing parameters like motility and membrane integrity are significantly compromised. The use of new extender constituents is an approach that can be used to improve the effectiveness of cryopreservation. Accordingly, we used honey (1.25, 2.5, 5, and 10%), coenzyme Q10 (100 and 200 µM), and ß-carotene/α-tocopherol (500 µM/620 µM and 250 µM/310 µM) as candidate components for rabbit-sperm extenders during cryopreservation. Ejaculates from commercial adult rabbit bucks (n = 5) were cryopreserved using conventional freezing. Several post-thawing sperm parameters were assessed, including total motility, membrane integrity, viability, nuclear membrane integrity, acrosome reaction, and mitochondrial membrane potential and activation. Additionally, we performed hormonal analyses of the seminal plasma. Moreover, we analyzed the post-thawing levels of a molecular marker of sperm quality, proAKAP4, which was used in rabbits for the first time. Our findings showed that the 2.5% honey supplementation increased the post-thawing sperm motility (13.75 ± 3.75%) compared to the greater concentrations employed. However, the post-thawing motility was negatively affected by the coenzyme Q10 (0%, in both groups) but was not affected by the ß-carotene/α-tocopherol supplementation (22 ± 18.15%, and 11.67 ± 10.17%). In conclusion, the cryopreservation protocols of this study did not help to maintain the sperm parameters after thawing. Further studies are required to identify novel protocols to mitigate the damage caused to rabbit sperm during cryopreservation.

Sentinel Node Biopsy in Patients With Breast Carcinoma Without Axillary Involvement at Diagnosis Receiving Primary Systemic Therapy.

BACKGROUND: Primary systemic therapy (PST) has acquired great importance in breast cancer (BC) in the last few years. In this scenario, even if it is accepted to perform SLNB before PST, most of the guidelines remark the advantages of this practice after it, such as avoiding another surgery to the patient, a rapid start of the treatment and no need of axillary dissection in cases of pathologic complete response (pCR). Nevertheless, the lack of knowledge of the initial axillary state and the need to practice axillary dissection with any axillary disease are claimed to be some other disadvantages. There are no randomized studies yet that can conclude the optimal timing of SLNB in PST, so for the moment we may settle for our common practice. PATIENTS AND METHODS: We studied all the cases attended in the Breast Unit that joined the inclusion criteria between 2011 and 2019 in our hospital and we compared the group with SLNB before PST with the group with SLNB after PST in terms of unnecessary axillary dissection and description features. RESULTS: We included 223 female patients diagnosed with BC and without clinical nor radiological axillary disease (cN0), who had received NAC and SLNB performed before or after it. We observed a higher proportion of high-grade histological tumors (G3), tumors with aggressive phenotypes (Basal like and Her 2 enriched), and younger women in the group of SLNB before NAC compared with the SLNB after NAC group (P < .01). Despite this, we did not find any difference in the number of positive SLNBs or in the number of ALND performed between the 2 groups. We found a higher proportion of ALND with all the lymph node (LN) negatives in the SLNB before NAC group. CONCLUSION: Taking into account that in the observation period we did not use ACOSOG Z0011 criteria with all the SLNBs, we figure out what would have been the real results nowadays following these criteria. In this scenario we conclude that patients with luminal phenotype seemed to benefit from practicing SLNB before NAC in terms of avoiding axillary dissections. We could not make any conclusion in the rest of the phenotypes. However, prospective studies are needed to confirm if this affirmation could be proved.

Optimized Fast Filtration-Based Sampling and Extraction Enables Precise and Absolute Quantification of the Escherichia coli Central Carbon Metabolome.

Precise and accurate quantification is a prerequisite for interpretation of targeted metabolomics data, but this task is challenged by the inherent instability of the analytes. The sampling, quenching, extraction, and sample purification conditions required to recover and stabilize metabolites in representative extracts have also been proven highly dependent on species-specific properties. For Escherichia coli, unspecific leakage has been demonstrated for conventional microbial metabolomics sampling protocols. We herein present a fast filtration-based sampling protocol for this widely applied model organism, focusing on pitfalls such as inefficient filtration, selective loss of biomass, matrix contamination, and membrane permeabilization and leakage. We evaluate the effect of and need for removal of extracellular components and demonstrate how residual salts can challenge analytical accuracy of hyphenated mass spectrometric analyses, even when sophisticated correction strategies are applied. Laborious extraction procedures are bypassed by direct extraction in cold acetonitrile:water:methanol (3:5:2, v/v%), ensuring compatibility with sample concentration and thus, any downstream analysis. By applying this protocol, we achieve and demonstrate high precision and low metabolite turnover, and, followingly, minimal perturbation of the inherent metabolic state. This allows us to herein report absolute intracellular concentrations in E. coli and explore its central carbon metabolome at several commonly applied cultivation conditions.

Penicillium chrysogenum as a fungal factory for feruloyl esterases.

Plant biomass is a promising substrate for biorefinery, as well as a source of bioactive compounds, platform chemicals, and precursors with multiple industrial applications. These applications depend on the hydrolysis of its recalcitrant structure. However, the effective biological degradation of plant cell walls requires several enzymatic groups acting synergistically, and novel enzymes are needed in order to achieve profitable industrial hydrolysis processes. In the present work, a feruloyl esterase (FAE) activity screening of Penicillium spp. strains revealed a promising candidate (Penicillium rubens Wisconsin 54-1255; previously Penicillium chrysogenum), where two FAE-ORFs were identified and subsequently overexpressed. Enzyme extracts were analyzed, confirming the presence of FAE activity in the respective gene products (PrFaeA and PrFaeB). PrFaeB-enriched enzyme extracts were used to determine the FAE activity optima (pH 5.0 and 50-55 °C) and perform proteome analysis by means of MALDI-TOF/TOF mass spectrometry. The studies were completed with the determination of other lignocellulolytic activities, an untargeted metabolite analysis, and upscaled FAE production in stirred tank reactors. The findings described in this work present P. rubens as a promising lignocellulolytic enzyme producer. KEY POINTS: • Two Penicillium rubens ORFs were first confirmed to have feruloyl esterase activity. • Overexpression of the ORFs produced a novel P. rubens strain with improved activity. • The first in-depth proteomic study of a P. rubens lignocellulolytic extract is shown.

Meta-GWAS identifies the heritability of acute radiation-induced toxicities in head and neck cancer.

BACKGROUND AND PURPOSE: We aimed to the genetic components and susceptibility variants associated with acute radiation-induced toxicities (RITs) in patients with head and neck cancer (HNC). MATERIALS AND METHODS: We performed the largest meta-GWAS of seven European cohorts (n = 4,042). Patients were scored weekly during radiotherapy for acute RITs including dysphagia, mucositis, and xerostomia. We analyzed the effect of variants on the average burden (measured as area under curve, AUC) per each RIT, and standardized total average acute toxicity (STATacute) score using a multivariate linear regression. We tested suggestive variants (p < 1.0x10-5) in discovery set (three cohorts; n = 2,640) in a replication set (four cohorts; n = 1,402). We meta-analysed all cohorts to calculate RITs specific SNP-based heritability, and effect of polygenic risk scores (PRSs), and genetic correlations among RITS. RESULTS: From 393 suggestive SNPs identified in discovery set; 37 were nominally significant (preplication < 0.05) in replication set, but none reached genome-wide significance (pcombined < 5 × 10-8). In-silico functional analyses identified "3'-5'-exoribonuclease activity" (FDR = 1.6e-10) for dysphagia, "inositol phosphate-mediated signalling" for mucositis (FDR = 2.20e-09), and "drug catabolic process" for STATacute (FDR = 3.57e-12) as the most enriched pathways by the RIT specific suggestive genes. The SNP-based heritability (±standard error) was 29 ± 0.08 % for dysphagia, 9 ± 0.12 % (mucositis) and 27 ± 0.09 % (STATacute). Positive genetic correlation was rg = 0.65 (p = 0.048) between dysphagia and STATacute. PRSs explained limited variation of dysphagia (3 %), mucositis (2.5 %), and STATacute (0.4 %). CONCLUSION: In HNC patients, acute RITs are modestly heritable, sharing 10 % genetic susceptibility, when PRS explains < 3 % of their variance. We identified numerus suggestive SNPs, which remain to be replicated in larger studies.

Efficacy of an asynchronous telerehabilitation program in post-COVID-19 patients: A protocol for a pilot randomized controlled trial.

BACKGROUND: About 40% of patients who have had COVID-19 still have symptoms three months later whereas a 10% may experience physical and/or psychological consequences two years later. Therefore, it is necessary to perform preventive interventions when patients are discharged from the hospital to decrease the aforementioned sequelae. The purpose of this pilot-controlled trial will be to determine the efficacy of a rehabilitation program on functional status and psychosocial factors for post-COVID-19 patients when it is delivered through a tele-care platform versus a booklet-based rehabilitation. METHODS: The estimated sample size will be of 50 participants who have been discharged after COVID-19 and have a level of fatigue equal or greater than 4 on the Fatigue Severity Scale. The primary outcome will be the severity of fatigue. Participants will be randomly allocated to an "asynchronous telerehabilitation group" or to a "booklet-based rehabilitation group". Treatment in both groups will be the same and will consist of a combination of therapeutic exercise and an educative program. Treatment outcomes will be evaluated the last day of the intervention and at three- and six-months follow-up. DISCUSSION: The telerehabilitation intervention appears to be a viable and efficacy option in decreasing severe fatigue and other fitness variables such as strength and aerobic capacity, similar to other traditional rehabilitation formats such as through an explanatory booklet. CLINICAL TRIAL REGISTRATION: This trial has been prospectively registered at clinialtrials.gov identifier: NCT04794036.

No Association Between Polygenic Risk Scores for Cancer and Development of Radiation Therapy Toxicity.

PURPOSE: Our aim was to test whether updated polygenic risk scores (PRS) for susceptibility to cancer affect risk of radiation therapy toxicity. METHODS AND MATERIALS: Analyses included 9,717 patients with breast (n=3,078), prostate (n=5,748) or lung (n=891) cancer from Radiogenomics and REQUITE Consortia cohorts. Patients underwent potentially curative radiation therapy and were assessed prospectively for toxicity. Germline genotyping involved genome-wide single nucleotide polymorphism (SNP) arrays with nontyped SNPs imputed. PRS for each cancer were generated by summing literature-identified cancer susceptibility risk alleles: 352 breast, 136 prostate, and 24 lung. Weighted PRS were generated using log odds ratio (ORs) for cancer susceptibility. Standardized total average toxicity (STAT) scores at 2 and 5 years (breast, prostate) or 6 to 12 months (lung) quantified toxicity. Primary analysis tested late STAT, secondary analyses investigated acute STAT, and individual endpoints and SNPs using multivariable regression. RESULTS: Increasing PRS did not increase risk of late toxicity in patients with breast (OR, 1.000; 95% confidence interval [CI], 0.997-1.002), prostate (OR, 0.99; 95% CI, 0.98-1.00; weighted PRS OR, 0.93; 95% CI, 0.83-1.03), or lung (OR, 0.93; 95% CI, 0.87-1.00; weighted PRS OR, 0.68; 95% CI, 0.45-1.03) cancer. Similar results were seen for acute toxicity. Secondary analyses identified rs138944387 associated with breast pain (OR, 3.05; 95% CI, 1.86-5.01; P = 1.09 × 10-5) and rs17513613 with breast edema (OR, 0.94; 95% CI, 0.92-0.97; P = 1.08 × 10-5). CONCLUSIONS: Patients with increased polygenic predisposition to breast, prostate, or lung cancer can safely undergo radiation therapy with no anticipated excess toxicity risk. Some individual SNPs increase the likelihood of a specific toxicity endpoint, warranting validation in independent cohorts and functional studies to elucidate biologic mechanisms.

Experimental determination of Escherichia coli biomass composition for constraint-based metabolic modeling.

Genome-scale metabolic models (GEMs) are mathematical representations of metabolism that allow for in silico simulation of metabolic phenotypes and capabilities. A prerequisite for these predictions is an accurate representation of the biomolecular composition of the cell necessary for replication and growth, implemented in GEMs as the so-called biomass objective function (BOF). The BOF contains the metabolic precursors required for synthesis of the cellular macro- and micromolecular constituents (e.g. protein, RNA, DNA), and its composition is highly dependent on the particular organism, strain, and growth condition. Despite its critical role, the BOF is rarely constructed using specific measurements of the modeled organism, drawing the validity of this approach into question. Thus, there is a need to establish robust and reliable protocols for experimental condition-specific biomass determination. Here, we address this challenge by presenting a general pipeline for biomass quantification, evaluating its performance on Escherichia coli K-12 MG1655 sampled during balanced exponential growth under controlled conditions in a batch-fermentor set-up. We significantly improve both the coverage and molecular resolution compared to previously published workflows, quantifying 91.6% of the biomass. Our measurements display great correspondence with previously reported measurements, and we were also able to detect subtle characteristics specific to the particular E. coli strain. Using the modified E. coli GEM iML1515a, we compare the feasible flux ranges of our experimentally determined BOF with the original BOF, finding that the changes in BOF coefficients considerably affect the attainable fluxes at the genome-scale.

[SARS-CoV-2 infection in children: Clinical characteristics and dynamics of SARS-CoV-2 transmission in a private health center. Uruguay]. / Infección por SARS-CoV-2 en niños: Características clínicas y dinámica de la transmisión de SARS-CoV-2 en un centro de salud privado. Uruguay.

BACKGROUND: To date, the prevalence and severity of the COVID-19 disease in children is lower than in adults. There are controversies regarding the dynamics of transmission and the role they play in the spread of the disease. AIM: To describe the clinical characteristics and transmission dynamics of patients under 15 years of age reported for suspicion and/or contact for COVID-19 in the period March 13 - November 20, 2020, in a private comprehensive health provider (Médica Uruguaya Medical Assistance Corporation, MUCAM). METHODS: Descriptive, retrospective study, in which clinical manifestations, epidemiological notion, secondary cases, severity and evolution are described. The risk and rate of secondary intradomiciliary attack were estimated. RESULTS: 539 patients met the inclusion criteria. The diagnosis was confirmed in 29 (5.3%): 13 (7.0%) of the 351 symptomatic children and 16 (4.5%) of the 188 asymptomatic. 100% of the confirmed cases and 85% of the unconfirmed cases had the notion of contact (p < 0.05). The OR for infection from an indoor contact was 26.5 (9.8-71.7) and the rate of secondary indoor attack 23% ± 4.1. CONCLUSIONS: In this series, mild and asymptomatic forms predominated in patients under 15 years of age. One in five exposed indoors contracted the disease, this notion of contact being decisive to indicate confirmatory studies. Most of the children did not continue the chain of transmission.

Microbial Isolation and Characterization of New Antibiotic-Producing Strains from Decayed Wood.

Microbial drug resistance is increasing over the last years, becoming one of the most important health concerns in the twenty-first century. It encourages the discovery of new antibiotics. Thus, novel antibiotics discovered by exploring different environments that previously have been left out of the scientific focus is a realistic opportunity. One of these habitats can be forest deadwood, which is a specific niche inside of the forest that provides shelter and nutrition to a great variety of organisms, such as fungi, bacteria, or saproxylic insects. Different studies have found the existence of complex antagonisms and symbiotic interactions among them, which points at decayed wood as a competitive environment. Besides, it is an interesting niche to look for new antibiotic producer microorganisms and active chemicals. This chapter describes isolation and screening methods of novel producers of antimicrobial compounds from decayed wood.

Screening of Antibiotic Gene Clusters in Microorganisms Isolated from Wood.

The biosphere of Earth is made up of a variety of ecosystems governed by complex biological interactions, some of them mediated by microbial bioactive secondary metabolites. These metabolites such as antibiotics (e.g., polyketides and nonribosomal peptides) have been receiving increasing attention, due to their multiple pharmaceutical uses. Besides, antibiotic resistance is on the rise, and it is currently regarded as one of the greatest threats to global human health. The screening of novel antimicrobial polyketides and nonribosomal peptides in poorly studied ecosystems is an interesting alternative to address the problem of antibiotic resistance. This chapter updates a molecular method to identify antibiotics gene clusters and their subsequent production and activity validation. On the one hand, a PCR method based on degenerated primers for nonribosomal peptide synthases (NRPS) and the polyketide synthases (PKS) genes is used as an initial fast screening. On the other hand, a bioassay-based method is the protocol selected for the production confirmation and antibacterial effect estimation. These methods are applied to screen Actinobacteria and Penicillium species as main antibiotic producers isolated from wood.

Validation of Polymorphisms Associated with the Risk of Radiation-Induced Oesophagitis in an Independent Cohort of Non-Small-Cell Lung Cancer Patients.

Several studies have identified single-nucleotide polymorphisms (SNPs) associated with adverse effects in non-small-cell lung cancer (NSCLC) patients treated with radiation therapy. Here, using an independent cohort, we aimed to validate the reported associations. We selected 23 SNPs in 17 genes previously associated with radiation-induced oesophagitis for validation in a cohort of 178 Spanish NSCLC patients. Of them, 18 SNPs were finally analysed, following the methods described in the original published studies. Two SNPs replicated their association with radiation-induced oesophagitis (rs7165790 located in the BLM gene: odds ratio (OR) = 0.16, 95% CI = 0.04-0.65, p-value = 0.010; rs4772468 at FGF14: OR = 4.36, 95% CI = 1.15-16.46, p-value = 0.029). The SNP rs2868371 at HSPB1 was also validated but displayed an opposite effect to the formerly described (OR = 3.72; 95% CI = 1.49-9.25; p-value = 0.004). Additionally, we tested a meta-analytic approach including our results and the previous datasets reported in the referenced publications. Twelve SNPs (including the two previously validated) retained their statistically significant association with radiation-induced oesophagitis. This study strengthens the role of inflammation and DNA double-strand break repair pathways in the risk prediction of developing radiation-induced oesophagitis in NSCLC patients. The validated variants are good candidates to be evaluated in risk prediction models for patient stratification based on their radiation susceptibility.

A Tri-Band Cooled Receiver for Geodetic VLBI.

This paper shows a simultaneous tri-band (S: 2.2-2.7 GHz, X: 7.5-9 GHz and Ka: 28-33 GHz) low-noise cryogenic receiver for geodetic Very Long Baseline Interferometry (geo-VLBI) which has been developed at Yebes Observatory laboratories in Spain. A special feature is that the whole receiver front-end is fully coolable down to cryogenic temperatures to minimize receiver noise. It was installed in the first radio telescope of the Red Atlántica de Estaciones Geodinámicas y Espaciales (RAEGE) project, which is located in Yebes Observatory, in the frame of the VLBI Global Observing System (VGOS). After this, the receiver was borrowed by the Norwegian Mapping Autorithy (NMA) for the commissioning of two VGOS radiotelescopes in Svalbard (Norway). A second identical receiver was built for the Ishioka VGOS station of the Geospatial Information Authority (GSI) of Japan, and a third one for the second RAEGE VGOS station, located in Santa María (Açores Archipelago, Portugal). The average receiver noise temperatures are 21, 23, and 25 Kelvin and the measured antenna efficiencies are 70%, 75%, and 60% in S-band, X-band, and Ka-band, respectively.

Corrigendum: ddRAD Sequencing-Based Identification of Genomic Boundaries and Permeability in Quercus ilex and Q. suber Hybrids.

[This corrects the article DOI: 10.3389/fpls.2020.564414.].

ddRAD Sequencing-Based Identification of Genomic Boundaries and Permeability in Quercus ilex and Q. suber Hybrids.

Hybridization and its relevance is a hot topic in ecology and evolutionary biology. Interspecific gene flow may play a key role in species adaptation to environmental change, as well as in the survival of endangered populations. Despite the fact that hybridization is quite common in plants, many hybridizing species, such as Quercus spp., maintain their integrity, while precise determination of genomic boundaries between species remains elusive. Novel high throughput sequencing techniques have opened up new perspectives in the comparative analysis of genomes and in the study of historical and current interspecific gene flow. In this work, we applied ddRADseq technique and developed an ad hoc bioinformatics pipeline for the study of ongoing hybridization between two relevant Mediterranean oaks, Q. ilex and Q. suber. We adopted a local scale approach, analyzing adult hybrids (sensu lato) identified in a mixed stand and their open-pollinated progenies. We have identified up to 9,435 markers across the genome and have estimated individual introgression levels in adults and seedlings. Estimated contribution of Q. suber to the genome is higher, on average, in hybrid progenies than in hybrid adults, suggesting preferential backcrossing with this parental species, maybe followed by selection during juvenile stages against individuals with higher Q. suber genomic contribution. Most discriminating markers seem to be scattered throughout the genome, suggesting that a large number of small genomic regions underlie boundaries between these species. A noticeable proportion of the markers (26%) showed allelic frequencies in adult hybrids very similar to one of the parental species, and very different from the other; a finding that seems relevant for understanding the hybridization process and the occurrence of adaptive introgression. Candidate marker databases developed in this study constitute a valuable resource to design large scale re-sequencing experiments in Mediterranean sclerophyllous oak species and could provide insight in species boundaries and on adaptive introgression between Q. suber and Q. ilex.