Variable-selection ANOVA Simultaneous Component Analysis (VASCA)

Motivation: ANOVA Simultaneous Component Analysis (ASCA) is a popular method for the analysis of multivariate data yielded by designed experiments. Meaningful associations between factors/interactions of the experimental design and measured variables in the dataset are typically identified via significance testing, with permutation tests being the standard go-to choice. However, in settings with large numbers of variables, like omics (genomics, transcriptomics, proteomics and metabolomics) experiments, the ‘holistic’ testing approach of ASCA (all variables considered) often overlooks statistically significant effects encoded by only a few variables (biomarkers). Results: We hereby propose Variable-selection ASCA (VASCA), a method that generalizes ASCA through variable selection, augmenting its statistical power without inflating the Type-I error risk. The method is evaluated with simulations and with a real dataset from a multi-omic clinical experiment. We show that VASCA is more powerful than both ASCA and the widely adopted false discovery rate controlling procedure; the latter is used as a benchmark for variable selection based on multiple significance testing. We further illustrate the usefulness of VASCA for exploratory data analysis in comparison to the popular partial least squares discriminant analysis method and its sparse counterpart.Agencia Andaluza del Conocimiento, Regional Government of Andalucia , in SpainEuropean Commission B-TIC-136-UGR20State Research Agency (AEI) of SpainEuropean Social Fund (ESF) RYC2020-030536-IAEI PID2020-118139RB-I0

Antimicrobial, Antioxidant, and Immunomodulatory Properties of Essential Oils: A Systematic Review

Essential oils (EOs) are a mixture of natural, volatile, and aromatic compounds obtained from plants. In recent years, several studies have shown that some of their benefits can be attributed to their antimicrobial, antioxidant, anti-inflammatory, and also immunomodulatory properties. Therefore, EOs have been proposed as a natural alternative to antibiotics or for use in combination with antibiotics against multidrug-resistant bacteria in animal feed and food preservation. Most of the results come from in vitro and in vivo studies; however, very little is known about their use in clinical studies. A systematic and comprehensive literature search was conducted in PubMed, Embase®, and Scopus from December 2014 to April 2019 using di erent combinations of the following keywords: essential oils, volatile oils, antimicrobial, antioxidant, immunomodulation, and microbiota. Some EOs have demonstrated their efficacy against several foodborne pathogens in vitro and model food systems; namely, the inhibition of S. aureus, V. cholerae, and C. albicans has been observed. EOs have shown remarkable antioxidant activities when used at a dose range of 0.01 to 10 mg/mL in cell models, which can be attributed to their richness in phenolic compounds. Moreover, selected EOs exhibit immunomodulatory activities that have been mainly attributed to their ability to modify the secretion of cytokines.Part of the research currently in progress in the authors’ laboratory is funded by the company PAYMSA, S. A. through the grant #4501 managed by the Fundacion General Empresa-Universidad de Granada

Effects of Probiotics on Metabolic Syndrome: A Systematic Review of Randomized Clinical Trials

The aim of this systematic review is to evaluate whether the use of probiotics has any effect on the components of metabolic syndrome (MetS) before patients develop type 2 diabetes. A qualitative systematic review, following the Cochrane methodology, and a comprehensive literature search of randomized controlled trials (RCTs) were conducted in PubMed and Scopus from inception until 4 July 2019. According to our inclusion criteria, nine clinical studies were finally analyzed, corresponding to six RCTs. Probiotics intake in patients with MetS resulted in improvements in body mass index, blood pressure, glucose metabolism, and lipid profile in some studies. Regarding inflammatory biomarkers, probiotics also positively affected the soluble vascular cell adhesion molecule 1 (sVCAM-1), interleukine-6 (IL-6), tumor necrosis factor alpha (TNF-alpha), vascular endothelial growth factor (VEGF), and thrombomodulin. Despite the diversity of the published studies, the intake of probiotics for patients with MetS may offer a discrete improvement in some of the clinical characteristics of the MetS and a decrease in inflammatory biomarkers. Nevertheless, these beneficial effects seem to be marginal compared to drug therapy and a healthy lifestyle and clinically non-relevant

The Role of Probiotic Lactic Acid Bacteria and Bifidobacteria in the Prevention and Treatment of Inflammatory Bowel Disease and Other Related Diseases: A Systematic Review of Randomized Human Clinical Trials

Inflammatory bowel disease (IBD), which includes Crohn’s disease (CD) and ulcerative colitis (UC), is a chronic inflammation of the small intestine and colon caused by a dysregulated immune response to host intestinal microbiota in genetically susceptible subjects. A number of fermented dairy products contain lactic acid bacteria (LAB) and bifidobacteria, some of which have been characterized as probiotics that can modify the gut microbiota and may be beneficial for the treatment and the prevention of IBD. The objective of this review was to carry out a systematic search of LAB and bifidobacteria probiotics and IBD, using the PubMed and Scopus databases, defined by a specific equation using MeSH terms and limited to human clinical trials. The use of probiotics and/or synbiotics has positive effects in the treatment and maintenance of UC, whereas in CD clear effectiveness has only been shown for synbiotics. Furthermore, in other associated IBD pathologies, such as pouchitis and cholangitis, LAB and bifidobacteria probiotics can provide a benefit through the improvement of clinical symptoms. However, more studies are needed to understand their mechanisms of action and in this way to understand the effect of probiotics prior to their use as coadjuvants in the therapy and prevention of IBD conditions

Study of the fetal and maternal microbiota in pregnant women with intrauterine growth restriction and its relationship with inflammatory biomarkers: A case-control study protocol (SPIRIT compliant)

In general terms, fetal growth restriction (FGR) is considered the impossibility of achieving the genetically determined potential size. In the vast majority of cases, it is related to uteroplacental insufficiency. Although its origin remains unknown and causes are only known in 30% of cases, it is believed to be related to an interaction of environmental and genetic factors with either a fetal or maternal origin. One hypothesis is that alterations in the gastrointestinal microbiota composition, and thus alteration in the immune response, could play a role in FGR development. We performed an observational, prospective study in a subpopulation affected with FGR to elucidate the implications of this microbiota on the FGR condition. A total of 63 fetuses with FGR diagnosed in the third trimester as defined by the Delphi consensus, and 63 fetuses with fetal growth appropriate for gestational age will be recruited. Obstetric and nutritional information will be registered by means of specific questionnaires. We will collect maternal fecal samples between 30 to 36 weeks, intrapartum samples (maternal feces, maternal and cord blood) and postpartum samples (meconium and new-born feces at 6 weeks of life). Samples will be analyzed in the Department of Biochemistry and Molecular Biology II, Nutrition and Food Technology Institute of the University of Granada (UGR), for the determination of the gastrointestinal microbiota composition and its relationship with inflammatory biomarkers. This study will contribute to a better understanding of the influence of gastrointestinal microbiota and related inflammatory biomarkers in the development of FGR. Trial registration: NCT04047966. Registered August 7, 2019, during the recruitment stage. Retrospectively registered. Ongoing research. Keywords: fetal growth restriction, gastrointestinal microbiota, inflammatory biomarker

Effects of dietary inclusion of sunflower soap stocks on colour, oxidation and microbiological growth of meat from light fattening lambs

[EN] Thirty-two lambs were finished on a total mixed ration (TMR) pelleted alone (00SS) or including sunflower soap stock (SS): 15SS (15 g SS per kg TMR), 30SS (30 g SS per kg TMR) and 60SS (60 g SS per kg TMR). Lambs (8 per group) were slaughtered at 27 kg live weight. Colour evolution, lipid oxidation, microbial growth and detection of diarrhoeagenic Escherichia coli were studied in meat samples. SS in the diet reduced meat lipid oxidation (P 0.05) on the cholesterol oxidation products. Meat from 60SS and control animals (00SS) revealed greater discoloration (P < 0.05) than 15SS. SS supplementation did not affect the microbiological populations, whereas high doses of SS seemed to increase the proliferation of diarrhoeagenic E. coli on day 14 (P < 0.10). These results suggest that the rate of SS inclusion in the diet of fattening lambs should not be above 15 g SS per kg TMR.S

Biological Effects of Maslinic Acid on Human Epithelial Cells Used in Tissue Engineering

In the present work, we evaluated the potential of maslinic acid (MA) to improve currently available keratinocyte culture methods for use in skin tissue engineering. Results showed that MA can increase cell proliferation and WST-1 activity of human keratinocytes after 24, 48, and 72 h, especially at the concentration of 5 μg/ml, without affecting cell viability. This effect was associated to a significant increase of KI-67 protein expression and upregulation of several genes associated to cell proliferation (PCNA) and differentiation (cytokeratins, intercellular junctions and basement membrane related genes). When human keratinocytes were isolated from skin biopsies, we found that MA at the concentration of 5 μg/ml significantly increased the efficiency of the explant and the cell dissociation methods. These results revealed the positive effects of MA to optimize human keratinocyte culture protocols for use in skin tissue engineering.PE-0395-2019 Consejería de Salud y Familias, Junta de Andalucía, SpainB-CTS-450-UGR20 (proyectos de I + D + i en el marco del Programa Operativo FEDER Andalucía 2014-2020, Universidad de Granada and Consejería de Transformación Económica, Industria, Conocimiento y Universidades)Spanish Plan Nacional de Investigación Científica, Desarrollo e Innovación Tecnológica (I + D + i) of the Spanish Ministry of Science and Innovation through grants FIS PI20/0317, FIS PI21/ 0980 and ICI19-00024 (BIOCLEFT) from Instituto de Salud Carlos III, co-financed by the European Regional Development Fun

Pyrosequencing Analysis Reveals Changes in Intestinal Microbiota of Healthy Adults Who Received a Daily Dose of Immunomodulatory Probiotic Strains

The colon microbiota plays a crucial role in human gastrointestinal health. Current attempts to manipulate the colon microbiota composition are aimed at finding remedies for various diseases. We have recently described the immunomodulatory effects of three probiotic strains (Lactobacillus rhamnosus CNCM I-4036, Lactobacillus paracasei CNCM I-4034, and Bifidobacterium breve CNCM I-4035). The goal of the present study was to analyze the compositions of the fecal microbiota of healthy adults who received one of these strains using high-throughput 16S ribosomal RNA gene sequencing. Bacteroides was the most abundant genus in the groups that received L. rhamnosus CNCM I-4036 or L. paracasei CNCM I-4034. The Shannon indices were significantly increased in these two groups. Our results also revealed a significant increase in the Lactobacillus genus after the intervention with L. rhamnosus CNCM I-4036. The initially different colon microbiota became homogeneous in the subjects who received L. rhamnosus CNCM I-4036. While some orders that were initially present disappeared after the administration of L. rhamnosus CNCM I-4036, other orders, such as Sphingobacteriales, Nitrospirales, Desulfobacterales, Thiotrichales, and Synergistetes, were detected after the intervention. In summary, our results show that the intake of these three bacterial strains induced changes in the colon microbiota.This study utilized fecal samples from the clinical trial NCT01479543 that was supported by Hero Spain S. A. through contract #3582 with the Fundacion General Empresa Universidad de Granada. Carolina Gomez-Llorente is the recipient of a postdoctoral fellowship of the University of Granada

Gene expression profiling in the intestinal mucosa of obese rats administered probiotic bacteria

This paper will be part of Candido Robles-Sanchez's doctorate, which is being completed as part of the 'Biochemistry and Molecular Biology Program' at the University of Granada, Spain. This work was funded by the company Hero Spain, S. A. (grant #3545 managed by Fundacion General EmpresaUniversidad de Granada) and by CEIBiotic, University of Granada, Spain (grant CEI2013P-11).We investigated whether the administration of Lactobacillus paracasei CNCM I-4034, Bifidobacterium breve CNCM I-4035 and Lactobacillus rhamnosus CNCM I-4036 modulate the expression of genes in the intestinal mucosa of obese Zucker rats. Forty-eight Zucker-Lepr(fa/fa) and 16 Zucker lean Lepr(+/fa) rats were used. Eight Zucker lean Lepr(+/fa) and 8 Zucker-Lepr(fa/fa) rats were euthanized as a reference. The remaining 40 Zucker-Lepr(fa/fa) rats were then assigned to receive 10(10) colony forming units (CFU) of one of the three probiotic strains, a mixture of L. paracasei CNCM I-4034 and B. breve CNCM I-4035, or a placebo by oral administration for 30 days. An additional group of 8 Zucker lean Lepr(+/fa) rats received the placebo for 30 days. Over 27,000 rat genes were studied using a DNA array. Four animals per group were used. Total RNA was extracted from intestinal mucosa and cDNA was synthesized, fragmented and labeled. Labeled cDNA was hybridized using GeneChip kits, and the latter were scanned. Intensity values of each probe were processed and normalized to obtain an individual value for each set of probes.Company Hero Spain, S. A. 3545CEIBiotic, University of Granada, Spain CEI2013P-1

Cell Models and Their Application for Studying Adipogenic Differentiation in Relation to Obesity: A Review

Over the last several years, the increasing prevalence of obesity has favored an intense study of adipose tissue biology and the precise mechanisms involved in adipocyte differentiation and adipogenesis. Adipocyte commitment and differentiation are complex processes, which can be investigated thanks to the development of diverse in vitro cell models and molecular biology techniques that allow for a better understanding of adipogenesis and adipocyte dysfunction associated with obesity. The aim of the present work was to update the different animal and human cell culture models available for studying the in vitro adipogenic differentiation process related to obesity and its co-morbidities. The main characteristics, new protocols, and applications of the cell models used to study the adipogenesis in the last five years have been extensively revised. Moreover, we depict co-cultures and three-dimensional cultures, given their utility to understand the connections between adipocytes and their surrounding cells in adipose tissue