Miracle-dz/UniFAR-FTUs huggingface dataset:
Colonization with Altered Schaedler Flora Impacts Leukocyte Adhesion in Mesenteric Ischemia-Reperfusion Injury

The microbiota impacts mesenteric ischemia-reperfusion injury, aggravating the interaction of leukocytes with endothelial cells in mesenteric venules. The role of defined gut microbiomes in this life-threatening pathology is unknown. To investigate how a defined model microbiome affects the adhesion of leukocytes in mesenteric ischemia-reperfusion, we took advantage of gnotobiotic isolator technology and transferred altered Schaedler flora (ASF) from C3H/HeNTac to germ-free C57BL/6J mice. We were able to detect all eight bacterial taxa of ASF in fecal samples of colonized C57BL/6J mice by PCR. Applying qRT-PCR for quantification of species-specific 16S rDNA sequences of ASF bacteria, we found a major shift in the abundance of ASF 500, which was greater in C57BL/6J mice relative to the C3H/HeNTac founder breeding pair. Using high-speed epifluorescence intravital microscopy to visualize the venules of the small bowel mesentery, we found that gnotobiotic ASF-colonized mice showed reduced leukocyte adherence, both pre- and post-ischemia. Relative to germ-free mice, the counts of adhering leukocytes were increased pre-ischemia but did not significantly increase in ASF-colonized mice in the post-ischemic state. Collectively, our results suggest a protective role of the minimal microbial consortium ASF in mesenteric ischemia-reperfusion injury.
Maternal High-Fat Diet Modulates Cnr1 Gene Expression in Male Rat Offspring

In recent years, strong evidence has emerged that exposure to a maternal high-fat diet (HFD) provokes changes in the structure, function, and development of the offspring’s brain and may induce several neurodevelopmental and psychiatric illnesses. The aims of this study were to evaluate the effects of a maternal HFD during pregnancy and lactation on depressive-like behavior and Cnr1 gene expression (encoding the CB1 receptor) in brain structures of rat offspring and to investigate the epigenetic mechanism involved in this gene expression. We found that a maternal HFD during pregnancy and lactation induced a depressive-like phenotype at postnatal days (PNDs) 28 and 63. We found that a maternal HFD decreased the Cnr1 mRNA levels in the prefrontal cortex with the increased levels of miR-212-5p and methylation of CpG islands at the Cnr1 promoter and reduced the level of Cnr1 gene expression in the dorsal striatum with an increased level of miR-154-3p in adolescent male offspring. A contrasting effect of a maternal HFD was observed in the hippocampus, where upregulation of Cnr1 gene expression was accompanied by a decrease of miR-154-3p (at PNDs 28 and 63) and miR-212-5p (at PND 63) expression and methylation of CpG islands at the Cnr1 promoter in male offspring. In summary, we showed that a maternal HFD during pregnancy and lactation triggered several epigenetic mechanisms in the brains of rat offspring, which may be related to long-lasting alterations in the next generation and produce behavioral changes in offspring, including a depressive-like phenotype.
Enhancement of the Diversity of Pollinators and Beneficial Insects in Intensively Managed Vineyards

Simple Summary The continuous intensification of agricultural production has resulted in higher yields and more yield security. However, these achievements went along with the substitution of heterogeneous agricultural landscapes by homogeneous ones with poor crop diversity, short crop rotations, and thanks to the high efficacy of modern herbicides and also to minimum in-crop diversity. A severe increase in plot size led to the elimination of ecologically valuable structural elements that had provided floral resources and nesting sites. Over the few last decades, several studies have been conducted to try to find solutions against insect decline and to preserve biodiversity. In the present study, the integration of cover plants between the lines of the vineyards to enhance biodiversity is shown. The benefits of the cover plants use are presented based on the results achieved on five intensive wine farms in Spain. Our findings suggest that the use of cover plants provide a wide range of enhancements in the insect community with a significant increase both in the number of species and the number of individuals showing an important influence over time, which would tend to have a significant conservation impact thanks to its effect as a reservoir of species. Abstract (1) Modern, intensive agricultural practices have been attributed to the loss of insect biodiversity and abundance in agroecosystems for the last 80 years. The aim of this work is to test whether there are statistically significant differences in insect abundance between different zones and over time on the vineyard field. (2) The study was carried out in five intensive wine farms in Spain over a three-year period (2013–2015). Each field was divided into two zones, one where cover plants were planted, and another remained unchanged (without cover). (3) A clear trend to increase the average number of insect species and individuals throughout the years in all farms was observed. Moreover, the zones with cover plants showed a significant difference with respect to the zones without. (4) The use of permanent cover plants allows creating areas of refuge for the insects favouring their conservation and reducing the agriculture impact in the insect decline.
Physical Activity Interventions and Their Effects on Cognitive Function in People with Dementia: A Systematic Review and Meta-Analysis

Background: Physical activity (PA) has emerged as an alternative nonpharmacological approach to effectively address the effects of dementia. The primary aim was to identify and summarize PA interventions and their effects on cognitive function among persons with dementia (PwD). Methods: A systematic review was conducted with a meta-analysis using different electronic databases, such as PubMed, Embase, APA PsycNET, and the Web of Science. The identified and selected studies were randomized controlled trials (RCTs) that were written in English, published between 2000 and 2020, and implemented among PwD who received a PA intervention and whose cognitive function was measured at baseline and during a follow-up. Results: Twenty-two PA intervention studies met the eligibility criteria and showed a medium-size effect on the cognitive function of PwD, 0.4803 (95% CI = 0.1901–0.7704), with a high percentage of heterogeneity (I2 = 86%, p ≤ 0.0001). Moreover, this review complements other reviews by including eight studies that have not previously been considered. Overall, studies have methodological limitations. However, six studies implemented in the past five years have shown more robust methodological designs, including larger sample sizes and more comprehensive measurement tools. Conclusion: It is not yet possible to draw a conclusion on the ideal PA intervention for this population due to the high proportion of heterogeneity within the included studies. More emphasis is needed on the intensity of PA monitoring and adherence to such programs.
Genetic Parameters for Different Measures of Feed Efficiency and Their Relationship to Production Traits in Three Purebred Pigs

Residual feed intake (RFI) gained attention as a potential alternative to the feed conversion ratio (FCR). Thus, this study aimed to estimate genetic parameters for different feed efficiency (FE) traits (FCR, RFI1 to RFI5) and their genetic correlation to on-test daily weight gain (ADG), backfat (BFT), loin muscle area (LMA), lean percentage (LP), and total feed intake (FI) for 603 Male Duroc (DD), 295 Landrace (LL), and 341 Yorkshire (YY). The common spatial pen effect was also estimated in these traits. Five RFI measures were estimated by regressing daily feed intake on initial testing age (ITA), initial testing weight (IBW), and ADG for RFI1; other models were the same as RFI1 except for additional BFT for RFI2; LMA for RFI3; BFT and LMA for RFI4; BFT, LMA, and average metabolic body weight (AMBW) instead of IBW for RFI5. Genetic parameters estimated using two animal models and the REML method showed moderate heritability for FCR in all breeds (0.22 and 0.28 for DD, 0.31 and 0.39 for LL, 0.17 and 0.22 for YY), low heritability for the majority of RFI measures in DD (0.15 to 0.23) and YY (0.14 to 0.20) and moderate heritability for all RFI measures in LL (0.31 to 0.34). Pen variance explained 7% to 22% for FE and 0% to 9% for production traits’ phenotypic variance. The genetic correlation revealed that selection against less complex RFI1 in DD and LL and RFI2 in YY would bring the most advantageous reduction to FI (0.71 for DD, 0.49 for LL, 0.43 YY) without affecting ADG in all breeds (0.06 for DD, −0.11 for LL, 0.05 for YY), decrease in BFT, and increase in LP in DD (0.51 in BFT, −0.77 in LP) and LL (0.45 in BFT, −0.83 in LP). Therefore, inclusion of these breed-specific RFI measures in the future selection criteria would help improve feed efficiency in the swine industry.
Understanding Wine through Yeast Interactions

Wine is a product of microbial activities and microbe–microbe interactions. Yeasts are the principal microorganisms responsible for the evolution and fulfillment of alcoholic fermentation. Several species and strains coexist and interact with their environment and with each other during the fermentation course. Yeast–yeast interactions occur even from the early stages of fermentation, determining yeast community structure and dynamics during the process. Different types of microbial interactions (e.g., mutualism and commensalism or competition and amensalism) may exert positive or negative effects, respectively, on yeast populations. Interactions are intimately linked to yeast metabolic activities that influence the wine analytical profile and shape the wine character. In this context, much attention has been given during the last years to the interactions between Saccharomyces cerevisiae (SC) and non-Saccharomyces (NS) yeast species with respect to their metabolic contribution to wine quality. Yet, there is still a significant lack of knowledge on the interaction mechanisms modulating yeast behavior during mixed culture fermentation, while much less is known about the interactions between the various NS species or between SC and Saccharomyces non-cerevisiae (SNC) yeasts. There is still much to learn about their metabolic footprints and the genetic mechanisms that alter yeast community equilibrium in favor of one species or another. Gaining deeper insights on yeast interactions in the grape–wine ecosystem sets the grounds for understanding the rules underlying the function of the wine microbial system and provides means to better control and improve oenological practices.
Analytical Rheology of Honey: A State-of-the-Art Review

Honey has been used as a nutraceutical product since ancient times due to its nutritional and medicinal properties. Honey rheology influences its organoleptic properties and is relevant for processing and quality control. This review summarizes the rheological behaviour of honeys of different botanical source(s) and geographical locations that has been described in the literature, focusing on the relation between rheological parameters, honey composition (moisture, water activity, sugar content, presence of colloidal matter) and experimental conditions (temperature, time, stress, shear rate). Both liquid and crystallized honeys have been addressed. Firstly, the main mathematical models used to describe honey rheological behaviour are presented highlighting moisture and temperature effects. Then, rheological data from the literature regarding distinct honey types from different countries is analysed and results are compared. Although most honeys are Newtonian fluids, interesting shear-thinning and thixotropic as well as anti-thixotropic behaviour have been described for some types of honey. Rheological parameters have also been successfully applied to identify honey adulteration and to discriminate between different honey types. Several chemometric techniques have also been employed to obtain the complex relationships between honey physicochemical and rheological properties, including partial least squares (PLS), principal component analysis (PCA) and artificial neural networks (ANN).
Bifidobacterium animalis subsp. lactis BB-12 Protects against Antibiotic-Induced Functional and Compositional Changes in Human Fecal Microbiome

The administration of broad-spectrum antibiotics is often associated with antibiotic-associated diarrhea (AAD), and impacts gastrointestinal tract homeostasis, as evidenced by the following: (a) an overall reduction in both the numbers and diversity of the gut microbiota, and (b) decreased short-chain fatty acid (SCFA) production. Evidence in humans that probiotics may enhance the recovery of microbiota populations after antibiotic treatment is equivocal, and few studies have addressed if probiotics improve the recovery of microbial metabolic function. Our aim was to determine if Bifidobacterium animalis subsp. lactis BB-12 (BB-12)-containing yogurt could protect against antibiotic-induced fecal SCFA and microbiota composition disruptions. We conducted a randomized, allocation-concealed, controlled trial of amoxicillin/clavulanate administration (days 1–7), in conjunction with either BB-12-containing or control yogurt (days 1–14). We measured the fecal levels of SCFAs and bacterial composition at baseline and days 7, 14, 21, and 30. Forty-two participants were randomly assigned to the BB-12 group, and 20 participants to the control group. Antibiotic treatment suppressed the fecal acetate levels in both the control and probiotic groups. Following the cessation of antibiotics, the fecal acetate levels in the probiotic group increased over the remainder of the study and returned to the baseline levels on day 30 (−1.6% baseline), whereas, in the control group, the acetate levels remained suppressed. Further, antibiotic treatment reduced the Shannon diversity of the gut microbiota, for all the study participants at day 7. The magnitude of this change was larger and more sustained in the control group compared to the probiotic group, which is consistent with the hypothesis that BB-12 enhanced microbiota recovery. There were no significant baseline clinical differences between the two groups. Concurrent administration of amoxicillin/clavulanate and BB-12 yogurt, to healthy subjects, was associated with a significantly smaller decrease in the fecal SCFA levels and a more stable taxonomic profile of the microbiota over time than the control group.
Improvement of Lipid Profile after One-Anastomosis Gastric Bypass Compared to Sleeve Gastrectomy

Fewer studies compared the improvement of plasma lipid levels after different types of surgery, in particular compared to one-anastomosis gastric bypass (OAGB). The aim of our study was to investigate how laparoscopic sleeve gastrectomy (LSG) and OAGB impact on weight loss and lipid profile 18 months after surgery, in patients with severe obesity. Forty-six patients treated with OAGB were matched to eighty-eight patients submitted to LSG. Weight loss after OAGB (33.2%) was more evident than after LSG (29.6%) (p = 0.024). The difference in the prevalence of dyslipidemia showed a statistically significant reduction only after OAGB (61% versus 22%, p < 0.001). After adjustment for delta body mass index (BMI), age and sex, we demonstrated a statistically significant decrease of the differences between the changes before and after (delta Δ) the two surgery procedures: Δ total cholesterol values (p < 0.001), Δ low density lipoprotein-cholesterol values (p < 0.001) and Δ triglycerides values (p = 0.007). Patients with severe obesity undergoing to OAGB presented a better improvement of lipid plasma values than LSG patients. The reduction of lipid plasma levels was independent of the significant decrease of BMI after surgery, of age and of sex.
A Sensitive SERS Method for Determination of Pymetrozine in Apple and Cabbage Based on an Easily Prepared Substrate

Residual pesticides are one of the major food safety concerns around the world. There is a demand for simple and reliable methods to monitor pesticide residues in foods. In this study, a sensitive method for determination of pymetrozine in apple and cabbage samples using surface-enhanced Raman spectroscopy (SERS) based on decanethiol functionalized silver nanoparticles was established. The proposed method performed satisfactorily with the linear detection range of 0.01–1.00 mg/L and limit of detection (LOD) of 0.01 mg/L in methanol. In addition, it was successfully used to detect pymetrozine in apple and cabbage samples, the LOD was 0.02 and 0.03 mg/L, respectively, and the recoveries of spiked cabbage and apple ranged 70.40–104.00%, with relative standard deviations below 12.18% and 10.33% for intra-day and inter-day tests. Moreover, the results of the correlation test with real cabbage samples of liquid chromatography-tandem mass spectrometry showed that they were highly correlated (slope = 0.9895, R2 = 0.9953). This study provides a sensitive approach for detection of pymetrozine in apple and cabbage, which has great potential for determination of pymetrozine residues in food products.
High Therapeutic and Esthetic Properties of Extracellular Vesicles Produced from the Stem Cells and Their Spheroids Cultured from Ocular Surgery-Derived Waste Orbicularis Oculi Muscle Tissues

Extracellular vesicles (EVs) are paracrine factors that mediate stem cell therapeutics. We aimed at evaluating the possible therapeutic and esthetic applications of EVs prepared from the waste human facial tissue-derived orbicularis oculi muscle stem cells (OOM-SCs). OOM-SCs were isolated from the ocular tissues (from elders and youngsters) after upper eyelid blepharoplasty or epiblepharon surgeries. EVs were prepared from the OOM-SCs (OOM-SC-EVs) and their three-dimensional spheroids. OOM-SCs showed a spindle-like morphology with trilineage differentiation capacity, positive expression of CD105, CD 90, and CD73, and negative expression of CD45 and CD34, and their stem cell properties were compared with other adult mesenchymal stem cells. OOM-SC-EVs showed a high inhibitory effect on melanin synthesis in B16F10 cells by blocking tyrosinase activity. OOM-SC-EVs treatment led to a significant attenuation of senescence-associated changes, a decrease in reactive oxygen species generation, and an upregulation of antioxidant genes. We demonstrated the regeneration activity of OOM-SC-EVs in in vitro wound healing of normal human dermal fibroblasts and upregulation of anti-wrinkle-related genes and confirmed the therapeutic potential of OOM-SC-EVs in the healing of the in vivo wound model. Our study provides promising therapeutic and esthetic applications of OOM-SC-EVs, which can be obtained from the ocular surgery-derived waste human facial tissues.
Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights into the Origin and Distribution of Nitrogen Fixation across Bacteria and Archaea

The phylogeny of nitrogenase has only been analyzed using the structural proteins NifHDK. As nifHDKENB has been established as the minimum number of genes necessary for in silico prediction of diazotrophy, we present an updated phylogeny of diazotrophs using both structural (NifHDK) and cofactor assembly proteins (NifENB). Annotated Nif sequences were obtained from InterPro from 963 culture-derived genomes. Nif sequences were aligned individually and concatenated to form one NifHDKENB sequence. Phylogenies obtained using PhyML, FastTree, RapidNJ, and ASTRAL from individuals and concatenated protein sequences were compared and analyzed. All six genes were found across the Actinobacteria, Aquificae, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Deferribacteres, Firmicutes, Fusobacteria, Nitrospira, Proteobacteria, PVC group, and Spirochaetes, as well as the Euryarchaeota. The phylogenies of individual Nif proteins were very similar to the overall NifHDKENB phylogeny, indicating the assembly proteins have evolved together. Our higher resolution database upheld the three cluster phylogeny, but revealed undocumented horizontal gene transfers across phyla. Only 48% of the 325 genera containing all six nif genes are currently supported by biochemical evidence of diazotrophy. In addition, this work provides reference for any inter-phyla comparison of Nif sequences and a quality database of Nif proteins that can be used for identifying new Nif sequences.
Design and Testing of Effective Primers for Amplification of the orf7 Gene of Phage WO Associated with Andricus hakonensis

Simple Summary Andricus hakonensis is thought to contain the most complex and diverse phage types known and should be an ideal model material for studying interactions among bacteriophages, bacteria and eukaryotes. As shown in previous studies, existing primers are not effective enough to amplify all virus groups in A. hakonensis. Based on a comprehensive analysis of all virus groups reported to date, we designed a relatively conservative primer for virus detection. This primer can accurately and efficiently detect the presence of phage WO in arthropod hosts. Using gene alignment, clear evidence was provided for the existence of hitherto unreported base deletions, which are an important cause of diversity in phage WO associated with A. hakonensis. Abstract Phage WO was first characterized in Wolbachia, an obligate intracellular Rickettsiales known for its ability to regulate the reproduction of arthropod hosts. In this paper, we focus on the study of virus diversity in Andricus hakonensis and the development of highly effective primers. Based on the existing Wolbachia genome sequence, we designed primers (WO-TF and WO-TR) to amplify the full-length orf7 gene of phage WO. Surprisingly, sequencing results showed a high abundance of other phage WO groups in A. hakonensis, in addition to the four groups previously identified. The results also showed that A. hakonensis contained most of the known types of orf7 genes (I, III, IV, V and VI) and the level of diversity of harbored phage WO was very high. Therefore, we speculated that existing primers were not specific enough and that new primers for the detection of phage WO were needed. Based on the existing orf7 gene sequence, we designed specific detection primers (WO-SUF and WO-SUR). Sequencing results showed that the primers effectively amplified all known types of phage WO. In addition to amplifying most of the known sequences, we also detected some new genotypes in A. hakonensis using the new primers. Importantly, all phage WO groups could be efficiently detected. Combined with the results of previous studies, our results suggest that A. hakonensis contains the largest number of phage types (up to 36 types). This study is novel in that it provides practical molecular evidence supporting base deletions, in addition to gene mutations and genetic recombination, as an important cause of phage WO diversity.