Miracle-dz/UniFAR-FTUs huggingface dataset:
Abstract 844: High-resolution microbiome profiling and meta-analysis yields insight into microbial consortia associated with colorectal cancer

Colorectal cancer (CRC) continues to be the second leading cause of cancer-related deaths globally. While multiple environmental factors are associated with incidence of CRC, multiple studies have reported that CRC is frequently linked with an altered colonic microbiota both in terms of taxonomic composition as well as structural organization. However, differences in study design and analysis methodologies among CRC microbiome profiling studies have generated inconsistent findings. To identify bacterial taxa consistently associated with CRC, we applied a uniform microbiome analysis methodology to sequence datasets followed by meta-analysis. Raw 16S rRNA amplicon sequence datasets from 12 studies including two new Malaysian cohorts were collected and analyzed using the Resphera Insight high-resolution taxonomic assignment protocol. Taxonomic abundances within each dataset were then assessed for significant enrichment or depletion in colorectal carcinoma samples versus controls. Alpha diversity and differences in predicted functional capacity were assessed utilizing QIIME and PICRUSt, respectively. Several bacterial species were consistently enriched in colorectal carcinoma samples relative to healthy controls including Fusobacterium nucleatum, Fusobacterium necrophorum, Leptotrichia trevisanii, Bacteroides fragilis, Parvimonas micra, Peptostreptococcus stomatis, and Gemella morbillorum. In contrast to other studies that have generally described Fusobacteria as enriched in CRC relative to controls, we identified multiple fusobacterial members that were often not strongly linked with CRC including Fusobacterium varium and Cetobacterium somerae. Evaluating functional predictions inferred from taxonomic composition, we observed consistent enrichment of specific KEGG categories in CRC including glycosyltransferases and carbohydrate digestion and absorption. Applying a uniform high-resolution analysis protocol for microbiome profiling enabled detection of specific species that were strongly associated with CRC across multiple studies. These findings demonstrate that higher level analyses (e.g. those at the genus or family level) may be insufficient for detection of indicator taxa in some populations. Citation Format: James R. White, Julia Drewes, Cynthia L. Sears. High-resolution microbiome profiling and meta-analysis yields insight into microbial consortia associated with colorectal cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 844.
Habitat use by American black bears in the urban–wildland interface of the Mid-Atlantic, USA

Abstract Despite a large body of literature that reports habitat use in non-urban areas, we lack a fundamental understanding of how American black bears (Ursus americanus; hereafter, black bear) use habitats in the urban–wildland interface in the eastern United States. This lack of information is problematic for bear managers in areas where bear populations are large and adjacent to urban areas. To better understand characteristics of urban–wildland habitat occupied by black bears, we conducted a study to understand habitat use of black bears in 7 urban areas in New Jersey, Pennsylvania, and West Virginia. We fit data from 77 individual black bears with Global Positioning System–Global System for Mobile Communications collars during 2010–2012 in Johnstown, State College, and Scranton, Pennsylvania; northwestern New Jersey; and Beckley, Charleston, and Morgantown, West Virginia. We fit resource selection functions using generalized linear mixed models in R with different combinations of study area, human impact (human density and housing density), habitat (distance to roads, patch size), land cover (deciduous forest, evergreen forest, mixed forest, shrubland, grassland, pasture, barren, open-, low-, medium-, and high-intensity development, woody wetlands, and herbaceous wetlands), topographic (elevation and slope), and other variables (year, period of day [night or day], age and sex of the individual bear). Black bears used habitat similarly among study areas and between sexes. Black bears used forested slopes and riparian corridors in the urban–wildland interface. Black bears on the urban–wildland interface selected habitats similarly to wildland bears within the body of literature. Habitat selection was similar for males and females, regardless of study area, time of day, season, or year. Our results indicate that managers can employ the same suite of management tools to reduce human–bear conflicts at the urban–wildland interface that they use to deal with black bear conflicts in wildland areas.
Comparative Cell Toxicology: The Basis for In Vitro Toxicity Testing

If “cell toxicology” is defined as the discipline aimed at studying the general principles of chemical interference with cellular structures and/or functions, then “comparative cell toxicology” may be defined as the study of the variety of responses to xenobiotics using: (a) different endpoints within one cell type; (b) cell types from different tissues from one species; and (c) homologous cell types from different species. If the full potential of in vitro models for toxicity testing is to be realised and the scientific basis for hazard assessment improved, then comparative cell toxicological approaches have to be developed further. In the present paper, an approach using different in vitro systems is described. The approach is aimed at the assessment of the basic toxicological characteristics of chemicals.
The Role of GroE Chaperonins in Developing Biocatalysts for Biofuel and Chemical Production

As the need and interest for producing renewable biofuels and biochemical has grown, new avenues to improve product yields and productivity have been explored. Specifically, improving the tolerance of host microbes towards stressors, such as heat shock or the presence of harmful solvents, has been an especially important route to improve industrial-scale chemical production. In this review, we discuss recent advances in microbial engineering for renewable chemical production through the introduction and expression of chaperonins, especially the bacterial GroE complex. The GroE complex provides a closed-off environment and allows vital proteins to enter and engage in post-translational folding or refolding in a more-ideal environment, allowing the microbe to possess increased survival rates in low/high temperatures or in high concentrations of otherwise harmful end-products. Overall, we highlighted how chaperonin systems such as the GroE complex could have many industrially-relevant uses in the coming years.
ALTERNATIVE THERAPIES BEYOND ANTIBIOTICS: HELICOBACTER PYLORI ERADICATION

Helicobacter pylori is a Gram-negative human gastric pathogen infecting about 30% of children and 60% of adults worldwide and has a possible etiologic role in peptic and gastric ulcers, gastric adenocarcinoma and more rarely, lymphoma of the mucosa-associated lymphoid tissue. Currently, this is managed by the use of a triple therapy, involving the co-administration of two antibiotics (with macrolides, fluoroquinolones, amoxicilin, nitroimidazoles and tetracycline among the most prescribed ones) and ranitidine bismuth and/or a proton pump inhibitor. However, as for other bacteria, during the last decades we have been observing the continuous growth of the number of antibiotic resistant H. pylori strains, especially in countries in which antibiotic prescription is more common. The high prevalence rates worldwide and the real risk of severe gastric diseases development demand the need for good strategies for H. pylori eradication. Still growing antibiotic resistance rate already leads to treatment failure in about 20% of the H. pylori-infected patients, but depending on the therapeutic schema and strain resistance pattern, the failure rate can reach 70%, which has led to the search for alternative therapies. This review focuses on the state of the art of alternative strategies for combating H. pylori infection, not involving the use of antibiotics, currently under investigation, namely vaccines, bacterial photodynamic inactivation, phage therapy, the use of probiotics and natural compounds.
Differential Effects of Small Molecule WNT Agonists on the Multilineage Differentiation Capacity of Human Mesenchymal Stem Cells.

Human bone marrow-derived mesenchymal stem cells (MSCs) are promising candidates for cell-based therapies, but loss of expansion and differentiation potential in vitro limits their applicability. Recently we showed that WNT3A protein promoted MSC proliferation and enhanced their chondrogenic potential, while simultaneously suppressing the propensity of the cartilage to undergo hypertrophic maturation. Since WNT3A protein is costly and rapidly loses its activity in culture, we investigated the possibility of replacing it with cheaper commercially available WNT agonists, specifically lithium chloride (LiCl), CHIR99021 (CHIR), SKL2001, and AMBMP. Of these, we found that only CHIR and LiCl stimulated MSC proliferation. Moreover, CHIR enhanced the chondrogenic capacity of MSCs, whereas LiCl predominantly increased the osteo- and adipogenic capacity. The different WNT agonists also differentially impacted the surface marker profile of the MSCs, possibly explaining the observed differences. Moreover, CHIR suppre.
Adaptation and plasticity in aboveground allometry variation of four pine species along environmental gradients

Abstract Plant species aboveground allometry can be viewed as a functional trait that reflects the evolutionary trade‐off between above‐ and belowground resources. In forest trees, allometry is related to productivity and resilience in different environments, and it is tightly connected with a compromise between efficiency‐safety and competitive ability. A better understanding on how this trait varies within and across species is critical to determine the potential of a species/population to perform along environmental gradients. We followed a hierarchical framework to assess tree height‐diameter allometry variation within and across four common European Pinus species. Tree height‐diameter allometry variation was a function of solely genetic components –approximated by either population effects or clinal geographic responses of the population's site of origin– and differential genetic plastic responses –approximated by the interaction between populations and two climatic variables of the growing sites (temperature and precipitation)–. Our results suggest that, at the species level, climate of the growing sites set the tree height‐diameter allometry of xeric and mesic species (Pinus halepensis, P. pinaster and P. nigra) apart from the boreal species (P. sylvestris), suggesting a weak signal of their phylogenies in the tree height‐diameter allometry variation. Moreover, accounting for interpopulation variability within species for the four pine species aided to: (1) detect genetic differences among populations in allometry variation, which in P. nigra and P. pinaster were linked to gene pools –genetic diversity measurements–; (2) reveal the presence of differential genetic variation in plastic responses along two climatic gradients in tree allometry variation. In P. sylvestris and P. nigra, genetic variation was the result of adaptive patterns to climate, while in P. pinaster and P. halepensis, this signal was either weaker or absent, respectively; and (3) detect local adaptation in the exponent of the tree height‐diameter allometry relationship in two of the four species (P. sylvestris and P. nigra), as it was a function of populations' latitude and altitude variables. Our findings suggest that the four species have been subjected to different historical and climatic constraints that might have driven their aboveground allometry and promoted different life strategies.
Hazards Associated with Holding and Reheating Foods at Vending Sites in a Small Town in Zambia.

Hazard analyses were done at 11 cooked-food-vending sites and related food-vending operations in a small-town market along a highway in Zambia. The analyses consisted of observations and time-temperature measurements at the vending sites and interpretations of results of laboratory tests of samples of foods (including leftovers) collected after holding and reheating. Salmonellae were isolated from dried ants, a cooked meatball on display, and pumped river water used by the vendors. Ants for sale at the market contained 107 Bacillus cereus cells per g. Nshima (boiled maize meal) was held at high temperatures in pans over glowing charcoal in which steam was generated throughout the entire holding period during the day, preventing bacterial growth. Large populations of B. cereus , however, were isolated from a sample left overnight at ambient room temperature. Cooked foods other than nshima were held at room or outdoor ambient temperatures throughout the day and overnight. High aerobic mesophilic colony, thermotolerant coliform and, in a few foods, Escherichia coli counts were found in foods after several hours of holding during the day of preparation and of foods held overnight. Temperatures attained during reheating were variable and sometimes would have resulted in survival of foodborne pathogens that multiplied during holding.
Gene and Protein Expressions Induced by 17β-estradiol and Parathion in Cultured Breast Epithelial Cells

Cancer of the breast is the most common form of malignant disease occurring among women of the western world and environmental substances seem to be involved in the etiology of this disease. Many studies have found an association between human cancer and exposure to agricultural pesticides and among them parathion, the organophosphorous pesticide used in agriculture to control mosquito plagues. The association between breast cancer and prolonged exposure to estrogens suggests that this hormone also may have a role in such process. However, the causative factors for breast carcinogenesis remain an enigma. The objective of this study was to determine the effects of 17β-estradiol (E2) and parathion on cell transformation of human breast epithelial cells in vitro. The results of this study showed that parathion alone and in combination with E2 induced malignant transformation of an immortalized human breast epithelial cell line, MCF-10F, and the malignant feature was confirmed by anchorage independency and invasive capabilities. Parathion alone efficiently elevated the expression of EGFR, c-Kit, Trio, Rac 3, Rho-A, and mutant p53 proteins. Analysis of gene expression using commercially available human cell cycle array revealed transcriptional alterations in 22 out of a total of 96 genes. Among them, nine genes involved in the regulation of cell cycle were altered. These included cyclins (A1, A2, C, G1, G2, and H), cyclin-dependent kinases (CDKs), and minichromosome maintenance deficient (MCM). Results suggest that parathion has the potency to cause malignant transformation of breast epithelial cells through modulation of expression of cell cycle regulated genes.
Motive for Killing: What Drives Prey Choice in Wild Predators?

17 Carnivorous animals are assumed to consume prey to optimize energy intake. Recently, 18 however, studies using Nutritional Geometry (NG) have demonstrated that specific blends of 19 macronutrients (e.g. protein, fat and in some cases carbohydrates), rather than energy per se , 20 drive the food selection and intake of some vertebrate and invertebrate predators in the 21 laboratory. A vital next step is to examine the role of nutrients in the foraging decisions of 22 predators in the wild, but extending NG studies of carnivores from the laboratory to the field 23 presents several challenges. Biologging technology offers a solution for collecting relevant 24 data which when combined with NG will yield new insights into wild predator nutritional ecology.
Mycobacterium bovis: realities and challenges for the veterinary biopharmaceutical industry

Mycobacterium bovis is the main etiological agent of bovine tuberculosis, bacterial diseases of world distribution, chronicle, of easy transmission, debilitating, zoonotic and antropozoonotic that affects any organ and which can be presented without symptoms On this base, it was carried out a study with the objective of approaching the current state and the scientific-technological projections for the prevention and diagnosis of the bovine tuberculosis, caused by M. bovis. It was demonstrated that the 45.09% of the original articles on inmunoprophylaxis against bacteria, registered in the Scopus database and contextualised until principles of 2014, were focused toward M. bovis. In spite of the advances in molecular biology and the hopes deposited in the Ag85A, Rv0287, Rv0288, Rv0251c, MPB70, MPB83, ESAT-6 and CFP-10 molecules, jointly with their combinations, it will continue absent in the market an effective, safety and differentiating vaccine; as well as a robust DIVA diagnosis system. It can be concluded that in the next 5 years, an officially recognized vacinal formulation will continue absent and that the tuberculin test in spite of its weaknesses will continue being the main tool of surveillance.
Genotoxic evaluation of the Ergene River, Turkey, on mosquito fish, Gambussia affinis (Baird and Girard, 1853) using the piscine micronucleus assay

The Ergene River is located in the Thrace Region of Turkey and is polluted by industrial and municipal waste. In the present study, we investigated the genotoxic and cytotoxic effects of water samples on Gambussia affinis in vivo using the piscine micronucleus (MN) test. Fish were exposed to 50, 100, 150 and 300 mL L -1 of water samples for 24 hrs, and MN, nuclear abnormalities (NA), polychromatic-normachromatic erythrocytes (PCEs/NCEs), and apoptotic erythrocytes were evaluated. In addition, water samples were analysed to determine the concentrations of the heavy metals. The results showed that MN, NA, and apoptosis frequencies significantly increase at all concentrations compared to the control. A significant correlation was found between genotoxicity endpoints and the concentration of water samples. The PCE-NCE ratio was significantly decreased at all treatments. The metal content of river water was not associated with the increase in the seasonal frequency of genotoxicity endpoints. The results indicated that the Ergene River has genotoxic and cytotoxic effects on erythrocytes of G. affinis in an in-vivo piscine MN test that could be due to organic and inorganic effluents.
Expression, Purification and in vitro Enzyme Activity Assay of Plant Derived GTPase

[Abstract] Based on gene expression data after biotic stress, the GTPase RabA4c has been suggested to regulate pathogen-induced callose biosynthesis in the model organism Arabidopsis thaliana. We studied the function of RabA4c in its native and dominant negative (dn) isoform. In planta, RabA4c overexpression prevented penetration of the virulent powdery mildew Golovinomyces cichoracearum into epidermal leaf cells. This penetration resistance was caused by enhanced callose deposition at sites of attempted fungal penetration at early time points of infection. By contrast, RabA4c (dn) overexpression did not increase callose deposition or penetration resistance. In this protocol, we describe the expression, purification and activity assay of the heterologously expressed GTPase RabA4c from A. thaliana based on the publication Ellinger et al. (2014). We fused RabA4c to the fluorophore mCitrine and expressed this protein in the yeast strain Pichia pastoris GS115. For purification of RabA4c, we used the GFP-Trap_A kit (Chromo Tek) which specifically binds to GFP derivatives like mCitrine. The enzyme activity assay was done by using the GTPase Assay Kit from Innova Biosciences. In general, we followed the instructions made by the manufacturers.
Correlation between the Change of Intracellular Free Calcium Ion and Autophagy Induced by Quercetin in Hep G2 Cells

Reagent staining. The results showed that the viabilities of Hep G2 cells were decreased and the autophagy was induced after treated with quercetin at concentration range of 0 ~ 50 μ g / mL , while that of HL7702 cells were not changed significantly. Meanwhile , we also observed the effects of quercetin on intracellular free calcium ion and the relationship between autophagy and change of the ( Ca 2 + ) i in Hep
OXIDATIVE STRESS, SARCOPENIA, ANTIOXIDANT STRATEGIES AND EXERCISE: MOLECULAR ASPECTS

Sarcopenia could be currently defined as a geriatric syndrome initially characterized by a decrease in muscle mass that will get worse causing deterioration in strength and physical performance. A negative protein turnover, impaired mitochondrial dynamics and functions, a decreased muscle regeneration capacity, as well as an exacerbation of apoptosis are usually considered to be cellular mechanisms involved in muscle atrophy leading to sarcopenia. Here, we first present that muscle overproduction of reactive oxygen and nitrogen species (RONS) and oxidative stress observed during aging, are associated with sarcopenia, and then discuss how RONS are involved in redox-sensitive signaling pathways leading to sarcopenia. The identification of cost-effectiveness interventions to maintain muscle mass and physical functions in the elderly is one of the most important public health challenges. Here, we also discuss about the efficiency of different kind of current antioxidant strategies against sarcopenia and future strategies. Since exercise is the best strategy to prevent and reverse sarcopenia, we also highlight that exercise acts as an antioxidant.
A pyometra managed by laparoscopic ovariohysterectomy in a dog

L'objectif de cet article est de decrire un cas de pyometre traite par ovariohysterectomie sous coelioscopie. Une chienne Caniche de 15 ans atteinte d'un syndrome de Cushing presente des pertes vulvaires purulentes. Une echographie abdominale confirme l'existence d'un pyometre a col ouvert. Une ovariohysterectomie sous coelioscopie est decidee afin de limiter la taille des plaies et diminuer les problemes de cicatrisation pouvant etre associes a l'hypercorticisme. La chirurgie a dure 85 minutes, la chienne est ambulatoire 3 heures apres l'intervention. Aucune complication n'a ete rencontree. Les ovariectomies ainsi que les ovariohysterectomies sont frequemment effectuees sur des chiennes en bon etat general. Cette intervention peut aussi etre envisagee lors de pyometre a col ouvert sans accroitre le taux de complication. Dans notre cas, la coelioscopie a permis de limiter les complications comme une dehiscence de plaie sur une chienne âgee, obese et presentant une faiblesse de la paroi abdominale associee a son hypercorticisme.
Determination metabolic and nutritional status in dairy cows during early and mid lactation

The objective of the present study was to investigate nutritional and metabolic status in Simmental cows during early and mid-lactation. Fifteen early lactating cows and 15 mid lactating cows were chosen for the investigation. Blood samples were collected to measure beta-hydroxybutyrate (BHB), nonesterified fatty acids (NEFA), triglycerides (TG), glucose and the activity of aspartate transaminase (AST). Early lactation as compared to mid lactating cows were found to have significantly higher (P<0.05) blood serum concentrations of NEFA, BHB and AST and lower blood serum concentrations of glucose (P 0.05). Significantly negative correlations were observed between BHB and glucose (P<0.01), BHB and TG (P<0.05), NEFA and glucose (P<0.05). Significantly positive correlations were observed between NEFA and BHB (P<0.05), NEFA and AST (P<0.05), glucose and TG (P<0.01). The results suggest that these parameters can serve as useful indicators of the nutritional and metabolic status of dairy cows during lactation. [Projekat Ministarstva nauke Republike Srbije, br. TR 31001]