Miracle-dz/UniFAR-FTUs huggingface dataset:
Avaliação in vitro da adsorção de aflatoxina B1 por produtos comerciais utilizados na alimentação animal

The aim of this study was to evaluate the aflatoxin B 1 (AFB 1 ) adsorption capacity, in vitro , by commercial products used in animal feed. Many studies are being conducted for the decontamination of aflatoxins in feed. The commercial products destined to fish feed that are available as probiotics and are formed by strains of bacteria and yeasts used in most mycotoxins adsorption assays. Three commercial products were studied: A, consisting of Bacillus subtilis , Bifidobacterium bifidum , Enterococcus faecium and Lactobacillus acidophilus ; B, consisting of dry yeast of Saccharomyces cerevisiae from brewery; and C, consisting of Bacillus subtilis, Bacillus licheniformis and Bacillus pumilus . Five suspensions of the maximum dose recommended by the manufacturer of each product (0; 25; 50; 75 and 100%) were tested against AFB 1 (1000 ng.mL -1 ) in microtubes to determine the adsorption capacity. To simulate the pH of the stomach and intestine of the Nile tilapia ( Oreochromis niloticus ), phosphate buffered saline solutions (PBS) at pH 1.5 and 7.5, respectively, were formulated. Microtubes were introduced into a centrifuge with mechanical agitation at 37oC for 1 h and then centrifuged for 10 min at 14.000 rpm; the supernatants were quantified by high-performance liquid chromatography. The commercial products in the maximum concentration were capable of adsorbing AFB 1 in amounts from 45.01 to 129.59; from 123.90 to 215.59; and from 209.98 to 370.73 (ng.mL -1 ), respectively. It was concluded that all commercial products, which are added to animal feed, adsorbed AFB 1 under simulated gastrointestinal pH conditions and are potential candidates for AFB 1 adsorption for future in vivo studies.
Effect of Prostaglandin E 2 on Human Dental Follicle Cells during Osteogenic Differentiation

Stem/progenitor cells isolated from human dental follicles differentiate into osteogenic cells. To investigate factors associated with osteogenic differentiation/mineralization in human dental follicle cells(hDFCs), we performed gene expression profiling of hDFCs during osteogenic differentiation. Cyclooxygenase(COX)-1 and -2 were up-regulated in hDFCs cultured in osteogenic induction medium(OIM)compared to growth medium(GM). Prostaglandin E2(PGE2), which is the most studied prostanoid derived from arachidonic acid through the actions of COXs, may regulate bone metabolism. All PGE2 E-type prostanoid receptors(EP), EP1-EP4, were expressed in hDFCs. Real-time PCR showed that the expression of EP2 and EP4 was increased in hDFCs cultured in OIM and GM at days 10 and 17 compared to day 0. We investigated the action of PGE2 in osteogenic differentiation using hDFCs. PGE2 decreased gene expression levels of osterix and alkaline phosphatase, which are factors associated with osteogenic differentiation. PGE2 elicited inhibitory action on matrix mineralization of hDFCs as seen with alizarin red S staining. These findings suggest that PGE2 may inhibit osteogenic differentiation/mineralization of stem/progenitor cells.
Aroma and sensory characteristics of Slavonian plum brandy

Quality of plum brandy is influenced by many factors, such as: climate characteristics, soil characteristics, characteristics of plum (Prunus domestica) varieties and technological characteristics of manufacturing process. The aim of this work was determination of the quality of Croatian “home-made” plum brandies produced by authentic production process from the Croatian region of Slavonia. For detection of volatile flavor components and quality of plum brandy, gas-chromatography and sensory analysis were applied. Home-made Croatian plum brandies as distillates of Prunus domestica contain numerous ingredients. Some of these ingredients are desirable and important for the quality of distillates, and some are undesirable. The obtained results show that all samples had a higher content of aldehydes and higher alcohols, ethanol content was in range 43.02 – 44.5 % vol.
Wild horses of the Great Basin

This is the first thorough study of the biology and ecology of American wild horses, a book with insights for all biologists and important implications and recommendations for conservationists and range managers. Berger blends theory with valuable new data on age, weight, demography, food resources, habitat, reproduction, social behavior, and competitive abilities. One of his most dramatic findings is the occurrence of induced abortions among pregnant mares when one stallion displaces another as master of a harem of females. Cloth $24.95 348 pages 27 b&w photographs, 39 line drawings
Food and feeding ecology of the Tasmanian short-tailed shearwater (Puffinus tenuirostris, Temminck): insights from three complementary methods

The diet of seabirds is usually studied by the identification of prey items recovered from their stomachs. This method is however limited to recently ingested prey and to non-digestible hard parts, precluding the determination of marine resources consumed by birds during long foraging trips. Thus, alternative indirect approaches are necessary to assess the potential importance of digested prey from long-term foraging activity. In this study, we present three complementary techniques to determine the prey of breeding short-tailed shearwaters (Puffinus tenuirostris) when they feed for themselves during long foraging trips: (1) conventional food analysis, (2) stable isotope analysis of carbon and nitrogen signatures (δ13C and δ15N) of plasma, and (3) lipid analysis of stomach oil and the use of fatty acids and fatty alcohols as trophic markers (stomach oil is of dietary origin). Dietary analysis showed that fish dominated by mass over crustaceans (82 and 18%, respectively). Two euphausiids Euphausia vallentini (a sub-Antarctic species) and Nyctiphanes australis (a Tasmanian species), and fish postlarvae represented more than 94% of the total number of food items, with myctophid fish of larger size dominating by mass. Plasma isotopic signature of birds suggested that shearwaters foraged mainly in Antarctic waters (δ13C = -23.8‰), and fed at a trophic level close to that of a myctophid-eater, the king penguin (δ15Nshort-tailed shearwater = 8.7‰, δ15Nking penguin = 9.8‰). Comparisons between fatty -acid and -alcohol patterns of stomach oil wax esters with those of potential prey also suggested a food based on myctophids (Electrona antarctica, Krefftichthys anderssoni and Gymnoscopelus braueri). To conclude, both lipid and stable isotope methods emphasized the importance of myctophids in the nutrition of short-tailed shearwaters during the chick-rearing period when adult birds feed for themselves. This study illustrates the interest of using both direct and indirect methods to determine trophic relationships between marine organisms.
Evaluation of antioxidant and antimicrobial potentials of Eclipta prostrata collected from the Nepal region

Eclipta prostrata is a perennial herb which is used to treat various ailments as a part of the traditional medicine in different parts of the world. Considering the ethnopharmacological importance of the plant, the antioxidant and antimicrobial activity of the leaf extract were evaluated. Antioxidant activity was determined using DPPH scavenging activity assay, ferric reducing power assay and total antioxidant assay. The phenol and flavonoid content were also quantitatively determined. The extract was able to scavenge DPPH free radical and reduce ferric ion. It showed a significant amount of phenol and flavonoid content. It inhibited the growth of pathogenic gram-positive and gram-negative bacteria effectively. Further study needs to be done for identifying the future applications of E. prostrata in drug and food industry.
Pollen tube growth and guidance: Occam’s razor sharpened on a molecular AGP Rosetta Stone

Occam’s Razor suggests a new model of pollen tube tip growth based on a novel Hechtian oscillator that integrates: (1) a periplasmic AGP-Ca2+ calcium capacitor with tip-localised arabinogalactan glycoproteins (AGPs); (2) tip-focussed cytosolic Ca2+oscillations; (3) Hechtian strands evidence of adhesion between the plasma membrane and the cell wall of the growing tip. Thus Hechtian adhesion, as a piconewton force transducer, couples the internal stress of a rapidly growing wall to the plasma membrane. Such Hechtian transduction via stretch-activated Ca2+ channels and H+-ATPase proton efflux dissociating periplasmic AGP-Ca2+, creates a Ca2+ influx that activates exocytosis of wall precursors. In effect a highly simplified primary cell wall regulates its own synthesis and a Hechtian growth oscillator regulates overall tip growth. By analogy with the Rosetta Stone that translates trilingual inscriptions as a single identical proclamation, the Hechtian Hypothesis translates classical AGPs and their roles as a Ca2+ capacitor, pollen tube guide and wall plasticiser into a simple but widely applicable model of tip growth. Even wider ramifications of the Hechtian oscillator may implicate AGPs in osmosensing or gravisensing and other tropisms, leading us yet further towards the Holy Grail of plant growth.
Lophodermium resinosum sp. nov. from red pine (Pinus resinosa) in Eastern Canada

A morphologically distinct Lophodermium species was collected from fallen secondary needles of Pinus resinosa Aiton over two consecutive years in Eastern Ontario; subsequent herbarium studies confirmed its presence in Nova Scotia, Quebec, and Maine. Symptomatic needles frequently exhibited red bands and completely subepidermal ascomata and conidiomata. Ascospore isolates from specimens were used to reconstruct phylogenies inferred from internal transcribed spacer rDNA and partial actin gene sequences. Both phylogenetic analyses delineated the specimens from other sequenced Lophodermium species. Phylogenetic evidence combined with morphological characters of ascomata and conidiomata supported the distinctiveness of this species, described here as Lophodermium resinosum sp. nov.
Review article Mutations in a- and b-tubulin encoding genes: Implications in brain malformations

The tubulin gene family is mainly expressed in post-mitotic neurons during cortical development with a specific spatial and temporal expression pattern. Members of this family encode dimeric proteins consisting of two closely related subunits (a and b), representing the major constituents of microtubules. Tubulin genes play a crucial role in the mechanisms of the Central Nervous System development such as neuronal migration and axonal guidance (axon outgrowth and maintenance). Different mutations in a/b-tubulin genes (TUBA1A, TUBA8, TUBB2A, TUBB4A, TUBB2B, TUBB3, and TUBB) might alter the dynamic properties and functions of microtubules in several ways, effecting a reduction in the number of functional tubulin heterodimers and causing alterations in GTP binding and disruptions of the binding of other proteins to microtubules (motor proteins and other microtubule interacting proteins). In recent years an increasing number of brain malformations has been associated with mutations in tubulin genes: malformations of cortical development such as lissencephaly and various grades of gyral disorganization, focal or diffuse polymicrogyria and open or closed-lips schizencephaly as likely consequences of an altered neuronal migration process; abnormalities or agenesis of the midline commissural structures (anterior commissure, corpus callosum and fornix), hypoplasia of the oculomotor and optic nerves, dysmorphisms of the hind-brain as expression of axon guidance disorders. Dysmorphisms of the basal ganglia (fusion between the caudate nucleus and putamen with absence of the anterior limb of the internal capsule) and hippocampi were also observed. A rare form of leukoencephalopathy characterized by hypomyelination with atrophy of the basal ganglia an cerebellum (H-ABC) was also recently described. The present review, describing the structural and functional features of tubulin genes, aims to revise the main cerebral associated malformations and related clinical aspects, suggesting a genotype–phenotype correlation.
GENOME-WIDE DETECTION OF QTL AND CNVS IN DAIRY CATTLE POPULATION

3 Abbreviations . 6 Part 1 GENOME SCAN FOR THE QTL IDENTIFICATION INVOLVED IN THE PHENOTYPIC VARIATION OF THE ECONOMICALLY IMPORTANT TRAITS IN DAIRY CATTLE . 7 References . 15 1 – Quantitative trait loci mapping for conjugated linoleic acid, vaccenic acid and 9-desaturase in Italian Brown Swiss dairy cattle using selective DNA pooling. Animal genetics, 2014: 45, 485–499. 17 Abstract . 18. 18 Introduction . 19 Materials and Methods . 21 Results and Discussion . 27 Conclusions . 32 References . 32 Table . 39 Figure . 48 2 – Genome-wide association study for somatic cell score in Valdostana Red Pied cattle breed using pooled DNA. BMC Genetics, 15:106 (doi:10.1186/s12863-014-0106-7) . 55 Abstract . 56. 56 Background . 57 Results and discussion . 58 Conclusions . 63 Methods . 64 References . 68 2 Table . 72 Figure . 76 Additional File . 78 Part 2 GENOME SCAN FOR THE CNVS DISCOVERY IN DAIRY CATTLE . 95 References . 105 3 – Identification and validation of copy number variants in Italian Brown Swiss dairy cattle using Illumina Bovine SNP50 Beadchip. Short Communication. Submitted Animal Genetics . 109 Abstract . 110. 110 Text . 111 References . 116 Table . 121 Figure . 123 Supplementary Information . 124 General Discussion . 155 International and National Conferences: Posters . 159
PML nuclear bodies and chromatin dynamics: catch me if you can!

Abstract Eukaryotic cells compartmentalize their internal milieu in order to achieve specific reactions in time and space. This organization in distinct compartments is essential to allow subcellular processing of regulatory signals and generate specific cellular responses. In the nucleus, genetic information is packaged in the form of chromatin, an organized and repeated nucleoprotein structure that is a source of epigenetic information. In addition, cells organize the distribution of macromolecules via various membrane-less nuclear organelles, which have gathered considerable attention in the last few years. The macromolecular multiprotein complexes known as Promyelocytic Leukemia Nuclear Bodies (PML NBs) are an archetype for nuclear membrane-less organelles. Chromatin interactions with nuclear bodies are important to regulate genome function. In this review, we will focus on the dynamic interplay between PML NBs and chromatin. We report how the structure and formation of PML NBs, which may involve phase separation mechanisms, might impact their functions in the regulation of chromatin dynamics. In particular, we will discuss how PML NBs participate in the chromatinization of viral genomes, as well as in the control of specific cellular chromatin assembly pathways which govern physiological mechanisms such as senescence or telomere maintenance.
Methanogenic archaea in peatlands.

Methane emission feedbacks in wetlands are predicted to influence global climate under climate change and other anthropogenic stressors. Herein, we review the taxonomy and physiological ecology of the microorganisms responsible for methane production in peatlands. Common in peat soils are five of the eight described orders of methanogens spanning three phyla (Euryarchaeota, Halobacterota and Thermoplasmatota). The phylogenetic affiliation of sequences found in peat suggest that members of the thus-far-uncultivated group Candidatus Bathyarchaeota (representing a fourth phylum) may be involved in methane cycling, either anaerobic oxidation of methane and/or methanogenesis, as at least a few organisms within this group contain the essential gene, mcrA, according to metagenomic data. Methanogens in peatlands are notoriously challenging to enrich and isolate; thus, much remains unknown about their physiology and how methanogen communities will respond to environmental changes. Consistent patterns of changes in methanogen communities have been reported across studies in permafrost peatland thaw where the resulting degraded feature is thermokarst. However much remains to be understood regarding methanogen community feedbacks to altered hydrology and warming in other contexts, enhanced atmospheric pollution (N, S, metals) loading, and direct anthropogenic disturbances to peatlands like drainage, horticultural peat extraction, forestry, and agriculture, as well as post-disturbance reclamation.
Inter‐laboratory variation in corticosterone measurement: Implications for comparative ecological and evolutionary studies

Interspecific comparisons of endocrine data are useful for drawing broad conclusions concerning the role of ecological variables in the evolution of physiological pathways. However, comparisons of endocrine data generated by different research groups are problematic, due to inter‐laboratory variation in measured hormone values. To date, we know of no study which has quantified the extent of inter‐laboratory variation in the measurement of hormone levels, outside of biomedical studies. To evaluate the extent to which laboratories differ in their measurement of hormones, we prepared seven samples of avian plasma with known concentrations of corticosterone and sent them for blind analyses to 19 laboratories and asked them to report the methods used and the values obtained. Both absolute hormone concentrations and the ratios between samples were equally variable, up to an order of magnitude different for some concentrations. Laboratory identity accounted for more than 80% of the variation in reported corticosterone, but we could not identify any methodological factors that consistently contributed to this inter‐laboratory variation. In addition, laboratory measurement error was significantly correlated with the latitude of the primary study species for each laboratory, suggesting that inter‐laboratory variation has the potential to drive trends in corticosterone datasets. Inter‐laboratory variation in corticosterone measurement may have serious implications for quantitative comparisons of endocrine values across laboratories, although comparisons of qualitative patterns may be more robust because rank order of the samples was relatively consistent across laboratories. Ignoring laboratory effect and the non‐independence of data may lead to an inflated rate of Type I error and spurious correlations.
Transcriptome analysis of the brain under diapause and nondiapause conditions in the blowfly Protophormia terraenovae

The blow fly Protophormia terraenovae responds to photoperiod and temperature to control reproductive diapause. Differentially expressed genes (DEGs) in the brain are investigated under diapause‐inducing and diapause‐averting conditions in search of potential genes for diapause induction. Total RNA is extracted from female brains 1–2.5 days after adult emergence under an LD 18 : 6 h photocycle at 25 °C as nondiapause samples and 3, 3.5, 7 and 7.5 days after adult emergence under an LD 12 : 12 h photocycle at 20 °C as diapause samples. From our transcriptome analysis, 626 350 654 reads are assembled into 126 231 contigs, from which 46 844 contigs (37.1% of the total) are annotated as protein‐coding genes. Among them, the expression levels in 549 contigs are specifically up‐regulated under diapause‐inducing (44.1%) or diapause‐averting (55.9%) conditions. Using quantitative real‐time reverse transcriptase‐polymerase chain reaction analysis, higher expression levels under diapause‐inducing conditions are found in a contig encoding angiotensin‐converting enzyme (ACE). Expression levels of the contig significantly increase 3 days after changing the photoperiod to diapause‐inducing short days. Rabbit antisera against 17 amino acid peptides included in P. terraenovae‐ACE stain one pair of cells lateral to the oesophageal foramen. These results suggest that the expression of a small number of genes is associated with the regulation of diapause in response to photoperiod and temperature, and ACE in the immunoreactive cells might respond to short days, which is why it is involved in diapause induction.
Structural basis of Mfd-dependent transcription termination

Abstract Mfd-dependent transcription termination plays an important role in transcription-coupled DNA repair, transcription-replication conflict resolution, and antimicrobial resistance development. Despite extensive studies, the molecular mechanism of Mfd-dependent transcription termination in bacteria remains unclear, with several long-standing puzzles. How Mfd is activated by stalled RNA polymerase (RNAP) and how activated Mfd translocates along the DNA are unknown. Here, we report the single-particle cryo-electron microscopy structures of T. thermophilus Mfd-RNAP complex with and without ATPγS. The structures reveal that Mfd undergoes profound conformational changes upon activation, contacts the RNAP β1 domain and its clamp, and pries open the RNAP clamp. These structures provide a foundation for future studies aimed at dissecting the precise mechanism of Mfd-dependent transcription termination and pave the way for rational drug design targeting Mfd for the purpose of tackling the antimicrobial resistance crisis.
Mechanism of MicroRNA miR-520g Pathogenesis in CNS-PNET

We recently discovered a high-level amplicon spanning the chr19q13.41 microRNA cluster in CNS Primitive Neuroectodermal Tumour, which results in striking upregulation of miR-520g. Constitutive over-expression of miR-520g in untransformed human neural stem cells enhanced cell growth, restricted differentiation down the neuronal lineage, and promoted expression of neural stem/progenitor cell markers. We thus hypothesize that ectopic miR-520g expression promotes tumourigenesis in part by inhibiting cellular differentiation. Consistent with this proposition, miR-520g is silenced upon embryonic stem cell differentiation and its expression is absent from most adult tissues. Moreover, expression analysis of miR-520g overexpressing cells revealed significant dysregulation of developmental signalling pathways. Further efforts focused on elucidating mechanisms of miR-520g function led to the identification of a cell cycle inhibitor, p21, as an important candidate target. These findings collectively suggest that miR520g may modulate differentiation by regulating developmental signalling pathways and cell cycle exit of neural stem/progenitor cells.