Miracle-dz/UniFAR-FTUs huggingface dataset:
The Measurement of Sulfur-Containing Aroma Compounds in Samples from Production-Scale Brewery Operations

A method employing solid-phase microextraction followed by gas chromatography and detection by chemiluminescence has been used to measure sulfur-containing volatile substances in a range of beers and brewery process samples. Commercial beers were very similar in the types of sulfur-containing molecules contained. All beers tested, including ales, featured high levels of dimethyl sulfide, as well as methanethiol and S-methyl thioacetate. Only one beer was free from sulfur dioxide and only one was devoid of dimethyl disulfide. None of the beers contained detectable levels of ethanethiol, diethyl sulfide, or ethyl methyl sulfide. S-methyl thioacetate is most conspicuously a product of yeast metabolism, being produced from methanethiol. However, it is likely that the levels of dimethyl sulfide, sulfur dioxide, and perhaps methanethiol at the end of fermentation are a balance of substantial purging loss and replenishment by the action of yeast. There is an increase in the level of S-methyl thioacetate, at the expense of methanethiol, in ale that is naturally conditioned in the bottle. Prolonged postfermentation conditioning in tank also leads to an increase in the level of certain sulfur-containing volatiles, especially dimethyl sulfide and S-methyl thioacetate. Higher levels of sulfur volatiles were found in the same beer when packaged in kegs as opposed to bottles, presumably because of the extent to which volatiles are lost during purging operations.
Biosynthetic Gene Clusters of Benzoisochromanequinone Antibiotics in Streptomyces spp. –Identification of Genes Involved in Post-PKS Tailoring Steps–

Benzoisochromanequinone (BIQ) antibiotics are a class of aromatic polyketides produced by Streptomyces spp. A polyketide synthase (PKS, Type II) is involved in the formation of each BIQ chromophore. The first PKS genes were cloned in S. coelicolor A3(2), producer of the typical BIQ antibiotic, actinorhodin; sequence analysis of the PKS genes revealed their clustering with all the other relevant biosynthetic genes (the act cluster). A number of PKS genes have been discovered in the producers not only of other BIQs, but also of other classes of aromatic polyketides, using the act PKS genes as hybridisation probes. Among them similar genetic organisations were identified for the genes encoding the minimal PKS components -KS (ketosynthase), CLF (chain length factor), ACP (acyl carrier protein)- and their closely associated proteins: KR (ketoreductase), ARO (aromatase), and CYC (cyclase). In spite of the increasing knowledge of PKS genes themselves, various biosynthetic problems remain to be solved. As one of the most extensively studied examples at the genetic level, BIQ antibiotics are useful model compounds to be studied to understand the whole biosynthetic pathways of aromatic polyketides. This review describes the genes from the act and gra (granaticin biosynthetic gene cluster in S. violaceoruber Tu22) clusters involved in post-PKS modifying (tailoring) steps to complete BIQ biosynthesis.
Lavorazioni su conchiglia di Pseudunio auricularius (Mollusca, Bivalvia) nel Neolitico antico a Isorella (BS), Italia settentrionale

The Early Neolithic site oflsorella, in the Brescia Province, attributed to the Vho Group, provided in the past several fragments of the freshwater bivalve Pseudunio auricularius. The recent wet sieving of the deposit allowed the recovery of many fragments of Unio cf. mancus and some small semifinished broken objects. The examination of these items and the comparison between the shell structures of the freshwater bivalves and those of Spondylus sp. and Glycymeris sp. show that the records have been obtained from the shell of P. auricularius. The new finds represent the missing link in the working process between the shell of P auricularius and the final artefacts.
Approaches For Inferring Past Population Size Changes From Genome-wide Genetic Data.

The history of populations or species is of fundamental importance in a variety of areas. Gaining details about demographic, cultural, climatic or political aspects of the past may provide insights that improve the understanding of how populations have evolved over time and how they may evolve in future. Different types of resources can be informative about different periods of time. One especially important resource is genetic data, either from a single individual or a group of organisms. Environmental conditions and circumstances can directly affect the existence and success of a group of individuals. Since genetic material gets passed on from generation to generation, traces of past events can still be detected in today’s genetic data. For many decades scientists have tried to understand the principles of how external influences can directly affect the appearance and features of populations, leading to theoretical models that can interpret modern day genetic variation in the light of past events. Among other influencing factors like migration, natural selection, etc., population size changes can have a great impact on the genetic diversity of a group of organisms. For example, in the field of conservation biology, gaining insights into how the size of a population evolves may assist in detecting past or ongoing temporal reductions of population size. This seems crucial since the reduction in size also correlates with a reduction in genetic diversity which in turn might negatively affect the evolutionary potential of a population. Using computational and population genetics methods, sequences from whole genomes can be scanned for traces of such events and, therefore, assist in new interpretations of historical details of populations or groups of interest. This thesis focuses on the detection and interpretation of past population size changes. Two approaches to infer particular parameters from underlying demographic models are described. The first part of this thesis introduces two summary statistics which were designed to detect fluctuations in size from genome-wide Single Nucleotide Polymorphism (SNP) data. Demographic inferences from such data are inherently complicated due to recombination and ascertainment bias. Hence, two new statistics are introduced: allele frequency-identity by descent (AF-IBD) and allele frequency-identity by state (AF-IBS). Both make use of linkage disequilibrium information and exhibit defined relationships to the time of the underlying mathematical process. A fast and efficient Approximate Bayesian Computation framework based on AF-IBD and AF-IBS is constructed that can accurately estimate demographic parameters. These two statistics were tested for the biasing effects of hidden recombination events, ascertainment bias, and phasing errors. The statistics were found to be robust to a variety of these tested biases. The inference approach was then applied to genome-wide SNP data to infer the demographic histories of two
TROPHIC RELATIONSHIPS OF TWO SYMPATRIC SPECIES OF RANIDELLA (ANURA)

The diets of breeding males of Ranidella signifera and R. parinsignifera were compared for 2 yr. In each year, the size-frequency distributions of prey were similar, as were the taxonomic representations of prey in the diets. The amounts of prey consumed at any given time also were similar. Thus, these species of Ranidella, which are morphologically alike and occupy similar microhabitats, are not differentiated with respect to diet. Prey species character- ized by small size (i.e., <1.2 mm long) were consumed most consistently by both species of Ranidella. Investigation of size-frequency distributions of available prey showed that smaller prey were numerically most dominant.
The complete mitochondrial genome of Oreolalax lichuanensis (Amphibia, Anura, Megophryidae)

Abstract The complete mitochondrial genome of the Oreolalax lichuanensis was determined. It is a circular molecule of 17 702 bp in size and consists of 13 protein-coding genes, 23 tRNA genes, two rRNA genes and a control region (D-loop). The base composition on light strand was 28.0% A, 32.2% T, 24.9% C and 14.9% G. Compared with most other vertebrates, this mitogenome appear a tandem duplication of tRNA-Met gene. This study will facilitate the further research of the population genetics of this species and systematic study of the genus Oreolalax.
Interspecies study of the enteric nervous system and related pathologies

The enteric nervous system (ENS) modulates a number of digestive functions including well known ones, i.e. motility, secretion, absorption and blood flow, along with other critically relevant processes, i.e. immune responses of the gastrointestinal (GI) tract, gut microbiota and epithelial barrier . The characterization of the anatomical aspects of the ENS in large mammals and the identification of differences and similarities existing between species may represent a fundamental basis to decipher several digestive GI diseases in humans and animals. In this perspective, the aim of the present thesis is to highlight the ENS anatomical basis and pathological aspects in different mammalian species, such as horses, dogs and humans. Firstly, I designed two anatomical studies in horses:  “Excitatory and inhibitory enteric innervation of horse lower esophageal sphincter”.  “Localization of 5-hydroxytryptamine 4 receptor (5-HT4R) in the equine enteric nervous system”. Then I focused on the enteric dysfunctions, including:  A primary enteric aganglionosis in horses: “Extrinsic innervation of the ileum and pelvic flexure of foals with ileocolonic aganglionosis”.  A diabetic enteric neuropathy in dogs: “Quantification of nitrergic neurons in the myenteric plexus of gastric antrum and ileum of healthy and diabetic dogs”.  An enteric neuropathy in human neurological patients: “Functional and neurochemical abnormalities in patients with Parkinson's disease and chronic constipation”. The physiology of the GI tract is characterized by a high complexity and it is mainly dependent on the control of the intrinsic nervous system. ENS is critical to preserve body homeostasis as reflect by its derangement occurring in pathological conditions that can be lethal or seriously disabling to humans and animals. The knowledge of the anatomy and the pathology of the ENS represents a new important and fascinating topic, which deserves more attention in the veterinary medicine field.
Inhibitory effects of antagonistic bacteria inhabiting the rhizosphere of the sugarbeet plants, on Cercospora beticola Sacc., the causal agent of Cercospora leaf spot disease on sugarbeet

: In the present study, the antagonistic capability of bacterial agents inhabiting the rhizosphere of sugarbeet plants were evaluated against Cercospora beticola Sacc. under laboratory and greenhouse conditions. After preliminary screening using the dual culture method, 14 strains with higher antagonistic capability were selected for further inhibitory assays against C. beticola . Bacterial strains were identified based on the sequence data of the small subunit-rDNA (SSU-rDNA) gene. Based on the SSU sequence data, the identity of bacterial strains were determined as Bacillus (10 strains: RB1, RB2, RB3, RB4, RB5, RB6, RB7, RB8, RB9, RB10), Paenibacillus (two strains: RP1, RP2), Enterobacter (one strain: RE), and Pseudomonas (one strain: RPs). The results obtained in this study showed that in all of the assays (dual culture, volatile and non-volatile metabolites) bacterial antagonists significantly inhibited the growth of C. beticola compared to the control. Bacillus (RB2) showed the highest inhibition rate on C. beticola in all of the assays. Based on the results of the laboratory assays, three bacterial strains RB2 ( Bacillus ), RPs ( Pseudomonas ), and RE ( Paenibacillus ) were selected for greenhouse assays. The experiment was designed based on a completely randomised design (CRD) with the application of antagonists prior to, simultaneously, and after inoculation with C. beticola on sugarbeet leaves. The reduction in disease severity was evaluated seven days after inoculation. The results of greenhouse assays were consistent with the results of laboratory studies. The obtained results showed that bacterial antagonists significantly reduced the disease severity when compared to the control.
The Influence of Spacing on Field-grown Perennial Crops

Achillea ‘Coronation Gold’, A. millefolium L. ‘Rose Beauty’, Physostegia virginiana L. ' Liatris pycnostachya Michx. , and Salvia leucantha Cav. were planted on 30-, 60-, 90-, or 120-cm centers. Data were collected for 2 or 3 years, depending on species. In all instances the number of flowering stems per plant increased but the number of stems per square meter decreased as spacing increased with time. Stem lengths of Achillea ‘Coronation Gold’, A. millefolium ‘Rose Beauty’, and Physostegia virginiana were affected signficantly by spacing but flower size and stem diameter remained unchanged regardless of planting distance.
Relationships among Three Non-Destructive Seedling Vigour Traits in Maize

Three non-destructive methods of seedling vigour assessment were compared in a pot experiment and two soil fertility environments in a field experiment. Ten and 23 maize (Zea mays L.) genotypes were evaluated in the pot and field experiments, respectively. The experimental design was a randomized complete block with three replicates. The seedling vigour traits investigated were seedling height, seedling length and vigour score on a scale of 1 to 9 (where 1= excellent vigour; 9 = very poor vigour). Data were collected at 2 and 4 weeks after planting (WAP) in pots, and 4 WAP in the field. The maize genotypes showed genetic variation for the three seedling vigour traits studied. Seedling height, seedling length and vigour score were significantly (P < 0.01) correlated in pots and in the field. Phenotypic correlation ranged from -0.76 to 0.89 in pots and -0.51 to 0.96 in the field while genotypic correlation ranged from -0.91 to 1.04 in pots, and -0.57 to 0.96 in the field. Heritability for the three traits was moderate to high (0.38-0.67) in pots and high in the field (0.71-0.88). Any one of the three traits could, therefore, be used for the assessment of seedling vigour in maize. Vigour score integrates qualitative and quantitative aspects of seedling performance. The ease and rapid nature of its determination place it at advantage over the other two seedling vigour traits.
Diversity and Physiological Characteristics of Culturable Bacteria from Marine Sediments of Ross Sea, Antarctica

The affiliations and physiological characteristics of culturable bacteria isolated from the sediments of Ross Sea, Antarctica were investigated. Sixty-three isolates obtained by cultivation were grouped into 21 phylotypes affiliated with the phyla Actinobacteria and Bacteroidetes and with the classes Alphaproteobacteria and Gammaproteobacteria by phylogenetic analysis of 16S rRNA gene sequences. Based on phylogenetic analysis (<98.65% sequence similarity), approximately 49% of total isolates represented potentially novel species or genus. Among them, extracellular protease, lipase, and exopolysaccharide activities at 10℃ or 20℃ were detected in approximately 46%, 25%, and 32% of the strains, respectively. Forty-three isolates produced at least one type of extracellular material and 21 of them produced at least two extracellular protease, lipase, and/or exopolysaccharides. Our findings indicate that culturable bacterial diversity present within the marine sediments of Ross Sea, Antarctica may contribute to the hydrolysis of the major organic constituents which is closely related with carbon and nitrogen cycling in this environment.
THE USE OF OTOLITHS AND VERTEBRAE IN THE IDENTIFICATION AND SIZE-ESTIMATION OF FISH IN PREDATOR-PREY STUDIES

Relationships between the size of otoliths and vertebrae, and body length are presented for eleven teleost species of the north-east Atlantic. Relationships between teleost size and weight are also presented for these species. These equations can be used to reconstruct the original dimensions of prey from the size of hard structures found in food samples of marine piscivores. For each fish species we selected otoliths and vertebrae which possessed unique features enabling diagnosis of specimens to the level of genus or species. Linear and non-linear functions provided the best fit for relations between hard structure size and fish length, and exponential functions yielded the best predictors for fish weight. For some species, the relationships obtained in this study differed from similar functions obtained by other authors at different locations. This calls for caution when using equations derived from specimens on other locations, especially if precise quantitative data are required.
Plasma membrane cholesterol in myocardial muscle and capillary endothelial cells. Distribution of filipin-induced deformations in freeze-fracture.

: Glutaraldehyde-fixed rabbit myocardium was treated with the polyene antibiotic, filipin, which binds specifically to sterols in membranes, producing distinct 25 nm-diameter deformations. These deformations (lesions) serve as labels for the presence of cholesterol-rich membranes and membrane domains. The distribution and density of filipin-induced lesions was examined in the plasma membranes of cardiac muscle and capillary endothelial cells by freeze-fracture electron microscopy. In the exposed fracture faces of endothelial plasma membranes, more than 99% of the surface area was covered with lesions, whereas about 90% of the plasma membrane area in the muscle cells remained unaffected by the treatment. Muscle cell plasma membranes revealed a patchy response; the lesions occurred in clusters which were separated by interconnecting expanses of unaffected membrane. Endothelial cell plasmalemmal vesicles, and muscle cell caveolae and transverse tubules displayed the same response to filipin as neighbouring areas of plasma membrane. However, gap junctions and desmosomes of the muscle intercalated disc membrane, and coated pits in both cell types were completely resistant to filipin treatment. These results provide evidence that the plasma membranes of the two cell types possess markedly different overall cholesterol levels, and that each has a characteristic pattern in the planar distribution of cholesterol.
Niche-adaptive evolution in Campylobacter jejuni

Campylobacter jejuni is the leading causative agent of human bacterial gastroenteritis. Human C. jejuni infection (campylobacteriosis) is frequently associated with poultry; through consumption of undercooked products, cross contamination from raw meats, or through direct contact with birds or their faecal matter, however it is established that poultry is not the sole cause of C. jejuni infection in humans. This research reveals new information on the MLST ST403 Clonal Complex, a previously identified C. jejuni lineage associated with the porcine host. ST403CC C. jejuni have also been linked with other mammalian hosts to a lesser degree, and have been implicated in human campylobacteriosis, however to date this clonal complex has not been linked to poultry. The original hypothesis of this research predicted that due to sharing a host niche commonly associated with C. coli, the porcine ST403CC may show evidence of increased recombination with C. coli, however this was not observed. Six ST403CC isolates of porcine origin were subjected to phenotype testing and whole genome sequencing; these isolates were capable of invasion in vitro, and were revealed both to have acquired seemingly lineage specific content, in the form of Restriction-Modification (R-M) system associated genes, and to have undergone degredation of certain loci. The ST403CC isolates also exhibited a distinct pattern of reduced genomic recombination compared to non-ST403CC C. jejuni, with evidence of lineage specific recombination events. Both generalist & specialist lineages have previously been revealed in C. jejuni. The research presented here identifies a new specialist lineage which is associated with mammalian hosts, and not found in poultry.
Allozyme variation in Abeliophyllum distichum NAKAI, an endemic tree species of Korea

Abeliophyllum distichum NAKAI is a geographically restricted tree species, found only in Korea. Genetic variation at 11 isozyme loci was analyzed from 120 individuals. Low level of genetic diversity was observed (A=1.6, P = 36.4%, H c =0.098), which is a typical pattern shown in endemic rare tree species. Most (94%) of the total genetic diversity was found within populations and estimated gene flow was moderately high (Nm=2.29), Ecology and life-history characteristics of A. distichum coupled with low level of genetic diversity suggested that there should be a special emphasis on the conservation study for this species.
Systematic discovery and characterization of stress-related microRNA genes in Oryza sativa

Abstract Abiotic stresses including drought, salinity, extreme temperatures, chemical toxicity and oxidative are the natural status of the environment to exert serious threats to agriculture. Abiotic stress-related microRNAs (ASmiRNAs) are a group of microRNAs (miRNAs) regulating stress responses in plants. However, the systematic investigation of ASmiRNAs is limited in Rice (O. sativa), a typical abiotic stress-resistant crop species. In the present work, we systematically investigated ASmiRNAs in silico. First, we identified 177 putative ASmiRNAs in O.sativa. Second, we found most ASmiRNAs were driven by TATA-promoter and most stress-related miRNA promoter regions contained the stress-related elements. Third, we found many ASmiRNAs families were species/family specific and a set of miRNAs might derive from genomic repeat-sequences in O. sativa. Finally, we found the ASmiRNAs in O. sativa target 289 genes with 1050 predicted target sites in which 98% sites have cleavage activity and 2% sites have translation inhibition activity. In conclusion, our findings provide an insight into both the function and evolution of ASmiRNAs and improve our understanding on the mechanism of abiotic stress resistance in O. sativa.