Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic characterization of wild and farmed European seabass in the Adriatic sea: assessment of farmed escapees using a Bayesian approach

&NA; Hybridizations between domesticated escaped farmed fish and wild conspecifics may increase genetic diversity or break down locally adapted gene complexes, thus reducing competitive ability and overall fitness. We examined the genetic structure of six farmed populations of European seabass, Dicentrarchus labrax, of different geographical origin, and ten neighbouring wild populations in the Adriatic Sea using 10 microsatellite loci. All loci were polymorphic, with mean expected heterozygosity >74% in all 16 populations. Overall number of alleles as well as short‐term effective population size were smaller in farmed (A = 18.7; Ne = 56.1) than in wild populations (A = 21.2; Ne = 180.6). The global FST of 0.0672 across loci showed significant population subdivision. Strong genetic differences between farmed fish and their wild conspecifics enabled the identification of seabass escapees back to their origins and the estimation of the extent of hybridization. Bayesian assignment analyses clustered wild populations together, whereas each farmed populations was assigned to a separate cluster. Intraspecific hybridization was highest in wild populations in areas impacted by fish farms, where highly admixed populations had decreased genetic diversity. The results of this study represent a solid foundation required to establish a genetic register of European seabass wild and farmed populations in the eastern Adriatic Sea that are required to establish a seabass DNA register.
VEGFA amplification/deletion in human breast tumors.

e21017 Background: The anti-VEGF antibody, bevacizumab, has been FDA approved for the treatment of breast cancer. While germline variability (i.e. single nucleotide polymorphisms) may serve as a predictive marker for anti-VEGF therapy, to date tumor-specific variability has not. More specifically, amplification or deletion of the VEGFA gene has not been studied or evaluated as a predictive or prognostic biomarker for breast cancer. Methods: A VEGFA/centromere enumerization-6 (CEN-6) probe was created and validated using DNA clones and restriction enzyme fragment measurements. The final product contained a RP11-710-L16 probe covering 183 KB including the VEGFA gene and flanking regions. The CEN-6 probe was developed with fluorescein isothiocyanate labeled peptide nucleic acid oligonucleotides. VEGFA and CEN-6 probes were tested on metaphase spreads to exclude cross-hybridization to other chromosomes. A tissue microarray containing 93 breast cancers was analyzed for the presence of VEGFA gene amplification .
Bifidogenic Effect of Glucooligosaccharide Prepared from Glucose by Extrusion Process

In order to investigate effect of glucooligosaccharide (GOS) prepared by extrusion process as a bifidogenic factor, cultivation of Bifidobacterium sp. , Bacteroides fragilis and Clostridium perfringens was done and analyzed. B. fragilis and C. perfringens were able to utilize only 16% and 11% of the oligosaccharides in GOS, respectively, whilst Bifidobacterium sp. FBD-22 could utilize 38%. Especially, many kinds of oligo saccharides in GOS were able to be utilized selectively only by Bifidobacterium sp. In case that GOS, as a carbon source, was used in the co-cultivation by Bifidobacterium sp. , B. fragilis and C. perfringens, growth of Bifidobacterium sp. was not influenced by the existence of B. fragilis and C. perfringens. Bifidobacterium sp. showed advantage on carbon source competition for GOS with B. fragilis. Acetic acid, antimicrobial agent in the intestine, was produced two times more from GOS than glucose in co-cultures of three strains. Therefore, it is suggested that GOS can be a potent bifidogenic factor which proliferates the population of Bifidobacterium sp. and may finally improve the intestinal environments of human.
Estudo do padrão de adesão agregativa de Escherichia coli do sorotipo O142:H34.

VASCONCELLOS, F. M. Study of the aggreggative adherence pattern of Escherichia coli from serotype O142:H34. 2014. 112 p. Ph. D. thesis (Biotechnology) – Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, 2014. Enteropathogenic Escherichia coli is one of the diarrheagenic E. coli (DEC) pathotypes, an important agent of acute diarrhea in children, especially in developing countries. Strains of this pathotype induce histopathological changes in the intestinal epithelium known as attaching and effacing (A/E) lesion. The classification of EPEC in the subgroups typical and atypical is based on the presence or absence of the plasmid E. coli adherence factor (pEAF), respectively. Somatic antigen (O) typing of EPEC strains associated with diarrhea led to the definition of 12 classical EPEC serogroups, among which is the serogroup O142. A previous study characterizing EPEC O142 described a strain of serotype O142:H34 (Ec48/66) presenting some important characteristics: the presence of the eae gene (which encodes the adhesin intimin of EPEC), the absence of the pEAF (determinant of typical EPEC), reactivity with the probe fragment CVD432 (indicative of the virulence plasmid of enteroaggregative E. coli, or EAEC) and the expression of the aggregative adherence pattern (characteristic of EAEC). This strain has an unusual combination of EPEC and EAEC virulence genes, making difficult its classification. Furthermore, the adhesin mediating the aggregative adherence othis strain was not characterized. Thus, the present study aimed to evaluate the role of fimbrial structures in the establishment of the aggregative adherence pattern of E. coli strain serotype O142:H34 and evaluate its classification. The strain Ec46/88 was able to adhere to HeLa, HEp-2, HT-29 and T84 cell in the aggregative adherence pattern, as well as to cause the A/E lesion in HeLa and HT-29 cells. A survey of several virulence factors of EAEC and other E. coli pathotypes detected the presence of aggDBCA, which comprise the operon encoding the EAEC AAF/I fimbriae, and ecpRABCDE, which encode the E. coli common pilus (ECP). The agg operon was sequenced exhibiting high identity (96%) of aggDBC with the same genes present in EAEC 17-2, and aggA (99%) with a gene encoding the variant AggA457. The genes of the ecp operon showed high identity (99%) with the same operon of EPEC E2348/69. Mutants in the genes encoding AAF/I and ECP ushers (aggC and ecpC, respectively) were obtained. The analysis of the interaction of both mutants with HeLa cells showed the maintenance of the aggregative adherence and the ability to cause the A/E lesion. However, the aggC mutant presented significant decrease in the number of adherent bacteria. Phylogenetic analysis in relation to other DEC pathotypes situated this strain in the group consisting predominantly of EPEC. The data obtained indicated that the Ec48/66 strain is an atypical EPEC able to cause the A/E lesion in vitro and to express the aggregative adherence pattern, which is partially dependent on a variant of AAF/I fimbriae, but not on ECP fimbriae.
Laboratory evaluation of Lactobacillus johnsonii CRL1647 metabolites for biological control of Musca domestica

The house fly, Musca domestica L. (Diptera: Muscidae), is a key problem in animal producing and rearing areas. Currently, the use and abuse of chemical pest‐control compounds has generated resistance in M. domestica and, hence, new approaches are required. In this work, the potential entomopathogenic activity of Lactobacillus johnsonii Fujisawa et al. CRL1647 was evaluated against M. domestica, under laboratory conditions. Bioassays were done for three consecutive years using bacterial cell suspensions (CS) and cell‐free supernatants (CFS) under controlled conditions (27 ± 1 °C, 57 ± 2% r.h., and L12:D12 photoperiod). Both the CS and CFS displayed high levels of larvicidal (96%) and pupicidal (97%) activities. Chemical characterization of the CFS revealed that the bioactive metabolites are acidic compounds, not affected by thermal treatment or by trypsin. Organic acids were identified and quantified by high‐performance liquid chromatography (HPLC); only lactic acid (129.7 ± 1.0 mM), acetic acid (37.3 ± 0.8 mM), and phenyllactic acid (0.3 ± 0.1 mM) were detected. A significant decrease in fecundity of the house flies was observed in females from larvae fed on CFS; male fertility was not affected. Interestingly, only the mixture of organic acids exerted the biological effects. These results suggest that the metabolites synthesized by L. johnsonii CRL1647 can be used in a novel biocontrol strategy against house flies.
A Simple New Technique for Ectomycorrhizal Formation between Cantharellus and Dendrocalamus strictus

In vitro ectomycorrhizal formation is important in establishing an ectomycorrhizal relationship between a host tree and mushroom mycelia. Moreover, axenic conditions are considered essential for the synthesis of ectomycorrhiza under laboratory conditions. There have been several attempts in the past to evolve new methods of ectomycorrhizal formation between pine seedlings and fungal mycelia, but there have been few reports with angiosperm trees. In an attempt to design equipment that would require limited space and yet permit the observation of ectomycorrhiza formation, we developed a flask-filter paper technique for in vitro ectomycorrhizal formation between Cantharellus tropicalis and Dendrocalamus strictus. The characteristic feature of this technique is that root and shoot parts extend within a flask forming typical ectomycorrhiza in aseptic synthesis. Hence, this technique enabled Dendrocalamus plants to grow axenically and develop an ectomycorrhizal association with Cantharellus mycelium. This method is simple and will help in the in vitro study of other mycorrhizal fungi which form ectomycorrhiza with other angiosperm trees.
Using the Free Program MEGA to Build Phylogenetic Trees from Molecular Data

Abstract Building evolutionary trees can be an excellent way for students to see how different gene sequences or organisms are related to one another. Molecular Evolutionary Genetics Analysis (MEGA) software is a free package that lets anyone build evolutionary trees in a user-friendly setup. There are several options to choose from when building trees from molecular data in MEGA, but the most commonly used are neighbor joining and maximum likelihood, both of which give good estimates on the relationship between different molecular sequences. In this article, we describe how to collect data from GenBank, insert the data into a text editor, import the data into MEGA, and use the dataset to create phylogenetic trees.
The reproductive biology of two small southern African mammals, the spiny mouse, Acomys spinosissimus (Rodentia: Muridae) and the Eastern rock elephant-shrew, Elephantulus myurus (Macroscelidea: Macroscelididae)

34 Introduction . 35 Materials and Methods . 36 General . 36 Histology . 38 Hormone analysis . 39 Relative age classes . 40 © University of Pretoria TABLE OF CONTENTS III Data analysis . 41 Results . 42 Climate data . 42 Body mass . 42 Males . 42 Females . 43 Discussion. 45 Acknowledgements . 50 References . 50 Tables . 56 Figure legends . 60 Figures . 61 CHAPTER 2 . 66 SEASONAL REPRODUCTION IN MALE AND FEMALE EASTERN ROCK ELEPHANT-SHREWS (ELEPHANTULUS MYURUS) FROM SOUTH AFRICA Abstract . 67 Introduction . 68 Materials and Methods . 70. 67 Introduction . 68 Materials and Methods . 70 General . 70 Histology . 71 Hormone analysis . 73 Relative age classes . 74 Data analysis . 75 Results . 76 General . 76 Body mass . 77 Months . 78 Relative age classes . 79 Month and relative age class . 80 Discussion. 81 Acknowledgements . 87 References . 87 Tables . 93 © University of Pretoria TABLE OF CONTENTS IV Figure legends . 98 Figures . 100 CHAPTER 3 . 109 REPRODUCTIVE PHOTORESPONSIVENESS IN MALE SPINY MICE (ACOMYS SPINOSISSIMUS) FROM SOUTH AFRICA Abstract . 110 Introduction . 111 Materials and Methods . 113. 110 Introduction . 111 Materials and Methods . 113 Histology . 114 Testosterone analysis . 115 Data analysis . 115 Results . 115 Discussion. 116 Acknowledgements . 121 References . 121 Figure legends . 127 Figures . 128 CHAPTER 4 . 130 REPRODUCTIVE RESPONSES TO PHOTOPERIOD IN MALE EASTERN ROCK ELEPHANT-SHREWS (ELEPHANTULUS MYURUS) FROM SOUTH AFRICA Abstract . 13
Health benefits of fibre, prebiotics and probiotics: a review of intestinal health and related health claims

Gastrointestinal health in regard to the gut microbiome is a rapidly emerging field and has many key components driving its emergence. Fibre, prebiotics and probiotics are all dietary components that can play a critical role in maintaining a healthy gut microflora. Fibre has long been appreciated for its influential role in cardiovascular disease, glycaemic control and weight management through various physiological mechanisms. Prebiotics have been shown to play an influential role in irritable bowel symptoms/disease, colon cancer, cardiovascular disease and overall digestive health. Together, various types of fibres and prebiotics have been targeted and synthesised to influence the gut microbiome, specifically Lactobacillus and Bifidobacterium populations. Lactobacillus spp. and Bifidobacterium spp. are common markers for gut health because they have been shown to down-regulate inflammation in the gastrointestinal tract, alleviate irritable bowel syndrome symptoms, stimulate immune functions, aid in mine.
West Nile virus in Europe : Host susceptibility, pathogenesis, and intervention studies

The aim of this thesis was to investigate the limited spread of WNV within Europe and to assess whether this virus could actually present a greater risk to Europe in the future. As a result, the following questions were addressed: 1) Are European strains of WNV less virulent than the American strains? 2) Are birds in Europe less susceptible to infection with WNV? 3) Would a vaccine be able to protect against infection with both lineage 1 and 2 WNVs?
Emballonuridae Gervais, 1855 (Chiroptera) of Reserva Biológica de Saltinho (Atlantic Forest), in Brazil, revealed by echolocation

Seventeen species of emballonurid bats are known in Brazil, but their distribution is often determined by patchy records. However, due to almost species-specific calls, echolocation can help to refine the distribution of emballonurids. Here we use acoustic samplings to assess and complement the list of emballonurids of Reserva Biologica Saltinho, an important Atlantic Forest remnant in Pernambuco state, Northeastern Brazil. We positively matched calls of Saccopteryx bilineata (Temminck, 1838) that was foraging along forest edges. However, a series of calls significantly different from those emitted by S. bilineata indicate the presence of a second Saccopteryx sonotype in the area. The lower frequencies in this sonotype presumably came from a larger species, indicating the possible existence of an undescribed cryptic species of Saccopteryx . We also detected Centronycteris maximiliani (Fischer, 1829), recorded 35 years after its first record in Pernambuco, and an undetermined species of Peropteryx Peters, 1867. Our data proved that echolocation is a very useful technique for inventorying poorly known and hard-to-capture emballonurid species, with the potential to reveal the cryptic richness.
BRYONIA ALBA L. AND ECBALLIUM ELATERIUM (L.) A. RICH. - TWO RELATED SPECIES OF THE CUCURBITACEAE FAMILY WITH IMPORTANT PHARMACEUTICAL POTENTIAL

The importance of the Cucurbitaceae family consists not only in the species that are widely known for various economically important human uses, but also in the species that have proven an important and promising potential concerning their biological activities. Bryonia alba L. and Ecballium elaterium (L.) A. Rich. are two species belonging to this family, that are known since ancient times for their homeopathic or traditional use in the treatment of numerous disorders. There is clear evidence that links between the two species are not only related to family morphological characters, but also to a certain degree to the sexual system and, most importantly, to the active principle content or to potential medicinal uses. All these elements helped to include both species in the same tribe and may result in important reasons for heading future studies towards the elucidation of their complete phytochemical composition and mechanisms of the biological activities. The present study aims to review the existing scientific literature on the two species and to offer sufficient evidence in order to justify a most detailed study of their pharmaceutical potential. Rezumat Importanţa familiei Cucurbitaceae constă nu numai in specii care sunt cunoscute in sens larg pentru utilizările economice, dar si in specii care si-au demonstrat un potenţial important si promiţător ca specii cu activitate biologică. Bryonia alba L. si Ecballium elaterium (L.) A. Rich. sunt două specii aparţinând familiei Cucurbitaceae care sunt cunoscute din cele mai vechi timpuri pentru utilizările in homeopatie sau in medicina tradiţională pentru tratamentul a numeroase afecţiuni. Există dovezi stiinţifice clare pentru legăturile dintre cele două specii, care se referă nu numai la caracterele morfologice specifice familiei, dar de asemenea intr-o anumită măsură si la sistemul sexual si, cel mai important, la conţinutul in principii active sau la potenţialele utilizări medicinale. Toate acestea au favorizat includerea ambelor specii in acelasi trib si reprezintă dovezi importante pentru indreptarea ulterioară a studiilor spre elucidarea completă a compoziţiei fitochimice si a mecanismelor implicate in activitatea biologică. Studiul de faţă isi propune asadar să ofere o trecere in revistă a dovezilor stiinţifice existente in literatura de specialitate legate de cele două specii si să ofere argumente suficiente pentru a justifica un viitor studiu amănunţit al potenţialului lor farmaceutic.
Cycloheximide Assays to Measure Protein Degradation in vivo in Plants

1Department of Biology, Shepherd University, Shepherdstown, WV, USA; 2Department of Translational Medicine, OncoMed Pharmaceuticals Inc., Redwood City, CA, USA; 3Joyable, San Francisco, CA, USA; 4International Maize and Wheat Improvement Center, Texcoco de Mora, Mexico, USA; 5Department of Molecular and Cellular Biology, College of Biological Sciences, University of California-Davis, Davis, CA, USA *For correspondence: jcallis@ucdavis.edu
Resposta inflamatória em asininos (Equus asinus) submetidos à ovariectomia

Proteinas de fase aguda sao glicoproteinas produzidas pelos hepatocitos e liberadas na corrente sanguinea em resposta a dano tecidual, decorrente de processos inflamatorios agudos. Atualmente, sao consideradas biomarcadores da resposta inflamatoria e infecciosa, quando comparada com outras variaveis como hipertermia, leucocitose e neutrofilia, porem em asininos ainda nao foram bem analisadas. Objetivou-se avaliar resposta inflamatoria aguda em asininos submetidos a ovariectomia por duas diferentes abordagens. Foram utilizados 18 animais, femeas adultas, pesando em media 100 kg, as quais foram divididas em dois grupos, de 09 animais cada, onde grupo I, foram ovariectomizadas por laparotomia e o grupo II por laparoscopia. Apos as cirurgias foram avaliadas as seguintes variaveis no sangue total: hemograma, fibrinogenio, haptoglobina, albumina, antitripsina, alfa-1 glicoproteina acida, ceruloplasmina, transferrina, imunoglobulinas A e G. Nos mesmos momentos, no liquido peritoneal, foram mensuradas: numero de hemacias e leucocitos, analise citologica diferencial (leucocitos e celulas mesoteliais), proteinas totais, pH e proteinas de fase aguda. Todas as variaveis foram analisadas antes das cirurgias, 12, 24, 48, 72 horas, 8 e 16 dias apos os procedimentos cirurgicos. Houve um aumento (p<0,05) do numero de leucocitos com neutrofilia apos as cirurgias, independente do procedimento cirurgico, no soro e liquido peritoneal. As proteinas de fase aguda tiveram comportamentos diferentes no sangue e liquido peritoneal. Neste trabalho identificamos, pela primeira vez, a proteina P23.000kD no soro e amostras peritoneais de asininos. O interesse sobre o papel das proteinas de fase aguda na medicina veterinaria, em especial em equideos vem crescendo, principalmente, visando utiliza-las como marcadores precoces do processo inflamatorio
Establishing Cardiac Measurement Standards in Three Avian Species

While radiographic standards for cardiac width have been developed for commonly treated mammalian species, no such standards exist for avian species. Therefore, cardiac abnor- malities in avian patients are often undiagnosed. In this study, linear multivariable equations were developed to provide a theoretical heart width in three avian species. Theoretical heart width was found to be directly related to the widths of the sternum and the thoracic cavity. With these few measurements, theoretical heart width can be calculated and compared with measured heart width.
Spatial Modeling of Deforestation in FMU of Poigar, North Sulawesi

Forest is a part of the ecosystem that provides environmental services. Deforestation may decrease forest function in an ecosystem. This study aims to build a spatial model of deforestation in a forest management unit (FMU) of Poigar. Deforestation analysis carried out by analyze the change of forest cover into non-forest cover with post classification comparison technique. Driving forces of deforestation carried out by spatial modeling using binary logistic regression models (LRM). Result of logistic regression model was used to predict the deforestation in 2013 and compare the prediction result with actual deforestation. The result showed that forest loss from the 2000 to 2013 period amounted 12,668.2 hectares. Deforestation in FMU of Poigar influenced by six factors there are distance from the road, distance from the settlement, distance from the river, population density, elevation and slope. Logistic regression model was built using five explanatory variables that are the distance from the road, distance from the river, population density, elevation and slope. Population density and accessibility is the most influented factor caused deforestation in FMU of Poigar. Prediction of deforestation could predict about 58 % of actual deforestation spatialy, so spatial models of deforestation could be an information to guidance on future management of FMU of Poigar.
The spleen of Physalaemus nattereri (Amphibia: Anura): morphology, melanomacrophage pigment compounds and responses to α-melanocyte stimulating hormone

Abstract The spleen is a lymphoid organ associated with defense mechanisms in anurans, and also it has pigmented cells. Melanomacrophages (MMs) are melanin-containing cells, which originated from hematopoietic stem cells and are found in hematopoietic organs. Melanin has bactericide and cytoprotective actions against free radicals. Furthermore, the α-melanocyte stimulating hormone (MSH) induces dispersion of melanosomes in melanocytes, besides having an anti-inflammatory action. Here, we describe the spleen morphology of Physalaemus nattereri and the response of splenic melanomacrophages to the α-MSH hormone. Animals were treated with α-MSH for 2, 6, 12, 24 and 48 h. Then, we measured the amount of melanin, lipofuscin and hemosiderin in each treatment. The spleen of P. nattereri is ovoid, and a connective tissue capsule covers the organ externally. There are no septa and the stroma is reduced. The parenchyma has two regions slightly separated from each other: white and red pulps. MMs occur in the red pulp. The α-MSH increased the volume of lipofuscin and hemosiderin in MMs after 6 h, but not melanin. Thus, the α-MSH altered only metabolic substances in splenic melanomacrophages, but not melanin, which usually is responsive to this hormone in hepatic MMs. Also, the description of the spleen morphology can help future comparative morphological and evolutionary studies on spleen morphology of vertebrates.