Miracle-dz/UniFAR-FTUs huggingface dataset:
The immediate impact of intertidal pebble fork harvesting on the warty venus Venus verrucosa benthic community

Recreational clam digging is a traditional activity on the large intertidal zone of the western coasts of the Cotentin (western English Channel). A variety of fishing gears are used to harvest the target species the warty venus Venus verrucosa (Linnaeus, 1758). In this note, the immediate effect (i.e., four days) of fork harvesting was studied during the March 2012 spring tide, following a control-impact design with a control station and three impacted stations using pebble forks. An immediate significant decreases of coarse sand and gravel benthic macrofauna is observed in fishing area. In the future, it is recommended that pebble fork fishing should be prohibited to harvest this target species.
Copepod assemblage structure (Crustacea: Copepoda) along a longitudinal environmental gradient in a tropical river-floodplain system, Brazil

Aim: In this study, we analyzed the structure of the copepod community along a longitudinal axis of the last undammed stretch of the Upper Paraná River floodplain, downstream of Porto Primavera reservoir. We hypothesized that (i) copepod assemblage would show an increase in the abundance of organisms, species richness and specific diversity with the distance from the Porto Primavera reservoir, due to the arrival of species from adjacent lakes and tributaries; (ii) copepod abundance and species richness would be higher in tributaries and adjacent lakes located at the floodplain, which show higher environmental heterogeneity and function as a species source; and (iii) spatial patterns of copepod assemblage structure are related to the environmental gradient, since copepods show a rapid response to the variation of environmental conditions. Method: Sampling was performed quarterly from August 2013 to July 2014, at the subsurface of the pelagic region. Sampling sites were located along the Paraná River, in seven of its tributaries, and in eight lakes located in its floodplain. Results: We identified 29 species belonging to two families: Cyclopidae (21 species) and Diaptomidae (eight species). On contrary of our first hypothesis, ANOVA results showed a significant decrease in copepod abundance in the downstream direction. Similarly, the tributaries showed higher values of ecological attributes in the upstream stretch. RDA results showed that in axis 1, the Paraná River and the lakes were positively correlated with conductivity, pH, temperature and suspended organic matter, characterized by the most abundant copepod species. The tributaries, on the other hand, were negatively correlated with turbidity, total nitrogen, total phosphorus and depth. Axis 2 showed a positive correlation of the Paraná River with conductivity and suspended organic matter, and a higher abundance of Argyrodiaptomus azevedoi, Notodiaptomus iheringi, N. henseni, N. cearensis 2 Palhiarini, W.S. et al. Acta Limnologica Brasiliensia, 2017, vol. 29, e102 Serial Discontinuity Concept (Ward & Stanford, 1995), which complements the River Continuum Concept, highlights that river impoundments promote discontinuity in the longitudinal dynamics and alterations in biotic and abiotic components. However, aquatic communities and nutrients could show a gradient downstream of the dam, becoming gradually closer to the original conditions of the river. In some aquatic ecosystems, one can observe large reservoirs constructed in cascades, as is the case of the Paraná River (Agostinho et al., 2007). Despite having a 230 km undammed stretch, this river suffers the effects of 34 cascading reservoirs located upstream of Porto Primavera reservoir (Agostinho et al., 2008). The construction of Porto Primavera reservoir has drastically affected the Upper Paraná River floodplain, since discharge control altered the flood regime, nutrient concentration along the river
Selective interference with HDAC2 induces multiple effects on cell death signaling in colon cancer cells

HDAC inhibition blocks cell proliferation and induces apoptosis in cancer cells. So far, the role of the different HDAC isoforms in apoptosis have been little investigated. This study shows that the expression of Bcl-2 family members – Bak and Bim, but not Bcl-XL – is regulated by the expression of the HDAC2 isoform in HT-29 colon cancer cells. The survival of colon cancer cells is associated with Bak repression which is regulated by HDAC2. Furthermore, an synergistic effect between HDAC inhibition and 5-Flurouracil (5-FU) administration in the survival of DLD1-5-FU/R, but not of 5F12 colon cancer cells is described. These results support the idea that selective HDAC2 inhibition could be an appropriate strategy for the induction of cell death in colon cancer cells.
Quantifying the role of wood density in explaining interspecific variation in growth of tropical trees

Aim To evaluate how wood density relates to tree growth rates in simple models and two tropical forests. Location Barro Colorado Island, Panama; and Pasoh Forest Reserve, Malaysia. Time Period 1986–2010. Major Taxa Studied Trees. Methods We derived expected relationships of wood density with diameter growth at a given diameter under a null hypothesis that aboveground biomass growth is independent of wood density, and an alternative hypothesis that biomass growth scales with crown area, which itself increases with wood density. We tested these assumptions and predictions through analyses of interspecific relationships of wood density with height, crown area and diameter growth at constant diameter in two tropical forests. Results Height was unrelated to wood density, whereas crown areas showed a slightly positive relationship to wood density. Thus, the expected exponent of diameter growth with wood density was equal to minus one under the null hypothesis, and equal to the exponent of crown area with wood density minus one under the alternative hypothesis. Empirical relationships of diameter growth and biomass growth with wood density were broadly consistent with the null hypothesis that biomass growth is unrelated to wood density at both sites, except in trees < 13 cm in diameter at Barro Colorado Island, which showed more negative relationships. Main conclusions Although most previous analyses of growth with wood density have examined linear relationships, simple models suggest that both tree diameter growth and tree biomass growth are power functions of wood density. Analyses in two tropical forests showed that aboveground biomass growth was approximately constant with wood density, and thus, that diameter growth was inversely proportional to wood density, for most tree sizes, although confidence intervals on the scaling exponents were broad. More negative relationships of growth with wood density at small sizes might reflect differential environmental filtering, in which higher wood density trees are found in less favourable understorey environments.
Changes in proHB-EGF expression after functional activation of the immune system cells

The level of proHB-EGF expression on J774, Raji, KG-1 cells derived from different types of human and mouse immune system cells under the standard in vitro culture conditions and during functional activation of these cells was investigated. Changes in the prohB-eGF expression on the cell surface were found to depend on the density of cell population, the content of fetal bovine serum in the culture medium, the presence of mitogenic factors – bacterial lipopolysaccharide and recombinant soluble hB-eGF – rshB-eGF, as well as anti-mitogenic factor – diphtheria toxoid (CRm197). The results obtained are important for the understanding of the functional role of prohB-eGF receptor on the surface of macrophage-like cells and B lymphocytes and indicate the involvement of this receptor in immune response regulation in organism.
De novo assembly and characterization of the transcriptome of a wild edible mushroom Leucocalocybe mongolica and identification of SSR markers

ABSTRACT Leucocalocybe mongolica is a prestigious rare wild edible mushroom in Northeast Asia. It is the unique species of the genus and the studying of its phynotype and genome is crucial to genus and species classification. Beyond that, it has high application and ecological value in the industry of food and atmosphere investigation. On account of the fact that transcriptomic and genomic data of L. mongolica lacked in the biological information database, that is a limitation to further study. The transcriptome data were obtained by virtue of Illumina paired-end sequencing technology: 42,622,958 clean reads were achieved and 37,302 contigs were generated. These contigs were subsequently assembled into 13,821 unigenes. These unigenes were annotated within 7 public databases. The 3914 unigenes were associated with a COG classification. Throughout all of the unigenes, 6642 were classified as three functional groups; 3110 unigenes were selected from KEGG pathways, and taken to further clustering analysis for 5 main categories; 57 genes, potentially involved in terpenoid, steroid, and unsaturated fatty acids biosynthesis were identified and selected for further research. The total number of carbohydrate-active enzymes of L. mongolica is 446 and the number of carbohydrate binding module (CBM) is relatively low. CE11, GT19, GT51, GT56, GH131, GH133, GH135 constitute the characteristic carbohydrate-active enzymes subfamily compared to other edible mushrooms. The characteristic carbohydrate enzymes relative to other mushrooms could play a vital role on the metabolism of nutrients. In these generated sequences, 1860 SSRs were identified and characterized as molecular candidate markers existing L. mongolica.
Reproductive physiology of Arapaima gigas (Schinz, 1822) and development of tools for broodstock management

V ACKNOWLEDGEMENTS . VII LIST OF ABBREVIATIONS . 15 LIST OF SPECIES . 21 LIST OF FIGURES AND TABLES. 23 1. Chapter 1 . 35 GENERAL INTRODUCTION . 35 1.1. Biology of Arapaima gigas and prospects for aquaculture . 37 1.1.1. Natural history . 37 1.1.2. General physiology and life-history . 40 1.1.3. Prospects for aquaculture . 43 1.2. Physiology of fish reproduction . 45 1.2. 1. Oogenesis . 45 1.2. 2. Spermatogenesis . 48 1.2. 3. Neuroendocrine control of reproduction . 50 1.2. 4. Reproductive dysfunctions in captivity . 55 1.3. Reproduction of Arapaima gigas . 58 1.3. 1. General aspects. 58 1.3. 2. The cephalic secretion and chemical communication . 59 1.3. 3. Issues with captive reproduction . 61 1.4. Experimental aims . 64 2. Chapter 2 . 67 DDRAD SEQUENCING IN ARAPAIMA GIGAS: ANALYSIS OF GENETIC DIVERSITY AND STRUCTURE IN POPULATIONS FROM AMAZON AND ARAGUAIA-TOCANTINS RIVER BASINS. 67 Abstract . 69 2.
High degree of virulence gene diversity in Streptococcus pyogenes isolated in Central Italy

Background/Purpose(s) Globally, Streptococcus pyogenes poses a continuous burden to human health, causing both self-limiting and life-threatening diseases. Therefore, studying the profile of virulence genes and their combinations is essential to monitor the epidemiology and pathogenetic potential of this important species. Thus, the aim of this study was to analyze some genetic features of clinical strains collected in Italy in 2012. Methods We conducted fibronectin-collagen-T antigen (FCT) region typing and emm typing in 122 S. pyogenes strains. Furthermore, several additional virulence genes were screened by polymerase chain reaction. Results We found correlations between emm types and FCT region profiles. emm1 strains were mainly associated with FCT2 and FCT6, while emm89 and emm12 strains were associated with FCT4. FCT5 was mainly represented in emm4, emm6, and emm75 strains. Noteworthy, we defined subtypes for each FCT type based on the differences in single and multiple loci compared to the reference scheme used for the classification of the FCT region. In addition, new FCT types were identified. Cluster analysis based on virulence gene profiling showed a non-random distribution within each emm type. Conclusion This study showed the high variability of S. pyogenes strains and the great diversification that this pathogen has undergone during its evolution in the human host.
Impact of the Deep Sea Trawl Fishery on Demersal Communities of the Northern Tyrrhenian Sea (Western Mediterranean

The composition of the catch of the deep-sea trawl fleet of Porto Santo Stefano (northern Tyrrhenian Sea, western Mediterranean) was analysed. In the period 1995-1999 observations were carried out on board of commercial vessels, collecting data for about 500 trawling hours. Nephrops norvegicus, Parapenaeus longirostris and large specimens of Merluccius merluccius were the targets on the fishing grounds from 300 to 450 m, while Aristaemorpha foliacea , Aristeus antennatus and N. norvegicus on the fishing grounds from 450 to 650 m depth. By-catch dominated the biomass caught, and was characterised by a high degree of species richness, as a consequence of the reduced selectivity of the bottom trawl gear. An important fraction of the by-catch was constituted by commercially retained species, which provided an important added value to the landings. Catch of target species was entirely comme rcialised. Annual average discards were about 20% of the total catch. Discard of commercial species was mostly due to species under commercial size, while discard of non-commercial species was represented by a large number of small size species of fishes and crustaceans. The results seem to indicate that this kind of fishery achieves a fairly good compromise between efficiency of resource utilisation and impact on the demersal communities.
CSF biomarkers are differentially related to structural and functional changes in dementia of the Alzheimer’s type

The two cardinal pathologies of Alzheimer’s disease (AD) develop according to distinct anatomical trajectories. Cerebral tau-related pathology first accumulates in the mesial temporal region, while amyloid-related pathology first appears in neocortex. The eventual distributions of these pathologies reflect their anatomical origins. An implication is that the cardinal pathologies might exert preferential effects on the structurofunctional brain changes observed in AD. We investigated this hypothesis in 39 patients with dementia of the Alzheimer’s type. Interrelationships were analysed between cerebrospinal fluid (CSF) biomarkers of the cardinal pathologies, volumetric brain changes using magnetic resonance imaging, and brain metabolism using [18F]-FDG-PET. Amyloid-related pathology was preferentially associated with structurofunctional changes in the precuneus and lateral temporal regions. Tau-related pathology was not associated with changes in these regions. These findings support the hypothesis that tau- and amyloid-pathology exert differential effects on structurofunctional changes in the AD brain. These findings have implications for future therapeutic trials and hint at a more complex relationship between the cardinal pathologies and disruption of brain networks.
Are pollinators the agents of selection on flower colour and size in irises

Plant–pollinator interactions are believed to play a major role in the evolution of floral traits. Flower colour and flower size are important for attracting pollinators, directly influencing reproduction, and thus expected to be under pollinator-mediated selection. Pollinator-mediated selection is also proposed to play a role in maintaining flower colour polymorphism within populations. However, pigment concentrations, and thus flower colour, are also under selective pressures independent of pollinators. We quantified phenotypic pollinator-mediated selection on flower colour and size in two colour polymorphic Iris species. Using female fitness, we estimated phenotypic selection on flower colour and size, and tested for pollinator-mediated selection by comparing selection gradients between flowers open to natural pollination and supplementary pollinated flowers. In both species, we found evidence for pollen limitation, which set the base for pollinator-mediated selection. In the colour dimorphic Iris lutescens, while pigment concentration and flower size were found to be under selection, this was independent of pollinators. For the polymorphic Iris pumila, pigment concentration is under selective pressure by pollinators, but only for one colour morph. Our results suggest that pollinators are not the main agents of selection on floral traits in these irises, as opposed to the accepted paradigm on floral evolution. This study provides an opposing example to the largely-accepted theory that pollinators are the major agent of selection on floral traits.
In vitro evaluation of the effect of dibutyl phthalate on electrogenic sodium-linked glucose transport in isolated rabbit ileum

ABSTRACT Dibutyl phthalate, a known endocrine disruptor, is a commonly used plasticizer that influences the glucose homeostasis. The present study elucidates the effects of dibutyl phthalate (1 and 5 mmol/L) on electrogenic sodium-linked glucose transport in the isolated rabbit ileum with ‘Ussing chamber. ’ Serosal addition of dibutyl phthalate has no effect on glucose-based electrogenic changes in short circuit current, and no effect of dibutyl phthalate is observed on ileal tissue conductance and catalase activity. However, mucosal addition of dibutyl phthalate in the presence of glucose shows a trend of decrease in short circuit current compared with the control. This indicates that dibutyl phthalate may have a deleterious effect on the electrogenic intestinal glucose transport.
Significant associations between single nucleotide polymorphisms and photosynthetic parameters and grain yield in maize

Photosynthesis is the basis of maize (Zea mays L.) grain formation. To further understand the genetic basis of maize photosynthetic parameters and clarify the relationship between maize photosynthetic parameters and grain yield (GY), identifying quantitative trait loci (QTLs) underlying photosynthetic parameters and GY plays an important role in improving maize yield. In this study, a set of 260 maize accessions from different geographic origins were evaluated across three developmental stages in 2 yr to identify QTLs for photosynthetic parameters and grain yield using 2824 single-nucleotide polymorphisms (SNPs) via genome-wide association analysis. The analysis revealed that maize photosynthetic parameters are substantially correlated with GY at different developmental stages. Fourteen SNPs associated with photosynthetic parameters and GY were detected at the threshold of P ≤ 0.001 in 2 yr as well as over years. Moreover, PZE-102116144 and SYN35048 associated with stomatal conductance (gs), and PZE-101152541 associated with photosynthetic rate (PN), were identified at different developmental stages. Four loci were co-associated with two or more traits, such as PZE-101152541 was significantly co-associated with GY and PN (at 25 and 35 d after pollination [DAP]), PZE-102116144 with GY, gs (at 15 and 25 DAP), and PN (at 25 DAP), PZE-109061997 with intercellular CO2 concentration (Ci) (at 25 DAP) and transpiration rate (Tr) (at 25 DAP), PZE-110019199 with gs (at 25 DAP) and GY. Based on functional annotations, two genes were considered as potential candidate genes for the identified SNPs (PZE-101152541 and PZE-109016787). The SNPs and candidate genes identified in this study might provide instrumental information for understanding the genetic mechanism of maize photosynthetic parameters and yield.
Phytophthora alticola; emended description based on new collections and a neotype

A Phytophthora diversity study in native forests and plantations of exotic Acacia mearnsii and Eucalyptus grandis yielded several isolates of an apparently new species in Phytophthora Clade 4. Multi-gene phylogeny placed these isolates in a single monophyletic clade together with sequence of an isolate CBS 121939 linked to the description of Phytophthora alticola. The morphological features of these new isolates were substantially different to those presented in the original description of P. alticola, but identical to an ex-paratype isolate (CBS 121939) of that species. The original description of P. alticola was likely based on mixed cultures and has been previously recognised as nomen dubium. In order to clarify this confusion, we have designated a neotype and emended P. alticola based on these new collections.
CARACTERIZAÇÃO, AVALIAÇÃO ANTIOXIDANTE E CITOTÓXICA DOS EXTRATOS DA POLPA E DA CASCA DE TUCUMÃ (Astrocaryum aculeatum)

A identificacao de compostos bioativos em frutos brasileiros e de extrema importância para a bioprospeccao de substâncias naturais com potenciais farmacoterapeuticos. Da mesma forma, as avaliacoes de perfis de atividade antioxidante e de toxicidade fazem parte dos processos iniciais da exploracao de extratos vegetais, sendo incluidos nos parâmetros de eficacia e seguranca. Os frutos amazonicos tem se destacado por seus excelentes potenciais terapeuticos em diversos ensaios experimentais. Dentro desse contexto encontra-se o tucuma, um fruto amazonico oriundo de uma palmeira (Astrocaryum aculeatum), amplamente utilizado no estado do Amazonas para a fabricacao de doces, sorvetes, licores ou para o consumo in natura. Estudos demonstram a presenca de uma grande quantidade de carotenoides na polpa do fruto. No entanto, o fruto carece de informacoes relacionadas as propriedades antioxidantes e a presenca de outros constituintes quimicos. O objetivo deste trabalho foi avaliar os extratos etanolicos da polpa e da casca de tucuma quanto a presenca de compostos bioativos, atividade antioxidante e citotoxicidade. A identificacao de compostos bioativos e de polifenois totais foram realizadas por meio de Cromatografia Liquida de Alta Eficiencia (CLAE) e metodo de Folin-Ciocalteau, respectivamente. As avaliacoes antioxidantes foram feitas pelo metodo de sequestro de radicais 2,2- difenil-1-picril-hidrazil (DPPH) e teste de Total Reactive Antioxidant Potential (TRAP). Os ensaios de citotoxicidade foram realizados pelas tecnicas de 3-(4,5)-dimetiltialzolil -2,5 difeniltetrazolio (MTT) e exclusao por azul de Tripan. Os resultados demonstraram a presenca de uma grande quantidade de polifenois na casca (790,9 ± 43,65 mg/100g) e na polpa (663,9 ± 92,40 mg/100g) do fruto. Alem disso, foi verificada a presenca de compostos bioativos importantes, como flavonoides (casca = 77,9 ± 0,02 mg/100g; polpa = 40,6 ± 0,06 mg/100g), taninos (casca = 26,4 ± 0,01 mg/100g; polpa = 6,4 ± 0,05 mg/100g) e alcaloides (casca = 1,3 ± 0,29 mg/100g; polpa = 0,7 ± 0,05 mg/100g). Dentre os compostos identificados estavam beta-caroteno, rutina, quercetina, acido galico, acido cafeico e acido clorogenico, com concentracoes superiores na casca em relacao a polpa (com excecao do acido galico). Os extratos apresentaram alta atividade antioxidante, com valores de IC50 correspondentes a 8,98 ± 0,39 μg/ml (casca) e 11,24 ± 0,461 μg/ml (polpa), para o metodo de TRAP, e 102,38 ± 4,8 ng/ml (casca) e 224,57 ± 3,9 (polpa) para o metodo de DPPH. No entanto, em concentracoes superiores a 100 μg/mL, ambos os extratos apresentaram efeitos citotoxicos. Os resultados sugerem que os extratos etanolicos da polpa e da casca de tucuma apresentam alta atividade antioxidante, com a presenca de compostos bioativos que demonstram excelentes potenciais farmacoterapeuticos.