Miracle-dz/UniFAR-FTUs huggingface dataset:
The Characteristic of Mitochondrial Cytochrome C Oxidase 1 Gene of Kryptopterus apogon (Bleeker, 1851)

A study on sequence in the mitochondrial cytochrome c oxidase 1 gene of Kryptopterus apogon from Indragiri River of Riau Province In Indonesia has been conducted. This is a preliminary research on the mitochondrial cytochrome c oxydase 1 gene as molecular marker to obtain species diversity and and phylogenetic relationship on Kryptopterus from Indragiri River. Polymerase chain reactions (PCR) technique was applied to amplify cytochrome c oxidase 1 gene of 655 bp. The partial sequence of cytochrome c oxydase 1 gene was put on multiple alligment with other fishes in Siluriformes and Kryptopterus apogon from GenBank. Multiple alignment and analyzed using MEGA program version 3.0. Genetic distance based on nucleotide of cytochrome c oxidase 1 gene among Kryptopterus apogon (Indragiri river) and Kryptopterus apogon (GenBank) was 0.076. Their nucleotide substitutions consist of 42 nucleotide transitions and five nucleotide transversions. The phylogenetic relationship using Neighbor Joining method based on the sequence of nucleotide cytochrome c oxidase 1 gene among Kryptopterus apogon (Indragiri river) and Kryptopterus apogon (GenBank) form one phylogeny cluster with high bootstrap value.
Growth response of mature larch trees to simulated vole gnawing: 20-year results

ABSTRACT Growth consequences of Japanese larch caused by vole gnawing were evaluated using artificial girdling of differing severity, ranging from 50% to 95% of circumference. The treatments were applied to 37-year-old trees in a larch plantation in Hokkaido, northern Japan, and the stand was monitored for 20 years. None of the treated trees died; simulated girdling did not appear to cause serious reductions in diameter at breast height or tree height. The artificial scars gradually became occluded by callus, the extent of the scars decreasing by 10–17 percentage points every 5 years. These observations indicate that when thinning mature stands of larch, it is unnecessary to select trees commensurate with their wounding extent, in terms of future volume growth.
Bioenergetics of the Peruvian scallops (Argopecten purpuratus) in an environmental context limiting oxygen

During the past two decades, the scallop (Argopecten Purpuratus) culture developed in the Peruvian coastal bays. The trophic availability linked to the upwelling system supports the production scallop. However, the Peruvian coasts are also known to have a high environmental variability especially in oceanic domain. Although scallop farms are vulnerable to production hazards (mortality, low growth), environmental variability in coastal bays of Peru and its effects on growth, reproduction and survival of this socially sensitive resource have been poorly studied. Paracas Bay in Pisco Peru is a traditional farming area where scallop highs and lows in productivity related to environmental conditions were recorded throughout its history. In order increase our knowledge on this issue, this study arises from three approaches : (1) observation in situ, (2) experimental physiology and (3) modelling of the energy budget of A. Purpuratus. An environmental monitoring conducted in the Paracas Bay shows that the oceanographic variability can be important, especially during the summer. Temperature variations of 8°C and oxic conditions ranging from supersaturation to anoxia (absence of oxygen) in the course of a day were observed. The high frequency monitoring has revealed a chronic, severe and prolonged hypoxic condition in Paracas Bay. Scallops grown on the bottom, where exposure to hypoxia was important (47% of the observed time) showed lower growth and reproductions conditions. However, during the summer, prolonged and severe hypoxic events affected both deep culture – scallops grown in suspension and on bottom- causing weight somatic tissue losses and cessation of reproduction. During the laboratory experiments, scallops showed significant ability to regulate their oxygen uptake face to decreased oxygen saturation up to 24%. Surprisingly, we found that this species is able to maintain filtration, although diminished, even at low oxygen saturations (5%). Based on the physiological responses of the Peruvian scallops face to hypoxia and the energy performance aerobic end anaerobic metabolism ; it is hypothesized that there exist a restriction in the energy flow available for metabolism at oxygen saturations below the regulation capacity of the organism. Model simulations including this energy restriction (on assimilation and reserves mobilization fluxes) against hypoxia can reproduce successfully field observations of Paracas Bay : greater exposure to hypoxia results in a reduced growth and reproductive conditions. Although the scallop has physiological adaptations/metabolism to deal with limited oxygen conditions, growth and reproduction can be compromised, affecting culture productivity of this species (according to the frequency, duration and intensity hypoxia). The results of observations, experiments and simulations obtained during this study provide useful information to better manage of Peruvian scallop cultures (ex. Load capacity estimates in the bays, evaluations of adequate areas/depths for culture, etc.).
How network structure can affect nitrogen removal by streams

Streams and rivers can be highly reactive sites for nitrogen (N) transformation and removal. Empirical and model-based research show how location in a stream network affects rates of N removal. Because the structure of stream networks can vary widely and N cycling in headwater streams may affect N cycling in downstream reaches, we hypothesised that network structure may affect whole stream network processing of N. We generated three stream networks with the same catchment area but differing shapes, based on optimal channel network theory. We applied a model of nitrate (NO3−) transport and denitrification, and implemented model scenarios to examine how network shape affects NO3− removal with (1) increased NO3− loading from the catchment, (2) altered spatial distributions of NO3− loading and (3) decreased drainage density (i.e. loss of headwater streams). For all stream networks, the fraction of total NO3− removed decreased with increasing NO3− loading from the catchment. Stream networks in narrow catchments removed a higher fraction of NO3−, particularly at intermediate NO3− loading rates. Network shape also controlled the distribution of removal in small versus large streams, with larger streams removing a higher fraction of the total NO3− load in narrower networks. The effects of network shape on NO3− removal when the spatial distribution of NO3− loading was altered varied with the magnitude of NO3− loading. At low loads, NO3− was entirely removed when added to distal parts of the stream network, and about 50% removed when added near the outlet; there was no effect of network shape. At intermediate and high loads, the fraction of total NO3− load removed by the narrow stream network was 1.5× higher than the rectangular and square networks when NO3− was added to distal parts of the networks. Network shape did not have an effect when NO3− load occurred near the outlet, regardless of the magnitude of the NO3− load. The fraction of total NO3− removed by the stream network was up to 5% lower when drainage density was reduced from 1.0 to 0.74 km−1, with the least change for the narrow network. Reducing the drainage density also altered the role of small relative to large streams, with the net effect of moving the location of NO3− removal downstream. Overall, effects of network shape contributed up to 20% of the variation in the fraction of NO3− removed by stream networks. Network shape was most important at intermediate to high NO3− loads and when NO3− was loaded to distal parts of the catchment. The narrow network removed more NO3− across model scenarios, with elevated removal in larger streams explaining most of the difference. We suggest the shape of the catchment may modulate the degree to which large streams contribute to whole network NO3− removal.
Eucalyptus grandis resistance genes : an in silico search for potential targets in response to Myrtle Rust

Plants have evolved multiple layers of defence responses to pathogens. A first line of defence is the recognition and response to common pathogen-associated molecular patterns. Plants also exhibit pathogen-specific responses, which are mediated by expression of resistance genes (R-genes). Rgene products effectively block disease progression. A significant plant pathogen, which causes Myrtle Rust, has spread rapidly along the east coast of Australia since its first identification on the NSW Central Coast in 2010. This incursion is of concern due to the dominance of the Myrtaceae family in Australian vegetation. The recently published genome of Eucalyptus grandis has provided a valuable resource for the identification of potential resistance genes in this important Australian genus. In this study a search was conducted against the E. grandis genome for one important class of R-genes that incorporate nucleotide binding sites and leucine-rich repeat protein domains (NB-LRR). Predicted NB-LRR coding sequences were identified and analysis of the coding sequences revealed 11 gene models within the E. grandis genome. Scrutiny of these gene models, through E. grandis peptide homologues, identified a further 412 genes which contained both NB and LRR domains. The identification of these R-genes may provide researchers with a targeted approach to defence response studies to Myrtle Rust and other pathogens in E. grandis.
Molecular mechanisms that govern the establishment of sensory-motor networks

The ability to exert complex locomotor behaviors requires precise guidance of sensory and motor fibers to the extremities resulting in the formation of precise peripheral networks. The axon guidance receptor Neuropilin-1 plays a critical role for fasciculation, guidance decisions, and coupling of growth of these heterotypic fiber systems, mediating axon-environment, axon-axon, and axon-Schwann cell interactions. Validation and characterization of the expression patterns of candidate genes previously predicted by a whole-genome expression analysis of differentially projecting sensory and motor neurons further contributes to the decipherment of molecular mechanisms that govern sensory-motor network formation.
Wild Lactobacillus hilgardii (CCMA 0170) strain modifies the fermentation profile and aerobic stability of corn silage

ABSTRACT The wild Lactobacillus hilgardii (CCMA 0170) strain isolated from sugarcane silage showed good results as an inoculant in this silage, so the aim of this study was to evaluate its effect on corn silage. After harvested, three replicates for each fermentation time of corn silage: 19, 60 and 103 days were prepared with L. hilgardii or uninoculated (control silage). Experimental silos were opened and their chemical composition was determined. The silages opened after 103 days were also assessed for aerobic stability and microbial population after aerobic exposure. The new inoculant reduced the dry matter losses and conserved more water-soluble carbohydrates. The inoculated silage showed higher lactic acid bacteria populations and lower yeasts and filamentous fungi than the control silage. The concentration of lactic and acetic acid and 1,2-propanediol increased in inoculated silage. The population of filamentous fungi and yeasts after aerobic exposure in the inoculated silage was less than the minimum detectable (<2.0 log CFU g−1). Lactobacillus hilgardii CCMA 0170 presents qualities for a good microbial inoculant for corn silage, more research is needed to evaluate their performance in large-scale silos.
Unfold: an integrated toolbox for overlap correction, non-linear modeling, and regression-based EEG analysis

Electrophysiological research with event-related brain potentials (ERPs) is increasingly moving from simple, strictly orthogonal stimulation paradigms towards more complex, quasi-experimental designs and naturalistic situations that involve fast, multisensory stimulation and complex motor behavior. As a result, electrophysiological responses from subsequent events often overlap with each other. In addition, the recorded neural activity is typically modulated by numerous covariates, which influence the measured responses in a linear or nonlinear fashion. Examples of paradigms where systematic temporal overlap variations and low-level confounds between conditions cannot be avoided include combined EEG/eye-tracking experiments during natural vision, fast multisensory stimulation experiments, and mobile brain/body imaging studies. However, even “traditional”, highly controlled ERP datasets often contain a hidden mix of overlapping activity (e.g. from stimulus onsets, involuntary microsaccades, or button presses) and it is helpful or even necessary to disentangle these components for a correct interpretation of the results. In this paper, we introduce unfold, a powerful, yet easy-to-use MATLAB toolbox for regression-based EEG analyses that combines existing concepts of massive univariate modeling (“regression ERPs”), linear deconvolution modeling, and non-linear modeling with the generalized additive model (GAM) into one coherent and flexible analysis framework. The toolbox is modular, compatible with EEGLAB and can handle even large datasets efficiently. It also includes advanced options for regularization and the use of temporal basis functions (e.g. Fourier sets). We illustrate the advantages of this approach for simulated data as well as data from a standard face recognition experiment. In addition to traditional and non-conventional EEG/ERP designs, unfold can also be applied to other overlapping physiological signals, such as pupillary or electrodermal responses. It is available as open-source software at http://www.unfoldtoolbox. org.
Applications of Aptamers in Cancer Therapy

Aptamers are small and specific oligonucleotides [RNA or single-strand DNA (ssDNA)] with a high binding affinity against target protein. In vitro selection process of aptamer by selective evolution of ligands by exponential enrichment (SELEX) has been invented in 1990 by Larry Gold and Jack Szostak. SELEX is a random amplification of target protein with combined oligonucleotide libraries and selection of synthesized aptamer by magnetic beads, affinity chromatography, and capillary electrophoresis-based methods. According to their low molecular weight, non-immunogenic feature in vivo , low production cost, high thermal stability, increase in production potential, and ample of modification capacities, aptamers are becoming essential medical tools for diagnosis and treatment of diseases such as macular degeneration, hemophilia, heart disease, and various cancer types. The therapeutic potential of aptamers, with high binding affinity against carcinogenesis-associated growth factors, receptors, or proteins frequently overexpressed in specific cancers such as prostate, breast, colon, lung, leukemia, hepatocellular, and cervical carcinoma. The strategies for aptamer-based drugs in cancer therapy design/modify aptamers against cancer biomarkers, accelerate immunotherapy targeting immune system, and increase the drug delivery in cancer cells. In conclusion, aptamers are promising candidate drugs due to their antiproliferative effect on cancer cells and the drug delivery systems during cancer chemotherapy.
The phenotypic correlates of individual vulnerability to angling

english) . 4 Zusammenfassung (deutsch). 5 Background . 6 1. The mechanistic basis of individual vulnerability to passive gear . 7 1.1 Morphology . 7 1.2 Behavior . 8 1.3 Physiology . 11 1.4 Life-history . 13 1.5 Abiotic effects . 15 2. Fisheries induced selection vs natural selection . 17 3. Methodological issues . 21 4. Objectives and thesis structure . 23 5. Framework . 27 6. Methods overview . 28 6.1 Model systems . 28 6.2 Phenotypic trait assessments . 29 6.3 Carp . 30 6.3. 1 Morphology . 30 6.3. 2 Behavior . 30 6.3. 3 Physiology . 32 6.3. 4 Life-history . 34 6.3. 5 Vulnerability to angling . 34 6.3. 6 Survival fitness . 35 6.4 Amago salmon . 36 6.4. 1 Behavior, growth and vulnerability to angling . 36 6.5 Largemouth bass . 37 6.5. 1 Behavior, vulnerability to angling and reproductive success . 37 6.6 Pike . 38 6.6.1 Environmental correlates of catch rate . 38
Isolation and characterization of cinnamate 4-hydroxylase gene from cultivated ramie (Boehmeria nivea)

ABSTRACT The present study aimed to describe the cDNA cloning of the cinnamate 4-hydroxylase (C4H) gene from ramie, predict the protein sequence and perform phylogenetic and structural analyses of this gene. C4H catalyses the hydroxylation of trans-cinnamic acid to p-coumaric acid, which plays a crucial role in lignin biosynthesis. In the present study, the gene encoding C4H was cloned by polymerase chain reaction (PCR) technology from cultivated ramie (Boehmeria nivea) and named BnGC4H. In addition, bioinformatics and tissue expression analyses were performed. The results showed that the cloned BnGC4H cDNA contained a 1518-bp open reading frame encoding a 505–amino acid protein. The sequence of BnGC4H is available from the GenBank database with accession number KY937946. The amino acid sequence and structural analysis revealed that BnGC4H shared conserved domains with other C4H forms, including cytochrome P450 domain and trans-cinnamate 4-monooxygenase domain. The phylogenetic analysis indicated that BnGC4H was closely related to Aquilaria sinensis C4H and Ruta graveolens C4H. Real-time quantitative reverse transcription–PCR and RNA in situ hybridization showed that BnGC4H was strongly expressed in the xylem during the maturity stage. The findings provided a theoretical basis for further exploring the function of BnGC4H in the lignin biosynthesis and regulation in ramie.
Amblyomma yucumense Krawczak, Martins & Labruna, 2015 (Acari: Ixodidae) in Argentina

Amblyomma yucumense was recently described from specimens collected in the Turvo State Park, southern Brazil. In search of this tick species, free-living ticks were collected at the Mocona Provincial Park and the Yaboti Biosphere Reserve in Misiones province, Argentina. A total of 594 ticks were collected, of which 448 were Amblyomma brasiliense, 90 Amblyomma incisum , one Amblyomma ovale , 48 Haemaphysalis juxtakochi and seven A. yucumense. The latter was confirmed by the presence of certain morphological characters and the analysis of sequences of a 410-bp fragment of the mitochondrial 16S rDNA performed to representative specimens. The sequences showed 100% identity with that of A. yucumense from Turvo State Park in Brazil. Amblyomma yucumense , Amblyomma dubitatum and Amblyomma coelebs phylogenetically group together and are morphologically similar, though they seem to have distinct ecological preferences. Amblyomma coelebs has only been found in northern Misiones province, while the most numerous records of A. dubitatum come from the central area of the province. Until now, the distribution of A. yucumense in Argentina is restricted to Mocona and Yaboti. The findings in this study expand A. brasiliense , A. incisum , A. ovale and H. juxtakochi distribution ranges to the south, and we report for the first time the presence of A. yucumense in Argentina.
An investigation into glucagon receptor pharmacology

The glucagon receptor (GCGR), a family B G protein-coupled receptor (GPCR), plays an important role in regulating blood glucose levels through its ability to bind the 29 amino acid peptide hormone, glucagon (GCG). Antagonising GCG action is a potential therapeutic option for reducing hepatic glucose production. However, GCG-based therapy is currently limited to acute emergency treatment of hypoglycemia in patients with type 1 diabetes (T1D) (Habegger et al., 2010). Further insight into GCGR-mediated signalling pathways and mechanism of activation may provide the basis for therapeutic development. We investigated the ligand stimulated GCGR signalling using multiple assays including those measuring cAMP accumulation, ERK1/2 phosphorylation and intracellular Ca2+ (Ca2+ i) mobilisation. Through site directed mutagenesis and FACS analysis for the investigation of cell-surface expression, we identified several important residues. They included K16812.49, L16912.50 , H17012.51 and T1722.45 of the ICL1 region (G1651.63 -T1722.45 ) as potential determinant in signalling bias at the GCGR through Gq/11-coupling, C1712.44 as a critical determinant of GCGR expression and R1732.46 as an essential residue for G protein-coupling. Helix 8 residue E4068.49 was implicated in maintaining GCGR in an inactive state. Finally, TM4 residues G2714.49 , L2774.55 and V2804.58 were found to plays an important role in successful translation and/or trafficking of GCGR and (Ca2+ i) mobilisation. The GCGR-mediated pERK1/2 response way found to be both Gq/11 and β-arrestin1/2 mediated, whereas it was independent of PKA or Gβγ-subunits. The GCG analogue TH-GCG, contrary to previous reports (Wakelam et al., 1986, Lenzen et al., 1990), was characterised as a partial agonist at the GCGR, inducing a robust cAMP response but fails to induce a detectable Ca2+ i or IP1 response. We also identified a RAMP2-dependent potentiation of the GCG stimulated cAMP response at the GCGR. The research described in this thesis has produced novel data that contributes to a clearer understanding of GCGR pharmacology.
Analysis of copy number variation from germline DNA can predict individual cancer risk

Background Twin studies suggest that inherited factors are responsible for a substantial portion of many different forms of cancer. However, most of these inherited factors have yet to be identified. Most analyses of genome wide association data focus on the additive effects of single nucleotide polymorphisms found in germline DNA. The objective of this study is to test whether germline DNA copy number variation data can be used to predict whether a person will develop cancer. Methods We tested this objective using data compiled by The Cancer Genome Atlas (TCGA) project. The TCGA data consisted of information on DNA copy number variation extracted from the peripheral blood of 8,821 different patients, each of whom had one of 32 different types of cancer. We used a machine-learning algorithm to test how well we could classify whether or not a patient had a certain cancer based solely on this data. Results We found that all 32 different types of cancer tested could be predicted better than random chance using copy number variation data. Specifically, we measured the area under the receiver operator curve, known as the AUC, for ovarian cancer in women (0.89), glioblastoma multiforme (0.86), breast cancer in women (0.75), and colon adenocarcinoma (0.79), with a 95% confidence interval width of less than 0.01 in each case. Conclusions All cancers have a substantial inherited component. This method should be applicable to developing predictive genetic tests for conditions known to have a substantial genetic component.