Miracle-dz/UniFAR-FTUs huggingface dataset:
Induced Resistance to Ustilago maydis in Zea mays Inoculated in Non-Sterile Conditions

Plants are able to acquire induced resistance to pathogens (priming) by its previous exposure to biotic or abiotic stresses. To analyze whether this process is involved in the maize infection by Ustilago maydis , we have compared the infection occurring in plants inoculated under axenic conditions or in sterile soil to plants grown in non-sterile soil. Our results showed that plants grown under axenic conditions were more susceptible to infection than those inoculated in non-sterile soil. Accordingly, disease symptoms: chlorosis development, anthocyanin production, tumor development, and necrosis, were more and severe in axenic plants. In addition, cell death and reactive oxygen species production, as well as ethylene, were higher in axenic plants. These observations indicate for the first time, that different physical stressors and contact with microorganisms of the environment are responsible for the induction of resistance (priming) in this pathosystem.
SpotEgg: An image‐processing tool for automatised analysis of colouration and spottiness

Colouration and patterning are widespread amongst organisms. Regarding avian eggs, colouration (reflectances) has been previously measured using spectrometers whereas spottiness has been determined using human-based scoring methods or by applying global thresholding over the luminance channel on photographs. However, the availability of powerful computers and digital image-processing algorithms and software offers new possibilities to develop systematised, automatable, and accurate methods to characterise visual information in eggs. Here, we provide a computing infrastructure (library of functions and a graphical user interface) for eggshell colouration and spottiness analysis called SpotEgg, which runs over MATLAB. Compared to previous methods, our method offers four novelties for eggshell visual analysis. First, we have developed a standardised non-human biased method to determine spottiness. Spottiness determination is based on four parameters that allow direct comparisons between studies and may improve results when relating colouration and patterning to pigment extraction. Second, researcher time devoted to routine tasks is remarkably reduced thanks to the incorporation of image-processing techniques that automatically detect the colour reference chart and egg-like shapes in the scene. Third, SpotEgg reduces the errors in colour estimation through the eggshell that are created by the different angles of view subtended from different parts of the eggshell and the optical centre of the camera. Fourth, SpotEgg runs automatic Fractal Dimension analysis (a measure of how the details in a pattern change with the scale at which this pattern is measured) of the spots pattern in case researchers want to relate other measurements with this special spatial pattern. Finally, although initially conceived for eggshell analysis, SpotEgg can also be applied in images containing objects different from eggs as feathers, frogs, insects, etc., since it allows the user to manually draw any region to be analysed making this tool useful not only for oologist but also for other evolutionary biologists.
Present status of eriophyoid mites in Thailand

One of the common groups of phytophagous mites encountered on various plants in Thailand is that of the eriophyoid mites, which can be found on agricultural, horticultural, ornamental, and medicinal plants, including fruit and forest trees. Because there is a paucity of information on eriophyoid taxonomy in Thailand, where the host plants are so diverse, there is a need to investigate the presence of these tiny creatures – especially those species that can be harmful to economic crops. Here, the taxonomy of the eriophyoid mites in the collection of the ﬁrst author was revised, together with the taxonomy of those reported by other researchers. To date, a total of 215 species of eriophyoid mites have been recorded from Thailand. The family Eriophyidae comprises 157 species, whereas only 58 species are reported in the family Diptilomiopidae. These mites are found on 161 plant species under 60 host plant families; they are relatively more numerous ( ＞ 10 species) on plants in the families Fabaceae, Poaceae, Moraceae, Sapindaceae, Rubiaceae, Anacardiaceae, Myrtaceae, and Euphorbiaceae. Fortunately, only a few species are considered to be pests of our economic crops. Eight new genera were assigned as new names for those mites previously identiﬁed by the ﬁrst author and Professor Jan Boczek. Another 8 new genera and 10 new species were also added for unidentiﬁed eriophyoid mites in this collection where Diptilomiopus phylanthi (Chandrapatya, 1992), Liparus eugeniae Boczek, chonburi Chandrapatya, Konvipasruang & Amrine, 2016 for Aculops desmodii Chandrapatya & Boczek, 2000 preoccupied by Aculops desmodii (Keifer, 1964) and Diptilomiopus sakaena Chandrapatya, Konvipasruang & Amrine, 2016 for Diptilomiopus combretae (Chandrapatya & Boczek, 2002) preoccupied by Diptilomiopus combretae Wei & Lu, 2001. words:
Effect of rosette size, clonality and spatial distribution on the reproduction of Vriesea carinata (Bromeliaceae) in the Atlantic Forest of Paraná, southern Brazil

Plant size and clonality are important traits for explaining the reproductive effort of clonal plants. Larger plants can invest more resources into reproduction, and clonality is known to increase reproductive effort. Moreover, reproductive effort is influenced by environmental variation, and so the spatial distribution of plants may affect plant reproductive effort. We investigated the effect of plant size, clonality and spatial distribution on the reproductive effort of Vriesea carinata in the Atlantic Forest in the state of Parana, Brazil. We marked twenty individual plants and measured their rosette size, biomass and number, as well as rosette reproductive effort (number of flowers, fruits and seeds). We also evaluated the relationship between reproductive effort and spatial distribution of plants. Reproductive effort did not correlate with size, whereas greater clonal growth contributed to a lower reproductive effort because rosettes within clones that had more rosettes set fewer flowers. We found that plants growing closer to each other exhibited similar reproductive efforts independently of vegetative traits, because reproductive traits were spatially autocorrelated. In Vriesea carinata, the main drivers of reproductive effort are clonality, which decreases flower production, and spatial factors, which result in greater similarity in reproductive efforts among more proximate plants.
Endopolygalacturonase from Fusarium oxysporum f. sp. lycopersici : Purification, characterization, and production during infection of tomato plants

Production of extracellular pectinolytic enzymes by Fusarium oxysporum f. sp. lycopersici on different carbon sources was analyzed by zymograms of isoelectric focusing (IEF) gels. Pectinolytic isoforms with pIs ranging from 4.0 to 9.0 were detected. A polygalacturonase (PG; EC 3.2.1.15) was purified by preparative IEF and denominated PGI. The enzyme consisted of one major unglycosylated isoform with pI 7.0 and a molecular weight (MW) of 35,000 and three major N-glycosylated isoforms with pIs 6.0, 6.5, and 6.75 and a MW of 37,500. Absence of PG1 from the filtrate after tunicamycin treatment indicated that N-glycosylation was essential for its secretion. PG1 was active as a monomer and apparently hydrolyzed polygalacturonic acid simultaneously in an endo-and exomanner; hydrolysis of substrate bonds was 3% at 50% viscosity reduction indicating random cleavage, whereas analysis of reaction products showed early appearance of galacturonic acid. pH and temperature optima were 4.0 and 37°C, respectively. Sequencing of 11 N-terminal amino acids showed 91% identity to a Fusarium moniliforme endoPG. PG1 was approximately twice as resistant to inhibition by purified tomato PG-inhibitor protein as endoPGs from F. moniliforme and Aspergillus niger. Zymograms revealed the presence of the main PG1 isoform (pI 7.0) in stems of tomato plants infected with F. oxysporum f. sp. lycopersici, while a pectate lyase (pI 8.7) was detected in roots during early stages of infection.
Experimental Pipeline for SNP and SSR Discovery and Genotyping Analysis of Mango (Mangifera indica L.)

[Abstract] Establishing a reservoir of polymorphic markers is an important key for marker-assisted breeding. Many crops are still lack of such genomic infrastructure. Single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) are useful as markers because they are widespread over the genome and many technologies were developed for high throughput genotyping. We present here a pipeline for developing a reservoir of SNP and SSR markers for Mangifera indica L. as an example for fruit tree crops having no genomic information available. Our pipeline includes de novo assembly of reference transcriptome with MIRA and CAP3 based on reads produced by 454-GS FLX technology; Polymorphic loci discovery by alignment of Illumina resequencing to the transcriptome reference; Identifying a subset of loci that are polymorphic in the entire germplasm collection for downstream diversity analysis by genotyping with Fluidigm technology.
Generating new models to study propagation and pathology of alpha-synuclein in Parkinson's disease and multiple system atrophy

Synucleinopthies are neurodegenerative diseases characterised by the formation of α-synuclein-rich intracellular inclusions in neurons and glia. Traditionally, animalmodels and immortalized cell lines have been used to investigate why and how theseinclusions form, and how they impact on cellular function. Recent advances incellular reprogramming and directed differentiation have enabled the generation ofneurons and glia, providing new models to study alpha-synuclein biology in patienttailoredbrain cells.The work presented in this thesis aimed to establish a platform of novel models tofurther address questions relevant to α-synucleinopathies. We created a library ofhuman induced pluripotent stem cell lines from patients diagnosed with familialParkinson’s disease (PD) and multiple system atrophy (MSA), as well as healthycontrols, which we extensively characterized. Using these new cellular models, wegenerated defined regionalized cellular subtypes relevant for modelling PD and MSA,such as dopaminergic neurons, oligodendrocytes and astrocytes, using efficientdifferentiation protocols. In contrast to previous studies, we found that α-synuclein istransiently expressed in oligodendrocytes during development and in the adult humanbrain. We also devised a transgenic strategy for generating reporter lines, from whichpure populations of astrocytes could be obtained. These human astrocytes werecapable of releasing cytokines and chemokines in response to stressors, and readilytook up α-synuclein from their surroundings, demonstrating their relevance inmodelling of synucleinopathies. Braak’s hypothesis suggests that the pathology startsin the peripheral nervous system and progresses to the central nervous system (CNS),based on clinical observations of Lewy pathology distribution. We found thatfollowing injection into the intestinal wall of rats, α-synuclein was transported via thevagal nerve to the brain, thereby strengthening the hypothesis postulated by Braak.The models and cell systems presented in this thesis have provided unprecedentedpossibilities to address key questions relevant to the initiation and progression of α-synucleinopathies PD and MSA. (Less)
Prediction of soil salinity in the Yellow River Delta using geographically weighted regression

ABSTRACT It is essential to determine the content and spatial distribution of soil salinity in a timely manner because soil salinization can cause land degradation on a regional scale. Geographically weighted regression (GWR) is a local regression method that can achieve the spatial extension of dependent variables based on the relationships between the dependent variables and environment variables and the spatial distances between the sample points and predicted locations. This study aimed to explore the feasibility of GWR in predicting soil salinity because the existing interpolation methods for soil salinity in the Yellow River Delta are still of low precision. Additionally, multiple linear regressions, cokriging and regression kriging were added to compare the accuracy of GWRs. The results showed that GWR predicted soil salinity with high accuracy. Furthermore, the accuracy was improved when compared to other methods. The root mean square error, correlation coefficient, regression coefficient and adjustment coefficients between the observed values and predicted values of the validation points were 0.31, 0.65, 0.57 and 0.42, respectively, which were better than that of other methods, indicating that GWR is an optimal method.
Attenuation and Deconvolution

All seismic waves experience some degree of anelastic attenuation as they propagate because the earth is not a perfect, homogeneous, elastic solid. This causes the seismic wavelet to evolve as it propagates in a way characterized by progressive diminishment of high frequencies and progressive phase rotations. As a result, there is no single “wavelet” embedded in a seismic record, instead, there is a changing and evolving wavelet which has progressively lower bandwidth as traveltime increases. Mathematically, data with this property are said to be nonstationary. In contrast, the major wavelet shaping step in seismic data processing remains stationary spiking deconvolution, an algorithm that has changed very little since its introduction some 70 years ago. This algorithm explicitly assumes that seismic data are stationary, or equivalently, that the wavelet does not evolve. Data processors often cope with this conflict between physics and algorithmic assumptions by designing the deconvolution operator over a limited time window containing the exploration target. While this can optimize the image at target, the essential nonstationarity of the data is not addressed and the result is data with characteristic wavelet distortions at times outside the design window. I present a systematic study of this issue using a sophisticated synthetic dataset created with finite-difference modelling over a 2D earth whose stratigraphy comes from well logs and whose attenuation is prescribed by constantQQ theory. The study reveals the characteristic wavelet distortions that are present in real seismic data when the processing includes only stationary methods.
Comparison of the efficiency and relevancy of reference genes in crayfish tissue samples / Kerevit doku örneklerinde referans genlerin geçerlilik ve etkinliğinin karşılaştırılması

Abstract Objective: Relevancy of the reference genes have not been investigated in crayfish tissue samples. Various genes have been proposed for establishing a reference level to analyze qPCR results obtained in different tissue samples. However, majority of those genes have been investigated solely in mammalian species. There is no report related to the relevancy and the efficiency of those common reference genes in crayfish tissue samples yet. The primary aim of the present work is to compare the expression level of a set of reference genes in various crayfish tissue samples to establish a reliable reference gene for quantitative expression level comparisons. Methods: cDNA copies were synthesized by RT-PCR from equalised total RNA samples of nine different tissue samples. qPCR were performed on cDNA samples by using four different primer pairs specific for β-actin, Peptidylprolyl Isomerase B, Sarcoplasmic Calcium Binding Protein and 18S ribosomal RNA genes. Results: qActin2 amplified gene fragments for β-actin in all samples. Cycle time of the amplification reaction differed substantially between the investigated tissue types. A similar difference was observed between the melting curves of the products. The primer pair PPIB amplified gene fragments for Peptidylprolyl Isomerase B only in heart, muscle and intestine samples but not in the rest of the tissue samples. Further, both amplification and melting curves for heart, muscle and intestine were different. qSCP amplified some gene fragments for Sarcoplasmic Reticulum Binding Protein only in muscle, heart and ganglion samples. The 18S_1 amplified fragments for 18S. Amplification curves the samples superimposed on each other. Melting curves of the products were very similar. Variance of the obtained data was the lowest for 18S ribosomal RNA. Conclusion: In refer to present results; it is conceivable to propose that among all the genes investigated in the present study, expression level of ribosomal 18S RNA is the most homogeneously distributed one within the body parts of the crayfish. Further, it is minimally affected by extreme biological changes such as molting. Thus, 18S Ribosomal RNA would be suggested as a reference gene to be used when investigating tissue specific expression level of a gene in the crayfish.
A revision of the genus Trophon montfort, 1810 (Gastropoda:Muricidae) from southern South America

The genus Trophon from southern South America is revised and restricted to ten valid species from among the 36 nominal species still currently used. In addition, a new species, Trophon parodizi from Patagonian waters, is described. Adult specimens of the new taxon are illustrated, described and compared with other living species of the same genus and similar geographic distribution. Redescription and re-illustration of types, based on material from several institutions around the world are provided for Trophon geversianus (Pallas, 1774), T. plicatus (Light-foot, 1786), T. patagonicus (d'Orbigny, 1839), T. acanthodes Watson, 1882, T. pelseneeri Smith, 1915, T. amettei Carcelles, 1946, T. clenchi (Carcelles, 1953), T. wilhelmensis Ramirez-Bohme, 1981, and T. bahamondei McLean and Andrade, 1982. In addition, "Trophon" malvinarum Strebel, 1908, assigned to genera incerta, is also redescribed and illustrated.
GLUCOSE-INDUCED LIPID DEPOSITION IN GOOSE PRIMARY HEPATOCYTES IS DEPENDENT ON THE PI3K-Akt-mTOR SIGNALING PATHWAY

Previously we showed that fatty liver formation in overfed geese was accompanied by PI3K-Akt-mTOR pathway activation and changes in plasma glucose concentrations. Here, we show that glucose acts in goose hepatocellular lipid metabolism through the PI3K-Akt-mTOR signaling pathway. We observed that glucose increased lipogenesis, decreased fatty acid oxidation and increased very low density lipoprotein triglyceride (VLDL-TG) assembly and secretion. Co-treatment with glucose and inhibitors of the PI3K-Akt-mTOR pathway (LY294002, rapamycin, NVP-BEZ235) decreased the levels of factors involved in lipogenesis and increased the levels of factors involved in fatty acid oxidation and VLDL-TG assembly and secretion. These findings show that inhibition of the PI3K-Akt-mTOR pathway decreased glucose-induced lipogenesis, inhibited the downregulation of fatty acid oxidation by glucose and increased the upregulation of VLDL-TG assembly and secretion by glucose. The results presented herein provide further support for the role of the PI3K-Akt-mTOR pathway in lipid metabolism as we showed that in goose primary hepatocytes, glucose acts through the PI3K-Akt-mTOR-dependent pathway to stimulate lipid deposition by increasing lipogenesis and decreasing fatty acid oxidation and VLDL-TG assembly and secretion. DOI: 10.2298/ABS151210075H Key words: glucose; PI3K-Akt-mTOR pathway; lipogenesis; fatty acid oxidation; VLDL assembly and secretion Received: December 10, 2015; Revised: January 15; Accepted: January 16, 2016; Published online: August 19, 2016 How to cite this article: Han C, We S, He F, Qi S, Xiong X, Ye F, Liu D, Wan H, Liu H, Li L, Xu H, Xu F, Zeng X. Glucose-induced lipid deposition in goose primary hepatocytes is dependent on the PI3K-Akt-mTOR signaling pathway. Arch Biol Sci. 2016;68(4):853-61.
RGF-PCR: A technique to isolate different copies of a multi-copy gene

Isolation of different copies of a multi-copy gene from the genome is a difficult process. To overcome the difficulty, a novel method known as Restricted Genomic Fraction-Polymerase Chain Reaction' (RGF-PCR) has been developed. RGF-PCR is a combination of fractionation of the restricted genome and PCR methods. The transposon Mariner-Like Elements (MLEs) occur as multi-copy genes in the silkworm, Bombyx mori genome. Using RGF-PCR method, isolation of different copies of the multi-copy MLE from different loci of the silkworm genome has been demonstrated. Polymorphic copies of MLEs have been isolated from restricted genomic fractions of silkworm, and the nature of polymorphism has been analysed and presented in this paper.
Digestive Proteinases and Antioxidant Capacity from Pterophylla beltrani Bolivar & Bolivar1 Fed Two Natural Diets

Abstract. Insect diets are complex and usually contain antinutritional factors; because of this, modification of the digestive process and strategies to cope with the factors determines adaptation of each species. Pterophylla beltrani Bolivar & Bolivar is a forest pest that has two feeding regimes; P. beltrani feeds first on diverse vegetation but changes during the second regime to consume foliage of oaks (Quercus spp.). The goal of this work was to assess the status of digestive proteinases and phenolic-antioxidants in the two feeding regimes, as indicators of changes related to diet variation. Trypsin-like activity was confirmed by hydrolysis of a synthetic chromogenic substrate. Units of proteolytic activity were 25.2 to 46.1 for the first regime and 22.6 to 40.2 for the second. No differences in proteolytic profiles were detected between regimes. Total phenolic content was 1,152.2 and 759 GAE/ml for the first regime and 832.2 and 552.2 GAE/ml for the second when samples were extracted in water or ethanol, respectively. Differences in the antioxidant capacity also were observed in individuals from the different feeding regimes — large amounts of phenolics for the first regime and greater antioxidant capacity for the second. Diet allows differential accumulation of antioxidants that might be associated with physiological and ecological implications yet to be discovered.
The Impact of Local Governments’ Social Transfers on Poverty Reduction In Indonesia

ABSTRACT This research aims to examine the impact of intervention to poverty reduction, manifested through social transfers from local governments’ budget (APBD). We use provincial panel data to examine the extent of impact from such transfer to poverty alleviation performance. Using Beck and Katz’s OLS-PCSE estimator, we confirmed that higher amount of social transfer is indeed beneficial for further reduction in poverty incidence. Other explanatory variables, namely GDP per capita and human capital, also demonstrate significant effects in decreasing the number of poor people, while higher unemployment can lead to addition of the number of people living below the poverty line. These findings suggest that the declining trend in social transfers channelled by local governments might underlie the stagnation of poverty reduction in the last decades. We therefore suggest that ensuring the sustainability of transfers to the poor from local governments’ funds is very important to re-accelerate poverty reduction. Keywords: social transfer; local government; poverty reduction; OLS-PCSE estimator