Miracle-dz/UniFAR-FTUs huggingface dataset:
Disentangling the effects of environmental factors on the distribution of vascular plants in Japan: the importance of land use for common species on a macroscale

Background: All human land use (LU) affects the distribution of plant species; however, the impacts vary with the type/intensity of LU. For managing ecosystems, it is therefore essential to understand the effects of LU types on the distribution of plant species on a macroscale. Aims: The objectives of our study were to quantify the effects of various LU types on the distribution of vascular plant species in Japan and to determine in particular the extent to which LU was an important factor for the distribution of common species. Methods: Based on a logistic regression model and variation partitioning being applied to each plant species, we evaluated the partial deviance by six LU types, four climatic types and three topographic and geological factors for 647 plant species at 14,412 sites in Japan. Results: The effect of LU was significant for species present at multiple sites. Of the six LU types, secondary vegetation and plantation were the most important factors determining species distribution for many species. Conclusions: Our results suggest that distribution of the common species is largely affected by LU on macroscale. The design of LU relating to secondary vegetation and plantations will thus be important in determining changes in the vegetation composition within Japan.
Estudos em Pitcairnia azouryi (Bromeliaceae), uma espécie endêmica de inselbergues da Floresta Atlântica

This study reports the discovery of new areas of occurrence of Pitcairnia azouryi Martinelli & Forzza, and the study of their populations regarding its genetic diversity, the amount of nuclear DNA and the chromosome number. Seven new areas of occurrence for this species were located between the northern state of Rio de Janeiro (RJ) and the southern state of Espírito Santo (ES), and georeferenced to the other studies. Leaf samples of 13-15 individuals were collected in five of these populations (PLB Pedra Lisa Burarama, PA Pedra das Andorinhas, PTI Pedra Três Irmãs, PPC Pedra Parada Cristal and PLC Pedra Lisa Campos), totaling 66 individuals. Nine SSR markers were used in PCRs. Genetic polymorphisms were identified from polymorphism between individuals sampled, detected by electrophoresis on acrylamide gel 8%. The parameters of diversity and genetic structure of populations were calculated using the software Fstat, PopGene and Structure. The flow cytometry analysis was performed using leaf samples obtained from adult individuals of five populations. Cytogenetic analyzes were performed with roots obtained from germinated seeds collected in two populations. The nine SSR primers produced satisfactory amplification products, and proved to be polymorphic. The number of alleles per loci ranged between two and eight. The values of gene diversity index (Gd) and the fixation index (Fis) in populations ranged from 0.459 to 0.578 and 0.047 to 0.208, respectively. The Fst values observed showed that 81.20% of the total genetic variation is found within populations and the occurrence of gene flow (Nm) 1,073 (average number of migrants per generation). Bayesian analysis indicated that a model of k = 3 populations is able to better capture the variation in the data on the genetic structure. The high variation of fixation index added to the large genetic variation within and moderate genetic differentiation among populations suggest the occurrence of the founder effect in the dispersion of new individuals in new locations, followed by genetic drift, especially for the population of Campos dos Goytacazes. The flow cytometry analysis showed that the nuclear DNA content is 2C = 1.16 picograms in all populations analyzed, except on PLC population, in which was measured twice of DNA content (2C= 2.32 picograms). This result was explained by cytogenetic analysis which revealed individuals with 2n = 50 chromosomes in ES and individuals 2n = 100 chromosomes in RJ. This result may be due for PLC's geographical isolation, environmental characteristics of different evolutionary processes.
Symposium: Genetic aspects of male (in)fertility

The Y chromosomal azoospermia factor (AZF) is essential for human spermatogenesis. It has been mapped by molecular deletion analyses to three subintervals in Yq11, AZFa, AZFb, and AZFc, containing a number of genes of which at least some control, post-transcriptionally, the RNA metabolism of other spermatogenesis genes, functionally expressed at different phases of the spermatogenic cycle. Intrachromosomal recombination events between homologous large repetitive sequence block in Yq11 are now recognized as the major cause of the AZFa, AZFb and AZFc microdeletions, and an overlap of the AZFb and AZFc regions was revealed by sequence analysis of the complete Yq11 region. The increasing knowledge of the expression patterns of AZF genes in human germ cells suggests that the DBY gene is the major AZFa gene, the RBMY gene the major AZFb gene, although a functional expression of the other AZFa/b genes in the male germ line is also most likely. Genetic redundancy might exist in AZFc because a number of gene copies in the large P1 palindrome structure in distal AZFc were found to be deleted also in fertile men.
Gas exchange and carbon metabolism in leaves of crabwood ('Carapa guianensis' Aubl.) in three mechanisms and suspension of water stress

Crabwood or Andiroba (in Brazil) is an arboreal species with variations in their physiological processes from soil and climatic conditions induced, such as lack or excess water. The objective of this study was to evaluate the effects of drought and flooding in gas exchange, abscisic acid, starch, total soluble carbohydrates, sucrose in Andiroba leaves with seven months of age and resilience of these young plants after cessation of stress. The experiment was conducted in a greenhouse. The experimental design was completely randomized in a factorial 3x5 (three water conditions: control, water deficit and flooding and 5 periods reviewed. 0, 10, 20, 30 and suspension of water stress after 72h) with 5 repetitions, totaling 75 sample units. Significant decreases were observed in water potential, stomatal conductance, transpiration and starch content, and significant increase in abscisic acid (ABA) content, total soluble carbohydrates and sucrose, with significant values on the 30th day of the experiment. After the water stress, the plants failed to recover the initial values of all variables, recovering only the sucrose levels. Andiroba is satisfactorily tolerant to water stress imposed in this experiment, but does not show a rapid recovery after the suspension of water stress, with higher sensitivity to water stress.
Multiplex polymerase chain reaction assay for the detection of Neisseria gonorrhoeae in urogenital specimens

A set of PCR primers were designed to detect a broad range of Neisseria species, including Neisseria meningitidis and Neisseria gonorrhoeae. All the three sets of primers could detect the Neisseria DNA at concentrations as low as 25 fg of bacterial DNA. The specificity of primers for Neisseria species was checked by using DNA from other bacteria found as commensal organisms. The primers targeting the 23S rRNA and nspA genes could amplify when the DNA from any of the Neisseria species commonly found as contaminants of clinical samples was used as template. A third set of primers targeting orfl gene was also designed and was found to be highly specific for N. gonorrhoeae. The in-house developed multiplex PCR method was compared with culture method for its ability to detect N. gonorrhoeae infections using 238 clinical swabs, obtained from patients visiting Safdarjung Hospital, New Delhi. The sensitivity of the culture method was 96%, while with multiplex-PCR, a sensitivity of 100% was observed. Sequence analysis of the gene for the outer membrane protein, nspA, from 140 clinical isolates of N. gonorrhoeae revealed no intraspecies divergence. The high specificity and sensitivity coupled with low cost and rapidity of the method described here provide a substantial advantage over the labour-intensive and time-consuming culture method currently used in hospitals in India.
Survey of Grapevine Viruses in Jordan

Field surveys were carried out in grapevine growing areas during the growing season 2003-2004 to evaluate the phytosanitary status of grapevines in Jordan. Samples from 1025 grapevines were collected and individually tested by Double Antibody Sandwich-Enzyme Linked Immunosorbent Assay (DAS-ELISA). Results showed that viruses were widespread in all orchards surveyed. About 33.6% of the samples (344 out of 1025) were virus-infected by one (25.1%), two (6.1%) or more (2.3%) viruses. However, remarkable differences in incidence were observed between the different viruses. The most prevalent being the Grapevine Leaf Roll associated Virus 1 (GLRaV-1) (13.7%) followed by Grapevine virus A (GVA) (12.2%), Grapevine Leaf Roll associated Virus 3 (GLRaV-3) (6.6%), Grapevine Fan Leaf Virus (GFLV) (5.0%), Tomato Ring Spot Virus (ToRSV) (4.7%), and the lowest was Grapevine Leaf Roll associated Virus 2 (GLRaV-2) (2.4%). Infection percentages were higher in nurseries (51.7%) than in commercial vineyards (30.6%).
EST-SSR Analysis and Cross-species Transferability Study in Lavandula

[Abstract] The genus Lavandula comprises of several economically important lavender species that are mainly cultivated worldwide for essential oil production. Identification of lavender species and their cultivars has been a huge bottleneck in lavender industries due to lack of appropriate identification mechanisms. Recent advances in modern technologies would help to address these identification issues through development of potential molecular markers, including simple sequence repeats (SSRs). SSRs can be developed from specific species, and can be potentially used for related species, which lack the source sequences to develop species-specific SSRs. Here, we describe the guidelines and steps of identifying and analyzing SSRs from expressed sequence tag (EST) sequences of lavender species. We also detail the validation procedures of selected EST-SSRs in distinguishing source (donor) species as well as related species.
Molecular phylogenetic hypotheses for the evolution of scleractinian corals

The evolutionary history of scleractinian corals is based on knowledge of skeletal characters and their 250 million yr fossil record. However, homologies of skeletal characters are not well-understood and fossil documentation of these characters is incomplete. As a result, relationships among families and suborders are poorly understood. We have analyzed a 225 bp segment of the nuclear 28S ribosomal RNA gene from 45 species of corals and a 566 bp segment of the mitochondrial 16S ribosomal RNA gene from 68 species. Unlike previous analyses of smaller numbers of taxa, the dataset presented here includes both reef-building and non-reef-building taxa from 20 of 24 families and all seven suborders. Nuclear sequences analyzed under maximum parsimony and minimum evolution criteria did not resolve relationships among families and suborders. Similar analyses of mitochondrial sequences resulted in a robust phylogenetic hypothesis. The mitochondrial hypothesis, like previous analyses of a subset of these data, did not agree with morphological hypotheses about relationships among families and suborders, and supports a polyphyletic origin of the scleractinian skeleton. Instead of seven major monophyletic groups as hypothesized from morphological data, mitochondrial data suggest that the Scleractinia is represented by two major clades. Relationships within these major clades are not clearly differentiated but each Glade is comprised of families from different morphological suborders as defined by Veron (1995). The mitochondrial topology gives no support for the morphological suborders Archaeocoeniina, Fungiina, Caryophylliina, or Meandriina as monophyletic groups but is consistent with a monophyletic Faviina, Poritiina, and Dendrophylliina. Monophyletic morphological families are supported with the exception of the Faviiidae, Caryophylliidae, Poritidae, and Oculinidae. The mitochondrial topology also supports the most recent taxonomic treatments of Psammocora and Fungiacyathus, genera that have been the subject of taxonomic debate.
Larval helminths parasitizing freshwater fishes from the Atlantic coast of Nicaragua

During a survey of the parasitic helminths of 8 fish species from the South Atlantic Autonomous Region, Nicaragua, 23 helminth species were collected. Sixteen of them were digenean species in metacercarial stage: Apharyngostrigea sp. , Ascocotyle (Ascocotyle) tenuicollis, Ascocotyle (Phagicola) mollienisicola, Ascocotyle (Phagicola) diminuta, Ascocotyle (Phagicola) nana, Cladocystis trifolium, Clinostomum complanatum, Clinostomum sp. , Cryptogonimidae gen. sp. , Diplostomum compactum, Heterophyidae gen. sp. , Oligogonotylus manteri, Posthodiplostomum minimum, Proterodiplostomidae gen. sp. , Stunkardiella minima, and Uvulifer sp. ; 1 was a cestode larva: Proteocephalidea gen. sp. ; and 6 were larval nematodes: Brevimulticaecum sp. , Contra-caecum sp. type II, Eustrongylides sp. , Falcaustra sp. , Serpinema trispinosum, and Spiroxys sp. With the exception of O. manteri, this is the first reported occurrence of these helminth species in Nicaragua. The larval helminth fauna in freshwater fishes from Nicaragua closely resembles that of freshwater fishes from southeastern Mexico.
Phenology of spawning for the common frog (Rana temporaria L.) in Finland from 1846 to 1986

The onset and changes in the timing of spawning of the common frog (Rana tempo raria L.) in Finland was studied through the 3888 records received through enquiries car ried out by the Finnish scientific society "Finska Vetenskaps Societeten-Suomen Tiedeseura" in each year over the period 1846-1986. Spawning begins at the end of April in southwestern Finland and gradually proceeds towards northeastern parts of central Fin land and from there to the north. The mean date of the first spawning of the year is 18 April. The maximum delay between the mean dates of all the records of spawning from the southernmost (lat. 60°N) and northernmost Oat. 70°N) 100x100 km Finnish uniform grid squares is 35 days. The mean date of spawning correlates well with mean air temperatures (April in southern, and May in northern, Finland) and with the dates when the ground was no more permanently snow covered. A long-term skift towards earlier spawning (2-13 days de pending on the indice used and the area studied) during the observation period of about 150 years can be seen after smoothing the means of 10-year periods with a 50-year moving average. This long-term change is in accordance with the changes observed in spring temperatures in Finland during the same period. The "greenhouse effect" causing a worldwide increase in the mean air temperatures probably influences the onset of spawning in amphibian populations and accordingly its impacts should be monitored in this respect in other areas as well.
Effect of diesel exhaust on the host response to respiratory viral infection: involvement of toll-like receptor 3

Jonathan Ciencewicki: Effect of Diesel Exhaust on the Host Response to Respiratory Viral Infection: Involvement of Toll-like Receptor 3 (Under the direction of Dr. Ilona Jaspers) Adverse effects resulting from exposure to air pollutants have become an increasing problem worldwide. Particularly levels of air pollutants have been associated with increases in the susceptibility and response to many respiratory diseases. Of the numerous air pollutants, diesel exhaust (DE) has become a major concern since it can account for a significant amount of the pollutants generated by motor vehicles in many areas. Previous results in our laboratory have demonstrated that prior exposure of respiratory epithelial cells to DE enhances the susceptibility to influenza infections. In this work, these results were confirmed and expanded upon both in vitro and in vivo. The effects of DE on the expression and signaling of toll-like receptor 3 (TLR3), which has previously shown to be needed for a complete innate immune response to influenza infections as well as other respiratory viral infections, were examined as well as mechanistic aspects involved in the observed effects. Increased expression and signaling of TLR3 was observed in respiratory epithelial cells exposed to DE prior to infection with influenza, resulting in an enhancement of the influenza-induced inflammatory and interferon (IFN) responses. A positive-feedback loop involving type I IFNs and DE-induced effects on epithelial cell tight junctional complexes played a role in the observed effects. In vivo exposure of mice to DE enhanced the susceptibility to influenza infections and decreased expression of surfactant proteins A and D, which are an important part of the innate immune defense against influenza and other
Three-dimensional analysis of the senescence program in rice (Oryza sativa L.) coleoptiles: Investigations by fluorescence microscopy and electron microscopy

The cytological sequence of senescence-related changes in coleoptiles of rice (Oryza sativa L. cv. Nippon-bare) was studied using fluorescence and electron microscopy. The coleoptiles reach full size 3 d after sowing, then rapidly senesce and wither completely by day 7. The interveinal region in cross-sections taken 1 mm from the tip of the coleoptile was selected for this analysis. Fluorescence microscopy using samples embedded in Technovit 7100 resin, electron microscopy and immunoelectron microscopy using DNA-specific antibodies were used to elucidate the sequence of senescence-related events. These occur in the following order: (i) degradation of the chloroplast DNA (cpDNA): (ii) condensation of the nucleus in conjunction with a decrease in the size of the dense-chromatin region, shrinkage of the chloroplast, degradation of ribulose-1, 5-bisphosphate carboxylase oxygenase, dilation of the thylakoid membranes, increase in size and number of osmiophilic globules, condensation of the cytoplasm; (iii) disorganization of the nucleus, degeneration of the tonoplast; (iv) complete loss of the cytoplasmic components, distortion of the cell wall, invasion of microorganisms into the intercellular spaces and ultimately into the cell itself. The mitochondria maintain their ultrastructural integrity and a constant level of mitochondrial DNA throughout senescence, In young mesophyll cells, invagination of the tonoplast into the vacuole frequently occurs. This occasionally includes cytoplasmic material, which is digested in the vacuole as senescence proceeds. Immunoelectron microscopy suggests that cpDNA degradation involves rough digestion first, rather than rapid, direct decomposition of the DNA into nucleotides. The fragmented cpDNA is then dispersed throughout the chloroplast and cytoplasm.
Genetic diversity of the semi-feral Marismeño horse breed assessed with microsatellites

Abstract Marismeño horses originated from primitive horses living around the marshes of the Guadalquivir River in Southern Spain. Throughout their evolution, they have experienced crosses with other breeds, first with horses from North Africa and thereafter with other horses. However, they have not lost their ability to adapt to the demanding marsh environment. Recently, a studbook of the breed was established, and the Breeders Association started a conservation programme. To study the relationship of the Marismeño with other breeds, a microsatellite analysis was developed, which included other ancient Southern Iberian horse populations, such as the Sorraia and Retuertas breeds. Candidates of recent crossbreeding with Marismeño horses, such as the Hispano-Arabian and the Spanish Purebred, were studied, and the Thoroughbred and the Arabian breed were used as international references. The results indicated that the Marismeño horse population maintains a great genetic diversity. Despite recent crossbreeding, the fixation index and the Hardy-Weinberg equilibrium analysis disclosed a certain homogeneity degree. A dendrogram was built using the obtained genetic distances, and clustering was performed with the software STRUCTURE, and the results reflected the genetic differentiation of the Marismeño horse from the other autochthonous Iberian breeds, although the Marismeño population has maintained a tight relationship with the Spanish Purebred. Remarkably, some relatedness between the Marismeño and the Barb horse breeds could be observed and was most likely derived from an ancient gene flow between the horses of the Iberian Peninsula and North Africa.
Changes in productivity in the virgin olive oil sector: An application to Protected Designations of Origin in Spain

Virgin olive oil is a key ingredient of the renowned Mediterranean diet. In this context, the main objective of this study was to estimate and decompose productivity change for Protected Designations of Origin (PDOs) in the Spanish virgin olive oil sector for the period 2008-2013. To this end, we introduced a Luenberger-type indicator based on a specific weighted additive model in Data Envelopment Analysis (DEA), which, in contrast to previous studies, captured all sources of inefficiency and avoided infeasibilities. Regarding the results, we found a reduction in productivity, in average terms, in the first periods analyzed (-0.12 and -1.65), followed by an improvement (0.79 and 0.54), that in the last period analyzed (2012-2013), however, returned to adverse figures (-0.47). In Spain, where foreign competition is weak, the most productive PDOs were those with an important number of oil mills and packaging/marketing companies such as “Montes de Toledo” and “Siurana”; productivity changes were mainly the consequence of downwards and upwards of the frontier of the technology over time. These changes were explained, to a certain extent, by the evolution of the economic crisis; and the productivity of the sector declined, in general, from 2008 to 2010, improving thereafter except for the last registered period, 2012-2013, where expectations for market recovery exceeded actual sales.
Enhancing growth, yield, biochemical, and hormonal contents of snap bean (Phaseolus vulgaris L.) sprayed with moringa leaf extract

ABSTRACT Increasing growth and productivity of food crops via safe biostimulants is a very important issue in the current years. This study aimed to investigate the potential of moringa leaf extract (MLE) in improving the performance of snap bean (Phaseolus vulgaris L.) cv. ‘Paulista’ under field conditions. Hormonal analysis of MLE revealed its richness of various classes of phytohormones particularly salicylates. The results revealed that all MLE concentrations had a positive effect on growth, biochemical, yield, and yield related traits as well as yield quality of snap bean compared to control, and the effect was dose-dependent. Moreover, increasing pods yield of snap bean may be related to gibberellins (GA7) content than other plant hormones. In conclusion, the leaf extract of moringa provides a good source of phytohormones that have a positive role to stimulate growth and productivity of snap bean plants.