Miracle-dz/UniFAR-FTUs huggingface dataset:
Lack of regeneration and climatic vulnerability to fire of Scots pine may induce vegetation shifts at the southern edge of its distribution

Aim Forest ecosystems dominated by fire‐sensitive species could suffer shifts in composition under altered crown fire regimes mediated by climate change. The aims of this study were to: (1) study the spatio‐temporal patterns and the climatic distribution of fires in Scots pine (Pinus sylvestris) forests during the last 31 years in north‐eastern Spain, (2) evaluate the climatic vulnerability to fire of these forests in Spain, (3) analyse the regeneration of Scots pine after fire, and (4) predict the mid‐term maintenance or replacement of Scots pine in burned areas.
The contribution of developmental palaeontology to extensions of evolutionary theory

Evo-devo is featuring prominently in current discussion to extend evolutionary theory. Developmental palaeontology, the study of life history evolution and ontogeny in fossils, remains an area of investigation that could benefit from, but also illuminate, the discourse and research agenda of evo-devo. Understanding how and why evolution proceeds in phenotypic space is an important goal of evo-devo and one that can be significantly enriched through the examination of development in the fossil record (Palaeo-evo-devo). Such an approach permits developmental pathways to be extended into the past, constraining hypotheses of developmental evolution in ways that cannot be predicted by patterns observed from extant taxa alone. The comparison of developmental dynamics among extant and extinct taxa yields a more complete understanding of the temporal persistence of factors that shape evolution in phenotypic space. As more data are compiled that document ‘fossilized ontogenies’, a stage will emerge from which insights into the evolution of development can begin to appraise those phenotypes that are inaccessible to evo-devo.
SHERLOC: An Investigation for Mars 2020

Abbey1, S. Asher2, A. Burton, M. Fries3, P. Conrad4, S. Clegg5, K. S. Edgett6, B. Ehlmann7, W. Hug8, R. Reid8, L. Kah9, K. Nealson10, T. Nelson5, M. Minitti11, J. Popp12, F. Langenhorst12, P. Sobron13, A. Steele14, N. Tarcea12, R. Wiens5, K. Williford 1, R. A. Yingst11. 1Jet Propulsion Laboratory, California Institute of Technology, Pasadena Ca, 91109 (Brandi.L.Carrier@jpl.nasa.gov, Rohit.Bhartia@jpl.nasa.gov, Luther.Beegle@jpl.nasa.gov),2University of Pittsburgh, 3Johnson Space Center, 4Goddard Space Flight Center, 5Los Alamos National Laboratory, 6Malin Space Sciences, 7California Institute of Technology, 8Photon Systems Inc., 9University of Tennessee, 10University of Southern California, 11Planetary Science Institute, 12University Of Jena, 13SETI Institute, 14Carnegie Institute Washington
Heterosis and Combining Ability of Fruit and Bean Characters in Ethiopian Origin Coffee (Coffea arabica L.) Hybrids

A half diallel analysis involving five parents, ten F1 hybrids and one check hybrid was studied for fruit and bean traits to generate information on heterosis and combining ability. The genotypes were evaluated in a randomized complete block design (RCBD) with three replications at Melko, Metu and Tepi research centers. The analysis of variance revealed highly significant difference among genotypes at (p<0.05) for all fruit and bean characters. This consistent significant difference for different traits suggests the presence of genotypic difference among parental lines and hybrids evaluated. Majority of fruit and bean characteristics showed negative heterosis over mid-parent and better-parent values. This may generally suggesting dominance of the small sized fruit and bean character over large sized parents. Both the additive and non-additive gene actions were involved in the control of the characters studied for fruit length, fruit width, fruit thickness, bean length, bean width, bean thickness and 100-bean weight. Keywords: Heterosis , Combining ability , G ene action, GCA, SCA,
Natural and artificial evolution in the serine proteases of Streptomyces griseus

The natural diversity of the Streptomyces griseus serine protease family was investigated; the insights gained were used to design enzymes with altered specificities. Genes encoding S. griseus protease E and two previously uncharacterized proteases (S. griseus proteases C and D, SGPC and SGPD) were isolated and sequenced. A shuttle vector was constructed to allow for genetic manipulations in Escherichia coli and protein secretion in Bacillus subtilis; the recombinant gene products were purified and characterized. The two newly characterized enzymes possessed domains unique among bacterial proteases: SGPC contained a carboxyl-terminal domain homologous to chitin binding domains while SGPD possessed an unusually long amino-terminal prepeptide with characteristics of mitochondria1 import signals. Furthermore, recombinant SGPD existed as a very stable homodimer. The S. griseus proteases are secreted in a promature form, and autocatalytic removal of the propeptide is essential for activity. S. griseus protease B (SGPB, a previously characterized enzyme) has primary specificity for large hydrophobic substrates. We genetically substituted the Leu residue at the promature junction PI site of SGPB with various amino acids; substitution with poor SGPB substrates reduced or abolished active protease secretion in E. coli. Thus, it was demonstrated that the specificity of SGPB is constrained by the promature junction sequence; active protease production is dependent on the efficiency of autocatalytic processing. The link between substrate specificity and proteolytic activity was used to select enzymes with altered primary specificities: loss of proteolytic activity due to mutations at the promature junction PI site could be restored by compensatory changes in enzyme specificity. Sequence alignments and crystallographic data were used to design an E. coli expression library containing 29,952 possible SGPB mutants with variations at seven sites involved in conferring primary specificity. A visual screening strategy allowing for the rapid analysis of up to 106 individual variants was developed to detect active protease secretion. The expression library was screened in conjunction with various promature junction sequences; variants producing increased proteolytic activity were isolated. Variant enzymes with increased specificity towards various hydrophobic and polar substrates were isolated.
Characterization of the mechanism of action of new HIV-1 reverse transcriptase-associated ribonuclease H inhibitors

HIV-1 the Reverse Transcriptase (RT), the most renowned retroviral specific enzyme, was the first anti-HIV target to be exploited, as. HIV-1 RT combines two functions essential for viral replication: DNA polymerase, synthesis DNA either in a RNA dependent (RDDP) or DNA dependent (DDDP) manner, and Ribonuclease H (RNase H) . The RNase H activity catalyzes highly specific hydrolytic events on the RNA strand of the RNA/DNA replication intermediate, critical to the synthesis of integration-competent double-stranded proviral DNA. Because of its essential role, RNase H is a promising target for drug development. However, despite years of efforts, no RNase H inhibitor (RHI) has yet reached clinical approval. In this work we pursued the identification and characterization of new promising RHIs targeting either the RNase H active site itself (RNase H active site chelating agents) or both RNase H and RDDP activities (allosteric dual inhibitors). The first approach faced the challenging nature of the RNase H active site region, the morphology of wich is, more open than that of the relatively similar,HIV-1 integrase (IN). This hampers the identification of a druggable pocket. We initially used Foamy Virus RT as a tool, to perform NMR and docking analyses on the interaction between FV RT RNase H domain and a previously identified diketo acid (DKA) derivative, inhibitor RDS1643. The amino acid residues of the FV RNase H active site region (T641, I647, Y672 and W703) were established to be important for the interaction with the inhibitor and analogous residues were successfully identified in the HIV-1 RNase H domain using structural overlays. Further docking and site directed mutagenesis studies were performed using six couples of ester/acid DKA, derived from RDS1643, showing for the first time, a broad interaction between RHIs and conserved residues in the HIV-1 RNase H active site region (R448, N474, Q475, Y501 and R557). Moreover, ester and acid derivatives exhibited a different binding orientation, that reflected a different specificity for RNase H versus IN. Among the synthesised derivatives one, RDS1759, showed to be an RNase H selective active site inhibitor characterized also, for the first time,in cell-based assays. The second approach focused on the determination of the mechanism of action of a new isatine-derived RNase H/RDDP dual inhibitor, RMNC6. Docking analysis and site directed mutagenesis results suported the hypothesis of a two-sites mode of action, with an independent role for two pockets,to be further characterized for a rational optimization of the scaffold.
Catalogue of the type material in the entomological collection of the University of La Laguna (Canary Islands, Spain). I. Arachnida

A catalogue of arachnid type specimens of the collection kept at the Department of Animal Biology, University of LaLaguna (Spain) is presented. It harbours type material of 104 species belonging to 23 families of arachnids, representedby 21 holotypes and 164 paratypes for 23 species of pseudoscorpions, and 49 holotypes, 218 paratypes and 3 syntypes for81 species of spiders. This collection is using the criteria and standards of the Global Biodiversity Information Facility(GBIF) for cataloguing and computerization of the specimens. Type specimens were checked with the original descriptions, and relevant additional information from original labels not included in GBIF was registered.
MARKER ASSISTED SELECTION FOR RESPONSE ATTACK OF VENTURIA INAEQUALIS IN DIFFERENT APPLE GENOTYPES

Apple scab caused by Venturia inaequalis, is an important disease, spread worldwide, having a major negative impact in apple production. In this study, there were analyzed four apple cultivars (Liberty, Florina, Starkrimson, Golden Spur), used as genitors in a diallel cross, and their seedlings. In the field, plants selection was done after presence or absence of the scab on leaves, and afterwards, phenotipically selection was completed by marker assisted selection. The molecular analysis conducted with the markers AL-07, AM-19 and U1400, detects the presence of the Vf gene, introgressed from Malus floribunda 821, which confers resistance to the pathogen, in the parental cultivars Liberty and Florina, and in all the F1 hybrids belonging these two genitors. Starkrimson and Golden Spur were susceptible scab parents with recessive homozygous genotype (vfvf), while Liberty and Florina were identified as heterozygous scab resistant parents with genotype (Vfvf). From the 60 apple seedlings analyzed, grouped in six combinations after their genitors (in each combinations were selected ten hybrids, among them five resistant and five susceptible to apple scab attack) 28 were resistant and heterozygous for Vf gene (Vfvf) and 32 were susceptible to scab with recessive homozygous genotypes (vfvf), being obtained almost Mendelian ratio for response to the pathogen, 50% resistant: 50% susceptible. Seedlings belonging to Starkrimson x Golden Spur were only recessive homozygous genotype (vfvf), and in combination resistant x resistant (Liberty x Florina) were identified susceptible and resistant offspring, but at last, only with heterozygous for Vf gene (Vfvf) and no one with dominant homozygous genotypes (VfVf).
Caractérisation fonctionnelle des interactions virus-kinases lors de l'entrée cellulaire du virus de l'hépatite C

Le virus de l'hepatite C (HCV) est une cause majeure de maladie chronique du foie et de carcinome hepatocellulaire. Les options therapeutiques pour traiter l'hepatite chronique sont limitees par des couts eleves, des effets secondaires et une resistance virale. L'entree du HCV est la premiere etape d'interaction entre le virus et la cellule hote. Elle est requise pour l'initiation, la propagation et le maintien de l'infection, ce qui en fait une cible prometteuse pour les traitements antiviraux. L’entree du HCV necessite l'interaction cooperative de plusieurs facteurs cellulaires, y compris CD81 et claudine-1 (CLDN1). Nous avons recemment identifie un role pour le recepteur a l’EGF (EGFR) et le recepteur a l’ephrine A2 (EphA2) dans l'entree du HCV par la regulation de la formation du complexe de co-recepteurs CD81-CLDN1, ce qui suggere que la signalisation de ces recepteurs joue un role dans l'entree du virus. Nous avons voulu identifier les mecanismes moleculaires de signalisation de l’EGFR requis pour l'entree du HCV et avons identifie HRas comme un transducteur de signalisation cle de l'hote. Des etudes d'imagerie ont revelees que la signalisation de HRas peut moduler la diffusion et le trafic membranaire de CD81, ce qui permet l’assemblage du complexe de recepteurs. De plus, HRas s’associe avec les recepteurs de l'hote CD81 et CLDN1 et des facteurs d’entree du HCV inconnus jusque la: l’integrine beta1 et Rap2B. Le HCV profite donc de la signalisation de HRas pour l'entree cellulaire. Ces donnees ameliorent notre comprehension des mecanismes moleculaires de l'entree du HCV induite par l’EGFR et ouvrent de nouvelles perspectives pour le developpement d'antiviraux.
Growth Pattern and Content of Tropane Alkaloids of Metabolic Engineered Scopolia parviflora Hairy Root Lines

Hyoscyamine and scopolamine are two most common tropane alkaloids found in the Solanaceae. The pEB expression vector carrying Nspmt gene was transformed to Agrobacterium rhizogenes. The growth of transgenic hairy roots were approximately to 80% of the wild type root. Transgenic hairy roots are less developed on only their branch roots than those of the wild type root. The extracts from Nspmt transgenic hairy root lines, 3 and 5 contained between 3.52 and 4.23 mg/g dry weight as hyoscyamine and did between 5.23 to 6.40 mg/g dry weight as scopolamine. These results showed that the overexpression of the pmt gene enhanced tropane alkaloids production of S. parviflora transformed roots and this improvement affected both hyoscyamine and scopolamine production.
Profil des vendeurs de viande de chasse et évaluation de la biomasse commercialisée dans les marchés municipaux de Brazzaville, Congo

Durant quatre semaines, une enquěte quantitative et qualitative sur la commercialisation de la viande de chasse a été menée sur 21 marchés de Brazzaville. L'objectif de cette étude était de définir le profil du vendeur et d'évaluer les quantités de viande de chasse commercialisées sur les marchés municipaux enquětés. Les résultats obtenus indiquent que les femmes (52%) ont été les plus impliquées dans ce commerce. Le revenu mensuel moyen d'un vendeur au marché a été estimé à 210 428 (420 USD) ± 49 128 (98,256 USD) FCFA. L'âge moyen des vendeurs était de 39 ± 10 ans et 69% d'entre eux avaient pour niveau scolaire les deux degrés de l'enseignement secondaire. Pendant l'étude, 3 711 carcasses de gibiers ont été répertoriées, représentant une biomasse d'environ 35 790 kg. Au total, 35 espèces dont 9 légalement interdites de chasse ont été inventoriées lors des ventes. Les mammifères constituaient 93,8% des animaux chassés avec trois ordres dominants, les artiodactyles (49,2%), les rongeurs (22,6%) et les primates (17,7%). Parmi ces trois ordres, les céphalophes, les potamochères, les athérures et les cercopithèques étaient les plus représentés. Le piégeage, méthode qui entraîne beaucoup de perte d'animaux, représentait le mode de capture le plus important, suivi de la chasse au fusil. Le Chemin de Fer Congo Océan et la Route Nationale n°2 ont été utilisés régulièrement dans le transport de viande de gibiers, à hauteur de 72%. Cette étude suggère une gestion durable des ressources fauniques et une mise en place d'un cadre légal et réglementaire adapté au contexte actuel du commerce de la viande de chasse au Congo-Brazzaville.
Consequence of 2012 Mw 8.6 Northern Sumatra Earthquakes towards Sundaland Plate

The impact of postseismic decay has been concerned mostly with the edge of plate boundaries. But great earthquakes (larger than M8.0) can cause widespread postseismic decay in areas well beyond any recognised plate boundaries. The Mw 8.6 and 8.2 northern Sumatra doublet earthquakes occurred on 11 April 2012, near the intersection of the Indian, Australian and Sundaland plate, have caused an extensive coseismic offset and postseismic decay over the region. In this study, the longterm GPS time-series (1999 – 2014) suggests that the postseismic decay associated with the 2012 doublet earthquakes have had a significant effect on the eastern boundary of the Sundaland plate up to the western region of Peninsular Malaysia. Before the 2004 Mw 9.1 Aceh and 2005 Mw 8.6 Nias earthquakes, the average velocity of continuous GNSS sites in Peninsular Malaysia is moving 31 ± 2.1 mm/yr southeast relative to ITRF2008. The postseismic decay of these two great earthquakes have caused Peninsular Malaysia to slightly deviate into the south-southeast direction with a lower average velocity by 10 ± 5.5 mm/yr. After 2012 northern Sumatra earthquakes Peninsular Malaysia returns to its original course of motion before the 2004 and 2005 earthquakes, with slightly lower average velocity at 25 ± 2.4 mm/yr. In this paper, the GPS network and availability of data are summarised. Next, the GPS processing strategies and deformation analysis used in this study are discussed. The paper then focuses on the impact of coseismic and postseismic deformation of the 2012 Mw 8.6 and 8.2 northern Sumatra earthquakes towards Sundaland plate vectors. Lastly, a new rotation vector for Sundaland plate is defined in ITRF2008 by using 10 selected cGPS sites that are assumed to be located in the stable block, based on the 1999 – 2004 time-series data.
Comparative analyses of adaptive phenomena in eukaryotic systems

All phenotypic adaptations are encoded in the genome, although untangling the relationships between specific phenotypes and genomic changes is complicated by the fact that at the molecular level, most changes are associated not with selection but neutral processes. Distinguishing between the two is necessary for reliable interpretation of any potential signature of selection. In this respect, this thesis addresses three aspects of genome evolution: biasing factors for the interpretation of protein evolutionary rates, the adaptive significance of presence/absence variation (PAV) in the model plant A. thaliana and the evolution of alternative splicing alongside increasing organism complexity. A comparative genomics approach is used throughout, taking advantage of the increasing availability of high-throughput sequencing data. We show that (i) lineage-specific substitutions and the differential conservation of the edges of exons influence interpretations of protein evolutionary rate, (ii) that PAV in A. thaliana can be explained without invoking adaption, despite enrichments for PAV events in genes considered as positively selected, and (iii) that alternative splicing is amongst the strongest predictors of organism complexity, consistent with an adaptive role of transcript diversification in determining a genome’s functional information capacity. Taken together, we find that the signatures and targets of adaptation can either be masked by, or re-interpreted in the context of, non-adaptive processes and that with the increasing availability of high-throughput data, such considerations are of increasing relevance.
Alternate level clustering for drum transcription

This paper introduces a clustering-based unsupervised approach to the problem of drum transcription. The proposed method is based on a stack of multiple clustering and segmentation stages that progressively build up meaningful audio events, in a bottom-up fashion. At each level, the inherent redundancy of the repeating events guides the clustering of objects into more complex structures. Comparison with state-of-the-art approaches demonstrate the potential of the proposed approach, both in terms of efficiency and of ability to generalize.
Characterization of Arabidopsis thaliana SR protein genes: mutations, alternative splicing, and ESE selection

Title of Document: CHARACTERIZATION OF ARABIDOPSIS THALIANA SR PROTEIN GENES: MUTATIONS, ALTERNATIVE SPLICING, AND ESE SELECTION. Jason Edmonds, Doctor of Philosophy, 2007 Directed By: Associate Professor, Stephen M Mount, Department of Cell Biology and Molecular Genetics RNA processing in eukaryotes is a highly complex process requiring numerous steps and factors that can play roles in the regulation of functional protein production. SR proteins are a well-defined family of splicing factors identified by a conserved RNA Recognition Motif (RRM) and carboxyl-terminal arginine/serine (RS) repeats. SR proteins are known to bind to mRNA precursors via Exonic Splicing Enhancers, and to recruit U2AF and the U1 snRNP to promote splicing. I have identified mutations in five Arabidopsis thaliana SR protein genes that result in altered phenotypes. Two (scl28-1 and srp31-1) result in embryonic lethal phenotypes, while three others (sc35-1, sr45-1, and srp30-1) result in viable and fertile plants with a range of phenotypes. I have also found that mutations in individual SR protein genes can effect the ability of a specific sequence to act as an ESE and hence affect splicing efficiency. Because 16 of the 20 Arabidopsis thaliana SR proteins themselves are alternatively spliced, I have looked for cross regulation using RT-PCR analysis of isoform accumulation in alternatively spliced SR protein genes. I found that SR proteins do, in fact, regulate the alternative splicing of gene targets and do so in both a gene and a tissue specific manner. In order to begin to fully understand the relationship between individual SR proteins it is essential to know when and where they are expressed throughout development. I have studied the expression pattern of 16 of the 20 SR proteins in the roots of wild-type plants as well as sc35-1, srp30-1, and sr45-1 mutants. I have identified both spatial and temporal expression patterns for these 16 proteins relative to specific tissues that compose the root. CHARACTERIZATION OF ARABIDOPSIS THALIANA SR PROTEIN GENES: MUTATIONS, ALTERNATIVE SPLICING, AND ESE SELECTION.
The encyclopedia of fungi of Britain and Europe

The biology of fungi nomenclature and systematics foraying and conservation chemical tests photography Ascomycetes - cup fungi, Morels and Helvellas, truffles, others Homobasidiomycetes - fairy clubs, chanterelles, tooth fungi, encrusting forms and other brackets, agaricales, cortinariales, russulales, boletales, gastromycetes (puff balls etc) heterobasidiomycetes myxomycetes (limited examples).
Swimming performance of lake sturgeon (Acipenser fulvescens)

Fishways have traditionally been designed to provide safe passage for jumping fish and only recently have non-jumping species been considered. Concern over dwindling populations of lake sturgeon (Acipenser fulvesens) has focused attention on fishway designs that accomodate its swinuning abilities. The objective of this study was to derive models that describe swinuning endurance and critical speed (5 crn/s increment, 10 minute interval) for lake sturgeon. Critical speed increased with temperature (7-21° C) and with total length (12-132 cm). Endurance at sustained and prolonged swinuning speeds (those maintainable for more than 20 seconds) increased with temperature but was independent of temperature at higher burst speeds. Endurance increased with total length at all speeds. Swinuning performance of lake sturgeon, relative to body length, is inferior to that of salmonids. Fishway designers need to consider swimming ability, space requirements and behavior of lake sturgeon to ensure them safe passage of migratory obstructions. Sci. 2063,