Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of arachidonic acid supplementation and cyclooxygenase/lipoxygenase inhibition on the development of early bovine embryos

The effect of arachidonic acid (AA) cascade on bovine embryo development in a granulosa cell co-culture system was studied. Arachidonic acid (100 µM) was supplemented from 1-cell to 8-16 cell block stage (first three days of co-culture) and from 1-cell to hatching. Specific cyclooxygenase (indomethacin, 28 µM) and lipoxygenase (nordihydroguaiaretic acid - NDGA, 28 µM) inhibitors were used from 1-cell to 8-16 cell block stage with AA. Embryo development was assessed by cleavage, day 7-day 8 and hatched embryo rates and by measuring growth rates through development stages found in days 7-10 of culture (day 0 = insemination day). Embryo quality was scored at day 8. A 6.5-10.4% increase on cleavage rate after AA supplementation was found. This AA supplementation from 1-cell to hatching delayed embryo growth rate beyond day 7 and a reduction on hatching rate was detected. When AA supplementation was restricted to the first three days of co-culture those negative effects were overcome. Also, indomethacin and NDGA prevented the positive effect of AA and induced a significant reduction on cleavage, respectively. NDGA further decreased day 7 embryo rate and quality. Results suggest that AA has a two-phase action on bovine embryos, promoting early development and impairing embryo growth from day 7 onwards and hatching rates. Both cyclooxygenase and lipoxygenase were found to be important pathways to promote cleavage.
The presence–absence matrix reloaded: the use and interpretation of range–diversity plots

Aim A great deal of information on distribution and diversity can be extracted from presence–absence matrices (PAMs), the basic analytical tool of many biogeographic studies. This paper presents numerical procedures that allow the analysis of such information by taking advantage of mathematical relationships within PAMs. In particular, we show how range–diversity (RD) plots summarize much of the information contained in the matrices by the simultaneous depiction of data on distribution and diversity. Innovation We use matrix algebra to extract and process data from PAMs. Information on the distribution of species and on species richness of sites is computed using the traditional R (by rows) and Q (by columns) procedures, as well as the new Rq (by rows, considering the structure of columns) and Qr (by columns, considering the structure by rows) methods. Matrix notation is particularly suitable for summarizing complex calculations using PAMs, and the associated algebra allows the implementation of efficient computational programs. We show how information on distribution and species richness can be depicted simultaneously in RD plots, allowing a direct examination of the relationship between those two aspects of diversity. We explore the properties of RD plots with a simple example, and use null models to show that while parameters of central tendency are not affected by randomization, the dispersion of points in RD plots does change, showing the significance of patterns of co-occurrence of species and of similarity among sites. Main conclusion Species richness and range size are both valid measures of diversity that can be analysed simultaneously with RD plots. A full analysis of a system requires measures of central tendency and dispersion for both distribution and species richness.
Does trophy hunting matter to long‐term population trends in African herbivores of different dietary guilds?

The persistence of large African herbivores in trophy hunting areas is still unclear because of a lack of data from long‐term wildlife monitoring outside national parks. We compared population trends over the last 30 years in Hwange National Park, Zimbabwe, and the neighbouring Matetsi Safari Area where large herbivores were harvested at an average yearly rate of 2%. We investigated whether trophy hunting altered densities and the proportion of adult males in several large herbivore species. Large herbivores generally thrived as well, or even better, in the hunting areas than in the national park. The proportion of adult males did not differ between the two zones, except for species with higher harvest rates and proportionally more males harvested. Densities were not lower in the hunting areas than in the national park, except for elephant and impala. Large herbivores generally declined throughout the 30‐year period in both zones, particularly selective grazers. This is probably because of their greater sensitivity to variation in rainfall compared with other herbivores. Rainfall indeed declined during the study period with droughts being particularly frequent during the 1990s. Browsers, mixed feeders and non‐selective grazers generally declined less in the hunting areas than in the national park, possibly because of lower densities of natural predators and elephants outside the park. Our study highlighted that large herbivores may persist in trophy hunting areas as well as in national parks. When rigorously managed, trophy hunting areas may be relevant conservation areas for large herbivores, particularly under the current global decline of wildlife abundance across Africa.
Differentiation of Photorespiratory Activity between Mesophyll and Bundle Sheath Cells of C4 Plants I. Glycine Oxidation by Mitochondria

Mitochondria were isolated from mesophyll protoplasts and bundle sheath protoplasts or strands which were obtained by enzymatic digestion of six C4 species: Zea mays, Sorghum bicolor, Panicum miliaceum, Panicum capillare, Panicum maximum and Chloris gayana, representative of three C4 types. Photorespiratory glycine oxidation and related enzyme activities of mesophyll and bundle sheath mitochondria were compared. Mesophyll mitochondria showed good P/O ratios with malate and succinate as substrate but lacked the ability to oxidize glycine. On the other hand, mitochondria isolated from bundle sheath protoplasts of P. miliaceum and bundle sheath strands of Z. mays possessed glycine oxidation activity similar to that of mitochondria from C3 plant leaves. The two enzymes involved in glycine metabolism in mitochondria, serine hydroxymethyltransferase and glycine decarboxylase, were also assayed in the mitochondria of the two cell types. The activities of the two enzymes in bundle sheath mitochondria were in the range found in C3 mitochondria. In contrast, the activities in mesophyll mitochondria were either not detectable or far lower than those in bundle sheath mitochondria and ascribed to contaminating bundle sheath mitochondria. The present results indicate the deficiency of a complete glycine oxidation system in mesophyll mitochondria and also a differentiation between mesophyll and bundle sheath cells of C4 plants with respect to the photorespiratory activities of the mitochondria.
Partial genome transfer through micronuclei in plants

Introduction 97 Microcell hybridization: a historical and methodological summary 99 Micronucleation in plant cells 100 Cell division activity 102 Species/genotype 103 Plant tissue 103 Synchronization 103 Sequential treatments 105 Methods 105 Isolation of micronucleated protoplasts 105 Micronuclei 105 Isolation 105 Enrichment 105 Transfer 106 Microprotoplasts 107 Isolation 107 Enrichment 108 Fusion 108 Perspectives 109
Climacium (Climaciaceae): species relationships and biogeographic implications

Abstract Climacium is a small but morphologically distinctive genus (“tree mosses”) with four species distributed primarily in the Northern Hemisphere. Climacium dendroides occurs around the globe at northern latitudes with disjunct populations in Mexico and New Zealand, whereas C. americanum and C. kindbergii are endemic to eastern North America and C. japonicum is limited to eastern Asia. Using nucleotide sequence data from five plastid loci plus the nuclear ribosomal ITS region we assessed evidence for monophyly of taxonomic species and tested the hypothesis that C. americanum and C. kindbergii from eastern North America have a sister group relationship with C. japonicum from eastern Asia. Climacium japonicum is resolved as sister to a clade containing the circumboreal C. dendroides, C. americanum, and C. kindbergii. Climacium americanum and C. kindbergii were not resolved as monophyletic based on sequence data but together they composed the sister lineage to C. dendroides. Geographically disjunct populations of C. dendroides in Asia, Mexico, the United States, and Canada vary at only a few polymorphic nucleotide sites across the three loci. The disjunctive New Zealand plants of C. dendroides are related to Asian accessions.
Interpretations and Comparisons of Constants in the Species-Area Relationship: An Additional Caution

Les precautions prealables sur la fausse interpretation de la valeur de Z (S=CA z : S=abondance des especes, A=zone, C et Z constantes) sont soulignees. L'exposant peut etre surestime et le cœfficient sous estime et ainsi compromettre les conclusions de comparaison entre des groupes d'archipels ou taxonomiques
Identification of an IQGAP1/AKAP79 complex in β‐cells

IQGAP1, is a recently discovered scaffold protein proposed to regulate membrane cytoskeleton events through protein–protein interactions with F‐actin, E‐cadherin, β‐catenin, and CLIP170. The binding of IQGAP1 to its partners is regulated by calcium/calmodulin (Ca++/CaM) and the small molecular weight guanine nucleotide triphosphatases (GTPases), Cdc42, and Rac1. Here we identify a novel IQGAP1 scaffolding function by isolating the cyclic AMP dependent kinase (PKA) with IQGAP1. IQGAP1 was co‐purified with PKA using 5′‐cyclic AMP (cAMP) affinity chromatography and PKA activity was co‐immunoprecipitated with IQGAP1 using an anti‐IQGAP1 antibody. The association of IQGAP1 with PKA was shown to occur through a direct interaction between A kinase anchoring protein 79 (AKAP79) and the carboxyl‐terminal domain of IQGAP1. This suggests that cAMP/PKA may be coupled with Ca++/CaM and GTPases through an IQGAP1/AKAP79 complex. J. Cell. Biochem. 90: 97–108, 2003. © 2003 Wiley‐Liss, Inc.
Breeding of Flocculent Industrial Saccharomyces cerevisiae Strains by Introducing the Flocculation Gene FLO1(Microbiology & Fermentation Industry)

We have cloned a DNA fragment bearing the putative FLO1 gene that controls flocculence in Saccharomyces cerevisiae and showed that the cloned gene is on chromosome 1. The flocculation property conferred by the cloned gene in a YCp-type plasmid (single-copy plasmid) was diminished in MATa/MA α cells, which suggests that the expression of the putative FLO1 gene may be repressed by the MAT information. Introduction of the DNA fragment in a YRp-type plasmid (multi-copy plasmid) into several non-flocculent industrial yeast strains, including bottom- and top-fermenting brewing yeasts, and those for making whisky, wine, sake, and shochu could convert them to flocculent ones.
Application of nonlinear regression analysis to the estimation of kinetic parameters for two enterotoxigenic strains ofBacillus cereus spores

Abstract Two enterotoxigenic Bacillus cereus strains, isolated from cooked chilled foods containing vegetables, were characterized in relation to safe food production by studying their heat resistance characteristics. The kinetic parameters of thermal resistance were determined by one-step nonlinear regression and were compared with those calculated by using two linear regressions. Results showed that the new analysis methodology applied in this study can improve the estimation ofD - and z - values. Great differences were found in the thermal resistance of the two strains. TheD90°C were 4·04 and 39 min for the AV TZ415 and AV Z421 strains respectively. Growth studies indicated that the two strains were able to grow at refrigeration temperatures, but the minimum growth temperature for the AV Z421 strain was 10°C, while the less heat-resistant strain, AV TZ415, grew at 5°C.
Induction and Proliferation of Adventitious Roots from 'Aloe vera' Leaf Tissues for 'in vitro' Production of Aloe-emodin

We have inspected aloe-emodin and aloin compounds in different tissues of 'Aloe vera' which were grown in Aloe farm for three years. Surprisingly, aloe emodin contents were much richer in the roots (574.8 92.4 μg/g) than in leaves (5.52 0.32 μg/g) that encouraged us to establish adventitious root culture system of the plant. The optimal condition for induction and proliferation of adventitious roots using young 'Aloe vera' leaves was established by treatments of variety of conditional media and auxin supplements. Adventitious root induction was suitable by enrichment of 0.5 mg/L 1-naphthalene acetic acid (NAA) and 0.2 mg/L 6-benzylaminopurine (BA) in Murashige and Skoog (MS) medium. However root proliferation was hindered by accumulation of phenolic compounds in the media that was overcome by pre-washing of the adventitious roots with more than 4 g/L of polyvinylphyrollidine (PVP) analogs increasing the survival rate (up to 60 %). Inspection of aloe-emodin contents in various adventitious roots grown different basal medium revealed that aloe-emodin accumulation is much higher on B5 medium (133.08 0.12 μg/g) than on MS medium (3.56 0.26 μg/g).
Cytomegalovirus-specific T-cell dynamics in HIV infection

T Inn order to detect epitope-specifi c CD4 T cells in mycobacteria l or viral infections in thee context of human class II major histocompatibilit y complex protein HLA-DR3, twoo novel HLA-DR3 tetrameri c molecules were produced successfully . One containedd an immunodominant , HLA-DR3 -restricted T-cel epitope derived from the 655 kDa heat shock protein of Mycobacterium tuberculosis, peptide 1-13. For the other tetramer ,, we identified a new HLA-DR3-restricted T-cel epitope derived from cytomegaloviruss pp65 lower matrix protein, peptide 510-522, which induced high levelss of IFNy-producing CD4 T cells in three out of four HLA-DR3-positive cytomegalovirus-seropositiv ee individuals up to 0.87% of CD4 T cells by intracellular cytokinee staining. In PBMC from Mycobacterium tuberculosis-exposed, M. bovis BCG-vaccinate dd or cytomegalovirus-seropositiv e individuals, we were able to directlyy detect with both tetramer s epitope-specifi c T cells up to 0.62% and 0.45% of thee CD4 T-cel population reactive to Mycobacterium tuberculosis and CMV, respectively. After a six-day culture with peptide p510-522, the frequency of CMVspecificc tetramer-binding T cells was expanded up to 9.90% tetramer CFSE cells withinn the CD4 T-cel population, further confirming the specificity of the tetrameri c molecules. Thus, HLA-DR3/peptide tetrameri c molecules were shown to be promisingg clinical tools to investigat e HLA-DR3-restricted antigen-specifi c CD4 Tcellss in clinical disease or following vaccination in detail.
Probabilistic Reference to Suspect or Victim in Nationality Extraction from Unstructured Crime News Documents

There is valuable information in unstructured crime news documents which crime analysts must manually search for. To solve this issue, several information extraction models have been implemented, all of which are capable of being enhanced. This gap has created the motivation to propose an enhanced information extraction model that uses named entity recognition to extract the nationality from crime news documents and coreference resolution to associate the nationality to either the suspect or the victim. After the proposed model extracts the nationality, it references it to the suspect or victim by looking up all of the victim related keywords and the suspect related keywords within the text, and their corresponding distances from the position of the nationality keyword. Based on their total distances, a probability score algorithm decides whether the nationality is more likely to belong to either the victim or the suspect. Two experiments were conducted to evaluate the nationality extractor component and the reference identification component used by the model. The former experiment had achieved 90%, 94%, and 91% for precision, recall, and F-measure values respectively. The latter experiment had achieved 65%, 68%, and 66% for precision, recall, and F-measure respectively. The model had achieved promising results after evaluation. Keywords: information extraction, named entity recognition, coreference resolution, crime domain
Conservation implications of adaptation to tropical climates from a historical perspective

Tropical climates and the biodiversity associated with them have long interested natural historians. Alexander von Humboldt inspired a generation of scientists, such as Charles Darwin and Alfred Russel Wallace, to observe and study tropical ecosystems. More recently, the mid‐20th century saw Theodosius Dobzhansky and Daniel Janzen lay the foundations for studying adaptation to tropical climates. Now in the 21st century, we are beginning to realize the threats posed by current and future climate change to tropical populations which, despite relatively low levels of projected warming for low‐latitude regions, face potentially significant detrimental impacts. Building on the insights of researchers in decades and centuries past, improved understanding of tropical ecology, evolution and biogeography will help us to conceive how future global change will impact on biodiversity.
Host range expansion of native insects to exotic trees increases with area of introduction and the presence of congeneric native trees

Summary Exotic tree species are widely used in forest plantations for their often high productivity and performance compared to native trees. However, these advantages may be compromised by herbivore damage. A list of European insect species that have expanded their host range to one of 28 exotic tree species introduced to Europe was compiled from a systematic literature review. The number of successful expansions was analysed using three predictors: (i) phylogenetic relatedness between exotic and European tree species; (ii) area covered by exotic tree species in Europe; and (iii) time since their introduction into Europe. In total, 590 host expansions of native insects to exotic trees were found, mainly of polyphagous species (43%); 25% of the cases reported some type of damage. Bark and wood borers, and defoliators were the dominant guilds. The number of recruited native insect species and cases where major damage occurred was positively correlated with the geographical extent of exotic trees in Europe and the presence of congeneric native trees. Synthesis and applications. The use of exotic tree species creates opportunities for native insect herbivores to expand their host range and increase their damage if they are widely planted next to native congeners. Risk assessment studies are recommended when introducing new tree species for forestry plantations. Risk assessments should include trials on susceptibility to any potential damaging organisms in the introduced range.
Introgression and phylogeography of Betula nana (diploid), B. pubescens (tetraploid) and their triploid hybrids in Iceland inferred from cpDNA haplotype variation

Aim The objective was to find direct genetic evidence supporting introgressive hybridization between tetraploid tree birch (Betula pubescens) and diploid dwarf birch (B. nana), via triploid hybrids, and to investigate an association between the introgression and phylogeographical distribution of Icelandic birch.
Twelve novel polymorphic microsatellites in a marine fish species, yellow croaker Larimichthys polyactis

We isolated 12 polymorphic microsatellites from an important marine food fish Larimichthys polyactis and characterized them in 32 unrelated individuals. Among the 12 microsatellites, four were tetranucleotide repeats and eight were dinucleotide repeats. The allele number ranged from five to 25 with an average of 15.4/locus; average expected heterozygosity was 0.81, ranging from 0.57 to 0.95, whereas the observed heterozygosity ranged from 0.34 to 1.00 (average: 0.78). Nine of the 12 markers conformed to Hardy–Weinberg equilibrium and showed no sign of linkage. These microsatellites will be useful for population genetic studies and selective breeding programs of this species.
Lignocellulosic biomass: Biosynthesis, degradation, and industrial utilization

Lignocellulose biomass derived from plant cell walls is a rich source of biopolymers, chemicals, and sugars, besides being a sustainable alternative to petrochemicals. A natural armor protecting living protoplasts, the cell wall is currently the target of intense study because of its crucial importance in plant development, morphogenesis, and resistance to (a)biotic stresses. Beyond the intrinsic relevance related to the overall plant physiology, plant cell walls constitute an exquisite example of a natural composite material that is a constant source of inspiration for biotechnology, biofuel, and biomaterial industries. The aim of the present review is to provide the reader with an overview of the current knowledge concerning lignocellulosic biomass synthesis and degradation, by focusing on its three principal constituents, i.e. cellulose, hemicellulose (in particular xylan), and lignin. Furthermore, the current industrial exploitation of lignocellulose from fast growing fibre crops (such as hemp) is highlighted. We conclude this review by suggesting approaches for further research to fill gaps in our current knowledge and to highlight the potential of biotechnology and bioengineering in improving both biomass biosynthesis and degradation.