Miracle-dz/UniFAR-FTUs huggingface dataset:
A classification of Selaginella (Selaginellaceae) based on molecular (chloroplast and nuclear), macromorphological, and spore features

The largest genus of seed-free vascular plants Selaginella alone constitutes the family Selaginellaceae, the largest of the lycophyte families. The genus is estimated to contain ca. 800 species distributed on all continents except Ant-arctica, with the highest species diversity in tropical and subtropical regions. The monophyly of Selaginella has rarely been doubted, in contrast its infrageneric classification has been contentious. In the present study, based on chloroplast and nuclear DNA evidence, macromorphology, spore features, and/or distribution information, Selaginella is classified into six subgenera: S. subg. Selaginella , S. subg. Boreoselaginella , S. subg. Pulviniella , S. subg. Ericetorum , S. subg. Heterostachys , and S. subg. Stachygynandrum . The latter three subgenera are further classified into six, five, and seven sections, respectively. All of these infrageneric divisions, identified with molecular data, are supported by non-molecular features. A key to infrageneric taxa is given. Thirty-seven infrageneric taxa published in earlier literature are lectotypified and classified into those infrageneric taxa here recognized. A nomenclatural account of each infrageneric taxon is given.
Seed dormancy in six cold desert Brassicaceae species with indehiscent fruits

Abstract The dispersal unit of many species of Brassicaceae is an indehiscent fruit, but relatively few studies have tested the effect of the pericarp on seed germination in this family. Our aim was to determine the effect of the pericarp on seed dormancy in six species of Brassicaceae native to the cold desert of north-west China. Intact dispersal units and isolated seeds of Chorispora sibirica, Euclidium syriacum, Goldbachia laevigata, Spirorrhynchus sabulosus, Sterigmostemum fuhaiense and Tauscheria lasiocarpa were stored dry at ambient laboratory conditions for 0–12 months and tested for germination in light and in dark at 5/2, 15/2 and 30/15°C. The amount of water absorbed by fruits and by seeds within the fruits was determined. For four species, intact fruits, isolated seeds and isolated seeds plus the removed pericarps were used to test for the mechanical versus possible chemical role of the pericarp in seed dormancy. Fresh isolated seeds, which have a fully developed embryo, germinated to lower percentages and rates than afterripened seeds. Thus, seeds have non-deep physiological dormancy. The pericarp significantly reduced germination, but inhibition was not due to lack of water uptake by seeds or to chemical inhibitors. Afterripened seeds of the six species germinated to 0–50% inside the fruits. We conclude that the pericarp plays a dominant role in seed dormancy of the six study species, and it does so by mechanically restricting embryo growth. Thus, the pericarp has the potential to spread germination over an extended period of time.
INFLUENCE OF SOLE GRASSES AND GRASS-LEGUME MIXTURES ON QUALITY ESTIMATION USING IN VITRO GAS PRODUCTION TECHNIQUE

The research was carried out to evaluate the effect of forage mixtures on the nutritive quality of Stylosanthes hamata legume , Panicum maximum and Pennisetum purpureum grasses. Stylosanthes hamata was harvested at five months after sowing while P. maximum and P. purpureum were harvested at eight weeks after planting. The experiment was a completely randomised design with forage proportion of 100% grass or legume and grass-legume mixture of 50%:50%, 75%:25%, 25%:75% replicated three times. There were significant (P<0.05) differences in all the parameters investigated. The crude protein content ranged from 8.94% in sole P. maximum to 14.12 % in sole S. hamata while neutral detergent fibre ranged from 42.00 in sole S. hamata to 65.00% in sole P. purpureum. Sole S. hamata produced the highest gas at 48 h of incubation while the least gas volume was recorded for sole grasses. Increased gas production was observed in the mixtures than in sole grasses. Metabolisable energy value ranged from 6.20 MJ kg -1 DM -1 in sole P. purpureum to 9.09 MJ kg -1 DM -1 in sole S. hamata . Potential gas production from the insoluble fraction of the forage species ranged from 15.65 in sole P. maximum to 17.01 ml/200mgDM in sole S. hamata . From this study it can be concluded that grass-legume mixtures are the most appropriate feed for ruminants based on their higher nutritive qualities than in sole grasses.
Cytological Effects of Mutagenic Agents and NaCl on Mitotic Division in Two Iraqi Rice (Oryza sativa L.) Genotypes

This study was carried out to determine the effects of NaCl (0.00, 50, 100, 150, 180 or 200) mM and two different types of mutagens chemical mutagen ethyl methyl sulphonate (EMS) at 0.5% and physical mutagen UV-B irradiation (40 min time exposure), on mitotic division in two Iraqi rice genotypes Amber 33 (A33) and Amber Baghdad (AB). Different concentrations of NaCl were used. Mitotic index (MI %) was decreased significantly by increasing NaCl concentration, however the highest mitotic index was recorded in mutated genotypes with EMS and UV-B. Different abnormal chromosomes were noticed in mutated plants. Results showed high percentage of abnormal chromosomes in EMS mutated genotypes. In addition no significant differences between genotypes in mean of mitotic index with respect to all experiments. [DOI: 10.22401/JNUS.20. 1.16]
Taxonomic status of two morphotypes of Coryphaena hippurus (Perciformes: Coryphaenidae)

Dois morfotipos de Coryphaena hippurus (dourado e palombeta) encontrados ao longo da costa brasileira sao considerados especies diferentes por pescadores e mercadores das regioes de desembarque do estado do Rio de Janeiro. Alem disso, esses morfotipos sao comercializados por valores diferentes e sofrem diferentes pressoes de pesca. Desta forma, a definicao do status taxonomico desses morfotipos e importante, tanto em termos economicos quanto biologicos. A fim de investigar esse problema foi utilizado o metodo de eletroforese de aloenzimas com a amostragem de dezessete loci para 117 individuos dos dois morfotipos de C. hippurus obtidos em desembarques pesqueiros na regiao de Cabo Frio/RJ (Brasil). Os dados indicaram uma homogeneidade entre os conjuntos genicos dos morfotipos. A despeito disso, diferencas entre os conjuntos genicos de dourado e palombeta foram encontradas, devido, especialmente, ao locus alcool desidrogenase. A hipotese de selecao natural e discutida como possivel explicacao para esses resultados.
A standard operating procedure for outlier removal in large-sample epidemiological transcriptomics datasets

Transcriptome measurements and other –omics type data are increasingly more used in epidemiological studies. Most of omics studies to date are small with samples sizes in the tens, or sometimes low hundreds, but this is changing. Our Norwegian Woman and Cancer (NOWAC) datasets are to date one or two orders of magnitude larger. The NOWAC biobank contains about 50000 blood samples from a prospective study. Around 125 breast cancer cases occur in this cohort each year. The large biological variation in gene expression means that many observations are needed to draw scientific conclusions. This is true for both microarray and RNA-seq type data. Hence, larger datasets are likely to become more common soon. Technical outliers are observations that somehow were distorted at the lab or during sampling. If not removed these observations add bias and variance in later statistical analyses, and may skew the results. Hence, quality assessment and data cleaning are important. We find common quality assessment libraries difficult to work with for large datasets for two reasons: slow execution speed and unsuitable visualizations. In this paper, we present our standard operating procedure (SOP) for large-sample transcriptomics datasets. Our SOP combines automatic outlier detection with manual evaluation to avoid removing valuable observations. We use laboratory quality measures and statistical measures of deviation to aid the analyst. These are available in the nowaclean R package, currently available on GitHub (https://github.com/3inar/nowaclean). Finally, we evaluate our SOP on one of our larger datasets with 832 observations.
Mutation rates in seeds and seed-banking influence substitution rates across the angiosperm phylogeny

1) Background Seed-banking (the ability to persist in the soil over many generations) is usually considered as a dormant stage where genotypes are “stored” as a bet-hedging strategy in response to unpredictable environments. However, seed dormancy may instead have consequences for the integrity of the DNA and generate novel mutations. 2) Methods We address this paradox by building phylogenies based on the plastomes and nuclear ITS of species belonging to ten angiosperm clades. In each clade, the substitution rate (branch-length) of a seed-banking species is compared with that of a closely-related non-seed-banking species. 3) Results Seed-banking species show as high or higher substitution rates than non-seedbanking species, and therefore mutations occur in dormant seeds at a rate at least as high as in above-ground plants. Moreover, seed born mutations have the same probability to reach fixation as those from above ground. Our results are robust to differences in selection, generation time, and polymorphism. 4) Conclusions Mutations occurring in seeds, and thus seed-banking, affect the population diversity of plant species, and are observable at the macro-evolutionary scale. Our study has consequences for seed storage projects, since the stored seeds are likely to accumulate mutations at a higher rate than previously thought.
In vitro-assisted single-seed descent for breeding-cycle compression in subterranean clover (Trifolium subterraneum L.)

Abstract. Subterranean clover (Trifolium subterraneum L.) is widely grown for its forage and ability to fix atmospheric nitrogen. Development of new varieties is constrained by the slow turnover time of generations, with only one generation per year possible under field conditions. We present an in vitro-assisted single-seed descent (IVASSD) technique, which enabled turnover of 2.7–6.1 generations per year across a diverse range of 27 T. subterraneum cultivars encompassing subspecies subterraneum, yanninicum and brachycalycinum. The IVASSD protocol accelerated the generation cycle in two ways: (i) time to floral initiation was minimised by growth under controlled temperature and extended photoperiod; and (ii) the seed-filling period was truncated and embryo and seed-coat dormancy avoided by the in vitro germination of immature seed on B5 medium plus L6KK overlay (0.525 mg gibberellic acid and 1.5 mg indole-butyric acid L–1). For the first time, an IVASSD system was validated on a full-scale breeding population with the production of 175 F7 recombinant inbred lines from an F4 population in less than one year. All F7 plants obtained were morphologically normal and fertile.
Numerical simulation of subsynoptic-scale cyclogenesis around an idealized antarctic continent / Simulación numérica de ciclogénesis a escala subsinóptica alrededor de un continente antártico idealizado

Abstract A three-dimensional numerical model of 100- km horizontal resolution was used to simulate subsynoptic-scale cyclogenesis around an idealized Antarctic continent. The simulation resolved a series of subsynoptic-scale cyclones around the idealized continent. These cyclones form adjacent to the confluence zones of katabatic winds. Their movements indicate an eastward direction going away from their initial point of formation. Baroclinic instability appears as primary mechanism for the development of these cyclones. Resumen Un modelo numerico tridimensional de 100 km de resolucion horizontal, fue utilizado para simular ciclogenesis a escala subsinoptica alrededor de un continente antartico idealizado. La simulacion resuelve una serie de centros depresionarios alrededor del continente idealizado. La formacion de los ciclones ocurre adyacentes a las zonas de convergencia del flujo de vientos catabaticos. Su desplazamiento indica una direccion al este alejandose de su area de formacion inicial. La inestabilidad baroclinica aparece como mecanismo primario para el desarrollo de estos ciclones
Taxonomy of actinomycetes in the deep-sea Calyptogena communities and characterization of the antibacterial compound produced by Actinomadura sp. DS-MS-114

ABSTRACT Fifteen actinomycetes were isolated from deep-sea sediments in Calyptogena communities in the Japan Trench (depth: 5352 m) and Sagami Bay (depth: 1171 m) under incubation at 4–37 °C. A relatively large number of colonies were obtained with incubation at 30 °C from the deep-sea sediment of Sagami Bay. We found Rhodococcus, Nocardioides and Micromonospora actinomycetes in both sediments, and additionally isolated an Aeromicrobium actinomycete from the Japan Trench and Streptomyces and Actinomadura actinomycetes from Sagami Bay. Actinomadura sp. DS-MS-114 isolated from the deep-sea sediment in Sagami Bay produced an antibacterial compound against Staphylococcus aureus NBRC12732T. Structural analysis by liquid chromatography–high-resolution electrospray ionization mass spectrometry (LC-HRESIMS) and proton nuclear magnetic resonance (1H-NMR) indicated that the antibacterial compound was 5,6-dihydro-1,8-dihydroxy-3-methylbenz[a]anthracene-7,12-quinone, which is known as an immunosuppressant. The deep-sediment in the Calyptogena community may be useful as a source of various actinomycetes producing physiologically active substances.
Investigation on Antioxidant Compounds from Marine Algae Extracts Collected from Binuangeun Coast, Banten, Indonesia

Marine algae contains bioactive secondary metabolites that have potential to be developed as antioxidant. The aims of this research were to investigate antioxidant activity and total phenolic compound of marine algae collected from Binuangeun Beach, Banten and to characterize antioxidant compounds from selected algae species. Antioxidant activity was determined by 1,1-diphenyl-2-picrylhydrazyl radical (DPPH) assay and Ferric Ion Reducing Antioxidant Power (FRAP) Assay, while total phenolic content was estimated by Folin-Ciocalteau method. Isolation of bioactive antioxidant compound was performed using SiO2 column chromatography and preparative high performance liquid chromatography (HPLC). The antioxidan activity evaluation was conducted to methanol extracts from 20 species (7 Chlorophyta, 9 Phaeophyta and 4 Rhodophyta). Results showed that Padina australis extract was found to be the most active. The major bioactive antioxidant compound was identified as fucoxanthin and a polar compound that was suspected as phenolic compound. The extracts of P. australis presented the highest phenolic content (58.59 mg GAE/g). A significant correlation between antioxidant capacity and total phenolic content was found, indicating that phenolic compounds are the major contributors to the antioxidant properties of P. australis.
High-throughput analysis of endogenous fruit glycosyl hydrolases using a novel chromogenic hydrogel substrate assay

A broad range of enzyme activities can be found in a wide range of different fruits and fruiting bodies but there is a lack of methods where many samples can be handled in a high-throughput and efficient manner. In particular, plant polysaccharide degrading enzymes – glycosyl hydrolases (GHs) play an important role in fruit development and ripening processes by modulating the plant cell wall. Knowledge about these enzymes is important for research in fruit development and also important for industry regarding postharvest properties. Although advances in genetic control and cell wall biochemistry have led to a more profound understanding of the importance of GH activity and regulation, current methods for determining glycosyl hydrolase activity are lacking in throughput and fail to keep up with data output from transcriptome research. Here we present the use of a versatile, easy-to-handle, multiplexed and highly reproducible method using CPH assays where different fruits have been screened for enzyme activity. Additionally, the importance and impact of the extraction method and buffer conditions on the assay are investigated. We will show that one experimental setup can be used for testing all enzymes.
Proteomic Profiling of Mammalian COPII Vesicles

Intracellular transport and homeostasis of the endomembrane system in eukaryotic cells depend on formation and fusion of vesicular carriers. COPII vesicles export newly synthesized secretory proteins from the endoplasmic reticulum (ER). They are formed by sequential recruitment of the small GTP binding protein Sar1, the inner coat complex Sec23/24, and the outer coat complex Sec13/31. In order to investigate the roles of mammalian Sec24 isoforms in cargo sorting, we have combined in vitro COPII vesicle reconstitutions with SILAC-based mass spectrometric analysis. This approach enabled us to identify the core proteome of mammalian COPII vesicles. Comparison of the proteomes generated from vesicles with different Sec24 isoforms confirms several established isoform-dependent cargo proteins, and identifies ERGIC1 and CNIH1 as novel Sec24C‐ and Sec24A-specific cargo proteins, respectively. Proteomic analysis of vesicles reconstituted with a Sec24C mutant, bearing a compromised binding site for the ER-to-Golgi QSNARE Syntaxin5, revealed that the SM/Munc18 protein SCFD1 binds to Syntaxin5 prior to its sorting into COPII vesicles. Furthermore, analysis of Sec24D mutants implicated in the development of a syndromic form of osteogenesis imperfecta showed sorting defects for the three ER-to-Golgi QSNAREs Syntaxin5, GS27, and Bet1.
The importance of facilitative interactions on the performance of Colobanthus quitensis in an Antarctic tundra

1Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile 2Instituto de Ecología y Biodiversidad (IEB), Santiago, Chile 3Laboratorio de Fisiología y Biología Molecular Vegetal, Instituto de Agroindustria, Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Forestales, Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile 4Laboratorio Cultivo de Tejidos Vegetales, Centro de Biotecnología, Departamento de Silvicultura, Facultad de Ciencias Forestales, Universidad de Concepción, Concepción, Chile
Structure of the Main Olfactory Bulb and Immunolocalisation of Brain-Derived Neurotrophic Factor in the Olfactory Layers of the African Grasscutter (Thryonomys swinderianus - Temminck, 1827)

The present study has provided some novel findings on the structure of the olfactory bulb in the African grasscutter, by basic neuro-anatomical technique and immunhistochemical technique, using antibody specific to brain-derived neurotrophic factor. Brain samples extracted from neonates on postnatal day 3, juveniles on postnatal day 72 and adults on postnatal day 450 were utilised for the study. There was a consistent increase in the relative weight of the olfactory bulb with advancement in age, but a significant (P < 0.05) decrease in the relative length from 20.81 ± 0.37 on postnatal day 3 to 17.75 ± 0.45 on postnatal day 72. The concentric lamina organization of the olfactory bulb was evident on postnatal day 3, but the glomerular layer was completely absent. The layer was evident on postnatal days 72 and 450. The mean diameters of each glomerulus on postnatal days 72 and 450 were 86.82 ± 0.25 µm and 117.14 ± 0.32 µm, respectively. The difference was significant (P < 0.05). The zones of the external plexiform layer were undifferentiated on postnatal day 3. There was a decrease in the number of mitral cell lines, but increase in size of each mitral cell, with advancement in age. Brain-derived neurotrophic factor was moderately immunolocalised in the olfactory nerve layer on postnatal day 3, but negative on postnatal days 72 and 450. Cell bodies of the periglomerular short-axon neurones mildly expressed brain-derived neurotrophic factor on postnatal days 72 and 450. The granule cells did not express brain-derived neurotrophic factor on all postnatal periods. The functional significance of the results was discussed.
Field experiment on longevity of the seeds in the soil seed bank (initial seed burial experiment at the University of Natural Resources and Life Sciences (BOKU)

70 packages (bags of fine net-like polyethylene tissue) with common ragweed seeds collected in 2010 from an arable field nearby Unterpurkla, in Styria, Austria (each net filled with 50 seeds) were buried in the soil at 10 cm depth in early spring 2011. Every year in spring the germination test procedure will be performed on the seeds of a subsample of 7 randomly selected bags. Additionally every year the germinability of seeds from the same base sample stored continuously at 4°C under dry conditions will be tested.
Allopatric divergence and secondary contact without genetic admixture for Arichanna perimelaina (Lepidoptera: Geometridae), an alpine moth endemic to the Hengduan Mountains

Mountain systems, especially at high altitudes, are an excellent model for determining the mechanisms underlying high species diversity and endemism. Herein, we elucidate the evolutionary history of the alpine moth Arichanna perimelaina (Wehrli), which is endemic to the Hengduan Mountains (HM) region in southwest China, based on three mitochondrial genes and two nuclear genes. Our results revealed six deeply divergent clades that corresponded to populations in different mountain systems in the HM region. Bayesian divergence time estimations suggested a mid‐ to late Pleistocene genetic divergence. The results also showed that the Mt Yulong (YL) region was a refugium and valley corridors established by glaciation during the Pleistocene allowed populations on the separate mountains to migrate. The reproductive isolation among the different clades on contact zone in the YL region may be associated with the asynchronous mating rhythms and/or the divergent mate recognition caused by the ecological source of divergent selection. Allopatric divergence associated with complex topographies and climatic oscillations, regional dispersal via valley corridors and the suitable refugium of the YL region shaped the genetic divergence and distribution pattern of A. perimelaina in the HM region. These findings highlight the essential role of complex terrain and climatic fluctuations in shaping the unique phylogeographic history of a narrow alpine moth, and provide insights into the mechanisms underlying high species richness and endemism in the HM region.