Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of mannitol metabolism genes in Saccharina explains its key role in mannitol biosynthesis and evolutionary significance in Laminariales

As a unique photosynthetic product in brown algae, mannitol exhibits high synthesis and accumulation in Saccharina japonica. Mannitol acts as a carbon-storage compound and is an osmoprotectant, imparting increased tolerance to osmotic stress. However, the underlying biochemical and molecular mechanisms in macroalgae have not been studied. Analysis of genomic and transcriptomic data has shown that mannitol metabolism in S. japonica is a circular pathway composed of four steps. In this study, one S. japonica mannitol-1-phosphate dehydrogenase (M1PDH2) and two mannitol-1-phosphatase (M1Pase) proteins were recombinantly expressed to analysis enzyme biochemical properties. RNA sequencing and droplet digital polymerase chain reaction were used to analyze the gene expression patterns of mannitol metabolism in different generations, tissues, sexes, and abiotic stresses. Our findings revealed insights into the mannitol synthesis pathways in brown algae. All genes were constitutively expressed in all samples, allowing maintenance of basic mannitol anabolism and dynamic maintenance of the “saccharide pool” in vivo as the main storage and antistress mechanism. Enzyme assays confirmed that the recombinant proteins produced mannitol, with the specific activity of SjaM1Pase1 being 1.8–4831 times that of other algal enzymes. Combined with the transcriptional analysis, SjaM1Pase1 was shown to be the dominant gene of mannitol metabolism. Mannitol metabolism genes in multicellular filamentous (gametophyte) and large parenchyma thallus (sporophyte) generations had different expression levels and responded differently under environmental stresses (hyposaline and hyperthermia) in gametophytes and sporophytes. The considerable variation in enzyme characteristics and expression of mannitol synthesis genes suggest their important ecophysiological significance in the evolution of complex systems (filamentous and thallus) and environmental adaptation of Laminariales.
The Secret Lives of Roots

Below-ground carbon, including roots, is a crucial factor in the overall carbon cycle. But how much carbon do roots transfer below ground, and how long does it stay? In their Perspective, [Trumbore and Gaudinski][1] highlight the report by [ Matamala et al . ][2], who use a new isotope method to measure root lifetimes. Their results suggest that the bulk of fine root mass has a lifetime of 4 to 6 years. However, in situ studies of root growth and mortality generally yield much shorter lifetimes. Trumbore and Gaudinski suggest that these disparate results may be reconciled by acknowledging the complexity of root populations, and that sampling studies must reflect that complexity. [1]: http://www.sciencemag. org/cgi/content/full/302/5649/1344 [2]: http://www.sciencemag. org/cgi/content/short/302/5649/1385
Genetic Differentiation and Population Genetic Structure of the Chinese Endemic Dipteronia Oliv. Revealed by cpDNA and AFLP Data

Dipteronia Oliv. is an endangered genus found in China with two species, D. sinensis and D. dyeriana. Previous morphological, cytogenetic, and molecular studies have suggested that D. dyeriana is a species related to D. sinensis. However, it is unclear how the two species diverged and whether gene flow exists between these two species. Here, we performed a molecular study at the population level to characterize genetic differentiation and decipher the phylogeographic history for Dipteronia species based on newly sequenced chloroplast DNA (cpDNA) and amplified fragment length polymorphisms (AFLP) date retrieved from our previous studies. No haplotype was shared between the two species in the cpDNA network. However, the phylogenetic analysis suggested that a haplotype found in D. sinensis (H4) showed a closer relationship with haplotypes of D. dyeriana. Based on our estimated time of divergence, these two cpDNA haplotype lineages of Dipteronia diverged at about 31.19 Ma. Furthermore, two genetic clusters with asymmetric gene flow were supported based on the structure analysis, which corresponded with the two Dipteronia species, and we also detected a low level of asymmetric gene flow between these two species according to the MIGRATE analysis using AFLP data. During the Last Glacial Maximum (LGM, c.21 kya BP), the genus’ predicted distribution was more or less similar to that at present, which was also supported by the mismatch analyses that showed no population expansion of the two Dipteronia populations after the LGM. The combined cpDNA and AFLP data revealed significant genetic differentiation between the two Dipteronia species with asymmetric gene flow, which can be explained by the varying phylogeographical histories of these two species.
Effect of dietary bile acids on growth, body composition, lipid metabolism and microbiota in grass carp (Ctenopharyngodon idella)

To investigate the effects of dietary bile acids (BA) on growth and metabolism of lipid in grass carp (Ctenopharyngodon idella, C. idella) at high dietary lipid level, a basal diet (50 g kg–¹ lipid, 5L group) was supplemented with 20 g kg–¹ soybean oil (70 g kg–¹ lipid, 7L group); then, 0.06 g/kg BA was added in 7L diet to form the third diet (7L+BA group). The 96 C. idella (69.86 ± 6.24 g) were divided into three groups (duplicate per group) and fed three diets, respectively, for 8 weeks, and then, growth and lipid metabolism were determined. Results showed that growth of fish in 7L+BA group was significantly higher than 5L and 7L groups. The lipid level in whole body, hepatopancreas and muscle of grass carp in 7L+BA group were significantly lower than 7L group. Relative expression of lipid catabolism genes in hepatopancreas and muscle of 7L+BA group was significantly higher than 5L group. The amount of microbiota in intestine of fish in 7L+BA group was significantly higher than the other two groups. The present results indicated that BA in 7L diet improved growth of fish by increasing protein synthesizing, decreasing lipid content in fish body and by regulating amount of microbiota in intestine of fish.
Inbreeding effects on some reproductive traits in Markhoz goats

The objective of this study was to estimate the inbreeding coefficient and its effects on reproductive traits in Markhoz goats. The pedigree file included 5351 kids produced by 234 bucks and 1470 does. Average inbreeding coefficient for the whole population was 2.68%, and the minimum and maximum inbreeding coefficients were 0.05% and 31.25%, respectively. Average coefficient of inbreeding for inbred population was 5.17% and the number of inbred animals in the population was 2777. For investigating effects of inbreeding coefficient on reproductive traits, 3443 records were available for litter size at birth (LSB), litter size at weaning (LSW), total litter weight at birth (TLWB) and mean of litter weight at birth (MLWB). Furthermore, available records for total litter weight at weaning (TLWW) and mean of litter weight at weaning (MLWW) were 2918. Inbreeding depression was estimated as the linear regression of performance on the individual inbreeding coefficient of kids and dams using the most appropriate animal model based on Akaike’s information criterion. Furthermore, inbreeding depressions for LSB and LSW were estimated using threshold and Poisson models. Regression coefficients of LSB, LSW, TLWB, TLWW, MLWB and MLWW on inbreeding coefficient of kids were –0.035, –0.019, –0.077 kg, –0.782 kg, –0.009 kg and –0.332 kg, respectively. Furthermore, regression coefficients of LSB, LSW, TLWB, TLWW, MLWB and MLWW on inbreeding coefficient of dams were 0.064, –0.013, 0.241 kg, 0.638 kg, 0.028 kg and –1.783 kg, respectively. The obtained results from this study showed that inbreeding depression is controlled by an appropriate mating system policy.
Chemical identification of 2,4-dinitrophenol (2,4-DNP) by GC-MS in fat burners and studies of its in vitro hepatotoxicity

v RESUMO . viii GENERAL INDEX . xi FIGURES INDEX . xiv ABBREVIATIONS LIST INDEX . xix PART 1 – INTRODUCTION . 1 1.1. The problem of ‘fat burners’ . 2 1.2. Trends in 2,4-dinitrophenol (2,4-DNP) use . 3 1.3. Legislation and epidemiology . 4 1.4. Chemical structure, physicochemical properties and commercial presentation . 12 1.5. Pharmacokinetics . 16 1.6. Pharmacodynamics . 17 1.7. Toxic effects, diagnosis and therapy associated with intoxication . 18 1.8. Analytical methods for 2,4-dinitrophenol (2,4-DNP) determination in commercial products and biological matrices . 19 PART 2 – OBJECTIVES . 23 PART 3 – CHEMICAL CHARACTERIZATION OF COMMERCIAL WEIGHT LOSS PRODUCTS . 24 CHAPTER 1: MATERIALS AND METHODS . 24 3.1.1. Reagents . 25 3.1.2. ‘Fat Burners’ . 25 3.1.3. Standards and samples preparation . 26 3.1.4. Derivatization and injection . 27 3.1.5. GC-MS conditions . 28 CHAPTER 2: RESULTS AND DISCUSSION . 29 3.2. 1. Research of 2,4-dinitrophenol (2,4-DNP) in weight loss commercial products . 30
Water potential in peach branches as a function of soil water storage and evaporative demand of the atmosphere

1Part of Master’s Dissertation of the first author. 2PhD student, no PPG-Management and Conservation of Soil and Water (MACSA), Universidade Federal de Pelotas, Pelotas RS, FAPEG Scholar. Email: alexbeckermonteiro@gmail.com 3Researcher at EMBRAPA Clima Temperado, Pelotas RS. Email: carlos.reisser@embrapa.br 4PhD student at PPG-Management and Conservation of Soil and Water (MACSA), Universidade Federal de Pelotas, Pelotas RS. Email: luciano.romano@cas. ifmt.edu. br 5Associate Professor III, Departamento de Engenharia Rural, Universidade Federal de Pelotas, Pelotas RS. Email: lctimm@ufpel.edu. br 6Professor, Universidade Federal do Pampa, Campus Itaqui RS. Email: m.toebe@gmail.com Abstract-The use of water potential indicators in the plant has been adopted in irrigation management, in recent years, since it is accepted that the plant is the best indicator of its own water status. The objective of this study was to verify the relationship between water potential in peach tree branches and the evaporative demand of the atmosphere and the water availability in two textural classes of an Aquertic Hapludalf soil, aiming to adopt irrigation management strategies based on the water potential in the plant. Research was carried out in a commercial peach orchard, cv. Esmeralda, in the municipality of Morro Redondo-Rio Grande do Sul state, Brazil. Four peach tree rows were evaluated, being two irrigated and two non irrigated. The irrigation management was based on the replacement of the potential crop evapotranspiration. It was concluded that the water potential in the peach tree branch is positively related with the evaporative demand of the atmosphere and negatively related with soil water storage. Future studies should adopt irrigation management strategies for peach trees based on the water potential mainly for the irrigation management of post-harvest peach trees.
In vitro propagation and reintroduction of golden paintbrush (Castilleja levisecta), a critically imperilled plant species

Abstract: Golden paintbrush (Castilleja levisecta Greenm.) is a hemiparasitic herbaceous perennial native to the Pacific Northwest of North America and is considered critically imperilled with only 11 populations remaining in the wild. The main objective of this study was to develop ex situ and in situ conservation through micropropagation and field plantings. In vitro cultures were initiated using nodal explants from two plants raised from seeds collected from a natural population. Shoots were then multiplied on Murashige and Skoog basal medium with 2.0 µmol L-1 6-benzylaminopurine (BA), 3.0 µmol L-1 kinetin (Kn), 2.2 g L-1 phytagel, and 3% sucrose. Explant position on source plants, culture vessel design, and application of different plant growth regulator levels for BA, Kn, and thiadiazuron (TDZ) were tested to optimize micropropagation protocols. Clones from the plants showed differences in plant height and number of nodes in response to various BA and TDZ concentrations. In vitro shoots were successfully rooted under ex vitro conditions using commercial rooting powder (0.8% indole-3-butyric acid) with an average of ∼17 roots per shoot and acclimatized in the greenhouse with 100% survival rate. Two-month-old plants were transferred to a Parks Canada restoration site at Fort Rodd Hill, Victoria, BC, with 7.5% survival. The use of micropropagation in combination with reintroduction efforts offers an excellent opportunity for conserving endangered plant biodiversity in vitro and facilitating in situ conservation efforts by providing plants for reintroduction.
NuMA is a negative regulator of 53BP1 in DNA double-strand break repair

Accumulation of 53BP1 at DNA breaks determines DNA repair pathway choice and promotes checkpoint activation. Here, we show regulation of 53BP1 beyond repair foci. 53BP1 movements are constrained in the nucleoplasm and increase in response to DNA damage. 53BP1 interacts with the structural protein NuMA, which controls 53BP1 diffusion. This interaction, and colocalization between the two proteins in vitro and in breast tissues, is reduced after DNA damage. In cell lines and breast carcinoma, NuMA prevents 53BP1 accumulation at DNA breaks and high NuMA expression predicts better patient outcomes. Manipulating NuMA expression alters PARP inhibitor sensitivity of BRCA1-null cells, end-joining activity, and immunoglobulin class switching that rely on 53BP1. We propose a new mechanism that involves the sequestration of 53BP1 by NuMA in the absence of DNA damage. Such mechanism may have evolved to disable repair functions and may be a decisive factor for tumor responses to genotoxic treatments.
Intronic non-coding RNAs within ribosomal protein coding genes can regulate biogenesis of yeast ribosome

The genome of the budding yeast (Saccharomyces cerevisiae) has selectively retained introns in ribosomal protein coding genes. The function of these introns has remained elusive in spite of experimental evidence that they are required for the fitness of yeast. Here, we computationally predict novel small RNAs that arise from the intronic regions of ribosomal protein (RP) coding genes in Saccharomyces cerevisiae. Further, we experimentally validated the presence of seven intronic small RNAs (isRNAs). Computational predictions suggest that these isRNAs potentially bind to the ribosomal DNA (rDNA) locus or the corresponding rRNAs. Several isRNA candidates can also interact with transcripts of transcription factors and small nucleolar RNAs (snoRNAs) involved in the regulation of rRNA expression. We propose that the isRNAs derived from intronic regions of ribosomal protein coding genes may regulate the biogenesis of the ribosome through a feed-forward loop, ensuring the coordinated regulation of the RNA and protein components of the ribosomal machinery. Ribosome biogenesis and activity are fine-tuned to the conditions in the cell by integrating nutritional signals, stress response and growth to ensure optimal fitness. The enigmatic introns of ribosomal proteins may prove to be a novel and vital link in this regulatory balancing act.
Shape description by a distribution function based on skeleton structure

A new method of describing the shape of a silhouette for data compression is proposed. A silhouette is decomposed into a union of components. Each component is defined as a density distribution function. The algorithm of shape decomposition is based on the skeleton structure. The components are represented in a tree structure according to the sequence of silhouettes. The latter are generated by applying a Gaussian filter to the original contour at varying levels. Simulation reveals that the proposed technique requires fewer bits than other shape decomposition schemes at the same degree of approximation. <<ETX>>
Indicadores de calidad del suelo en el agroecosistema caña de azúcar (Saccharum spp.)

Indicadores de calidad edafica del agroecosistema cana de azucar (Saccharum spp.), cultivo de vital importancia economica y social en el estado de Tabasco, Mexico, fueron analizados en dos epocas del ano, a partir de la caracterizacion y el diagnostico nutrimental del suelo y la densidad de longitud de raices finas (DLRF). Se establecieron ocho perfiles, cuatro en la epoca seca y cuatro en la humeda, y se tomaron muestras de suelo y biomasa radical en ocho profundidades, se hizo taxonomia de suelo para conocer la unidad, la cual correspondio a un Vertisol Stagnico VRst (Eutrico). El diagnostico mostro, en general, contenidos nutrimentales bajos y muy bajos, con excepcion del P en los primeros 30 cm y CIC hasta los 50 cm. Los indicadores quimicos destacaron la importancia de la MO del suelo y su alta correlacion con el COS, N y P. El Ca y Mg tambien mostraron correlaciones altas entre si. La macrofauna, como indicador biologico, fue escasa sobre todo en la epoca seca, lo que sugirio degradacion del suelo. La DLRF fue estadisticamente mayor en la epoca humeda en las tres primeras profundidades, en tanto que en la epoca seca fue homogenea en casi todas. La distribucion vertical de las raices finas (<3 mm), extractoras de nutrimentos, indico una importante exploracion hasta los 140 cm de profundidad
A blight disease on highbush blueberry associated with Macrophomina phaseolina in Serbia

Abstract Unusual blight-like symptoms appeared on highbush blueberry plants in Serbia during August 2015 and infected plants showed browning and reddening of leaves, drying of foliage and brown discolouration of internal vascular stem tissues. The objective of this study was to isolate and confirm a causal agent of the disease. Five diseased blueberry plants (2-year-old), with visible brown discolouration in the wood, were collected for isolation on potato dextrose agar (PDA). Morphological analysis of the selected fungal isolates showed the presence of abundant black, round to oblong, or irregularly shaped microsclerotia immersed in the PDA. Dark, globose pycnidia formed on water agar with an initially hyaline, granular content and single-celled conidia, indicating the presence of plant pathogenic fungus Macrophomina phaseolina associated with symptomatic plant tissues. Pathogenicity was confirmed on potted blueberry plants based on the initial symptoms of leaves turning yellowish to brown at the leaf edges, followed by the defoliation of leaves of the inoculated stems. Discolouration of vascular tissues was also observed on transverse sections of inoculated stems. The pathogen M. phaseolina was confirmed using molecular analysis of the ITS1-5.8S-ITS2 region of rDNA and a part of the TEF-1α gene region. This is the first report of M. phaseolina causing a blight disease on highbush blueberry in Serbia. The study should help in elucidating disease symptomatology and provide information on the risk which this fungus could pose in blueberry production.
Sperm quality and egg size in brown trout: implications for sperm competition and cryptic male choice

Salmonid males have developed altemative reproductive strategies (genetically based life history programmes that affect an individual 's allocation o f resources to reproduction) as a means to achieve successful reproduction in unpredictable environments. For exarnple, anadromous males undertake migrations to the resource-rich ocean, and precociously mature parr, who mature sexually in the nascent river with comparatively few resources available for growth (THORPE et al. 1998). These strategies are not exclusively genetically deterrnined, but rather phenotypically plastic, since additive genetic and environmental effects and growth conditions are implicated in the process of salmonid sexual maturation (BOHLIN et al. 1994, GARANT et al. 2003). Mating strategies in the brown trout (Sa/mo trutta, L.) are conditional and are influenced by the arnount offood available to juveniles, which deterrnines individual growth rates (ALM 1959, BOHLIN et al. 1994, HUTCHINGS & MYERS 1994, THORPE et al. 1998). Slower growth rate, caused by access to fewer resources, leads to the need for migration, with a consequence of delayed sexual maturation (BERGLUND 1992). Such conditional mating strategies favour fast-growing and early maturing males to adopt a sneaking spawning behaviour. An optimal energy allocation strategy for ensuring reproductive success of a given male depends on its condition (GROSS 1996) and on the information available to competing males (MAYNARD SMITH 1982, HACCOU & IWASA 1995). Parr and adult males commonly participate in the spawning of a single female, with the consequence that sperrn competition between these reproductive phenotypes regularly occurs. Because access to a female's redd yields the greatest reproductive success in salmonids, an intensive selection of male body size occurs (GRoss 1985, FLEMING & GRoss 1994). Adult males that delay sexual maturation are older and significantly bigger than parr males due to greater arnount of resources in oceanic habitat as compared to the ecological conditions in the freshwater habitat. These older males possess a long nose and kype, which are used to fight for spawning areas (FLEMING & GRoss 1994), and have an adipose fin, which functions as a badge to attract females (JÃRVI 1990). Adult males are dominant over parr males and guard the female on spawning grounds.
First record of Molossus pretiosus Miller, 1902 (Chiroptera, Molossidae) for the Cerrado of Bahia, northeastern Brazil

Molossus pretiosus Miller, 1902 is known from two localities in Brazil: one in the Caatinga of Minas Gerais, and other in the Pantanal of Mato Grosso do Sul. We report here the first record of M. pretiosus for the Cerrado of Bahia, Northeastern Brazil. This record extends the distribution of this species by about 200 km northward.
The role of heterotrophic nanoflagellates and ciliates and their different fates in fishless and fish-stocked ecosystems

Heterotrophic nanoflagellates (HNF) and ciliates are ubiquitous and comprise a substantial proportion of microbial food webs. They are thought to be major consumers o f bacteria and autotrophic picoplankton production (e.g. WEISSE 1990), and are themselves preyed upon by larger zooplankton (e.g. PACE & VAQUE 1994). The significance of microbial food webs was first demonstrated in oligotrophic marine ecosystems where nutrient inputs are low and largely regenerated, maintaining low levels o f harvestable biological production (PoMEROY 1974, AZAM et al. 1983). Recent evidence, however, suggests that microbial food webs may be significant components of some eutrophic and even hypenrophic lakes, accounting for >50% ofthe annual carbon production and most of the remineralization of nutrients (e.g. RIEMANN & S0NDERGMRD 1986, VOROS et al. 1991). Thus, although their importance has been realized, their role in the eutrophication process has not been well studied. CHRISTOFFERSEN et al. (1993) reported the effects of filter-feeding planktivorous fish on a plankton community, including the structure of the microbial food web. However, in their results, changes in HNF density were not clear, and those of ciliates were not investigated. As yet, there have been no reports on the roles or fates of HNF or ciliates in the presence of introduced filter-feeding fish. The objectives of this study were, using enclosures, (l) to estimate the changes in HNF and ciliate density in an ecosystem in which filter-feeding silver carp (Hypophthalmichthys molitrix) had been stocked, compared with those in a similar but fishless ecosystem, and (2) to estimate growth rates of HNF and grazing rates on HNF and ciliates to evaluate their fàtes in the two ecosystems.