Miracle-dz/UniFAR-FTUs huggingface dataset:
Biochemical Characterization and Immunohistochemical Identification of Vitellin in the Ovary of Kuruma Prawn (Marsupenaeus japonicus)

Vitellin(Vn)was purified from the mature ovaries of the kuruma prawn (Marsupenaeus japonicus) with gel filtration, polyacrylamide gel electrophoresis(PAGE), and electro-elution. Native-and SDS-PAGE revealed that the purified Vn was a lipo-glyco-caroteno-protein of 530 kDa consisting of four subunits (70,83,105, and 190 kDa). Gly, Ala, and Glu were the dominant amino acids of Vn. The antiserum against the purified Vn, which was raised in a rabbit, immunoreacted with vitellogenin (VTG) in the hemolymph and Vn in the ovary by immunodiffusion and Western blotting. Positive immunoreaction with the antiserum was detected in the cytoplasm of oocytes at the late perinucleolus stage. However follicle cells surrounding the oocytes were not immunostained at any developmental stage. No immunoreaction was detected in the cortical rods of mature oocytes. Immunohistochemical observation revealed that the accumulation of Vn in the cytoplasm of the oocytes began at the early vitellogenic stage. These results indicate that the level of in situ cellular VTG in follicle c lls is below the limit of immunodetection.
Aquatic mammals from the Mexican Caribbean; a review

We present a review of the aquatic mammal species occurring in the Mexican Caribbean. Several published sources were reviewed to find information about aquatic mammals reported for the Mexican Caribbean. Additionally, we consulted 29 national and international collections and museums. Based on documents, collections, direct records and local news, we analyzed 18 confirmed species of aquatic mammals for the study area [Tursiops truncatus, Stenella clymene, S. frontalis, S. longirostris, Steno bredanensis, Grampus griseus, Globicephala macrorhynchus, Peponocephala electra; Pseudorca crassidens, Orcinus orca, Physeter macrocephalus, Kogia breviceps, K. sima, Ziphius cavirostris, Mesoplodon europaeus, Trichechus manatus manatus, Lontra longicaudis annectens and Monachus tropicalis (extinct)]. In order to gather solid baseline information that enhances efficient long-term management, regular and systematic population censuses of the aquatic mammal community are recommended. We recommend the use of the “Mexican Caribbean” area as a separate unit of management and conservation, differently as has been included in the macro region “Gulf of Mexico/Mexican Caribbean”.
A cladistic reappraisal of the fossil flatfishes record consequences on the phylogeny of the Pleuronectiformes (Osteichthyes : Teleostei)

Le but de cet article est de presenter les resultats d'une etude cladistique des Pleuronectiformes fossiles afin de preciser l'histoire evolutive de ce groupe de Teleosteens. L'attribution de certains fossiles aux Pleuronectifonnes ou a une famille de poissons plats a ete confirmee ou contredite. Des dates minimales d'apparition de certains groupes ont ete proposees : le Lutetien (Eocene moyen) pour les Soleidae, le Miocene moyen pour les Bothidae, et non l'Eocene comme on le croyait auparavant. Cependant de nombreux fossiles n'ont pu etre places dans une famille precise. En effet, l'absence de definition de certaines familles de poissons plats au moyen de caracteres apomorphes a empeche de mener plus loin la recherche de la position phylogenetique de certains fossiles. En consequence, notre comprehension de l'histoire evolutive des poissons plats est encore fragmentaire et des travaux sur les especes actuelles sont necessaires afin de placer certains fossiles plus precisement dans l'arbre phylogenetique des poissons plats.
Invasive willows drive instream community structure

Summary Exotic invasive species are known to influence taxonomic communities and ecological processes. Few studies have examined the impact on taxonomic communities across trophic levels because it is time consuming and requires a wide range of identification skills. Here, we examined the impacts of invasive willow trees (Salix spp.) on microbial and macroinvertebrate composition using a combination of high resolution ecogenomic and classical approaches. Aquatic communities were compared and contrasted between stream reaches with and without willow infestation in three temperate Australian streams. Willows significantly altered in-stream fungal, algal and macroinvertebrate communities. Macroinvertebrate diversity was similar between riparian types. Willow-infested sites were characterised by lower macroinvertebrate abundance and Australian biotic index scores, indicating the presence of taxa generally more tolerant to pollution. At invaded sites, grazers were replaced by generalist collector–gatherer taxa and the proportions of macroinvertebrate functional-feeding groups (FFG) were altered such that the primary trophic pathway was changed from an autotrophic algal-based pathway to a heterotrophic, detrital-based pathway. Riparian invasion by willows may change the primary source of energy from autotrophy to heterotrophy in small streams, with knock-on effects on community structure across trophic levels.
A genomic approach to selecting robust and versatile SNP sets from next-generation sequencing data for genome-wide association study in citrus cultivars

The large-scale genotyping assay is a prerequisite for modern genetic analysis, and single-nucleotide polymorphism (SNP) markers that enable high-throughput genotyping are widely used for genome-wide association studies (GWAS) and genomic selection (GS). However, SNP markers randomly selected from limited genome data often fail in genotyping certain citrus crosses because of high genetic diversity and frequent polymorphism among accessions. Ambiguous markers that may yield false genotyping results add undesired bias to GWAS and GS. In this study, we aimed to select an SNP marker set that minimise genotyping failure among a wide range of citrus varieties. We initially selected 15 ancestral varieties for an SNP discovery panel. Possible SNP regions among the cultivars in the panel were extracted by next-generation sequencing (NGS). The selected SNPs were evaluated for their scores and also their distances to adjacent SNPs. We consequently selected the 756 most discriminative SNPs according to their position in the reference genome sequence and designed a GoldenGate SNP array. Genotyping of 120 citrus cultivars passed 674 SNP markers according to their scores. The robustness and versatility of the passed SNP markers were evaluated with nine validated trios, and consistent SNP markers were selected. Using these consistent markers, we confirmed cross combinations of 71 trios. Equivocal SNP markers that showed combination-dependent aberrant segregation were eliminated, leaving 598 SNP markers. The genotypes obtained with the selected SNP markers were consistent in the 80 trios. These results demonstrate SNP discovery in diverse citrus cultivars using NGS technology and SNP marker design according to a reference genome, and show that validating genotypes with multiple trios permitted the design of robust and versatile SNP markers. They will contribute to accurate GWAS and GS analysis in citrus cultivars.
Mitigating impacts of weeds and kangaroo grazing following prescribed fire in a Banksia woodland

icant Banksia/Tuart woodland reserves. Summary Banksia woodlands are renowned for their flammability and prescribed fire is increasingly employed to reduce the risk of wildfire and to protect life and property, particularly where these woodlands occur on the urban interface. Prescribed fire is also employed as a tool for protecting biodiversity assets but can have adverse impacts on native plant communities. We investigated changes in species richness and cover in native and introduced flora following autumn prescribed fire in a 700-hectare Banksia/Tuart (Eucalyptus gomphocephala) woodland that had not burnt for more than 30 years. Effectiveness of management techniques at reducing weed cover and the impacts of grazing by Western Grey Kangaroo (Macropus fuliginosus) postfire were also investigated. Thirty plots were established across a designated burn boundary immediately before a prescribed fire in May 2011, and species richness and cover were measured 3 years after the fire, in spring of 2013. Fencing treatments were established immediately following the fire, and weed management treatments were applied annually in winter over the subsequent 3 years. Our results indicate that autumn prescribed fire can facilitate increases in weed cover, but management techniques can limit the establishment of targeted weeds postfire. Postfire grazing was found to have significant adverse impacts on native species cover and vegetation structure, but it also limited establishment of some serious weeds including Pigface (Carpobrotus edulis). Manipulating herbivores in time and space following prescribed fire could be an important and cost-effective way of maintaining biodiversity values.
Effects of reducing compounds on Agrobacterium-mediated transformation of sweet potato

Reducing compounds have so far been used for improvement of Agrobacterium-mediated transformation of crop plants with a strong ability to give rise to tissue browning, but not for that of sweet potato. Therefore, we examined the effects of commercially available five reducing compounds (L-ascorbic acid, L-cysteine, dithiothreitol, 2-mercaptoethanol, and reduced glutathione) on parameters associated with Agrobacterium system prior to applying them to sweet potato transformation. The parameters chosen in this study are enzymatic browning caused by sweet potato leaves, callus formation from the leaves and vir gene expression in Agrobacterium. All five reducing compounds restrained acute browning at concentrations of 20-60 mM, of the buffer in which the wound leaves were incubated. However, the reducing compounds except reduced glutathione arrested callus formation from the healthy leaves at 10 mM or less. Thus, we tested whether reducing compounds at these low concentration ranges can suppress tissue browning of sweet potato leaves which is slowly occurred under hygromycin B, and found that all of them failed. Furthermore, the compounds except 2-mercaptoethanol repressed vir gene expression at concentrations of 1-10 mM, which is essential to transfer T-DNA molecules from the bacteria to plant cells. Based on the results, we discuss usage of the reducing compounds on sweet potato transformation.
The Influence of Different Protein, Fat and Mineral Levels on the Digestibility of Fat and Fatty Acids Measured at the Terminal Ileum and in Faeces of Growing Pigs

Abstract The influence of dietary protein, fat and mineral levels on crude fat and fatty acid digestibility was investigated in growing pigs. The experiment was a factorial design with two levels of protein (normal and high), two levels of dietary fat (3 and 15% of DM) and three levels of minerals (50, 100 and 150% of Danish Standard). Four litters, each of six female pigs, were used in the experiment. Increasing the dietary protein content resulted in a moderate but significant increase in the ileal digestibility of fatty acids. The increase was most pronounced for the saturated fatty acids. Addition of animal fat to the basal diet caused a substantial increase in ileal digestibility of all fatty acids except stearic acid (18:0). A variation in the dietary mineral content of ±50% of the Danish Standard had no significant influence on ileal digestibility of crude fat and fatty acids. Apparently, microbial hydrogenation occurred in the hind-gut, but the increase in stearic acid (18:0) excretion could not b.
Population survey of predatory insects in sugarcane in the municipality of União, Piauí state, Brazil, using light trap

Predatory insects are important to control agricultural pests. Knowledge of predators in sugarcane culture may allow for chemical control reduction. This study aimed to record predator entomofauna associated with sugar­cane commercial cultivation in the municipality of Uniao, State of Piaui. Insects were collected with a light trap, "Luiz de Queiroz" model, equipped with a F15 T8 BL lamp positioned 1.5 meters above ground in the geo­graphical coordinates of 21 ° 22' 30" S and 48 ° 13' 0" W. The trap was turned on at 6 p.m. and turned off at 6.00 a.m., and sampling was conducted once a week. In a total of 52 collections, 83 predator species distri­buted in 07 orders, 17 families, and 45 genera were collected. Coleoptera and Hymenoptera orders were the most diverse, with 56 and 15 species, respectively. Selenophorus sp.1 (Coleoptera: Carabidae) was the spe­cies with the highest number of individuals among Coleoptera, and Linepithema humile (Mayr, 1868) (Hymenoptera: Fomicidae) was the species with trhe highest number among Hymenoptera.
Haloferax Volcanii Strategies to Regulate Type IV Pilus Dependent Adhesion and Microcolony Formation

Microorganisms can utilize type IV pili to initiate and maintain biofilms microbial communities that provide protection against stressful conditions. Because environmental conditions change suddenly, microorganisms have evolved multiple mechanisms to rapidly transition from a planktonic to sessile cell state. Despite the presence of archaea alongside bacteria throughout the environment, including the human microbiome, little is known about how these organisms form and maintain biofilms. Here we use genetic, microscopic and biochemical techniques to investigate multiple strategies the model archaeon Haloferax volcanii employs to permit effective adhesion and microcolony formation, early steps in biofilm formation and maturation, as well as eventual dispersal from biofilms. First, we identified six pilins, PilA1-6, each with a highly conserved hydrophobic stretch (H-domain). Each of these pilins can adhere to surfaces when expressed individually in trans but with diverse phenotypes. PilA1 and PilA2, which in wild-type planktonic cells appear to be the most abundant pilins, adhere less well than wild-type, while PilA3 and PilA4 adhere better. Conversely, PilA5 and PilA6 form microcolonies significantly earlier than wild-type. We furthermore showed that N-glycosylation, dependent on the oligosaccharyltransferase, AglB, regulates the functions of these pilins. A mutant lacking all six pilins, ΔpilA[1-6], has a severe motility defect that can be complemented by expression of any individual PilA pilin in trans. Surprisingly, a hybrid protein containing only the H-domain of the PilA pilins could restore motility in the ΔpilA[1-6] strain, contributing to a model in which pilins sequester a motility inhibitor within the membrane of planktonic cells. Motility was also shown to be regulated by the flagellin FlgA2. Strains lacking flgA2 are hypermotile with longer, more abundant flagella, implicating FlgA2 as an additional factor in inhibiting dispersal from biofilms. From these results, we have demonstrated numerous mechanisms to regulate biofilm formation and dispersal in Hfx. volcanii. These novel mechanisms, some of which are likely conserved across the bacterial and archaeal domains, will advance our understanding of critically understudied members of the microbiome. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor Mecky Pohlschroder
Genetic variation for nitrogen use efficiency in a set of recombinant inbred lines II-QTL detection and coincidences

The development of varieties with a better nitrogen use efficiency (NUE) is a means for modern agriculture to decrease environmental pollution by nitrates and to maintain a sufficient net income. Such development will be more efficient if the genetic basis of NUE is is known. QTLs for vegetative development, grain yield and its components and grain composition (starch, protein, amino acids) were studied with and without nitrogen fertilization (N + and N-), using a set of 99 recombinant inbred lines crossed to a tester. QTLs for traits of vegetative development, grain yield and its components were grouped in clusters. For such traits, more QTLs were detected in N + than in N-, and QTLs in N- were a subset of QTLs in N + . Only some QTL x N level interactions were detected. For grain protein content, more QTLs were detected in N- than in N + . All these detected N- QTLs coincided with QTLs detected for vegetative development and grain yield in N + . QTLs for N-uptake were mainly detected in N + , whereas QTLs for nitrogen utilisation efficiency were mainly detected in N-. As a whole, genetic variability was expressed differently in N + and N-. Several coincidences between genes encoding for enzymes of N and C metabolism and QTLs for vegetative development and grain yield and its components were observed. This was the case for genes of glutamine synthetase, ADPGppase, sucrose phosphate synthase, sucrose synthase and invertase. All coincidences were consistent with the expected physiological effects of such genes which appear to be good candidate genes for QTLs of grain yield and its components.
Random amplified polymorphic DNA (RAPD) finger prints evidencing high genetic variability among marine angiosperms of India

In India 14 seagrass species can be found with monospecific genera (Enhalus, Thalassia and Syringodium), Cymodocea with two species and Halophila and Halodule represented by more than two taxonomically complex species. Considering this, the present study was made to understand the level and pattern of genetic variability among these species collected from Tamilnadu coast, India. Random amplified polymorphic DNA (RAPD) analysis was used to evaluate the level of polymorphism existing between the species. Out of the 12 primers tested, 10 primers amplified 415 DNA fragments with an average of 41.5 fragments per primer. Of the total 415 amplified fragments only 123 (29.7%) were monomorphic and the remaining 292 (70.3%) were polymorphic for Indian seagrass species. Among the 10 primers used four are identified as the key primers capable of distinguishing all the Indian seagrasses with a high degree of polymorphism and bringing representative polymorphic alleles in all the tested seagrasses. From the present investigation, this study shows that the RAPD marker technique can be used not only as a tool to analyse genetic diversity but also to resolve the taxonomic uncertainties existing in the Indian seagrasses. The efficiency of these primers in bringing out the genetic polymorphism or homogeneity among different populations of the Halophila and Halodule complex still has to be tested before recommending these primers as an identification tool for Indian seagrasses.
Monitoring rumen environment in finishing Lidia bulls

Objective . The aim of this work was to characterize the changes in rumen pH and temperature in finishing Lidia breed bulls reared on pasture and fed a total mixed ration (TMR). Materials and methods . Five 4-year-old Lidia bulls received approximately 10 kg of the TMR per animal and day in the morning. Bulls could move freely in a 17-ha fenced area and express normally their feeding behaviour. Internal wireless boluses were used to collect pH and temperature values every 10 minutes throughout the measurement period. Results . Average daily pH was 6.2. Average and maximum daily temperatures were not high enough to be indicative of disease (infections of other pathologies). Conclusions. When rations and feeding systems are appropriately managed, Lidia bulls can be supplemented with concentrates in the finishing stages of their productive cycle without impairing the rumen environment. Objetivo. El presente trabajo pretendio caracterizar las modificaciones que se producen en el pH y la temperatura ruminal de los toros de lidia, criados con un sistema de alimentacion basado en el suministro de una mezcla unifeed seca durante la etapa de acabado. Materiales y metodos . Se utilizaron 5 toros cuatrenos de la raza de Lidia alimentados con, aproximadamente, 10 kg/animal y dia de la mezcla unifeed a primera hora de la manana. Los toros disponian de un espacio cercado de 17 ha, que les permitiria expresar sus patrones de comportamiento de pastoreo en libertad con plena normalidad. El pH y la temperatura ruminal se midio de forma continua utilizando una sonda interna sin cables. Resultados . El pH medio fue de 6.20. Ni los valores de temperatura ruminal medios ni los maximos registrados son excesivamente altos como para ser indicativos del desarrollo de patologias o infecciones que pudieran afectar al estado de los animales. Conclusiones. Mediante el manejo adecuado de las raciones y del sistema de alimentacion, puede llevarse a cabo una suplementacion con alimentos concentrados para toros de lidia en la fase de remate de manera adecuada y respetuosa con su ambiente ruminal.
Catalysis of iron core formation in Escherichia coli bacterioferritin

Iron is an essential element for almost all life, so iron homeostasis is an important concern for most living organisms. The chemical properties of iron as represented by the low aqueous solubility of ferric iron and the toxicity of hydroxyl radicals it can produce by means of the Fenton reaction make achievement of iron homeostasis both challenging and crucially important. Bacterioferritin (BFR) is a bacterial member of the ferritin family of proteins that stores iron as a microcrystalline ferric hydroxide core of ~2700 iron atoms. This core is surrounded by 24 identical protein subunits, each possessing a dinuclear iron centre that catalyzes the oxidation of Fe to Fe. This structure affords storage, solubility and bioavailability of iron. To improve our incomplete knowledge of the mechanism of iron core formation, the properties of an assembly variant (Glu128Arg/Glu135Arg) and the wild-type of Escherichia coli BFR have been characterized by X-ray crystallography, site-directed mutagenesis, and iron oxidation kinetics. The crystal structure of the variant included two ethylene glycol (EG) molecules adjacent to the dinuclear (ferroxidase) site that catalyzes iron oxidation. One EG resides in the ferroxidase pore that provides a route from the solvent to the ferroxidase site. The other EG resides at the inner surface of the protein where the iron core presumably binds and is surrounded by three acidic residues: Glu47, Asp50, and Asp126. Kinetics studies revealed that Glu47Gln, Asp50Asn and Asp126Asn substitutions in the assembly variant and the wild-type 24-mer retarded iron core formation and that Glu47 is important in iron oxidation at the ferroxidase site whereas Asp50 and Asp126 are important for iron core nucleation. The 3-fold channel, 4-fold channel, B-site channel and the ferroxidase pore of