Miracle-dz/UniFAR-FTUs huggingface dataset:
Simulating forage production of Marandu palisade grass (Brachiaria brizantha) with the CROPGRO-Perennial Forage model

Abstract. Forage-based livestock systems are complex, and interactions among animals, plants and the environment exist at several levels of complexity, which can be evaluated using computer modelling. Despite the importance of grasslands for livestock production in Brazil, tools to assist producers to make decisions in forage–livestock systems are scarce. The objective of this research was to use the CROPGRO-Perennial Forage model to simulate the irrigated and rainfed growth of Marandu palisade grass (Brachiaria brizantha (A. Rich.) Stapf. cv. Marandu), the most widely grown forage in Brazil, by using parameters previously calibrated for the tall-growing cv. Xaraes of the same species, under non-limiting water conditions. The model was calibrated for the irrigated experiment and then tested against independent data of the rainfed experiment. Data used to calibrate the model included forage production, plant-part composition, leaf photosynthesis, leaf area index, specific leaf area, light interception and plant nitrogen (N) concentration from a field experiment conducted during 2011–13 in Piracicaba, SP, Brazil. Agronomic and morpho-physiological differences between the two grasses, such as maximum leaf photosynthesis, N concentration and temperature effect on growth rate, were considered in the calibration. Under rainfed conditions, the simulations using the Penman–Monteith FAO 56 method gave a more realistic water stress response than the Priestley and Taylor method. After model parameterisation, the mean simulated herbage yield was 4582 and 5249 kg ha–1 for 28 days and 42 days irrigated, and 4158 and 4735 kg ha–1 for 28 days and 42 days rainfed, respectively. The root-mean-square error ranged from 464 to 526 kg ha–1 and the D-statistic from 0.907 to 0.962. The simulated/observed ratios ranged from 0.977 to 1.001. These results suggest that the CROPGRO-Perennial Forage model can be used to simulate growth of Marandu palisade grass adequately under irrigated and rainfed conditions.
Caracterização florística e fitossociológica de um trecho sazonalmente inundável de floresta aluvial, em Araucária, PR.

The shrub-arboreal component of a floodplain forest, located in the alluvial plain of the Barigui River in Araucaria-PR was studied. The researched area was limited to places of same soil type (Glei soil) and the level of the water table was measured in a central point of the 20 plots of 100 m 2 , correlating this physiographic feature with the obtained phytosociologic parameters. The individuals with minimal perimeter of breast height (PBH) of 15 cm were valued, resulting in 29 species found. The most important was Sebastiania commersoniana (Baillon) L.B. Smith and R.J. Downs (branquilho), followed by Allophylus edulis (A.St.-Hil., Cambess. e A.-Juss.) Radlk. (vacum). The small sise of the individuals, the large number of individuals with multiple boles and the expressive importance of dead trees were atributed to enviromental stress. Less flooded places provided better diametric development and only at the micro-topographic elevations most species of lower phytosociologic values were established.
Effects of different batches of Neoparamoeba perurans and fish stocking densities on the severity of amoebic gill disease in experimental infection of Atlantic salmon, Salmo salar L.

Currently, there are two methods of inducing laboratory-based amoebic gill disease (AGD) in Atlantic salmon, Salmo salar L. : cohabitation with infected fish or exposure to a suspension of amoebae. Amoebic gill disease cannot be induced with cultured amoebae; therefore, the only source of the infective organism is salmon with the disease. For experimental purposes and to maintain pathogen supply, salmon are kept in an infection tank and amoebae are isolated from salmon once the disease establishes. In this way, discrete batches of amoebae are collected periodically. This study investigated the infective ability of different batches of amoebae. Furthermore, the effect of stocking density of salmon on the progression of AGD was also examined. The infective ability of different batches of amoebae isolated periodically from AGD-affected salmon varied in terms of quantifiable pathology. Salmon stocking density had a significant impact on survival after amoebae challenge, with morbidity beginning 23 days post challenge in tanks stocked at 5.0 kg m -3 and 29 days for those stocked at 1.7 kg m -3. For uniform initiation of AGD in multiple tanks, amoebae batches should be equally divided and added to tanks until the required concentration is reached and to maintain a standard biomass between replicate tanks and treatments. © 2010 The Authors. Aquaculture Research © 2010 Blackwell Publishing Ltd.
Regulation of NF-κB action by reversible acetylation

Abstract While the proximal cytoplasmic signalling events controlling the activation of NF-kappaB are understood in considerable detail, the subsequent intranuclear events that regulate the strength and duration of NF-kappaB action remain poorly defined. Recently, we have demonstrated that the RelA subunit of the NF-kappaB heterodimer is subject to reversible acetylation. The p300/CBP acetyltransferases play a major role in the in vivo acetylation of RelA principally targeting lysines 218, 221 and 310 for modification. Acetylation of these distinct lysine residues regulates different functions of NF-kappaB, including transcriptional activation, DNA binding affinity, I-kappaBalpha assembly and subcellular localization. Specifically, acetylation of lysine 221 enhances DNA binding and impairs assembly with I-kappaBalpha while acetylation of lysine 310 is required for full transcriptional activity of RelA independent of changes in DNA binding or I-kappaBalpha binding. In turn, acetylated RelA is deacetylated by histone deacetylase 3 (HDAC3). Deacetylation of lysine 221 promotes high-affinity binding of RelA to newly synthesized I-kappaBalpha proteins whose expression is activated by NF-kappaB. I-kappaBalpha binding to deacetylated RelA promotes rapid nuclear export of the NF-kappaB complex. This export is dependent on CRM1 binding to a nuclear export signal present in I-KBalpha and promotes replenishment of the cytoplasmic pool of latent NF-kappaB/I-kappaBalpha complexes thus readying the cell for response to the next NF-kappaB inducing stimulus Together, these studies highlight how reversible acetylation of RelA serves as an intranuclear molecular switch promoting both positive and negative regulatory effects on nuclear NF-kappaB action.
Nucleotide Sequencing and Pcr-Sscp of Mx1 Gene in Chicken

Mx1 is an interferon induced gene which inhibits the proliferation of single stranded RNA viruses. The size of Mx1 gene of chicken (Gallus gallus) is 21289 bp, having 14 exons and the coding sequence is 2118 bp long. Differential antiviral activity of Mx protein has been proved in various species including chicken. Polymerase Chain Reaction and subsequent Single Stranded Conformation Polymorphism (PCR-SSCP) analysis of 284 bp fragment of this gene was conducted to screen 153 birds of Aseel breed of chicken. Three genotypes viz. AB (0.74), BC (0.12) and AC (0.14) with three different alleles viz. A (0.44), B (0.43) and C (0.13) were identified. The homozygous genotypes i.e. AA, BB and CC could not be found in this population. Nucleotide sequencing of different alleles was done and submitted to the NCBI GenBank data (Acc. No.-GQ912704, GQ912705 and GQ912706). Nucleotide sequences were aligned with that of the corresponding Mx1 gene sequences of different breeds of chicken using DNASTAR Lasergene Software which revealed variations at five positions (91st, 107th, 113th, 194th and 231st). There is an urgent need of wide search for detection of polymorphism in Mx1 gene of different breeds of chicken and its possible association with the traits of economic importance.
Marking methods in small mammals: ear‐tattoo as an alternative to toe‐clipping

In a field study on the behavioural response of grey-sided voles Clethrionomys rufocanus to predator odour ear tattoos were used for individual marking of the voles in the field. The study was conducted over three summer seasons in the tundra of northern Norway. In this paper we report our experience with ear-tattooing in order to compare it with other methods used for marking small mammals. Methods should be compared for their different influences on physiology and behaviour and to find alternatives to the widely used toe-clipping. Looking for alternatives becomes mandatory because in many countries this method needs a special permit or is totally prohibited by law. Marking a vole with ear-tattoos took us 2 min on average. The rate for the first recapture after marking voles was 87%. This is much higher than reported recapture rates for toe-clipped voles. From all recaptured individuals we were able to identify > 89.9% of the codes. The time lag between marking and first recapture was higher than the lag between second and third recapture, which indicates a trauma caused by the marking procedure. However, there was no evidence of any weight loss as reported for other marking methods, and most of the tattooed animals did not show any behaviour indicating irritation after being marked. It is concluded that ear-tattooing, as an alternative to other methods of marking small mammals is useful even in the field. However, to assess different advantages and disadvantages in other circumstances, the chosen method should be examined critically before use.
Cytological observations on the so‐called neoblasts in the serpulid Spirorbis

The purported “neoblasts” of the serpulid Spirorbis have been studied in Spirorbis (Paradexiospira) vitreus and Spirorbis (Laeospira) borealis at both the light and electron microscopic levels. These perivasal cells occur in greatest abundance around the ventral blood vessel of the achaetous region. In light microscope preparations, the perivasal cells are intensely basophilic, containing basally situated nuclei, and relatively large nucleoli. The fine structure of the perivasal cells reveals that they contain an abundance of rough endoplasmic reticulum, well‐developed Golgi complex, heterogeneous dense bodies, and cytolysomes. The respiratory pigment chlorocruorin, which has a diameter of about 230 Å and is believed to be composed of two superimposed hexagonal components, has been localized within: cisternae of the rough endoplasmic reticulum, elements of the Golgi complex, and membrane‐bounded vesicles at the base of the perivasal cells. Evidence is advanced which strongly suggests that molecules of chlorocruorin are transported from the perivasal cells into the lumen of the vessel by reverse pinocytosis. It is concluded that whatever other functional role(s) the perivasal cells of Spirorbis may have, a major function is the synthesis and secretion of chlorocruorin. Whether the perivasal cells can be considered to be pluripotent is discussed.
The effects of symbiont induced haploid thelytoky on the evolution of brevipalpus mites

Bacterial symbionts that manipulate the reproduction of their host to increase their own transmission are widespread. Most of these bacteria are Wolbachia, but recently a new bacterium, named Cardinium, was discovered that is capable of the same manipulations. In the host species Brevipalpus phoenicis (Acari: Tenuipalpidae) this bacterium induces thelytoky by feminizing unfertilized haploid eggs. The related species B. obovatus and B. californicus are thelytokous too, suggesting that they reproduce in the same remarkable way as B. phoenicis. Here we investigated the mode of thelytokous reproduction in these three species. Isofemale lines were created of all three species and 19 lines were selected based on variation in mitochondrial COI sequences. All B. phoenicis and B. californicus lines (10 and 4 lines, respectively) produced males under laboratory conditions up to 6.7%. In contrast, males were absent from all B. obovatus lines (5 lines). Additional experiments with two B. phoenicis isofemale lines showed that males can be produced by very young females only, while older females produce daughters exclusively. For most lines it was shown that they are indeed feminized by a bacterium as treatment with antibiotics resulted in increased numbers of males up to 13.5%. Amplification and identification of specific gyrB sequences confirmed that those lines were infected with Cardinium. Three out of the five B. obovatus lines did not produce males after treatments with antibiotics, nor did they contain Cardinium or any other bacterium that might induce thelytoky. In these lines thelytoky is probably a genetic property of the mite itself. Despite the different causes of thelytoky, flow cytometry revealed that all 19 lines were haploid. Finally, the taxonomic inferences based on the mitochondrial COI sequences were incongruous with the classical taxonomy based on morphology, suggesting that a taxonomic revision of this group is necessary.
New Cases of Parthenogenesis and Polyploidy in the Genus Ramazzottius (Tardigrada, Hypsibiidae) and a Hypothesis Concerning Their Origin

Summary Specimens of the genus Ramazzottius Binda and Pilato, 1986 (Eutar-digrada, Hypsibiidae) were obtained from 2 moss and 1 lichen sample(s) collected in the Emilian Apennine Mountains. R. tribulosus was only found in one sample, whereas R. oberhaeuseri was found in all three. The first species had only diploid specimens, with 6 bivalents during the first meiotic division; the second had only females showing various polyploid cytotypes in addition to the diploid bisexual cytotype cited for this area. One of the triploid and the tetraploid cytotypes were characterized by the presence of univalents at oocyte metaphase. In contrast, another cytotype had “bivalents” in triploid number. Though the large number of cytotypes found in a single sample may be attributed to chance, it is better explained by an in loco origin, at least in some cases.
In Vitro Resistance by Fish Pathogens to Aquacultural Antibacterials, Including the Quinolones Difloxacin (A-56619) and Sarafloxacin (A-56620)

Abstract Two new quinolone antibacterials, difloxacin (A-56619) and Sarafloxacin (A-56620), were compared with oxolinic acid, oxytetracycline, and ormetoprim-sulfadimethoxine in vitro for their activities against common bacterial pathogens of fish. The objectives were to determine (1) the frequencies of in vitro resistance to antibacterials at eight times the minimum inhibitory concentration (MIC), (2) the rates and extents of decrease in antibacterial susceptibility when organisms were serially transferred to increasing concentrations of drug, (3) the stability of the decreased susceptibility, and (4) cross-resistance to other antibacterials by organisms with developed resistance. The frequency of spontaneous resistance to all antibacterials at eight times the MIC was low, 10-7-10-10. Quinolone-selected mutants that showed low-level resistance would be inhibited by achievable in vivo levels of difloxacin or Sarafloxacin. Oxolinic acid would not inhibit such mutants. The rate of susceptibility decrease du.
Genetic diversity of Artemia populations in Lake Urmia, Iran

Urmia Lake is one of the largest permanent hypersaline lakes in the world, located in northwestern Iran. It is one the permanent habitats for the genus Artemia. This thesis deals with the study of the genetic diversity of the Artemia population in the lake. It was assumed that the information obtained by conducting several genetic and life span characterization studies can provide better insight into the Artemia population in Urmia Lake. Additionally the aim of this study was to assess and improve molecular analyses as a tool to describe inter- and intraspecific diversity of the Artemia populations from Iran. In this thesis, a new molecular marker was developed to identify the parthenogenetic strain co-occurring with bisexual Artemia in Urmia Lake. In addition, in order to investigate the temporal population diversity of Artemia from Urmia Lake, subfossil cyst samples were recovered from the sediment which was dated to 5000-6700 YBP and identified as parthenogenetic Artemia. Another study of this thesis describes the population diversity among Artemia samples, originating from different areas of Urmia Lake, using a mtDNA molecular marker and various phenotypic characteristics. The experimental data bring us to the conclusion that only combined efforts in which selectable molecular markers are joined with phenotypic traits, covering representative numbers of populations, can provide sufficient complementary information for a maximal understanding of the biodiversity of the genus Artemia in Urmia Lake.
Allometry of the leg bones of moas (Dinornithes) and other birds

The body masses of various moas have been estimated, measurements have been made of their leg bones and allometric equations have been calculated. Corresponding equations have been calculated for various groups of living birds, using new data and data from the literature. The two families of moas are compared with each other, with modern ratites and with flying birds. Shortening of the tarsometatarsus in moas and narrowing of the pelvis in other ratites are interpreted as adaptations concerned with balancing the bird on its feet. following reduction of the wings.
Morphological variation between allopatric populations of Steinernema kraussei (Steiner, 1923)(Rhabditida: Steinernematidae)

Morphometrics of four Canadian, three US and two European isolates representing distinct geographic populations of Steinernema kraussei (Steiner, 1923) were compared and analysed by multivariate analysis. A total of 540 individuals (270 males and 270 third-stage infective juveniles) representing the nine populations was measured. Fourteen morphometric variables were selected and subjected to principal component and canonical analyses. Results from both analyses indicate that there are morphological differences among the studied isolates, and that these differences are congruent with their geographic origin. The European isolates were shown to be distinctly different from the North American isolates. Within the North American isolates, the western isolates were distinguished from the eastern one (Parishville). No significant differences were observed between the two European isolates studied. Ont ete comparees et etudiees par analyse multivariable les caracteristiques morphometriques de quatre isolats canadiens, trois isolats americains et deux isolats europeens representant des populations geographiques distinctes de Steinernema kraussei. Un total de 540 individus (270 mâles et 270 juveniles infestants de troisieme stade) representant les neuf populations a ete mesure. Quatorze variables morphometriques ont ete selectionnees et soumises a des analyses en composantes principales et canonique. Les resultats des deux analyses montrent qu’il existe des differences morphologiques entre les isolats etudies et que ces differences sont congruentes avec leur origine geographique. Les isolats europeens sont apparus comme etant nettement differents des isolats nordamericains. Dans le groupe des isolats nord-americains, les isolats de l’ouest ont ete differencies de celui de l’est (Parishville). Aucune difference significative n’a ete observe entre les deux isolats europeens etudies.
Codon usage and coevolution of the large and small subunits of ribulose‐1,5‐bisphosphate carboxylase/oxygenase

As the most abundant protein on Earth, ribulose‐1,5‐bisphosphate carboxylase/oxygenase (RuBisCO) is the key enzyme in carbon fixation of photosynthesis in all green plants. It is hexadecimal polymer, consisting of two kinds of subunits, large and small ones, which are encoded by different genomes. The large subunit (LSU) is encoded by the chloroplast genome; the small one by the nuclear genome. The function of RuBisCO relies on the two subunits, and only when they are combined to be hexadecimal, can it carry out its whole function. However, how the LSU and small subunits evolved, and if they coevolved, has remained mysterious. In this study, based on data in 21 species, phylogenies were analyzed on two subunits, respectively, and a mirror tree was reconstructed to reveal phylogenetic similarity. Furthermore, a comparative analysis method, using the codon usage bias and correlation calculation for RuBisCO subunits, was carried out. The relative synonymous codon usage (RSCU) values of LSU and small subunits were calculated. Finally, a novel parameter, RSCU distances‐based correlation (RDC), for evaluating molecular coevolution was proposed based on Pearson's correlation coefficient between RSCU value matrices of two subunits. The results show that the topological similarity of the mirror tree gave positive evidence of coevolution between subunits. Similarly, the RDC was high, at 0.558, revealing that the RuBisCO subunits coevolved to an extent. The results confirmed that coevolution happened between the two subunits of RuBisCO, although they were encoded by different genomes. This study added new evidence that functional constraint plays an important role in the evolution of the two subunits.
Semisynthesis of Erythropoietin Analog Having Three Oligosaccharides

An erythropoietin (EPO) analog having three complex-type biantennary sialyloligosaccharides was prepared. The full-length EPO glycopeptide was prepared through native chemical ligation of a triglycosylated peptide-αthioester corresponding to EPO 1–32 amino acid residues, which was synthesized chemically, and a polypeptide corresponding to EPO 33–166 amino acid residues, which was prepared by E. coli expression. Oxidative folding of the full-length glycopolypeptide afforded the biologically active EPO analog.
Simultaneous enhancement of microalgae biomass growth and lipid accumulation under continuous aeration with 15% CO2

To overcome the opposing trends in biomass yield and lipid accumulation, Chlorella PY-ZU1 cultures were continuously aerated with 15% CO2 to simultaneously enhance biomass yield (2.78 g L−1) and lipid content (47.04%). Microalgal cells consumed almost all the nitrate in the culture after 1 day to synthesize 24 mg L−1 of chlorophyll, which supported a peak growth rate of 0.675 g L−1 per day. Meanwhile, increased expression of key enzymes related to lipid synthesis (e.g., acetyl coenzyme A) enhanced lipid productivity to 192.10 mg L−1 per day. During the growth process, the carbon content of the dried biomass increased from 47.00% to 56.02% while the nitrogen content decreased from 6.36% to 1.99%. The unsaturated fatty acids decreased and saturated fatty acids increased, thus improving the anti-oxidation stability of microalgal biodiesel.