Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation of genes similar to DREB1/CBF from sweet cherry (Prunus avium L.)

The C-repeat (CRT) dehydration responsive element (CRT/DRE) is a cis-acting DNA element, which stimulates transcription in response to low temperature and drought stress. Recently, the DREB1/CBF (regulatory factor that binds to the CRT/DRE elements and promotes expression of multiple low-temperature-induced genes resulting in cold-acclimation) has been identified in Arabidopsis thaliana L. We have isolated a genomic clone from Prunus avium L. (sweet cherry) that was predicted to include three DREB1/CBF-like genes. Two (D2A and D2B) of the genes were deduced to have a complete open reading frame (ORF) and the other (D2Ctr : truncated D2C) was deduced to have an incomplete ORF. Each putative protein had an EREBP/AP2 DNA binding domain motif and a potential nuclear localization signal in the N-terminal region. Furthermore, the D2A and the D2B proteins had an acidic C-terminal region. The D2A and the D2B proteins were found to be 53 and 53.5% identical to DREB1B/CBF1, respectively. However, the EREBP/AP2 conserved domain of the three D2 proteins showed a high identity (74-79%) with that of each DREB1/CBF. In addition, the TATA-box and G-box sequences, and MYB- and MYC-recognition sites were predicted along with in the 5' other conserved sequences of all three genes. The expression of the D2 genes was found to be induced by low temperature in P. avium.
Ablastic and Trypanocidal Antibodies against Trypanosoma Duttoni

The non-pathogenic trypanosomes, the members of which infect various rodents and are morphologically similar to Trypanosoma lewisi of the rat, present a number of immunological problems of peculiar interest. As far as these infections have been studied, they are characterized by an initial period of rapid reproduction of the parasites followed by a period during which reproduction is either completely inhibited or greatly reduced, and they are generally terminated by self-cure with a subsequent immunity of variable length. This peculiar development, which has been studied extensively in T. lewisi, is associated with the formation of the two following antibodies (Taliaferro, 1932): (1) The inhibition of reproduction is associated with a passively transferable antibody, termed ablastin, which has the specific property of inhibiting reproduction of the organisms and possesses many of the classical features of ordinary antibodies, but differs from them in that it exhibits no marked in vitro affinity for the organisms.
Ergot alkaloid concentrations in tall fescue hay during production and storage.

Common tall fescue [Lolium arundinaceum (Schreb.) Darbysh. = Schedonorus arundinaceus (Schreb.) Dumort. ] is infected with a fungus that produces ergot alkaloids, a class of compounds associated with fescue toxicosis. The objective of this research was to monitor the change in concentrations of ergot alkaloids from time of clipping through storage of tall fescue hay. A 2-yr field study was conducted in Mt. Vernon, MO, in which tall fescue was baled at high moisture (204-219 g H 2 O kg ―1 dry matter [DM]) and low moisture (102-112 g H 2 O kg ―1 DM) then stored for 18 mo. Hay samples were collected over the 540-d period from clipping through storage and analyzed for ergovaline and total ergot alkaloid concentration. Data were analyzed using standard ANOVA procedures and break-point regression. In both years, ergovaline concentrations decreased sharply within the first month after harvest and gradually over the remaining 17 mo. In three of the four cases, most of the ergovaline disappearance occurred within 3 d after clipping. The final ergovaline concentration remained above 250 μg kg ―1 DM, which is still considered toxic to livestock. In the first year, ergot alkaloid concentration followed a pattern similar to ergovaline concentration. In the second year, however, the decrease in total ergot alkaloid was gradual throughout the entire 18 mo. A general recommendation to producers would be to delay feeding toxic tall fescue hay until at least 1 mo after clipping.
Flavonols from the Ripe Fruits of Opuntia ficus‐indica Var. saboten Protect Neuronal PC‐12 Cells against Oxidative Stress

Fruits of prickly pear cactus Opuntia ficus-indica have been traditionally used as a folk medicine with various pharmacological activities, partly due to their antioxidative flavonoids. The ripe fruits of O. ficus-indica var. saboten were extracted with 70% v/v aqueous ethanol to obtain phenolic extracts, which were separated into five fractions of n-hexane, chloroform, ethyl acetate, n-butanol and water. The ethyl acetate fraction showed the highest levels of total phenolics, total flavonoids and antioxidant capacity among the fractions tested. A reversed-phase high-performance liquid chromatography and quadrupole time-of-flight liquid chromatography-mass spectrometry analysis of the ethyl acetate fraction revealed seven major flavonols: isorhamnetin-3-O-glucoside, isorhamnetin-3-O-rutinoside, kaempferol, kaempferol-3-O-glucoside, kaempferol-7-O-neohesperidoside, quercetin and quercetin-3-methylether. The ethyl acetate fraction increased the in vitro viability of neuron-like PC-12 cells against intracellular oxidative stress in a dose-dependent manner. These results suggest that the ethyl acetate fraction rich in flavonols protecting neuronal cells from oxidative stress may be utilized as a functional food ingredient for nutraceuticals. Practical Applications Fruits of Opuntia ficus-indica var. saboten are edible berries with a thick skin and many seeds, and have long been used as an oriental folk medicine with various health-promoting effects, in part due to antioxidative phenolics. Antioxidative flavonols such as isorhamnetin, kaempferol and quercetin in the O. ficus-indica var. saboten ripe fruit were identified and quantified as major phenolics, indicating that its extract can be standardized to use as an antioxidant source for product development in food manufacture. The O. ficus-indica var. saboten ripe fruit phenolics attenuated intracellular oxidative stress and reduced the release of intracellular lactate dehydrogenase in the cytosol of neuron-like PC-12 cells. Therefore, the ethyl acetate fraction rich in flavonols might be utilized as a food ingredient for nutraceuticals.
Complexation between milk proteins and polysaccharides via electrostatic interaction: principles and applications – a review

Summary This article details recent research conducted on the complexation between milk proteins and polysaccharides and the properties of the complexes, and the application of such relationships to the food industry. Complexation between proteins and polysaccharides through electrostatic interactions gives either soluble complexes in a stable solution or insoluble complexes, leading to phase separation. The formation and the stability of these complexes are influenced by pH, ionic strength, ratio of protein to polysaccharide, charge density of protein and polysaccharide as well as processing conditions (temperature, shearing and time). The functional properties of milk proteins, such as solubility, surface activity, conformational stability, gel-forming ability, emulsifying properties and foaming properties, are improved through the formation of complexes with polysaccharides. These changes in the functional properties provide opportunities to create new ingredients for the food industry.
Fractal Analysis for Morphological Description of Corn Roots under Nitrogen Stress

A means of quantification of plant root branching, specifically under stress, is of importance for evaluating the contribution of plant roots to water and nutrient uptake and subsequently plant growth. An experiment was conducted to describe the morphology of corn (Zea mays L.) root systems using fractal analysis and also to determine if a root's fractal dimension (D) is altered by N stress. Corn genotypes (B73 × LH105 and N74 × Mo17) were planted in peg boxes, 1.2 m long, 1.2 m deep, and 0.05 m wide filled with 20:80 soil to sand mixture and were grown with N rates of 0, 10, 20 and 30 mg kg −1 . Thirty-nine days after planting, the mixture was gently washed from the roots and the roots were divided into nine sections (squares of side 304.8 mm) and slide photographs were taken from each section [. ]
Effects of Heart Fatty Acid-binding Protein Genotype on Intramuscular Fat Content in Duroc Pigs Selected for Meat Production and Meat Quality Traits

Using multi-trait animal model BLUP, selection was conducted over seven generations for growth rate (DG), real-time ultrasound loin-eye muscle area (LEA), backfat thickness (BF), and intramuscular fat content (IMF) to develop a new line of purebred Duroc pigs with enhanced meat production and meat quality. This study was intended to investigate the relationship between restriction fragment length polymorphism (RFLP) of a heart fatty acid-binding protein (H-FABP) gene and intramuscular fat content (IMF) of this Duroc purebred population. The present experiment examined the RFLP of 499 slaughtered pigs. The DNA was separated from the blood or ear tissue of the pigs, which were slaughtered at 105 kg of body weight. Intramuscular fat content of the longissimus muscle was measured using chemical analysis. A significant difference was detected in the breeding value of IMF among the H-FABP PCR RFLP genotypes. The AA genotype has a significantly larger positive effect on the IMF breeding value than do the Aa and aa genotypes for the MspI RFLP. In addition, the DD genotype has a significantly greater positive effect on IMF breeding value than the Dd and dd genotypes for the HaeIII RFLP. For the HinfI RFLP, the hh genotype has a significantly larger positive effect on IMF breeding value than the HH genotype. Multiple regression analysis was performed using the IMF breeding values as the dependent variable and the three H-FABP genotypes as independent variables. Results revealed that the contribution of the genotypes to variation in IMF breeding values was approximately 40%. These results demonstrated that H-FABP RFLPs affect IMF in this Duroc population.
Differential Dynamic Signal Processing in Frog Vestibular Neurons

XX Central vestibular neurons process head movement-related signals. Characterization of these neurons and the knowledge about their connectivity is crucial to confer them a particular role in gaze and posture stabilization. Different aspects of the sensory-motor transformation were studied in vestibular neurons recorded from isolated brain preparations of adult frogs. The preparation includes the N.VIII with its individual labyrinthine nerve branches. XX Vestibular neurons subdivide into tonic and phasic neurons based on differential intrinsic membrane properties and might be suited to process different dynamic components of vestibular signals. Intracellular injections of oscillatory frequency-modulated currents showed that tonic neurons form neuronal elements with low-pass filter properties. In contrast, phasic neurons exhibited a pronounced subthreshold resonance at ∼40 Hz due to the activation of prominent potassium conductances, which conferred to these neurons band-pass filter-like properties. In addition, the different filter behaviors of the two neuronal subtypes correlate with a differential processing of synaptic sensory inputs that renders tonic neurons well-suited for synaptic integration and phasic neurons for signal detection. XX The different response dynamics of labyrinthine synaptic inputs in tonic and phasic vestibu-lar neurons is likely the result of a combination of specific intrinsic membrane properties and a differential contribution of synaptic inputs from local circuits. Application of GABAergic and glycinergic antagonists revealed that a semicircular canal-specific disynaptic inhibition is present only in phasic but not in tonic neurons. This inhibitory input on phasic neurons renders the monosynaptic excitatory response more transient, which complies with the high-dynamic, intrinsic properties of this neuronal subtype. Tonic neurons, in contrast, receive inhibitory inputs with considerably longer latencies and are thus not controlled by a short-latency inhibitory side-loop. XX The simulation of natural head movement-related activity patterns of labyrinthine afferents by electrically stimulating the afferents with frequency-modulated pulse trains revealed distinct differences in the synaptic response dynamics of tonic and phasic neurons. Tonic neurons transformed the frequency waveform of this stimulus in an almost linear fashion, whereas the synaptic compound responses in phasic neurons exhibited large peak leads thereby generating highly asymmetric response profiles. A modeling approach showed that the asymmetry of the latter neurons was due to membrane properties but was substantially reinforced by GABAergic and glycinergic inhibitory inputs from cerebellar and local vestibular networks. XXThus, the co-adaptation of intrinsic and network properties establishes two distinct neuron types that are well-suited for parallel processing of head movement-related signals with different dynamics.
Relationship between the vitellin concentration in the hemolymph and oocyte necroses during the annual reproduction cycle in the Japanese scallop, Mizuhopecten yessoensis

Summary A specific and sensitive enzyme-linked immunosorbent assay (ELISA) was developed for measurement of vitellin in the hemolymph and ovary of the Japanese scallop, Mizuhopecten yessoensis. We observed two peaks of vitellin concentration in the hemolymph during the annual reproductive cycle. The peaks corresponded with the occurrence of two types of oocyte necrosis, type I and type II. Type I necrosis occurs in the early phase of vitellogenesis and is characterized by necrotic oocytes that do not have a germinal vesicle. Type II necrosis occurs during the mid-to late-phase of vitellogenesis and peaks just before spawning. It is characterized by necrotic oocytes whose germinal vesicle is strongly stained by eosin, i.e., the germinal vesicle has lost basophilic properties. In immunohistochemical examinations, oocytes and auxiliary cells (which are in contact with oocytes), reacted with anti-vitellin serum; mid-gut gland, adductor muscles, intestine, gonoduct, kidney, and gill do not. These results suggest that the presence of vitellin in the hemolymph is a result of leakage of yolk protein from necrotic oocytes.
Modern pollen spectra from dakhleh oasis, western egyptian desert

Abstract The Dakhleh Oasis lies at the heart of the Western Egyptian Desert. Measurable precipitation occurs at rare intervals and the mean annual rainfall is <0.5 mm. Artesian water supports the pastoral agricultural economy of the oasis. The vegetation consists of fragmentary natural communities of Saharo-Arabian species and a predominant anthropogenic component. Twenty-five samples were analysed for modern pollen—5 Tauber traps placed in a horticultural station; 18 surface muds from permanent pools or ditches; and 2 relict pond sediments on the plateaux above the oasis depression. The Tauber trap spectra are dominated by local, introduced taxa, with small percentages (1–3) of long-distance (Mediterranean region) elements and Saharo-Arabian, native elements (0–2). The relict pond samples and to a lesser extent the ditch and pond muds contain constant though small percentages (5–7%) of native desert species of indicator value, large proportions of ubiquitous taxa (chiefly Cheno-Amaranth, Cyperaceae and G.
Reply from Gordon B. Drummond and Brian D. M. Tom

We thank Dr Hopkins and his co-authors for their trenchant criticism of the articles that have been published in this series. They take us to task for a number of errors and omissions, many of which we would refute, although we do agree that in one case (our statement about 95% confidence intervals) we were wrong. We wrote: The 95% confidence values for the mean indicate that we’d be 95% likely to get another estimate of the mean within this range, using another set of data samples from the same population. This was incorrect. When samples are taken from a population, each sample will yield a different estimate of the confidence interval of the mean. If we were to take sample after sample from a population, and use each sample to calculate a 95% confidence interval for the mean value, in the long run 95% of these confidence intervals would include the actual mean of the entire population. In many other respects, we appear to agree. We suggest that their final judgment of our objectives should be more positive as we develop the themes further. We are far from the first to be aware that data presentation and analysis need to be improved. Dr Hopkins has himself written of the difficulty in using ‘innovative and controversial practices’ and cited previous attempts to promote better practice, including several of his own, although we read a note from the editor of one of his articles that he himself has been subject to strong disagreement (Hopkins et al. 2009). Why have previous attempts to improve data presentation and statistical rigour failed? There are probably several reasons, perhaps the most important of which is the
Taxonomy, phylogeny and biogeography of the lichen genus Peltigera in Papua New Guinea

The lichen genus Peltigera is represented in Papua New Guinea by 15 species, including 6 described as new for science: P. cichoracea, P. didactyla, P. dolichorhiza, P. erioderma, P. extenuata, P. fimbriata sp. nov., P. granulosa sp. nov., P. koponenii sp. nov., P. montis-wilhelmii sp. nov., P. nana, P. oceanica, P. papuana sp. nov., P. sumatrana, P. ulcerata, and P. weberi sp. nov. Peltigera macra and P. tereziana var. philippinensis are reduced to synonymy with P. nana, whereas P. melanocoma is maintained as a species distinct from P. nana pending further studies. The status of several putative taxa referred to P. dolichorhiza s. lat. in the Sect. Polydactylon remains to be studied on a wider geographical scale and in the context of P. dolichorhiza and P. neopolydactyla. The phylogenetic affinities of all but one regional species (P. extenuata) are studied based on inferences from ITS (nrDNA) sequence data, in the context of a broad taxonomic sampling within the genus. A key to all species is provided and available data on their ecology and general distribution are discussed. The species P. canina, P. horizontalis, P. laciniata, P. malacea, P. polydactylon and P. tomentosa are excluded from the lichen checklist of Papua New Guinea. All lichenicolous fungi observed on Peltigera thalli in Papua New Guinea are listed.
Lignocellulolytic enzymes produced by tropical white rot fungi during biopulping of Acacia mangium wood chips

Pycnoporus coccineus and Coriolus versicolor are among the tropical white rot basidiomycetes that degrade lignin selectively. In this research work, crude enzyme produced during biopulping using both fungi were extracted, filtered and assayed using specific substrates. Both the peroxidases enzyme activities and residual lignin content were measured for the incubation period of 20, 40 and 60 days of biopulping. For both fungi, manganese peroxidase is predominant and highly expressed thus shows the highest rate compared to other ligninolytic enzymes activities in all of extract preparations. After 60 days of inoculation, manganese peroxidase activities are recorded as 270.51 U/mL and 274.36 U/mL for C. versicolor and P. coccineus, respectively. On the evaluation of the lignin content after biopulping, the lignin content showed significant decreased. Wood chip biotreated with C. versicolor showed higher percentage in lignin loss (9.42%) compared to with P. coccineus (8.10%).
Modulation of inflammatory and immune responses by short-chain fatty acids.

: Short-chain fatty acids (SCFAs) are the main metabolic products of anaerobic bacterial fermentation in the intestine. In addition to their important role as fuel for intestinal epithelial cells, SCFAs modulate different processes in the gastrointestinal (GI) tract and in other tissues such as adipose and immune tissues. In this chapter, we first present a brief description of basic aspects of SCFA physiology, such as production, absorption and metabolism. The main mechanisms by which SCFAs act on cells and the effects of these fatty acids in isolated leukocytes are then discussed. We also highlight the results obtained by studies performed in vivo using SCFAs in the treatment of inflammatory pathologies. A brief discussion about the perspectives in this research field is presented at the end of the chapter.
Structural and functional impacts of albumin oxidation by hypochlorite: Possible changes in drug binding characteristics upon myeloperoxidase-mediated oxidation in Vivo

Interaction of drugs with serum albumin, the most abundant protein in plasma, has a great significance in pharmaceutical sciences. It can affect the biological activity, toxicity, and pharmacokinetics of drugs and design of dosages. Determination of the impact of chemical modifications of albumin and its structural changes upon interaction with drugs are very important when drugs bind with albumin to a significant degree. Hypochlorite is naturally produced by activated phagocytes in vivo at inflammatory conditions. In current study, the effects of hypochlorite-mediated oxidation on the albumin stability, surface hydrophobicity and its interaction with furosemide were investigated using intrinsic and extrinsic fluorescence techniques. Bovine serum albumin (BSA) was chemically modified with sodium hypochlorite under nondenaturing conditions. The Job’s plot indicated that the drug binds to the unmodified and modified BSAs with a 1:1 stoichiometry. Fluorescence quenching data showed that the albumin affinity for the drug as well as its surface hydrophobicity increases under the effect of protein oxidation. Measurement of conformational stability indicated that oxidized BSA is less stable compared to the unmodified protein. Thermodynamic analyses of the binding process showed that the major forces involved in the interaction of furosemide to the unmodified and oxidized BSA are same (hydrophobic). Increment of protein surface hydrophobicity (PSH) as well as the decrement of protein stability may reminiscent of higher protein structural flexibility upon oxidation which may affect the drug binding site.
Linaceae and Ctenolophonaceae especially of Malesia, with notes on their demarcation anf the realtionships with Ixonanthaceae

Linaceae, Ctenolophonaceae and Ixonanthaceae are regarded as separate families. In Linaceae two subfamilies are recognized, only one of which occurs in Malesia, Hugonioideae, with three genera, Hugonia, Indorouchera, Philbornea. In Hugonia two sections are recognized, sect. Hugonia with H. costata Miq. and sect. Durandea with H. jenkinsii F.v. Muell. In Indorouchera two species are recognized, I. contestiana (Pierre) Hall. f. and I. griffithiana (Planch.) Hall. f. Philbornea has only one species, P. magnifolia (Stapf) Hall. f. Ctenolophonaceae contains only the genus Ctenolophon with two species, of which one, C. parvifolius Oliv. , in Malesia. This is a precursor for the Flora Malesiana treatment. Delimitation and subdivision are discussed with chapters on anatomy, floral morphology, embryology, etc.