Miracle-dz/UniFAR-FTUs huggingface dataset:
Cellular mechanisms involved in stress-induced coma and CNS spreading depression in the locust.

Spreading depression (SD) is an interesting and important phenomenon due to its role in mammalian pathologies such as migraine, seizures, and stroke. Until recently investigations of the mechanisms involved in SD have mostly utilized mammalian cortical tissue, however in my thesis I demonstrated that SD-like events occur in the CNS of an invertebrate model, Locusta migratoria. Locusts enter comas in response to stress during which neural and muscular systems shut down until the stress is removed, and this is believed to be an adaptive strategy to survive extreme environmental conditions. Using the ventilatory central pattern generator (vCPG) as a model circuit I was able to show that stress-induced arrest of vCPG function is associated with SD-like events in the locust metathoracic ganglion (MTG) that closely resemble cortical SD (CSD) in many respects, including mechanism of induction, extracellular potassium ion ([K]o) changes, and propagation in areas equivalent to mammalian grey matter. SD-like events in the locust were characterized as abrupt [K]o increases associated with electrical activity silence in the locust CNS that propagate to other areas within the MTG. In this thesis I described the generation of comas by several cellular stressors (hyperthermia, metabolic stressors, Na/K-ATPase inhibition, and KCl) and the associated SD-like events in the locust, provide a description of the similarities to CSD, and show how they can be manipulated both by stress preconditioning and pharmacologically. I showed that hyperthermic vCPG arrest can be preconditioned by prior heat shock (HS) treatment and induced-thermotolerance was associated with an increased rate of [K]o clearance associated with vCPG recovery that was not linked to changes in ATP levels or total
Interactome INSIDER: a multi-scale structural interactome browser for genomic studies

Protein interactions underlie nearly all known cellular function, making knowledge of their binding conformations paramount to understanding the physical workings of the cell. Studying binding conformations has allowed scientists to explore some of the mechanistic underpinnings of disease caused by disruption of protein interactions. However, since experimentally determined interaction structures are only available for a small fraction of the known interactome such inquiry has largely excluded functional genomic studies of the human interactome and broad observations of the inner workings of disease. Here we present Interactome INSIDER, an information center for genomic studies using the first full-interactome map of human interaction interfaces. We applied a new, unified framework to predict protein interaction interfaces for 184,605 protein interactions with previously unresolved interfaces in human and 7 model organisms, including the entire experimentally determined human binary interactome. We find that predicted interfaces share several known functional properties of interfaces, including an enrichment for disease mutations and recurrent cancer mutations, suggesting their applicability to functional genomic studies. We also performed 2,164 de novo mutagenesis experiments and show that mutations of predicted interface residues disrupt interactions at a similar rate to known interface residues and at a much higher rate than mutations outside of predicted interfaces. To spur functional genomic studies in the human interactome, Interactome INSIDER (http://interactomeinsider.yulab.org) allows users to explore known population variants, disease mutations, and somatic cancer mutations, or upload their own set of mutations to find enrichment at the level of protein domains, residues, and 3D atomic clustering in known and predicted interaction interfaces.
Fitness‐related offspring sex allocation of Anastatus disparis, a gypsy moth egg parasitoid, on different‐sized host species

Anastatus disparis (Ruschka) (Hymenoptera: Eupelmidae) is an egg parasitoid and considered a potential biological control agent of the gypsy moth, Lymantria dispar (L.) (Lepidoptera: Lymantriidae). Only male offspring of A. disparis emerge from single eggs of L. dispar in the laboratory, and A. disparis exhibits low parasitism on L. dispar in the field. We therefore selected several lepidopteran species with various body sizes to evaluate the optimal egg size for hosting A. disparis. In addition, we explored whether the nutritional content of a single L. dispar egg influences the sex of A. disparis offspring and why female offspring can be reared from L. dispar eggs in the field. The results indicated that host egg size decisively influenced the body size and sex ratio of the parasitoid offspring. Therefore, larger hosts, especially the largest eggs of Antheraea pernyi Guérin‐Méneville (Saturniidae), might increase the fitness of A. disparis females. Lymantria dispar eggs concealed in the larger egg shell of A. pernyi produced female A. disparis, suggesting that adult A. disparis should prefer hosts with larger bodies and that the nutritional content of L. dispar eggs did not play a decisive role in the sex allocation of A. disparis. The results also indicated that the egg mass and the fur cover of L. dispar egg masses might be the key factors inducing female A. disparis to lay female offspring in L. dispar eggs.
OCCURRENCE AND CHARACTERIZATION OF Colletotrichum fuscum

During 2012–2014 in southeastern Poland the species Colletotrichum fuscum was isolated from the leaves of oregano (Origanum vulgare L.) showing the symptoms of necrotic, concentrically zoned spots with a lighter center and a slightly raised edge. Morphology of nine randomly chosen isolates from the fungus population and reference isolate CBS obtained from CBS-KNAW Fungal Biodiversity Centre were studied. Each isolate was cultured on PDA medium, at the temperatures 24°C for 14 days. The character of the cultures, the color of the averse and the reverse, the formation of morphological structures of the fungus, i.e. acervuli, conidia, appressoria and chlamydospores were studied. Ultrastructural observations of morphological structures were undertaken using scanning electron microscopy. The presence of setose acervuli, conidia, chlamydospores and appressoria was visible. Moreover, studies on the biotic effect between C. fuscum and other species of phyllosphere fungi of oregano showed that all tested fungi inhibited the growth of C. fuscum, but the size of the limiting effect was different. Fungi from genera Trichoderma and Clonostachys were found out to be the most effective and positive antagonists. Alternaria alternata, Botrytis cinerea and Fusarium spp. – despite the high values of IBE were considered negative antagonists.
Biochemical Responses of Soybean (Glycine max L. Merr.) to Proton Beam Irradiation

The present study evaluated the biochemical effects of proton beam irradiation in soybean. Seeds of two Korean elite cultivars (Kwangan and Pungsannamul) were irradiated by a 57-MeV proton beam in the range of 50-400 Gy. We measured the contents of malondialdehyde (MDA), antioxidant enzymes, and chlorophyll. MDA contents in proton beam-irradiated plants were higher than those in control plants. The activity of antioxidant enzymes differed between the two cultivars. In Kwangan, ascorbate peroxidase (APX) activity increased by 29% relative to the control at 55 Gy and decreased by 58% at 308 Gy. Superoxide dismutase (SOD) and peroxidase (POD) activities decreased by 47 and 25% relative to the control at 55 Gy and recovered to 87 and 56% of that at 55 Gy with 172 Gy and 117 Gy, respectively. In Pungsannamul, APX and SOD decreased by 32 and 35% relative to the control at 62 Gy, with the highest value observed at 243 Gy. In terms of the chlorophyll content, the two varieties responded similarly to proton beam irradiation, whereas in Kwangan, no significant reduction was observed above 100 Gy when compared with the control. Proton beam irradiation affected chlorophyll b more than chlorophyll a. These results show that the activity of antioxidant enzymes decreased in response to irradiation with approximately 50 Gy proton beams, then increased gradually with increasing doses, followed by a moderate decrease at higher doses. According to correlation with MDA contents and antioxidant enzyme activities, defense system of Pungsannamul was less activated by proton-beam irradiation than that of Kwangan.
Risk Factors of Osteoporosis in Rheumatoid Arthritis Patients; Glucocorticoid, Inactivity, or Nutrient Deficiencies

Received:April 21, 2017, Revised:April 22, 2017, Accepted:April 22, 2017 Corresponding to:Yoon-Kyoung Sung, Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, 222 Wangsimni-ro, Seongdong-gu, Seoul 04763, Korea. E-mail:sungyk@hanyang.ac. kr Copyright c 2017 by The Korean College of Rheumatology. All rights reserved. This is a Free Access article, which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited. Editorial pISSN: 2093-940X, eISSN: 2233-4718 Journal of Rheumatic Diseases Vol. 24, No. 2, April, 2017 https://doi.org/10.4078/jrd.2017. 24.2. 63
Effects of Varying Dietary Protein Level on Growth, Nutrient Utilization and Body Composition of Juvenile Blackfin Sea Bream, Acanthopagrus berda (Forsskal, 1775)

The optimum dietary protein requirement of juvenile blackfin sea bream, Acanthopagrus berda (live body weight 8.1-89.2 g) was investigated. Fish juvenile were collected from Sonari Channel Hawks bay and were maintained in recirculating water system (rearing glass aquaria of 120 lit, water temperature 25C). Four isoenergetic (20.1 kJ/g digestible energy) diets were formulated to contain protein levels of 20%, 30%, 40% and 50%, and fed one of the experimental diets at a daily ration of 2% body weight for 90 days. Higher weight gain and growth rate were observed in the fish fed with 40% and 50% protein diets. Broken line regression analysis generated an optimum protein levels of 42.0% for blackfin sea bream. Fish whole body composition showed that lipid content of the fish fed with 40% and 50% was lower and moister content was higher. The hepatosomatic index (HSI) of the fish fed with 40% and 50% was greater than that of the fish fed with 20%-30% protein level. No significant difference was observed in protein and ash contents of whole fish for the diets of 20% to 50% protein. Fish fed 40% and 50% protein diets showed higher nitrogen gain and nitrogen retention efficiency than those fed on other diets. These results suggest that under similar culture conditions, the optimum protein level of the juvenile sea bream (from initial weight of 8.1 g to 89.2 g) is 42.0%.
Optimization of medium components for the production of milk clotting enzyme by a filamentous fungus A26 in solid state fermentation using rice bran

Microbial production of milk clotting enzyme by an airborne filamentous fungus A26 was studied in solid state fermentation using rice bran as a substrate. Effects of various nitrogen sources on milk clotting activity (MCA) and specific activity of milk clotting/mg protein (SPA) were investigated using a completely randomized design. The highest levels of MCA (1,467 S.U./ml) and SPA (3,861 S.U./mg protein) were obtained when ammonium sulfate was supplied to provide 0.05% nitrogen. Impacts of glucose, lactose, and ammonium sulfate on MCA were evaluated by response surface methodology. The results suggested that glucose, lactose, and ammonium sulfate enhanced MCA. Within the ranges of concentration studied, the highest MCA at 1,727 S.U. /ml was predicted by the model when glucose, lactose, and ammonium sulfate were supplied at 0.040, 0.040, and 0.004 g/g rice bran, respectively
Development of Novel Approach for In Situ Generation of Oxidative Stress using KillerRed in C. elegans

Oxidative stress has been implied in a wide variety of diseases, such as cancer, myocardial infarction, and neurodegenerative diseases including Parkinson's diseases (PD). PD is characterized by the degeneration of dopaminergic (DA) neurons; genetic studies have identified gene mutations causal to PD. Accumulating studies hypothesize that these genes protect DA neurons against oxidative stress. However, lack of experimental tools to target oxidative stress in specific cells has prevented direct evaluation of the hypothesis. We established a novel method to use KillerRed (KR), a genetically-encoded protein that generates radicals upon light activation. We showed its efficacy in live animals by cell-specific ablation of neurons in C. elegans. We applied KR to degenerate DA neurons. By controlling the level of stress via activation light, the protective role of PD-gene, LRRK2, against oxidative stress was confirmed. Thus, we established a method to address the role of oxidative stress in a cell-specific manner.
Nutrient status of soil and winter wheat (Triticum aestivum L.) in response to long-term farmyard manure application under different climatic and soil physicochemical conditions in the Czech Republic

ABSTRACT Long-term field experiments with annual crop rotation were established in 1955 and 1956 at three locations (Lukavec, Čáslav, Ivanovice) in the Czech Republic, which differ in their climate and soil physicochemical properties. The effect of cattle farmyard manure (FM) and a combination of FM and mineral (NPK) fertilizer application (FMNPK) on nutrient status of soil and the response of winter wheat, and nutrient content of wheat grain and straw were evaluated after ~60 years since the establishment. The results showed higher pseudototal (aqua regia soluble) contents of phosphorus and sulfur from FM and FMNPK application compared with control, whereas the labile and moderatory labile content of individual nutrients (except calcium) varied between treatments. The nutrient content of wheat grain and straw was more significantly (p < 0.05) affected by the location and growing season than by the fertilizers. The substantial changes in wheat nutrient uptake occurred for the weakly acidic loamy Gleyic Phaeozem, whereas the lowest response due to fertilizer application was observed for the acidic Cambisol (sandy loam texture). Even after six decades of FM and FMNPK application, the effectiveness of these treatments was predominantly influenced by the soil and climatic conditions at the individual locations.
THIS ARTICLE HAS BEEN RETRACTED  Repeated massage‐like stimulation induces long‐term effects on nociception: contribution of oxytocinergic mechanisms

Massage‐like stroking induces acute antinociceptive effects that can be reversed by an oxytocin antagonist, indicating activation of oxytocin on endogenous pain controlling systems. We now demonstrate an increase in hindpaw withdrawal latencies (HWLs), in response to thermal and mechanical stimuli, which was present after six treatments of massage‐like stroking every other day and which continued to increase through the remaining seven treatments. Repeated massage‐like stroking also resulted in increased oxytocin‐like immunoreactivity (oxytocin‐LI) levels in plasma and periaquaductal grey matter (PAG). Furthermore, increases in HWLs were also present after injections of oxytocin into the PAG (0.1, 0.5 and 1.0 nmol). Intra‐PAG oxytocin injection of 1 nmol followed by 1 or 20 nmol of naloxone attenuated the increments in HWL. Also, there was a dose‐dependent attenuation of the oxytocin‐induced antinociceptive effects following intra‐PAG injection of the µ‐opioid antagonist β‐funaltrexamine (β‐FNA) and the κ‐opioid antagonist nor‐binaltorphimine (nor‐BNI) but not the δ‐antagonist naltrindole. The long‐term antinociceptive effects of massage‐like stroking may be attributed, at least partly, to the oxytocinergic system and its interaction with the opioid system, especially the µ‐ and the κ‐receptors in the PAG.
Settlement of Ostrea edulis is determined by the availability of hard substrata rather than its nature: implications for stock recovery and restoration of the European oyster

1. Since the collapse of the Ostrea edulis stock in the mid-1800s the oyster has struggled to re-establish itself in self-sustaining assemblages in Europe. 2. It is now widely recognized that O. edulis is an integral component of a healthy biologically functional benthic environment and as such, the restoration of wild stocks has become a matter of urgency. 3. A major limiting factor in O. edulis stock recovery is the availability of suitable substrate material for oyster larvae settlement. 4. This research re-examined the larval settlement potential of several naturally occurring in-situ shell materials (e.g. Mytilus edulis , Modiolus modiolus , O. edulis ) with the aim of determining the most appropriate for large-scale restoration projects. 5. A positive correlation between available shell material and settlement was determined and analysis using PERMANOVA did not identify an attachment preference by O. edulis to any particular shell type. 6. The findings suggest that if restoration efforts were coordinated with applied hydrodynamic and habitat suitability modelling in conjunction with naturally occurring shell substrate concentrations, a cost-effective recovery for O. edulis assemblages in the wild could be achieved.
Dynamique, evolution et expression de genomes de bacteries lactiques : cas du metabolisme des pyrimidines chez lactobacillus plantarum ccm 1904

Lactobacillus plantarum est une bacterie lactique utilisee pour diverses fermentations dans l'industrie agro-alimentaire. Malgre la grande taille de son genome, la souche ccm 1904 est auxotrophe pour de nombreux acides amines et vitamines ; elle est cependant prototrophe pour les pyrimidines. Par sa grande diversite d'organisations genomiques, le metabolisme des pyrimidines constitue un modele interessant pour l'etude de la dynamique et de l'evolution des genomes. Chez plusieurs bacteries gram positives, les genes intervenant dans la biosynthese de novo des pyrimidines sont organises en un grand operon pyrr-p-b-c-aa-ab-k-db-f-e. Mais l'operon pyr de l. Plantarum est incomplet : pyrr-b-c-aa-ab-db-f-e. Par ailleurs, les bacteries lactiques possedent un second gene pyrd distinct (pyrda) ; pyrda et pyrdb codent chacun une dihydro-orotate deshydrogenase fonctionnelle. Les travaux realises au cours de cette these ont permis de mettre en evidence plusieurs originalites propres a l. Plantarum : - l'existence d'un gene pyrd unique, de type b. La construction d'un mutant delete du gene pyrdb par mutagenese dirigee par pcr a conduit a l'obtention d'une souche auxotrophe pour les pyrimidines. Le gene pyrda aurait ete perdu par adaptation a de nouvelles niches ecologiques ou sa presence n'est pas indispensable ; - l'absence du gene pyrk codant une sous-unite de la dihydro-orotate deshydrogenase b. Son absence pourrait etre liee a la non-utilisation du fer par les lactobacilles ; - le groupement, ailleurs sur le chromosome, des genes upp (uracile phosphoribosyltransferase) et pyrp (uracile permease) intervenant dans la voie de sauvetage de l'uracile. Cette situation pourrait correspondre a un deplacement recent du gene pyrp hors de l'operon pyr. De plus, l'etude de mutants de regulation construits par mutagenese dirigee par pcr a permis de montrer que l'expression de l'operon pyr est regulee par attenuation transcriptionnelle mediee par la proteine pyrr.
Effect of aqueous extracts of allelopathic Artemisia annua on germination andearly growth of Isabgol (Plantago ovate)

In order to consider the allelopathic effect of aqueous extracts of Artemisia annua on germination and early growth of Isabgol (Plantago ovate), an experiment was conducted using a completely randomized design with five treatments (control, 25%, 50%, 75% and 100% concentration of aqueous extracts) and four replications in the laboratory. Results analyzed by SAS software with means subjected to Duncan test at 5% probability level showed that effect of different concentrations of Artemisia annua extract was significant on germination percentage and rate, plumule and radicle lengths and fresh and dried weights of seedlings.
Genetic Parameters for Clinical Mastitis, Fertility and Somatic Cell Score in Czech Holstein Cattle

Abstract Cases of mastitis (CM) from 38,236 lactations belonging to 16,497 cows were recorded on seven farms in the Czech Republic from 1996 to 2014. Clinical mastitis was analyzed with linear animal model as an all-or-none trait for each recorded lactation (CM305) and separately for each trimester of lactation (CM1, CM2, and CM3). Bivariate linear animal models were used to estimate the genetic correlation between these CM traits and lactation means for somatic cell score (SCS305), the interval between calving and first insemination (INT) and days open (DO). Factors included in the linear model were parity, herd, year of calving, calving season, fixed linear and quadratic regression on age at first calving, fixed linear and quadratic regression on milk production in the corresponding parity, permanent environmental effect of the cow, and additive genetic effect of the cow. Estimated heritabilities of the CM traits ranged from 0.01 to 0.03. Permanent environmental effects accounted for approximately two-thirds of the phenotypic variance. Genetic correlations of SCS305 with CM traits were 0.85±0.029, 0.81±0.086, 0.82±0.087, and 0.67±0.088 for CM305, CM1, CM2, and CM3, respectively. Genetic correlations of INT with CM305, CM1, CM2, and CM3, respectively, were 0.22±0.065, 0.19±0.084, 0.20±0.121 and 0.15±0.121: and genetic correlations of DO and the four CM traits were 0.28±0.079, 0.26±0.101, 0.43±0.134, and 0.15±0.131. For the 140 sires in the dataset, Spearman rank correlations among breeding values for the four CM traits and for SCS305 were uniformly high at 0.99±0.001.
The production of VLCPUFAs in plants

Very long-chain polyunsaturated fatty acids (VLCPUFAs) like eicosapentaenoic acid (EPA) or docosahexaenoic acid (DHA) are health-beneficial components in the human diet. However, due to overfishing and pollution of the sea, oily sea fish as the main dietary source for these important fatty acids is decreasingly available. A promising solution to this shortfall is the production of VLCPUFAs in transgenic oilseed crops. Although this goal has already been reached to some extent, there are still challenges which need to be met. These are the specific accumulation of VLCPUFAs in the neutral lipid fraction of seeds as well as absolute product yields, especially in case of DHA. Those aspects of heterologous VLCPUFA production might be improved by transfer of specific acyltransferases and superior desaturases from suitable VLCPUFA-producing organisms into seed lipid metabolism. Therefore, nucleotide sequences from two Ostreococcus species potentially encoding acyltransferases or a Δ4-desaturase, respectively, were characterized by expression in yeast. In these studies, none of the analyzed putative acyltransferases revealed specificity for VLCPUFAs. In contrast, the front-end desaturase Old4p from Ostreococcus lucimarinus was found to prefer VLCPUFAs to shorter-chain fatty acids and to desaturate both (n-3)- and (n-6)-substrates bound to lipids. In addition to the yeast experiments, acyltransferases were also introduced individually and in combination with VLCPUFA-producing enzymes into Arabidopsis thaliana. Upon separate expression, a putative acyl-coenzyme A:lyso-phosphatidylcholine acyltransferase (LPCAT) sequence from O. lucimarinus produced the strongest effects by enhancing levels of polyunsaturated fatty acids at the expense of monounsaturated fatty acids in total seed lipids. However, the combination of acyltransferases with VLCPUFA-producing enzymes did not lead to higher yields in transgenic seeds. Besides the expression studies performed with the microalgal acyltransferase sequences, also endogenous acyltransferase activities of the two different host plants A. thaliana and Camelina sativa were investigated by using both species for VLCPUFA-production and comparing product yields.