Miracle-dz/UniFAR-FTUs huggingface dataset:
Unique Epigenetic Features of Ribosomal RNA Genes (rDNA) in Early Diverging Plants (Bryophytes)

Introduction: In plants, the multicopy genes encoding ribosomal RNA (rDNA) typically exhibit heterochromatic features and high level of DNA methylation. Here, we explored rDNA methylation in early diverging land plants from Bryophyta (15 species, 14 families) and Marchantiophyta (4 species, 4 families). DNA methylation was investigated by methylation-sensitive Southern blot hybridization in all species. We also carried out whole genomic bisulfite sequencing in Polytrichum formosum (Polytrichaceae) and Dicranum scoparium (Dicranaceae) and used available model plant methyloms (Physcomitrella patents and Marchantia polymorpha) to determine rDNA unit-wide methylation patterns. Chromatin structure was analyzed using fluorescence in situ hybridization (FISH) and immunoprecipitation (CHIP) assays. Results: In contrast to seed plants, bryophyte rDNAs were efficiently digested with methylation-sensitive enzymes indicating no or low levels of CG and CHG methylation in these loci. The rDNA methylom analyses revealed variation between species ranging from negligible (<3%, P. formosum, P. patens) to moderate (7 and 17% in M. polymorpha and D. scoparium, respectively) methylation levels. There were no differences between coding and noncoding parts of rDNA units and between gametophyte and sporophyte tissues. However, major satellite repeat and transposable elements were heavily methylated in P. formosum and D. scoparium. In P. formosum rDNA, the euchromatic H3K4m3 and heterochromatic H3K9m2 histone marks were nearly balanced contrasting the angiosperms data where H3K9m2 typically dominates rDNA chromatin. In moss interphase nuclei, rDNA was localized at the nucleolar periphery and its condensation level was high. Conclusions: Unlike seed plants, the rRNA genes seem to escape global methylation machinery in bryophytes. Distinct epigenetic features may be related to rDNA expression and the physiology of these early diverging plants that exist in haploid state for most of their life cycles.
Field Efficiency of Humic Substances, Boric Acid and some Novel Insecticides against Aphis gossypii Glover and Bemisia tabaci (Gennadius) on Cotton Plants

Nutritive acids improve the plant growth via increasing its carbohydrates content and nutrients uptake, and enhance the plant resistance to biotic and a biotic stress factors. Accordingly, field experiments were conducted at Sakha Agricultural Research Station, Kafr EL-Sheikh Governorate, Egypt during seasons 2016 and 2017 to evaluate the insecticidal activity of the nutritive acids (boric acid, humic acid and fulvic acid), pymetrozine, dinotefuran and thiamethoxam against Aphis gossypii Glover and Bemisia tabaci (Gennadius) on cotton plants under the field conditions. The toxicity of the binary mixtures of the nutritive acids with the tested insecticides against the two insects was evaluated as well. The tested compounds were applied at their field recommended rates. Pymetrozine, dinotefuran and thiamethoxam applied separately exhibited high efficiency against A. gossypii (causing 90.10 – 97.48% reduction), B. tabaci adults (recording 88.07 – 94.68% reduction) and B. tabaci immature stages (producing 87.29 – 92.43% reduction). Boric acid, humic acid and fulvic acid resulted in a considerable toxicity to both A. gossypii (31.60 – 55.21% reduction) and B. tabaci adults (29.51 – 43.70% reduction) and immature stages (22.46 – 37.94% reduction). Among the tested nutritive acids, humic acid proved to be the most potent against A. gossypii, while fulvic acid was the most effective on B. tabaci. Binary mixtures of the nutritive acids with the tested insecticides resulted in insignificant changes in the insecticides activity against the two pests. These results suggest that boric acid, humic acid and fulvic acid could be effectively used to improve the cotton plant growth (as recommended) and, at the same time, to control A. gossypii and B. tabaci. Further studies are required to clarify the mode of action through which the nutritive acids cause their insecticidal activity against sucking insects on cotton plants.
Quality comparison of retorted Samgyetang made from white semi-broilers, commercial broilers, Korean native chickens, and old laying hens

Objective The aim of this study was to compare the quality characteristics of retorted Samgyetang (Korean ginseng chicken soup) made from white semi-broilers (WSB; Ross× Hyline white, 3 weeks old), commercial broilers (CB; Ross, 4 weeks old), Korean native chickens (KNC; Hanhyup-3-ho, 12 weeks old) and old laying hens (OLH; Hyline white, 72 weeks old) and to explore the possibility of using the carcasses of KNCs and OLHs as raw material for product diversification. Methods Raw and cooked meat quality, fatty acid composition and consumer acceptance were analyzed. Results Among the chicken breeds, OLH and KNC showed a higher shear force value than WSB and CB due to high insoluble collagen contents. However, the meat of KNC was more tender than that of OLH. The meat of OLH was characterized by the lowest moisture content and highest crude fat content. The meat of KNC was characterized by a higher proportion of saturated fatty acids, α-linolenic acid and arachidonic acid than that of OLH. The meat of OLH showed the highest content of unsaturated fatty acid, particularly linoleic acid, in its thigh meat. Electronic nose readings revealed that the meat aroma pattern was clearly different across breeds. OLH had the lowest overall acceptance score, while no differences were found in flavor, texture, juiciness and appearance among WSB, CB, and KNC. Conclusion KNC shows potential as raw material for Samgyetang, while additional preprocessing methods, such as tenderization and fat removal, are required for the utilization of OLH as raw material for retorted Samgyetang.
In vitro activity of fosfomycin on biofilm in community-acquired Staphylococcus aureus isolates

Objective: Staphylococcus aureus is a significant pathogen microorganism that can lead to serious infections. In this study, we researched the activity of biofilm formation and fosfomycin on biofilm in community-acquired S. aureus isolates that were drawn from human noses. Methods: Microtitration plate method was used to determine biofilm formation. The effect of fosfomycin on sessile cells was studied on biofilm matrix composed around plastic beads. The icaA, icaD, icaB, icaC, bap, eno, fnbA, fnbB, clfA, clfB, fib, ebpS, cna and mecA genes were screened by Polymerase Chain Reactions (PCR). Results: S. aureus was isolated from 87 samples (13.2%) out of a total 658 nasal samples. We found that 10 of these isolates (11.4%) were methicillin-resistant S. aureus (MRSA). A total of 86 isolates had the ability to form biofilm. The biofilm inhibitor concentration (BIC) and minimum biofilm eradication concentration (MBEC) of fosfomycin were determined as 8 µg/ml and 32 µg/ml, respectively. In the molecular detection results of biofilm-related genes of these isolates, ica-dependent genes were determined to be quite high. However, no bap gene was observed to be positive in any of the isolates. Among the other genes, the most frequent genes to be declared positive were eno (97.6%) and fnbA (94.1%). Conclusion: This study indicates that prevalence of biofilm genes in S. aureus isolates in nasal flora is high and fosfomycin is an effective anti-biofilm agent alone. However, to increase fosfomycin’s efficiency, there is a need for more combination studies to make it more effective.
Cyclin B1 scaffolds MAD1 at the corona to activate the spindle assembly checkpoint

The Cyclin B:CDK1 kinase complex is the master regulator of mitosis that phosphorylates hundreds of proteins to coordinate mitotic progression. We show here that, in addition to these kinase functions, Cyclin B also scaffolds a localised signalling pathway to help preserve genome stability. Cyclin B1 localises to an expanded region of the outer kinetochore, known as the corona, where it scaffolds the spindle assembly checkpoint (SAC) machinery by binding directly to MAD1. In vitro reconstitutions map the key binding interface to a few acidic residues in the N-terminus of MAD1, and point mutations in this region remove corona MAD1 and weaken the SAC. Therefore, Cyclin B1 is the long-sought-after scaffold that links MAD1 to the corona and this specific pool of MAD1 is needed to generate a robust SAC response. Robustness, in this context, arises because Cyclin B1-MAD1 localisation becomes MPS1-independent after the corona has been established. We demonstrate that this allows corona-MAD1 to persist at kinetochores when MPS1 activity falls, ensuring that it can still be phosphorylated on a key C-terminal catalytic site by MPS1. Therefore, this study explains how corona MAD1 generates a robust SAC signal and why stripping of this pool by dynein is essential for SAC silencing. It also reveals that the key mitotic kinase, Cyclin B1-Cdk1, scaffolds the pathway that inhibits its own degradation.
Antinociceptive Activity of Petroleum Ether Fraction of Clinacanthus nutans Leaves Methanolic Extract: Roles of Nonopioid Pain Modulatory Systems and Potassium Channels

Methanolic extract of Clinacanthus nutans Lindau leaves (MECN) has been reported to exert antinociceptive activity. The present study aimed to elucidate the possible antinociceptive mechanisms of a lipid-soluble fraction of MECN, which was obtained after sequential extraction in petroleum ether. The petroleum ether fraction of C. nutans (PECN), administered orally to mice, was (i) subjected to capsaicin-, glutamate-, phorbol 12-myristate 13-acetate-, bradykinin-induced nociception model; (ii) prechallenged (intraperitoneal (i.p.)) with 0.15 mg/kg yohimbine, 1 mg/kg pindolol, 3 mg/kg caffeine, 0.2 mg/kg haloperidol, or 10 mg/kg atropine, which were the respective antagonist of α2-adrenergic, β-adrenergic, adenosinergic, dopaminergic, or muscarinic receptors; and (iii) prechallenged (i.p.) with 10 mg/kg glibenclamide, 0.04 mg/kg apamin, 0.02 mg/kg charybdotoxin, or 4 mg/kg tetraethylammonium chloride, which were the respective inhibitor of ATP sensitive-, small conductance Ca2+-activated-, large conductance Ca2+-activated-, or nonselective voltage-activated-K+ channel. Results obtained demonstrated that PECN (100, 250, and 500 mg/kg) significantly (P<0.05) inhibited all models of nociception described earlier. The antinociceptive activity of 500 mg/kg PECN was significantly (P<0.05) attenuated when prechallenged with all antagonists or K+ channel blockers. However, only pretreatment with apamin and charybdotoxin caused full inhibition of PECN-induced antinociception. The rest of the K+ channel blockers and all antagonists caused only partial inhibition of PECN antinociception, respectively. Analyses on PECN's phytoconstituents revealed the presence of antinociceptive-bearing bioactive compounds of volatile (i.e., derivatives of γ–tocopherol, α–tocopherol, and lupeol) and nonvolatile (i.e., cinnamic acid) nature. In conclusion, PECN exerts a non-opioid-mediated antinociceptive activity involving mainly activation of adenosinergic and cholinergic receptors or small- and large-conductance Ca2+-activated-K+ channels.
The rhizosphere effect of some wheat cultivars on inorganic phosphorus fractions in a phosphorus-deficient calcareous soil

Knowledge of the distribution and changes of soil phosphorus fractions in the rhizosphere, helps to determine efficiency of different crop cultivars in phosphorus acquisition. This study was conducted in order to evaluate the rhizosphere effect of some wheat cultivars on inorganic phosphorus fractions. A greenhouse experiment as a factorial in completely randomized design was conducted with 10 treatments and 3 replications. Experimental factors were different plant cultivars (4 wheat cultivars and control) and soil-sampling zone (rhizosphere and non-rhizosphere). A rhizobag technique was used to separate rooted and non-rooted inside each pot representing the two soil sampling zones. Based on fractionation results, the order of inorganic phosphorus fractions in the studied soil were apatite-P> OCP-P> DCP-P> Al-P> Fe-P> O-P which were found to be in the order of 830, 123, 17, 16, 14 and 0 g kg-1, respectively. The concentration of the most inorganic phosphorus fractions between rhizosphere and non-rhizosphere soil was significantly different. All plant cultivars decreased inorganic phosphorus forms significantly. This difference was not equal for all cultivars and all fractions. Organic P was significantly higher in the rhizosphere soil compared to non-rhizosphere soil. Soluble phosphorus was not significantly differed between rhizosphere and non-rhizosphere soil. Root induced chemical changes; root morphology, microbial populations, pH changes etc. can be determining factors on phosphorus depletion differences among plant cultivars and soil sampling zone. Key words: Phosphorus, fractionation, rhizosphere, rhizobag, wheat.
Emergency response to emerging diseases: TiLV in tilapia

Tilapia lake virus (TiLV) is a novel RNA virus resembling Orthomyxovirus. It has been recently re-classified to Tilapia tilapinevirus species, under Tilapinevirus genus, Amnoonviridae family (ICTV, 2018). Since the first discovery in Israel in 2014, so far TiLV has been reported from 14 countries in three continents (Asia, Africa, and South America). Thailand is one of the affected countries that reported emergence of this virus in 2017. Initially, we employed nested RT-PCR primer sequences previously published for TiLV diagnosis. However, the resulting amplification of nonspecific fish genes led us to modify the nested RT-PCR protocols into a semi-nested RT-PCR by omitting a non-specific primer to avoid false positive results. Subsequently, our molecular work together with histopathology and sequence analysis confirmed the presence of TiLV infection in Thailand. Prior to the publication of our manuscript, we informed the Thai Department of Fisheries of our discovery of TiLV in Thailand. Our publication was preceded by a brief article at the website of the Network of Aquaculture Centers in Asia-Pacific in which we warned of the spread of TiLV and offered free use of a newly improved, semi-nested RT-PCR method and positive control plasmid for detection of TiLV. To date, we have provided positive controls in response to 44 requests from 24 countries who have expressed their appreciation for our attempt to help in emergent controlling the spread of this fish pathogen. Our current study focuses on genetic diversity of TiLV and development of detection method that covers all genetic variants.
A Pesca no Pantanal de Mato Grosso do Sul, Brasil: Descrição, Nível de Exploração e Manejo(1994-1999

Nesta tese foi analisada a situacao atual da pesca no Pantanal de Mato Grosso do Sul, incluindo a atividade dos pescadores profissionais artesanais e a dos pescadores esportivos. Compararam-se as caracteristicas atuais da pesca e de periodos anteriores, procurando-se relaciona-las com as alteracoes naturais do ecossistema, qualidade ambiental, politica e legislacao pesqueira. Ha um indicativo geral de que os recursos pesqueiros encontram-se relativamente pouco explorados, o que foi corroborado pela relacao da captura versus esforco para a pesca total e para as principais especies,com excecao do pacu Piaractus mesopotamicus. Verificou-se que a producao da pesca profissional e esportiva pode ser explicada,alem do esforco, pela altura do rio,temperatura e mes ou periodo hidrologico, e suas interacoes. Nesta tese procurou-se valorizar o bem estar do homem e a necessidade de se planejar o desenvolvimento integrado pa regiao para a efetiva conservacao dos recursos pesqueiros do Pantanal.
Quantitative intravital imaging of Plasmodium falciparum sporozoites: A novel platform to test malaria intervention strategies

Malaria infection starts with the injection of motile Plasmodium sporozoites into the host’s skin during a mosquito bite. Previous studies using the rodent malaria model indicate that the dermal inoculation site may be where sporozoites are most vulnerable to antibodies, yet, functional in vivo assays with human malaria parasites are lacking. Here, we present the first characterization of P. falciparum sporozoites in the skin, comparing their motility to two rodent malaria species and investigating whether the environment of its natural host influences P. falciparum sporozoite motility using a human skin xenograft model. The combined data suggest that in contrast to the liver and blood stages, the skin is not a species-specific barrier for Plasmodium. We observe that P. falciparum sporozoites inoculated into mouse skin move with similar speed, displacement and duration, and enter blood vessels in similar numbers as the rodent parasites. Thus, interventions targeting P. falciparum sporozoite migration can be tested in the murine dermis. Importantly, to streamline quantification of sporozoite motility, we developed a toolbox allowing for automated detection and tracking of sporozoites in intravital microscopy videos. This establishes a platform to test vaccine candidates, immunization protocols, monoclonal antibodies and drug candidates for their impact on human malaria sporozoites in vivo. Screening of intervention strategies for in vivo efficacy against Pf sporozoites using this new platform will have the potential to validate targets prior to expensive clinical trials.
Herbivore intraspecific variation and evolutionary divergence drive trophic cascade strength

Trophic cascades—the indirect effect of predators on non-adjacent lower trophic levels—are important drivers of the structure and dynamics of ecological communities. However, the influence of intraspecific trait variation on trophic cascade strength remains largely unexplored, which limits our understanding of the mechanisms underlying ecological networks. Here we experimentally investigated how herbivore intraspecific genetic variation and evolutionary divergence related to host-plant specialization influences trophic cascade strength in a terrestrial tritrophic system. We found that the occurrence and strength of the trophic cascade are strongly influenced by herbivores’ intraspecific variation and evolutionary divergence but are not associated with density-dependent effects mediated by herbivore population growth rate. Our findings stress the importance of intraspecific trait diversity and evolutionary adaptations as drivers of trophic cascade strength and underline that intraspecific variation should not be overlooked to decipher the joint influence of evolutionary and ecological factors on the functioning of multi-trophic interactions.
Antibacterial and cytotoxic activities of high altitude essential oils from Nepalese Himalaya

Essential oils of Rhododendron anthopogon, Artemisia vulgaris, Zanthoxylum armatum,Acrous calamus, Cinnamomum glaucescens, Nardostachys grandiflora and Abies spectabilis are studied for antibacterial and cytotoxic activities, and are evaluated with standard antibiotics for the synergistic potentiality against human pathogenic bacteriaStaphylococcus aureus, Escherichia coli and Klebsilla pneumonia. Antibacterial activity was performed by cup-plate method and cytotoxicity was evaluated by brine shrimp lethality test. Essential oils of C. glaucescens, R. anthopogon and Z. armatum were found to have higher antibacterial activity against E. coli, S. aureus and K. pneumonia, respectively. The best synergism of R. anthopogon oil and erythromycin was found in 20,000 µg/20 µl. Similarly, synergism of essential oil was done in four different concentration (20000/20, 10000/20, 5000/20, 2500/20, 1000/20, 500/20, 250/20 and 125 µg/20 µl). The best result was shown in 125 µg/20 µl against E. coli. Key words: High altitude medicinal plants, essential oils, human pathogen, bacteria, cytotoxicity.
Ecology and Diversity of Plankton in Kotmale Reservoir, Sri Lanka

Present study investigated the relationship between plankton communities and environmental variables in five different locations of the Kotmale Reservoir during the period of June 2008 to May 2011. A total of 123 plankton species were recorded with 85 species of phytoplankton and 38 species of zooplankton. The relative abundance data indicate that Aulacoseira granulata (31.06%), Botryococcus braunii (12.34%) and Microcystis sp. (11.93%) were the dominant phytoplankton species while Acanthocystis turfacea (52.22%) was the dominant zooplankton species. Staurastrum cingulum was the dominant species in sites where the immediate catchment is covered with reservation forest with no significant inflow streams. Aulacoseira granulata, Fragellaria capucina and Navicula sp. were abundant in locations where the highest total phosphorus (TP) values were recorded. The main inflow streams, Puna Oya and Pundalu Oya appear to bring nutrient rich waters from its catchment with dense tea estates, agricultural lands, industries and villages. Microcystis sp. was abundant in locations where the highest values for TP, dissolved phosphorus (DP), ammonia, conductivity and turbidity were recorded. Botryococcus braunii was dominant in the location where Puna Oya reaches the reservoir. Staurastrumlepta canthum was abundant in the location located closer to the dam where the water body mostly contains limnetic characteristics. Among the zooplankton, cladocera species were abundant in sites where Staurastrum cingulum was identified. Rotifers and ciliate protozoans were identified closer to the dam and at the sites with high dominance of Microcystis sp. Accordingly, it was apparent that the distribution and abundance of these plankton species depend on the prevailing environmental conditions which ultimately show their ability to use as environmental indicators.
CONFOCAL MICROSCOPY STUDIES OF LIVING FUNGAL HYPHAE AND CONIDIA USING RHENIUM (I) TRICARBONYL COMPLEXES AS FLUORESCENT DYES.

Botrytis cinerea is a ubiquitous necrotrophic filamentous fungal pathogen, causing the “grey mold” disease in a wide range of plants, including species of importance in the food industry. Recently, we reported the use of fac -[Re(I)(CO)3(2,2’-bpy) L ]PF6 ( C3 ) and fac -[Re(I)(CO)3(4,4’-dimethyl-2,2’-bpy) L ]PF6 ( C4 ) complexes as biomarkers for yeasts and bacteria. Nevertheless, the use of these complexes to stain filamentous fungi, such as Botrytis cinerea , has not been explored so far. Since Botrytis cinerea exhibits a dynamic multilayer cell wall that changes the composition during normal growth, in both their hyphae and conidia, is not possible to directly extrapolate the use of both C3 and C4 as biomarkers for Botrytis cinerea without an experimental approach. In this work, we explored new features of the luminescent compounds C3 and C4 as biomarkers for the higher filamentous fungi Botrytis cinerea , including conidia and juvenile hyphae. We found that, with the new protocol proposed, both C3 and C4 were suitable to stain conidia with a simple procedure since no cell permeabilization is required. Additionally, these results suggest that C3 and C4 can selectively stain living conidia, allowing the differentiation from non-germinating conidia. This point opens a new focus of development for rhenium (I) tricarbonyl complexes as new fluorescent biomarkers for Botrytis cinerea with potential properties as vital staining.