Miracle-dz/UniFAR-FTUs huggingface dataset:
The starter effect of non-symbiotic microbial bioproducts on wheat.

Microbial groups developed in the rhizosphere ensure the stability and dynamics of nutrient transfer processes to plants. Additional soil inoculation with rhizospheric bacteria acts to expand the ecological niche, supplements the activity, the number of individuals and promote plant growth. In today’s agriculture, there is a need for the usage of rhizosphere microflora and integrative approaches to stimulate plant growth. The aim of the study is to evaluate the use of biofertilizers as starter stimulators in autumn wheat. Different concentrations of Bactofil, containing rhizospheric bacteria, were applied in small rhizothrones. Evaluation of relationships between bacterial inoculum and plant reveals the degree of applicability and adaptation to the soil conditions of exogenous microflora. Doses of 15.6 x 108 and 20.8 x 108 cells/m2 stimulates the root elongation and higher level of mycorrhization. Bioproducts can be viable solutions to stimulate the initial development of wheat plants.
Detección del Sugarcane mosaic virus (SCMV) en Saccharum spp. en México y origen filogenético de un aislado de Jalisco

Sugarcane mosaic virus (SCMV) is one of the main viral agents that infect sugarcane ( Saccharum spp.). SCMV detection in Mexico has been based on typical symptomatology of the disease, which is not conclusive. Additionally, there is limited information about their phylogenetic origin. The objective of this work was to detect the presence and distribution of SCMV in the sugarcane growing areas of the Mexican Pacific using RT-PCR, and to determine the phylogenetic origin of one isolate from Jalisco. The results showed the wide distribution of SCMV in sugarcane areas of the Mexican Pacific. The virus was found in 33 of the 242 samples analyzed, corresponding to 13.63%. The varieties Mex 69-290 and CP 72-2086 presented the most severe mosaic symptoms. Phylogenetic analysis using partial HC-Pro sequences of SCMV isolate from Jalisco (JalMex-126) suggests a close relationship with isolates from India, Australia, China and Argentina, and thus likely share a common genetic origin and have been dispersed to through infected sugarcane germplasm.
Optimization of Proteasomal Degradation Reporter (eDeg-On) System for CRISPR-mediated Whole-genome Knockout Screens

Optimization of the Proteasomal Degradation Reporter (eDegOn) System for CRISPR-mediated Whole-genome Knockout Screens by Yiwen Liu Protein folding and clearance of misfolded proteins are crucial to maintain cellular homeostasis (Jariel-Encontre et al., 2008). Misfolded proteins may associate with other cellular components and possibly impair their functions. They may also self-associate to form insoluble aggregates, which are the hallmarks of a number of neurodegenerative diseases, such as Parkinson’s (Olanow and McNaught, 2006) and Alzheimer’s (Oddo, 2008). The ubiquitin proteasome system (UPS) is the main pathway that catalyzes the degradation of soluble misfolded proteins in mammalian cells. Therefore, enhancing the UPS activity through activation of proteasomal degradation is considered a promising strategy to ameliorate phenotypes associated with the accumulation of misfolded proteins. Modulation of specific UPS components, for instance, results in increased degradation of target proteins (Rechsteiner and Hill, 2005 and Vilchez et al., 2012). However, our current understanding of the molecular mechanism underlying proteasomal degradation is still limited, limiting the rational design of pharmacologic strategies to enhance UPS activity. As a result, proteasome activators are rare and remain poorly characterized (Huang and Chen, 2009). To overcome these limitations, researchers in my group developed a cellbased platform (the eDeg-On system) to monitor changes in UPS activity. This genetic circuit links increase in UPS activity to an increase in fluorescent output, thereby providing a reliable tool for the discovery of proteasome activators. The CRISPR-cas technology has emerged as powerful technique to introduce genetic modifications at the whole-genome scale. I optimized the eDeg-On system and evaluated it for pooled screening of whole-genome CRISPR-mediated knockout library. I replaced the antibiotic resistance gene in the eDeg-On system and assessed the response of HEK293 cells stably expressing the eDeg-On system to modulation of proteasomal degradation. To evaluate the use of a stable cell line expressing the eDeg-On system as a reporter assay in the context of a pooled CRISPR-mediated screen, I conducted mock screens using different ratios of positive and negative controls. The results obtained demonstrate that the eDeg-On system can be used as a reporter assay for CRISPR-mediated whole-genome knockout screens. The use of the eDeg-On system to conduct genetic screen for the discovery of molecules that function as proteasome regulators will contribute to the development of therapeutic strategies for protein misfolding diseases. Further applications of this study include targeting the UPS function for therapeutic applications as well as for enhancing the production of recombinant proteins in industrial settings.
Studies on thermal, optical and bio-physical behavior of maize hybrids as influenced by plant population and levels of fertilization in irrigated eco-system.

A field experiment was conducted for two consecutive years (2013 and 2014) at Agricultural Research Station, Mudhol located at 16023’56.4’’ North latitude, 7506’33’’ East longitude and at an altitude of 577.6 meters above mean sea level under assured irrigated ecosystem. Treatments comprises of three maize hybrids (H1-NK-6240, H2-Super 900-M and H3-Arjun), two plant populations (P1-1, 11, 111 and P2-83, 333 plants ha -1) and five fertility levels (F1-N(150)P2O5(65)K2O(65), F2-N(187)P2O5(81)K2O(81), F3-N(225)P2O5(97)K2O(97), F4-N(262)P2O5(114)K2O(114) and F5-N(300)P2O5(130)K2O(130) kg ha -1). Among the hybrids significantly higher canopy temperature was recorded with Arjun at grain filling stage (29.43 oC) and light transmission ratio at seedling, silking and grain filling state (42.23, 11.34 and 6.32 %, respectively) resultant to significantly lower light absorption at silking and grain filling was associated with former hybrid (86.66 and 93.68%, respectively). Significantly higher leaf area at seedling, silking and grain filling state was higher with NK-6240 (6.44, 47.65 and 53.59 dm2 plant-1, respectively), leaf area index (0.62, 4.60 and 5.17, respectively) and total dry matter production (6.87, 78.32 and 242.87 g plant-1) and significantly higher grain yield was recorded with NK-6240 (10.14 t ha-1) and was comparable with Super 900-M. Among the plant population higher plant population transmitted lower light at seedling, silking and grain filling stage (39.90, 6.48 and 4.99%, respectively) and absorbed higher amount of light (60.10, 93.52 and 95.01%, respectively). Leaf area per plant (6.75, 47.37 and 52.55 dm2 plant1) and total dry matter (6.82, 77.04 and 222.77 g plant-1) was higher with lower plant density and LAI (0.61, 4.59 and 5.26, respectively) and grain yield (9.80 t ha-1) was higher with higher plant population. Among the fertility levels, application of N(150)P2O5(65)K2O(65) kg ha -1 recorded higher canopy temperature, higher light transmission ratio and lower absorption ratio. In the contrary N(300)P2O5(130)K2O(130) kg ha -1 recorded higher leaf area per plant (7.59, 50.81 and 57.34 dm2 plant-1, respectively), leaf area index (0.73, 4.77 and 5.54, respectively), total dry matter production (7.56, 87.58 and 242.03 g plant-1) and grain yield (10.42 t ha-1).
Ricasolia amplissima (Lobariaceae): one species, three genotypes and a new taxon from south-eastern Alaska

Abstract The genetic diversity within the foliose form of Ricasolia amplissima from Europe and North America was studied using molecular phylogenetic analysis of the nuclear ITS and RPB2, and mitochondrial SSU. Boundaries between closely related species were also examined using morphological and chemical patterns. Four species of the recently reinstated lichen genus Ricasolia De Not. were phylogenetically verified which necessitated a new combination, Ricasolia japonica (Asah.) Cornejo. Analyses suggest that the generic type taxon R. amplissima (Scop.) De Not. belongs to a species complex that shows two evolutionary centres, one in Europe, North Africa, Asia Minor and the Macaronesian Islands, the other from north-western North America on exposed shores of mainly forested marine islands in south-eastern Alaska, where it shows strong habitat specificity. The Alaskan lineage is very similar to the European lineage but it differs by the lack of scrobiculin and other chemical substances. It is described here as R. amplissima subsp. sheiyi Derr & Dillman.
ANTI-INFLAMMATORY ACTIVITY OF SYZYGIUM AROMATICUM SILVER NANOPARTICLES: IN VITRO AND IN SILICO STUDY

Â Â Objective: In the present study, antioxidant and anti-inflammatory activity of Syzygium aromaticum (clove) silver nanoparticles (clove AgNPâ€™s) was evaluated.Methods: Gas chromatography-mass spectrometry technique was used to identify the compounds present in the aqueous extract of clove. Fourier transform infrared (FT-IR) analysis was done to characterize the clove silver AgNPâ€™s. 1,1-diphenyl-2-picrylhydrazyl (DPPH) assay was performed to evaluate the antioxidant property of nanoparticles (0.05 and 0.25 mg/ml) and aqueous extracts (0.05, 0.1, and 0.25 mg/ml) of clove. The anti-inflammatory property of the clove AgNPâ€™s was determined by inhibition of protein denaturation and downregulation of interleukin-1 beta. In silico molecular docking studies was performed using Schrodinger Maestro software.Results: Eugenol was found to be highest with 16.27%. The AgNPâ€™s exhibited dose-dependent antioxidant property. AgNPâ€™s scavenged 80% of radical at the concentration of 0.25 mg/ml. The scavenging activity of AgNPâ€™s markedly increased when compared to aqueous extract at the same concentration. Inhibition of protein denaturation assay also revealed AgNPâ€™s showing the highest activity (66%) when compared with drug aspirin (55%) and aqueous extract (56%). In the enzyme-linked immunosorbent assay (ELISA) method, AgNPâ€™s showed better inhibition (80%) when compared to aqueous extract (60%). Among 15 compounds, two compounds (eugenol and methyl 14-methylpentadecanoate) showed good glide energy, docking score, and hydrogen-bonded active site interactions with the protein interleukin-1 beta.Conclusion: As AgNPâ€™s were more active than the aqueous extract, it may be considered for pharmacological activity against inflammatory disorders.
Short communication: Functional genetic diversity of chestnut (Castanea sativa Mill.) populations from southern Spain

Aim of the study: To evaluate the adaptive genetic variability of chestnut ( Castanea sativa Mill.) populations from southern Spain in relation to bud burst and water stress. Area of study: Andalusia (southern Spain) where many chestnut groves were progressively abandoned and have become ‘naturalized’. Material and methods: A total of 126 chestnut trees from eight populations were assessed by means of nine genic microsatellite loci (expressed sequence tag simple sequence repeat markers) related to bud burst and water stress. Main results: Significant differences in genetic diversity were detected within and among populations, not found with neutral microsatellite markers. The structure analysis indicated the presence of two different gene pools. Research highlights: These results could contribute to the development of conservation strategies for this species in southern areas exposed to the effects of climate change. The genetic diversity of these populations could be useful in minimizing this risk and other predictable factors related to global change.
Toxoplasma gondii infection in sheep and free-range France: seroprevalence and isolate genotyping by microsatellite analysis.

Ingesting meat of free-range livestock, mainly sheep, is associated with human toxoplasmosis in European countries. Data on Toxoplasma gondii infection in French ovine livestock are relatively scarce. Sera from 164 lambs and 93 ewes slaughtered in HauteVienne district, France, were tested by a direct agglutination test. Antibodies to T. gondii were found in 36 (22.0%) lambs and in 61 (65.6%) ewes. In addition, to attempt parasite isolation for genotyping, hearts from 50 other ewes were obtained from a local slaughterhouse, and were screened by a direct agglutination test. T. gondii was isolated in 8 of 30 seropositive hearts bioassayed in mice. All isolates were type IIbygenetic characterization atfive microsatellite loci (TUB2, TgM-A, W35, B17, B18). These results indicate that ovines slaughtered inFrance may be highly infected by T. gondii witha potential risk of parasite transmission to humans by consumption of undercooked meat. Multilocus microsatellite analysis shows the predominance of type II in sheep as previously described in humans. # 2006 Elsevier B.V. All rights reserved.
The Efficacy of Some Detergents on Some Intestinal Parasites and Their Histopathological Effects

Detergents or surfactant are chemical substances that used for cleaning purposes. The chemical compositions of the detergents are varying greatly according to application demands and commercial competitive. The aim of the present study was to, investigate the effect of common substances, used by people in our area for cleaning vegetables and fruits. On killing some parasitic stages and also studying their histopathological effects on mice intestine. Four types of ordinary commercial detergents were used (Altunsa, Bonux, Ariel , ABC) at concentrations of 1.5, 3, 4.5 g\l against E. hitolytica , E. coli , G. lamblia cysts and H. nana eggs. The parasitic stages were incubated with the detergents used for 2, 5, 15, 30 minutes. In order to detect the efficacy of the detergents the incubated stages were administered to laboratory mice. Histological sections of mice intestinal parts were done to find out the histopathological effect of the detergents. The detergents varied in their actions on tested parasitic stages, the most effective was Ariel and ABC type followed by Bonux. The lowest efficacy was for Altunsa type. Incubating the parasitic stages with the detergent for 2 minutes had no impact with some detergents, while 5 minutes was enough for killing the stages with all detergents. The histopathological examination of intestinal parts had not revealed any dimorphty or changes comparing to the control group except in that leaved for more than 5 minutes. The conclusion is that some detergents can be used for cleaning vegetables, killing and removing parasitic stages. Detergents do not cause histopathological effects if its residues removed thoroughly and not leaved on vegetables for long period of time.
Chemokines and peptides that promote and inhibit CMV entry

Human cytomegalovirus (HCMV) infection in utero can lead to congenital sensory neural hearing loss and mental retardation. Reactivation or primary infection can increase the morbidity and mortality in immune suppressed transplant recipients and AIDS patients. The current standard of care for HCMV disease is nucleoside analogs, which can be nephrotoxic. In addition resistance to current treatments is becoming increasingly common. In an effort to develop novel CMV treatments, we tested the effectiveness of the D-form of a novel heparan sulfate binding peptide, p5RD, at reducing infection of ganciclovir (GCV) resistant HCMVs in vitro and MCMV in vivo. HCMV infection was reduced by greater than 90% when cells were pretreated with p5RD. Because p5RD acts by a mechanism unrelated to those used by current antivirals, it was effective at reducing GCV resistant HCMVs by 85%. We show that p5RD is resistant to common proteases and serum inactivation, which likely contributed to its ability to significantly reduced infection of peritoneal exudate cells and viral loads in the spleen and the lungs in vivo. The ability of p5RD to reduce HCMV infectivity in vitro including GCV resistant HCMVs and MCMV infection in vivo suggests that this peptide could be a novel anti-CMV therapeutic.
Antioxidant Properties of Scomber japonicus Hydrolysates Prepared by Enzymatic Hydrolysis

ABSTRACT The antioxidant properties of the Pacific chub mackerel (Scomber japonicus) muscle protein hydrolysates prepared by enzymatic hydrolysis were investigated. After enzyme hydrolysis at 50°C for 60 min, more than 80% of the S. japonicus muscle protein was hydrolyzed. The highest 2,2-Diphenyl-1-picrylhydrazyl (DPPH) radical-scavenging activity (71.69%) occurred in whole muscle protein hydrolysates treated at 50°C for 30 min with Protamex, and the highest 2,2ʹ-azino-bis(3-ethylbenzothiazolin-6-sulfonic acid) (ABTS) radical-scavenging activity (95.39%) was observed in white muscle protein hydrolysates treated at 50°C for 30 min with Neutrase. The highest superoxide dismutase (SOD)-like activity (32.84%) was recorded in white muscle protein hydrolysates treated at 50°C for 120 min with Protamex. Changes in the molecular weight distribution of S. japonicus muscle proteins after enzymatic hydrolysis were observed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). A robust and a convenient enzyme hydrolysis technique for obtaining S. japonicus muscle protein hydrolysates with useful biological activities, within a short time (<2 h) is proposed.
Does the Vulnerable sun bear Helarctos malayanus damage crops and threaten people in oil palm plantations?

Abstract Largely as a result of the expansion of oil palm Elaeis guineensis, forest fragmentation has occurred on a large scale in Borneo. There is much concern about how forest-dependent species, such as the Vulnerable sun bear Helarctos malayanus, can persist in this landscape. The absence of sufficient natural food in forest fragments could drive sun bears into oil palm plantations, where they risk coming into conflict with people. We interviewed oil palm plantation workers and farmers in the Lower Kinabatangan region of Sabah, Malaysian Borneo, to ascertain if sun bears were utilizing plantations, if they were causing damage to the crop, and how the bears were perceived by people. To obtain a comparative baseline we extended these questions to include other species as well. We found that bears were rarely encountered in plantations and were not considered to be destructive to the oil palm crop, although they were generally feared. Other species, such as macaques Macaca spp. , bearded pigs Sus barbatus, and elephants Elephas maximus, had more destructive feeding habits. Sun bears could use this readily available food resource without being targeted for retribution, although incidental human-related mortality remains a risk. Although bears could gain some nutritional benefit from oil palm, plantations do not provide the diversity of food and cover available in a natural forest.
By-catch in the commercial beam trawl fishery for Rapa Whelk in the Black Sea

In this work, the by-catch was investigated in commercial beam trawls used in the rapa whelk ( Rapana venosa ) fishery, in trials at sea between September 1, 2015 and April 30, 2016. Four commercial boats using beam trawls were chartered and catch data was collected from a total of 87 hauls. Hauls were performed between 7.1–28.3 meters deep for a duration of 20–77 minutes and haul speed varied between 1.4 – 2.7 knots. A total of 28 by-catch species were identified, which amount in average to 11.4% of the total number of specimens in the by-catch. Two different groups were identified in the by-catch (G1: 7-18 m, G2: 19-26 m) according to depth. Although there is a reduction in the amount of by-catch for G2 group, no significant difference was found between groups (p>0.05). According to Generalized Additive Models (GAM) results, the variables affecting the by-catch amount were identified as fishing area, depth, haul duration, and amount of captured rapa whelk (p<0.01). In addition, a large proportion of immature individuals of striped venus clams ( Chamelea gallina ), blood cockles ( Anadara kagoshimensis ), Mediterranean mussels ( Mytilus galloprovincialis ) and wedge clams ( Donax trunculus ) were caught as by-catch during the study. Finally, the impact of commercial beam trawls on the demersal macrofauna is discussed.
Biotic interactions, climate and disturbance underlie the distribution of two Julbernardia tree species in miombo woodlands of Africa

Abstract: Occurrence data for Julbernardia globiflora and J. paniculata at 617 sites in the miombo woodland region of central, eastern and southern Africa and forest inventory data for 512 woodland plots in Zambia were used to determine species distribution and dominance. Distribution of the two Julbernardia species overlaps in the central region of the miombo woodland range while the eastern and western range regions are exclusively for only one of the two species. In the region of co-occurrence, there is a clear spatial separation in the dominance of the two species. In old-growth woodland a significant proportion of the variation in the dominance of J. globiflora was explained by the dominance of J. paniculata while mean annual maximum temperature and tree species richness negatively affect the dominance of J. paniculata. Old-growth woodland clearing changes the local climatic conditions and alters the way Julbernardia species in re-growth stands respond to potential evapo-transpiration (PET). Climate change, especially global warming, may further reinforce the impacts of PET to differentially favour J. globiflora. Because of this altered response of Julbernardia species in re-growth miombo, preserving old-growth miombo and preventing present human disturbances in designated areas, such as forest reserves and national parks, may be a useful climate adaptation strategy for these species.
Hybrid Songbirds are Deficient in Learning and Memory

Identifying the phenotypes underlying postzygotic reproductive isolation is crucial for fully understanding the evolution and maintenance of species. One potential postzygotic isolating barrier that has not yet been examined is learning and memory ability in hybrids. Learning and memory are important fitness-related traits, especially in scatter-hoarding species, where accurate retrieval of hoarded food is vital for winter survival. Here, we test the hypothesis that learning and memory ability can act as a postzygotic isolating barrier by comparing these traits among two scatter-hoarding songbird species, black-capped (Poecile atricapillus), Carolina chickadees (Poecile carolinensis), and their naturally occurring hybrids. In an outdoor aviary setting, we find that hybrid chickadees perform significantly worse on an associative learning spatial task and are worse at solving a novel problem compared to both parental species. Deficiencies in learning and memory abilities could therefore contribute to postzygotic reproductive isolation between chickadee species. Given the importance of learning and memory for fitness, our results suggest that these traits may play an important, but as yet overlooked, role in postzygotic reproductive isolation.