Miracle-dz/UniFAR-FTUs huggingface dataset:
Study of heterotic expression and inbreeding depression in okra [Abelmoschus esculentus (L)]

The present investigation was undertaken to assess the genetic potential of okra genotypes through breeding and selection in nine genotypes of five crosses (Cross I - Punjab-7 x Arka Anamika, Cross II - Punjab-7 x Parbhani Kranti, Cross III - Hissar Unnat x GAO-5, Cross IV - Varsha Uphar x Phule Utkarsha and Cross V- Pusa Sawani x GAO-5). Among the crosses, Varsha Uphar x Phule Utkarsha exhibited significant positive relative heterosis, heterobeltiosis and inbreeding depression for fruit yield per plant in tune of 33.60, 24.67 and 26.32 per cent, respectively. This hybrid also showed significant heterosis for other yield contributing traits viz; number of internodes per plant, number of branches per plant and fruit length.
Long-term use of green manure legume and chemical fertiliser affect soil bacterial community structures but not the rate of soil nitrate decrease when excess carbon and nitrogen are applied

Legumes add not only nitrogen (N), but also carbon (C) to soils, so their effects on the soil microbial community may be different from those of chemical fertiliser. Soil microbes often compete with plants for N when excess C is applied due to their increased N immobilisation potentials and denitrification. In the present study we evaluated the effects of the 9-year use of a green manure legume (hairy vetch; Vicia villosa) in a greenhouse tomato system on soil microbial community structures as well as on the decrease of nitrate when rice straw was incorporated into the soil. Soil microbial community structures and their diversity were altered by the long-term use of legumes. The ratios of Acidobacteria, Gemmatimonadetes and Proteobacteria increased in the hairy vetch soils. The rates of decrease in nitrate were similar in soils with a history of chemical fertiliser and hairy vetch, following the addition of rice straw. In addition, during incubation with added rice straw, the difference between the two soil microbial community structures became less clear within 2 weeks. Thus, we conclude that even though growing a green manure legume changed soil bacterial community structures, this did not result in relatively faster loss of available N for plants when rice straw was added to the soils.
The expression of growth factor signaling genes in co-culture IVM

The objective of this study was to determine the expression of growth factor signaling genes in human adiposederived stem cells (ASCs), porcine oocytes, and cumulus during in vitro maturation (IVM). The human ASCs (from 2 young and 2 old donors) were used for the co-culture IVM system. The maturation rate was examined based on polar body extrusion. The expression of the growth factor signaling genes from ASCs, oocytes, and cumulus were measured using qPCR. All data were analyzed using ANOVA followed by Tukey’s test. The expression of the h-IGF1 signaling genes from human ASCs cells showed similar values in all groups and the h-FGF2 expressions were higher in the young donors than the old ones. The p-FGF2, p-FGFR2, and p-TGFβ1 expressions in the oocytes as well as p-IGFR in the cumulus that were co-cultured from the young donors showed higher values than the old and control groups. The apoptotic ratio (p-BAX/p-BCL2) from the oocytes and cumulus in both co-culture groups also showed lower levels than the control (P<0.05). Oocyte maturation rates were significantly increased in all co-cultured groups (Y1 (85.9 ± 2.2%), Y2 (91.2 ± 1.1%), O1 (86.3 ± 1.5%), and O2 (86.5 ± 2.3%)) compared with the control (76.7 ± 1.1%; P<0.05). Although the expression of growth factor signaling genes was varied, young donors’ ASCs might support in vitro maturation beħer than those from old donors.
Seasonal and relative abundance of stem-borer and leaf-folder in wet land rice eco-system

Seasonal abundance of rice stem-borer and leaf-folder was monitored in wet land rice during kharif 2016 at ICAR-National Institute of Biotic Stress Management, Raipur by erecting yellow stem-borer sex pheromone and light traps. Three species of stem-borer including yellow stem-borer, Scirpophaga incertulas, stripped stem-borer, Chilo suppressalis and white stem-borer, Scirpophaga innotata were found attacking rice, among them, Sc. incertulas dominated. First catch of female of yellow stem-borer in light trap appeared during 1st week of August 2016 (31st MSW) which caused 1.1% dead heart, thereafter reached the first peak catch during 3rd week of August 2016 (33rd MSW) and second peak during 4th week of August 2016 (35th MSW) which caused the dead heart of 3.60 and 3.83%, respectively. Leaffolder damage was low throughout the crop period. Relative humidity and rainfall were positively correlated with trap catches while maximum (26.0 0C to 29.3 0C) and minimum (17.4 0C to 25.5 0C) temperatures were positively correlated to damage caused by two insects.
Isolation and identification of plant growth promoting rhizobacteria from maize (Zea mays L.) rhizosphere and their plant growth promoting effect on rice (Oryza sativa L.)

Th e use of plant growth promoting rhizobacteria is increasing in agriculture and gives an appealing manner to replace chemical fertilizers, pesticides, and dietary supplements. Th e objective of our research was to access the plant growth promotion traits of Pseudomonas aeruginosa, P. fl uorescens and Bacillus subtilis isolated from the maize (Zea mays L.) rhizosphere. In vitro studies showed that isolates have the potential to produce indole acetic acid (IAA), hydrogen cyanide, phosphate solubilisation, and siderophore. RNA analysis revealed that two isolates were 97% identical to P. aeruginosa strain DSM 50071 and P. aeruginosa strain NBRC 12689 (AK20 and AK31), while two others were 98% identical to P. fl uorescens strain ATCC 13525, P. fl uorescens strain IAM 12022 (AK18 and AK45) and one other was 99% identical to B. subtilis strain NCDO 1769 (AK38). Our gnotobiotic study showed signifi cant diff erences in plant growth variables under control and inoculated conditions. In the present research, it was observed that the isolated strains had good plant growth promoting eff ects on rice.
In vitro physical mutagenesis of giant reed (Arundo donax L.)

Giant reed (Arundo donax L.) is a C3 perennial, warm‐season, rhizomatous grass of emerging interest for bioenergy and biomass derivatives production, and for phytoremediation. It only propagates vegetatively and very little genetic variation is found among ecotypes, basically precluding breeding efforts. With the objective to increase the genetic variation in this species, we developed and applied a mutagenesis protocol based on γ‐irradiation of in vitro cell cultures from which regenerants were obtained. Based on a radiosensitivity test, the irradiation dose reducing to 50% the number of regenerants per callus (RD50) was estimated at 35 Gy. A large mutagenic experiment was carried out by irradiating a total of 3120 calli with approx. 1×, 1.5× and 2× RD50. A total of 1004 regenerants from irradiated calli were hardened in pots and transplanted to the field. Initial phenotypic characterization of the collection showed correlated responses of biomass‐related quantitative traits to irradiation doses. Approx. 10% of field‐grown clones showed remarkable morphological aberrations including dwarfism, altered tillering, abnormal inflorescence, leaf variegation and others, which were tested for stability over generations. Clone lethality reached 0.4%. Our results show for the first time that physical mutagenesis can efficiently induce new genetic and phenotypic variation of agronomic and prospective industrial value in giant reed. The methodology and the plant materials described here may contribute to the domestication and the genetic improvement of this important biomass species.
Genotoxicity of haloacetic acids, aspirin and ibuprofen in human cells : genotoxic effects of water disinfectant by-products in human blood and sperm and bulk and nano forms of aspirin and ibuprofen in human blood of respiratory disease patients

This project focuses on two important topics which may pose hazards to human health. Firstly, drinking water disinfection by-products (DBPs), which are generated by the chemical disinfection of water have been investigated. What has not been shown is the effect of DBPs in human germ cells as well as somatic cells and whether oxidative stress is involved in the mechanism of genotoxic action. Three different DBPs (halo acetic acids: HAAs), together with the antioxidants – catalase and butylated hydroxyanisole (BHA), were investigated in peripheral blood cells and sperm from healthy individuals using the Comet assay and lymphocytes only using the micronucleus assay. Secondly, nanoparticles of the non-steroidal anti-inflammatory drugs (NSAIDs), aspirin and ibuprofen, have been investigated in patients with respiratory diseases, in the micronucleus assay and the Comet repair assay. NSAIDs inhibit cyclooxygenase enzyme activity, which plays part in tumour progression. In the Comet assay, BHA and catalase were able to reduce DNA damage in both cell types compared to HAAs alone. Similarly, in the micronucleus assay, micronuclei were reduced with the antioxidants, suggesting oxygen radical involvement in both assays. With the NSAIDs,
Assessment of the Prophylactic Activity of the Ethanolic Extract of Momordica charantia Leaves against Acetaminophen-Induced Liver Impairment in Wistar Rats

Background: Various parts of M. charantia have been reported to possess pharmacological properties against some diseases due to its phytochemicals constituents. Aim: This research was aimed at assessing the prophylactic effect of the ethanol extract of M. charantia against acetaminophen-induced liver damage in Wistar rats. Methodology: A total of sixteen rats were randomly divided into four groups with four rats in each group. The experiment spanned through fourteen days. Group 1 served as the control, group 2 received 1500 mg/kg per body weight (pbw) of acetaminophen orally throughout, group 3 received 250 mg/kg (pbw) of extract throughout while group 4 received 250 mg/kg (pbw) of extract for six days and thereafter was given 1500 mg/kg (pbw) acetaminophen orally from day 7 to day 14. The biochemical parameters of liver function- aspartate transaminase (AST), alanine transaminase (ALT), alkaline phosphatase (ALP), and protein levels were determined. In addition the following antioxidant parameters- reduced glutathione (GSH) and malondialdehyde (MDA) were also measured from the serum of experimental animals. Histopathological changes in the liver were also investigated. Results: Results show that the oral pre-treatment with extract of M. charantia (250 mg/kg body weight) revealed significant (P<0.05) reduction of serum activities of ALT, AST and ALP. Also, pre-treatment with the extract caused a significant (P<0.05) increase in total protein and GSH level with a significant (P<0.05) decrease in the MDA compared to the control group. Histopathological analysis confirmed the amelioration of liver damage and reduced laceration caused by acetaminophen. Conclusion: This study substantiates the prophylactic activity of M. charantia leaf ethanol extract against liver impairment which might be attributed to some of its intrinsic phytochemical constituents which possess anti-oxidant activities.
Quantifying long-term predictability in microbial plankton dynamics

Determining predictability in community turnover is a key ecological question. In the microbial world, seasonality has been reported for communities inhabiting temperate zones, but not much is known on seasonality for individual species. Specifically, we have a vague understanding on the amount of species displaying predictability during temporal community turnover as well as on their dynamics. Here we developed a ‘Recurrence Index’ to quantify predictability in microbial species. Applying our index to 18S rDNA metabarcoding data from one of the longest temporal observatories of marine plankton we determined that 13% of the picoeukaryotic and 19% of the nanoeukaryotic species, accounting for about 40% of the community abundance in both fractions, feature predictable dynamics when sampled monthly during 10 years. Thus, most of the species analysed had unpredictable temporal abundance patterns. Altogether, we show that species with both predictable and unpredictable temporal dynamics can occur within the same seasonal microbial community.
Decomposing the neural pathways mediating value-based choice

Understanding the neural implementation of value-based choice has been an important focus of neuroscience for several decades. Although a consensus has emerged regarding the brain regions involved, disagreement persists regarding precise regional functions and how value information flows between value-based choice regions. In the current study, we isolate neural activity related to decision-making using a gambling task where expected gains and losses are dissociated from the received outcomes of choices. We apply multilevel modelling and mediation analysis to formally test whether brain regions identified as part of the value-based choice network mediate between perceptions of expected value and choices to take or pass a gamble. A critical function in decision-making is accruing and representing value information to drive choice. Several regions have been assigned this role, including ventromedial prefrontal (vmPFC) and posterior parietal cortex (PPC), and the ventral striatum (VStr). The implied chain of events is one where regions that support the process of gathering relevant information mediate the relationship between choice and representations of value in other brain regions. Here, we formally test whether distinct brain regions express interregional mediation consistent with this chain of processes. We observe that activity in vmPFC does not predict choice, but rather is highly associated with outcome evaluation. By contrast, both PPC and VStr (bilaterally) mediate between expected value and choice. Interregional mediation analyses reveal that VStr fully mediates between PPC and choice. Together these results suggest that VStr, and not vmPFC nor PPC, functions as an important driver of late stage choice. Significance Statement Making choices that maximize gain and minimize loss is critical for success. Our paradigm and analytic approach allowed isolation of choice-related neural signals from outcome-related signals. The vmPFC is involved at outcome rather than at choice. Isolating choice-related neural activity, we formally demonstrate that VStr and PPC mediate between expected value and choice. Our approach adds significant innovation by using generalized multilevel modelling to predict behavior with concurrent neural activity and formally testing the fully mediated pathway from stimulus through neural activity to behavior. Applying interregional multilevel mediation analysis, we demonstrate that ventral striatum comprises a final, critical step in processing value-based choice, mediating the relationship between value representation and choice.
Effect of Omega-3 and Multivitamins on Aluminum-Induced Changes in Serum and Tissue Enzyme Activities in Rats

The present work was designed to study the effect of omega-3 and multivitamins on aluminum-induced changes in some tissue enzymes level in male albino rats. For the present work, seventy adult male rats were randomly divided into seven groups; fed on normal diet and treated as follows: Control group 1supplied with tap water. Group 2 supplied with 0.2 ml/rat of the vehicle (oil ). Group 3 supplied orally with 0.2 ml/rat aluminum solution. Group 4 supplied orally with 0.2 ml/rat aluminum solution and diluted acetic acid solution (0.5 %). Group 5 supplied orally with 0.2 ml/rat aluminum solution and omega-3. Group 6 supplied orally with 0.2 ml/rat aluminum solution and multivitamins. Group 7 supplied orally with 0.2 ml/rat aluminum solution and both antioxidants, omega-3 and multivitamins. After treating the animals with the tested materials daily for 30 days, the activities of serum alkaline Phosphatase (ALP), acid Phosphatase (ACP), Alanine Transaminase (ALT) and Aspartate Transaminase (AST) were increased while their activities in liver and brain tissues were significantly decreased. The toxicity of Aluminum was enhanced in the presence of acid as indicated by further changes in the levels of above parameters as compared with those of Al treated animals. The toxic effect of Al, in the presence of antioxidants such as omega-3 and multivitamins, was comparatively reduced and the studied parameters showed tendencies to change toward the normal levels. Thus, animals treated with Al in the presence of above antioxidants showed slight decreases in the activities of tissues ALP, ACP, ALT and AST. From the results of the present study, it can be concluded that the toxic effect of Al in the presence of acid was enhanced, whereas its toxicity was greatly reduced in the presence of the antioxidants such as omega-
Pathogenic variability of Plasmopara halstedii infecting sunflower in the Czech Republic

Plasmopara halstedii was isolated from diseased sunflowers collected from eight locations in the Czech Republic from 2007 to 2014. Races of the pathogen were determined based on 84 isolates collected during the study. In total, eight races of P. halstedii were detected using a set of nine sunflower differential lines. Races 700, 704, 705, 710, 714 and 715 were proven by soil drench inoculation and two additional races (730 and 770) proposed by the previously applied leaf disc inoculation method. Race 700 was the most dominant in the Czech P. halstedii populations, with race 710 being the second most frequent. Race 704 and 714 were found over three seasons, while other races were recorded only in one growing season (race 730 in 2010, and the new races 705 and 715 in 2014). A comprehensive study was further conducted for isolates collected in 2013-2014 using an extended differential set consisting of 15 sunflower lines. According to the latter methodology which marks races with five-digit virulence codes, races 70060, 70471, 70571, 71060, 71461 and 71571, were recorded. The growing complexity of P. halstedii pathogenicity exhibited by ability to infect higher number of differential genotypes and resulting in determination of the new pathogen races (virulence profiles) 70571, 71461 and 71571 is alarming. Though the limited number of isolates studied cannot characterize the entire pathogen diversity in the Czech Republic, the trend towards more diverse virulence in P. halstedii populations is clearly demonstrated by the new records of races 704, 705, 714 and 715, all capable of overcoming the resistance gene Pl6. This article is protected by copyright. All rights reserved.
Punctuated evolution shaped modern vertebrate diversity

The relative importance of different modes of evolution in shaping phenotypic diversity remains a hotly debated question. Fossil data suggest that stasis may be a common mode of evolution, while modern data suggest very fast rates of evolution. One way to reconcile these observations is to imagine that evolution is punctuated, rather than gradual, on geological time scales. To test this hypothesis, we developed a novel maximum likelihood framework for fitting Lévy processes to comparative morphological data. This class of stochastic processes includes both a gradual and punctuated component. We found that a plurality of modern vertebrate clades examined are best fit by punctuated processes over models of gradual change, gradual stasis, and adaptive radiation. When we compare our results to theoretical expectations of the rate and speed of regime shifts for models that detail fitness landscape dynamics, we find that our quantitative results are broadly compatible with both microevolutionary models and with observations from the fossil record.
Predator-prey / Obligate Mutualism in Information System Security and Usage

: In this paper, I model the interaction of an information system, its users, and its attackers as an ecological system with three populations. I model the relationship between users and the system as an obligate mutualism and the relationship between the system and the attackers as a predator-prey relationship. Sensitivity analysis on a numerical example suggests that the model is consistent with expectations of economic reality. Critical point analysis suggests that defenses that reduce the reward to attackers are superior to those that reduce damage to assets.
Evolutionary genomics of genes involved in the environmental adaptation of metazoans

In evolutionary biology, it is well recognized that environments with distinct biotic and abiotic conditions impose selective pressures to species. Moreover, the survival of organisms in such particular conditions requires adaptive evolution through the maintenance of advantageous mutations by natural selection. Therefore, identifying specific regions of the organisms’ genome with signatures of selection can be insightful to understand the species evolutionary history and highlight important functional changes occurring in relevant protein-coding genes. Metazoans are an ideal group to perform molecular evolutionary studies, because they have numerous morphological, physiological, behavioral and ecological specializations and have invaded several habitats including marine, freshwater, and terrestrial ecosystems. The prime aim of this thesis is to study the adaptive evolution of protein-coding genes from two contrasting metazoan groups (invertebrates of the Class Cephalopoda – squids, cuttlefishes, octopuses and Nautilus, and vertebrates of the Class Aves – birds) for which adaptive selection at the molecular level is poorly known, despite their high diversity and adaptations to extreme environments (distinct temperature, pressure, depth, etc.). This was accomplished by the use of different Maximum likelihood codon-based models of molecular evolution that estimate the non-synonymous to synonymous substitution rate ratio (! ). This parameter measures the form and strength of selective pressure on the protein-coding genes: 0< ! <1 indicates purifying selection; ! = 1 indicates that mutations are neutral; and ! > 1 is indicative of positive selection or fixation of advantageous mutations. Part I of this thesis (chapters 2 and 3) focuses on the analyses of complete mitochondrial genomes of the Class Cephalopoda (metazoan invertebrates). In chapter 2, 17 species of cephalopods were initially considered, while in chapter 3 the analyses of mitochondrial genomes were extended to a total of 37 species. Here, two major objectives are explored. First, the Cephalopoda mitochondrial phylogeny (successfully determined and in agreement with previous studies) and second, test for evidence of adaptive selection in the 13-mitochondrial protein-coding genes (mt genes: seven NADH dehydrogenases, nd1–nd6 and nd4l, for Complex I; cytochrome b, cytb, for Complex III; three cytochrome c oxidases, cox1–cox3, for Complex IV; and two ATPases, atp6 and atp8, for Complex V) for the oxidative phosphorylation (OXPHOS) respiratory system. An important finding of this study was the discovery of positive selection in the Octopodiformes lineage, cephalopods with eight arms