Miracle-dz/UniFAR-FTUs huggingface dataset:
Immunomodulatory properties of water soluble arabinoxylans from extruded rice bran and wheat pentosan in an in vitro model of human monocytes and macrophages

Arabinoxylans (AXs) are major components of non-starch polysaccharides (NSPs). Recently, AXs have attracted a great deal of attention, because of their possible antitumor and immunomodulation activities. These activities have been suggested to be related to the content of low molecular weight (Mw) AXs, in particular those with a Mw below 32 kDa. Rice bran and wheat pentosan are rich sources of AXs. However, extraction of AXs is difficult and often gives low yield. Various methods have been used to increase the extraction yield of AXs with varying degrees of success, such as alkaline hydrolysis and enzymatic treatment. However, some of these treatments have been reported to be either expensive or produce hazardous wastes and non-environmentally friendly. Extrusion processing has been used to increase the solubility of cereal dietary fibre, however, these studies used alkaline or enzyme treatments with the extrusion to maximise the extraction yield. The use of extrusion alone as a pre-treatment method to increase the extraction yield and reduce the molecular weight (Mw) of AXs from rice bran or wheat endosperm pentosan has not been investigated. Hence, the current study aimed to determine if extrusion alone could change the extraction yield and Mw of the AXs. Wheat endosperm pentosan and rice bran were extruded with a twin-screw extruder at screw speeds of 80 and 160 revolutions per minute (rpm). It was found that the extraction yield of AXs increased with an increase in screw speed and was accompanied by a decrease in the Mw of the AXs. In vitro studies using immunoassays to measure proinflammatory markers showed that AXs from extruded rice bran and wheat pentosan significantly (P<0.05) increased nitric oxide (NO) and tumour necrosis factor α (TNFα) production from both U937 monocytes and macrophages in a concentration-dependent manner at (50, 500 and 1000 μg/ml), respectively. Moreover, the immunomodulatory activity of AXs was associated with the very low Mw of AXs. Moreover, inhibition of toll like receptor 4 (TLR4), which is known to be the receptor for bacterial lipopolysaccharides (LPS), significantly inhibited the AXs-induced increase in NO and TNFα production in both U937 monocytes and macrophages (P<0.05), suggesting the actions of AXs may be mediated at least in part through TLR4. The findings of this study indicate that AXs may compete with LPS for the same receptor TLR4, resulting in decreasing the inflammatory response that LPS produces during the infection. Thus AXs can produce a non-detrimental moderate increase in the inflammatory response.
Investigating fish behavioural responses to LED lights in trawls and potential applications for bycatch reduction in the Nephrops-directed fishery

for bycatch reduction in the Nephrops-directed fishery DTU Orbit (07/11/2019) Investigating fish behavioural responses to LED lights in trawls and potential applications for bycatch reduction in the Nephrops-directed fishery Light-emitting diodes (LEDs) have been tested in trawl fisheries to reduce the bycatch of unwanted species through behavioural stimulation. Previous studies used LED lights to either highlight escaping routes or increase the contact rate with square-mesh panels. However, phototactic responses (moving towards or away from light sources) to LED lights could also be exploited to separate species during the catching process. We investigated if either positive or negative phototaxis can be used to improve fish vertical separation from Nephrops (Nephrops norvegicus) in the aft section of a horizontally separated trawl codend. The aim was to increase the proportion of fish entering the upper compartment. We conducted two different experiments in front of the separation into compartments, inserting green LED lights in the upper and lower netting panel, respectively. Species vertical separation was analysed and compared in two identical trawls towed in parallel, one equipped with lights and one without. We obtained significant changes in vertical separation, but no clear species-specific phototactic response was identified. Neither of the light positions improved fish separation from Nephrops. However, the potential of LED lights as behavioural stimulators is confirmed, and a more mechanistic understanding of light and fish vision may improve the results of future applications.
Soil Reception and Activity of Acetochlor, Alachlor, and Metolachlor as Affected by Wheat (Triticum aestivum) Straw and Irrigation

Acetochlor [2-chloro-N-(ethoxymethyl)-N-(2-ethyl-6-methylphenyl)acetamide], alachlor [2-chloro-N-(2,6-diethylphenyl)-N-(methoxymethyl)acetamide], and metolachlor [2-chloro-N-(2-ethyl-6-methylphenyl)-N-(2-methoxy-1-methylethyl)acetamide] were applied in 280 L of water/ha to plots covered with 0 to 6720 kg/ha of wheat (Triticum aestivum L.) straw. At straw levels of 1120 kg/ha or greater, 50% or less of the applied herbicides were received by the soil surface before irrigation. Sprinkle irrigation (1.3 cm) washed 15 to 20% of the originally applied herbicide into the soil regardless of straw level. More metolachlor was retained on the straw than acetochlor or alachlor. Analysis of the wheat straw indicated that little water-extractable herbicide remained for all herbicides. Initial herbicidal activity on grain sorghum [Sorghum bicolor (L.) Moench. ] was reduced by the presence of wheat straw at the time of application, with acetochlor being least affected and alachlor most affected. Ten days after treatment, less than 10% of the original alachlor and acetochlor remained in the soil. When planted at this time, grain sorghum response was inversely related to the amount of straw mulch that was originally present. Metolachlor residues in the soil on day 10 were 11 to 26% of that on day 0 and there was comparably less reduction in activity on grain sorghum.
Isolation of innate immune response genes, expression analysis, polymorphism identification and development of genetic markers for linkage analysis in common carp (Cyprinus carpio)

Since the late 1990s, common carp and koi production enterprises around the world have suffered enormous losses due to a viral disease caused by cyprinid herpesvirus-3 (CyHV-3). Genetic variation in resistance to CyHV-3 infection was observed in different common carp strains, indicating that disease resistance can be improved by selective breeding. Marker-assisted selection is a breeding strategy that can accelerate genetic gain; however, this approach requires genetic markers and a genetic linkage map. To develop molecular tools for breeding CyHV-3resistant aquaculture stock, several candidate genes for antiviral innate immune response from common carp were isolated, and single nucleotide polymorphisms (SNPs) were identified. SNP markers for common carp immune response genes were developed for testing their linkage to disease resistance and for generating a genetic linkage map. Common carp immune response genes were isolated using degenerate primers developed from conserved peptide regions among other fish species for polymerase chain reaction (PCR) amplification. The amplified products were cloned and sequenced. Gene-specific primers were designed based on the isolated carp gene sequences to amplify gene fragments from genomic DNA of three carp strains and koi. The amplified products were cloned and sequenced to identify SNPs. For the genes that are duplicated, locus-specific primers were used for PCR amplification.
Weed management studies in kharif onion (Allium cepa L.) on yield attributes

The present investigation entitled "Weed management studies in kharif Onion (Allium cepa L.)" was conducted at Horticulture Complex, Dept. of Horticulture, Maharajpur, Jawaharlal Nehru Krishi Vishwa vidyalaya, Jabalpur (M.P.) during the year 2016-17. The treatments consisted of Ten combination of different agro input management practices viz., Oxyflurofen 23.5% EC + one hand weeding at 40-60 DAT (T1), Oxyflurofen 23.5% EC + one hand weeding at 30 DAT + Quizalofop Ethyl 5% EC at 60 DAT (T2), Pendimethalin 30% EC + one hand weeding at 30 DAT + Quizalofop Ethyl 5% EC at 60 DAT (T3), Black Plastic Mulch (T4), Organic Mulch6 t/ha (T5), Weedy check (T6), Silver Plastic Mulch (T7), Organic Mulch9 t/ha (T8), Organic Mulch12 t/ha (T9), Weed free check (T10), Significantly maximum 260.31 q/ha and 267.31q/ha marketable and total yield respectively was recorded under the treatment T4. Whereas, the lowest 140.02 q/ha and 147.36 q/ha yield was observed in T6. And minimum weed index was observed (-7.36%) in the treatment T4. The highest bolters percentage (2.70%) was recorded in the treatment T6. The highest (3.78%) value of doubles was recorded in the treatment T6. and the lowest doubles percentage 1.09% was recorded under the T10.
Rescue and characterisation of Oropouche virus in mammalian cell lines

II Publications based on this thesis . III Acknowledgments . IV Declarations . X List of abbreviations . XIX Chapter I. General Introduction . 2 1.1 The family Bunyaviridae . 3 1.1.1 The bunyavirus virion and genome . 6 The protein coding regions . 10 The untranslated regions . 16 1.1.2 The life-cycle of a bunyavirus particle in mammalian cells . 18 Attachment and entry . 18 Membrane fusion . 19 Transcription and Replication . 19 Release . 21 1.1.3 Host responses to bunyavirus infection . 24 The type 1 interferons and bunyaviruses . 24 Bunyaviruses and the antiviral response . 31 Programmed death of a bunyavirus-infected cell . 32 1.2 Oropouche virus . 33 1.2.1 Epidemiology . 33 1.2. 2 Clinical profile . 38 1.2. 3 Molecular Epidemiology . 38 1.2. 4 Pathogenesis . 39 1.2. 5 Virus-host interaction . 41 1.2. 6 Antivirals and OROV . 41 1.3 Reverse genetics . 42 1.3. 1 A brief history . 43 1.3. 2 Bunyavirus reverse genetics . 43 1.4 Aims . 49 Chapter II. Materials and Methods . 52 2.1 Materials . 52 2.1.1 Bacterial strains . 52 2.1.2 Eukaryotic cell lines . 52 2.1.3 Viruses . 54 2.1.4 Oligonucleotides . 55 2.1. 5 Plasmids . 64
Population structure and genetic diversity in the invasive freshwater snail Galba schirazensis (Lymnaeidae)

We studied the population genetic structure of the freshwater snail Galba schirazensis (Kuster, 1862), a potential vector of infectious diseases such as fascioliasis. Galba schirazensis has now a worldwide distribution but a poorly known origin because this species has been distinguished only recently from the morphologically similar and cosmopolitan Galba truncatula. We developed specific microsatellite markers and sequenced a mitochondrial gene (cytochrome oxidase subunit I) to study individuals of G. schirazensis from the Old World and New World. We found very low genetic diversity within populations, no heterozygotes, and marked population structure—a pattern observed in other highly selfing lymnaeid species with recently enlarged distributions as a result of biological invasions. The total lack of observed heterozygosity in the few populations of G. schirazensis that displayed some allelic diversity suggests high selfing rates. We also found that the center of diversity, and by extension the origin a.
Evaluating correlation of the native Inaba strain with the dominant isolated strains in outbreaks occurred in Iran at 2013 by Pulsed Field Gel Electrophoresis

Objectives: The aim of this study was to analyze the isolated cholera strains at outbreak 2013 for studying the their similarity and compare their homology in order to find out the route of infection either emerge from abroad or reemerge from inside native strains. Methods: All diagnosed V. cholerae isolates were entered to the study after re-identification at referral laboratory of Health Ministry based on standard procedures. These specimens were examined for specific serogroups by O1 polyvalent and Ogawa/Inaba nonspecific antisera and tested by MIC Test Strip Method against Ciprofloxacin, Nalidixic Acid, Cefixime, Ampicillin, Tetracycline, Trimethoprim-Sulfamethoxazole, and Erythromycin. Results: A total of 257 clinical Vibrio cholerae was isolated in an outbreak of Iran at 2013. The dominant causative type was Inaba. In Antibiotic susceptibility test isolates were 100% resistant to all except Erythromycin that just 23% of strains were sensitive. Homology of isolates was investigated through genotyping by PFGE method and their clonality was compared with previous isolated Iranian native strain. Overall 92% of analyzed strains showed a homolog pattern. These strains were located in 8 clusters. Although isolated strains at 2011 had 80 % homology with recent isolates, located in complete distinct cluster than all strains isolated at 2013. PFGE analysis revealed no dissimilarity between those stains resistant and sensitive to Erythromycin. Conclusion: This study confirmed that isolated Inaba strains at 2013 had different clonality pattern in PFGE than previously identified, suggested have foreign route from the neighboring countries. J Microbiol Infect Dis 2016;6(4): 184-189
Biomimetic Calcium Phosphates Derived from Marine and Land Bioresources

This chapter aims to establish the key factors for technological optimization of biogenic calcium phosphate synthesis from marine and land resources. Three natural calcium sources—marble, seashell and bovine bone—were considered as raw materials. The pro- posed materials are suitable candidates for the synthesis of bone substitutes similar to the inorganic bone component. The synthesis processes were developed based on the investi- gations of thermal phenomena (TGA-DSC analysis) that can occur during thermal treatments. By this method, we were able to determine the optimum routes and temperatures for the complete dissociation of calcium carbonate as well as risk-free deproteinization of bovine bone. An exhaustive characterization, performed with modern and comple- mentary techniques such as morphology (SEM), composition (EDS, XRF) and structure (FT-IR, XRD), is presented for each precursor. The final chemical composition of ceramic products can be modulated through a careful control of the key parameters involved in the conversion, in order to create long-term performant biphasic apatite biomaterials, with broad medical applicability. Identifying the suitable strategies for this modulation contributes to an appreciable advance in orthopedic tissue engineering.
In vitro antitumor activity of patulin on cervical and colorectal cancer cell lines

Background and Purpose: Patulin is a mycotoxin produced by some molds, especially Aspergillus and Penicilium, and is responsible for mycotoxicosis in animals and humans. There is still not very detailed data about the anti-cancer potency of patulin, but some reports demonstrated that it induces cellular apoptosis and toxicity. Materials and Methods: To determine the efficacy of patulin as a therapeutic strategy for cervical and colorectal cancers, we investigated its effects on HeLa,SW-48, and MRC-5 cell lines. Cell lines were exposed to various concentrations of patulin (i.e., 0.5, 1, 2, and 4 µM), then using methyl thiazolyl tetrazolium (MTT) and bromo-2′-deoxyuridine (BrdU) assays, the rates of apoptosis and cell viability were determined. Results: The obtained results showed a significant reduction in cell viability and apoptosis induction in a dose-dependent manner. Among all the cell lines, the highest growth inhibition rate was obtained at the 4 μM concentration of patulin. Conclusion: Our results suggested that patulin could significantly decrease tumor growth in human cervical and colorectal cancer models.
Influence of some biotic and abiotic inducers on Fusarium wilt disease incidence of lupin (Lupinus albus) on disease resistance and protein pattern

Two biotic inducers (Pseudomonas fluorescens and P. putida) and three abiotic inducers (copper sulphate, indole butyric acid and potassium chloride) were tested for their ability to induce resistance in lupin plants against wilt disease caused by Fusarium oxysporum f. sp. lupini. Application of the inducers, as seed treatment, significantly reduced wilt disease incidence under greenhouse conditions. Potassium chloride and Pseudomonas fluorescens were superior. SDSPAGE analysis of lupin seedlings revealed that seed treated with biotic and abiotic inducers resulted in a rapid induction of different novel PR-protein in shoot and root of lupin seedlings upon infection with the pathogen. These new proteins were not detected in untreated healthy or infected control seedlings.
Subcutaneous implantation of the light-activated pit and fissure resin-based sealant prototypes LAS-clear and LAS-opaque resulted in a mild transient tissue reaction

The objective of this study was to evaluate the biocompatibility of the light-activated pit and fissure resin-based dental sealant prototypes, LAS-clear and LAS-opaque, after subcutaneous implantation in rats for 7, 30, and 60 days. The commercial light-activated resin-based sealants, Delton-clear (DC), Helioseal clear (HC), Helioseal opaque (HO), and Clinpro Sealant (CL) served as control. Twenty-four 8-week-old male Sprague-Dawley rats were used in this study. Two rows of three 5 mm subcutaneous incisions were created on the back of each rat parallel to the midline. The materials were randomly implanted and the incisions were closed using sutures. The implants were left in situ for 7, 30, and 60 days. The implanted samples and the surrounding skin were removed, sectioned, and stained for histopathological evaluation. Results revealed that the scores of inflammatory cell infiltration of the DC, HC, LAS-clear, HO, CL, and LAS-opaque groups were not significantly different at 7, 30, and 60 days post-operation (p>0.05). The average total inflammatory cell infiltration score was highest at day 7 and lowest at day 30. Even though all the material revealed a persistent inflammatory response mediated by lymphocytes and macrophages at all time point evaluation, the tissue reaction of all groups to material implantation was that of typical wound healing. The tissue response scores of the DC, HC, LAS-clear, HO, CL, and LAS-opaque were not significantly different at 7, 30, and 60 days post-operation. The tissue response observed was material encapsulation without marked pathology. The capsule thickness was gradually increased in a time-dependent manner. In conclusion, the LAS-clear and LAS-opaque materials were biocompatible with the subcutaneous layer.
Effects of nutrient solution temperature on the concentration of major bioactive compounds in red perilla

Red perilla ( Perilla frutescens ) is used as food, stomachic and antitussive crude drugs, and anti-allergy supplements. The major bioactive compounds of red perilla are perillaldehyde ( PA ) , rosmarinic acid ( RA ) , luteolin ( LU ) , and anthocyanin ( ANT ) . In this study, we investigated the effects of 6 days low ( 10, 12, and 15 ° C ) and control ( 20 ° C ) nutrient solution temperature ( NST ) treatments on plant growth and major bioactive compound concentrations in red perilla leaves at the node position. No significant difference was detected in the dry weight of leaves of the main shoot, which is the main part harvested, among the treatments. However, leaf water content ( % ) tended to decrease with a decrease in NST, especially in plants grown at 10 ° C NST, which exhibited values significantly lower than those of plants grown at 15 ° C and 20 ° C NSTs. PA and ANT concentrations in the 3rd to 5th nodes did not differ among treatments. Conversely, RA concentration increased with a decrease in NST, irrespective of the node position. LU concentration at 10 ° C NST was the highest in all treatments, irrespective of the node position. This suggested that the production of bioactive compounds under the low NSTs differed depending on leaf maturity stage and compound. Additionally, the contents of RA and LU in the whole plant increased because there was no reduction in growth of the harvested part under the low NSTs. Therefore, 6 days exposure to root-zone temperatures at 10 ° C appears to be an effective method to increase both RA and LU concentrations and their contents in the whole plant of red perilla for its use as a crude drug or medicinal material.
Genetic and biological aspect of residual feed intake in pigs

Improving feed efficiency is one of the major objectives in animal breeding programs, in particular in view of increasing feed costs and increasing demands on feed crops and land for biofuel production. Residual feed intake (RFI) is a measure of feed efficiency that has improved statistical properties over traditional measures of feed efficiency that are based on the ratio of feed intake and growth. During the growing period, RFI is defined as the difference between the observed feed intake and expected feed intake based on average requirements for maintenance and growth. In pigs, RFI of individuals can be estimated as the residual of a model for feed intake that includes growth rate and backfat as covariates, possibly along with metabolic body weight (Mrode and Kennedy, 1993). Variation in RFI captures differences in efficiency of digestion, efficiency of metabolic utilization of feed energy, maintenance requirements, tissue turn over rates, activity, and stress, among others. The contribution of these components to RFI has been studied in poultry (Luiting, 1990) and beef cattle (Herd and Arthur, 2009), but has not been evaluated in pigs. To this end, selection experiments for RFI were initiated at INRA and Iowa State University (ISU) in 2000, both in Large White pigs. The INRA experiment consists of a line that is selected for increased RFI and a line selected for reduced RFI. At ISU a line is selected for reduced RFI, along with a line that was randomly selected for five generations and for increased RFI in the last generation reported here. In both experiments, selection is primarily among boars from first parity sows, which are evaluated for feed intake under group-housing with single space electronic feeders. At INRA, selection is for own phenotype for RFI measured as an index of daily feed intake, growth rate, and backfat within contemporary group. At ISU, selection is for BLUP EBV for RFI from an animal model for average daily feed intake with covariates for growth rate and backfat by generation. Further details of each experiment are in Gilbert et al. (2007) and Cai et al. (2008) and Bunter et al. (2010). Both sets of lines have been the subject of investigations into the genetic and biological basis of RFI, details of which can be found elsewhere. Objectives of this paper are to summarize the major findings of these studies, focusing on consistencies and differences of findings between the two experiments. Results presented apply to data collected during the first 6 generations of both experiments.