Miracle-dz/UniFAR-FTUs huggingface dataset:
7-Piperazinethylchrysin inhibits melanoma cell proliferation by targeting Mek 1/2 kinase activity

Purpose: To investigate the growth-inhibitory effect of 7-piperazinethylchrysin (PEC) on melanoma cell lines.Methods: Cell viability was analyzed by trypan blue exclusion assays and the cell cycle by flow cytometry using ModFit LT software. Specifically, cells were stained with propidium iodide (0.5 mg/mL) supplemented with RNase A (50 mg/mL), and analyzed using flow cytometry and ModFit LT software.Results: In A375 and B16F10 cell cultures, proliferation was reduced to 79 and 72 %, respectively, on treatment with 30 μM PEC. PEC increased the proportion of A375 cells in G1/G0 phase to 71.23 %, versus 42.76 % in untreated cells. In B16F10 and A375 cells, treatment with PEC caused the inhibition of Mek 1/2 kinase activity and suppressed Erk 1/2 phosphorylation. The level of cAMP-response element binding protein was increased by PEC. The expression of microphthalmia-linked transcription factor was also increased by PEC treatment. Marked enhancement was observed in the level of tyrosinase in melanoma cells on treatment with PEC. Analysis of PBG-D expression showed a marked increase in B16F10 and A375 cells on the addition of PEC to cell cultures at 72 h. The level of PBG D expression was increased by 9- and 8.5-fold in B16F10 and A375 cells, respectively, on incubation with 30 μM PEC. The addition of a Mek 1/2 inhibitor (U0126) to the cultures promoted PEC-mediated growth inhibition.Conclusion: PEC inhibited melanoma cell proliferation, apparently by blocking the cell cycle at G0/G1 and downregulating the Ras/Raf/Mek/Erk pathway.Keywords: Tyrosinase, Kinase, Microphthalmia, Phosphorylation, 7-Piperazinethylchrysin
Heterosis Studies for Growth, Earliness, Fruit Yield and Yield Components in Chilli (Capsicum annuum L.)

Chilli (Capsicum annuum L.) is one of the most important commercially grown spice cum vegetable in the world. The quality in chilli is determined by pungency level, oleoresin, fruit colour, fruit size, pericarp thickness, external glossiness and ascorbic acid content Dhall (2008). Dry matter content of red chilli fruit is an important quality character for the dry powder and dry fruit purpose, which are the major export items of chilli. Even though India ranks first in chilli area and production, the yield potential is low due to poor yielding varieties and high incidence of pests and diseases. From a practical point of view, standard heterosis is the more important of the two levels of heterosis because it is aimed at developing desirable hybrids superior to the existing high yielding commercial varieties. Heterosis breeding is an important genetic tool that can facilitate yield enhancement from 30-400% and helps to enrich many other desirable quantitative traits in crops Srivastava (2000).
Evaluation of natural oils for the development of cheap and sustainable solution for mosquito problem in the poor community

http://dx.doi. org/10.21276/IJRDPL.22780238. 2017.6(3). 2641-2647 ABSTRACT: Mosquitoes and their increasing number are responsible for causing millions of deaths around the world. Another important aspect is global warming that has already altered the distribution of vector borne diseases (IPCC fourth assessment report). Uses of synthetic insecticides to control vector mosquitoes has not only affected humans but has also caused adverse environmental effects in addition to high operational cost. Chemical mosquito repellent has a remarkable safety profile, but they are toxic to human health causing various side effects. Hence giving importance to health of human beings together with the environment, a mosquito repellent solution was prepared. The solution was prepared using the natural oils such as neem (Azadirachta indica), lemon grass (Cymbopogon flexuosus). All the oils were experimented using different concentrations. The experiment was conducted in a society where the people were already suffering from vector borne diseases such as malaria, dengue and chikungunya. The solution proved to be very effective for repelling of the mosquitoes and also did not cause any effect on the human beings. In addition to this, the solution is affordable by the poor communities.
Machine Learning for Investigating Post-Transcriptional Regulation of Gene Expression

RNA binding proteins (RBPs) and non-coding RNAs (ncRNAs) are key actors in post-transcriptional gene regulation. By being able to bind messenger RNA (mRNA) they modulate many regulatory processes. In the last years, the increasing interest in this level of regulation favored the development of many NGS-based experimental techniques to detect RNA-protein interactions, and the consequent release of a considerable amount of interaction data on a growing number of eukaryotic RBPs. Despite the continuous advances in the experimental procedures, these techniques are still far from fully uncovering, on their own, the global RNA-protein interaction system. For instance, the available interaction data still covers a small fraction (less than 10%) of the known human RBPs. Moreover, experimentally determined interactions are often noisy and cell-line dependent. Importantly, obtaining genome-wide experimental evidence of combinatorial interactions of RBPs is still an experimental challenge. Machine learning approaches are able to learn from the data and generalize the information contained in them. This might give useful insights to help the investigation of the post-transcriptional regulation. In this work, three machine learning contributions are proposed. They aim at addressing the three above-mentioned shortcomings of the experimental techniques, to help researchers unveiling some yet uncharacterized aspects of post-transcriptional gene regulation. The first contribution is RNAcommender, a tool capable of suggesting RNA targets to unexplored RBPs at a genome-wide level. RNAcommender is a recommender system that propagates the available interaction data, considering biologically relevant aspects of the RNA-protein interactions, such as protein domains and RNA predicted secondary structure. The second contribution is ProtScan, a tool that models RNA-protein interactions at a single-nucleotide resolution. Learning models from experimentally determined interactions allows to denoise the data and to make predictions of the RBP binding preferences in conditions that are different from those of the experiment. The third and last contribution is PTRcombiner, a tool that unveils the combinatorial aspects of post-transcriptional gene regulation. It extracts clusters of mRNA co-regulators from the interaction annotations, and it automatically provides a biological analysis that might supply a functional characterization of the set of mRNAs targeted by a cluster of co-regulators, as well as of the binding dynamics of different RBPs belonging to the same cluster.
The anti-apoptotic Mcl-1 protein controls the type of cell death in Theiler’s virus-infectedBHK-21 cells

Theiler’s murine encephalomyelitis virus (TMEV) is a highly cytolytic RNA virus that produces a persistent central nervous system infection and immune-mediated demyelination in susceptible strains of mice. TMEV-infected macrophages (mφs) undergo apoptosis which reduces the yield of infectious progeny (<10 pfu/cell), whereas TMEV infection of other rodent cells in vitro, e.g. baby hamster kidney cells (BHK-21), produces a canonical necrotic cytopathic effect with high virus yields (200-500 pfu/cell). In this study, we found that while most TMEV-infected BHK-21 cells became necrotic, ~20% of cells underwent apoptosis. Mcl-1, an anti-apoptotic Bcl-2 family member, was highly expressed in BHK-21 cells, but levels decreased upon infection, consistent with the onset of apoptosis. Infection in BHK-21 cells in which Mcl-1 expression was knocked down using silencing (si) RNA that an ~ 3-fold increase in apoptotic cell death compared to that in parental cells. Infection of stable Mcl-1-knock-down cell lines led to restricted viral titers, unlike the high viral titers observed in parental cells. The apoptotic program switched on by TMEV replication appeared to be similar to that in mouse M1-D mφs, with hallmarks of activation of the intrinsic apoptotic pathway in a tumor suppressor protein p53-dependent manner. Subsequent activation of the Bcl-2 BH-only pro-apoptotic Noxa protein led to degradation of Mcl-1, activation of Bax and cleavage of caspases-9 and -3. Together, these results indicate that Mcl-1 acts as a critical pro-survival factor that protects against apoptosis in a p53-dependent manner and restricts the production of infectious virus in BHK-21 cells.
Incompatibility and Pollination of Distylous Psychotria serpens (Rubiaceae) in the Ryukyu Islands, Japan

Psychotria serpens (Rubiaceae) is usually distylous in floral morphology, but uncertainty still remains as to whether the two morphs of the species have self- and intramorph-incompatibility system and also on the efficiency of pollinators. We examined self- and intramorph-incompatibility as well as efficiency in flower visitors to carry out pollination in natural populations. Pollination experiments indicated that P. serpens is self- and intramorph-incompatible, as in other typical distylous species. Flowers of the two morphs produced nectar from the base of the corolla tube and attracted various insects, such as short-tongued wasps, bees, hoverflies, butterflies, etc. Among the flower visitors, the short-tongued wasps, bees and hoverflies were considered to be efficient pollinators for P. serpens in the Ryukyu Islands.
Response of broiler chickens to dietary inclusion of fermented canola meal under heat stress condition

Abstract Feeding high levels of canola meal to monogastric animal require reducing antinutritional factors such as glucosinolates and fibre. Solid state fermentation is known to reduce antinutritional factors and improve nutritional quality of feedstuffs. In this study, canola meal was treated with Lactobacillus salivarius in solid state fermentation for 30 days and included in diet with 4 levels of 0 (control), 10, 20, and 30%. From 29 to 35 days of age, equal number of birds from each dietary treatment was exposed to either 23 ± 1 °C (unheated) or 36 ± 1 °C (heated). Results showed that irrespective of temperature, weight gain (WG) and feed conversion ratios (FCR) were not affected by inclusion of fermented canola meal (FCM). Diet also did not affect carcass yield, plasma triiodothyronine (T3) and tetraiodothyronine (T4), and body temperature. As expected, heated birds had lower carcass yield and T3 than their unheated counterparts. In conclusion, although dietary inclusion of FCM at levels more than 10% retarded growth performance during 1 to 28 days of age, no detrimental effects on performance was observed when FCM included up to 30% during 29 to 35 days of age under both unheated and heated conditions.
Characterisation of the selectivity and binding interactions of berberine derivatives with G-quadruplex DNA and a DNA/RNA hybrid

VI TABLE OF CONTENTS VIII CHAPTER 1 – GENERAL INTRODUCTION 1 1.1 GENERAL INTRODUCTION ON NUCLEIC ACIDS.1 1.2 DNA REPLICATION . 3 1.3 TELOMERIC DNA . 5 1.3. 1 Telomere nucleoprotein interactions. 7 1.3. 2 Telomerase. 9 1.4 G-QUADRUPLEX STRUCTURES . 11 1.4. 1 Biological impact of G-quadruplexes . 14 1.5 TARGETING TELOMERASE . 15 1.5. 1 Direct telomerase inhibition . 15 1.5. 2 G-quadruplex binding ligands . 17 1.6 METHODS FOR CHARACTERISING G-QUADRUPLEXES . 20 1.6. 1 Circular dichroism spectroscopy . 20 1.6. 2 Electrospray ionisation mass spectrometry. 25 1.7 SCOPE OF THESIS . 31 CHAPTER 2 – METHODS & MATERIALS 33 2.1 MATERIALS. 33 2.2 OLIGONUCLEOTIDES . 33 2.2.1 Purification of oligonucleotides . 33 2.2.2 Preparation of secondary oligonucleotide structures . 35 2.3 LIGAND PREPARATION . 37 2.3. 1 Determining ligand extinction coefficients . 38 2.3. 2 Preparing ligand-oligonucleotide mixtures. 38 2.4 MASS SPECTROMETRY ANALYSIS . 38 2.4. 1 Waters Q-ToF UltimaTM conditions . 38 2.4. 2 Waters SynaptTM HDMSTM conditions . 39
Comparative Analysis For Production Traits Of Local Chicken And Isa Brown In Kgr-Iraq /

The research work has been constructed at Sulaimani Research Station–Director of Agricultural Research to study the effect of three lines of local chickens: Pure black (line 1), Black with brown Neck (line 2), White (line 3) and Isa Brown (line 4) at four periods (19-32, 33-43, 44-60 and 61-75 weeks) on egg production traits. The age at first day of egg production, first week of production, sexual maturity, when reach to 50% and peak egg production and long duration of peak egg production were recorded. In addition to estimate the egg/hen/all periods, egg/hen/week, egg/ hen/ all period% and hen day egg production%. No significant difference between lines on age at first day of egg production, first week of production, sexual maturity and reach to peak production. Line 2 significantly (p<0.05) reach to 50% before other lines about 8-21 weeks. Moreover, line 3 significantly (p<0.05) has the shorter duration of egg production compared with other lines. Hen day egg production% at age at sexual maturity, at 50% production and throughout long duration of production did not significantly differed between lines. Peak production% of line 2 was significantly (p<0.05) higher than other lines. Egg weight was significantly (p<0.05) higher in line 4 compared with lines 1,2 and 3, but did not significantly differed with line 3 in egg/ hen/ all periods and egg/ hen/ week. As for percentage of egg production, line 2 was significantly (p<0.05) higher in percentages (33.20 and 34.30%) for egg/ hen/ periods% and Hen Day Production%, respectively. As the age increased the egg weight was increased, while egg/ hen/ period, egg/ hen/ week and percentage of egg production were significantly (p<0.05) higher at period 3.
Can the Cure for Chagas’ Disease be Found in Nature?

Nature is a skilled factory that produces a wide variety of secondary metabolites known as natural products. Those compounds synthesized by living organisms are usually related to their vital processes. Many drugs used nowadays, had its origins in medici- nal plants and other organisms such as herbs, fungi and sponges. Hence, those sources constitute a viable alternative to conventional medicine in many developing countries. In other hand, protozoan diseases like Chagas, represent a health threat causing mortality to populations around the world. The classic treatment for Chagas’ disease is chemo- therapic and includes benznidazole and nifurtimox, although, the search for new drugs still remains. Triatomines that may spread Chagas can also be controlled making use of the insecticide property of certain plants. After literature survey it was found, classes of natural products, plant extracts, essential oils, and other natural sources that have shown activity against T. cruzi . In this context, many substances were tested in vitro and in vivo assays to verify trypanocidal efficacy. Promising results were published regarding to compounds arising from plants and sponges that showed high toxicity on different forms of the parasite with low toxicity on mammalian cells, although few were clinically tested on Chagas’ disease.
Response of a Multiple-Resistant Palmer Amaranth (Amaranthus palmeri) Population to Four HPPD-Inhibiting Herbicides Applied Alone and with Atrazine

Control of multiple-resistant Palmer amaranth populations in corn will rely heavily on the use of POST 4-hydroxyphenylpyruvate dioxygenase (HPPD)-inhibiting herbicides. Therefore, field and greenhouse experiments were conducted to: (1) evaluate Palmer amaranth control with four HPPD inhibitors alone and in combination with atrazine at two application timings and (2) investigate the joint activity of HPPD-inhibiting herbicides and atrazine in atrazine-resistant (AR) and atrazine-susceptible (AS) Palmer amaranth populations. Control of the AR Palmer amaranth population varied among the HPPD-inhibiting herbicides with tolpyralate > tembotrione = topramezone > mesotrione based on GR50 values in the greenhouse. In the field, Palmer amaranth control was lower when the HPPD-inhibiting herbicides, with the exception of tolpyralate, were applied to 15- vs. 8-cm-tall Palmer amaranth. Tolpyralate controlled Palmer amaranth ≥95% at both application timings. The addition of atrazine (560 g ai ha-1) improved Palmer amaranth control with mesotrione and topramezone at the 8-cm application timing and with mesotrione and tembotrione at the 15-cm application timing. In the greenhouse, joint activity of mesotrione and atrazine and tembotrione and atrazine was synergistic with both the AR and AS Palmer amaranth populations. In the AR population, an additional 980 g ai ha-1 of atrazine (8X) was needed to cause a synergistic response compared with the AS population. Synergistic responses with mesotrione were detected with all atrazine rates for the AS population and for atrazine rates ranging from 280 to 2,240 g ai ha-1 for the AR population. Only additive responses were observed when atrazine was applied with tolpyralate and topramezone, indicating that joint activity in the form of synergism occurs more readily with the triketones compared with the benzopyrazoles. When faced with an AR Palmer amaranth population, the addition of atrazine to HPPD inhibitors may increase the overall success of weed management due to joint activity. Nomenclature: Atrazine; mesotrione; tembotrione; tolpyralate; topramezone; Palmer amaranth, Amaranthus palmeri S. Wats. ; corn, Zea mays L.
The effects of rumen-protected choline and l-carnitine supplementation in the transition period on reproduction, production, and some metabolic diseases of dairy cattle

ABSTRACT This experiment was designed to examine the effects of l-carnitine and choline on production parameters, reproduction indices, as well as ketosis and fatty liver indicators in pre- and post-partum Holstein cows. A number of 120 dairy cows were randomly allocated to four treatment groups: protected choline (60 gm/day per cow), l-carnitine (50 gm/day per cow), choline + l-carnitine (60 + 50 gm/day per cow), and control group (without supplement). Treatments were given from one week before calving to four weeks after calving. Milk and blood samples were collected at the time of calving till four successive weeks. Results showed that combined choline and l-carnitine supplementation increased milk fat % (3.93 ± 0.11), but decreased solids-non-fat % (8.04 ± 0.10) and lactose % (3.92 ± 0.05). Reproduction indices – including service/conception rate (1.24 ± 0.40), calving to first visible oestrus (53.36 ± 8.20), calving to first service (59.07 ± 4.20 days), and days open (63.36 ± 8.10 days) – were improved for combined choline and l-carnitine group. A significantly lower level of aspartate aminotransferase (50.16 ± 5.96) and a higher level of beta hydroxy butyrate acid (0.31 ± 0.10) were observed in blood serum when combined choline and l-carnitine was supplemented. In conclusion, concomitant administration of choline and l-carnitine improved reproduction indices as well as the liver health index in Holstein cows.
Modeling Groundwater Flow at a Hydraulic Fracturing Site Near Pavillion, Wyoming

This thesis uses the GIS-conceptual model approach to create groundwater models investigating groundwater contamination near Pavillion, Wyoming. This area was part of a study by the US Environmental Protection Agency (EPA) in 2009 that claims domestic water well contamination originated from hydraulically fractured natural gas wells. Hydraulic fracturing is the process of injecting water, sand, and chemicals into gas and oil wells in order to stimulate well production. This has caused concern over groundwater contamination. The models show natural groundwater flow systems generally move from west to east, however, a recharge area near the center of the model locally disrupts that pattern. Fivemile Creek is the primary discharge zone, located towards the northern end of the model. Once gas production is included in the model, the groundwater flow systems change drastically; injection wells induce areas of high head that cause groundwater to flow away from them, while extraction wells draw groundwater towards them. This flow system alteration affects where advective groundwater transport carries dissolved methane. Groundwater flow patterns change direction in response to varying monthly extraction and injection rates, however proper well casing can mitigate these effects by isolating the flow occurring within a well from the surrounding groundwater flow systems. The resulting models support the EPA’s conclusion that hydraulic fracturing was the most likely cause of water contamination in the area by showing that deep contaminants found at the EPA monitoring well can be traced back to a gas development well, while shallower contaminants could have originated from other areas that are not within the vicinity of natural gas wells. Proper casing is crucial for minimizing the disturbance and anthropogenic methane contamination of natural groundwater flow systems. The methodology of this thesis can be used to create groundwater models of any area where enough data is available to create realistic groundwater models.
Selection and validation of reference genes for real-time qRT-PCR normalization in different tissues of Eucalyptus tereticornis

Abstract Reference genes are generally used as endogenous normalization factor for relative quantification of target genes in quantitative real-time PCR (qRT-PCR). The present work aimed at identifying suitable reference genes for normalization of qRT-PCR data in tissues of Eucalyptus tereticornis. The expression levels of housekeeping genes like Actin (EtAct2), Isocitrate dehy - drogenase (EtIDH), ribosomal RNA (Et18s rRNA), SAND family protein (EtSAND), Histone protein (EtH2B), α-Tubulin (EtTUB), and eukaryotic initiation factor (EteIF4B) were studied to characterize their normalization stability in different tissues including young leaves, internodes, developing and mature xylem. The expression level of these genes was analyzed using different algorithms like geNorm, NormFinder and Best- Keeper. Among the seven reference genes analyzed, EtAct2 was expressed with less variance and was found to be the most stable reference gene across different tissues using all the three programs, while the least stable gene identified was EtH2B. Further, the normalization efficiency of the reference genes were assessed to predict the expression levels of three primary cell wall specific cellulose synthase transcripts (EtCesAs) in E. tereticornis tissues. The relative expression of EtCesA4, EtCesA5 and EtCesA6 was determined to be 3-19 fold higher in leaf and internode tissues when compared to developing and mature xylem tissues. This study will allow accurate normalization of qRT-PCR experiments across different tissues in E. tereticornis for future genomic research in this tropical eucalypt species.