Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of Herbicide and Insecticide Interaction on Soil Entomofauna Under Maize Crop

Abstract The aim of this study was to evaluate the impact of the herbicide mixture nicosulfuron+atrazine, with or without the insecticide chlorpyrifos, onto soil entomofauna under maize crop. The treatments, applied 25 days after maize emergence, were represented by a weeded control without insecticide and herbicide, a weeded control with chlorpyrifos, and mixtures of nicosulfuron+atrazine, with or without chlorpyrifos. Arthropods populations, on the soil surface, as well as inside the soil under maize, were principally represented by mites (Arachnida: Acari), decomposer collembolans (Hexapoda:Parainsecta:Collembola) and predator ants (Hymenoptera:Formicidae). The nicosulfuron+atrazine mixture with chlorpyrifos and the isolated chlorpyrifos reduced the population dynamics of all insect groups on the soil surface compared to the weeded control. In the soil, mite and ant populations were reduced after application of the herbicide mixture with chlorpyrifos and of the isolated chlorpyrifos.
EFFECTS OF DIFFERENT METHODS OF FERMENTATION ON MICROBIOLOGY, PROXIMATE AND MINERAL COMPOSITIONS OF COCOA BEAN (THEOBROMA CACAO (L.)

The study investigated effects of different methods of fermentation on microbiology, proximate and mineral composition of cocoa bean (Theobroma cacao (L.). Open, close and local methods of fermentation of cocoa beans were carried out separately for five days. Microbial analysis was carried out using pour-plate technique while proximate and mineral analyses were determined using standard methods. The bacterial count of cocoa beans at 5th day of fermentation ranged from 2.0 x 104cfu/ml in local method to 1.0x 102cfu/ml in close method. The bacteria isolated and identified included Bacillus subtilis,B. cereus,B.licheniformis,Micrococcus luteus and Staphylococcus aureus. Fungi count also ranged from 1.03x 104sfu/mlin local method to 1.0x 102sfu/ml in close method. Fungi isolated and identified included Aspergillus niger,A. flavus,Neurospora crassa and Saccharomyces cerevisiae. The pH of the fermenting cocoa beans ranged from 8.0 in local to 3.5 in close method. Also, the proximate analyses of the fermenting beans showed that the moisture content ranged from 55.56 to 50.89%; fat from 23.56to 21.93%;protein from 13.46 to 11.06%;ash from 5.94 to 5.91% and carbohydrate from 13.46to11.06%. All values ranged from close to local method with open method having higher values than close but lower than local method. There was a significant increase in the concentration of calcium, copper, iron, sodium potassium and magnesium in the fermenting cocoa beans.Keywords: Cocoa bean, fermentation, microbiology, proximate, mineral
Mathematical Modeling of Intracellular Calcium Signaling: A Study of IP 3 Receptor Models

3 Dedication . 4 Acknowledgements . 5 List of Tables . 9 List of Figures . 10 List of Acronyms . 14
Population Dynamics of Digitaria spp Submitted to Selection Pressure by Herbicides in Sugarcane Crop

Abstract The objective of this research was to study population dynamics of the weed crabgrass, genus Digitaria, submitted to selection pressure by herbicides currently applied in sugarcane crops in Brazil. In the first experiment two crabgrass species (Digitaria nuda and Digitaria ciliaris) and eight herbicide treatments applied in preemergence were used, and control percentage was evaluated at 7, 14, and 21 days after herbicide application (DAA). In the second experiment the level of tolerance through dose-response curve was determined for the species D. nuda and D. ciliaris, to the herbicides imazapyr, tebuthiuron, ametryne, and metribuzin. All the herbicides studied were efficient in controlling D. ciliaris, however, for D. nuda the best results were obtained only with ametryne, metribuzin, and isoxaflutole. The relation (T/S) between the rate required to reduce plant dry biomass (GR50) at 21 DAA of D. nuda and D. ciliaris was 16 for imazapyr and 6.3 for tebuthiuron, showing differential susceptibility of species; however for ametryne the rate T/S of 1.1 showed that D. nuda was not tolerant to this herbicide. For metribuzin, at 1.92 kg a.i. ha-1, reduction of dry biomass was 80 and 90% to D. nuda and D. ciliaris, respectively. Even being controlled by metribuzin, D. nuda presented a higher level of tolerance to this herbicide, what was confirmed by the relationship T/S 14.4. As general conclusion of the research, it can be stated that the species D. nuda is more tolerant to ALS inhibiting herbicides and substituted urea, when compared with D. ciliaris; probably, D. nuda was selected by repetitive use of these herbicides.
The role of O-linked protein glycosylation in β-cell dysfunction (review)

Although only recently described, the pathway of O-linked protein glycosylation is already being implicated in diseases as diverse as cancer and Alzheimer's. Unlike the better known N-linked pathway, O-linked protein glycosylation is a dynamic and regulated event, much like tyrosine phosphorylation. During the process of O-glycosylation, the enzyme O-GlcNAc transferase (OGT) uses the substrate UDP-N-acetylglucosamine (UDP-GlcNAc) to attach a single O-linked N-acetylglucosamine (O-GlcNAc) to nuclear and cytosolic proteins on serine or threonine residues. Conversely, the enzyme O-GlcNAc-selective N-acetyl-beta-D-glucosaminidase (O-GlcNAcase) removes the O-GlcNAc, returning the protein to its baseline state until the cycle repeats itself. Although proving to be of interest in many different tissues, this pathway is especially important in pancreatic beta-cells. The beta-cell is unique in containing much more OGT than any other cell type. This enables beta-cells to respond to physiological increases in the glucose concentration by converting glucose to the OGT substrate UDP-GlcNAc, thereby dynamically coupling intracellular O-linked protein glycosylation to the extracellular glucose concentration. As a result, the beta-cell also appears to be especially susceptible to disruption of the O-glycosylation pathway. The diabetogenic agent streptozotocin (STZ), a UDP-GlcNAc analogue, causes beta-cell toxicity by irreversibly inhibiting O-GlcNAcase, while the diabetogenic agent alloxan (ALX), also a UDP-GlcNAc analog irreversibly inhibits OGT. This review will summarize what is currently known about beta-cell O-glycosylation and expand upon historical observations of chemically-induced beta-cell toxicity in animals to develop a model suggesting how beta-cell O-glycosylation is also involved in the development and progression of type 2 diabetes in humans.
The effect of single epidural plus intramusculer injection of FSH on superovulatory response in Anatolian Black cow

Bu calisma superovulasyon olusturmak icin tekrarlanan dozlarda yapilan FSH uygulama sayisini azaltmak, FSH’nin tek uygulama seklinde epidural-im olarak uygulanmasinin superovulasyon olusturma yonunde etkisini belirlemek ve bu uygulamanin Yerli Kara inekte etkisini ortaya koymak amaciyla tasarlandi. Elde edilen sonuclar gunde iki kez azalan dozlarda yapilan FSH uygulama sonuclari ile karsilastirildi. Bu calismada 21 bas Yerli Kara inek kullanildi. Yerli Kara ineklere 1.56 g progesteron iceren Cue-mate uygulandi. Inekler FSH uygulama sekli ve dozuna bagli olarak 3 gruba (D1, D2 ve E) ayrildi. Grup D1’e toplam 490 IU FSH ve grup D2’ye toplam 700 IU FSH superovulasyon prokolunun 7. gununde baslamak uzere 4 gun sure ile azalan dozlarda im olarak uygulandi. Grup E’ye ise FSH superovulasyon prokolunun 7. gununde 175 IU epidural, 175 IU im olmak uzere tek uygulama biciminde yapildi. Superovulasyon protokolunun 9. gununde Cue-mate cikarildi ve gruplardaki tum ineklere 500 µg prostaglandinF2α yapildi. 11. gun aksam ve 12. gun sabah olmak uzere 12 saat ara ile tum ineklere Yerli Kara bogalardan alinan spermalar ile suni tohumlama yapildi. Superovulasyon uygulanan inekler suni tohumlama uygulamasindan 7 gun sonra cerrahi olmayan yontemle embriyo elde etme calismasina alindi. Elde edilen embriyolar Uluslararasi Embriyo Transferi Birliginin bildirdigi kistaslara gore siniflandirildi. Gruplar arasinda ortalama CL sayilari yonunden istatistiki bir farklilik gozlenmedi. Ortalama CL sayilari grup D1’de 3.7 ± 0.56; grup D2’de 3.4 ± 0.55 ve grup E’de 6.0 ± 1.14 olarak belirlendi. Transferedilebilir embriyo oranlari gruplar arasinda farkli degildi (10/42, %23.8 grup D1; 14/32, %43.8 grup D2 ve 19/82, %23.2 grup E). Transferedilemez embriyo oranlari da gruplar arasinda farkli bulunmadi (32/42, %76.2 grup D1; 18/32, %56.2 grup D2 ve 63/82, %76.8 grup E). Tum gruplar da UFO orani benzerdi (17/77, %22.1 grup D1; 13/71, %18.3 grup D2 ve 28/132, %21.2 grup E). Embriyo geri kazanim orani gruplar arasinda farkli bulundu (59/77, %76.6 grup D1; 45/71, %63.4 grup D2 ve 110/132, %83.3 grup E). Sonuc olarak, superovulasyon olusturma yonunden FSH’nin tek uygulama seklinde yapilan epidural-im uygulamasinin azalan dozlarda yapilan FSH uygulamasi ile karsilastirildiginda sonuclarin azalan dozlarda yapilan uygulamaya yakin oldugu belirlendi. Ancak transferedilebilir embriyo orani hem epidural-im uygulamada hem de azalan dozlarda yapilan uygulamalarda dusuk bulundu. Transferedilebilir embriyo oranini artirmak icin farkli irklarda daha ileri calismalarin yapilmasi gerektigi benimsendi
CHARACTERIZATION OF A GTP-BINDING DNA APTAMER

iii ACKNOWLEDGEMENT iv LIST OF FIGURES vii LIST OF ABBREVIATIONS ix CHAPTER 1: INTRODUCTION 1.1 Guanosine-5’-triphosphate (GTP) and G-protein-coupled receptor (GPCR) 1 1.1.1 GPCR drug screening assays 3 1.2 Functional Nucleic acids (FNAs) and In vitro selection 7 1.3 Fluorescent Aptamer-based Sensors 1.3. 1 Aptamers and sensor anatomy 10 1.3. 2 Label-free approach 11 1.3. 3 Single-labeled signaling aptamers 14 1.3. 4 Double-labeled signaling aptamers 15 1.3. 5 Structure-switching signaling aptamers 18 1.4 Applications using Aptamers 20 1.5 Research Objective 25 CHAPTER 2: APTAMER CHARACTERIZATION BY STRUCTURE-SWITCHING 2.
Fine Tuning of CFTR Traffic and Function by PDZ Scaffolding Proteins

Cystic fibrosis (CF) is the most common lethal genetic disorder in Caucasian population (Welsh et al., 1995). This pathology is due to mutations in the CF transmembrane conductance regulator (CFTR) encoding gene leading to alterations or loss of function of this channel (Kerem et al., 1989; Riordan et al., 1989; Rommens et al., 1989). CF affects several organs such as sweat glands, reproductive system and gastrointestinal tract, but the first cause of morbidity and mortality is respiratory system affections. While gene therapy for replacement of CFTR was a promising curative approach since the discovery of the CFTR gene, it turned to be more difficult than initially thought and no cure has arisen so far. Protein-protein interactions are powerful regulators of both protein trafficking and function, and can be enhanced or prevented by small molecules and short peptides (Zhang et al., 2011). Modulating these protein interactions are becoming a hopeful approach to develop new treatments for various diseases, including CF.
Characterization and Targeting of the Aldehyde Dehydrogenase Subpopulation in Ovarian Cancer

Abstract : Despite a common outstanding response to primary therapy, most ovarian cancer patients will experience recurrence due to what is often microscopic undetectable disease. One possible cause of this is a chemoresistant population of cells with stem cell characteristics. We have examined one potential population in particular, the ALDH-positive population. We have shown that ALDH1A1-positive cells are more tumorigenic than ALDH1A1-negative cells, contribute to poor patient outcomes, and contribute to chemoresistance. These effects can be reversed by downregulating ALDH1A1 expression with nanoparticle-delivered siRNA. Additionally, we have shown that CSCs are clinically significant, in that chemoresistant tumors have increased density of ALDH and CD133 cells. Importantly, they do not seem to explain the entire story, as there are still many CSC-negative cells present at the conclusion of treatment. Specifically, endoglin (CD105) and hedgehog family members (Gli1 and Gli2) appear to play important roles in chemotherapy resistance, and when targeted enhance response to chemotherapy. To further identify other important players, we have further developed the patient-derived xenograft (PDX) model where patient samples are directly implanted into mice, and when formed, treated with chemotherapy. The treated tumors, like patient specimens, are enriched with ALDH1-positive cells. Further characterization of the surviving population is underway, in conjunction with separately-funded protocols.
The environmental impacts of biomass crops: use by birds of miscanthus in summer and winter in southwestern England

We compared birds in a group of established and well-managed miscanthus (Miscanthus x giganteus) fields in Somerset and East Devon, southwestern England, with plots of short rotation coppice (SRC) willow, arable crops and grassland in two winters and one summer. Following early spring cutting, 19 miscanthus fields grew taller, initially produced greater cover and were less weedy than SRC. As stubble in May, the miscanthus contained broadly similar species at similar densities to arable and grassland comparison plots. By July, at 2-m-tall, miscanthus held higher densities of birds but of fewer species, most of them characteristic of woodland and scrub. SRC, previously identified as being a beneficial crop for many birds, always contained more species and individuals than miscanthus. Throughout each of two winters, 15 miscanthus plots remained unharvested and contained more wood/scrub species such as Blackbirds Turdus merula, tits, Reed Buntings Emberiza schoeniclus and Woodcock Scolopax rusticola than the comparison plots, which held more corvids and Skylarks Alauda arvensis amongst others. Similar overall mean densities of birds in the miscanthus and the comparison plots masked relatively low density variance in miscanthus and very high variance in the comparison plots. Unharvested miscanthus crops grown in place of habitat types supporting flocks of wintering birds would displace these flocks. Miscanthus plantations with open patches attracted more finches and waders in winter. The two previous studies of birds in miscanthus in the UK found more species and more individuals than we did in summer and winter. Both these studies documented high levels of weediness and patchy crop growth. In the context of this previous work our data suggest that bird use of miscanthus in summer and winter is likely to be variable, affected by region, weediness, crop structure and patchiness. While large-scale cropping of SRC in England is likely to have a positive overall impact on a suite of common farmland and woodland birds, our data suggest that miscanthus in the southwest of England may have an approximately neutral effect. However, some open farmland specialist species may be lost when planting either crop.
Effects of nitrogen on development and growth of the leaves of vegetables. 3. Appearance and expansion growth of leaves of spinach

In a series of greenhouse and field trials, spinach cv. Trias plants were supplied with different amounts of N fertilizer in various split applications. Rates of leaf emergence and expansion were recorded, as well as final leaf size. The rate of leaf appearance varied between 0.16 and 0.57/day across experiments, but was hardly affected by N treatment. The rate of leaf expansion and mature leaf area increased with leaf number, reaching maximum values at leaf pair 3+4 or 5+6 and decreasing subsequently. Both characteristics were positively correlated with N supply. The duration of expansion was not influenced by N treatments and varied between 15 and 30 days in most experiments. The rate of leaf expansion was the main factor determining mature leaf size. Specific leaf area over all green leaves slowly decreased with time in most experiments and was around 300 cmsuperscript 2/g. As the differences in the number of leaves were small, the differences in total green leaf area per plant resulted from differences in the areas of individual mature leaves.
THE EFFECT OF ANTIOXIDANTS ON THE BOND STRENGTH OF RESIN COMPOSITE TO BLEACHED ENAMEL

Aim : This study aimed to assess the effect of treating bleached enamel with antioxidants on the value of shear bond strength of resin composite to enamel. Also, a comparison was set between the natural antioxidant used (5% pomegranate solution) and the chemical one (10 % sodium ascorbate gel). Materials and Methods : Fifty six human freshly extracted sound upper anterior teeth were used. The specimens were randomly divided into four main groups as follow : Group I : control(no bleaching) ; Group II : bleached then treated with the chemical antioxidant ; Group III : bleached then treated with the natural antioxidant; Group IV : bleached with no antioxidant treatment. Each group was further sub-divided into two sub-groups according to whether the restoration was performed immediately or delayed (after one month incubation in artificial saliva) (n=7). The variables were as follow: No bleaching immediate restoration (control) ; no bleaching delayed restoration after incubation for one month in artificial saliva ; bleached followed by application of a chemical antioxidant (10% sodium ascorbate gel) for 10 min then immediate restoration;bleached followed by application of a chemical antioxidant (10% sodium ascorbate gel) for 10 min then delayed restoration; bleached followed by application of a natural antioxidant (5% pome granate solution) for 10 min then immediate restoration ; bleached followed by application of a natural antioxidant (5% pome granate solution) for 10 min then delayed restoration ; bleached with no application of an antioxidant then immediate restoration ; bleached with no application of an antioxidant then delayed restoration. The data were statistically analyzed using two way ANOVA test, one way ANOVA test, Tuckey’s post-hoc tests and pair wise student T-test. Results : Regarding the mean shear bond strength values (immediate restoration) ; the control sub-group (immediately restored) demonstrated the highest values followed by the bleached subgroups treated with the natural antioxidant (5% pomegranate solution), then the bleached subgroups treated with the chemical antioxidant (10% sodium ascorbate gel). The bleached subgroups that were not treated with the antioxidants showed the least values. Regarding the subgroups that undergone a delayed investigation ; the sub-groups treated with the natural antioxidant demonstrated the highest shear bond strength values followed by the sub-groups treated with chemical antioxidants then the control group while the bleached sub-groups that were not treated with the antioxidants showed the least values of mean shear bond strength
Interference of maternal immunity with immune response of broiler chicks vaccinated with Gumboro vaccine.

This study was aimed to evaluate the levels of maternal immunity and to find the proper time for vaccination against infectious bursal disease (IBD) in broiler chicks with studying levels of total protein, albumin and globulin. One hundred twenty chicks were used and 20 of them were tasted respectively at age of 1, 7, 14, 21, 28, 35 days. It was observed that the levels of maternally derived antibody (MDA) were detectable up to 14 days of age and then declined to low levels in 21 days using ELISA test whereas globulin level did not show any significant change during the period of study. One hundred forty chicks were used to find the proper time of vaccination; they were divided in to seven groups, and vaccinated with live attenuated intermediate vaccine against IBD with different vaccination programs. The study showed that the second group which vaccinated 7 days and boostered at 14 days old was the best one. Ten chicks of each group were scarified at 28 days and 35 days for blood collection. It was demonstrated that the second group presented a significant elevation in levels of specific antibodies against IBD and globulin.
Spatial Distribution and Mobility of the Ran and the Bicoid proteins in Live Systems

The small GTPase Ran is a key regulator of nuclear pore complex mediated nucleocytoplasmic transport. To examine how Ran distribution and mobility contributes to its role in nuclear transport, we analyzed the behavior of an EYFP-Ran fusion protein in HeLa cells using several quantitative fluorescence imaging techniques. Similar to the endogenous Ran, on average ~ 70% EYFP-Ran localized to the nucleus. In contrast to previous reports, we observed no immobile fractions of EYFP-Ran in cells. The majority of the EYFP-Ran molecules were freely diffusing but a smaller population of EYFP-Ran displayed significantly slower mobility, resulting in an overall average apparent diffusion coefficient of ~5 μm /s. The fraction of slower moving EYFP-Ran was larger within nuclei, suggesting that nuclear ligands such as RCCl or transport receptor complexes strongly influence the nuclear dynamics of Ran. The average residence time of Ran at the nuclear envelope was measured to be --20 ms and we estimate that at steady state ~200 endogenous Ran molecules are present at each nuclear pore complex. This high number suggests that in addition to being present at the nuclear pore within transport complexes, Ran might also dynamically associate with the nuclear envelope, thereby raising the effective concentration of the protein around the pores.
Ultrastructural, morphological and molecular characterization of heterotopic cells in the hippocampus in epileptic Dcx knockout (KO) mice

Mutations in the doublecortin gene (DCX) are responsible for type 1 lissencephaly and subcortical band heterotopia. This thesis work concerns the characterization of abnormally positioned 'heterotopic' neurons present in the Dcx knockout (Dcx KO) mouse model of hippocampal dysplasia and epilepsy. The pyramidal cell layer of the hippocampal CA3 region in Dcx mutants is divided into two heterotopic cell layers instead of a single layer observed in the wild type (WT). Global gene expression analyses of the knockout neurons revealed information concerning their generation and migration, which helps us understand why their positioning is abnormal. KO layers were shown to differ from each other and from WT at postnatal day 0. Common perturbed mechanisms affect intracellular organelles including mitochondria and Golgi apparatuses. Studying perturbed mechanisms specific to the individual KO layers shows defined but distinct neurogenesis time windows of each layer that correspond to a different maturity status in early postnatal stages. Layer specific molecular markers and bromo-deoxyuridine (BrdU) birth dating experiments in KO and WT mice, suggest that there is an inversion of the neuronal layers of the Dcx KO CA3 region, compared to WT. Complementing these gene expression data, ultrastructural and morphological analyses of abnormal Dcx KO neurons compared to WT, in their tissue environment of the developing brain (postnatal day 0) revealed the nature of the lamination defect and the state of CA3 cells in this model. Potential organelle abnormalities, including mitochondrial defects and modifications of the Golgi apparatus, were identified in mutant cells, as well as significantly increased cell death in CA1 and CA3 regions. Oligodendrocyte precursor cells and somatostatin-positive interneurons were found interspersed within the pyramidal cell layers in early postnatal stages, and this was not the case in WT. These results therefore open up new directions in order to better understand the pathophysiology of a sepectrum of severe disorders associated with heterotopic neurons in the brain, presenting in human patients with severe epilepsy and, developmental delay, and intellectual disability