Miracle-dz/UniFAR-FTUs huggingface dataset:
An investigation into the RNA-binding protein UNR and its interactors

Recent work linked the RNA-binding protein UNR to a number of human pathologies although little is currently known about how UNR functions in human cells. This thesis aims to elucidate how UNR functions by, among other things, discovering novel UNR-interacting proteins and transcripts and proteins that are differentially expressed in the presence or absence of UNR. It is shown that UNR levels decrease with increasing cell confluency in cultured HeLa cells but that they increase with increasing confluency in the wild type TP53-containing U2OS cell line. UNR is shown to colocalise to stress granules with TP53 in arsenite-stressed HeLa cells. A number of novel UNR-interacting proteins were discovered in three cell lines (HeLa, U2OS and SaOS-2), including HUWE1, NARR, SQSTM1 and LDB1. GO-term overrepresentation analysis confirmed that UNR is an RNA-binding protein as ‘RNA binding’ and ‘poly(A) RNA binding’ were the top two overrepresented molecular function GO terms by p-value across each of the cell types. Less expected overrepresented GO terms pertained to selenium metabolism and the extracellular exosome. There was no evidence for conservation of UNR-interacting transcripts across the cell types but there were some similar significantly overrepresented GO terms among the respective UNR-interacting transcripts. These included terms pertaining to RNA and the nucleus. The most significant UNR-interacting transcript in HeLa cells was PABPC1 and that the PABP protein was also significantly upregulated following UNR knockdown in HeLa cells. ‘Poly (A) RNA binding’ was a significantly overrepresented GO term among proteins differentially regulated following UNR knockdown in HeLa and U2OS cells. ‘Adherens junction’ was another significantly overrepresented GO term using proteins that were higher in abundance in siUNR-treated HeLa cells and either higher or lower in abundance in either arsenite-stressed or unstressed U2OS cells. UNR was observed at cell-cell junctions in HeLa and U2OS cells by immunofluorescence microscopy.
Predation on Hypsiboas bischoffi (Anura: Hylidae) by Phoneutria nigriventer (Araneae: Ctenidae) in southern Brazil

value regarding their trophic level in the food chain since they are both prey and predators (Toft, 1980; Duellman and Trueb, 1994; Stewart and Woolbright, 1996; Feio et al., 1998), and can effectively control populations of invertebrates such as mosquitoes ( agman and Shine, 2005). As ectotherms, they are highly efficient at converting energy from food into their own tissues. Therefore, they have an important role in the energy flow of the ecosystem as prey for invertebrates (Toledo, 2003; Toledo, 2005; Moura and Azevedo, 2011), birds (Toledo et al., 2005; Toledo et al., 2007; Andrade et al., 2013) and mammals (Santos, 2009; Shalk and Morales, 2012). Among invertebrates, spiders are an important group that prey upon amphibians (Menin et al., 2005; Toledo et al., 2007; Pombal Jr., 2007). Herein, we report Phoneutria nigriventer predating upon an individual of Hypsiboas bischoffi. The predation was observed on the 24 February 2013, during a field study in the National Forest of Piraí do Sul (24°34’S; 49°55’W). This National Park is located in the municipality of Piraí do Sul, State of Paraná, in the south of Brazil and comprises an area of around 150 ha, consisting mainly of Araucaria forest (Moro et al., 2009). The encounter was observed around 21:00h during a survey of breeding sites (Scoot and Woodward, 1994). The site was an old artificial tank, which now harbours a swamp. An agonistic call was emitted by the H. bischoffi, being a defensive strategy that has been reported many times before (Sazima, 1975; Hödl and Gollmann, 1986; Azevedo-Ramos, 1995; Williams et al., 2000). The agonistic call made it possible to locate the frog while it was being predated by Phoneutria nigriventer (Figure 1). After the call, the frog was found completely paralyzed by the venom of P. nigriventer. The spider, standing on the branch of a herbaceous plant, held the frog by insertingits helicerae into the frog’s dorsal region. This spider belongs to the Ctenidae family, known for preying Herpetology Notes, volume 10: 403-404 (2017) (published online on 22 July 2017)
Humoral immune response in mice immunized by oral route with phaseolamine extracted from common bean (Phaseolus vulgaris)

ABSTRACT The prevalence of obesity is increasing in Brazil, generating high costs for the health system. In the search for alternative therapies to control the obesity, several researches seek active compounds in natural products in order to find better pharmacological effects. Inhibitors of α-amylase such as phaseolamine extracted from common beans (Phaseolus vulgaris) have shown satisfactory results in weight loss. The present study aimed to verify the possibility of phaseolamine-causing allergic reactions through the humoral response in mice sensitized with phaseolamine. Swiss female mice (n = 10) were sensitized orally with 100 µg of lyophilized phaseolamine diluted in water for 10 consecutive days and reinforced on the 21th and 35th days after the beginning of this experiment. The production of immunoglobulins IgG, IgG1 and IgE was measured by ELISA and western blotting. The immunological response was investigated and it was found that phaseolamine induced the synthesis of IgG and did not induce the synthesis of IgG1 and IgE. The present study indicates that the product did not cause allergic reactions.
Seasonal variations of ω3 polyunsaturated fatty acids in muscle of Capoeta caelestis

In this study, seasonal variations of fatty acid amounts in muscle tissues of Capoeta caelestis were investigated. We have found that the ω3 contents of C. caelestis in spring, summer, autumn and winter were 17.43%, 15.29%, 17.54%, 13.63% in female and 16.96%, 19.25%, 18.66%, 14.76% in male, respectively. The amounts of ω3 polyunsaturated fatty acids were higher than those of ω6 polyunsaturated fatty acids. The eicosapentaenoic acid amounts were always higher than the docosahexaenoic acid amounts in C. caelestis. Female C. caelestis presented a higher amount of eicosapentaenoic acid and docosahexaenoic acid than males. The amounts of docosahexaenoic acid to eicosapentaenoic acid varied from 0.44% to 0.56% in females and from 0.45% to 0.59% in males in different seasons. The levels of eicosapentaenoic acid + docosahexaenoic acid in female muscles changed from 10.34% to12.51% and in male muscles from 11.16% to 15.41%, respectively. It was seen that the ω3 polyunsaturated fatty acid amounts of C. caelestis reached the highest level in summer and autumn in both sexes. Therefore, it can be concluded that the nutritional value of this fish is better in the both seasons with respect to the ω3 polyunsaturated fatty acid amounts.
Reproductive ecology of the semi-evergreen tree Vitex negundo (Lamiaceae)

Vitex negundo is a small aromatic semi-evergreen tree often cultivated as an ornamental plant. It sheds foliage and produces new foliage almost simultaneously in December-April and flowers in June-November. The flowers are homogamous, herkogamous, self-compatible and exhibit a facultative xenogamous breeding system. They are bi-labiate, gullet type and are pollinated nototribically by bees, wasps and butterflies, while collecting nectar, and also by bees, which pollinate it sternotribically, while collecting pollen. Trigona bee is the primary nectar robber, because it bores holes at the base of the corolla tube to collect nectar. Other bees and wasps are principally legitimate foragers, but they collect nectar illegitimately, if they happen to reach the hole in the corolla tube made by Trigona. Nectar robbing by Trigona indirectly increases the pollen dispersal distance by pollinators and promotes outcrossing rate in this tree. Fruits are non-fleshy and disperse by gravity, and subsequently become hydrochorous and anthropochorous. The seeds did not germinate naturally during the study period and, hence, detailed studies on seed dormancy and seed viability are suggested to understand the seed biology. V. negundo is grown commercially as a crop in certain parts of the world and for ornamental purposes in parks, gardens and the backyards of houses both in urban and rural areas. Therefore, the reproductive biology information reported now is useful to understand the various aspects of its sexual reproduction and, accordingly, to take measures for the protection of its pollinator fauna for the production of genetically superior seeds in natural areas. Finally, it is suggested that V. negundo should be used
Defining the role of LRIG1 dependent EGFR signalling on airway homeostasis and lung cancer development

Aberrations of EGFR signalling drive cancer development. In squamous cell lung cancer, EGFR is overexpressed. LRIG1 is a negative regulator of EGFR and patient pre-invasive squamous cell lung cancer samples show LRIG1 loss, suggesting involvement in early disease pathogenesis. In skin and gut homeostasis, LRIG1 regulates stem cells. In the upper airway, basal cells act as stem cells and are the putative origin of squamous cell lung cancer. I hypothesise LRIG1 has a key role in the airway homeostasis and its loss tilts this towards pre-invasive squamous cell lung cancer development. Lrig1 EGFP-ires-CreERT2 mice delineated airway LRIG1 expression. Flow sorted LRIG1-positive and -negative murine basal cells were used in 2D and 3D colony-forming, spheroid and proliferation assays. A murine squamous cell lung cancer model was set up through application of N-Nitrosotris-(2-chloroethyl)urea (NTCU). Pre-invasive lesions and tumour development were compared between wild-type (WT), LRIG1-heterozygous and LRIG1-null animals. Human basal cells obtained from bronchoscopy were sorted according to LRIG1 expression and used directly in colony-forming assays or maintained in primary culture to assess the effect of shRNA knockdown of LRIG1. LRIG1 is expressed by 50% of airway basal cells. LRIG1-expressing murine basal cells exhibit increased colony-forming capacity (p=0.0133), spheroid formation (p=0.0020) and proliferation (p=0.0011) compared to LRIG1-negative cells. Similarly, LRIG1-expressing human airway basal cells isolated from endobronchial brush biopsy samples exhibit increased colony-forming capacity (p=0.0067) and proliferation (p=0.0153). Topical application of NTCU to mice recapitulates the development of human pre-invasive and squamous cell lung cancer lesions after 23 weeks. Results show lesions in LRIG1-null mice to be larger than those of WT animals. shRNA knockdown of LRIG1 in cultured human airway basal cells alters cell phenotype, leading to increased colony-forming efficiency and greater proliferation at cell confluence. LRIG1 has an important role in stem cell homeostasis of the human and murine airway epithelium. Loss of LRIG1 promotes lesion development in a murine squamous cell lung cancer mouse model and alters behaviour of human epithelial cells in culture, indicating a potential target for the treatment of squamous cell lung cancer in humans.
Evidence that Marine Temperatures Influence Growth and Maturation of Western Alaskan Chinook Salmon

AbstractChinook Salmon Oncorhynchus tshawytscha from western Alaska have experienced recent declines in abundance, size, and age at maturity. Declines have led to hardships for the region’s subsistence and commercial salmon harvesters, prompting calls to better understand factors affecting the life history of these populations. Western Alaskan Chinook Salmon are thought to spend their entire marine residency in the Bering Sea. The Bering Sea ecosystem demonstrates high interannual variability that is largely driven by the annual extent of sea ice. However, warming is expected to supersede interannual variability in the next several decades as a consequence of climate change. We investigated the influence of sea surface temperatures (SSTs) on the life history of western Alaskan Chinook Salmon by using information from two regional populations subject to long-term monitoring. We found strong correlations between early marine growth and SSTs. Warmer SSTs appeared to lead to a younger age at maturity, largely.
MOLECULAR DIAGNOSIS OF Guignardia citricarpa IN ASYMPTOMATIC SWEET ORANGE TISSUE

Citrus black spot, a fungal disease caused by the quarantine fungus Guignardia citricarpa, restricts the exportation of fresh fruit to countries in the European Union. The occurrence of latent infections and the time required for diagnosis using conventional methods have brought about the need to validate fast, efficient and reproducible molecular techniques to detect the pathogen in asymptomatic tissue. As such, this study aims to detect G. citricarpa in the symptomatic fruit and asymptomatic leaf tissue of sweet oranges by conventional and real-time polymerase chain reaction (PCR). Specificity and limit of detection (LOD) were assessed in tissue samples of fruit lesions and asymptomatic leaves. Low concentrations of the fungus were found in asymptomatic leaves. Under these conditions, real-time PCR proved to be viable, reproducible and highly sensitive to detection of the pathogen.
Effects of conservation biological control practices on predatory arthropod assemblages and molecular identification of cucumber beetle biological control agents

ii Acknowledgements.iv Vita.v List of Tables.vii List of Figures.viii Chapter 1: Effects of conservation biological control practices on predatory arthropod assemblages and cucumber beetle biological control in cucurbits.1 Abstract.
Toxicity of Some Pesticides Against Tetranychus urticae and its Predatory Mites under Laboratory Conditions

The relative toxicity of some pesticides to the two-spotted spider mite Tetranychus urticae and its predatory mites, Phytoseiulus persimilis and Amblyseius californicus, was evaluated under laboratory conditions. Three pesticides namely, dimethoate, bifenthrin and hexythiazox were tested against mite populations. According to LC50 value, the toxicity of pesticides to the adult two-spotted spider mite was respectively bifenthrin (1.82 ppm), dimethoate (117.97 ppm), hexythiazox (537.45 ppm/24 h. 175.75 ppm/72 h). For P. p ersimilis and A. californicus , the toxicity of pesticides according to LC values and IOBC toxicity category, bifenthrin and dimethoate were harmful while hexythaizox was harmless after 24 h, moderately harmful after 72 h. The Ovicidal/Ovolarvicidal test indicated that hexythiazox and bifenthrin were extremely toxic to T. urticae eggs and larvae. Toxicity of hexythiazox to A. californicus and P. persimilis larvae was less than the other pesticides. The Nymphicidal test indicated that the activity of bifenthrin was very strong on T. urticae nymphs, but the activity of dimethoate was fairly weak and less than hexythaizox. Dimethoate was toxic to A. californicus and P. persimilis nymphs whilst bifenthrin and hexythiazox were moderately harmful. Hexythiazox appeared to be a promising candidate for a mite management program for T. urticae. A. californicus was more tolerant than P. persimilis to the tested pesticides.
Molecular and phenotypic characterization of symbiotic Rhizobium isolated from some wild Vicia species under Egyptian conditions

Two naturally growing symbiotic N2-fixing Rhizobia coded as Vs1 and Vc1 from active root nodules of Vicia sativa and V. cinerea as wild plants were isolated, respectively. Cultures of both Rhizobium isolates were purified and used for inoculation of certain differentiated legume hosts. Nodulation test indicated successfully formation of active root nodules onViciafaba and Pisumsativumcultivatedin germination tubes containing Hoagland's medium (Nitrogen free) under sterilized conditions. Rhizobium isolates were re-isolated from both host plants and their characteristics were in vitro investigated. Based on their morphological, cultural and biochemical properties, both Rhizobium isolates of Vs1 and Vc1were found to have similar characteristics of the reference strain Rhizobium leguminosarumbiovarviciae. To evaluate nitrogen fixation, efficacy of both isolates in comparison with the reference strain to form root nodules on faba bean and pea plants in Leonard’Jars was also tested. Results indicated superiority of Vc1 in forming larger number and dry weight of nodules than Vs1 on both host plants. To confirm these findings, genetic diversity of both Vs1 and Vc1 compared with the reference strain by RAPD and SRAP DNA fingerprinting was assessed, isolate VS1 was grouped with the reference strain in one cluster with 84% and 95% based on RAPD and SRAP similarity, respectively. However, isolate VC1 was highly diverged and located in different group with lower similarity 51% and 59% based on RAPD and SRAP similarity with Vs1, respectively.
GSTF1 gene expression at local Albanian wheat cultivar Dajti under salinity and heat conditions

Abstract Plants have evolved effective defense mechanisms against stress-induced oxidative damages, among which an important role play glutathione S-transferases (GSTs). This huge class of proteins have been reported to increase in a number of crops under temperature and saline stresses. However, different wheat cultivars display specific characteristics of expression. In our study we controlled the transcription of GSTF1 gene at leaves of wheat (Triticum aestivum L.) of local cultivar Dajti, evaluated previously as resistant toward salt and temperature stresses. Three different concentrations of NaCl, 50, 100, 200mM, were applied at plants germinated in Hoagland culture, and total ARN was extracted from leaves collected at 0-3-6-10-24-72 hrs after treatment. Seeds from the same cultivar were germinated in Hoagland culture under heat treatment, keeping controls at 25°C/20°C and the rest under a 35°C /25°C-day/night regime in a growth chamber. Total RNA was extracted after one week, 30, and 45 days following HT. RT-PCRs were performed using primers specific for GSTF1. Concentration of amplicons was evaluated in agarose gels. In conclusion, the transcription of GSTF1 at Dajti cultivar is reduced during the time of exposure on saline conditions, does not depend on salt concentration, and is not affected by prolonged temperature stress.
Warning Signals of Adverse Interactions between Climate Change and Native Stressors in British Columbia Forests

We examine the direct effects of multiple disturbance agents on individual tree development and stand productivity in 15–40-year-old managed forests in British Columbia, Canada. Our primary interest was to establish a baseline assessment of damage in these forests and, especially, to focus on the degree to which biotic and abiotic stressors cause physical damage and diffuse mortality. Based on extensive climate data for the study area and the ecology of the disturbance agents we explore possible interactions between individual stressors and climate. Mean annual temperature increased by over 1 °C in the last century and annual precipitation increased by 8%, with that in the summer increasing by 18%. Disturbance agents were a central driver of mortality, growth and physical damage and their combined impact in lodgepole pine stands was as much as four times greater than expected particularly in the dominant trees most counted upon for stand productivity and timber supply. Climate-mediated disturbances accounted for five of the top six damage agent categories in terms of percent of basal area impacted but the lack of long-term disturbance monitoring data, a global information gap, limits our ability to conclusively link high damage rates to climatic changes.
Biochemical factors associated with cassava resistance to whitefly infestation

Cassava ( Manihot esculenta Crantz) an important food security crop, is inflicted by whitefly ( Bemisia tabaci ) worldwide, causing direct damage of up to 80% of yield loss. Although resistance to the pest has been associated with antibiosis, changes that occur in metabolite activity, and their effect on the pest have not been fully elucidated. A study was carried out to evaluate changes in peroxidase, tannin and flavonoid activity in cassava genotypes attacked by B. tabaci in order to contribute to knowledge on whitefly resistance in cassava. Five genotypes showing resistance, and three susceptible, were selected based on whitefly count and leaf damage scores, and assayed for peroxidase, tannin and flavonoid activity. There were significant differences among genotypes for leaf damage (P 2.5) was incurred by UG 130068. All genotypes showed significant (P < 0.05) differences for peroxidase activity, with CS1-144 having a high activity rate three months after planting. The lowest activity was observed in UG 120170, a susceptible genotype. A significant (P < 0.01) negative correlation (r = -0.84) was observed between peroxidase activity and cassava leaf damage scores, as well as between tannin and damage (r = -0.57), indicating that peroxidase and tannin play a part in cassava resistance to B. tabaci . Key Words: Antibiosis, Bemisia tabaci , flavonoids, peroxidase, tannins
Kinetics and mechanism of ozone inactivation of protozoan cysts

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Generation and validation of a floxed FosB mouse line

Expression of the FosB gene has been studied extensively in many fields using a variety of tools. However, previous techniques have had a variety of caveats, from potential off-target effects (e.g., overexpression of FosB, ΔFosB, or a dominant negative mutant of JunD, termed ΔJunD) or confounding developmental effects (e.g., the constitutive FosB knockout mouse). Therefore, we sought to create a floxed FosB mouse line that will allow true silencing of the FosB gene with both spatial and temporal control. Here, we detail the cloning strategy, production, and validation of the floxed FosB mouse. We demonstrate methodology for breeding and genotyping, and show that viral-mediated expression of Cre recombinase in a targeted, discrete brain region ablates expression of the FosB gene in floxed but not wild type mice. Thus, the floxed FosB mouse presented here represents an important new tool for the continued investigation of this critical gene.