Miracle-dz/UniFAR-FTUs huggingface dataset:
The Cul3 Ubiquitin Ligase: An Essential Regulator of Diverse Cellular Processes

i ACKNOWLEDGMENTS: . ii LIST OF TABLES: . v LIST OF FIGURES . vi LIST OF ABBREVIATIONS USED . viii GLOSSARY . x CHAPTER 1: Introduction and Background . 1 THE CUL3 UBIQUITIN LIGASE . 2 CELL CYCLE REGULATION: Basic mechanisms controlling proliferation . 10 CELL CYCLE REGULATION: Cyclins and Cdks . 11 CELL CYCLE REGULATION: Mechanisms controlling cyclin E abundance . 15 CUL3 AND DISEASE: Cancer . 16 CUL3 AND DISEASE: FHHt hypertension: . 18 CUL3 AND DISEASE: Neuronal, eye, and skin conditions . 19 SIGNIFICANCE . 20 REFERENCES . 21 CHAPTER 2: The N-terminus of Cyclin E is Required for Cul3-mediated Degradation . 29 INTRODUCTION AND BACKGROUND: . 30 RESULTS: . 32 Cyclin E binds directly to Cul3 independently of BTB domain-containing proteins . 32 Mutations in the N-terminal region of cyclin E prevent degradation by the Cul3 complex . 37 Lysine 48 on cyclin E serves as a ubiquitination site for Cul3 . 42 The N-terminal domain of cyclin E is required for degradation . 45 Cul3 cannot degrade endogenous LMW cyclin E . 46 Cyclin E2 is not a substrate of Cul3 . 47 Loss of Cul3 results in early accumulation of cyclin E after release from serum starvation . 48 RhoBTB3 interacts with UbE2E1 to facilitate complex formation . 52 DISCUSSION: . 56 MATERIALS AND METHODS . 63 REFERENCES . 66 CHAPTER 3: Identifying Possible Roles of Cul3 and Klhl3 in the Kidney . 70 BACKGROUND: The role of Cul3 and Klhl3 in FHHt . 71 RESULTS: . 75 Identifying proteins that interact with Klhl3 . 75 Dynamitin/p50 binds Klhl3 . 77 P50 is stabilized in the presence of an FHHt-associated Klhl3 mutant . 80 P50 binds Cul3 . 82 Cul3 and Klhl3 ubiquitinate p50/dynamitin in vitro . 83 iv P50 levels appear to remain unchanged in vivo . 85 Transfected p50 is destabilized by Cul3 . 86 DISCUSSION: . 86 FUTURE DIRECTIONS: . 87 The possibility of aquaporin regulation by Cul3 . 88 Other identified proteins that may interact with Klhl3 . 94 MATERIALS AND METHODS . 95 REFERENCES . 97 CHAPTER 4: Conclusions, Discussion, and Future Directions . 101 RESEARCH QUESTION 1: What is the nature of the interactions between Cul3, Cdk2, and the LRR protein MUF1? 103 BACKGROUND: LRR proteins and Cul3 . 103 BACKGROUND: LRR5 (FMOD), LRR3 (SALM1) and Cul3 . 106 BACKGROUND: LRR5 (FMOD) interacts with the BTB protein FAZF . 107 RESULTS: Exploring the interactions between the LRR protein MUF1, Cul3, and Cdk2 . 109 MUF1 binds Cdk2 . 112 Levels of MUF1 and cyclin E . 112 DISCUSSION: . 115 RESEARCH QUESTION 2: How does loss of Cul3 affect breast cancer cells? 118 RESEAERCH QUESTION 3: What other modifications may affect cyclin E in vivo? 119 RESEARCH QUESTION 4: How do BTB proteins affect the binding of E2 enzymes to Cul3based complexes? 123 RESEARCH QUESTION 5: Do changes in Nrf2 activity affect regulation of AQP2 in Cul3 conditional knockout or Cul3Δ403-459 mice? 125 FINAL THOUGHTS . 127 METHODS: . 127 REFERENCES . 128 TERMINAL REFERENCE SECTION . 132
Endophytic bacterial diversity of Avicennia marina helps to confer resistance against salinity stress in Solanum lycopersicum

ABSTRACT The current study aimed to explore the endophytic bacterial diversity of Avicennia marina and the potential roles of these endophytes in counteracting saline conditions in tomato plants. Molecular analysis revealed strains from Paenibacillus, Bacillus, Microbacterium, Citrobacter, Lysinibacillus, Halomonas, Virgibacillus, Exiguobacterium, and Vibrio. However, Bacillus pumilus AM11 and Exiguobacterium sp. AM25 showed significantly higher growth in saline media. In response to salinity stress, tomato plants treated with AM11 and AM25 showed significantly higher (∼15–23%) biomass, photosynthetic rate and pigment accumulation compared to controls. Salinity-exposed plants had significantly reduced growth and increased (three-fold) lipid peroxidation, whilst glutathione, catalase, and peroxidase activities were significantly reduced. In contrast, AM11, AM25, and methionine improved these physiochemical attributes. The study concludes that the application of bacterial endophytes from plants growing in saline conditions can offer other plants similar stress-resistance potential. Such halophytic bacterial strains can be used to improve plant growth in saline conditions.
MOLECULAR DYNAMICS STUDY OF CYTOCHROME C – LIPID COMPLEXES

The interactions between a mitochondrial hemoprotein cytochrome c (cyt c) and the model lipid membranes composed of zwitterionic lipid phosphatidylcholine (PC) and anionic lipids phosphatidylglycerol (PG), phosphatidylserine (PS) or cardiolipin (CL) were studied using the method of molecular dynamics. It was found that cyt c structure remains virtually unchanged in the protein complexes with PC/PG or PC/PS bilayers. In turn, protein binding to PC/CL bilayer is followed by the rise in cyt c radius of gyration and root-mean-square fluctuations. The magnitude of these changes was demonstrated to increase with the anionic lipid content. The revealed effect was interpreted in terms of the partial unfolding of polypeptide chain in the region Ala15-Leu32, widening of the heme crevice and enhancement of the conformational fluctuations in the region Pro76-Asp93 upon increasing the CL molar fraction from 5 to 25%. The results obtained seem to be of utmost importance in the context of amyloidogenic propensity of cyt c.
Why do female desert lizards construct burrows to lay eggs

Many oviparous animals construct well-designed nests to provide relatively favourable conditions for their eggs and hatchlings, but the direct evidence that nest structure can determine their reproductive success is insufficient. In the present study, we explored the structure of nests and its effect on nest environments and reproductive success in the toad-headed agama (Phrynocephalus przewalskii). We observed that female P. przewalskii constructed burrow nest consisting of an inclined tunnel and an expanded chamber. We constructed artificial nests with or without the burrow to determine how burrows influence nest environments, egg survival and successful emergence of hatchlings. Our results indicated that burrow nests had higher and more stable humidity than non-burrow nests. More importantly, egg survival and the emergence success of hatchlings were significantly higher for burrow nests than for non-burrow nests. Therefore, our manipulation experiments provide direct evidence that maternal nest construction behaviour could determine parental reproductive success in reptile.
Snowshoe hare multi‐level habitat use in a fire‐adapted ecosystem

Prescribed burning has the potential to improve habitat for species that depend on pyric ecosystems or other early successional vegetation types. For species that occupy diverse plant communities over the extent of their range, response to disturbances such as fire might vary based on post-disturbance vegetation dynamics among plant communities. Although responses of snowshoe hares (Lepus americanus) to fire have been studied in conifer-dominated forests in northern parts of the species’ range, there is a lack of information on snowshoe hare habitat use in fire-dependent communities in southern parts of their range. We used global positioning system (GPS) and very high frequency (VHF) radio-collars to monitor the habitat use of 32 snowshoe hares in a scrub-oak (Quercus ilicifolia)-pitch pine (Pinus rigida) barrens complex in northeastern Pennsylvania where prescribed fire has been used for habitat restoration. The area contained stands that underwent prescribed burning 1–6 years prior to our study. Also, we investigated fine-scale determinants of habitat use within stands. We found that regardless of season, hares did not select for areas that had been burned within 6 years prior. Hares primarily used stands of older scrub oak, conifer, or hardwoods, which contained dense understory vegetation and canopy cover. Hare habitat use also was positively associated with stand edges. Our results suggest that hares do not respond to prescribed burning of scrub oak in the short-term. In addition, by focusing on structural determinants of habitat use, rather than broad-scale characteristics such as stand type, management strategies for snowshoe hares can be adapted over the extent of their range despite the multitude of different land cover types across which the species occurs. 2017 The Wildlife Society.
Antimicrobial Activity of Leave Extracts of Bryophyllum pinnatum and Aspilia africana on Pathogenic Wound Isolates Recovered from Patients Admitted in University of Port Harcourt Teaching Hospital, Nigeria

The incidence of antibiotic resistance among bacteria to synthetic drugs is on the increase, as such there is the need for new and safer antimicrobials especially, from natural sources like plants. Leaves of Bryophyllum pinnatum and Aspilia africana are among the many that have been used by rural dwellers as medicines to treat infections. Methanol, hot water and ethanolic extracts of the leaves of Bryophyllum pinnatum and Aspilia africana were obtained and their antimicrobial activity testing against three microorganisms isolated from wound which includes Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa. The results indicated that the methanol extract of both plants had higher antimicrobial activity against the test isolates as compared with their ethanol extracts; while the hot water extracts had no antimicrobial activity against the isolates. Ethanol extracts of both plants showed little antimicrobial activity against the test isolates. S. aureus was more susceptible to methanolic extract of B. pinnatum with a zone of inhibition of 4 mm, E. coli was 3.0 mm while that of P. aeruginosa was 1.0 mm. Susceptibility pattern of the isolates to A. africana showed that P. aeruginosa was more susceptible with a zone of inhibition of 6.0 mm; that of S. aureus was 5.0 mm while that of E. coli was 3.0 mm. This shows that methanolic extracts of Bryophyllum pinnatum and Aspilia africana can be used against pathogenic organisms including Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa which can cause slow healing of wounds.
Investigating the molecular mechanisms of vomocytosis

The opportunistic fungal pathogen Cryptococcus neoformans is the major etiological agent of the life threatening disease cryptococcosis, which is responsible for over half a million human deaths per annum. Professional phagocytes, such as alveolar macrophages, phagocytose inhaled spores and attempt to destroy the pathogen. However, this process is inefficient in immunocompromised hosts, such as those suffering from HIV/AIDS. In such hosts the macrophage is thought to behave like a “Trojan Horse”, acting as both a cryptococcal dissemination vector and as a protective niche against antifungal agents/cells present in the circulation. Vomocytosis, first discovered in C. neoformans, is a non-lytic expulsive mechanism whereby C. neoformans or C. gattii exit the macrophage leaving both pathogen and the host macrophage with a morphologically normal phenotype. The clinical implications of vomocytosis are poorly understood however; data from this research suggests that the induction of a pro-inflammatory response increases vomocytosis rates, suggestive of a pathogen escape mechanism from a harsh antimicrobial environment i.e. the pro-inflammatory primed macrophage. Regulating the rates of vomocytosis in vivo may have dramatic consequences on pathogen dissemination and also patient prognosis. For instance, enhancing the rate of vomocytosis within circulation could allow other antifungal cells and compounds access to destroy the freshly released cryptococci, hence reducing pathogen burden and improving patient prognosis.
The habitat and abundance of two wintergreen orchids (Aplectrum hyemale and Tipularia discolor) in western North Carolina1

Abstract Aplectrum hyemale and Tipularia discolor are wintergreen orchids native to the eastern and central United States. Each produces a single leaf in late fall that persists through the winter and senesces in early spring. Both species occur in scattered patches in the understory of deciduous forests, and although they overlap in range and often co-occur in the landscape, their habitat and photosynthetic potential have not been compared directly. In this study we examine the relative abundance of A. hyemale and T. discolor in western North Carolina and quantify habitat characteristics and levels of leaf chlorophyll for each species. We conducted broad-scale surveys (walkabouts) of seven sites in Pisgah National Forest during the winter and collected habitat data in 26 patches of each species in one mesic forest. Both species shared similar habitat attributes at this site (plants located ∼ 2 m from overstory trees of similar diameter in ∼ 45% sunlight). However, across all sites, T. discolor was three times more abundant than A. hyemale, more likely to occur in large patches (> 20 plants), and more consistently distributed across a range of slope aspects. In contrast, A. hyemale occurred most often on slopes facing 91–180°, and at elevations > 750 m. Whereas A. hyemale was most often associated with Liriodendron tulipifera overstory trees, T. discolor was often in close proximity to Quercus spp. as well as L. tulipifera. Leaf chlorophyll was twice as high in A. hyemale, which could support differences in photosynthetic strategies, or reflect differences in leaf size and morphology.
Entomopathogens in conjunction with imidacloprid could be used to manage wireworms (Coleoptera: Elateridae) on spring wheat

Abstract We examined the effect of biopesticides used alone, mixed with other biopesticides, or in conjunction with an imidacloprid against wireworms (Coleoptera: Elateridae) in spring wheat Triticum aestivum Linnaeus (Poaceae) (variety: Duclair). The study was conducted at Ledger and Valier, Montana, United States of America in 2015 and 2016. Ten biopesticides (spinosad, azadirachtin, pyrethrin, Beauveria bassiana (Balsamo-Crivelli) Vuillemin (Fungi: Clavicipitaceae) GHA (Mycotrol), B. bassiana ANT-03 (BioCeres), Chromobacterium subtsugae Martin et al. (Bacteria: Neisseriaceae), Burkholderia Yabuuchi et al. (Burkholderiaceae) species, Metarhizium brunneum Petch (Fungi: Clavicipitaceae) ESC1 (MbESC1), and M. brunneum F52 (MetF52) as microsclerotial and corn grit-based granules) were tested in addition to thimet and imidacloprid. Treatment efficacy was based on plant stand protection, wireworm populations, and yield. In 2015, there was considerable variation between sites in treatment efficacy. Mycotrol, BioCeres, MetF52+spinosad, and MetF52+imidacloprid applications protected seedlings from wireworm damage better than the control at Ledger, while only MetF52 at Valier. Wireworm populations were significantly higher with Mycotrol, spinosad, MetF52+spinosad, MbESC1 (25 g/L), and MetF52 treatments, compared with control, at 14 and 28 days post application at Ledger, but without effect at Valier, 2015. We found significantly higher yield in plots treated with imidacloprid+MetF52 and Mycotrol+azadirachtin (Xpulse) compared with control at Ledger. In 2016, no significant treatment effects were observed at either site. In summary, this study provides insight on what treatments should be explored in more detail despite variable results.
In Silico Analysis and Molecular Docking Studies of Cajanus cajan Lectin against Aminopeptidase-N Receptor from Acyrthosiphon pisum

Legume lectins are structurally and evolutionarily related to a well-defined group of lectins that were originally discovered in the seeds of legumes like jack bean, common bean, pea, peanut and soybean. Many of these lectins have been purified and characterized with respect to their structure, sugar-binding specificity and biological activity (Sharon and Lis, 1990; Van Damme et al., 1998; Peumans and Van Damme, 1999). Legume lectins exhibited fairly homogeneous molecular structure with ~30kDa subunits (Van Damme et al., 2007). These lectins shared extensive sequence homology and three dimensional structural similarities, but differed in carbohydrate specificity (Rouge et al., 1991). The monomer structure is characterized by presence of the ―jelly roll‖ motif that is often associated with carbohydrate-binding activity. The ―jelly roll‖ is characterized by the presence of three sets of antiparallel β-sheets. The sheets are connected by several loops of varying lengths (Loris et al., 1998; Vijayan and Chandra 1999). Two metal ions, calcium and a transition metal, found in all the legume lectin structures are essential for the International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 7 Number 06 (2018) Journal homepage: http://www.ijcmas. com
European Bison: Status Survey and Conservation Action Plan

This review of the European bisons (Bison bonasus) status clearly indicates that, through proper management and conservation, its present numbers and distribution have improved significantly since its extinction in the wild at the beginning of the 20th century. The Action Plan briefly summarizes the history of extinction in the wild and present status of the European bison, as well as the reasons of extinction. The ecology of the species has been reviewed and threats, including recent diseases, are described. The Action Plan also puts forward future goals in conservation and management of European bison. These include recommendations for captive breeding and reintroduction to natural ecosystems, and the propagation of captive animals with known pedigrees for the preservation of the species and to maintain its genetic purity.
Grain-yield stability among tropical maize hybrids derived from doubled-haploid inbred lines under random drought stress and optimum moisture conditions

Abstract. Drought is a devastating environmental stress in agriculture and hence a common target of plant breeding. A review of breeding progress on drought tolerance shows that, to a certain extent, selection for high yield in stress-free conditions indirectly improves yield in water-limiting conditions. The objectives of this study were to (i) assess the genotype × environment (GE) interaction for grain yield (GY) and other agronomic traits for maize (Zea mays L.) across East African agro-ecologies; and (ii) evaluate agronomic performance and stability in Uganda and Tanzania under optimum and random drought conditions. Data were recorded for major agronomic traits. Genotype main effect plus GE (GGE) biplot analysis was used to assess the stability of varieties within various environments and across environments. Combined analysis of variance across optimum moisture and random drought environments indicated that locations, mean-squares for genotypes and GE were significant for most measured traits. The best hybrids, CKDHH1097 and CKDHH1090, gave GY advantages of 23% and 43%, respectively, over the commercial hybrid varieties under both optimum-moisture and random-drought conditions. Across environments, genotypic variance was less than the GE variance for GY. The hybrids derived from doubled-haploid inbred lines produced higher GY and possessed acceptable agronomic traits compared with the commercial hybrids. Hybrid CKDHH1098 ranked second-best under optimum-moisture and drought-stress environments and was the most stable with broad adaptation to both environments. Use of the best doubled-haploids lines in testcross hybrids make-up, well targeted to the production environments, could boost maize production among farmers in East Africa.
Germination biologies and seedbank dynamics of Acacia shrubs in the Western Desert: implications for fire season impacts on recruitment

In arid Australia, fires in different seasons often result in markedly different recruitment rates of woody plants, and this can have important and long-lasting impacts on post-fire community structure and composition. The current study investigated ecological mechanisms behind this effect in four widespread arid Acacia species: Acacia aptaneura, Maslin & J.E. Reid Acacia kempeana F.Muell. , Acacia maitlandii F.Muell. and Acacia melleodora Pedley. Specifically, the study examined whether increased recruitment after summer compared with winter burning relates to (1) higher soil temperatures during summer fires having increased capacity to overcome dormancy of seeds with heat-stimulated germination; (2) warmer soil temperature conditions after summer fires providing more favourable incubation temperatures for germination; and/or (3) summer fires coinciding with seasonal fluxes in seedbank densities, which may occur in response to granivory and/or rapid rates of seed deterioration after dispersal. Results supported hypotheses (1) and (2), as germination of all species responded positively to heat shock and warmer incubation temperatures. Some support was also demonstrated for hypothesis (3), as seedbank densities were shown to fluctuate seasonally, most likely in response to strong granivory. This multi-species study provides insights into mechanisms behind enhanced shrub recruitment after arid zone summer fires; and reinforces the notion that season of burn can be a strong determinant of regeneration trajectories of woody plants after fire.
Microbial Dynamics and Biogas Production during Single and Co-digestion of Cow Dung and Rice Husk

Anaerobic digestion is achieved by the combined effort of hydrolytic, acetogenic and methanogenic bacteria. Microbial dynamics and biogas production during anaerobic digestion of cow dung and rice husk were studied in this research. The experiment lasted for 30 days using a 10 litre scale bio-digester. All proximate parameters reduced significantly after digestion for CD (cow dung), RH (rice husk), and CD:RH (cow dung and rice husk) except moisture content that increased in all the substrates. Ash content (1.08–1.67 mg) and crude fibre (1.27–1.96 mg) increased in CD only. The pH ranges for the substrates were CD (7.0–7.5), RH (6.1–7.6), and CD:RH (6.1–7.8). Temperature ranges were CD (27.4 o C–33.5 o C), RH (27.2 o C–33.3 o C) and CD:RH (27.3 o C–33.4 o C). The total biogas production of the substrates and the components of each gas produced were, CD (4327.65 cm 3 :62.4% CH 4 , 37.4% CO 2 , 0.2% H 2 S), RH (150 cm 3 :100% CO 2 ), and CD:RH (4730.55 cm 3 :73.8% CH 4 , 25.8% CO 2 , 0.4% H 2 S). Percentage distribution of digester’s micro flora include aerobes 40.75%, anaerobes 31.25%, fungi 25% and methanogenic bacteria 3%. Hydrolytic bacteria and fungi isolated were Bacillus spp, Enterobacter spp, Pseudomonas spp, Proteus spp, Micrococcus spp, Aspergillus spp, Penicillium spp and Streptococcus spp . Acetogens isolated were Clostridium spp, Streptococcus spp and Pseudomonas spp. Methanococcus spp and Methanobacterium spp were the only isolated methanogen. Rice husk produced the least amount of biogas.
Effect of Fungicides and Plant Extracts in the Management of Foliar, Twig and Fruit Diseases of Citrus (Citrus limon)

A research work was conducted on citrus plants raised at GPC, of Fruit Tree Improvement Project (FTIP) at Horticulture Farm, Bangladesh Agricultural University, Mymensingh, to investigate the effect of fungicides and plant extracts in controlling the scab, die-back and canker. Three fungicides viz. Cupravit 50 wp (0.4%), Dithane M-45 (0.3%), Rovral 50 WP (0.2%) and extracts of 3 plants viz. Neem {Azadirachta indica), Ginger {Zingiber officinale) and Garlic {Allium sativum) were applied for controlling the citrus (C. limon) diseases (scab, die-back and canker). All the fungicides showed significant effect in the control of the above mentioned citrus diseases. The highest reduction of the scab, die-back and canker diseases was recorded applying Rovral 50 WP. Neem leaf extract was the most effective in controlling canker of leaf and fruit. Garlic extract and Neem leaf extract were the most effective in controlling die-back of twig and branches of citrus, respectively. From the above results it can be concluded that Rovral 50 WP is the most effective chemical for controlling all citrus (C. limon) diseases and citrus canker can successfully be controlled specially by Neem leaf and garlic extract. J. Environ. Sci. & Natural Resources, 10(1): 93-100 2017