Miracle-dz/UniFAR-FTUs huggingface dataset:
Copper-responsive transcriptional regulation in Candida albicans

Candida albicans is a commensal fungus of humans and can cause opportunistic infections if the host immune system is compromised. C. albicans infections can range from relatively minor subcutaneous infections to life-threatening systemic candidiasis. Copper is an essential nutrient for almost all organisms, and the coppercontaining protein superoxide dismutase is required for the virulence of C. albicans in a mouse model. Previous work in our laboratory has shown that copper uptake and regulation in C. albicans has some similarities to Saccharomyces cerevisiae, including the activation of the copper transporter gene CaCTRI in low copper conditions by the transcription factor CaMaclp. However, further analysis in this study has demonstrated that the actual mechanism of regulation by CaMaclp is different from that of S. cerevisiae Maclp. This thesis demonstrates for the first time that the CaMACI gene is transcriptionally autoregulated in a copper-dependent manner. This is in contrast to the S. cerevisiae MAC1 homologue, which is constitutively transcribed. The presence of one binding site for CaMaclp in the promoters of CaCTRI, CaMACI and the ferric/cupric reductase gene CaFRE7 is sufficient for copper-responsive regulation. In contrast, two promoter elements are essential for normal levels of copper-dependent activation by S. cerevisiae Maclp. CaMaclp is also involved in the regulation of the ironresponsive transcriptional repressor gene SFU1 and the alternative oxidase gene AOX2. This work describes key features of the copper uptake system in the human pathogen C. albicans that distinguishes it from similar processes in the model yeast S. cerevisiae. Transcriptional autoregulation of the CaMACI gene could enable C. albicans to respond more precisely to environmental changes, conferring an adaptation to the human host that may be an advantage in the disease process.
Forage intake and performance of cattle in silvopastoral systems and monoculture of Marandu in PreAmazon region

This work aimed to evaluate dry matter intake (DMI) and performance of F1 Nellore x Guzera with live weight (LW) of 180±15 kg (5 months) on pastures of Brachiaria brizantha cv. Marandu in silvo-pastoral systems composed of babassu palm (Attalea speciosa) and monoculture systems in Pre-Amazonic region of Maranhão state, Brazil. Animals were evaluated in four systems: 0, 80, 131 and 160 adult palms ha -1 , characterizing monoculture (MC), low density (LD), average density (AD) and high density palm trees (HD), respectively, during the rainy (RS) and dry season (DS). Comparing seasons, only DMI in MC and AD were affected. DMI was between 2.6% LW for the RS and 2.8% LW for the DS, These values are very close as suggested by NRC, which is 2.7% LW for animals in this category. Higher average daily gain per ha was observed in animals kept in pastures with LD (0.750 g.day -1 and 84.37 kg.ha -1 , respectively). It was observed that animal performance was influenced by density of palm trees and the DMI by season, probably by the sward structure. Animal performance and production forage biomass were higher in 0 and 80 palm systems. This greater forage biomass allow higher stocking rate and, consequently higher animal production per ha.
Rooting Characteristics and Antioxidant Pigment Responses of Three Hybrid Bermudagrass [ Cynodon dactylon (L.) Pers. × Cynodon transvaalensis Burtt- Davy] Cultivars Exposed to Drought

18 Introduction . 19 Materials and Methods . 21 Plant Culture . 21 Plant Propagation . 22 Rainout Box . 24 Experimental Design . 24 Drought Conditions . 25 Data Collection . 25 viii Results . 28 Discussion . 30 CHAPTER III ANTIOXIDANT PIGMENT RESPONSES OF THREE HYBRID BERMUDAGRASS CULTIVARS EXPOSED TO DROUGHT . 34 Abstract . 35 Introduction . 36 Materials and Methods . 44 Plant culture . 44 Rainout box . 46 Drought Conditions . 47 Experimental Design . 47 Data Collection . 49 Statistical analysis . 51 Results and Discussion . 52 CHAPTER IV CONCLUSIONS . 63. 35 Introduction . 36 Materials and Methods . 44 Plant culture . 44 Rainout box . 46 Drought Conditions . 47 Experimental Design . 47 Data Collection . 49 Statistical analysis . 51 Results and Discussion . 52 CHAPTER IV CONCLUSIONS . 63 REFERENCES . 67 APPENDIX . 77 VITA . 109
The effects of caffeine on the renal antioxidant activity in rats / Ratlarda böbrek antioksidan aktivitesi üzerine kafeinin etkileri

Abstract Objective: In our study, the short-term effects of caffeine on the renal antioxidant activity in rats were investigated. Methods: Caffeine was given orally at two different doses: 30 mg/kg and 100 mg/kg (a high non-toxic dose). The current study included 30 rats, which were divided into 3 groups: a control group and two caffeine-treated groups. Group 1 was given caffeine at 30 mg/kg and Group 2 was given caffeine at 100 mg/kg for 14 days. We measured advanced oxidation protein products (AOPP), malondialdehyde (MDA) and nitric oxide (NO) levels in the kidney tissue following caffeine administration. In addition, we also evaluated superoxide dismutase (SOD), and glutathione S transferase (GST) activities in the kidney tissue. Results: Our results showed that caffeine administration decreased lipid peroxidation and advanced oxidation protein products in kidney. Especially, MDA levels in the kidney tissue of the caffeine-treated groups decreased significantly as a result of the dose. NO levels in the kidney tissue of the caffeine-treated groups were higher than those in the control group. GST activities in the kidney tissue of rats in the caffeine groups also increased significantly. In our study, we did not observe significant changes in renal SOD activities upon caffeine consuption. Conclusion: These results show that short-term consumption of two different doses of caffeine may protect against oxidative stress in the kidney tissue of rats. This effect is related to the caffeine dosage. Determining the mechanisms and antioxidant effects of caffeine at suitable dose requires advanced animal and human studies.
New species of gobiid fishes of the genera Lythrypnus, Elacatinus and Chriolepis from the eastern tropical Pacific

Se describen ocho especies nuevas de peces de la familia Gobiidae del Pacific Tropical. Se recolectaron Lythrypnus lavenbergi, L. 01- phigena y L . cobalus en aguas profundas frente a la Isla del Coco; L . insularis proviene de las Islas Revillagigedo, fuera de la costa mexicana. L . cobalus se distingue de L. dalli (Gilbert), que habita mas al norte, por diferencias en el numero de radios y por su tamano diminuto, pero ambos se parecen por su coloracion. Las especies nominales L. crinIlus Ginsburg y L. latifascia Ginsburg se consideran sinonimos deL . dalli. L . pulchellus Ginsburg de las costas de Mexico y Centroamerica es muy similar a L. rhizophora (Heller & Snodgrass) de las islas oceanicas Coco y Galapagos, aunque aparentemente presentan diferencias importantes en la coloracion en vida. Las especies Elacatinus inomatus, de la costa centroamericana y E. nesiotus, de la Isla del Coco aparentemente son "especies gemelas". Chriolepis cuneata de la costa continental se parece mas a otras especies del continente y C. dialepta de la Isla del Coco es mas parecida a otra forma insular, C. lepidota Findley de la Isla Malpelo, Colombia.
Is there a difference of temperature sensitivity between marine phytoplankton and heterotrophs?

The temperature sensitivity of phytoplankton growth rates, parameterized as the activation energy (Ea) in the Boltzmann‐Arrhenius equation, is critical to determining how global warming will affect marine ecosystems and the efficiency of the biological pump in the ocean. We applied both linear and nonlinear regression models to two laboratory temperature‐growth experimental datasets to estimate the Ea of each taxon of phytoplankton and heterotrophic protists. We found that phytoplankton Ea and normalized growth rates depended strongly on community composition. Diatoms grew more rapidly and had lower Ea values, whereas cyanobacteria grew more slowly and had higher Ea values. The phytoplankton Ea was underestimated by a single OLS regression on the pooled dataset because slowly growing cyanobacteria dominated in warm, oligotrophic ocean gyres, and rapidly growing diatoms dominated in cold, nutrient‐rich waters. By contrast, the median Ea values estimated from individual experiments did not differ between phytoplankton and heterotrophic protists. Our results suggest that phytoplankton community composition needs to be considered when trying to predict the effects of ocean warming on ecosystem productivity and metabolism.
EFFECT OF CALCIUM AND POTASSIUM COMPOUNDS ON VEGETATIVE GROWTH, FRUITING, YIELD AND FRUIT QUALITY OF GUAVA (Psidium guajava L.) cv. L-49

of THESIS Submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Horticulture Supervisor Submitted by Prof. B.K. Singh Sanjay Kumar Vishwakarma DEPARTMENT OF HORTICULTURE INSTITUTE OF AGRICULTURAL SCIENCES BANARAS HINDU UNIVERSITY VARANASI 221 005 INDIA I.D. No. PH-104
Comparison of stability methods in elephant-grass genotypes for energy purposes

Elephant grass is a plant of tropical origin with high biomass-production potential that stands out today as an alternative energy source. The potential of its genotypes depends on the genotype × environment interaction. The objective of this study was to estimate the genotype × environment interaction and compare stability methods in elephant grass for biomass production in a biannual cutting regime. The experiment was conducted in a randomized block design with two replicates and evaluations of 73 elephant-grass genotypes in six cuts. The trait dry matter yield was utilized for the analysis of the genotype × environment interaction and the stability. The stability analysis methods employed were those of Yates and Cochran, Plaisted and Peterson, Wricke, Annicchiarico, Lin and Binns, and Huehn. Kang and Phan’s ranking was adopted for all the methods. Spearman’s coefficient was utilized to evaluate the degree of agreement between the different methods employed. Significant differences were observed for the genotype × environment interaction. Non-parametric Lin and Binns’ and Annicchiarico’s methods were more discriminating than the analysis of variance methods in the evaluation of stability and productivity of the tested genotypes. Key words: Pennisetum purpureum, energy alternative, biomass production, genotype by environment interaction.
Survival of Shigella flexneri on Vegetables and Detection by Polymerase Chain Reaction.

Commercially prepared and packaged fresh vegetables were tested to determine the types and levels of indigenous microflora. Sixteen species of bacteria from 11 genera were identified and titers of up to 1 × 1010 cells per gram of vegetable were observed. To evaluate the survival of Shigella spp. on packaged vegetables, an avirulent insertion mutant of Shigella flexneri 5 (pHS 1059) was added to vegetables. This strain survived in phosphate-buffered saline at pH 7.3 at 5 to 10°C for more than 3 months. It also survived for several days at both ambient and refrigerator temperatures when inoculated onto various commercially prepared vegetables. A rapid method for detecting Shigella spp. on vegetables was developed by using the polymerase chain reaction (PCR) to amplify a 118-base-pair DNA fragment from the S. flexneri virulence-associated spa region. The PCR also generated the corresponding fragments from S. sonnei , S. boydii , and Shigella sp. This fragment was also observed when S. flexneri cells were used to artificially contaminate sterile and nonsterile vegetables, but no amplified fragment was observed when the normal microflora of the vegetables were eluted and tested by PCR.
Vigor and skill in the acrobatic mating displays of a Neotropical songbird

Animal social behaviors are often mediated by signals that provide information about signaler attributes. Although some signals are structurally simple, others are temporally dynamic and multifaceted. In such cases, exaggeration of some display components is likely to curtail the expression of others. We quantified features of the acrobatic, multimodal “leap display” of blue-black grassquits (Volatinia jacarina), which appears to entail moderate-to-high performance levels in terms of vigor and skill. We video recorded and quantified leap parameters (height, duration, rotation angle, launch velocity, and number of wing beats) and assessed how these parameters covaried with each other and with vocal parameters, display rates, and body mass index. Our analyses revealed correlations among multiple performance variables: leap height, duration, launch velocity, and number of wing beats. Leap height also correlated positively with song duration. By contrast, no leap parameters covaried with rotation angle. Our analyses also revealed a trade-off in vigor and skill-based leap attributes: birds with a lower body mass index showed a negative relationship between leap heights and the proportion of displays that included leaps (vs. perched vocalizations only). Our results identify directions of display evolution subject to mechanical or timing constraints and provide evidence that display attributes that emphasize vigor and skill may limit one another. Our results also support a key expectation of handicap models of display evolution, which is that costs of display execution should be borne disproportionately by signalers of lower quality.
EPA and DHA Modulate Macrophage-Derived Inflammation and Subsequent Skeletal Muscle Inflammation

EPA AND DHA MODULATE MACROPHAGE-DERIVED INFLAMMATION AND SUBSEQUENT SKELETAL MUSCLE INFLAMMATION Diane Mieko Sepa-Kishi Advisor: University of Guelph, 2013 Dr. Lindsay E. Robinson Macrophage-derived inflammation contributes to chronic inflammation in adipose tissue in obesity and is also linked to the development of skeletal muscle (SM) insulin resistance. The long-chain n-3 PUFA have been shown to modulate cytokine secretion from macrophages, though subsequent effects on SM inflammation and function are unknown. A model of macrophage conditioned media (MCM) was used to examine effects of n-3 PUFA on macrophage inflammation and consequent effects on SM cells. Treatment of RAW 264.7 macrophages with long-chain n-3 PUFA decreased LPS-induced MCP-1 and IL-6 gene expression and MCP-1 secreted protein. In turn, MCM from n-3 PUFA-treated macrophages decreased TNF-α and IL-6 gene expression in LPS-stimulated L6 SM cells, but did not affect insulin-stimulated pAkt content. Long-chain n-3 PUFA did not affect gene expression of inflammatory signaling intermediates NF-κB and TLR4. Overall this thesis suggests that longchain n-3 PUFA are important nutritional strategies for reducing macrophage-derived inflammation, with ensuing benefits in SM inflammation.
Control of globin gene expression by Kruppel-like factors

Kruppel-like factors (KLFs) are a family of seventeen proteins designated KLF1 to KLF17. KLFs are transcriptional factors that bind GC-rich sequences such as CACCC elements. The DNA binds to KLFs via three carboxyl-terminal Cys-2/His-2 zinc fingers. KLFs control cell differentiation and embryonic development. They are also implicated in a number of cellular functions such as erythropoiesis, proliferation and tissue development. This review will focus primarily on KLFs that are involved in haemoglobin control. These include KLF1, KLF2, KLF3, KLF8 and KLF10. The connection between human KLF1 and elevated foetal haemoglobin was first identified in a study done by (Borg et al., 2011) on a large Maltese family with Hereditary Persistence of Foetal Haemoglobin (HPFH) where a nonsense mutation in the Erythroid Kruppel-Like Factor 1 gene (KLF1 ) was identified as the main cause of HPFH. KLF2 is a positive regulator of mouse and human embryonic B-globin genes and it overlaps with KLF1 in embryonic erythropoiesis. KLF3 and KLF8 expression is driven by KLF1 while together KLF3 and KLF8 participate in the silencing of embyronic globin expression during development. KLF10 expression was also shown to be associated with high foetal haemoglobin levels in Bthalassaemia patients undergoing hydroxyurea treatment.
Survey for ticks on feral swine within a cattle fever tick-infested landscape in Texas, U.S.A.

Abstract We collected ticks from feral swine, Sus scrofa L. , during 1–3 September 2015, in pastures known to be infested by southern cattle ticks, Rhipicephalus (Boophilus) microplus (Canestrini), at the Laguna Atascosa National Wildlife Refuge in Cameron County, Texas, U.S.A. All 81 examined feral swine were infested by ticks, but none was infested by R. microplus. Tick species collected were Amblyomma maculatum Koch, Amblyomma mixtum Koch, Amblyomma tenellum Koch, Dermacentor halli McIntosh, and Dermaentor variabilis (Say). This is the first formal report of A. tenellum infesting feral swine.
High fodder value and feeding likelihood favour endozoochorous plant dispersal

Questions In pasture-dominated landscapes, endozoochory by large herbivores is an important vector of plant dispersal. Conditions influencing the potential for endozoochorous dispersal of plant species by grazers are, however, still poorly known. Here, we assess the impact of feeding habits and functional traits on the likelihood of endozoochorous dispersal by cattle (ruminant) and horses (non-ruminant). Location Pasture of 27 ha in NW-Germany year-round grazed by free-ranging cattle and horses. Methods Vegetation relevees were established in 45 plots, in which dung samples of cattle and horses were collected. The number and composition of seedlings emerging from dung samples were compared with the vegetation of the study site in terms of plant functional trait composition. For the first time, feeding habits were included in the analysis. Generalized linear models were used to identify traits that increased the potential for endozoochorous dispersal. Results A total of 65 species germinated from the dung samples. These species had higher average fodder and nutrient indicator values than the species composition of the vegetation. Especially species found in horse dung were more tolerant of grazing and had more elongated seeds. The likelihood of endozoochorous dispersal was higher for common than for rare species and was influenced by feeding habits. Conclusions The likelihood of plant species being dispersed endozoochorously can be linked to different functional traits and is dependent on the type of grazer and the population size of target species in the vegetation. Differences between cattle and horses in seed dispersal may result from species-specific grazing habits and different digestion modes. This article is protected by copyright. All rights reserved.
Sexing of Phylloscopus based on multivariate probability of morphological traits

ABSTRACT Sexes cannot be distinguished with certainty by human observers in many avian species. However, some apparently monomorphic species have small but measurable sexual dimorphisms in biometry, which can be used to determine sex. Here, we develop a method based on multivariate probabilities to improve sexing in three Phylloscopus species. We captured 16 124 Common Chiffchaffs (P. collybita), Iberian Chiffchaffs (P. ibericus) and Willow Warblers (P. trochilus) during postnuptial migration in the Doñana National Park (SW Spain). We estimated the probability of them being male or female based on a combination of the density distributions of wing and tarsus lengths. Density distributions were derived as two normal components of the mixture distribution in both traits. Discriminatory ability was compared under different assumptions. 95% of Common Chiffchaffs, 92% of Iberian Chiffchaffs and 87% of Willow Warblers were sexed with 95% confidence. These percentages are greater than those reported for these species using sexing methods based only on wing length. Our method was not affected by changes between years in the degree of dimorphism or mixture of populations from different geographical origins. In the Iberian Chiffchaff and the Willow Warbler, sexing was improved when our method was applied to immatures and adults separately. Sex ratio was estimated to be two females per male in the Common Chiffchaff and the Willow Warbler. In the latter species, females migrated one week later than males. Sex ratio in the Iberian Chiffchaff was 1:1. Our sexing method could be used for other species with known and apparent dimorphism or to any data set of birds with biometric measures.
Diet of the Nankeen Kestrel Falco cenchroides on Christmas Island

This note reports on the diet of the Nankeen Kestrel Falco cenchroides on Christmas Island (Indian Ocean) from remains located at perches in 2005 and 2008. The dominant prey item was the Giant Grasshopper Valanga irregularis . Other prey included the Christmas Island Swiftlet Collocalia linchi natalis and the introduced Grass Skink Lygosoma bowringii .
Effect of hen age and storage time on egg weight loss and hatchability results in turkeys

Abstract The aim of this study was to determine the effect of egg water loss during storage and incubation on hatch rates in heavy-type broad-breasted white BUT Big 6 turkeys. Turkey hens started laying eggs at 30 weeks of age. In weeks 2, 8, 16 and 21 of the laying season, 1512 eggs were selected randomly and divided into 4 groups of 378 eggs each. The groups of eggs were stored for 7, 10, 13 or 17 days before incubation. At the beginning and end of the storage period and on days 9, 15, 21 and 24 of incubation, eggs were weighed to determine the percent water loss relative to the egg’s weight. Four incubation cycles of 378 eggs each were performed for each storage period. A total of 16 incubation cycles were carried out (4 weeks of the laying season × 4 egg storage periods) and the following parameters were determined (%): egg fertilization, dead embryos, unhatched eggs and hatchability results from fertilized eggs. The percentages of dead embryos and unhatched poults with physical defects and abnormal position were determined in hatchery waste from each incubation cycle. Egg water loss varied throughout storage and reached 0.57% of total egg weight after 7 days, 0.79% after 10 days, 0.87% after 13 days and 1.28% after 17 days (P≤0.05). After 7 days of storage, egg water loss during a 15-day and 21-day incubation period reached 5.76% and 8.72%, and lower values were noted after 17 days of storage (P≤0.05). Egg water loss of 1.28% during storage resulted in a high rate of early embryonic mortality (14.81%) and a low hatch rate (72.12%) (P≤0.05). High water loss in stored eggs contributed to a higher percentage of congested embryos. During storage, egg water loss reached 0.72% in week 2 of the laying season, 0.78% in week 8 and ≥1% in weeks 16 and 21 of the laying season (P≤0.05). Egg water loss during a 21-day incubation period was similar in weeks 2, 8 and 16 of the laying season, and lower in week 21 (P≤0.05). The hatchability of turkey eggs was lowest in weeks 16 and 21 of the laying season (P≤0.05). Low water loss during incubation contributed to a high rate of late embryonic mortality (13.2%). High water loss during egg storage is accompanied by lower water loss during incubation. Water loss should be monitored after storage and on days 15 and 21 of incubation to evaluate water metabolism in hatching eggs.