Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of DNA transposable elements in the Tasmanian devil (Sarcophilus harrisii) genome

The Tasmanian devil (Sarcophilus harrissi) is a carnivorous marsupial residing in Tasmania. Its population is being driven to extinction by a transmissible cancer, devil facial tumor disease (DFTD), which has already caused a decline in the population by 60% since 1996 [4]. Very few transmissible cancers have been identified and include a non-fatal cancer in canines. By comparison DFTD in nearly 100% fatal [5]. As a result of their diminishing population, Tasmanian devils were classified as an endangered species in 2009 by the IUCN (International Union for Conservation of Nature). Efforts to repopulate Tasmanian devils are underway with a captive breeding program (Conservation Society of Australia). The possibilities of developing a vaccine may not be unreasonable because DFTD cells are genetically identical [ 4]. In order to understand DFTD, the genome of the Tasmanian devil (which has been sequenced and data are publicly available) needs to be better examined. Cancer may be associated with transposable elements [ 1]. Mobility of these DNA sequences may be associated with the development of cancers in human cell lines. Identification of transposable elements within the Tasmanian devil genome could be a step towards understanding of the causes DFTD and perhaps help save this species.
Analysis of transcription and protein expression changes in the 786-O human renal cell carcinoma tumor xenograft model in response to treatment with the multi-kinase inhibitor sorafenib (BAY 43-9006)

Proc Amer Assoc Cancer Res, Volume 47, 2006 906 Renal cell carcinoma (RCC) is the 6th leading cause of cancer death and is marked by a high prevalence of mutations of the VHL gene which results in the deregulation of VEGF and increased tumor angiogenesis. BAY 43-9006 (sorafenib) is an orally active, multi-kinase inhibitor that targets the serine/threonine kinase RAF (RAF-1 and B-RAF) and receptor tyrosine kinases (VEGFR-2/PDGFR-β) involved in tumor growth and angiogenesis. It is currently being evaluated in phase III clinical trials for the treatment of RCC, hepatocellular carcinoma and melanoma. In the VHL-/- 786-O tumor xenograft model, once daily oral dosing of sorafenib produces partial tumor growth inhibition at 15 mg/kg and complete tumor stasis at doses of 30 mg/kg or higher associated with inhibition of tumor microvessel formation and visible areas of tumor necrosis (Chang, YS et al. EORTC 2005). To gain a better understanding of the early gene and protein expression changes associated with tumor stasis upon treatment with sorafenib, drug and vehicle treated tumors were harvested at 4 and 24 hours after the third 60 mg/kg dose. Affymetrix GeneChip™ analysis revealed significant increases in mRNA levels of the inflammatory and angiogenic cytokines, IL-6 and IL-8, as well as the matrix metalloproteinases, MMP-1 and MMP-10 upon treatment with sorafenib. These changes were confirmed by Taqman using human mRNA specific primers. Sorafenib induced modest increases in expression of the angiogenic factor, VEGF, whereas no significant changes were observed in the mRNA levels of the angiogenic factors, FGF-1 and FGF-2, or TGF-α, a known autocrine growth factor for RCC. Measurement of protein levels of IL-6, IL-8, MMP1 and VEGF from vehicle and sorafenib-treated 786-O tumor extracts were determined by ELISA using antibodies specific for the human protein. Increases in mRNA expression in sorafenib-treated 786-O RCC tumors corresponded to increases at the protein level, which were statistically significant for IL-6, IL-8, and MMP-1. The observed changes in VEGF expression are consistent with published clinical observations of modulation of VEGF in the plasma or serum of patients treated with inhibitors targeting VEGFR. Additional studies are underway to evaluate the utility of IL-6, IL-8, and MMP-1 as pharmacodynamic biomarkers for clinical response to sorafenib.
BIOCHEMICAL STUDY ON ENZYMATIC ANTIOXIDANT IN ASTHMATICS

Oxidative stress contributes to the pathophysiology of respiratory disorders and other chronic diseases associated with asthma. Increased levels of oxidants are considered a marker of the inflammatory process. The objective of the present study was to investigate the levels of antioxidants status in asthmatic patients in comparison with healthy volunteers. Lipid peroxidation assay, Superoxide Dismutase (SOD), Glutathione Peroxidase (GPx), Catalase (CAT), was determined in 95 asthmatic patients based on severity. The results of the present study suggest that downward and elevated level of antioxidants are associated with the severity of asthma, The results revealed the existence of an increased oxidative stress and reactive oxygen species in asthmatics, with altered antioxidant capacities.
Effect of Quercus infectoria and Zataria multiflora extracts on the expression of Apo-B100 and PPAR-α in liver and adipose tissues in insulin resistant rats

Background: Insulin resistance can increase the risk of metabolic syndrome. Studies have shown that expression of PPAR alpha improved insulin function in patients with insulin resistance. Also ApoB100 is an essential ligand for the receptors of low-density lipoproteins (LDL). Increased plasma level of apoB100 is a risk factor for cardiovascular disease (CVD) and its increased production leads to insulin resistance. The aim of this study was to evaluate the effects of Q. Infectoria and Z. multiflora extracts on the expression of PPARα and Apo-B100 genes in adipose and hepatic tissues of insulin-resistant rats Materials and methods : Forty Wistar rats were divided into 1- healthy control, 2- high fat control, 3- fenofibrate,4- Q. Infectoria and 5- Z. multiflora groups. All groups were fed with high fat diet for 6 weeks expect for the healthy control. Glucose tolerance test was performed to confirm insulin resistance in rats. Then groups 3, 4, and 5 were treated by fenofibrate , Q. Infectoria and Z. multiflora extracts respectively. After sacrificing the rats, their liver and fat tissues were removed. Real-time PCR was used to assess PPARα and ApoB100 gene expressions. Results: All groups had significant weight gain after 8 weeks. Expression of PPAR-α and ApoB100 genes were the same in Q. Infectoria , Z. multiflora, fenofibrate and healthy control groups. Conclusion: In conclusion, Q. Infectoria and Z. multiflora extracts decreased ApoB100 and increased PPARα gene expressions but these changes were not statistically significant.
The effect of algal blooms on fish in their inshore nursery grounds in the Gulf of Gdańsk

Studies of cyanobacterial bloom dynamics show that the highest biomass accumulation of Nodularia spumigena is observed in the shallowest area of the Gulf of Gdańsk in summer. In the same region and time, the highest fish abundance is observed. Mostly young individuals of gobies, small sandeel, flounder, three-spine stickleback and young herring occur. In this work we compare how toxic blooms of cyanobacteria influence the number and structure of fish communities in a coastal zone. The results obtained in our study were rather unexpected. More fish species were caught and the biomass of fish was higher during a bloom than in a month following the sampling (no bloom).
Genetic analysis of rust resistance genes in global wheat cultivars: an overview

ABSTRACT Rust is the most devastating fungal disease in wheat. Three rust diseases, namely, leaf or brown rust caused by Puccinia triticina Eriks, stem or black rust caused by Puccinia graminis f. sp. tritici West, and stripe or yellow rust caused by Puccinia striiformis f. Tritici Eriks, are the most economically significant and common diseases among global wheat cultivars. Growing cultivars resistant to rust is the most sustainable, cost-effective and environmentally friendly approach for controlling rust diseases. To date, more than 187 rust resistance genes (80 leaf rust, 58 stem rust and 49 stripe rust) have been derived from diverse wheat or durum wheat cultivars and the related wild species using different molecular methods. This review provides a detailed discussion of the different aspects of rust resistance genes, their primitive sources, their distribution in global wheat cultivars and the importance of durable resistant varieties for controlling rust diseases. This information will serve as a foundation for plant breeders and geneticists to develop durable rust-resistant wheat varieties through marker-assisted breeding or gene pyramiding.
Characterization of protein and peptide sensing processes in the gut coupled to gastrointestinal hormone secretion using ex-vivo models

The gut hormones (GH) are secreted from intestinal L-cells in response to protein degradation products (peptide) present in the lumen after a meal and are known to participate in food intake control. However the sensing and the intracellular mechanisms underlying GH secretion to protein from intestinal L-cells have remained undefined and the current in vitro models are very limited for the study of nutrient sensing leading to GH secretion. By combining in vitro and ex vivo approaches, we have established and characterizeed physiologically relevant new models representatives of the small intestine. The present thesis also demonstrated that dipeptide sensing requires the activation of different cell types (enterocyte and enteroendocrine cells) and different transporter/receptors (PEPT1, T1R1/R3 umami and GPR93 receptor) acting as sensor. The subsequent network between signaling pathways and the subsequent crosstalk between cells triggers appropriate absorptive and secretory mechanisms.
Estudo da produção de biofilme de isolados de Leptospira spp

Leptospirosis is a zoonotic disease caused by a bacterium that can live a long time in appropriate environmental conditions. Biofilms are aggregations of microorganisms, has a defined architecture, and provides an ideal environment for the exchange of genetic material between cells, beyond to providing protection, temperature resistance and antimicrobial. As it happens with other spirochetes, the leptospira can change their morphology according to environmental changes, and these changes include the formation of biofilms. However are few research with biofilms produced by Leptospira spp, especially on isolated from clinical frames. The aim of this study was evaluate biofilm formation by four clinical isolates of Leptospira interrogans serovar Icterohaemorrhagiae e Canicola. For evaluation of biofilms in vitro and antimicrobial susceptibility, the following tests were performed: adhesion test on polystyrene plate, quantification of protein and polysaccharide, test for minimum inhibitory concentration with three antimicrobials drugs and three different doses. For visualization of the formed biofilm was performed confocal laser microscopy. In the adhesion test on polystyrene plate, all isolates were strongly adhered, characterized as having more polysaccharide than protein. In this research, tests shown that the isolated pathogenic of Leptospira spp has formed biofilm, and they possess antimicrobial resistance to high doses of antibiotics that are used routinely in animal and human clinical.
Effects of Moderate Shade on Citrus Leaf Gas Exchange, Fruit Yield, and Quality

High temperature stress during critical stages of cit rus flower and fruit development can reduce fruit yield and quality by reducing the supply of photosynthates. We conduct ed a 2-year trial to examine the potential of applying moderate shade at different physiological stages of fruit development to reduce high temperature stress, increase carbon fixation, yield, and fruit quality in citrus. Ten year-old 'Ruby Red' grape fruit (Citrus paradisi L.) and 8-year-old 'Hamlin' sweet orange {Citrus sinensis L. ) trees were shaded with 50% shade screens either continuously from post-bloom until harvest, from Apr. to July (early shade) or from Aug. until harvest (late shade). Leaf photosynthesis, fruit yield, and quality variables were evaluat ed. Mid-day leaf temperatures and leaf-to-air vapor pressure differences were reduced by shading, resulting in increased stomatal conductance and photosynthetic activity of shaded leaves compared to sunlit leaves. In grapefruit, late shading (Aug.-harvest) increased fruit yield by 35% in 1999. Continuous shade reduced fruit yields in both varieties. Grapefruit juice content was increased by the late and continuous shade treatments relative to the controls. Late shading significantly increased grapefruit juice yield per tree due to the greater fruit yield compared to control trees. Juice content of 'Hamlin' fruit was not affected by shade treatments, but the juice yield per tree was significantly reduced by the continuous shade treatment as a result of reduced fruit yield. Total soluble solids content of grapefruit and orange were reduced by continuous and late shade, however, fruit and juice yield per tree of late shaded grapefruit were increased, resulting in net increases in total solids per tree. An increase in yields and total solids per acre would offset the costs of shading and justify shading an orchard of high-value varieties for processing. The economic feasibility of this approach deserves further study.
Comparison of Archaeal Populations in Soil and Their Encapsulated Iron-Manganese Nodules in Four Locations Spanning from North to South China

ABSTRACT To characterize the archaeal community composition in soil originating iron-manganese nodules, four types of soils—brown soil, yellow-cinnamon soil, yellow brown soil and red soil—and their associated iron-manganese nodules were collected from Queyu (QY), Zaoyang (ZY), Wuhan (WH) and Guiyang (GY), China, respectively, and subjected to quantitative polymerase chain reaction, cloning and sequencing analyses. The results showed that the archaeal 16S rRNA gene copy numbers in nodules, ranging between 3.59 × 102 and 4.17 × 103 copies g−1 dry nodule, were about 50–1000 times lower than those in their corresponding soils (1.87 × 105 to 1.08 × 106 copies g−1 dry soil), correlating with the low organic matter in the nodules, while archaea accounted for a relatively higher proportion of total prokaryote in nodules than in soils. Community composition analysis suggested that the archaeal diversity in both soils and nodules were much lower than bacterial, but archaeal community structures were similar to each other among the soils and nodules from the same location but varied among four locations, converse to the previous observation that bacterial community shifted markedly between nodules and soils as the result of habitat filtering. The archaeal communities in both soils and nodules were predominated by Thaumarchaeota Group I.1b with the relative abundance ranging between 73.88 and 94.17%, except that Euryarchaeota dominated the archaeal community in one nodule sample (WHn) developed from lake sediment. The finding shed new light on the archaeal diversity and their ecophysiology in different habitats, and further supported the opinion that archaea are more adaptable to stress and unfavorable conditions.
Abstract P027: Preconditioning Cardiosphere-Derived Cells by Hypoxia and Prolyl Hydroxylase Inhibitors to Induce HIF-Related Metabolic Changes and C-Kit Expression

Cardiosphere-derived cells (CDCs) decrease loss of cardiac function following infarction, but the potential of CDC therapy is limited due to the low retention rate and the time required to obtain sufficient cells for transplantation. AIM: Here, we aimed to precondition CDCs by culturing under hypoxia, or with prolyl hydroxylase inhibitors (PHIs), to prepare the cells for the hypoxic environment within the infarcted heart. METHODS: Rat heart explants were cultured under hypoxia (2% O2) or normoxia (21% O2) to generate explant-derived cells (EDC). EDCs were isolated, cultured to form cardiosphere and expanded into monolayer CDCs. At 80% confluency, normoxic CDCs were treated with dimethyloxalyl glycine (DMOG), Ethyl 2-(2,3-dihyroxybenzamido) (KKC226) and FG-2216 for 24 h. RESULTS: Hypoxia, 1 mM DMOG, 0.5 mM KKC226 and 30 μM FG-2216 treated CDCs showed significantly increased HIF-1α protein expression (3.9-fold, 2.6-fold, 2.1-fold and 1.5-fold, respectively) and reduced oxygen consumption (81%, 32%, 47% and 35%, respectively), compared with normoxic CDCs. Hypoxia and PHI treatment increased protein levels of GLUT-1 (6.7-fold, 3.2-fold, 4.0-fold and 2.1-fold, respectively), resulting in significant increases in glucose uptake and lactate accumulation in the culture medium, compared with controls, commensurate with increased glycolytic metabolism after hypoxia or PHI treatment. Further, hypoxia and KKC226 increased c-Kit mRNA expression 5.1-fold and 1.5-fold, respectively. qRT-PCR confirmed increased CXCR-4 mRNA in all hypoxia and PHI-treated CDCs. EDC and CDC proliferation were 1.7-fold faster under hypoxia, compared with normoxia, but did not increase with PHI treatment. CONCLUSION: Hypoxia and PHIs stabilized and activated HIF, which induced metabolic changes in CDCs, including GLUT-1 upregulation and a switch to anaerobic glycolytic metabolism. All preconditioned cells had reduced oxygen consumption and were better adapted to survive within an hypoxic infarct scar. HIF-induced upregulation of CXCR-4 may increase the homing of these cells to the infarcted myocardium. Finally, increased proliferation and expression of the cardiac stem cell marker, c-Kit, could decrease the time required for cell expansion prior to therapy by a week.
Molecular confirmation of trematodes in the snail intermediate hosts from Ratchaburi Province, Thailand

*Corresponding author: Thapana Chontananarth, PhD, Center of Excellence in Animal, Plant and Parasite Biotechnology, Srinakharinwirot University, Bangkok 10110, Thailand. Tel: +6626495000, ext. 18514 Fax: +6622600127 E-mail: thapana@g.swu. ac.th Foundation Project: Supported by the Faculty of Science, Srinakharinwirot University, Thailand for providing funding and relevant facilities (Grant No. 471/2558) The journal implements double-blind peer review practiced by specially invited international editorial board members.
Preliminary Research on the Wheat Pests and on Their Integrated Control during 2015-2016, at Agricultural Research-Development Station Turda

In Transylvania, the evolution of wheat insect pests is strongly influenced by the ecotehnological conditions, by climate change and current technology (Malschi, 2009 Malschi et al., 2015). The paper presents the dynamics and importance of the main pests of wheat (thrips, aphids, leafhoppers, wheat flies, cereals sunbugs, investigated under the integrated pest control system suitable of the area. During 2015-2016, the investigations were conducted at the Agricultural Research and Development Station Turda, from the wheat no tillage cultural system with cereal rotation of three years and applying all zonal recommendations of technology and phytosanitary complex. The pest monitoring was performed based on the samples collected with entomological net, by decadal 100 sweep-net catches/sample. The study data shows the danger of the attack of abundant populations of wheat flies ( Phorbia securis, Delia coarctata, Opomyza florum , Oscinella frit etc.; wheat fleas ( Chaetocnema aridula ) and cereal leaf beetle ( Oulema melanopa ); leafhoppers ( Psammotettix alienus, Javesella pellucida, Macrosteles laevis ); aphids ( Sitobion avenae, Schizaphis graminum, Rhopalosiphum padi ); thrips ( Haplothrips tritici ), sunbugs ( Eurygaster maura, Aelia acuminata ) etc., and the necessity of applying insecticide treatments on the vegetation. Since 2015, a stronger impact of global warming on the wheat pests structure (%) are found. This change began on the last ten years. The importance of cereal sunbugs is increasing, well as the importance of the wheat flies, aphids and leafhoppers, which requires professional study on the pest dynamics and adequate integrated control of wheat pests.
The Birds of Cairns, Cooktown and the Atherton Tablelands

An account is given of the birds that were observed by the members of the Bird Observers Club, during their tour of an area in north-eastern Queensland, between September 26, 1964 and October 11, 1964, together with references to other records that have been made for the district.
Primer registro de Typhlocoelum cucumerinum (Trematoda: Typhlocoelidae) en Cairina moschata domestica (aves: Anatidae) en Colombia

This study records for the first time in Colombia the presence of trematode Typhlocoelum cucumerinum (Rudolphi, 1809) in domestic Muscovy ducks ( Cairina moschata domestica ). A total of 210 trematodes were collected from 42 adult individuals, 26 males and 16 females. Parasitic frequency was 57.14% and mean parasitic intensity was 8.75 parasites per animal. Results show the presence of trematodes in aquatic ecosystems in the Department of Cordoba (Colombia).
Arcuate ER alpha-mediated estrogen signaling pathways and regulation of KNDy-associated gene expression in female mice

OF THE DISSERTATION . ii ACKNOWLEDGEMENTS . iv TABLE OF CONTENTS . v LIST OF TABLES . viii LIST OF FIGURES . ix ASSOCIATED PUBLICATIONS . xi CHAPTER 1: LITERATURE REVIEW . 1 1.1 Importance of the problem . 2 1.2 Estrogen signals through multiple pathways . 3 1.3 Functions of estrogens . 8 1.4 Problems in reproduction associated with energy balance . 13 1.5 Functions of kisspeptin . 15 1.6 Additional signaling pathways intersect with kisspeptin signaling . 22 1.7 Summary and objectives of the thesis . 27 References . 29 Figures . 39 CHAPTER 2: REGULATION OF GENE EXPRESSION BY 17β-ESTRADIOL IN THE ARCUATE NUCLEUS OF THE MOUSE THROUGH ERE-DEPENDENT AND EREINDEPENDENT MECHANISMS . 43 2.1 Abstract . 44 2.2 Introduction . 45 2.3 Methods . 48 2.4 Results . 53 2.5 Discussion . 58 2.6 Acknowledgements . 68
Zooplankton body size versus taxonomy in Mediterranean wetlands: implications for aquatic ecosystem evaluation

Intrinsic ecological characteristics of Mediterranean wetlands make them excellent sites for studying biodiversity, but these wetlands have been studied much less frequently than temperate lakes. The invertebrates that inhabit them, and zooplankton specifically, play important roles in these wetlands. We compared the ability of taxon- and size-based analyses of the zooplankton community to predict the influence of environmental variables. We sampled environmental variables and zooplankton at 7 Mediterranean wetlands in the Iberian Peninsula (southern Spain) monthly along 1 hydroperiod cycle (2009–2010). We used 3 arrays for classifying the zooplankton community: 1) species occurring in >5% of the samples, 2) coarse-level taxa easily identified by a nonexpert (large branchiopods, small branchiopods, calanoid copepods, cyclopoid copepods, and harpacticoid copepods), and 3) 4 body-size classes (<1, 1–2.5, 2.5–10, and >10 mm in length). We used permutational analysis of variance (PERMANOVA) and canonical correspondence analysis (CCA) to test our hypotheses. Communities differed significantly among wetlands, and body size (55.8% of explained variance) was more useful than taxonomic composition (common taxa: 24.4%, coarse-level taxa: 26.5% of explained variance) for rapid assessment of the influence of the environmental variables on zooplankton community in temporary wetlands.