Miracle-dz/UniFAR-FTUs huggingface dataset:
Coccidiostats in poultry manure - a potential impact on metal accumulation in beneficial soil invertebrates.

Carboxylic ionophore antibiotics are used in veterinary medicine for prevention and treatment of coccidiosis in poultry. The most frequently used coccidiostats in Slovenia and in northern Europe are natural ionophores monensin, salinomycin, and lasalocid. As these substances are only partially metabolised in treated animals, the major part of coccidiostats consumed are excreted in active form. When poultry manure is used as fertiliser, part of the coccidiostats ends up in the environment. Ionophores act as cation transporters across cell membranes, so they can potentially also impact metal transport, especially in metal-burdened environments. We studied the bioaccumulation of copper in earthworms (Eisenia andrei) and isopods (Porcellio scaber) when concurrently exposed to monensin and Cu-contaminated artificial soil. Copper predominantly enters agricultural soils by use of Cu-based herbicides and manure from pig farms where it is used as a growth promoter. In the present study, animals were exposed for 14 or 28 days to environmentally realistic concentrations of Cu (80 and 160 mg/kg dry soil) and monensin (25 mg/kg dry soil). We found that monensin increases the uptake and accumulation of Cu in earthworms, while no impacts on isopods were observed. Thus we may conclude that in Cu-burdened environments like vineyards, Cu intake could decrease the toxicity threshold if monensin-contaminated manure from poultry farms was used frequently.
Metabolic, cardiac and ventilatory regulation in early larvae of the South African clawed frog, Xenopus laevis.

Early development of O2 chemoreception and hypoxic responses under normoxic (150 mmHg) and chronically hypoxic (110 mmHg) conditions were investigated in Xenopus laevis from hatching to 3 weeks post fertilization. Development, growth, O2 consumption, ventilatory and cardiac performance, and branchial neuroepithelial cells (NEC) density and size were determined. At 3 days post fertilization (dpf), larvae started gill ventilation at a rate of 28 ± 4 beats/min and showed increased frequency to 60 ± 2 beats/min at a PO2 of 30 mmHg. Also at 3 dpf, NECs were identified in the gill filament buds using immunohistochemical methods. Lung ventilation began at 5 dpf and exhibited a 3-fold increase in frequency from normoxia to a PO2 of 30 mmHg. Hypoxic tachycardia developed at 5 dpf, causing an increase of 20 beats/min in heart rate, which led to a 2-fold increase in mass-specific cardiac output at a PO2 of 70 mmHg. At 10 dpf, gill ventilatory sensitivity to hypoxia increased, which was associated with the increase in NEC density, from 15 ± 1 to 29 ± 2 cells/mm of filament at 5 and 10 dpf, respectively. Unlike the elevated rate, cardiac and ventilatory volumes were independent of acute hypoxia. Despite increased cardioventilatory frequency, larvae experienced an average of 80% depression in during acute hypoxia. Chronic hypoxia (PO2 of 110 mmHg) decreased mass-specific cardiac performance before 10 dpf. In older larvae (10 to 21 dpf), chronic hypoxia decreased acute branchial and pulmonary hypoxic hyperventilation and increased NEC size. Collectively, these data suggest that larvae exhibit strong O2-driven acute hypoxic responses post-hatching, yet are still O2 conformers. All acute hypoxic responses developed before 5 dpf, and then the effects of chronic hypoxia started to show between 7 and 21 dpf. Thus, the early formation of acute hypoxic responses is susceptible to the environment and can be shaped by the ambient PO2.
The deacetylase HDAC6 is an essential component of stress granules and plays a critical role in the cellular response to stress

The reversible acetylation of histones has a critical role in transcriptional regulation. Likewise reversible acetylation of non-histones proteins is also important for other cellular processes. Acetylation and deacetylation of histones and other proteins are catalyzed by opposing histone acetyl transferases (HATs) and deacetylases (HDACs) respectively. Among three classes of histone deacetylases, HDAC6 is a very unique class II HDAC enzyme which possesses two independent deacetylase domains and a Zn-UBP ubiquitin binding domain at the C-terminus. HDAC6 has been shown to interact with nuclear proteins as well as cytoplasmic proteins such as tubulin and HSP90. However, the physiological function of HDAC6 is not fully understood yet. Therefore, to further define the cellular function of HDAC6, an identification of novel interacting proteins has been undertaken. The first section of this thesis describes the identification of one novel HDAC6 interacting protein and the role of HDAC6 in stress granule (SG) formation in response to environmental stress. First of all, we identified new HDAC6 interacting proteins using proteomic affinity trap approach. Here, we focused that HDAC6 interacts and colocalizes with a previously identified stress granule component, G3BP (RasGAP associated endoribonuclease) in vitro and in vivo. We first discovered that HDAC6 is a stable and critical component of stress granules. Further experimental data suggested that HDAC6 can regulate the assembly of SGs via recruiting SG components to the microtubule system. Because of this HDAC6 may have an impact on various processes involoving RNA metabolism and we provide initial evidence that the miRNA pathway is indeed influenced by HDAC6 function. The second section of this thesis examines the role of HDAC6 in response to various stresses. The involvement of HDAC6, a multi-functional cytoplasmic deacetylase, in processes such as the clearance of cytotoxic aggregated misfolded proteins and the deacetylation of HSP90 chaperone, has prompted us to investigate a role for HDAC6 in cellular protection under stress condition. In hypoxia, HDAC6 regulated stability of HIF- 1α by controlling its deacetylation. Indeed, loss of HDAC6 rendered cells more sensitive to programmed cell death. Moreover, depletion of HDAC6 affected the recovery of cells from stress as well as the direct stress response, suggesting a significant role of HDAC6 as a cellular regulator of the stress response. In addition, a number of other putative HDAC6 interactors are presented, which were identified in the initial mass spectrometry screens. Several of these proteins encode cytoplasmic factors that have a role in RNA metabolism, protein translation or in cytoskeletal regulation. Therefore, it appears likely that at least some of these may turn out to be relevant partners contributing to HDAC6 function.
Conventional and organic cropping systems at Suitia IV: weeds

Weeds are postulated to be one of the most difficult problems in organic farming, where herbicides are not used. Possible substitutive methods for herbicides are, for instance, crop rotation, careful ploughing, fallowing, delayed cultivation before sowing and stubAbstract. At Suitia, Southern Finland, weed populations in different crop rotations at conventional and organic cropping systems were investigated in 1982—1988. The number ofweeds and the dry matteryields of weeds were greater in organic cropping (on average 324 weeds/m 2 and 425 kg DM/ha) compared toconventional cropping (94 weeds/m 2 and 61 kg DM/ha). There were least weeds in the conventionally cultivated ley. The first year, clover ley in organic cropping prevented the growth of weeds as well as the grass ley in conventional cropping. Overwintering damages in organically cultivated leys increased the amounts of weeds in the following ley years. Organically cultivated winter wheat reduced the amount and weight of weeds almost as well as conventionally cultivated winter wheat although its biomass was three-fourths of the conventionally cultivated winter wheat. The biomass of organically cultivated barley later on in the rotations was only one-fifth of the conventionally cultivated barley and had five times more weeds. In conventional cropping, the number of weeds in almost all weed species was decreased or stayed at the same level during the experiment. In organic cropping, the number of most weeds in weed species increased from the level for 1982. Most increased Stellaria media, Fallopio convolvulus, Lamium sp and Chenopodium album.
Efectos de los campos electromagnéticos pulsados (PEMF) en el cultivo de las stem cells circulantes

El diseno de este trabajo intenta establecer las condiciones de cultivo y la metodologia para la evaluacion del grupo de las SC adultas y del grupo de las SC adultas expuestas a PEMF, con el estudio de los siguientes objetivos: 1. - Estandarizacion de las condiciones de cultivo de las celulas mononucleares (CMN) de sangre periferica en medio liquido y de su irradiacion con Campos Electromagneticos Pulsados ( PEMF). 2. - Identificacion morfologica de los tipos celulares y evaluacion de la proliferacion e inmunofenotipo celular. 3. - Valorar los cambios de actividad celular inducidos por los PEMF mediante la cuantificacion de citoquinas y de la capacidad fagocitica. Se obtuvieron las siguientes conclusiones: - El cultivo de celulas mononucleares de sangre periferica produce fibroblast-like/fibrocitos con caracteristicas de tejido conjuntivo y de celulas macrofagicas (morfologia fibroblastica, Vimentina +, CD 68 + y NBT Test positivo). - El patron de produccion de citoquinas durante el cultivo registra un aumento progresivo de los niveles de GM-CSF, un descenso tambien progresivo de la IL-2, IL-1beta y de la IL-10, y un incremento de IFN-? y TNF-alfa el dia 14. - El protocolo de irradiacion PEMF disenado para este estudio con menores dosis y tiempos de irradiacion, consigue resultados equiparables a los utilizados en protocolos anteriores. - La irradiacion con PEMF produce un incremento muy significativo de la proliferacion celular, disminuyendo el numero de celulas alargadas el dia 14. - No se detectaron cambios significativos en los marcadores citoquimicos ni en la capacidad fagocitica tras la irradiacion PEMF. - La irradiacion PEMF no altera los niveles de IL-2, IL-4, GM-CSF e IFN-? - Se observo una disminucion muy significativa de los niveles de IL-1beta y de TNF-alfa en los cultivos irradiados con PEMF.
Transmission of European Stone Fruit Yellows Phytoplasma ('Candidatus Phytoplasma prunorum') during the propagation process

Th e study focused on the incidence of ’Candidatus Phytoplasma prunorum’ transmission during the propagation process. Two common commercial propagation procedures, whip grafting in winter and budding in summer, were applied. Infected scions were grafted on certifi ed apricot seedling rootstocks. Transmission of the pathogen was observed with both procedures. Whip grafting in winter, however, resulted in signifi cantly lower infection rates of the progeny (0 to 15 %) than budding in summer (46 to 88 %).
Security Issues In Wireless Sensor Network

Wireless Sensor Network is a network of devices that can convey the information congregated from a tested field through wireless connections. The data is sent from numerous nodes and gateways, the data is associated with other networks. Wireless Sensor Network has various potential advantages. It is an emergent technology utilized as a part of numerous application which incorporates security issues in this manner security plays an important role in Wireless Sensor Network. Wireless Sensor Network undergo from numerous restrictions including little memory, low calculation ability, restricted vitality assets and unreliable remote channels. These restraints make security a challenge in Wireless Sensor Network. The undertaken study aims to present the various security issues in Wireless Sensor Network and also discusses the protocols used to deal with these security challenges. This study is helpful for scholars, researchers and academicians.
Hyperinvasiveness in the major food-borne pathogen Campylobacter jejuni

Campylobacter jejuni is a common cause of human gastrointestinal infections. Invasion of host epithelial cells is believed to be an important virulence Mechanism of this bacterium. C. jejuni strains vary in their ability to invade the human epithelial cells and some of the strains are hyperinvasive. The aim of this work was to find the molecular basis of this hyperinvasive phenotype. The previously studied hyperinvasive phenotype of C. jejuni 01/51 in INT-407 cells was verified using Caco-2 cell based invasion assay and the assay was set up at Nottingham Trent University by selecting blood agar for 48 hours as the pre-assay bacterial growth conditions and 100 multiplicity of infection as the starting inoculum. Seven hundred and sixty eight mutants generated in this strain by random transposon insertional mutagenesis were screened for their ability to invade human intestinal epithelial cells in an in vitro model and 174 mutants were selected for further studies. The motility of selected mutants was determined and 40 mutants that showed more than 75% motility compared to wildtype strain, with a very low level of invasion were selected for reconfirmation of this reduced invasion phenotype using standard INT-407 and Caco-2 cells based invasion assays. Localisation of the transposon insertion site by plasmid rescue was attempted in 15 mutants that showed very low levels of invasion in both eukaryotic cell lines.
Estudo experimental sobre a intoxicação de Gallus gallus domesticus com semente de crotalaria spectabilis. II efeito em aves na fase final de crescimento

A Crotalaria spectabilis e uma leguminosa amplamente distribuida no Brasil, que pode ser utilizada como adubacao verde. Suas sementes podem ser colhidas junto com o milho ou outros graos quando invade plantacoes de cereais. Tendo-se em vista que o milho e um componente essencial da racao de aves de exploracao comercial, representando aproximadamente 60% da racao pronta, o presente estudo avaliou a acao toxica de sementes de Crotalaria spectabilis para aves de corte de linhagem comercial, durante os 28 primeiros dias de vida. Quatro grupos experimentais, subdivididos em grupos de machos e de femeas, foram tratados com racao inicial acrescida de sementes de Crotalaria spectabilis trituradas, nas proporcoes 0,0 (controle), 0,01%, 0,1% e 0,4%. As dietas contendo 0,4% e 0,1% provocaram quadro de intoxicacao a partir do terceiro dia (0,4%) ou da segunda semana (0,1%) de vida, provocando sintomas tais como tristeza, apatia, aglomeracao, penas arrepiadas, acentuada anorexia e abdomen abaulado. Houve evidente retardo de crescimento e alta mortalidade. Multiplas lesoes foram encontradas: ascite severa; degeneracao, necrose, apoptose e proliferacao conjuntiva hepaticas, com reducao do tamanho do orgao; reducao de tecido linfoide da bursa, com presenca de celulas picnoticas; lesoes degenerativas em rins; e calcificacao intersticial pulmonar, entre outras. As aves controle e aquelas que receberam 0,01% de sementes nao apresentaram alteracoes patologicas ou de desenvolvimento.
Monitoring Anticoagulant Rodenticides in Birds of Prey in the Wildlife Rehabilitation Setting

Author(s): Murray, Maureen | Abstract: Monitoring anticoagulant rodenticide (AR) exposures in birds of prey presented to a wildlife clinic or rehabilitation setting has several advantages and disadvantages. Advantages include the ability to document signs of toxicosis in live birds. Additionally, in birds that die due to AR toxicosis, post-mortem lesions in the non-frozen, non-autolyzed cadaver will illustrate patterns of AR-induced hemorrhage. In birds that die or are euthanized due to other causes, liver samples can be collected and analyzed for AR residues. Disadvantages include an inability to ascertain the dose of AR ingested. In birds with exposure to multiple ARs, the timing of ingestion is also unknown. The route of exposure and pathway through the food chain likewise are unknown. Importantly, determining the true incidence of toxicosis and mortality among the sampled birds is not possible because birds that are found and transported for care may not be reflective of mortalities in the overall population. Despite the limitations of this method of sampling, much useful information can be gathered, particularly in studies that are continued over time. Two such monitoring studies conducted in Massachusetts, USA over a ten-year period, showing widespread exposure among sampled birds, will be discussed. In addition, other information that is needed to enhance the data obtained by cadaver sampling will be high­lighted, particularly as these data gaps relate to evaluation of mitigation efforts.
Primary Hydatid Cyst of the Thyroid Gland Revealed by Primary Hypothyroidism

Introduction: The thyroid localization of the hydatid cyst (HC) remains exceptional and unusual even in countries where this Parasitosis is still endemic: its frequency varies from 0.1 to 0.6 ‰ depending on the series. It is most often asymptomatic or resulting in anterior cervical swelling or more rarely a hoarseness of the voice. We report an original observation of thyroid HC revealed by primary hypothyroidism. Observation: An eight-year-old patient with no notable pathological history was explored for normochromic normocytic anemia at 8 g/dl. The clinical examination found neither jaundice nor splenomegaly. There was anterior cervical swelling that was painless and lateralized to the right. No lymphadenopathy or other palpable mass was noted. Biology revealed peripheral hypothyroidism with TSH at 7.83 μIU/ml. The balance of hereditary hemolytic anemias was negative. Cervical ultrasonography and CT showed an anechoic anterior cervical mass 2.51 cm in diameter, occupying the right thyroid lobe, without micro calcifications, intracystic vegetation, or adenopathies. Hydatid serodiagnostic was positive. The diagnosis of thyroid HC was confirmed by histological examination post loboishmectomy. The total blood count and TSH were spontaneously corrected after one month of the surgery. Conclusion: The diagnosis of HC is worthy of mention in the presence of peripheral hypothyroidism with increased thyroid gland volume, especially in endemic areas. This location can sometimes hide associated thyroid neoplasia.
Identification à l'échelle génomique de gènes transcrits par deux isoformes de l'ARN polymérase III humaine

In eukaryotes, transcription is carried out by DNA-dependent RNA polymerases I, II and III (or I-V inplants). These RNA polymerases are specialized in the transcription of specific groups of genes.Human RNA polymerase III (Pol III) transcribes small noncoding RNAs involved in the regulation oftranscription (7SK RNA), RNA processing (U6 RNA, RNAse P, RNAse MRP), translation (tRNAs,5S RNA) or other cellular processes (vault RNAs [multidrug resistance], adenoviral RNAs [VA-I,VA-II], Epstein-Barr virus RNAs [EBER1, EBER2]). It has furthermore been reported that somemicroRNAs of viral or cellular origin may also be transcribed by Pol III.Interestingly, increased Pol III transcription levels accompany or cause cell transformation. Themechanisms underlying this phenomenon are still largely unknown. Recently, two distinct isoforms ofhuman Pol III have been discovered (Haurie et al., 2010). RPC32β-containing Pol IIIβ is ubiquitouslyexpressed and essential for growth and survival of human cells. In contrast, RPC32α-containing PolIIIα is dispensable for cell survival and its expression is restricted to undifferentiated embryonic stem(ES) cells and to tumor cells.The distinct effects of Pol IIIα and Pol III β on cell growth and transformation may be explained bythe transcription of isoform-specific target genes. To identify such isoform-specific target genes, wespecifically targeted RPC32α and of RPC32β subunits in chromatin immunoprecipitation (ChIP)experiments and analyzed the co-precipitated DNA sequences by high throughput sequencing (ChIPseq.). Genome wide localization of RPC32α and RPC32β subunits of Pol III revealed the presence of bothsubunits on many of the known Pol III-transcribed genes, suggesting redundant activities of bothisoforms of Pol III in transcription of these genes. We also found that some of the genes known to betranscribed by Pol III are only occupied by either RPC32α or by RPC32β, suggesting that these genesare exclusively transcribed by Pol IIIα or by Pol IIIβ, respectively. RPC32α and RPC32β ChIP-seq. results furthermore led to the identification of novel Pol III candidategenes in HeLa cells. Moreover, we found high levels of Pol IIIα or Pol III β at some of the annotatedtRNA pseudogenes, implicating that these genes may be transcribed. The functions of RNAstranscribed from novel putative Pol III genes or from tRNA pseudogenes remain to be determined.
The role of hypoxia signalling pathways in normal and leukaemic haemopoiesis

Although haemopoietic stem cells (HSCs) represent one of the best-defined stem cell systems, the pathways regulating HSC development and maintenance are not fully understood. HSCs reside in the hypoxic niche and maintain intracellular hypoxia. Hypoxia and hypoxia signalling pathways are thought to play a vital role in HSC maintenance. Hypoxia inducible factors (Hifs) are evolutionarily conserved and are the key regulators of hypoxia. Hifs consist of an unstable, oxygen-dependent α-subunit and an oxygen-independent stable β-subunit. The two main isoforms of Hif-α, namely Hif-1α and Hif-2α, are critical for the response to hypoxia. Hif-mediated pathways have been extensively studied and have been shown to regulate metabolic adaptation and to influence various cellular mechanisms, including cell growth, survival, differentiation and apoptosis, erythropoiesis and angiogenesis. Hif-1α has been shown to be essential for maintenance of HSC functions under stressful conditions of serial transplantation and aging, but the role of Hif-2α and the interplay between Hif-1α and Hif-2α in regulating HSC functions and their niche is not known. Hence, in this study, I have investigated the role of Hif-α in HSC functions. Furthermore, published evidence suggested that leukaemic stem cells (LSC) share the hypoxic properties with HSCs. Cited2, a hypoxia-inducible Hif-1α and Hif-2α target gene, is critical for embryonic and adult haemopoiesis and possesses oncogenic properties. I have investigated the role of Cited2 in AML generation. The results demonstrate that Hif-2α is not essential for maintenance of HSC functions in a cell-autonomous manner under steady state and stressful conditions of serial transplantation and aging. It is also evident that HSCs lacking Hif-2α together with Hif-1α successfully maintain normal haemopoiesis. However, the data in this thesis show that Hif-2α is essential for non-cell-autonomous maintenance of HSC functions, particularly in males and current work also indicate that a previously unappreciated complex interplay between Hif-1α- and Hif-2α-dependent signalling is required for adult HSC maintenance in a non-cell-autonomous manner. Additionally, the data demonstrate that haemopoietic stem and progenitor cells (HSPCs) lacking Cited2 display reduced transformation potential and failure to generate transplantable AML in vivo. Overexpression of Mcl-1 (an anti-apoptotic gene), in Cited2Δ/Δ cells bypassed their defective transformation potential forming transformed colonies in vitro. Hence, the data in this thesis provide evidence that Cited2 is essential for leukaemic transformation at least in part via Mcl-1 regulation.
Bioinformatics: Sequence and Genome Analysis

Preface Chapter 1. Historical introduction and overview Chapter 2. Collecting and storing sequences in the laboratory Chapter 3. Alignment of pairs of sequences Chapter 4. Introduction to probability and statistical analysis of sequence alignments Chapter 5. Multiple sequence alignment Chapter 6. Sequence database searching for similar sequences Chapter 7. Phylogenetic prediction Chapter 8. Prediction of RNA secondary structure Chapter 9. Gene prediction and regulation Chapter 10. Protein classification and structure prediction Chapter 11. Genome analysis Chapter 12. Bioinformatics programming using Perl and Perl modules Chapter 13. Analysis of microarrays