Miracle-dz/UniFAR-FTUs huggingface dataset:
Transmission of ‘Candidatus Liberibacter solanacearum’ by Bactericera trigonica Hodkinson to vegetable hosts

The bacterium ‘ Candidatus Liberibacter solanacearum’ is a recent plant pathogen of several crops in Solanaceae and Apiaceae and is associated with economically important diseases. The bacterium is a carrot seed borne pathogen that can also be transmitted from potato mother tubers and by psyllid vectors. The psyllid Bactericera trigonica Hodkinson was described carrying CaLso associated with vegetative disorders in carrot and celery crops in Spain and its competence to transmit this phloem-limited bacterium among vegetables is currently being investigated. Here electrical penetration graphs showed that B. trigonica fed in the phloem of carrot and celery and probed the phloem in potato, but not in tomato plants. The bacterium was efficiently transmitted to carrot and celery plants when either single B. trigonica or groups of ten fed on these species. An inoculation access period of 24 hours was sufficient for a single B. trigonica to transmit the bacterium to carrot (67.8%), celery (21.1%) and eventually to potato and tomato (6.0%). Higher transmission rates were obtained with 10 individuals on celery (100%), carrot (80%), potato (10%) and tomato (10%). Bactericera trigonica laid eggs, and the hatched nymphs develop into adult on carrot and celery, but not on potato and tomato. CaLso was detected in 20% of the eggs laid by females carrying the bacterium. The results confirmed that B. trigonica is a vector of the bacterium to carrot and celery, and it is discussed the potential role of this psyllid in the transmission of the pathogen to potato and tomato plants.
Séchage par atomisation des bactéries probiotiques : des mécanismes de protection à la production à l'échelle pilote

Les probiotiques sont des microorganismes vivants qui, ingeres en quantite suffisante, exercent des effets positifs sur la sante. La lyophilisation est aujourd’hui questionnee quant a sa consommation d’energie et son caractere discontinu. S’il offre une alternative pour produire massivement des poudres probiotiques a faible cout, le sechage par atomisation induit quant a lui des stress thermiques et oxydatifs conduisant a des pertes de viabilite redhibitoires.Dans ce travail, un procede innovant de sechage par atomisation est propose. Du lactoserum doux concentre (jusqu’a 30% p/p) est utilise a la fois comme support de culture et de sechage de P. freudenreichii et L. casei. Ce procede elimine les etapes intermediaires a risque de contamination eleve, accroit la biomasse et ameliore la viabilite des bacteriesLes mecanismes sous-jacents ont ete explores au plan de la resistance bacterienne et des conditions de sechage. Le milieu concentre induit une osmoadaptation des bacteries par expression de proteines de stress et accumulation de solutes compatibles, conduisant a une tolerance accrue des probiotiques a differents stress. La presence d’agregats et la concentration en Mg2+ du milieu concentre pourraient egalement etre impliquees.Le scale-up du procede a ete etudie : un schema technologique semi-industriel impliquant sechage par atomisation, sur bande et en lit fluidise a permis d’atteindre une viabilite de 100% (> 109 CFU g-1). Par ailleurs, la fonctionnalite des poudres probiotiques a ete evaluee in vitro and in vivo sur modele porcelet. Ce travail ouvre de nouvell
The effects of Hydroxypropyl-β-Cyclodextrin on the American Flagfish (Jordanella floridae) over one complete life-cycle

ii Acknowledgements . iii Index to Figures . vii Index to Tables . xi Index to Appendices . xii List of Abbreviations . xiii 1.0 Literature Review . 1 1.
Étude de la neuroinflammation suite à la lésion et la transplantation corticale

Les lesions du systeme nerveux central (SNC) entrainent une perte neuronale associee a des deficits fonctionnels importants. En reponse a une lesion, les capacites de repousse axonale et de regeneration spontanee des neurones du SNC sont limitees. Nous avons evalue, dans un modele de lesion corticale chez la souris adulte, le potentiel des greffes de neurones corticaux embryonnaires a reparer les voies corticales lesees. L'efficacite de cette approche therapeutique depend (1) du degre de survie des cellules greffees, (2) de la capacite des cellules greffees a se differencier en type neuronal approprie et (3) de la capacite des neurones greffes a restaurer les voies corticales endommagees de facon specifiques. Nous avons montre que les neurones embryonnaires corticaux d'origine du cortex moteur transplantes immediatement apres la lesion du cortex moteur adulte se differencient en neurones matures exprimant les memes neurotransmetteurs et marqueurs de couches corticales que ceux du cortex normal. De plus, les neurones transplantes developpent des projections vers les cibles corticales et sous corticales appropriees. Par ailleurs, nous avons etudie l'influence de la neuroinflammation post-lesionnelle sur la survie des neurones transplantes et, l'influence des neurones transplantes sur la neuroinflammation de l'hote.
Codon optimization of the prM-E coding region generates stable genome-length cDNA clone for a chimeric dengue 2/3 virus that can be propagated in Escherichia coli

Abstract In an effort to generate a chimeric dengue virus containing the prM-E sequence fromDENV-3 and with the rest of the viral genome derived from a DENV-2 strain 16681-3pm by in vitroligation of subgenomic fragments, it was found that the ligated chimeric genome could not be stablypropagated as genome-length cDNA clone in Escherichia coli. Native DENV-3 prM-E coding regionmay contain certain nucleotide sequence that results in plasmid instability when ampli fi ed in E. coli.In this study, we modi fi ed codons in the DENV-3 viral sequence into those that are most frequentlyused in human genome. Employing the Gibson assembly method, the modi fi ed prM-E fragmentwas introduced into the full-length cDNA clone of strain 16681-3pm to replace the correspondingsequence in a DENV-2 genome. The full-length plasmid cDNA clone intended for the generationof a chimeric virus, D3 prMEopt/16661-3pm, was successfully propagated in E. coli. In vitro transcription of this clone produced full-length RNA transcripts that generated infectious viruses whenintroduced into cultured mammalian cells. Based on kinetics experiments, the replication of D3prMEopt/16661-3pm with modi fi ed codons in the prM-E gene was comparable to the one generatedby the in vitro ligation approach. By combining the use of modi fi ed codons and the Gibson assemblymethod, a full-length cDNA clone of a chimeric virus containing the DENV-3 prM-E sequence canbe stably propagated in E. coli, facilitating further manipulation of the viral sequences. Availability ofsuch an infectious cDNA clone would provide a valuable tool for investigating the role of nucleotide/amino acid variations in the DENV-3 prM-E gene in viral replication, immunogenicity, and pathogenicity as well as accelerating dengue vaccine development.
Effect of Herbal Vitamin D3 on Reduced Levels of Phosphorous with Phytase Enzyme on Performance of Broiler Chicken

The present study was conducted to investigate the dietary effect of herbal vitamin D3 on reduced levels of phosphorous with phytase enzyme on performance of broiler chicken reducing phosphorous at graded level on performance, mineral retention, bone mineralization, carcass traits and biochemical parameter in commercial broilers. Four hundred twenty, day old commercial Vencobb 400Y broiler chicks were allotted to 21 replicate with 20 birds in each replicate. The birds were raised in deep litter system under uniform management and fed the respective diets. A corn-soybean meal based diet was prepared for starter and finisher broiler chicks to meet the nutritional requirements, as recommended by NRC (1994). Seven dietary
Germ line aging and regional epigenetic instability: age prediction using human sperm DNA methylation signatures

Background The relationship between aging and epigenetic profiles has been highlighted in many recent studies and models using somatic cell methylomes to predict age have been successfully constructed. However, gamete aging is quite distinct and as such age prediction using sperm is ineffective with current techniques. Results We have produced a model that utilizes human sperm DNA methylation signatures to predict chronological age by utilizing methylation array data from a total of 329 samples. The dataset used for model construction includes infertile patients, sperm donors, and individuals from the general population. Our model is capable of accurately predicting age with an r2 of 0.928 in our test data set. We additionally investigated the repeatability of prediction by processing the same sample on 6 different arrays and found very robust age prediction with an average standard deviation of only 0.877 years. Additionally, we found that smokers have approximately 5% increased age profiles compared to ‘never smokers. ’ Conclusions The aging calculator we have built offers the ability to assess “germ line age” by accessing genomic regions affected by age. Our data suggest that this model can predict an individual’s chronological age with a high degree of accuracy regardless of fertility status and with a high degree of repeatability. Additionally, our data appear to show age acceleration patterns as a result of smoking suggesting that the aging process in sperm may be impacted by environmental factors though this effect appears to be quite subtle.
Multimodal Machine Translation with Embedding Prediction

Multimodal machine translation is an attractive application of neural machine translation (NMT). It helps computers to deeply understand visual objects and their relations with natural languages. However, multimodal NMT systems suffer from a shortage of available training data, resulting in poor performance for translating rare words. In NMT, pretrained word embeddings have been shown to improve NMT of low-resource domains, and a search-based approach is proposed to address the rare word problem. In this study, we effectively combine these two approaches in the context of multimodal NMT and explore how we can take full advantage of pretrained word embeddings to better translate rare words. We report overall performance improvements of 1.24 METEOR and 2.49 BLEU and achieve an improvement of 7.67 F-score for rare word translation.
Ensaios biológicos in vitro e in vivo de novos compostos sintéticos sobre infecção por Trypanosoma cruzi

MASTER DISSERTATION IN BIOLOGIA CELULAR E MOLECULAR Julianna Siciliano de Araújo Among the protozoan parasites that cause human diseases, Trypanosoma cruzi stands out as the etiologic agent of Chagas' disease (CD), described in 1909 by Carlos Chagas. Drugs currently available for the treatment of this infection, benznidazole (BZ) and nifurtimox, show limited efficacy and are associated with serious adverse effects, highlighting the urgent need of developing new therapeutic options. In this context, our group has been working on different fronts in the investigation of agents with antiparasitic potential. In this study, a total of 35 compounds was established: 6-arylimidamides (AIAs) (DB1966, DB1967, DB1968, DB1979, DB1989 and DB1995), 9 mono-arylimidamides (DB1996, DB1997, DB1980, DB2001, DB2002, DB2003, DB2004, DB2006 and DB2007) and 20 phosphodiesterases inhibitors (VUF11848, VUF13522, VUF13526, VUF13527, VUF13536, VUF14256, VUF14656, VUF14703, VUF14767, VUF14768, VUF14852, VUF14907, VUF14975, VUFH1601, GBR11827, BS9538, IOTA0372, IGS1.1, IGS1. 18, IGS5.51), comparing to the data using BZ as reference drug. The results show that dicationic AIAs are significantly more active upon both bloodstream trypomastigotes and intracellular amastigotes compared to the monocationic ones, with nanomolar EC50 values (0.03 up to 1 μM). All bis-AIAs exhibited superior activity than BZ, especially DB1967 and DB1989 that, in vivo, were able to significantly reduce parasitemia levels in spite of not reaching protection against mortality comparable to BZ. For the PDE inhibitors, differential activity was observed depending on the evolutionary form assayed, with bloodstream trypomastigotes being less sensitive than intracellular forms. GBR11827 stands out for being the most active on bloodstream forms, for presenting the fastest action (6 h) and acting irreversibly. VUF13527 maintains similar profile of activity upon Y, Tulahuen and Colombian strains of T. cruzi (EC50 ranging 0.1 and 0.5 μM). The activity on axenic amastigotes and the previous treatment of the host cells with the compounds were also assessed and a potential modulating effect on the mammalian cell was discarded. Thus, this work contributes to the rational development of new molecules and even optimization of these molecules, aiming to identify new alternatives for CD treatment.
Biology and Management of the Buck Moth, Hemileuca maia (Lepidoptera: Saturniidae)

The genus Hemileuca Walker (Lepidoptera: Saturniidae) is widespread across North America, with about 20 species, including the buck moth, Hemileuca maia (Drury). This species is important as a periodic defoliator in oak forests of the eastern United States but is not considered to be destructive to forest resources. Buck moth populations are regulated naturally by environmental factors, particularly foliage quality, predators, parasitoids, and pathogens. The buck moth has become a species of conservation concern in northern states, where it is threatened by habitat loss, ﬁre suppression and other anthropogenic changes in habitat conditions, and perhaps by parasitoids introduced to control invasive Lepidoptera. In the South, the buck moth caterpillars attract attention because the urticating spines of its larvae cause painful stings that often require ﬁrst-aid advice. Although considered a nuisance in urban areas, this insect generally is not sufﬁciently abundant to warrant spe-ciﬁc control measures. If control is warranted, several biological and insecticidal options are available.
Investigation into pathological neuronal-myeloid cell interactions and rescue of hyper-reactive immune responses in Huntington's disease

The innate immune system is known to play a significant role in the pathogenesis of Huntington’s disease (HD). However, whether the myeloid cell activation and inflammation associated with neurodegeneration and disease progression in HD is protective or damaging remains to be clearly defined. Here, neuronal-myeloid cell interactions were examined in novel co-culture models of HD, with the aim of investigating the contribution of myeloid cells to neurotoxicity or neuroprotection in the pathogenesis of HD. HD and non-HD human NSC-derived neuronal cell lines expressing human huntingtin (HTT; full-length or exon 1) were developed and characterised. These cell lines can be differentiated into mature neuronal cultures, and HD neuronal cultures expressing mutant HTT exon 1 exhibit several characteristics of pathologically affected neurons in the HD patient brain. Additionally, a novel technique was discovered for the induced differentiation of primary blood monocyte cultures, from healthy volunteers or HD patients, into microglia-like cells (BMD-microglia). BMD-microglia are similar to human brain-resident microglia in vivo by both morphological and antigenic criteria. In co-culture, BMD-microglia rescued HD neurons from mutant HTT-induced neurotoxicity and reduced neuronal death. This was associated with elevated levels of brain-derived neurotrophic factor (BDNF) release and M2 polarisation shift. During chronic stimulation, HD patient BMD-microglia became more M2-polarised than healthy volunteer BMD-microglia and released BDNF at three-fold higher levels. In contrast, BMD-macrophages, differentiated from primary monocyte cultures from healthy volunteers or HD patients, were neurotoxic in co-culture with HD or non-HD neurons, and this was associated with increased release of the proinflammatory cytokines interleukin (IL)-1β, IL-6 and tumour necrosis factor (TNF)α. Inherent dysfunctional upregulation of cytokine release was also demonstrated in HD patient monocytes. Overall, the findings presented in this Thesis highlight myeloid cell phenotypes as an important modulator of neurotoxicity in HD, and harnessing the innate immune system in order to promote neuroprotective myeloid cell phenotypes whilst inhibiting neurotoxic phenotypes is an attractive therapeutic target. Laquinimod, a novel immunomodulatory drug which has been shown to have beneficial effects in multiple sclerosis patients, was shown here to dampen hyper-reactive cytokine production in HD patient monocytes. Modulation of peripheral immune responses has previously been demonstrated to impact on central pathology and disease progression in HD, and therefore laquinimod may be a promising candidate for dampening the harmful effects of a dysfunctional innate immune system in HD.
Resistance Exercise Elicits Selective Mobilization and Adhesion Characteristics of Granulocytes and Monocyte Subsets

Resistance exercise eliciting muscle damage results in an immune response, leading to increases in circulating cytokines, and immune cell mobilization. Classical monocytes respond to muscle damage, however, little is known about the intermediate or nonclassical monocyte response to resistance exercise. Moreover, the impact of polyphenol supplementation in conjunction with resistance exercise on the innate immune response is unknown. The purpose of this study was to examine the immune response following resistance exercise with (PPB) and without (PL) polyphenol supplementation. Thirty-nine untrained men were randomized into three groups: PPB (n=13, 21.8±2.5yrs, 171.2±5.5cm, 71.2±8.2kg), PL (n=15, 21.6±2.5yrs, 176.5±4.9cm, 84.0±15.7kg) or a control group (CON) (23.3±4.1yrs, 173.6±12.0cm, 77.8±15.6kg). Blood samples were obtained pre(PRE), immediately(IP), 1(1H), 5(5H), 24(24H), 48(48H) and 96(96H) hours postexercise (PPB/PL). CON rested for one hour between PRE and IP blood draws. Changes in granulocyte and monocyte subset proportions and adhesion characteristics (CD11b) were assessed via flow cytometry, while plasma cytokine concentrations and markers of muscle damage were analyzed via multiplex and spectrophotometric assays, respectively. Creatine Kinase and myoglobin were elevated at each time point for PPB and PL (p < 0.050). Monocyte chemoattractant protein-1 was significantly elevated at IP in PPB (p = 0.005) and PL (p = 0.006) and significantly greater than CON at 5H (PPB: p < 0.001; PL: p = 0.006). Granulocyte proportions were elevated at 1H (p < 0.001), 5H (p < 0.001) and 24H (p = 0.005; p = 0.006) in PPB and PL, respectively. Classical monocyte proportions were lower in PPB (p = 0.008) and PL (p = 0.003) than CON at IP, and significantly greater
Effect of time of day on foot performance

Abstract This study has been designed to assess the effects of time of day on foot performance in trained and untrained subjects. Two groups of 26 right-footed subjects each: a group of soccer players and a group of sedentary people participated in this study. Subjects had to actually perform three tests: kicking accuracy, dribbling, and a tapping task. The tests were accomplished with the right and the left foot at different hours of the day (07:00 h, 14:00 h, and 18:00 h). First, our results have shown that foot performance was significantly better in the afternoon (14:00 h) than in the evening (18:00 h) in all groups. We have found a better performance in trained compared to the untrained subjects for the right and the left foot in dribbling and tapping task. In conclusion, this study demonstrates that foot performance change during the day.
The Multiple Sclerosis Genomic Map: Role of peripheral immune cells and resident microglia in susceptibility

We assembled and analyzed genetic data of 47,351 multiple sclerosis (MS) subjects and 68,284 control subjects and establish a reference map of the genetic architecture of MS that includes 200 autosomal susceptibility variants outside the major histocompatibility complex (MHC), one chromosome X variant, and 32 independent associations within the extended MHC. We used an ensemble of methods to prioritize up to 551 potentially associated MS susceptibility genes, that implicate multiple innate and adaptive pathways distributed across the cellular components of the immune system. Using expression profiles from purified human microglia, we do find enrichment for MS genes in these brain - resident immune cells. Thus, while MS is most likely initially triggered by perturbation of peripheral immune responses the functional responses of microglia and other brain cells are also altered and may have a role in targeting an autoimmune process to the central nervous system. One Sentence Summary: We report a detailed genetic and genomic map of multiple sclerosis, and describe the role of putatively affected genes in the peripheral immune system and brain resident microglia.
Identifying Genetic Factors Influencing Sperm Mobility Phenotype in Chicken using Genome Wide Association Studies, Primordial Germ Cell Transplantation, and RNAseq.

Sperm mobility is a major determinant of male fertility in chicken. In spite of low heritability of reproductive traits, sperm mobility has high heritability index which suggests presence of quantitative trait loci (QTLs) governing the trait. Our research focused on three objectives: i) to identify the QTLs affecting low mobility phenotype in chicken, ii) to understand the impact of Sertoli-cells and germ cells interactions in influencing the mobility phenotype and iii) to identify the genes and gene networks differentially expressed in male and female PGCs. To detect the QTLs, genome wide association studies (GWAS) was conducted which revealed the presence of multiple minor alleles influencing the trait and indicated the role of epistasis. The second section of research involved isolation, culture and transfer of primordial germ cells (PGCs) to create high line germ line chimera chicken carrying low line PGCs. We established the culture of chicken PGCs isolated from the embryonic blood in a feeder free culture conditions but could not detect the presence of low line genotype in the semen of transgenic males. Our final study involved RNA-sequencing (RNAseq) of male and female PGCs to identify differentially expressed genes from their transcriptomes. We identified five candidate genes: 3-hydroxy-3methylglutaryl CoA reductase (HMGCA), germ cell-less (GCL), SWIM (zinc finger SWIM domain containing transcription factor), SLC1A1 (solute carrier family 1 member 1), UBE2R2L (ubiquitin conjugating enzyme) and validated their expression level in male and female PGCs by RT-qPCR. GCL was exclusively expressed in males while SLC1A1 & UBE2R2L were expressed only in female cPGCs. This present study provides novel gender specific germ cell markers in the broiler chicken. These results will help in elucidating the genetic programming of gender specific germ line development in broilers. ©2017 by Sohita Ojha All Rights Reserved