Miracle-dz/UniFAR-FTUs huggingface dataset:
Breeding density and nest-site selection of urban population of the fieldfare Turdus pilaris in Rzeszow (SE Poland)

Abstract Numerous studies have investigated the nest-site characteristics and selection of bird species, because these features often play a determining role in bird breeding success. In recent years researchers focused on urban environments as a source of novel conditions which provide breeding opportunities for species that are able to survive in human-altered environments. Although thrushes Turdus spp. are among the species which frequently inhabit urban areas, the fieldfare Turdus pilaris only recently has started to colonize human settlements and reports on populations in urban ecosystem are rare. The aim of our study was to investigate the fieldfare density and nest-site selection in urban parks of Rzeszow, Poland. We found that the average density of breeding pairs in study area was 2.92 pair/ha. Fieldfares nested entirely on deciduous trees, despite the presence of numerous coniferous trees in parks. They built their nests mostly on those tree species which were the most abundant in particular study plot, which indicates that the studied urban population of the fieldfare is rather opportunistic in the selection of a nest-tree species. Also nest-tree surroundings consisted of the trees that dominated in the parks. The results of our study suggest that the fieldfare is among the species that synurbize easily and may reach even higher breeding densities in towns than in natural habitats.
Investigation of Novel Progression-related Methylation Events and HOXD Genes in Prostate Cancer

Aberrant DNA methylation in gene promoters causes gene silencing and is a common event in prostate cancer development and progression. While commonly identified methylated genes have been analyzed for their potential clinical utility in a variety of cancers, few studies have attempted a genome-wide methylation approach to discover new and possibly improved biomarkers for prostate cancer. In order to identify DNA methylation changes associated with aggressive prostate cancer, we performed a genome-wide analysis of 40 prostate cancers using Agilent human CpG island microarrays. Methylation profiles of candidate genes were validated using quantitative MethyLight technology in an independent series of 219 radical prostatectomies and compared to clinicopathological parameters. The effects of methylation on expression of HOXD3 and HOXD8 and the possible role of HOXD8 in progression of PCa were also investigated.
Transfer of Wautersia numazuensis to Cupriavidus genus as Cupriavidus numazuensis comb. nov.

Abstract The phylogenetic analysis of the 16S rRNA gene sequence from strain TE26T and K6 belonging to Wautersia numazuensis (Kageyama et al., 2005a) was found deeply intermingled among the species of the genus Cupriavidus. The comparison showed that strain TE26T was closely related to C. pinatubonensis (99.1%), C. basilensis (98.7%), C. necator (98.7%) and C. gilardii (98.0%). However, DNA-DNA hybridization experiments (lower than 20%) demonstrated that strain TE26T is different from those Cupriavidus species. A comparative phenotypic and chemotaxonomic analysis (based on fatty acid profiles) in combination with the 16S rRNA phylogenetic analysis and the DNA-DNA hybridization results supports the incorporation of Wautersia numazuensis into the genus Cupriavidus. The proposal of this study includes the transfer of Wautersia numazuensis to Cupriavidus numazuensis comb. nov. The type strain is TE26T = LMG 26411T = DSM 15562T = CIP 108892T.
Simultaneous Production of Xylitol and Ethanol from Different Hemicellulose Waste Substrates by Candida tropicalis Strain Ly15

In the present study, we optimized the parameters for maximum yield of xylitol and ethanol by Candida tropicalis strain LY15 utilizing different Hemicellulosic Waste substrates (HWs) obtained by Acid-Alkaline hydrolysis method. Using the pomegranate peel as substrate, higher yield of xylose reductase, xylitol and ethanol were obtained. The optimal level of variables such as inoculum, HWs concentration, time period and RPM (agitation speed) were determined by the response surface methodology, with a significant co-efficient determination of R2= 0.89. Positive correlation was obtained with our experimental and predicted values. The interactions with the ideal levels of inoculum (1%), HWs (Pomegranate peel) (2%), time period (60 h) and RPM (140) showed highly significance values of xylose reductase (171.5 IU/mL), xylitol (55.57 g l-1) and ethanol (3.37 g l-1) at an incubation period of 60 h. The dual yield produced by Candida tropicalis strain LY15 using pomegranate peel makes the organism potent candidate for industrial application.
Evaluation of Cyanide Levels in Two Cassava Varieties ( Mariwa and Nyakatanegi ) Grown in Bar-agulu, Siaya County, Kenya

Mannihot esculenta Crantz (Cassava) is the second highest producer of carbohydrates after sugarcane. However, some varieties have high levels of cyanogenic glycosides and therefore are potentially toxic for human consumption. Nyakatanegi is one of the local varieties cultivated in Bar-agulu village in Siaya County (Kenya) and has been severally in the recent past reported to cause fatal cyanide toxicity. The other variety which is rarely associated with cassava poisoning is Mariwa. The objective of the current study was to determine cyanide levels in the two cassava varieties (Mariwa and Nyakatanegi) which are locally cultivated in Siaya County. The study was based on three laboratory assays: the picrate paper, picrate in solution and titration. Whole root cassava tubers were collected from a farmer in Bar-agulu village, Siaya County, packaged separately and transported to Mount Kenya University Pharmaceutical Chemistry Laboratory for analysis. Voucher specimens were authenticated in the cassava laboratories at Jomo Kenyatta University of Agriculture and Technology. It was observed that all the cortex samples of Nyakatanegi variety had the highest concentrations of cyanide giving 400 ppm for the picrate paper assay, 14.10 mg/Kg for the picrate in solution and 63 mg/Kg for the titration assays. On the other hand, the cortex samples of Mariwa reported cyanide concentrations of 30 ppm, 11.20 mg/Kg and 27.20 mg/Kg for the picrate paper, picrate in solution and titration assays respectively. The results showed higher amounts of cyanide in the tested cassava varieties than the WHO recommended levels (10 mg/Kg) especially the Nyakatanegi variety. Based on these results, sensitization campaigns are necessary to minimize cases of cyanide poisoning following cassava consumption.
NKT cell-mediated enhancement of humoral immunity against Clostridium difficile toxin B (IRC10P.406)

To develop more effective antibody-stimulating vaccines, we must improve our understanding of the mechanisms by which vaccines induce and maintain long-lasting humoral immunity. This is important for the development of new vaccines against emerging pathogens such as C. difficile. It is well-established that Natural Killer T (NKT) cells, activated with the glycolipid, α-galactosylceramide (α-GC) enhance humoral immunity, but the mechanisms by which they do so are poorly understood. Here we show that activated NKT cells enhance the antigen-specific IgG1 response and survival against C. difficile Toxin B (TcdB). We and others have shown that NKT cells may enhance priming of T helper (Th) cells. We therefore hypothesized that T helper and NKT subsets coordinate to enhance the humoral immune response against C. difficile. Flow cytometry analysis demonstrated that NKT cell activation with a-GC did not alter numbers of Th or follicular T helper (Tfh) cells, but increased the number of NKTfh cells. ELISPOT assays indicated that the α-GC enhanced secretion of IL-4 and IL-21 is mainly Th-derived. Adoptive transfer experiments show that α-GC did not alter the ability of Th cells to boost antibody production. This suggests that NKT cells may exert direct and indirect effects (via Th cells) on humoral immunity. Understanding the mechanisms by which NKT cells enhance humoral immunity will help in designing strategies to appropriately activate NKT cells and boost vaccine efficacy.
Environmentally sustainable pest control options for Drosophila suzukii

The spotted‐wing drosophila or cherry vinegar fly (Drosophila suzukii) is native to Asia but has invaded other continents since 2008 and has spread throughout Europe. The females have a serrated ovipositor allowing them to penetrate the skins of intact ripening fruits to deposit their eggs, and the developing larvae rapidly destroy the fruits close to harvest. Drosophila suzukii has a rapid life cycle and the larvae develop well beneath the fruit surface. This means that the use of pesticides is problematic and often not effective, first due to their restricted use close to harvest to protect consumers, and second because the larvae are deep enough inside the fruit to avoid contact. There are currently no effective and environmentally sustainable pest control methods for this species, resulting in extensive damage to fruit crops. Here, we review the current status of D. suzukii as a fruit crop pest and discuss the feasibility of current pesticide‐free control methods. We also consider the potential of new technologies as a basis for the urgently needed specific and long‐term control of this species.
Functional analysis of nucleoside diphosphate kinase from Mycobacterium avium subspecies paratuberculosis

Functional analysis of nucleoside diphosphate kinase from Mycobacterium avium subspecies paratuberculosis Ziad Marroushi Advisor: University of Guelph, 2017 Dr. Lucy Mutharia Mycobacterium avium subspecies paratuberculosis (Map), the causative agent of Johne’s disease, is an intracellular pathogen capable of surviving and replicating within macrophages for extended periods with minimal activation of the innate immune response. Mycobacterial secreted protein, nucleoside diphosphate kinase (Ndk), altered signalling pathways for macrophage activation, subverting host innate immune responses, disrupting maturation of membrane-bound phagosomes, and enabling the intracellular survival of mycobacteria within macrophages. Rab small GTPase proteins play a major role in phagosome maturation, facilitating the transition from early phagosomes to phagolysosomes, where bacteria are degraded. Nucleoside diphosphate kinase (Ndk) from Mycobacterium tuberculosis inactivated Rab proteins, leading to evasion of innate immunity by interfering with phagosome maturation. Ndk is also a housekeeping enzyme, important in the maintenance of nucleoside triphosphate (NTP) pools, with histidine at position 117 (H117) involved in autophosphorylation and phosphotransfer activity, and synthesis of NTPs. In my thesis research, I have cloned and expressed putative recombinant Map Ndk (Map rNdk) in E. coli and generated anti-Ndk polyclonal antibodies in rats. Native Map Ndk was detected by immunoprecipitation using anti-Ndk antibodies. The interaction of Map rNdk with bovine macrophage proteins involved in phagosome maturation (Rab5 and Rab7) and other Map proteins, as well as its immunogenicity during natural infection were examined. In contrast to studies with M. tuberculosis, no interactions were observed between Map rNdk and Rab5 or Rab7. Map rNdk-H117 catalytic mutants were constructed and
Mixed patterns of morphological adaptation to insularity in an aerial displaying bird, the Common Snipe Gallinago gallinago

On islands, colonizing birds may evolve behavioural and morphological adaptations to the new environment, often resulting in changes in body size and reduction or even total loss of flight. These island populations have therefore been used to test hypotheses related to adaptations for flight. However, in certain species in which flight is used not only in foraging and migration but also in mating displays, disentangling the effects of natural and social selection is difficult. Thus, sedentary populations of species that perform aerial displays (such as the Common Snipe Gallinago gallinago that breed in the Azores archipelago) may offer an opportunity to separate the effects of natural and social selection on morphology. If insular Common Snipe respond to the characteristic ecological context of oceanic islands, we expect them to differ from migratory conspecifics in body size and by having relatively smaller and more rounded wings. On the other hand, if social selection exerts a more powerful force over the morphology of this species, we expect that sedentary and migratory birds will not differ in flight‐related characters. We tested these hypotheses by comparing morphological characters measured on live Common Snipe captured in the Azores during the breeding season with those measured on migratory specimens hunted during autumn/winter in mainland Portugal. Sedentary Azorean birds were smaller and had relatively shorter tails but did not show the tendency for insular birds to possess more rounded wings as described in other taxa, including in the Azores. Bergman's rule might explain the difference in body size and shorter tails may be responsible for behavioural differences between populations. The lack of difference in wing shape might be explained by the need of the Common Snipe to perform aerial displays during courtship, suggesting an effect of social selection on the migratory strategy of this species.
Tissue Distribution and Properties of Glutathione S-transferases in Micromelalopha troglodyta (Lepidoptera: Notodontidae)

The small prominent, Micromelalopha troglodyta (Graeser) (Lepidoptera: Notodontidae), is an important pest of poplar in China. Glutathione S-transferases are known to be responsible for adaptation mechanisms of M. troglodyta. Thus, the tissue distribution and kinetic constants of glutathione S-transferase activity in the small prominent were studied. Significant differences in glutathione S-transferase (GST) activity and distribution percentages of GST activity and kinetic characteristics were observed among 4 tissues (head, midgut, fat body and integument). Furthermore, the inhibition of glutathione S-transferase activity in 4 tissues by 21 inhibitors was conducted. The results showed the inhibition of GST activity of different tissues by 21 inhibitors is different. For GST activity in heads, chlorpyrifos, profenofos, lambda-cyhalothrin, fipronil and quercetin were the best inhibitors tested. Tannic acid was the most potent inhibitor of midgut GST activity. In the fat body, GST activity was inhibited mos.
Identifizierung Hämolyse-assoziierter Faktoren des Lungenpathogens Legionella pneumophila und Charakterisierung der Patatin-ähnlichen Phospholipase A PatA

Legionella pneumophila, der Erreger einer schwer verlaufenden Pneumonie, der Legionarskrankheit, besitzt neben bekannten Virulenzfaktoren wie z. B. einem Typ IVB-Sekretionssystem sowie dessen sekretierten Effektoren, eine Vielzahl potentiell zytolytisch wirkender Proteine (Proteasen, Lipasen und Hamolysine), die zur Pathogenitat des Bakteriums und damit zur intrazellularen Vermehrung in Amoben und humanen Alveolarmakrophagen beitragen konnen. Zur Detektion zytolytischer Faktoren wurde ein Agarplatten-basiertes Screening-System angewandt, durch das 26 Gene identifiziert wurden, die vor allem das hamolytische Potential von L. pneumophila beeinflussten. Neben dem Gen fur das L. pneumophila Hitzeschockprotein 33 (Hsp33) wurden zwei Gene, aroC und pabB, die fur Enzyme des Shikimatweges bzw. der Folatbiosynthese codieren, als Hamolyse-assoziierte Faktoren identifiziert. Die aroC-Mutante war in ihrer Fahigkeit zur Pigmentbildung stark vermindert, wahrend die pabB-Mutante einen intrazellularen Vermehrungsdefekt in Acanthamoeba castellanii aufwies. Fur PatA, eine Patatin-ahnliche Phospholipase A von L. pneumophila, die uber das Dot/Icm Typ IVB-Sekretionssystem in die Wirtszelle injiziert wird und hamolytische Eigenschaften besitzt, wurde sowohl Phospholipase A- als auch Lysophospholipase A-Aktivitat gegenuber verschiedenen Phospholipidsubstraten inklusive Cardiolipin nachgewiesen. Fur diese lipolytischen Aktivitaten war das in ein G-X-S-X-G-Lipasemotiv eingebettete Serin 72 als Bestandteil einer katalytischen Diade mit Aspartat 288 essentiell. Nach Expression in humanen A549 Lungenepithelzellen lokalisierte PatA an der Zytoplasmamembran der Wirtszelle, wofur der C-terminale Proteinbereich verantwortlich war. Die Deletion zweier C-terminaler Proteinregionen, einer low complexity-Region zwischen den Aminosauren E519 bis E527 und einer putativen Transmembran-Domane im Bereich der Aminosauren K533 bis D555, fuhrte zum vollstandigen Verlust der Zytoplasmamembranlokalisation.
A Substrate for Stem Cell Culture and Differentiation

: Skin is the largest organ in vertebrates that is of great importance and performs as a protective barrier against the external world. It serves various functions such as protecting against external insults, fluid homeostasis, self-healing, and sensory detection. Skin disorders impose major financial and social burden. Therefore, the regeneration potential of the skin is an important area of research in tissue engineering (TE). This potential is due to the stem cells; they play a vital role in the skin regeneration process, since one of the main characteristics of the stem cells is their ability to differentiate into the organ specific specialized cells. Numerous factors such as growth factors, topography, etc. are involved in stem cell differentiation. In the current study, primary human keratinocytes were isolated from the foreskin samples and cultured. Then, the substrate was developed using PDMS (polydimethylsiloxane) silicon following keratinocyte fixation. This substrate can be used in further stem cell culture and differentiation studies.
Ammonium transporter genes in Chlamydomonas: the nitrate-specific regulatory gene Nit2 is involved in Amt1;1 expression

Ammonium transport is a key process in nitrogen metabolism. In the green alga Chlamydomonas, we have characterized molecularly the largest family of ammonium transporters (AMT1) so far described consisting of eight members. CrAmt1 genes have an interesting transcript structure with some very small exons. Differential expression patterns were found for each CrAmt1 gene in response to the nitrogen source by using Real Time PCR. These expression patterns were similar under high and low CO2 atmosphere. CrAmt1;1 expression was characterized in detail. It was repressed in both ammonium and nitrate medium, and strongly expressed in nitrogen-free media. Treatment with a Glutamine synthetase inhibitor released partially repression in ammonium and nitrate suggesting that ammonium and its derivatives participate in the observed repressing effects. By studying CrAmt1;1 expression in mutants deficient at different steps of the nitrate assimilation pathway, it has been shown that nitrate has a double negative effect on this gene expression; one related to its reduction to ammonium, and a second one by itself. This second effect of nitrate was dependent on the functionality of the regulatory gene Nit2, specific for nitrate assimilation. Thus, NIT2 would have a dual role on gene expression: the well-known positive one on nitrate assimilation and a novel negative one on Amt1;1 regulation.
Évolution de la virulence et infections multiples

Au sein des populations naturelles d'etres vivants circulent une diversite de parasites, qu'il s'agisse de plusieurs especes, souches ou plus generalement types. Si certains modeles d'epidemiologie evolutive integrent deja le polymorphisme des parasites, rares sont ceux pour lesquels la dynamique epidemiologique depend de la croissance intra-hote et des interactions que les parasites entretiennent lorsqu’ils infectent le meme hote. Les complexite combinatoire et dynamique explique pourquoi il n'y a pour l'heure pas de prediction generale de l'evolution de la virulence dans de tels contextes d'infections multiples. A la recherche d'une tendance generale d'evolution de la virulence, nous modelisons chaque niveau de dynamique sur lequel l'evolution des parasites repose. En particulier, nous etudions explicitement les interactions et l'issue de la competition au sein des hotes, les dynamiques epidemiologique et enfin adaptative. Sur l'exemple des infections chroniques causees par des micro-parasites transmis horizontalement, nous employons les approches propres aux systemes dynamiques et aux probabilites pour emboiter cette suite de dynamiques afin d'en explorer les consequences evolutives. Nous definissions notamment le concept de patron d'infection, a savoir l'ensemble des issues intra-hote associees a chaque configuration d'inoculation et decrivons cinq patrons jusqu'ici non decrits, lesquels echappent a la dichotomie classique entre super- et coinfection. Cette typologie nous permet par la suite d'envisager l'evolution de la virulence dans un cadre general. Nous observons en particulier une ineluctable mais bornee croissance evolutive de la virulence.
Industrial milk powder in bioassays for evaluation of cytotoxicity and genotoxicity

Considering the widespread consumption of milk powder by the general population as well as the lack of studies on the toxicity of such industrialized foods, this study evaluated the cytotoxic and genotoxic potential of powdered milk from four reputed companies in the food market of Brazil and other South American countries. Milk samples were evaluated in root meristem cells of Allium cepa L. , at concentrations of 0.065 and 0.13 g/mL, for 24 and 48 hours of exposure; and by means of cell viability in culture of cells of normal lineage, via MTT test, for 24 hours, at concentrations of 0.016; 0.032; 0.065 and 0.13g/mL. The concentration 0.13 g/mL was the one suggested for consumption in all milk packages evaluated in this study. In A. cepa, we observed that the milks, at both concentrations and at the two exposure times investigated, reduced the cellular proliferation of root meristems demonstrating a significant cytotoxicity. Furthermore, 0.13g/mL milks at the exposure time of 24h induced an expressive frequency of cellular alterations in the plant tissue, showing to be genotoxic. In the in vitro evaluation, three milks at 0.065 g/mL and all milks at 0.13 g/mL have significantly reduced cell viability, proving to be cytotoxic to the analyzed cell culture. Therefore, under the studied conditions, the powdered milks evaluated caused significant genetic instability to the cells of the test systems used.
Jaundice and photosensitization in indigenous sheep of Malaysia grazing on Brachiaria decumbens

Observations on twelve indigenous sheep grazed on pasture of Brachiaria decumbens in MARDI, Serdang was carried out. Within 44 days of grazing five animals died, all showing signs of jaundice and photoserisitization. All twelve animals showed significant reduction in body weight. There was also marked increase in SGOT (serum glutamate oxaloacetate transaminase) and total bilirubin with values ranging from 330-1891 U/I and 5.47-13.06 mg/100 ml respectively. Changes in haematological pictures (RBC, PCV, Hb and WBC) and plasma protein were also observed. On necropsy all five carcasses showed ulceration on the skin particularly around the eyelids, muzzle, both upper and lower lips, tips of ear and the vulva. They also showed varying degrees of jaundice. The liver was consistently slightly enlarged, firmer than normal and had pale mottling. Histopathology indicated centrilobular necrosis of the liver thus indicating that the jaundice was due to toxic damage. It was concluded that a Brachiaria or Brachiaria associated was the aetiological agent