Miracle-dz/UniFAR-FTUs huggingface dataset:
Cross-population analysis of high-grade serous ovarian cancer reveals only two robust subtypes

Background Four gene expression-based subtypes of high-grade serous ovarian cancer (HGSC), variably associated with differential survival, have been previously described. However, in these studies, clustering heuristics were consistent with only three subtypes and reproducibility of the subtypes across populations and assay platforms has not been formally assessed. Therefore, we systematically determined the concordance of transcriptomic HGSC subtypes across populations. Methods We used a unified bioinformatics pipeline to independently cluster (k = 3 and k = 4) five mRNA expression datasets with >130 tumors using k-means and non-negative matrix factorization (NMF) without removing hard-to-classify samples. Within each population, we summarized differential expression patterns for each cluster as moderated t statistic vectors using Significance Analysis of Microarrays. We calculated Pearsons correlations of these vectors to determine similarities and differences in expression patterns between clusters. We identified sets of clusters that were most correlated across populations to define syn-clusters (SC), and we associated SC expression patterns with biological pathways using geneset overrepresentation analyses. Results Across populations, for k = 3, moderated t score correlations for clusters 1, 2 and 3 ranged between 0.77-0.85, 0.80-0.90, and 0.65-0.77, respectively. For k = 4, correlations for clusters 1-4 were 0.77-0.85, 0.83-0.89, 0.51-0.76, and 0.61-0.75, respectively. Within populations, comparing analogous clusters (k = 3 versus k = 4), correlations were high for clusters 1 and 2 (0.91-1.00), but lower for cluster 3 (0.22-0.80). Results were similar using NMF. SC1 corresponds to mesenchymal-like, SC2 to proliferative-like, SC3 to immunoreactive-like, and SC4 to differentiated-like subtypes reported previously. Conclusions While previous single-population studies reported four HGSC subtypes, our cross-population comparison finds strong evidence for only two subtypes and our re-analysis of previous data suggests that results favoring four subtypes may have been driven, at least in part, by the inclusion of samples with low malignant potential. Because the mesenchymal-like and proliferative-like subtypes are highly consistent across populations, they likely reflect intrinsic biological subtypes and are strong candidates for targeted therapies. The other two previously described subtypes (immunoreactive-like and differentiated-like) are considerably less consistent and may represent either a single subtype or signal that is not amenable to clustering.
Population Genetics of the Homomorphic Self-incompatibility Polymorphisms in Flowering Plants

This paper surveys the results obtained from the investigation of the homomorphic self-incompatibility polymorphisms in 19 species of flowering plants in terms of the number and frequency of alleles in their populations, the distribution of alleles between these populations and the total number of alleles in the species, and assesses the extent to which these results conform with theoretical expectations. The survey shows that, contrary to theory, the populations of most species do not contain a very large number of alleles and the same appears to be true for the total number of alleles in the species. Populations of Trifolium repens and T. pratense, however, appear to possess a large number of alleles for reasons which are unknown. Data on the distribution of alleles range from complete overlap to considerable differentiation between populations in respect of the complement of alleles they contain. The frequencies of alleles in populations of most species with gametophytic systems of self-incompatibility appear to be equal, as the theory suggests; frequencies in populations of Papaver rhoeas and Lolium perenne, however, appear to be significantly unequal. Allele frequencies in populations of sporophytic species are, as expected, unequal, those of dominant alleles being lower than those of recessive alleles. The implications of these results are discussed and the need for further, more comprehensive information on the attributes of these polymorphisms in natural populations is stressed.
Adenovirus vector systems permitting regulated protein expression and their use for in vivo splicing studies

We have constructed two adenovirus-based gene expression vector systems permitting regulated protein expression. They are based on the tetracycline-regulated Tet-ON- and the progesterone antagonist RU 486-regulated gene expression systems, which were rescued into E1-deficient adenovirus vectors. The vectors function in a number of cell types representing a broad species-variety and the regulation of protein expression was shown to be tightly controlled in cells not permissive for virus replication. Furthermore, the adenovirus-Tet-ON system was shown to perform in mice after intramuscular administration.The novel adenovirus-vector systems were then used to study the effects of overexpression of selected proteins on adenovirus replication during a lytic infection, with focus on regulation of adenovirus alternative splicing. Expression of adenovirus transcription units is to a large extent temporally regulated at the level of alternative pre-mRNA splicing, where viral splice site usage shifts from proximal to distal splice site selection as infection proceeds. This makes adenovirus an appropriate model for mechanistic studies of regulated splicing. We show that overexpression of the essential host cell splicing factor ASF/SF2 inhibits this shift by promoting usage of proximal splice sites. As a consequence, the virus displayed a markedly inhibited growth. Interestingly, mRNA expression from the adenovirus major late promoter was almost completely lost as a consequence of ASF/SF2 overexpression. Collectively, the cellular splicing factor ASF/SF2 prevents adenovirus from entering the late phase of infection. This strongly argues for a need for the virus to block the splicing enhancer activity of ASF/SF2 for establishment of a lytic infection. Further, from analysis of the strict inhibition of late region 1 late pre-mRNA splicing we propose that the temporal regulation of alternative splicing is merely a consequence of fitness rather than profoundly deleterious effects of an unregulated expression. During our studies we noted that in 293 cells, which are used for growth of E1-deficient Ad vectors, an unwanted background reporter gene expression was evident in our vector systems. We therefore introduced an additional regulatory element, functioning as a transcriptional road-block, and showed that this methodological innovation represents a way to overcome the potentially deleterious effects of background reporter gene expression. This modified viral vector system should make it possible to reconstruct recombinant viruses expressing highly toxic proteins.In conclusion, this work presents a new in vivo model system to study proteins involved in RNA splicing and other gene regulatory mechanisms.
Detection of swarming and biofilm formation ability of Salmonella typhimurium isolated from landfills waste

Two hundred and twenty four soil samples has been collected from landfills waste and examined for the presence of Salmonella typhimurium. The results showed that 109 (45.41%) isolates belonged to Salmonella according to conventional biochemical test. PCR technique using InvA gene confirmed identification of 41(37.6%) isolates as S. typhimurium. The ability of S. typhimurium for motility and biofilm formation was investigated. The results estimated that out of 41 isolates only 32(48%) isolates showed swarming motility on BHI medium with 0.8% agar whereas only 32(78%) isolates have the ability of biofilm formation on polystyrene ( micro-titer plate assay) and 23(56%) isolates in the air liquid interface (pellicle formation). A significance differences has been found between pellicle formation and time resuming (t-test, ˂0.05) as well as a significance correlation has been found between biofilm formation and swarming motility (r12Bivariat,˂0.01).
Isolation and characterization of microsatellite markers for the seagrass Cymodocea nodosa

In order to study the spatial patterns of genetic diversity of a clonal marine angiosperm, the seagrass Cymodocea nodosa, microsatellite markers were obtained by screening a genomic library enriched for the (CT) dinucleotide motif. Of 38 primer pairs defined, 15 amplified polymorphic microsatellites and are described. These loci identified a number of alleles ranging from two to seven, and showed expected heterozygosity ranging from 0.35 to 0.76, when a group of 40 individuals from Cadiz Bay in Spain was analysed. Additionally, we describe here the multiplexing conditions for 12 of these loci.
Antifungal and antioxidant activity of Mentha longifolia (L.) Hudson (Lamiaceae) essential oil

Th e present study describes the antifungal and antioxidant activity of Mentha longifolia (L.) Hudson essential oil. Th is plant is native to Europe, Central Asia and Australia. It is used as carminative, stomachic and stimulant and also in aromatherapy. Th e essential oil profi le was determined by GC and GC-MS. Th e main compounds in the oil were trans-dihydrocarvone (23.64%), piperitone (17.33%) and cis-dihydrocarvone (15.68%). Minimum inhibitory concentrations (MIC) and minimum fungicidal concentrations (MFC) were recorded using the microdilution method. Commercial antimicotic bifonazol was used as a control. Th e concentration of 10 μl/ml showed fungicidal activity against Aspergillus and Fusarium species, Penicillium funiculosum and Trichoderma viride. Concentration of 5 μl/ml was effi cient against Trichophyton menthagrophytes and yeast Candida albicans. Th e most sensitive micromycetes were Cladosporium fulvum, C. cladosporium cladosporioides and Penicillium ochrochloron where concentration of 2.5 μl/ml was lethal. Th e antioxidant activity of essential oil was evaluated by means of the 2,2-diphenyl-1-picrylhydrazil (DPPH) radical scavenging method. Th e essential oil of M. longifolia was able to reduce DPPH radicals into the DPPH-H form, and this activity was dose-dependent. Th e oil exhibited signifi cant potential for antioxidant activity, and reduced DPPH to 50% (IC 50 =0,659 ml/ml of solution).
Characterisation of KCNQ expression and functional impact in the cerebral vasculature

Total RNA was extracted from SD rat and BALB/c mouse basilar arteries (rBA / mBA) and rat middle cerebral arteries (MCA) using the RNeasy mini spin columns (Qiagen, UK) and following DNase I treatment was reverse-transcribed to cDNA using M-MLV (Invitrogen, UK). KCNQ gene expression products were detected using primers specific for the 5 different isoforms. RNA derived from mouse heart and brain was used as positive controls. Isometric tension experiments were performed using segments of rat basilar artery mounted on a wire myograph and bathed in Krebs’ solution aerated with 95%O2 / 5 % CO2 at 37oC. KCNQ1 and KCNQ4 were expressed in the basilar arteries and MCA at sufficiently high levels to be detected easily after 35 PCR cycles (n=3 each). Nested PCR was employed to explore the expression of the isoforms further. Whilst this technique revealed some KCNQ2 to be present KCNQ3 and KCNQ5 were not detected. Appropriate amplicons were detected in the brain and heart samples. In the functional studies, the selective Kv7 channel blocker XE991 (10 μM) contracted rBA from baseline tension to 4.93 ± 0.69 mN in 14 of 15 preparations from 8 animals. This equated to 103 ± 31 % of the contraction produced by 60 mM KCl. The Kv7 channel activator flupirtine (1 and 10 μM) relaxed contractions produced by 1 μM 5HT with a mean relaxation of 72 ± 10 % (n=7 from 4 animals) at 10 μM. These were reversed completely by 10 μM XE991. These studies show that cerebral arteries express KCNQ1 and KCNQ4 prominently and modulation of the ion channels alters markedly cerebral artery basal or 5-HT-induced tone. As flupirtine does not activate Kv7.1 channels these data combined suggest that ion channels encoded by KCNQ4 are important determinants of cerebral blood flow.
Inheritance of Resistance to the Watermelon Strain of Papaya Ringspot Virus in the Cucumber Line TMG-1

The inbred cucumber (Cucumis sativus L.) line TMG-1 is resistant to three potyviruses: zucchini yellow mosaic virus (ZYMV), watermelon mosaic virus (WMV), and the watermelon strain of papaya ringspot virus (PRSV-W). In this study we sought to determine the genetics of resistance to PRSV-W. TMG-1 was crossed with WI-2757, an inbred line susceptible to all three viruses. Segregation data indicated that resistance to PRSV-W was due to a single dominant gene (proposed designation, Prsv-2). Enzyme-linked immunosorbent assay (ELISA) data suggested that the mechanism of resistance to PRSV-W differs from that for ZYMV and WMV, and may be better described as tolerance. Although the plants were free of symptoms, high PRSV-W titers existed in young expanding leaves of the TMG-1 plants and the WI-2353×TMG-1 F 1 progeny
Effects of delayed access to feed and different crude protein levels in broiler chicks after hatching 3. Morphological development of small intestine segments.

This experiment was conducted to investigate effects of delayed access to feed/water (immediately, after 12 h, 24 h and 48 h) and different dietary crude protein levels (low, normal and high) on morphological development of small intestine segments in broiler chicks after hatching. Delaying 24th h or more time in access to feed after hatching (P <0.01) significantly impaired mucosal development of small intestine. Increasing delayed access to feed after hatching decreased villus size and surface area except for villus width in small intestine segments. A significant interaction between feed accessing time and dietary CP levels for villus size was also observed indicating that high CP diet alleviated retardation of development of villus size and area for 48 h-delayed access to feed.
Benefits of morphological defence demonstrated by direct manipulation in larval dragonflies

Many prey species evolved morphological structures to hold off predators. As morphology and behaviour are frequently entwined, it is very difficult to demonstrate the assumed defence benefit of the morphological traits. Using a novel approach of directly manipulating morphological defence in larval dragonflies, we demonstrated that spines were an effective morphological defence against predatory fish. Our results showed that the survival probability of larval dragonflies being attacked from behind was four-fold higher in larvae possessing spines than in larvae without spines. However, spines were ineffective against attacks from the front. We discuss the relevance of our study for understanding inducible defence.
SALIVARICIN B GENE - ITS LOCALISATION AND RFLP ANALYSIS IN TWO POTENTIALLY PROBIOTIC LACTOBACILLUS SALIVARIUS STRAINS

The study has provided data on two Lactobacillus salivarius strains of poultry origin. The strains were investigated for the presence of genes encoding a bacteriocin: salivaricin B, and their localisation in chromosome or plasmid DNA. Specific primers were used to amplify a 224 bp fragment of salivaricin B gene (salB). RFLP analysis of PCR products revealed two DNA fragments of the predicted sizes upon digestion with NdeI and XapI. Analysis with SspI allowed obtaining variability in two fragments in comparison to computer analysis of both strains, suggesting their divergency. It may be assumed that the amplified DNA fragments of salB gene share great, but not complete similarity to the previously described sequence of salB gene. Two examined strains showed different plasmid profiles; however bands of similar sizes were seen in both profiles. Genes responsible for salivaricin production are located on chromosomal DNA. Properties of these strains, in particular the presence of genes encoding bacteriocin production, imply that they may be used as potential probiotics for poultry.
Deoxyribonucleic Acid Base Compositions, and Homology of "Microcyclus," Spirosoma, and Similar Organisms

The nonmotile, vibrioid, curly or ring-forming bacteria were examined to assess their systematic relationships through determination of the guanine-plus-cytosine contents of their deoxyribonucleic acids and the degrees of homology among the deoxyribonucleic acids of the various genera and species. Our results verify that Runella, Flectobacillus, Spirosoma, and Ancylobacter ("Microcyclus") are separate genera. However, our results also indicate that (i) "Ancylobacter eburneus" is not a separate species but is in fact a strain of Ancylobacter aquaticus, (ii) Flectobacillus marinus should not be used to create the new genus "Cyclobacterium" and the latter name should be discarded, and (iii) "Renobacter" is very similar to Ancylobacter, but these two genera exhibit very low levels of deoxyribonucleic acid-deoxyribonucleic acid homology and should probably remain separate at least until additional information is available.
Comparative population genetic structures of the fruit fly Urophora cardui and its primary parasitoid Eurytoma robusta

The interaction between two species may depend on geographic scale and this in turn can affect co‐evolution among them. The present study comparatively examines population genetic structures of the tephritid gall fly Urophora cardui and its primary ectoparasitoid Eurytoma robusta for inference of relative dispersal patterns and host‐parasitoid specificity. Genetic differentiation patterns indicated two levels of hierarchical structure in both species: locally similar distance‐dependencies but globally differences. Locally, both species showed isolation by distance and a high correlation between host and parasitoid FST for the same population‐pairs was found. At the local level, E. robusta populations were most structured. These findings suggest that locally E. robusta is tracking behind its host, U. cardui, and that colonisation of new patches by both species underlie a stepping‐stone dispersal process. The investigation as a whole showed that U. cardui populations were hierarchically structured across a genetic‐geographical cline. There was no sign of a comparable cline in E. robusta where populations globally became independent of one another and of the host. The different degree of hierarchical genetic structure of the two species suggests that dispersal processes or interactions differ relative to geographical scale and population history.
Modulation of Plasma Levels and Percentages of Incorporation of ω-3 PUFAs in Egg Yolk under the Influence of Supplementation Sources Rich in Omega 3 to Diet of Laying Hens

o Abstract: Hundred forty-four Shaver White laying hens were used over a 4 week experimental period to investigate the effect of 3% of soybean oil, corn oil (MIL), canola oil, flaxseed oil (LIN), salmon oil (SAL) or tuna and sardine oil (SR/AT) added to the diets, upon the fatty acid egg yolk composition, blood plasma levels and incorporation time of each fatty acid into the egg yolk. Hens were allocated into 72 cages and the experimental design was a 6 x 6 randomized factorial model. Hens fed 3% of different oils, responded with increased polyunsaturated fatty acids omega 3 (ω-3 PUFAs), except for corn oil. The addition of flaxseed, soybean or corn oil into the diet increased the PUFAs levels into the egg yolk and in the blood plasma. Adding tuna and sardine oil into the diet increased the concentration of yolk saturated fatty acids. The levels of ω-3 PUFAs were increased in the tuna and sardine oil treatment, while the flaxseed oil increased the plasma fatty acids. The deposition of 349.28 mg/yolk of α-linolenic fatty acids (ALA) was higher in the group fed LIN, while the higher equal to 157.13 mg DHA/yolk was observed in group SR/AT. In the plasma, deposition increased from 0.33% (MIL) for 6.29% ALA (LIN), while that of DHA increase of 0.47% (MIL) for 4.24% (SAL) and 4.48% (SR/AT) and of 0.98% (MIL) for 6.14% (SR/AT) and 8.44% (LIN) of ω-3 PUFAs. The percentage of EPA into the yolk and plasma was higher for the hens fed 3% tuna and sardine oil diet, as well as the levels of yolk DHA. The concentration of DHA into the plasma was higher for the salmon and tuna/sardine oil treatments. The PUFAs yolk decreased during the first eight days of experiment, while the ω-3 PUFAs increased during the same period. The concentration of ALA increased until ten days of experiment, while the percentage of EPA and DHA increased up to the eighth experimental day.
Sox2 is a Master Regulator of Differentiation in Respiratory Epithelium

ii Acknowledgements . v Table of contents . 1 List of Figures . 4 Chapter 1: Introduction . 6 Summary . 16 References . 19 Chapter 2. Sox2 Is Required for Maintenance and Differentiation of Bronchiolar Clara, Ciliated, and Goblet Cells. 22 Abstract . 23 Introduction . 24 Results . 27 Localization of Sox2 in the Respiratory Epithelium . 27 Progressive Deletion of Sox2 from Lung Epithelium . 27 Conditional Deletion of Sox2 Results in Cuboidal-to-Squamous Epithelium Lacking Goblet, Clara, and Ciliated Cells in the Conducting Airway Epithelium . 28 Sox2 Is Required for Differentiation of Goblet Cells Following Allergen Exposure . 29 Reduced Proliferation and Decrease in Cell Density in the Bronchioles of Sox2 Mice . 29 Sox2 Activates Promoter-Luciferase Constructs for Scgb1a1, FoxJ1, and Agr2 . 30 Sox2 Interacts with Smad3 and Inhibits TGF-ß1/Smad3 Signaling . 30 Discussion . 32 Summary . 35 Materials and Methods . 36 References . 42 Chapter 3. Sox2 activates cell proliferation and differentiation in the respiratory epithelium. 62 Abstract . 63 Introduction . 64 Materials and methods . 67
Effects of mulberry (Morus alba L) silage supplementation on the haematological traits and meat compositions of Hanwoo (Bos taurus coreanae ) steer

This study was conducted to evaluate the effect of dietary supplementation with mulberry silage on hematologic traits and meat compositions in Hanwoo (Bos taurus coreanae) steer fed total mixed rations and to determine application possibility of mulberry silage as a functional feed source in the beef industry. Twenty steer (622.5±12.7 kg) of the late fattening stage were assigned to either a group with mulberry silage supplementation (MSS) or without (control). No significant differences were found in serum total protein and albumin concentrations. There was no difference between control and MSS in serum cholesterol concentrations but a significant difference (P<0.05) was noted in serum cholesterol concentrations before and after the experiment for the MSS. Dry matter and ether extract content of Longissimus dorsi for MSS were significantly higher (P<0.05) than those for control. However, crude protein of L. dorsi was significantly lower (P<0.05) in MSS than in control. Although no significant change was apparent in content of saturated fatty acids in L. dorsi between control and MSS, some fatty acids including arachidate and behenate were significantly (P<0.05) changed with mulberry silage supplementation. Total free amino acids showed similar levels in the two groups. Levels of most free amino acids were significantly higher (P<0.05) in MSS than in control. In conclusion, MSS changed the serum biochemistry in Hanwoo steer of the late fattening stage and caused relative alterations of chemical composition in L. dorsi. Key words: Hanwoo steer, mulberry silage, meat composition, fatty acid composition, free amino acid.