Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection and characterization of chromosomal aberrations in human solid tumors using fluorescence in situ hybridization strategies

A novel approach to the identification of human chromosomes has been developed. Chromosomal in situ hybridization (or 'chromosome painting') has been performed using Alu element-mediated PCR products from small quantities (250-500) of flow-sorted normal and abnormal chromosomes. Chromosome paints for various normal chromosomes, including # 5, 6, 7, 14, 18, 19, 21, and 22, were generated and shown to be effective in the identification of the appropriate chromosomes. In addition, certain abnormal chromosomes, including a mental retardationassociated deletion chromosome 11 (q22-q23), the products of the constitutional translocation t(ll;22), and the CML-associated t(9;22), were used to generate region-specific paints. In each case, the appropriate regions of the chromosomes were highlighted and this strategy is, therefore, well suited to the identification of previously unidentified marker chromosomes. A further direct consequence of this work is that chromosome paints specific for the common aberrant chromosomes, such as the Philadelphia chromosome, can be generated and made widely available. These may find particular use in the analysis of complex or masked chromosomal translocations. Figures 1-9 are represented on Color Plate I
Using Chelator-Buffered Nutrient Solutions to Limit Ni Phytoavailability to the Ni-Hyperaccumulator Alyssum murale

Abstract Nickel (Ni) is essential for all plants due to its role in urease activation. Demonstration of Ni essentiality has required exceptional effort to purify nutrient solutions to remove Ni; thus, an improved technique would make study of Ni deficiency more available to diverse researchers. As part of our research on Ni hyperaccumulation by plants, we developed chelator-buffered nutrient solutions with very low buffered activity of free Ni2+, and tested growth of Alyssum murale (Goldentuft Madwort), A. corsicum (Madwort), A. montanum (Mountain Alyssum) and Lycopersicon esculentum (Tomato). We used a modified Hoagland nutrient solution with 2 mM Mg and 1 mM Ca to simulate serpentine soil solutions. We could use hydroxyethyl-ethylene-diaminetriacetate (HEDTA) to achieve Ni2+ activity levels as low as 10-16 M, and cyclohexane-ethylenediamine-tetraacetate (CDTA) to supply higher activities of buffered Ni2+ compared with HEDTA; however, we were unable to obtain proof of induced Ni-deficiency, even with urea-N supply in a 6-week growth period, apparently because seeds supplied enough Ni for growth. Yields were somewhat reduced at lower Ni activity by the end of the test period, but strong deficiency symptoms did not occur, apparently due to the supply of Ni from hyperaccumulator species seeds (contained 7000–9000 mg Ni kg-1). Chelator buffering supplied controlled levels of Ni2+ for all test species; very low plant Ni levels were attained when seed Ni was low. Reaching clear and strong Ni deficiency appears to require longer growing periods, using seed with exceedingly low initial endogenous Ni, or species possessing higher Ni requirements.
Maternal chitosan oligosaccharide supplementation affecting expression of circadian clock genes, and possible association with hepatic cholesterol accumulation in suckling piglets

Chitosan oligosaccharide (COS) has been shown to reduce lipid accumulation in liver in mice and rats. The purpose of this study was to investigate whether maternal COS feeding affects hepatic lipid metabolism via influencing the expression of circadian clock genes in piglets. From day (d) 85 of gestation to d 14 of lactation, sixteen pregnant sows were divided into a control group (basal diet without COS supplementation) and a COS group (30 mg COS/kg basal diet). After farrowing, one piglet per litter in each group was selected for the collection of plasma and liver samples on d 0 and d 14 of age, respectively. Interestingly and significantly, we found that maternal COS supplementation promoted plasma and hepatic cholesterol accumulation and up-regulated the mRNA level of negative-regulated element period 1 (Per1), and reduced the abundance of the positive elements, circadian locomotor output cycles kaput (CLOCK), and brain muscle Arnt-like 1 (BMAL1) in the suckling piglets on d 14. These alterations may promote the hepatic cholesterol accumulation, which, in turn, activates hepatic bile acid metabolism and attenuates the relative expression levels of lipid metabolism-associated genes in the liver. However, the expression of CLOCK and BMAL1 and the lipid profile in the plasma and liver were not affected by COS supplementation on d 0. Collectively, our results indicate that maternal supplementation with COS postpartum up-regulates cholesterol accumulation in suckling piglets at age d 14, in part, by the regulation of circadian clock genes.
Is there ‘a’ mixed race group in Britain? The diversity of multiracial identification and experience

In contemporary British society, references to ‘mixed race’ people and to various forms of mixing abound. But to what extent can we say that there is ‘a’ mixed race group in Britain today? If such a group exists, what commonalities underlie the experience of being mixed? In addressing this question, I draw on a study of the racial identifications of different types of mixed young people in Britain. I find that the meanings and significance of race and mixedness in these young people’s lives can vary considerably both across and within specific mixed groups. In conclusion, I argue that while there is evidence of a growing consciousness and interest in being mixed, we cannot (yet) speak of a coherent mixed group or experience in Britain.
`Little Chipmunk' Syndrome? Male Body Size and Dominance in Captive Yellow‐Pine Chipmunks (Tamias amoenus)

In mammals, large males are often assumed to have higher mating success because they have greater success at contest competition. This relationship is often used to explain the prevalence of male-biased sexual size dimorphism in mammals. However, in many small vertebrates, large individuals are not always dominant. Using staged dyadic encounters, we examined the relationship between male body size and social dominance in captive male yellow-pine chipmunks (Tamias amoenus), a species with female-biased sexual size dimorphism. The yellow-pine chipmunk has a mating system in which males participate in mating chases and dominant males may have an advantage in acquiring matings with oestrous females. Captive male chipmunks were aggressive in only 28% of 144 paired encounters; however, several lines of evidence indicated that smaller chipmunks were dominant over large chipmunks: (1) small males were dominant in more dyads than large males; (2) within dyads, dominant males were smaller than subordinate males; and (3) small males performed more aggressive behaviour than large males. These results are not consistent with the prediction that large males are typically dominant. If large chipmunks are able to gain matings with females because of qualities other than dominance (such as the ability to successfully find and/or chase receptive females), then the costs of aggression to large chipmunks may outweigh any potential benefits. Small males, but not large males, may improve their mating success by being aggressive.
The militarization of anti-poaching: undermining long term goals?

Summary Conservation is at a critical juncture because of the increase in poaching which threatens key species. Poaching is a major public concern, as indicated by the rises in rhino and elephant poaching, the United for Wildlife Initiative and the London Declaration, signed by 46 countries in February 2014. This is accompanied by an increasing calls for a more forceful response, especially to tackle the involvement of organized crime in wildlife trafficking. However, there is a risk that this will be counter-productive. Further, such calls are based on a series of assumptions which are worthy of greater scrutiny. First, calls for militarization are based on the idea that poverty drives poaching. Yet, poaching and trafficking are changing because of the shifting dynamics of poverty in supply countries, coupled with changing patterns of wealth in consumer markets. Second, the ways increases in poaching are being linked to global security threats, notably from Al Shabaab are poorly evidenced and yet circulate in powerful policy circles. There is a risk that militarization will place more heavily armed rangers in the centre of some of the most complex regional conflicts in the world (such as the Horn of Africa and Central Africa/Sahel region).
Discovery and characterization of prions in Saccharomyces cerevisiae

Some protein aggregates can perpetuate themselves in a self-templating protein-misfolding reaction. These aggregates, or prions, are the infectious agents behind diseases like Kuru and madcow disease. In yeast, however, prions act as epigenetic elements that confer heritable alternative phenotypes. Prion-forming proteins create bistable molecular systems whose semi-stochastic switching between functional states increases phenotypic diversity within cell populations. My thesis work explores the idea that rather than being detrimental, prions may commonly act to their host’s advantage. To broaden the known range of prion phenomena in S. cerevisiae, I, together with a postdoctoral fellow in our lab, systematically surveyed the yeast proteome for prion-forming proteins. Using a combination of computational, cell biological, and biochemical approaches, we ultimately identified 18 novel prion domains capable of driving phenotypic switching, and an additional 6 domains that were highly positive for prion-like aggregation in other assays. These results establish the critical importance of intrinsic amyloid-forming tendencies for prion behavior by Q/N-rich proteins. We further confirmed that one of these proteins, the transcription factor Mot3, forms a novel prion in its endogenous context. An analysis of these findings revealed a strong and unexpected amino acid bias in prionogenic proteins: prions were strongly enriched for asparagine (N), but not the chemically related amino acid glutamine (Q). We validated this finding using molecular simulations and experimental analyses of Q-to-N and N-to-Q variants of prion domains. N-rich sequences had an intrinsic tendency to both nucleate and propagate amyloid conformers. Q-rich proteins tended instead to make structurally non-constrained interactions leading to proteotoxic soluble and nonamyloid aggregated conformers. The appendices include works in progress. Each explores a different aspect of prion biology. Appendix A confirms a theoretical prediction that prions, if functional, should preferentially regulate certain rapidly evolving genes. I demonstrate with the newly discovered prion protein, Mot3, that prions accelerate the appearance of new phenotypes in important traits like mating behavior and cell-adhesion. I further identify naturally occurring prion states of Mot3 and other prion proteins in wild yeast isolates, and show that elimination of these prions has strong phenotypic effects in these strains. Appendix B, work done in collaboration with another lab, establishes that Nup100, a GLFG nucleoporin, is a prion. The conformational flexibility of GLFG nucleoporins is critical for the function of the nuclear pore complex, a molecular sieve that regulates all macromolecular transport between the nucleus and cytoplasm. Thesis supervisor: Susan Lindquist Title: Professor of Biology
The purification, characterization, serological activity and hepatotoxic properties of two cationic glycoproteins (α1 and ω1) from Schistosoma mansoni eggs

T cell-deprived mice acutely infected with S. mansoni suffer microvesicular hepatocyte damage which is not seen in infected, immunological intact animals. A cationic fraction (CEF6) of the PBS-soluble portion of S. mansoni eggs (SEA) induces antibodies which, on passive transfer, prevent hepatocyte damage. CEF6 contains 2 antigens, ω1 and α1, and has also been shown to be a useful serodiagnostic reagent. This paper describes the purification and characterization of the 2 antigens present in CEF6. ω1 is a monomeric glycoprotein with a pI > 9·0 and a molecular weight of 31 kDa. α1 consists of two immunologically cross-reactive dimers, 41 and 36 kDa in non-reducing conditions, each of which consists of one unique and one common glycoprotein subcomponent. In ELISA with mouse and human infection sera ω1 is shown to be S. mansoni specific and is better able to distinguish S. mansoni infections from other schistosome infections than are unfractionated SEA, CEF6 or α1. Passive transfer of monospecific anti-ω1 sera into S. mansoni infected, T cell-deprived mice completely prevented the occurrence of microvesicular hepatocyte damage in these animals. Monospecific anti-α1 serum had no hepatoprotective capacity.
Welfare improvement using alginic acid in rainbow trout (Oncorhynchus mykiss) juveniles

The present study explored alternative strategies to improve the health status and growth metabolism in cultured juvenile fish. In this context the effects of alginic acid administration on the welfare of rainbow trout juveniles were investigated. Both the hepatic gene expression of heat shock protein 70 and the cortisol plasma levels were evaluated in order to estimate the possible beneficial role of alginic acid in improving animal well-being. At the same time the body weight was measured and was correlated with the hepatic expression of insulin-like growth factor I, myostatin, and two isoforms of the thyroid receptor. Finally, improvement of the immune system was investigated by monitoring the expression of innate immune-related genes, such as interleukin1β, interleukin8 and toll-like receptor3, in the spleen. The data obtained demonstrated an improvement in the welfare of rainbow trout juveniles, revealed by growth and innate immune response enhancement by alginic acid administration. These results may be of great importance for the further development of more sustainable aquaculture practices, and can be considered as a biotechnological application to produce a safer product for human health.
Intake and Digestibility of Untreated and Urea Treated Rice Straw Base Diet Fed to Sheep

Rice straw as one of agricultural by-products has low quality due to low content of essensial nutrients like protein, energy, minerals and vitamin as well as poor palatability and digestibility. Therefore, the quality of rice straw needs to be improved in order to increase its utilization by gastrointestinal tract of ruminants. The purpose of this study is to compare untreated and urea treated rice straw as basal diets for sheep. Twelve mature Merino wethers (average body weight 53.62 + 3.44 kg) were separated into 4 groups based on their live weight with each groups assigned three diets, that are: diet 1 untreated rice straw with high forage legume content, diet 2 urea ensiled rice straw and diet 3 rice straw sprayed with urea solution at feeding time. Diets were allocated based on a randomized complete block design. Urea ensiled rice straw was prepared by spraying chopped straw with urea solution to yield straw containing 4% urea and 40% moisture, then kept in air tight polythylene bags for 6 weeks. The untreated, ensiled and urea supplemented rice straw were mixed with other feed ingredients to provide isoenergetic and isonitrogenous diets. Diets were formulated to meet maintenance requirement according to NRC. Sheep were adapted to experimental diets for 15 days, and after adaptation period, a metabolism trial was conducted. Results reveal that dry matter intake permetabolic body weight (DMI/W0.75), DE (digestible energi) intake and apparent digestibility of NDF (neutral detergent fibre) were not significantly different between diet 1 and diet 2. Apparent digestibility of DM (dry matter), OM (organic matter), and ADF (acid detergent fibre), as well as N retention were not significantly different between three diets. Positive result in N retention was only observed in diet 2, while others were negative. It may be concluded from this study that untreated rice straw basal diet supplemented with forage legume offer an alternative method other than urea ensiled for improving the nutritional value of rice straw as a ruminant feed on small farmer. Key words : Rice straw, urea treated, digestibility, and sheep
Dispharynx nasuta (Nematoda: Acuariidae) em Guira guira e Crotophaga ani (Cuculiformes: Cuculidae) no Estado do Rio Grande do Sul, Brasil

Nematodes of the genus Dispharynx (Railliet, Henry & Sisoff, 1912) are parasites of several groups of birds which have been primarily studied in birds of economic importance due to the injuries caused in the host proventricle. Dispharynx nasuta (Rudolphi, 1819) Stiles & Hassall, 1920, was found in two species of Cuculiformes, guira cuckoos, Guira guira Gmelin, 1788 and smooth-billed ani, Crotophaga ani Linnaeus, 1758, in the southern-most State of Brazil. From 2005 to 2008, 120 specimens of G. guira and 120 specimens of C. ani, were collected in Cacequi, Sao Vicente do Sul and Jaguari, Rio Grande do Sul State, Brazil. The prevalence of D. nasuta in G. guira was 28.3% and in C. ani 26.7%; the average intensity of infection was 8.81 (DP=18.41; Amplitude 1 - 82) helminths/host in G. guira and 5.10 (DP=6.17; Amplitude 1 - 30) in C. ani; the average abundance of infection was 2.28 (DP=10.02) helminths/host in G. guira, and 1.32 (DP=3.82) in C. ani, respectively. Comparative analysis between the species, sex, sexual maturity and seasonality showed that C. ani did not present significant differences with regard to any of the analyzed parameters. Guira guira presented some differences: females had more parasites than males (P=0.039); female birds collected in the winter (P=0.008) and male birds collected in the summer had more parasites (P=0.011); and immature males had more parasites than adult males (P=0.015). The injuries found in the proventricle of the parasitized birds were compatible with adenomatoid hyperplasia and with granulomatosis proventriculitis. This communication expands the number of host species and the geographic distribution of D. nasuta.
Comparison of three methods for determining the conductive xylem area of Scots pine (Pinus sylvestris)

Summary Three methods for the estimation of conductive xylem area were compared in several stands of Scots pine in northern Germany: (1) computer tomography (seven stands, 105 trees), (2) staining of increment cores (seven stands, 75 trees), and (3) resistance to penetration (two stands, 35 trees). The staining method gave significantly higher estimates of the proportion of conductive xylem area than the other methods. The results indicate that between true, stainable heartwood and conductive xylem there is a zone of relatively dry but chemically unaltered xylem, which the staining method identified as sapwood. Therefore the use of staining methods to estimate functional sapwood in Scots pine seems to be prone to significant errors. Estimates of stand transpiration based on sapflux density and sapwood area obtained by staining can result in an error of up to 15 per cent. This can be avoided by using techniques that are based on wood moisture content. With a combination of computer tomography and staining techniques it is possible to estimate the extent of the three zones of xylem, viz. true sapwood, the transition zone, and true heartwood. Resistance to penetration proved to be an efficient and inexpensive alternative to computer tomography.
An evolutionarily stable joining policy for group foragers

For foragers that exploit patchily distributed resources that are challenging to locate, detecting discoveries made by others with a view to joining them and sharing the patch may often be an attractive tactic, and such behavior has been observed across many taxa. If, as will commonly be true, the time taken to join another individual on a patch increases with the distance to that patch, then we would expect foragers to be selective in accepting joining opportunities: preferentially joining nearby discoveries. If competition occurs on patches, then the profitability of joining (and of not joining) will be influenced by the strategies adopted by others. Here we present a series of models designed to illuminate the evolutionarily stable joining strategy. We confirm rigorously the previous suggestion that there should be a critical joining distance, with all joining opportunities within that distance being accepted and all others being declined. Further, we predict that this distance should be unaffected by the total availability of food in the environment, but should increase with decreasing density of other foragers, increasing speed of movement towards joining opportunities, increased difficulty in finding undiscovered food patches, and decreasing speed with which discovered patches can be harvested. We are further able to make predictions as to how fully discovered patches should be exploited before being abandoned as unprofitable, with discovered patches being more heavily exploited when patches are hard to find: patches can be searched for remaining food more quickly, forager density is low, and foragers are relatively slow in traveling to discovered patches. Copyright 2005.
Water‐energy dynamics, climate, and prediction of woody plant species richness: an interim general model

Predictable geographic patterns in the distribution of species richness, especially the latitudinal gradient, are intriguing because they suggest that if we knew what the controlling factors were we could predict species richness where empirical data is lacking (e.g. tropics). Based on analyses of the macro‐scale distribution of woody plant species richness in Southern Africa, one controlling factor appears to be climate‐based water‐energy dynamics. Using the regression models of climate's relationship to species richness in Southern Africa, I was able to describe an Interim General Model (IGM) and to predict first‐order macro‐scale geographic variations in woody plant species richness for the continent of Africa, as well as elsewhere in the world—exemplified using South America, the United States and China.
UNIVERSIDADE FEDERAL DE PERNAMBUCO CENTRO DE CIÊNCIAS BIOLÓGICAS MESTRADO EM BIOQUÍMICA E FISIOLOGIA

Dengue Fever is an arboviruses transmitted by Aedes aegypti and mosquito control is fundamental to reduce disease spreading. A. aegypti larvae have developed resistance to organophosporous insecticides and the use of natural compounds that promote mortality may avoid emergence of resistant larvae due to rotation of insecticides. This work reports the larvicidal activity (LC50 of 0.925% w/v) of Moringa oleifera flower extract on fourth larval instars (L4) of A. aegypti. Proteinaceous trypsin inhibitor from M. oleifera flower (MoFTI, 169.9 kDa, Ki: 0.38 nM), triterpene (β-amyrin), sterol (β-sitosterol) and flavonoids (kaempferol and quercetin) were detected in the extract; lectin was absent. Trypsin from L4 gut extract was inhibited by MoFTI (Ki: 0.6 nM), however acetylcholinesterase (AChE) activity from total L4 extract was not altered. In vivo assay showed that gut trypsin activity from L4 treated with M. oleifera flower extract decreased along the time (0 to 1440 min) and was strongly inhibited (98.6 %) after 310 min incubation; AChE activity from total L4 extract was not affected in this period. The study points out M. oleifera flower extract as a biodegradable tool for A. aegypti larvae control and suggests that larvicidal mechanism involves inhibition of L4 gut trypsin by MoFTI.