Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential Processing of Cyclin E Variants in Normal vs Tumor cells and their Role in Breast Cancer Oncogenesis

Abstract : Cyclin E is a posftive regulator, which controls the transition of the Ol to S phase of the cell cycle. When associated with CDK2, it is responsible for cells passing through the restriction point, which is the barrier between Gi and S. This commits the cell to complete one round of cell division. Previous findings by this laboratory have found that overexpression of cyclin E and the presence of lower molecular weight isoforms (LMW) are found more often in breast tumors and cancer cell lines when compared to normal tissues and cells. Also, tumor cells, but not normal cells have the mechanisms to proteolytically cleave the fall length cyclin E into these LMW forms. An altered cyclin E may contribute to the deregulation of the Gi to S checkpoint and lead to tumorigenesis. Our laboratory has also identified through mutational and biochemical analysis, the region of cyclin E that is proteolyticaly cleaved to generate the LMW forms. Critical phosphorylation sites of cyclin B are responsible for the appearance of the LMW forms of cyclin B. To invesrigate the possible role of phosphorylation in the processing of cyclin B into these lower forms, two approaches have been employed, First, incubation of breast cancer cell line extracts expressing the LMW forms with phosphatases was examined via western blot analysis. (isualization of cyclin B showed downward shifts in both the fall length and lower forms in the presence of active dephosphorylation. Second, fall length and truncated cyclin E cDNAs were mutated at critical phosphorylation residues via site-directed mutagenesis. Transfection of these mutants into tumor cells capable of LMW form processing followed by western analysis indicates that at least one of the mutations results in the loss of2 lower forms of cyclin B. However, assays for kinase activity in the transfected tumor cells demonstrate no change activity of the mutants deficient in these phosphorylation sites.
Flor Yeast Proteomic Response to the Lack of Fermentable Carbon Source

Flor yeasts metabolism highly configures organoleptic properties in Sherry type wines during biological aging (Peinado et al., 2009). Along this process, the mentioned yeasts prevail by forming a biofilm in the wine surface and the presence of certain proteins involved in the response to stresses becomes essential for survival, among the most important ones: lack of fermentable carbon sources. The main aim of this study is to compare proteome data from the flor yeast Saccharomyces cerevisiae G1 in a typical biological aging condition (without fermentable carbon source) and in a fermentative condition (with fermentable carbon source). In this work, OFFGEL fractionator coupled to LTQ Orbitrap XL MS equipment were used trying to identify the maximum possible number of proteins related to the lack of fermentable carbon source stress in a synthetic biological aging and under a reference fermentative condition. As a result, 18 stress proteins responding to the lack of fermentable carbon source have been detected only in the biological aging condition or higher than in the reference condition which are involved in biofilm formation, perception of stimuli among other biological processes. This study together with other experiments that definitively confirm the necessity of these proteins synthesis, may lead to the genetic improvement of flor yeast strains aimed to enhance their survival during the biological aging process and hence the whole wine elaboration process.
Morphological diversity and DNA polymorphism of common oat (Avena sativa L.) breeding varieties cultivated in Poland

Morphological diversity and DNA polymorphism of common oat (Avena sativa L.) breeding varieties cultivated in Poland The aim of the work was characterization of morphological diversity and DNA polymorphism of common oat breeding varieties. 25 morphological traits and DNA polymorphism have been examined using AFLP and RAPD methods. It has been found, that identification of oat breeding varieties is possible based on the examined morphological traits. The examined accessions were differentiated by traits important for intraspecific taxonomy of oat: type of panicle, presence of awns, colour of grain, as well as other morphological traits, such as shape of panicle, and type of awns. Relationships of morphological traits of leaves, grains, and stem with some DNA fragments suggesting presence of molecular markers of these morphological traits have been found. Morphological similarity of breeding varieties doesn't correspond to affinity complied with DNA similarity of these objects. Breeding varieties distinguishing unique combination of morphological traits as well as different DNA polymorphism have been identified. They could be used in process of new varieties breeding. Complex characterization of the examined objects of oat collection, maintained in the National Centre for Plant Genetic Resources of Plant Breeding and Acclimatization Institute, will make possible its effective use in breeding and research works and will facilitate management of this collection.
Phylogenetic relationships of Luziola (Poaceae: Oryzeae) and related genera from aquatic habitats

Luziola is a small aquatic genus consisting of nine American species and belonging to Poaceae (subfamily Ehrhartoideae, tribe Oryzeae). We surveyed 160 morphological characters and performed phylogenetic analyses to determine relationships within the genus and between it and its closest relatives, and to deduce the evolution of a number of characters in relation to the aquatic habit. Our results confirm that Luziola is a monophyletic group and that Zizaniopsis is its sister group among taxa examined but revealed only a few clades within Luziola, the best supported of which consists of Luziola fragilis Swallen, Luziola fluitans (Michx.) Terrell & H. Rob. , and Luziola peruviana J.F. Gmel. We used this phylogenetic evidence to reconstruct the evolution of several characters hypothesized to be correlated to an aquatic life style, including reduction or absence of glumes, papillae arranged in horizontal rows on the lemmas, dumb-bell shaped silica bodies, and a change from hermaphrodite to unisexual florets.
Habitat use by fishes of Lake Superior. I. Diel patterns of habitat use in nearshore and offshore waters of the Apostle Islands region

Diel patterns of distribution of fishes in nearshore (15–80 m depth) and offshore (>80 m) waters of the Apostle Islands region of Lake Superior were described using bottom trawls, mid-water trawls, and acoustic gear during day and night sampling. These data revealed three types of diel migration: diel vertical migration (DVM), diel bank migration (DBM), and no migration. DVM was expressed by fishes migrating from benthopelagic to pelagic strata and DBM was expressed by fishes migrating horizontally from deeper waters in the day to shallower waters at night while remaining within the benthopelagic stratum. Most fishes that did not exhibit diel migration showed increased nighttime densities as a result of increased activity and movement from benthic to benthopelagic strata. Rainbow Smelt (Osmerus mordax), Cisco (Coregonus artedi), Bloater (C. hoyi), Kiyi (C. kiyi), juvenile Trout-Perch (Percopsis omiscomaycus), and adult siscowet (Salvelinus namaycush siscowet) exhibited DVM. Lake Whitefish (C. clupeaformis), lean Lake Trout (Salvelinus namaycush namaycush), and juvenile siscowet exhibited DBM. Adult Trout-Perch and adult Pygmy Whitefish (Prosopium coulteri) exhibited a mixture of DBM and DVM. Burbot (Lota lota), Slimy Sculpin (Cottus cognatus), Spoonhead Sculpin (C. ricei), and Deepwater Sculpin (Myoxocephalus thompsonii) did not exhibit diel migration, but showed evidence of increased nocturnal activity. Ninespine Stickleback (Pungitius pungitius) exhibited a mixture of DVM and non-migration. Juvenile Pygmy Whitefish did not show a diel change in density or depth distribution. Species showing ontogenetic shifts in depth distribution with larger, adult life stages occupying deeper waters included, Rainbow Smelt, lean and siscowet Lake Trout, Lake Whitefish, Pygmy Whitefish, Ninespine Stickleback and Trout-Perch. Of these species, siscowet also showed an ontogenetic shift from primarily DBM as juveniles to primarily DVM as adults. Across all depths, fishes expressing DVM accounted for 73% of the total estimated community areal biomass (kg ha−1) while those expressing DBM accounted for 25% and non-migratory species represented 2% of the biomass. The proportion of total community biomass exhibiting DVM increased with depth, from 59% to 95% across ≤30 m to >90 m depth zones. Along the same depth gradient, the proportion of total community biomass exhibiting DBM declined from 40% to 1%, while non-migrators increased from 1% to 4%. These results indicate that DVM and DBM behaviors are pervasive in the Lake Superior fish community and potentially provide strong linkages that effect coupling of benthic and pelagic and nearshore and offshore habitats.
Sympatric and allopatric combinations of hen fleas and great tits: a test of the local adaptation hypothesis

To test whether allopatric nest parasites differ from sympatric ones in their effect on various life history traits of their avian host, I designed a cross‐transfer experiment in which hen fleas (Ceratophyllus gallinae) were exchanged between great tit (Parus major) nests in two geographically widely separated areas. In neither of the areas did allopatric fleas influence body mass, tarsus length, wing length, duration of nestling period or mortality in great tit nestlings more severely than did sympatric fleas. Duration of incubation was also similar among females independent of experimental treatment. This lack of difference between allopatric and sympatric fleas is hypothesized to reflect the comparative harmlessness of hen fleas for their hosts.
Three‐Dimensional Reconstruction of Hematopoietic Organ of Bombyx mori Larva

Three‐dimensional reconstructions of a hematopoietic organ (HPO) from Bombyx mori larva were undertaken using light and electron microscopy. Each compact islet varied in sizes, but in the central area of the HPO their size became smaller. Compact islets and loose islets were made up of prohemocytes, plasmatocytes, and reticular cells, but there were differences in the proportions of these cells. Within the cytoplasm of reticular cells and within their cell projection, vacuoles were observed. Cell proliferation occurs primarily in the compact islets, and differentiation associated with the reticular cells occurs primarily in the loose islets. It can be inferred that reticular cells have a significant influence on proliferation and differentiation associated with hematopoiesis. According to the results of the 3‐D reconstruction, one reticular cell is in contact with eight or nine hemocytes. Each reticular cell is presumably of approximately ten hemocytes. Movies relevant to Figs. 3, 4 and 5 can be found at http://biotech.korea. ac.kr/ cellbio/pages/ 3D‐results.html.
DAISIE and arthropod invasions in Europe.

A milestone in the knowledge of alien species in Europe has been achieved by the DAISIE (Delivering Alien Invasive Species Inventories for Europe) project. Th rough the Sixth Framework Programme of the European Union, DAISIE has delivered a major portal for information on biological invasions that is publicly available at http://www. europe-aliens.org. Th e rationale was to develop a pan-European inventory of invasive alien species by integrating existing databases, to describe patterns and evaluate trends in biological invasions in Europe, identify priority species and assess their ecological, economic and health risks and impacts. Although an on-going process, the foundation, scope, and technological architecture of DAISIE was established through a consortium of leading researchers of biological invasions in Europe from 19 institutions across 15 countries and delivered through the cooperation of experts in ecology and taxonomy from throughout Europe that in total amounted to 182 contributors. Th e inventory, accounts, and distribution maps today provide the fi rst qualifi ed reference system on invasive alien species for the European region. Th e information presents an outstanding resource to synthesise current knowledge and trends in biological invasions in Europe. Th e data will help identify the scale and spatial pattern of invasive alien species in Europe, understand the environmental, social, economic and other factors involved in invasions, and can be used as a framework for considering indicators for early warning. A key component of DAISIE is Th e European Alien Species Database, an inventory of all alien species in Europe, and resulted from compiling and peer-reviewing national and regional lists of alien fungi, bryophytes, vascular plants, invertebrates, fi sh, amphibians, reptiles, birds and mammals. Data were collated for all 27 European Union member states (and separately for their signifi cant island regions), other European states (Andorra, Iceland, Liechtenstein, Moldova, Monaco, Norway, the European BioRisk 4(1): 1–3 (2010)
Genetic Relationships of Arctic Grayling in the Koyukuk and Tanana Rivers, Alaska

Abstract Electrophoretic data were used to examine the stock structure of Arctic grayling Thymallus arcticus collected from the Yukon River drainage, Alaska. Arctic grayling were sampled from Grayling Lake in the Koyukuk River drainage and from three tributaries (Caribou Creek, Goodpaster River, and Volkmar River) entering a 60-km stretch of the Tanana River. Of 30 protein-coding loci examined, three (Mdh-2, Pgm-1, and Sod-2, coding for malate dehydrogenase, phosphoglucomutase, and superoxide dismutase, respectively) were polymorphic. Differences in allele frequency between the Koyukuk and Tanana drainages accounted for about 5% of the observed variability, whereas differences among the collections from the Tanana drainage accounted for less than 1%. The difference observed between collections from the Koyukuk and Tanana rivers, major tributaries to the Yukon River, suggests that genetic comparisons are useful for biogeographical studies of Alaskan Arctic grayling. The small divergence exhibited among the.
Invasive Cane Toads as Prey for Native Arthropod Predators in Tropical Australia

Abstract: The successful spread of invasive Cane Toads (Rhinella marina) across tropical Australia has been attributed to a lack of biotic resistance, based upon the inability of most anuran-eating vertebrate predators to tolerate the powerful chemical defenses of the toads. However, despite their high species richness, invertebrates have been much less studied than vertebrates as predators of Cane Toads. Our field and laboratory studies show that toads are killed and consumed by a phylogenetically diverse array of arthropod taxa. No arthropod predators consumed toad eggs in our laboratory experiments, but fishing spiders, water beetles, water scorpions, and dragonfly nymphs killed toad tadpoles, and ants and fishing spiders killed metamorph toads. Published accounts report predation on toads by crustaceans and hemipterans also. In our experiments, no predators showed any overt ill effects from consuming toad tissue. Dragonfly nymphs (Pantala flavescens) and fishing spiders (Dolomedes facetus) selectively took Cane Toad tadpoles at higher rates than some simultaneously offered native frog tadpoles. In combination with published data, our experiments suggest that the tadpoles and metamorphs of Cane Toads face high predation rates from the diverse and abundant invertebrate fauna of aquatic and riparian habitats in tropical Australia. The invasion of Cane Toads can potentially have positive effects on populations of many native animal species.
Evaluation of technological and functional properties of a new probiotic Lactobacillus fermentum ME-3

Backround: In persons without clinical symptom it is difficult to assess an impact of probiotics regarding its effect on health. We evaluated the functional efficacy of the probiotic Lactobacillus fermentum ME-3 in healthy volunteers by measuring the influence of two different formulations on intestinal lactoflora, fecal recovery of the probiotic strain and oxidative stress markers of blood and urine after 3 weeks consumption. Methods: Two studies with healthy adults were performed; altogether 45 randomly allocated persons consumed either the ME-3 capsules/placebo or fermented goat milk/goat milk in a daily of dose 9.2 to 11.8 log CFU respec- tively for 3 weeks. The fecal lactoflora composition, fecal ME-3 recovery, effect of the consumption on intestinal lactoflora, and oxidative stress markers of blood (total antioxidative activity; total antioxidative status and glutathione red-ox ratio) and urine (8-isoprostanes) was measured. Results: ME-3 was well tolerated and a significant increase in total fecal lactobacilli yet no predominance of ME-3 was detected in all study groups. Fecal recovery was documented by molecular methods only in fermented milk group, however the significant improvement of blood TAA and TAS indices
Isolation, phylogenetische Analyse und Funktion von Wnt-Liganden aus Nematostella vectensis

Isolation, phylogenetische Analyse und Funktion von Wnt-Liganden aus Nematostella vectensis Die Wnt-Genfamilie kodiert fur sekretierte Signalmolekule, die uber verschiedene Signalkaskaden fundamentale Entwicklungsprozesse, wie axiale Musterbildung, Zellschicksalsentscheidungen und die Entstehung von Erkankungen, in allen daraufhin untersuchten Tieren auslosen. Im Menschen sind 12 Subfamilien der Wnt-Liganden identifiziert worden. Sechs dieser Subfamilien sind auch in Ecdysozoen ( zum Beispiel: Anopheles gambiae und Caenorhabditis elegans) vertreten. Die Cnidaria (Nesseltiere) sind eine evolutionar sehr ursprungliche Tiergruppe, deren Korper nur eine Korperachse, die oral-aboral Achse und zwei Keimblatter, Ectoderm und Endoderm besitzt. Die Anthozoa (Seeanemonen) gelten als die basale Gruppe der Cnidaria. In der Seeanemone Nematostella vectensis wurden zwolf verschiedene Wnt-Sequenzen identifiziert. Fur die vorliegende Arbeit wurden Fragmente der Wnt-Transkripte von N. vectensis komplettiert und nach der Errechnung von molekularen Stammbaumen mit der Ausstattung mit Wnt-Liganden anderer Tiere verglichen. Die einzelnen N. vectensis Wnt-Sequenzen lassen sich mit guter statistischer Unterstutzung in elf der zwolf im Menschen vorkommenden Wnt-Subfamilien einordnen. Funf der Subgruppen gingen in der Evolution der Ecdysozoa verloren. Nach der allgemein gultigen Auffassung besteht ein direkter Zusammenhang zwischen der Komplexitat des Genoms und der Morphologie von Organismen. Das wirft die Frage auf, zu welchem Zweck so einfache Organismen wie N. vectensis eine derart komplexe Ausstattung an Morphogenen besitzen. Die durchgefuhrten Expressionsanalysen zeigen, das acht der Transkripte, in einer gestaffelten Anordnung entlang der Korpersaule der Planulalarve, exprimiert sind. Funf im Ektoderm und drei im Endoderm. Eine solche Anordnung der Wnt-Expressionsdomanen ist auch im Gehirn von Wirbeltierembryonen zu finden. Das Expressionsmuster sowie Uber- und Fremdexpressionsexperimente in N. vectensis und Xenopus laevis, weisen darauf hin, das Wnt-Liganden eine zentrale Funktion in der Gastrulation und der Etablierung von Symmetrieachsen im Verlauf der Entwicklung von N. vectensis haben. Die komplexe Ausstattung an Wnt-Subfamilien mus in fruhen vielzelligen Organismen vor uber 650 Millionen Jahren entstanden sein, was darauf hinweist, das diese Gengruppe eine Rolle bei der Evolution der verschiedenen Korperbauplanen rezenter Organismen spielte.
Floral ontogeny of Hardenbergia violacea (Fabaceae: Faboideae: Phaseoleae) and taxa of tribes Bossiaeeae and Mirbelieae, with emphasis on presence of pseudoraceme inflorescences

The floral ontogeny of several Australian papilionoid taxa has been studied in Hardenbergia violacea L. (Phaseoleae); Kennedia rubicunda (Phaseoleae; inflorescences only); Bossiaea cordigera (Bossiaeeae); Gastrolobium truncatum, Mirbelia oxylobioides, and Pultenaea daphnoides (Mirbelieae). Species studied of Hardenbergia, Pultenaea, and Brachysema have pseudoracemose inflorescences comprised of triads of flowers, Kennedia rubicunda has paired flowers that resemble reduced pseudoracemes, while Gastrolobium truncatum and Mirbelia oxylobioides have pseudoracemes comprised of 2–10 flowers per ultimate unit. Pseudoracemes are a significant and overlooked feature in many taxa of tribes Bossiaeeae and Mirbelieae. Hardenbergia violacea has ultimate axillary units of three flowers, each with a subtending bract but no bracteoles. Floral ontogeny in H. violacea and P. daphnoides shows acropetal order among whorls, and unidirectional order starting from the abaxial side in sepal, petal, and stamen whorls, as in most papilionoid flowers. The carpel is initiated concurrently with the first antesepalous stamen primordium. Pultenaea daphnoides and Bossiaea cordigera have unidirectional sepal initiation starting abaxially, but simultaneous petal initiation, an unusual feature among papilionoids. In late stages of H. violacea and B. cordigera, a diadelphous stamen tube or sheath is formed, while in taxa of Mirbelieae the stamens remain free. The flowers in all taxa studied become strongly zygomorphic as evidenced by three petal morphs and upturning of the free portions of style and stamens late in development.
Emulsifying and Foaming Properties of Okara Protein Hydrolysates

Okara is a low-value coproduct of soy milk production. Its dry matter contains 25–30% protein that is of high nutritive quality, has an excellent efficiency ratio, and thus holds promise for applications in food systems. However, okara protein has low solubility. We here optimized its extraction and isolation from okara by using dilute sodium hydroxide and subsequent isoelectric precipitation. The obtained okara protein isolate (OPI) was hydrolyzed with different enzymes into a range of hydrolysates with different degrees of hydrolysis. Most hydrolysates had better emulsifying activity and produced more stable emulsions than OPI. In contrast, hydrolysis had no positive effect on foam-forming and foam-stabilizing activity of OPI proteins. Hydrolysis of OPI enhances the emulsifying capacity of the proteins. Furthermore, the emulsifying and foam-forming capacities of most of the OPI hydrolysates were similar to or even better than those of the commercial (soy) protein hydrolysates used in this study.
The Role of New Mutations in Evolution and Cloning: Genetic Analysis to Identify the Role of New Beneficial Mutations in Increasing Viability and Salt Tolerance in Drosophila Melanogaster and the Influence of Deleterious Mutations on Cloning Efficiency

Ron C. Woodruff, Advisor Mutation and selection are major driving forces of evolution. However, the role of new beneficial mutation is considered negligible in almost all evolutionary processes. In most cases it is difficult to separate the effect of pre-existing genetic variation at low frequencies from new mutations. In this study, experiments with Drosophila melanogaster were conducted to study the effect of new beneficial mutations on increases in viability and in adaptation to increased toxic levels of dietary salt. Completely homozygous stocks were used in the experiments to eliminate the effect of pre-existing genetic variation. In the viability experiment, a modification of Dobzhansky and Spassy assay (1947) was used to demonstrate that new beneficial mutations can quickly increase viability in Drosophila populations of different sizes. By use of inbred homozygous stock it was demonstrated that adaptation of Drosophila to increased salt tolerance due to new beneficial mutations can also occur quickly. We have also documented that the accumulation of deleterious mutations can reduce cloning efficiency in somatic cells. Overall, the results of these studies support the view that new mutations along with selection can have a major influence on cloning and the evolution of organisms.