Miracle-dz/UniFAR-FTUs huggingface dataset:
Targeting the Journey: From Embryogenesis to Cancer Stem Cell

When Michael Clarke (1) reported data for the existence of breast cancer stem cells, he introduced a new paradigm with the notion that at the heart of our failure to eradicate cancer is the continual repopulation of tumors by a small number of phenotypically distinct cells. In time, the stem cell characteristics became longevity, asymmetric cell division, self-renewal, quiescence and drug resistance. The offspring of these stem cells, often labeled progenitors, were following a failed path to differentiation and constituted the bulk of the tumor mass. This model, termed a hierarchical model, has been held in opposition to the traditional stochastic model, which held that one random cancer cell gives rise to two daughter cells, although it was understood by any cell biologist that at any given moment most cancer cells were quiescent and therefore also drug resistant, and that some cells in a heterogeneous population had managed to differentiate more than others. While the articles in this CCR Focus argue for the hierarchical model as opposed to the stochastic model, the jury is still out. And regardless of which model is accepted in time, the concept of “stemness” has prompted the introduction of at least 4 important new pathways to target. Embryonic stem cell pathways are dysregulated in cancer, and drugs targeting these pathways are in development. In the overview of this issue of CCR Focus by Guest Editor Percy Ivy, and in an elegant elaboration by Catherine O’Brien et al, the stem cell hypothesis is debated. But the lead compounds and potential drugs described, respectively, by experts Fumi Takahashi-Yanaga, Antonio Pannuti, Akil Merchant, Mark LaBarge and co-authors in the Wnt, Notch, Hedgehog, and Niche pathways make this critical point: we will have new drugs for cancer. Speaking to this are the responses in basal cell carcinoma and medulloblastoma observed with the Hedgehog inhibitor. The opportunity for drug development is the key contribution of the cancer stem cell hypothesis. As always, it is hoped that this issue of CCR Focus will challenge the expert, inform the interested nonexpert, and inspire strategies for the future.
SUPERAGREGATES FROM AMPHOTERICIN B MICELLES: A NEW WAY TO DECREASE ITS TOXICITY

INTRODUCTION The Amphotericin B in a micellar system (AmB) is a drug largely used for the treatment of systemic fungal infections, especially in immune-compromised patients. However, its use is limited due to its high toxicity, which is the main cause of side effects such as nephrotoxicity (1). There are several intravenous amphotericin B lipidic formulations that are less toxic, but presenting high cost. According to the literature, in aqueous solution there are the monomeric and aggregated forms of AmB, these latter being responsible for its side effects (2). Lately, it has been observed that the heating of AmB solutions generates “superaggregates” forms, which are produced by the condensation of monomeric and aggregate forms. This new state has been demonstrated to be less cytotoxic while keeping its activity (1). The aim of this work was not only to investigate the changes in the spectrum of the unheated and heated AmB solutions, following the bands of “superaggregates”, monomer and aggregates forms, but also to evaluate its toxicity.
Genetic relationships of common cocklebur accessions from the United States

Abstract DNA fragment analysis, based on amplification of intersimple sequence repeats by the polymerase chain reaction (ISSR-PCR), was used to assess genetic relationships of 217 U.S. accessions of common cocklebur. Twenty-four polymorphic markers were generated from six primers. Analysis of genetic similarity by clustering procedures resulted in separation of the accessions into two main clusters. Accessions within these two clusters were designated as either northern or southern genotypes. Forty-four of 48 accessions analyzed from Washington, Michigan, Iowa, and Ohio were northern genotypes, whereas 67 of 68 accessions analyzed from Mississippi, Arkansas, South Carolina, and North Carolina were southern genotypes. Accessions from Kansas, Missouri, and Illinois included 40 and 56 northern and southern genotypes, respectively, indicating a transition zone. In Illinois, accessions collected from northern and southern counties tended to be northern and southern genotypes, respectively. We conclude that much of the genetic variation among U.S. common cocklebur accessions is distributed along a latitudinal gradient.Nomenclature:Common cocklebur, Xanthium strumarium L. XANST.
Does mist-netting provide reliable data to determine the sex and age ratios of migrating birds? A case study involving the Great Tit (Parus major) and the Blue Tit (Cyanistes caeruleus)

Abstract Nowakowski J.K. , Chruściel J., Muś K. : Does mist-netting provide reliable data to determine the sex and age ratios of migrating birds? A case study involving the Great Tit (Parus major) and the Blue Tit (Cyanistes caeruleus). Ekologia (Bratislava), Vol. 32, No. 2, p. 173-185 , 2013. Ringing results of tits caught at two stations on the Polish Baltic coast were used to check if mistnetting could be successfully used to analyse the composition of sex and age classes of migrating birds. Four hypotheses are discussed, describing the distribution of age and sex classes during migration, and the consequences these distributions might have for the catching results. We analysed records of 59 000 Blue Tits and more than 84 000 Great Tits that were caught and we found a similarity in the results of catches at stations 188 km apart, and a higher similarity among catching sites 0.5-16 km apart. These results proved that mist-netting provides reliable data on the sex and age structure of migrating flocks, and that these data can generally be interpreted as representative for at least the area in a radius of more than 10 km. The results also showed a migratory divide through the central part of the Polish Baltic coastline between irruptive Blue Tits in the west and regular partial migrants in the east. Great Tits showed no tendency for irruptions anywhere in the study area. A high correspondence in the age and sex ratio was found for Great Tits and Blue Tits, in particular where both species are regular migrants. We found that the ratios of females and immatures did not differ by more than 1% over many years of study in these areas.
Ecophysiological Responses of Tall Fescue Genotypes to Endophyte Infection and Climate Change

OF THESIS ECOPHYSIOLOGICAL RESPONSES OF TALL FESCUE GENOTYPES TO ENDOPHYTE INFECTION AND CLIMATE CHANGE Tall fescue is a widely used forage grass in the eastern USA and can form a symbiosis with a fungal endophyte, which can be beneficial for the plant but can cause livestock health issues. Little is known regarding the symbiotic response to predicted climate change. To address this knowledge gap, I analyzed tall fescue variety trial data collected throughout the U.S., exploring relationships between climate variables and yield for two different fescue cultivars that were either endophyte-free or infected. This study showed no endophyte or cultivar effect on fescue yield, but identified temperature, precipitation and location as significant predictors of yield, suggesting that local conditions were more important than endophyte presence or fescue genotype for this dataset. Using a field experiment located in central Kentucky, I quantified the ecophysiological responses of four tall fescue genotypes to endophyte presence, elevated temperature and increased growing season precipitation. In this study, tall fescue genotype was as important as endophyte presence in determining ecophysiological responses to climate change treatments. My thesis illustrates that tall fescue response to climate change will depend on host genetics, the presence and genetics of the fungal endophyte symbiont, and the specific changes to the environment experienced at a site.
Viscosimetric study and synergistic antifungal activity of oils extract from three Algerian medicinal plants against toxigenic Aspergillus

Oils extracted from seeds of three medicinal plants used in Algerian folk medicine (Citrullus colocynthis, Nigella sativa and Linum usitassimum), were tested for their antifungal synergyagainst one strain of Aspergillus flavus toxin (A. flavus MTTC 2799) by the method of radial growth on solid medium Potateos Dextrose Agar (PDA). Antifungal results revealed that all oils tested at the concentration 1/5000 inhibited the growth of the studied fungus, where the best antifungal potency was observed for the L. usitassimum seed oil. The values ofantifungal indices (55.65, 48.65, 40.54) were recorded, respectively for L. usitassimum oil,C. colocynthis oil and N. sativa oil at concentrations of (1/5000, 1/500 and 1/2000). The results of the synergistic antifungal activity obtained by oils combination revealed that L.oil/C. oil showed the best antifungal effect (54.19%) before the L. oil/C.oil/N. oil system with 48.76% of inhibition. In order to explain the synergistic effect and the best behavior of oils, especially determination of optimal concentrations C* (C star) needed for antifungal synergistic activity, viscosimetric investigation was carried out at room temperature and at several concentrations. Key words: Viscosity, oil carbon chain, synergistic antifungal activity, oils, Aspergillus flavus.
The global threat of chikungunya virus

What is virus chikungunya? Chikungunya virus (CHIKV) is an emerging pathogen that belongs to the Togaviridae family. It causes chikungunya fever (CHIKF), a febrile illness associated with arthralgia and rash. The name chikungunya derives from a word in Makonde (Bantu language) meaning “that which bends,” describing the stooped appearance of those people suffering the characteristic painful arthralgia. Although in most cases this virus is not severe, it has become a global threat due to the emergence in recent years of several outbreaks that have affected a large part of the population and to the lack of effective vaccines and antivirals [1]. The chikungunya virus is divided into three distinct lineages [2] :  West African lineage.  Eastern / Central / Southern Africa lineage (ECSA). This group emerged a new lineage, the lineage of the Indian Ocean (IOL).  Asian lineage.
Possible interactions between the Fcε receptor and a novel mast cell function-associated antigen

We have recently described a monoclonal antibody, mAb G63, which identifies a novel membrane component of mast cells. This antigen is a glycoprotein with an apparent molecular mass of 28-40 kd, and is present on the surface of rat mucosal and serosal mast cells. Its density on cells of the mucosal mast cell line RBL-2H3 is 1 - 2 x 10(4) copies per cell. Crosslinking of this membrane protein by the intact mAb G63 results in a pronounced inhibition of the Fc epsilon RI-mediated secretion of RBL-2H3 cells. Here we show that crosslinking this novel membrane component inhibits biochemical processes initiated by Fc epsilon RI aggregation, such as the hydrolysis of phosphatidylinositides, the influx of Ca2+ ions, and the synthesis and release of de novo formed inflammatory mediators. Furthermore, by fluorescence microscopy, we show that crosslinking of Fc epsilon RI-IgE complexes by multivalent antigen results in redistribution of the membrane component recognized by G63, leading to its co-localization with the aggregated Fc epsilon RI. This localization is inhibited by NaN3, but not by colchicine or cytochalasin D. Fc epsilon RI crosslinking also promotes internalization of this novel membrane component. Taken together these data suggest that the mast cell membrane component recognized by mAb G63 is involved in the Fc epsilon RI-mediated stimulation of these cells, and thus can be considered a mast cell function-associated antigen (MAFA).
Evaluation of the in vivo role of p-glycoprotein in the maintenance of cholesterol homeostasis

Removal of cholesterol from the body is the final step in reverse cholesterol transport, the process by which excess cholesterol is moved from peripheral tissues to the liver for excretion. Several provocative studies led us to probe the contributions of P-glycoprotein (Pgp), an ATP-dependent transporter with broad range of hydrophobic substrates, to the removal of cholesterol and its bile acid metabolites from the body. We used knockout mice lacking both isoforms of Pgp (Abcb1a⁺/1b⁺) fed test diets containing elevated fat and/or cholesterol to determine if Pgp deletion affects murine cholesterol homeostasis. The knockout mice had the same cholesterol phenotype as wild-type mice, measured by cholesterol absorption, circulating lipoproteins, and hepatic storage of cholesterol. We examined the activation of two key regulatory pathways that maintain cholesterol homeostasis, Sterol Regulatory Element Binding Protein-2 (SREBP-2) and Liver X Receptor (LXR), to determine if the knockout mice maintain cholesterol balance through compensatory mechanisms. The knockout mice had decreased expression of SREBP-2-target genes in the jejunum and increased expression of LXR-target genes in the liver. These perturbations to cholesterol regulatory networks are indirect evidence that the knockout mice lacked a cholesterol efflux mechanism. We evaluated efflux of bile acids from the liver to the gallbladder in mice after nine weeks on the test diets. Knockout mice fed elevated fat or cholesterol had a 30-50% reduction in bile acid efflux capacity compared to wild type mice, suggesting that Pgp contributes to murine bile acid efflux. Subsequent analysis revealed that Pgp did not display specificity for a particular class of bile acids. In summary, we provide evidence that deletion of Pgp did not alter the cholesterol phenotype of mice; however, compensatory shifts in cholesterol regulatory networks maintained homeostasis in the knockout. Additionally, we show that Pgp knockout mice had a reduced capacity to efflux bile acids to the gallbladder. The nature of the changes to the cholesterol regulatory networks and the perturbations to bile acid efflux suggest that Pgp is a non-specific efflux transporter that recognizes both cholesterol and bile acids as substrates.
Proteolysis and Biogenic Amine Formation in Sterilized Edam‐Type Curd Slurry Inoculated with Probiotic Strains

Edam-type curd slurry inoculated with 1% Lactococcus lactis subsp. lactis KF147 as control and further added with Propionibacterium shermanii PS-4 + Bifidobacterium bifidum DSM 20082 (1:1), P. shermanii PS-4 + Lactobacillus acidophilus ATCC4356 or P. shermanii PS-4 + B. bifidum DSM 20082 + Lactobacillus acidophilus ATCC4356 (1:1:1), at a rate of 1%, were studied for their effect upon biogenic amine and proteolysis pattern during incubation at 30C for 21 days. Results showed no significant influence of any combination of probiotic microorganisms on total solids, salt and fat of Edam-type curd slurries, but some effect on pH and soluble nitrogen fractions; presence of P. shermanii + B. bifidum + Lactobacillus acidophilus led to the highest concentration (7.9%) of water-soluble nitrogen by the end of incubation. When inoculation included B. bifidum, a significant decrease in total biogenic amines (from 447 to 37 mg/kgDW) was observed by 21 days – with histamine decreasing from 84 to 25 and tyramine from 359 to 6 mg/kgDW. Practical Applications This study was aimed at investigating proteolysis and biogenic amine formation by selected probiotic bacteria added to Edam-type curd slurry. The nitrogen fractions and biogenic amines in control increased significantly throughout incubation at 30C. Inocula of P. shermanii + L. acidophilus + B. bifidum (1:1:1) could effectively reduce biogenic amine contents, especially histamine and tyramine. This observation has potential public health impact because regular curds are often above the maximum legal threshold in regions with warm weather and poor cold storage network. Furthermore, addition of probiotic L. acidophilus and B. bifidum improved the overall flavor profile, owing to extra soluble nitrogen produced.
The influence of calcium on phytase efficacy in non-ruminant animals

High dietary calcium (Ca) can negatively influence growth performance and reduce phosphorus, protein and amino acid digestibility in broilers and pigs. In addition, high dietary Ca will precipitate with phytate at pH conditions within the small intestine. Previous research reported that high dietary Ca significantly reduced phytase efficacy through precipitation with or competition for binding sites on the phytate molecule. However, microbial phytases are active at pH ranges where phytate is soluble and hydrolyse phytate rapidly to reduce the likelihood of phytate precipitating with Ca, suggesting the effect of dietary Ca on the efficacy of these phytases may be reduced. Even with such phytases there may still be problems observed due to particularly high concentrations of dietary Ca, which can occur as a result of a reduction in Ca not being applied in the presence of a phytase and/or if Ca concentrations in the diet exceed expectations. For example, when total Ca was analysed in 795 broiler and pig diets, on average, there was 0.22% more Ca present than expected. This means that if a diet was formulated to contain 0.80% total Ca, the analysed value could be as high as 1.02%, almost 25% above the expected dietary Ca concentration. The discrepancy between the expected and analysed total Ca may have implications on chemical and physical properties within the gastrointestinal tract, dietary phytate solubility, nutrient digestibility and phytase efficacy. The present paper aims to highlight factors influencing the effect of Ca on phytase efficacy, encompassing the differences among published book values for total Ca content of ingredients, the difference between Ca sources and their affinity for phytate, and finally how these factors influence the Ca to P ratio and thus phytase efficacy.
Identification and characterization of genes involved in Arabidopsis thaliana cell wall acetylation

Author(s): de Souza, Amancio Jose | Advisor(s): Pauly, Markus | Abstract: Most non-cellulosic plant cell wall polysaccharides including the hemicellulose xyloglucan and the pectic polysaccharides can be O-acetylated. This feature has direct significance in the use of these polymers in the food and biofuel industry. For example, increased pectin acetylation can reduce its gelling abilities and is hence detrimental in its application as a food thickener or emulsifier. In general, plant biomass with wall polymers with high acetate content can negatively influence biomass hydrolysis by fungal enzymes and interfere with downstream fermentation by yeasts.Genetic and biochemical approaches were used to identify genes involved in wall polymer acetylation in the model species Arabidopsis. A forward genetics approach was able to identify wall acetylation differences within a population of Arabidopsis ecotypes in both total wall acetate and xyloglucan O-acetylation. One of these naturally occurring mutant alleles of a recently identified putative xyloglucan acetyltransferase (AXY4) was found in the Ty-0 ecotype. Ty-0 completely lacks xyloglucan acetyl-substituents in roots and leaves, suggesting that the lack of XyG acetylation does not compromise the fitness of the ecotype in its ecological niche. In an attempt to further characterize the AXY4 protein, and characterize peptide domains involved in cell wall polymer recognition, a functional domain swap approach was utilized without success. A biochemical approach to identify and purify a putative xyloglucan acetylesterase was attempted also without success. Another way to modulate wall acetylation is by apoplastic plant acetylesterases, which naturally remove acetyl-substituents on polymers. To characterize genes in the Pectin acetyl esterase gene family in Arabidopsis thaliana, reverse genetics was used and lead to the identification of two genes responsible for altering wall acetate levels of pectins. Further pectin fractionation experiments suggest that PAE8 and PAE9 act predominantly but distinctively on pectic rhamnogalacturonan I. Pectin acetylesterase activity was demonstrated in vitro for the proteins encoded by PAE8 and PAE9. Through genetic means it is possible to increase wall acetate content, but this modification lead to a reduction in Arabidopsis inflorescence size giving insights about the function of acetylation of pectins.
EXPLOITATION OF RESISTANCE GENE ANALOGS ENCODING NBS-LRR DOMAINS IN WIDE HYBRIDIZATION OF COTTON

Resistance gene analogs (RGAs) are one of the rich families of R genes that share conserved motifs and encode NBS-LRR domains. Based on this property numerous RGAs were isolated from Gossypium arboreum based on reported sequences from G. hirsutum L. in the database and subsequently cloned for nucleotide sequencing analysis. The isolated RGAs from G. arboreum showed nucleotide and amino acid homology to the reported RGAs from G. barbadense and G. hirsutum but some of them were found to be unique in phylogenetic tree and they were considered as novel RGAs. There are two possibilities of their use either to as a probe for detection and isolation of full length R genes from crop plants or to use them as markers. So, the isolated unique RGAs were used as DNA markers in F 1 generation and back crosses of G. arboreum × G. anomalum , and F 1 population of G. arboreum × G. capitis-viridis . The series of assays proved that G. arboreum is free of diseases and an important source that could be used for the development of disease resistant cotton plants. Due to this property G. arboreum is being used in inter-specific hybridization. The isolated RGA as a marker confirmed the inter-specific F 1 generation and back crosses. The process of selection from inter-specific populations can be accelerated by the use of RGA markers and also could be used as an important tool to recover desirable plants containing resistance from G. arboreum .
A review of the genus Pellenes in the fauna of Central Asia and the Caucasus (Araneae, Salticidae)

The paper is a review of the genus Pellenes (s. lat.) in the fauna of Central Asia and the Caucasus. The genus Pellenes (s. lat.) is rede® ned and subdivided into four subgenera according to the structure of genitalia: Pellenes (s. str.), Pelpaucus subgen. nov., Pelmultus subgen. nov. and Pelmirus subgen. nov. Altogether 23 species have been treated, of which nine are described as new to science: Pellenes amazonka sp. nov. (female), P. badkhyzicus sp. nov. (male), P. borisi sp. nov. (female), P. karakumensis sp. nov. (male), P. bonus sp. nov. (male), P. pamiricus sp. nov. (male and female), P. pseudobrevis sp. nov. (male and female), P. sytchevskayae sp. nov. (male and female) and P. turkmenicus sp. nov. (male and female). Five species are newly synonymized: P. maderianus KulczynÂ ski, 1905 with P. epularis (O. P.-Cambridge, 1872); P. kulabicus Andreeva, 1976 and P. simoni (O. P.-Cambridge, 1872) with P. geniculatus (Simon, 1868); and P. albomaculatus Peng and Xie, 1993 with P. denisi Schenkel, 1963; P. tauricus (Thorell, 1875) is removed from synonymy with P. simoni (O. P.-Cambridge, 1872) and is shown to be a junior synonym of P. nigrociliatus (Simon in L. Koch, 1875). A lectotype is designated for Pellenes brevis Simon, 1868. P. campylophorous (Thorell, 1875) is recognized to be nomen dubium. Pellenes calvus (Simon, 1868) is excluded from the Central Asian fauna of Pellenes. Evarcha lapponica (Sundevall, 1832), comb. nov. (ex Pellenes), is proposed. Some