A data-driven integrative model of sepal primordium polarity in Arabidopsis

Flower patterning is determined by a complex molecular network but how this network functions remains to be elucidated. Here, we develop an integrative modeling approach that assembles heterogeneous data into a biologically coherent model to allow predictions to be made and inconsistencies among the data to be found. We use this approach to study the network underlying sepal development in the young flower of Arabidopsis thaliana. We constructed a digital atlas of gene expression and used it to build a dynamical molecular regulatory network model of sepal primordium development. This led to the construction of a coherent molecular network model for lateral organ polarity that fully recapitulates expression and interaction data. Our model predicts the existence of three novel pathways involving the HD-ZIP III genes and both cytokinin and ARGONAUTE family members. In addition, our model provides predictions on molecular interactions. In a broader context, this approach allows the extraction of biological knowledge from diverse types of data and can be used to study developmental processes in any multicellular organism.     

Agrobacterium tumefasciens-mediated transformation of the aquatic fungus Blastocladiella emersonii

Agrobacterium tumefaciens is widely used for plant DNA transformation and more recently, has also been used to transform yeast, filamentous fungi and even human cells. Using this technique, we developed the first transformation protocol for the saprobic aquatic fungus Blastocladiella emersonii, a Blastocladiomycete localized at the base of fungal phylogenetic tree, which has been shown as a promising and interesting model of study of cellular function and differentiation. We constructed binary T-DNA vectors containing hygromycin phosphotransferase (hph) or enhanced green fluorescent protein (egfp) genes, under the control of Aspergillus nidulans trpC promoter and terminator sequences. 24 h of co-cultivation in induction medium (IM) agar plates, followed by transfer to PYG-agar plates containing cefotaxim to kill Agrobacterium tumefsciens and hygromycin to select transformants, resulted in growth and sporulation of resistant transformants. Genomic DNA from the pool o resistant zoospores were shown to contain T-DNA insertion as evidenced by PCR amplification of hph gene. Using a similar protocol we could also evidence the expression of enhanced green fluorescent protein (EGFP) in zoospores derived from transformed cells. This protocol can also open new perspectives for other non-transformable closely related fungi, like the Chytridiomycete class.     

Oxidative Damage of Lysozyme and Human Serum Albumin and Their Mixtures. A Comparison of Photosensitized and Peroxyl Radical Promoted Processes

Oxidative modifications of lysozyme (Lyso) and human serum albumin (HSA) mediated by photoinduced processes and peroxyl radicals were studied. Both oxidative conditions were applied to the separate proteins and their mixtures. Dimerization and fragmentation of the proteins do not correlate with the formation of carbonyls or peroxides, implying that evaluation of these changes is not an index of the overall oxidative modification of a protein. The results obtained also show that the hypothesis that the electrostatic interactions of Lyso and HSA could facilitate the formation of Lyso-HSA dimers in the presence of a source of reactive oxygen species was verified in both ROS-producing systems.     

Inhibitory Effects of Bile Acids on Enzymatic and Pharmacological Activities of a Snake Venom Phospholipase A<Subscript>2</Subscript> from Group IIA

Bile acids, such as cholic acid (CA) and ursodeoxycholic acid (UDCA) have shown to decrease or increase the enzymatic activity of group IB pancreatic PLA₂, depending on the concentration used. Studies suggest that the inhibition of hydrolysis rate of the substrate is due to formation in aqueous phase of a complex between bile acid and PLA₂, which is catalytically inert. For this reason, we tested the inhibition of the enzymatic activity of group IIA snake venom PLA₂ by bile acids, using an aqueous phase model. In addition, we measured the ability of bile acids to inhibit the toxic effects caused by the mentioned toxin. UDCA and CA inhibited the enzymatic activity of the PLA₂ in a competitive mode. Moreover, these compounds inhibited myotoxic, cytotoxic and edema-forming activities induced by the toxin, but UDCA was more efficient than CA. It was demonstrated that bile acids interact directly with this protein by causing slight changes in the intrinsic fluorescence spectra. Preliminary molecular docking studies suggest that bile acids interact with amino acids at the active site of the PLA₂ through different interactions, CA showed hydrogen bonds with His48, whereas, UDCA displayed with Asp49. Results obtained herein may turn UDCA and CA into promising models for the development of new molecules with anti-inflammatory and anti-snake venom PLA₂ properties.     

Stem cells in brain tumorigenesis and their impact on therapy

The concept that the genesis of new cells in the adult mammalian brain is negligible has long influenced our perception and understanding of the origin and development of central nervous system (CNS) tumors. The discovery that neurons and glia are produced throughout life from neural stem cells provides new possibilities for candidate precursor cells of CNS neoplasms. The emerging hypothesis is that alterations in the cellular and genetic mechanisms that control adult neurogenesis might contribute to brain tumorigenesis. As such, opportunities become available to identify new therapeutic strategies.     

The response of Arctic vegetation and soils following an unusually severe tundra fire

Fire causes dramatic short-term changes in vegetation and ecosystem function, and may promote rapid vegetation change by creating recruitment opportunities. Climate warming likely will increase the frequency of wildfire in the Arctic, where it is not common now. In 2007, the unusually severe Anaktuvuk River fire burned 1039 km² of tundra on Alaska''s North Slope. Four years later, we harvested plant biomass and soils across a gradient of burn severity, to assess recovery. In burned areas, above-ground net primary productivity of vascular plants equalled that in unburned areas, though total live biomass was less. Graminoid biomass had recovered to unburned levels, but shrubs had not. Virtually all vascular plant biomass had resprouted from surviving underground parts; no non-native species were seen. However, bryophytes were mostly disturbance-adapted species, and non-vascular biomass had recovered less than vascular plant biomass. Soil nitrogen availability did not differ between burned and unburned sites. Graminoids showed allocation changes consistent with nitrogen stress. These patterns are similar to those seen following other, smaller tundra fires. Soil nitrogen limitation and the persistence of resprouters will likely lead to recovery of mixed shrub–sedge tussock tundra, unless permafrost thaws, as climate warms, more extensively than has yet occurred.     

Aluminium foil as an alternative substrate for the spectroscopic interrogation of endometrial cancer

Biospectroscopy has the potential to investigate and characterize biological samples and could, therefore, be utilized to diagnose various diseases in a clinical environment. An important consideration in spectrochemical studies is the cost‐effectiveness of the substrate used to support the sample, as high expense would limit their translation into clinic. In this paper, the performance of low‐cost aluminium (Al) foil substrates was compared with the commonly used low‐emissivity (low‐E) slides. Attenuated total reflection‐Fourier transform infrared spectroscopy was used to analyse blood plasma and serum samples from women with endometrial cancer and healthy controls. The 2 populations were differentiated using principal component analysis with support vector machines with 100% sensitivity in plasma samples (endometrial cancer = 70; healthy controls = 15) using both Al foil and low‐E slides as substrates. The same sensitivity results (100%) were achieved for serum samples (endometrial cancer = 60; healthy controls = 15). Specificity was found higher using Al foil (90%) in comparison to low‐E slides (85%) and lower using Al foil (70%) in comparison to low‐E slides in serum samples. The establishment of Al foil as low‐cost and highly performing substrate would pave the way for large‐scale, multicentre studies and potentially for routine clinical use.

     

Length‐weight relationships of fishes in the Mira basin,Colombia

This study estimated the a and b parameters of the length–weight relationships of 15 fishes from the Mira and Caunapí rivers, San Andrés de Tumaco, Nariño, Colombia. The specimens were captured during four samplings periods between 2015 and 2016 using a different a combination of fishing gillnets and electrofishing. The a values ranged from 0.0002 to 0.04 and b values ranged from 2.86 to 3.6. The data presented here are tentative estimates because the fish have been weighted and measured after fixation in formalin and ethanol, however, these data are references for weight‐length relationship for 15 species, the maximum weight for the same 15, and new maximum lengths for 3 species.     

Hydrophobicity of Antifungal β-Peptides Is Associated with Their Cytotoxic Effect on In Vitro Human Colon Caco-2 and Liver HepG2 Cells

The widespread distribution of fungal infections, with their high morbidity and mortality rate, is a global public health problem. The increase in the population of immunocompromised patients combined with the selectivity of currents treatments and the emergence of drug-resistant fungal strains are among the most imperative reasons to develop novel antifungal formulations. Antimicrobial β-peptides are peptidomimetics of natural antimicrobial peptides (AMPs), which have been proposed as developmental platforms to enhance the AMPs selectivity and biostability. Their tunability allows the design of sequences with remarkable activity against a wide spectrum of microorganisms such as the human pathogenic Candida spp., both in planktonic and biofilm morphology. However, the β-peptide’s effect on surrounding host cells remains greatly understudied. Assessments have mainly relied on the extent of hemolysis that a candidate peptide is able to cause. This work investigated the in vitro cytotoxicity of various β-peptides in the Caco-2 and HepG2 mammalian cell lines. Results indicated that the cytotoxic effect of the β-peptides was influenced by cell type and was also correlated to structural features of the peptide such as hydrophobicity. We found that the selectivity of the most hydrophobic β-peptide was 2–3 times higher than that of the least hydrophobic one, for both cell types according to the selectivity index parameter (IC50/MIC). The IC50 of Caco-2 and HepG2 increased with hydrophobicity, which indicates the importance of testing putative therapeutics on different cell types. We report evidence of peptide-cell membrane interactions in Caco-2 and HepG2 using a widely studied β-peptide against C. albicans.