How to measure top–down vs bottom–up effects: a new population metric and its calibration on Daphnia

Research on the role of top–down (predation) and bottom–up (food) effects in food webs has led to the understanding that the variability of these effects in space and time is a fundamental feature of natural systems. Consequently, our measurement tools must allow us to evaluate the effects from a dynamical perspective. A population‐dynamics approach may be appropriate to the task. More specifically, because food and predators both affect birth rate, birth rate dynamics may be a key to understanding their impact on the population of interest. Based on the Edmondson–Paloheimo model for birth rate, we propose a new population metric to assess the relative strength of top–down vs bottom–up effects. The metric is the ratio of contributions of changes in proportion of adults and fecundity to change in birth rate. Proportion of adults reflects a top–down effect (predators are assumed to be size‐selective), fecundity reflects a bottom–up effect, and birth rate appears as a common currency with which to compare the former and the latter. Using microcosm experiments and computer simulations on the cladoceran Daphnia, we calibrate the metric and show that, in both types of tests, the ratio of contributions is typically 0.5–0.7 under a strong bottom–up effect and 2.0–2.2 under a strong top–down effect. This provides experimental evidence that the ratio of contributions may allow one to distinguish a strong top–down effect from a strong bottom–up effect.     

The antileukemic activity of modified fibrinogen–methotrexate conjugate

Background

The search for new, innovative methods to treat all types of diseases, especially cancer-related ones, is a challenge taken by pharmaceutical companies and academic institutions. The use of conjugates containing widely-known and widely-used bioactive substances is one of the ways to solve this problem. Research into drug binding with macromolecular carrier systems has joined the search for new therapeutic strategies.

Methods

The main goal of this paper is the potential offered by the use of fibrinogen derivatives as an antileukemic drug carrier. Physicochemical properties of the obtained conjugate were analyzed, characterizing alterations in relation to the starting carrier and analyzing biological implications. The intraperitoneally (i.p.) inoculated P388 mouse leukemia model for in vivo studies was used.

Results and conclusions

Conjugates consisting of a fibrinogen derivative with a covalently bound anticancer drug were developed. Carrier preparation and a conjugate synthesis in aqueous solution were formulated, as well as purification of the conjugate was performed. The study showed that the survival of leukemia mice treated with FH–MTX conjugate was indeed significantly longer than survival in both untreated animals (control) and mice treated with unbound MTX. A significant increase in the antileukemic activity of MTX conjugated with hydrolysed fibrinogen was observed as compared with the unconjugated drug. Reported data suggest that hydrolysed fibrinogen can serve as a carrier molecule for the MTX drug with the aim of enhancing its antileukemic activity.

General significance

Conjugates consisting of a fibrinogen derivative with a covalently bound anticancer drug seem to be a promising anticancer drug.     

Therapeutic regulation of myeloid-derived suppressor cells and immune response to cancer vaccine in patients with extensive stage small cell lung cancer

Myeloid-derived suppressor cells (MDSC) are one of the major factors limiting the efficacy of immune therapy. In a clinical trial of patients with extensive stage small cell lung cancer (SCLC), we tested the possibility that targeting MDSC can improve the induction of immune responses by a cancer vaccine. Forty-one patients with extensive stage SCLC were randomized into three arms: arm A—control, arm B—vaccination with dendritic cells transduced with wild-type p53, and arm C—vaccination in combination with MDSC targeted therapy with all-trans-retinoic acid (ATRA). Interim results of the ongoing clinical trial are presented. Pre-treatment levels of MDSC populations in patients from all three arms were similar. Vaccine alone did not affect the proportion of MDSC, whereas in patients treated with ATRA, the MDSC decreased more than twofold (p = 0.02). Before the start of treatment, no patients had detectable p53-specific responses in IFN-γ ELISPOT. Sequential measurements did not show positive p53 responses in any of the 14 patients from arm A. After immunization, only 3 out of 15 patients (20 %) from arm B developed a p53-specific response (p = 0.22). In contrast, in arm C, 5 out of 12 patients (41.7 %) had detectable p53 responses (p = 0.012). The proportion of granzyme B-positive CD8⁺ T cells was increased only in patients from arm C but not in arm B. Depletion of MDSC substantially improved the immune response to vaccination, suggesting that this approach can be used to enhance the effect of immune interventions in cancer.     

A new species of Aspidistra (Ruscaceae s.l., Asparagales) from southern Vietnam, field observations on its flowering and possible pollination by flies (Phoridae)

The genus Aspidistra with almost 100 species is the most diverse in southern China and northern Vietnam. We describe a new species Aspidistra phanluongii N.Vislobokov from southern Vietnam. Species of Aspidistra are herbs characteristic of Southeast Asian forests. Flowering of these plants can be considered cryptic. There are no recorded field observations on phenology, biology of flowering or pollination of Aspidistra. Previously proposed pollinators of Aspidistra include collembolans, amphipods, fungus gnats (Diptera: Mycetophilidae, Sciaridae) and even slugs. We present observation data on the flowering of A. phanluongii in the wild. Flowers were visited by flies of Megaselia (Phoridae) and ants. Megaselia flies, well-known pollinators of numerous tropical plant species, are shown to be likely pollinators of Aspidistra phanluongii. The present study does not provide evidence of pollination by fungus gnats.     

114 Kinetic and thermodynamic basis for damaged bases excision by 8-oxoguanine-DNA glycosylases

DNA glycosylases play the opening act in a highly conserved process for excision of damaged bases from DNA called the base excision repair pathway. DNA glycosylases attend to a wide variety of lesions arising from both endogenous and exogenous factors. The types of damage include alkylation, oxidation, and hydrolysis. A major DNA oxidation product is 8-oxoguanine (8-oxoG), a base with a high mutagenic potential. In bacteria, this lesion is repaired by formamidopyrimidine-DNA glycosylase (Fpg), while in the case of humans this function belongs to 8-oxoG-DNA glycosylase (OGG1). We have attempted a comprehensive characterization of 8-oxoG recognition by DNA glycosylases. First, we have obtained thermodynamic parameters for melting of DNA duplexes containing 8-oxoG in all possible nucleotide contexts. The energy of stacking interactions of 8-oxoG was in strict dependence on 8-oxoG nucleotide environment, which may affect the recognition of damage and the efficiency of eversion of 8-oxoG from DNA helix by glycosylases. Next, we established how the flexibility of DNA context affects damage recognition by these enzymes (Kirpota et al., 2011). Then, we have found that DNA containing 8-oxoG next to a single-strand break provides a good substrate for Fpg, as soon as all structural phosphate residues are maintained. Using site-directed mutagenesis, we have addressed the functions of many previously unstudied amino acid residuess that were predicted to be important for Fpg activity by molecular dynamics simulation and phylogenetic analysis. Of note, many substitutions abolished the excision of 8-oxoG, but did not affect the cleavage efficiency of abasic substrates. Finally, we investigated the contribution of separated structural domains of Fpg to specific enzyme-substrate interaction. Surprisingly, despite the absence of the catalytic domain, C-terminal domain of Fpg possessed a low- residual ability to recognize and cleave abasic substrates. Our study sheds light on mechanism details of Fpg and OGG1 activity, with the ultimate goal of understanding how binding energy can be spent by these enzymes for catalysis.     

Potential CRF1R PET imaging agents: 1-Fluoroalkylsubstituted 5-halo-3-(arylamino)pyrazin-2(1H)-ones

A series of pyrazinones were prepared and evaluated as potential CRF₁R PET imaging agents. Optimization of their CRF₁R binding potencies and octanol–phosphate buffer phase distribution coefficients are discussed herein.     

Automated quantification of budding Saccharomyces cerevisiae using a novel image cytometry method

The measurements of concentration, viability, and budding percentages of Saccharomyces cerevisiae are performed on a routine basis in the brewing and biofuel industries. Generation of these parameters is of great importance in a manufacturing setting, where they can aid in the estimation of product quality, quantity, and fermentation time of the manufacturing process. Specifically, budding percentages can be used to estimate the reproduction rate of yeast populations, which directly correlates with metabolism of polysaccharides and bioethanol production, and can be monitored to maximize production of bioethanol during fermentation. The traditional method involves manual counting using a hemacytometer, but this is time-consuming and prone to human error. In this study, we developed a novel automated method for the quantification of yeast budding percentages using Cellometer image cytometry. The automated method utilizes a dual-fluorescent nucleic acid dye to specifically stain live cells for imaging analysis of unique morphological characteristics of budding yeast. In addition, cell cycle analysis is performed as an alternative method for budding analysis. We were able to show comparable yeast budding percentages between manual and automated counting, as well as cell cycle analysis. The automated image cytometry method is used to analyze and characterize corn mash samples directly from fermenters during standard fermentation. Since concentration, viability, and budding percentages can be obtained simultaneously, the automated method can be integrated into the fermentation quality assurance protocol, which may improve the quality and efficiency of beer and bioethanol production processes.     

Melanoma cells produce multiple laminin isoforms and strongly migrate on α5 laminin(s) via several integrin receptors

Melanoma cells express and interact with laminins (LMs) and other basement membrane components during invasion and metastasis. In the present study we have investigated the production and migration-promoting activity of laminin isoforms in melanoma. Immunohistochemistry of melanoma specimens and immunoprecipitation/western blotting of melanoma cell lines indicated expression of laminin-111/121, laminin-211, laminin-411/421, and laminin-511/521. Laminin-332 was not detected. In functional assays, laminin-111, laminin-332, and laminin-511, but not laminin-211 and laminin-411, strongly promoted haptotactic cell migration either constitutively or following stimulation with insulin-like growth factors. Both placenta and recombinant laminin-511 preparations were highly active, and the isolated recombinant IVa domain of LMα5 also promoted cell migration. Function-blocking antibodies in cell migration assays revealed α6β1 integrin as the major receptor for laminin-111, and both α3β1 and α6β1 integrins for laminin-332 and laminin-511. In contrast, isolated LMα5 IVa domain-promoted melanoma cell migration was largely mediated via αVβ3 integrin and inhibited by RGD peptides. Given the ubiquitous expression of α5 laminins in melanoma cells and in melanoma-target tissues/anatomical structures, as well as the strong migration-promoting activity of these laminin isoforms, the α5 laminins emerge as putative primary extracellular matrix mediators of melanoma invasion and metastasis via α3β1 and other integrin receptors.     

Octahedral (cyclopentadienyl)rhodium clusters [Rh6Cp6(μ6-C)] and [Rh6Cp6(μ3-CO)2]: Synthesis, structures and electrochemistry

The 86-electron dicationic octahedral rhodium clusters containing Cp (Cp = C₅H₅) ligands and either an interstitial carbon atom, [Rh₆Cp₆(μ₆-C)]²⁺ ([1]²⁺), or two carbonyl groups, [Rh₆Cp₆(μ₃-CO)₂]²⁺ ([2]²⁺), were synthesized in low yields by reactions of Rh₃Cp₃(μ-CO)₃ with RhCp(C₂H₄)₂ or [RuCp^∗(MeCN)₃]⁺ (Cp^∗ = C₅Me₅), respectively. The structures of [1]²⁺ and [2]²⁺ were determined by X-ray diffraction. Their electrochemical behavior proved that they possess a rather extended electron transfer activity. In accordance with DFT calculations, the nearly octahedral structure of [1]²⁺ and [2]²⁺ is retained both upon oxidation (2+/3+) and the first reduction (2+/+); however, the second reduction (+/0) results in the breaking of one (for [1]⁰) or two (for [2]⁰) Rh-Rh bonds. In the case of the related Dahl’s nickel cluster Ni₆Cp₆ the nearly octahedral structure is retained upon all redox steps (3+/2+/+/0/−/2−).