Metastasis as supra-cellular selection? A reply to Lean and Plutynski

In response to Germain (Biol Philos 27:785–810, 2012. doi: 10.1007/s10539-012-9334-2) argument that evolution by natural selection has a limited explanatory power in cancer, Lean and Plutynski (Biol Philos 31:39–57, 2016. doi: 10.1007/s10539-015-9511-1) have recently argued that many adaptations in cancer only make sense at the tumor level, and that cancer progression mirrors the major evolutionary transitions. While we agree that selection could potentially act at various levels of organization in cancers, we argue that tumor-level selection (MLS2) is unlikely to actually play a relevant role in our understanding of the somatic evolution of human cancers.     

A Cladist is a systematist who seeks a natural classification: some comments on Quinn (2017)

In response to Quinn (Biol Philos, 2017.  https://doi.org/10.1007/s10539-017-9577-z) we identify cladistics to be about natural classifications and their discovery and thereby propose to add an eighth cladistic definition to Quinn’s list, namely the systematist who seeks to discover natural classifications, regardless of their affiliation, theoretical or methodological justifications.     

Agomelatine and Duloxetine Synergistically Modulates Apoptotic Pathway by Inhibiting Oxidative Stress Triggered Intracellular Calcium Entry in Neuronal PC12 Cells: Role of TRPM2 and Voltage-Gated Calcium Channels

Calcium ion (Ca²⁺) is one of the universal second messengers, which acts in a wide range of cellular processes. Results of recent studies indicated that ROS generated by depression leads to loss of endoplasmic reticulum-Ca²⁺ homeostasis, oxidative stress, and apoptosis. Agomelatine and duloxetine are novel antidepressant and antioxidant drugs and may reduce oxidative stress, apoptosis, and Ca²⁺ entry through TRPM2 and voltage-gated calcium channels. We tested the effects of agomelatine, duloxetine, and their combination on oxidative stress, Ca²⁺ influx, mitochondrial depolarization, apoptosis, and caspase values in the PC-12 neuronal cells. PC-12 neuronal cells were exposed in cell culture and exposed to appropriate non-toxic concentrations and incubation times for agomelatine were determined in the neurons by assessing cell viability. Then PC-12 cells were incubated with agomelatine and duloxetine for 24 h. Treatment of cultured PC-12 cells with agomelatine, duloxetine, and their combination results in a protection on apoptosis, caspase-3, caspase-9, mitochondrial membrane depolarization, cytosolic ROS production, glutathione peroxidase, reduced glutathione, and lipid peroxidation, values. Ca²⁺ entry through non-specific TRPM2 channel blocker (2-APB) and voltage-gated Ca²⁺ channel blockers (verapamil and diltiazem) was modulated by agomelatine and duloxetine. However, effects of duloxetine on the Ca²⁺ entry through TRPM2 channels were higher than in agomelatine. Results of current study suggest that the agomelatine and duloxetine are useful against apoptotic cell death and oxidative stress in PC-12 cells, which seem to be dependent on mitochondrial damage and increased levels of intracellular Ca²⁺ through activation of TRPM2 and voltage-gated Ca²⁺ channels.     

The Origin and Evolution of Vertebrate Glycine Transporters

In the vertebrate central nervous system, glycinergic neurotransmission is regulated by the action of the glycine transporters 1 and 2 (GlyT1 and GlyT2)—members of the solute carrier family 6 (SLC6). Several invertebrate deuterostomes have two paralogous glycine carrier genes, with one gene in the pair having greater sequence identity and higher alignment scores with respect to GlyT1 and the other paralog showing greater similarity to GlyT2. In phylogenetic trees, GlyT2-like sequences from invertebrate deuterostomes form a monophyletic subclade with vertebrate GlyT2, while invertebrate GlyT1-like proteins constitute an outgroup to both the GlyT2-like proteins and to vertebrate GlyT1 sequences. These results are consistent with the hypothesis that vertebrate GlyT1 and GlyT2 are, respectively, derived from GlyT1- and GlyT2-like genes in invertebrate deuterostomes. This implies that the gene duplication which gave rise to these paralogs occurred prior to the origin of vertebrates. GlyT2 subsequently diverged significantly from its invertebrate orthologs (i.e., through the acquisition of a unique N-terminus) as a consequence of functional specialization, being expressed principally in the lower CNS; while GlyT1 has activity in both the lower CNS and several regions of the forebrain.     

Phosphoinositide 3-Kinase Pathway Mediates Early Aldosterone Action on Morphology and Epithelial Sodium Channel in Mammalian Renal Epithelia

Involvement of phosphoinositide 3-kinases (PI3Ks) in early aldosterone action on epithelial sodium channel (ENaC) in mammalian renal epithelia was investigated by hopping probe ion conductance microscopy combined with patch-clamping in this study. Aldosterone treatment enlarged the cell volume and elevated the apical membrane of renal mpkCCDc14 epithelia, which resulted in enhancing the open probability of ENaC. Inhibition of PI3K pathway by LY294002 obviously suppressed these aldosterone-induced changes in both cell morphology and ENaC activity. These results indicated the important role of PI3K pathway in early aldosterone action and the close relationship between cell morphology and ENaC activity in mammalian renal epithelia.     

Molecular Evolution and Functional Divergence of the Metallothionein Gene Family in Vertebrates

The metallothionein (MT) gene superfamily consists of metal-binding proteins involved in various metal detoxification and storage mechanisms. The evolution of this gene family in vertebrates has mostly been studied in mammals using sparse taxon or gene sampling. Genomic databases and available data on MT protein function and expression allow a better understanding of the evolution and functional divergence of the different MT types. We recovered 77 MT coding sequences from 20 representative vertebrates with annotated complete genomes. We found multiple MT genes, also in reptiles, which were thought to have only one MT type. Phylogenetic and synteny analyses indicate the existence of a eutherian MT1 and MT2, a tetrapod MT3, an amniote MT4, and fish MT. The optimal gene-tree/species-tree reconciliation analyses identified the best root in the fish clade. Functional analyses reveal variation in hydropathic index among protein domains, likely correlated with their distinct flexibility and metal affinity. Analyses of functional divergence identified amino acid sites correlated with functional divergence among MT types. Uncovering the number of genes and sites possibly correlated with functional divergence will help to design cost-effective MT functional and gene expression studies. This will permit further understanding of the distinct roles and specificity of these proteins and to properly target specific MT for different types of functional studies. Therefore, this work presents a critical background on the molecular evolution and functional divergence of vertebrate MTs to carry out further detailed studies on the relationship between heavy metal metabolism and tolerances among vertebrates.     

The Evolution of Reproduction-Related NLRP Genes

NLRP proteins are important components of inflammasomes with a major role in innate immunity. A subset of NLRP genes, with unknown functions, are expressed in oocytes and early embryos. Mutations of Nlrp5 in mice are associated with maternal-effect embryonic lethality and mutations of NLRP7 in women are associated with conception of biparental complete hydatidiform moles (biCHMs), suggesting perturbed processes of genomic imprinting. Recessive mutations on NLRP2/7 in humans are associated with reproductive disorders and appear to be induced by a demethylation of the maternal pronucleus. In this study, we find that radiation of NLRP genes occurred before the common ancestor of Afrotheria and Boreoeutheria, with the clade of oocyte-expressed genes originating before the divergence of marsupial and eutherian mammals. There have been multiple independent duplications of NLRP2 genes one of which produced the NLRP7 gene associated with biCHMs.     

Tonoplast Lipid Composition and Proton Pump of Pineapple Fruit During Low-Temperature Storage and Blackheart Development

Vacuole represents a major storage organelle playing vital roles in pH homoeostasis and cellular detoxification. The chemical and functional properties of tonoplast in response to chilling temperature and their roles in chilling injury are largely unknown. In the current study, lipid composition of tonoplast and the activities of two vacuolar proton pumps, H⁺-ATPase (V-ATPase) and H⁺-pyrophosphatase (V-PPase), were investigated in accordance with the development of blackheart, a form of chilling injury in pineapple fruit (Ananas comosus). Chilling temperature at 10 °C for 1 week induced irreversible blackheart injury in concurrence with a substantial decrease in V-ATPase activity. By contrast, the activity was increased after 1 week at 25 °C. The activity of V-PPase was not changed under both temperatures. Level of total phospholipids of tonoplast decreased at 10 °C, but increased at 25 °C. There was no change at the level of total glycolipids under both temperatures. Thus, low temperature increased the ratio of total glycolipids vs. total phospholipids of tonoplast. Phosphatidylcholine and phosphatidylethanolamine were the predominant phospholipids of tonoplast. Low temperature increased the relative level of phosphatidic acid but decreased the percentage of both phosphatidylcholine and phosphatidylethanolamine. Unsaturated fatty acids accounted for over 60 % of the total tonoplast fatty acids, with C18:1 and C18:2 being predominant. Low temperature significantly decreased the percentage of C18:3. Modification of membrane lipid composition and its effect on the functional property of tonoplast at low temperature were discussed in correlation with their roles in the development of chilling injury in pineapple fruit.     

The hand of man first then Santa Rosalia’s blessing: a critical examination of the supposed criticism by Samraoui (2017)

Samraoui (J Insect Conserv.  https://doi.org/10.1007/s10841-017-9966-2, 2017) claims that he shows evidence that our conservation plan of Urothemis edwardsii has failed and that natural dispersal was the only cause of the recent rapid range expansion of the species in Northeast Algeria. Here, we show that his analysis is biased, many of his arguments are erroneous and strongly contradictory, many key studies are dismissed, and the few data used as evidence to refute our conclusions rather confirm them. We also provide data to prove that our conservation plan did not cause any harm to the source population by comparing exuviae-based estimation of population size in 2012 and 2016. We discuss the need for future monitoring and management and highlight that the recommendations of Samraoui (J Insect Conserv, 2017) are misleading, and thus are unlikely to bring us closer to an effective long-term conservation of the species in the region. Beyond our criticism, we explain why we should not dismiss the direct and indirect implications of final instar larvae translocation in successful colonization of odonates in particular, which could also be applied to aquatic insects in general.     

Cardiotoxicity Induced by Antifungal Drugs

This review addresses the potential of antifungal drugs to cause cardiac toxicity. Many antifungal drugs, especially antifungal azoles, rarely cause torsades de pointes (TdP) and carry the risk of sudden death. Interventions to avoid TdP should include cautious use of azoles in combination with other drugs that cause QTc prolongation, and elimination of risk factors for TdP whenever possible. These risk factors include: hypokalemia, hypomagnesemia, severe bradycardia, and preexisting long QT syndrome. ECG monitoring should be considered when the use of multiple QT-prolonging drugs is unavoidable and TdP risk factors cannot be resolved. Itraconazole exhibits negative inotropic activity which may present as worsening heart failure in patients with preexisting heart failure. A few cases of severe bradycardia have also been described with voriconazole. Most cases of cardiac toxicity associated with amphotericin B are due to severe electrolyte abnormalities, rapid administration or overdose. Although cardiac toxicity is not common with the use of antifungal drugs, recognition of the potential to cause serious cardiac-related outcomes, evaluation of risk factors, and monitoring is warranted.     

Amphotericin B: How Much Is Enough?

The total curative dose of amphotericin B for any given fungal infection or specific patient is not precisely known. Prior to the availability of lipid formulations of amphotericin B (LFAB), dosing of amphotericin B was dictated by its associated toxicity. The unique pharmacokinetic features of each LFAB have led to differences in their recommended doses. Most published data have evaluated doses of 3–5 mg/kg/day, although niches exist for both higher and lower doses. Low-dose LFAB allows for intravenous broad-spectrum antifungal coverage without drug-drug interactions and with reduced toxicity. High-dose LFAB demonstrates increased fungal clearance in animal models, although this has not translated to improved clinical outcomes for most invasive fungal infections. Although available data do not demonstrate significant benefit associated with high-dose therapy, for liposomal amphotericin B, the data also demonstrate no significant harm. As such, the use of high-dose liposomal amphotericin B for salvage therapy may be a consideration.     

Large-Scale Chromosomal Changes and Associated Fitness Consequences in Pathogenic Fungi

Pathogenic fungi encounter many different host environments to which they must adapt rapidly to ensure growth and survival. They also must be able to cope with alterations in established niches during long-term persistence in the host. Many eukaryotic pathogens have evolved a highly plastic genome, and large-scale chromosomal changes including aneuploidy, and loss of heterozygosity (LOH) can arise under various in vitro and in vivo stresses. Both aneuploidy and LOH can arise quickly during a single cell cycle, and it is hypothesized that they provide a rapid, albeit imprecise, solution to adaptation to stress until better and more refined solutions can be acquired by the organism. While LOH, with the extreme case of haploidization in Candida albicans, can purge the genome from recessive lethal alleles and/or generate recombinant progeny with increased fitness, aneuploidy, in the absence or rarity of meiosis, can serve as a non-Mendelian mechanism for generating genomic variation.     

Different Incubation Times of Cells After Gene Electrotransfer in Fetal Bovine Serum Affect Cell Viability,but Not Transfection Efficiency

Electroporation as a delivery method is increasingly important in gene therapy, not only in vivo but also in in vitro experimental systems. Different applications of gene electrotransfer require high viability of cells and high transfection efficiency of gene electrotransfer. It was already demonstrated that the addition of fetal bovine serum (FBS) immediately after gene electrotransfer leads to improved cell survival and transfection efficiency. Therefore, the aim of the study was to determine whether prolonged incubation of cells in FBS, for more than standard 5 min, can lead to increased transfection efficiency and improved cell survival. Different murine melanoma and murine and human endothelial cell lines were transfected with plasmid encoding green fluorescent protein and then incubated for different periods of time in FBS (5–30 min). Transfection efficiency was determined by flow cytometry and fluorescence microscopy and cell survival by cell viability assay. Prolonged incubation of cells in FBS after gene electrotransfer had varying effect on cell survival, which was decreased in melanoma cell lines B16F1 and B16F10, minimally affected in SVEC4-10 and HUVEC cells and increased in 2H11 cell at 30 min of incubation time in FBS. On the other hand, transfection efficiency of gene electrotransfer was not affected by long incubation of cell in FBS, regardless of the cell line used. The results of our study emphasize the importance of optimization of gene electrotransfer protocol for particular cells and specific purposes of gene electrotransfer, taking into account the importance of transfection efficiency and cell survival.     

Comments on “a framework for assessing readiness for tiger reintroductions”

We comment on five aspects of Gray et al.’s (Biodivers Conserv,  https://doi.org/10.1007/s10531-017-1365-1, 2017a) framework for assessing the readiness of sites for tiger reintroductions. Clarifications in numbers of tigers, available habitat and prey requirements indicate that more land and additional recovery of preferred prey species will be critical for a successful reintroduction. A focus on threat assessments and mitigations will be more important than a focus on site management tools. Local attitudes and levels of poaching require more attention than in the current assessment, as they are likely to be major obstacles to successful large carnivore reintroductions in Asia. Given the limited resources for rangewide tiger conservation, the value of such long-term initiatives must be weighed relative to the urgent need to recover and secure existing tiger populations before they also become extinct.     

The hand of man or Santa Rosalia’s blessing? A rebuttal of the paper “on the restoration of the relict population of a dragonfly <Emphasis Type="Italic">Urothemis edwardsii</Emphasis> Selys (Libellulidae: Odonata) in the Mediterranean”

The intentional reintroduction and translocation of animals and plants has, over the last few decades, become an integral part of the panoply of conservation tools. In a recent published paper in J. Insect Conserv. (doi:  10.1007/s10841-016-9911-9), Khelifa et al. (2016) claimed to have restored the last relict population of Urothemis edwardsii (Selys) in the Mediterranean. Here, I provide evidence that their claims are unwarranted, and that what has occured is a natural process of colonisation by a Critically Endangered population which was confined to a single known site. In addition to several inaccuracies contained in the paper, I will demonstrate that the work was inappropriate and question the adopted methodology that may imperil the type population of U. edwardsii. I urge for the translocation initiative to be discontinued and discuss other safe approaches that may benefit the newly expanding population.     

The Phylogenetic Distribution and Evolution of Enzymes Within the Thymidine Kinase 2-like Gene Family in Metazoa

Deoxyribonucleoside kinases (dNKs) carry out the rate-determining step in the nucleoside salvage pathway within all domains of life where the pathway is present, and, hence, are an indication on whether or not a species/genus retains the ability to salvage deoxyribonucleosides. Here, a phylogenetic tree is constructed for the thymidine kinase 2-like dNK gene family in metazoa. Each enzyme class (deoxycytidine, deoxyguanosine, and deoxythymidine kinases, as well as the multisubstrate dNKs) falls into a monophyletic clade. However, in vertebrates, dCK contains an apparent duplication with one paralog lost in mammals, and a number of crustacean genomes (like Caligus rogercresseyi and Lepeophtheirus salmonis) unexpectedly contain not only the multisubstrate dNKs, related to Drosophila multisubstrate dNK, but also a TK2-like kinase. Additionally, crustaceans (Daphnia, Caligus, and Lepeophtheirus) and some insects (Tribolium, Danaus, Pediculus, and Acyrthosiphon) contain several multisubstrate dNK-like enzymes which group paraphyletically within the arthropod clade. This might suggest that the multisubstrate dNKs underwent multiple rounds of duplications with differential retention of duplicate copies between insect families and more complete retention within some crustaceans and insects. Genomes of several basal animalia contain more than one dNK-like sequence, some of which group outside the remaining eukaryotes (both plants and animals) and/or with bacterial dNKs. Within the vertebrates, the mammalian genomes do not contain the second dCK, while birds, fish, and amphibians do retain it. Phasianidae (chicken and turkey) have lost dGK, while it has been retained in other bird lineages, like zebra finch. Reconstruction of the ancestral sequence between the multisubstrate arthropod dNKs and the TK2 clade of vertebrates followed by homology modeling and discrete molecular dynamics calculations on this sequence were performed to examine the evolutionary path which led to the two different enzyme classes. The structural models showed that the carboxyl terminus of the ancestral sequence is more helical than dNK, in common with TK2, although any implications of this for enzyme specificity will require biochemical validation. Finally, rate-shift and conservation-shift analysis between clades with different specificities uncovered candidate residues outside the active site pocket which may have contributed to differentiation in substrate specificity between enzyme clades.     

Effect of Wheatgrass on Membrane Fatty Acid Composition During Hepatotoxicity Induced by Alcohol and Heated PUFA

Alcoholism is a broad term used for problems related to alcohol, medically considered as disease, specifically an addictive illness, abuse, and dependence. It is the major cause of liver disease in western countries. Alcoholic liver disease encompasses the hepatic alterations leading to fatty liver, hepatitis, and fibrosis or cirrhosis. Fried food items prepared with repeatedly heated polyunsaturated fatty acid (PUFA) exacerbate the disturbances induced by alcohol. The use of herbs to treat diseases is almost universal. Wheatgrass (WG) is used as a supplemental nutrition because of its unique curative properties. As it has antioxidant property, it prevents cancer, diabetes, and acts as liver cleanser. The present study was undertaken to evaluate the efficacy of WG on preserving membrane integrity in liver damage induced by alcohol and heated PUFA (ΔPUFA).The rats were divided into four groups. The animals in group 1 served as normal (standard diet), group 2 served as hepatotoxic (alcohol + ΔPUFA), group 3 served as treated (alcohol + ΔPUFA + WG), and group 4 served as WG control. The compositions of membrane fatty acid, total phospholipids, phospholipase A, C (PLA and PLC) were analyzed in liver to evaluate the effects of WG. Changes in fatty acid composition, decrease in phospholipids levels, and increase in PLA, PLC were observed in the diseased group. Restoration effect was seen in WG-treated rats. Histopathological observations were in correlation with the biochemical parameters. From the results obtained, we conclude that WG effectively protects the liver against alcohol and ΔPUFA-induced changes in fatty acid composition and preserves membrane integrity.     

Role of Structural Changes Induced in Biological Membranes by Hydrolysable Tannins from Sumac Leaves (Rhus typhina L.) in their Antihemolytic and Antibacterial Effects

In this study, we found that the sumac tannins (Rhus typhina L.) exert to a various extent antihemolytic effects and antibacterial activity against Bacillus cereus and Pseudomonas aeruginosa depending on structural specificity of bacteria and different mechanisms of their toxic action. The sumac tannins exert the most expressed activity against B. cereus. The antihemolytic effect of the sumac tannins seems to be connected to a greater extent with their modifying action on the erythrocyte membrane structure. It was found that the sumac tannins are incorporated into the erythrocyte membrane, causing transformation of discocytes into echinocytes and enhancing the rigidity of the hydrophilic region of the lipid bilayer. We suggest that the embedding of sumac tannins into the membrane of erythrocytes alters their physical properties and, as a consequence, can limit their interaction with bacterial toxins.     

Role for the TRPV1 Channel in Insulin Secretion from Pancreatic Beta Cells

Transient receptor potential channels have been put forward as regulators of insulin secretion. A role for the TRPV1 ion channel in insulin secretion has been suggested in pancreatic beta cell lines. We explored whether TRPV1 is functionally expressed in RINm5F and primary beta cells from neonate and adult rats. We examined if capsaicin could activate cationic non-selective currents. Our results show that TRPV1 channels are not functional in insulin-secreting cells, since capsaicin did not produce current activation, not even under culture conditions known to induce the expression of other ion channels in these cells. Although TRPV1 channels seem to be irrelevant for the physiology of isolated beta cells, they may play a role in glucose homeostasis acting through the nerve fibers that regulate islet function. At the physiological level, we observed that Trpv1 ^?/? mice presented lower fasting insulin levels than their wild-type littermates, however, we did not find differences between these experimental groups nor in the glucose tolerance test or in the insulin secretion. However, we did find that the Trpv1 ^?/? mice exhibited a higher insulin sensitivity compared to their wild-type counterparts. Our results demonstrate that TRPV1 does not contribute to glucose-induced insulin secretion in beta cells as was previously thought, but it is possible that it may control insulin sensitivity.     

Intrinsic antimicrobial properties of silk spun by genetically modified silkworm strains

The domesticated silkworm, Bombyx mori, is a fundamental insect for silk industry. Silk is obtained from cocoons, protective envelopes produced during pupation and composed of single raw silk filaments secreted by the insect silk glands. Currently, silk is used as a textile fibre and to produce new materials for technical and biomedical applications. To enhance the use of both fabrics and silk-based materials, great efforts to obtain silk with antimicrobial properties have been made. In particular, a convincing approach is represented by the enrichment of the textile fibre with antimicrobial peptides, the main effectors of the innate immunity. To this aim, silkworm-based transgenic techniques appear to be cost-effective strategies to obtain cocoons in which antimicrobial peptides are integrated among the silk proteins. Recently, cocoons transgenic for a recombinant silk protein conjugated to the silkworm Cecropin B antimicrobial peptide were obtained and showed enhanced antibacterial properties (Li et al. in Mol Biol Rep 42:19–25,  https://doi.org/10.1007/s11033-014-3735-z, 2015a). In this work we used the piggyBac-mediated germline transformation to generate several transgenic B. mori lines able to overexpress Cecropin B or Moricin antimicrobial peptides at the level of the silk gland. The derived cocoons were characterised by increased antimicrobial properties and the resulting silk fibre was able to inhibit the bacterial growth of the Gram-negative Escherichia coli. Our results suggest that the generation of silkworm overexpressing unconjugated antimicrobial peptides in the silk gland might represent an additional strategy to obtain antimicrobial peptide-enriched silk, for the production of new silk-based materials.