Insights into membrane translocation of the cell-penetrating peptide pVEC from molecular dynamics calculations

Discovery of cargo carrying cell-penetrating peptides has opened a new gate in the development of peptide-based drugs that can effectively target intracellular enzymes. Success in application and development of cell-penetrating peptides in drug design depends on understanding their translocation mechanisms. In this study, our aim was to examine the bacterial translocation mechanism of the cell-penetrating pVEC peptide (LLIILRRRIRKQAHAHSK) using steered molecular dynamics (SMD) simulations. The significance of specific residues or regions for translocation was studied by performing SMD simulations on the alanine mutants and other variants of pVEC. Residue-based analysis showed that positively charged residues contribute to adsorption to the lipid bilayer and to electrostatic interactions with the lipid bilayer as peptides are translocated. Translocation takes place in three main stages; the insertion of the N-terminus into the bilayer, the inclusion of the whole peptide inside the membrane and the exit of the N-terminus from the bilayer. These three stages mirror the three regions on pVEC; namely, the hydrophobic N-terminus, the cationic midsection, and the hydrophilic C-terminus. The N-terminal truncated pVEC, I3A, L5A, R7A mutants and scramble-pVEC make weaker interactions with the lipids during translocation highlighting the contribution of the N-terminal residues and the sequence of the structural regions to the translocation mechanism. This study provides atomistic detail about the mechanism of pVEC peptide translocation and can guide future peptide-based drug design efforts.     

Population dynamics of Monochamus carolinensis (Col., Cerambycidae) under laboratory conditions

The study of life history dynamics of the pine sawyer beetle Monochamus carolinensis (Olivier) is of interest because the beetles are vectors for the pinewood nematode, Bursaphelenchus xylophilus (Steiner and Buhrer) Nickle, the causal agent of pine wilt in susceptible pine trees. Previous observation of a laboratory colony of M. carolinensis suggested numbers of adult beetles reared from logs varied little in relation to oviposition densities among individual logs. Logs in laboratory colonies are routinely subjected to artificially high oviposition rates. The objectives of this study were to examine the relationship between initial oviposition rate, holding time (time between log cut and oviposition), log volume and area and adult survivorship in laboratory colony. This study examined the number of eggs, larvae, adults and generation survivorship in logs over a 2‐year period. The number of adults emerged per log was not related to the number of eggs laid. Late larval and adult numbers were significantly correlated with log size. Only 12% of the initial cohort completed development and emerged as adults. We attribute the high within‐log mortality of beetles to intraspecific competition and cannibalism.     

Signet ring cells in fine needle aspiration cytology of breast carcinomas: review of the cytological findings in ten cases identified by histology

Objective:  To establish whether the presence of signet ring cells (SRCs) in histology sections of breast carcinoma cases was reflected by their presence in fine needle aspiration cytology (FNAC) smears, correlating to the histological type of breast carcinoma.
Methods:  We reviewed the FNAC findings of ten cases that had been diagnosed as primary breast carcinoma with SRCs on histological sections between 1998 and 2007. Slides and histological sections were obtained from the archives of Ege University Hospital.
Results:  FNA smears were reviewed for the following cytomorphological features: background, cellularity, architecture, nuclear pleomorphism and the presence of SRCs. The background was bloody in eight cases, necrotic in one, and clean in one. There was no mucinous material in any of the cases. Cellularity was prominent in five cases (hypercellular), moderate in three (cellular) and low in two (hypocellular). Loosely cohesive groups of tumour cells of varying size were observed in all cases. A plasmacytoid appearance to some of the tumour cells was seen in all cases and discohesive tumour cells were present in eight. Nuclear pleomorphism was high in six cases and moderate in four. SRCs were observed in seven of the ten cases. Two of these seven cases also had a tubular pattern and one had tumour giant cells.
Conclusions:  FNAC should be evaluated carefully regarding the presence of SRCs when cells with a plasmacytoid appearance are observed in either hyper- or hypocellular smears. The presence of single SRCs in FNACs with hypercellularity, high nuclear grade and tubular formation or tumour giant cells may be a clue in favour of ductal carcinoma. The presence of single SRCs in FNACs with hypocellularity and mild to moderate nuclear grade may be suggestive of lobular carcinoma. However, larger studies would be needed to establish the predictive value of the presence of SRCs on FNAC.     

Proteomic insight into phenolic adaptation of a moderately halophilic Halomonas sp. strain AAD12

A gram-negative, moderately halophilic bacterium was isolated from ?amalt? Saltern area, located in the Aegean Region of Turkey. Analysis of its 16S rRNA gene sequence and physiological characteristics showed that this strain belonged to the genus Halomonas ; hence, it was designated as Halomonas sp. strain AAD12. The isolate tolerated up to 800 mg?L(-1) phenol; however, at elevated concentrations, phenol severely retarded cell growth. The increase in lag phase with increasing phenol concentrations indicated that the microorganism was undergoing serious adaptative changes. To understand the physiological responses of Halomonas sp. strain AAD12 to phenol, a 2-dimensional electrophoresis approach combined with mass spectrometric analysis was used. This approach showed that the expression of 14 protein spots were altered as phenol concentration increased from 200 to 800 mg?L(-1). Among the identified proteins were those involved in protein biosynthesis, energy, transport, and stress metabolism. So far, this is the first study on phenolic adaptation of a gram-negative, moderately halophilic bacteria using proteomic tools. The results provided new insights for understanding the general mechanism used by moderately halophilic bacteria to tolerate phenol and suggested the potential for using these microorganisms in bioremediation.     

Synthesis and Antioxidant Evaluation of O-Methylated Emodacidamides: Starting from Parietin,a Secondary Metabolite of Lichen Xanthoria parietina

Polyhydroxy-anthraquinones bearing amino acids are found rather seldom in nature. Emodacidamides, isolated from a marine-derived fungus, Penicillium sp. SCSIO sof101 by Luo et al. (2017) are the first natural example of amino acid conjugated anthraquinone. In this study, O-methylated emodacidamides and emodinic acid-anilides were synthesized starting from parietin, extracted from the lichen Xanthoria parietina (L.) Th. Fr. The structural elucidations of prepared compounds were confirmed by 1D and 2D NMR analyses including HSQC and HMBC techniques. In addition, all newly synthesized compounds were evaluated for the antioxidant activities with free radical 1,1-diphenyl-2-picrylhydrazyl (DPPH) scavenging. The synthesized compounds showed low to moderate antioxidant and DPPH scavenging activities. The antioxidant activities were supported within quantum chemical calculations using the DFT−B3LYP/6-311++G(d,p) level of theory. It is observed that the antioxidant activity of emodacidamides mostly depends on the phenolic groups on anthraquinone ring. The phenolic groups on other substituents help to improve antioxidant activity and also the position of hydroxy group is a decisive factor for antioxidant ability.     

Nebivolol And Quinapril Reduce P-Wave Duration And Dispersion In Hypertensive Patients

We aimed to investigate the effects of nebivolol and quinapril treatments on P-wave duration and dispersion in hypertensive patients. Hypertensive patients who were in sinus rhythm were assigned to the two treatment groups and received either 20 mg quinapril/day or 5 mg nebivolol/day. P-Wave dispersion (PWD) was measured at baseline and after four weeks of treatment and defined as the difference between the maximum (Pmax) and the minimum (Pmin) P-wave duration. The study group consisted of 54 patients (Mean age: 53 ± 9 years, 46% women) with 27 patients in each group. At 4-week follow up both treatment groups showed a significant reduction (p< 0.001) in systolic (SBP) and diastolic blood pressure (DBP). Heart rate (HR) reduction was significant in patients receiving nebivolol (P=0.001). Both groups showed a similar (P=0.413 for PWD, p=0.651 for Pmax) but significant reduction in PWD (nebivolol: -16± 14, P< 0.0001 and quinapril: -13± 11, P< 0.0001) and Pmax (nebivolol: -10± 11, P=0.001 and quinapril: -9± 11, P=0.001). A 2 (Time) x 2 (Group) mixed-model repeated-measures analysis of variance revealed that the main effect of Time was significant for Pmax (P=0.002) and PWD (P=0.008) after controlling for changes in SBP, DBP and HR. However, the main effect of Group and Time x Group interaction was not significant for both variables (All p values > 0.05). In conclusion, short-term treatment with nebivolol and quinapril produces a similar but significant reduction in Pmax and PWD in hypertensive patients. This effect is independent of blood pressure and heart rate changes.     

Alkaloids of turkish papaver tauricola

The major alkaloids of Papaver tauricola collected in three different parts of Anatolia have proved to be of the rhoeadine type. The three collections possessed different major alkaloids and the existence of chemical strains containing rhoeadine-type alkaloids, is indicated. In addition to the rhoeadine-type alkaloids (rhoeagenine, rhoeadine, oreogenine, oreodine, glaucamine, glaudine and epiglaudine), tetrahydroprotoberberine-(sinactine, scoulerine) and isopavine- (amurensinine) type alkaloids have been isolated as minor products. These findings contrast with the previous literature in which 1-benzyltetrahydroisoquinoline- and proaporphine types were reported to be the major alkaloids.     

pVEC hydrophobic N‐terminus is critical for antibacterial activity

Cell‐penetrating peptides (CPPs) are commonly defined by their shared ability to be internalized into eukaryotic cells, without inducing permanent membrane damage, and to improve cargo delivery. Many CPPs also possess antimicrobial action strong enough to selectively lyse microbes in infected mammalian cultures. pVEC, a CPP derived from cadherin, is able to translocate into mammalian cells, and it is also antimicrobial. Structure‐activity relationship and sequence alignment studies have suggested that the hydrophobic N‐terminus (LLIIL) of pVEC is essential for this peptide's uptake into eukaryotic cells. In this study, our aim was to examine the contribution of these residues to the antimicrobial action and the translocation mechanism of pVEC. We performed antimicrobial activity and microscopy experiments with pVEC and with del5 pVEC (N‐terminal truncated variant of pVEC) and showed that pVEC loses its antimicrobial effect upon deletion of the LLIIL residues, even though both peptides induce membrane permeability. We also calculated the free energy of the transport process using steered molecular dynamic simulations and replica exchange umbrella sampling simulations to compare the difference in uptake mechanism of the 2 peptides in atomistic detail. Despite the difference in experimentally observed antimicrobial activity, the simulations on the 2 peptides showed similar characteristics and the energetic cost of translocation of pVEC was higher than that of del5 pVEC, suggesting that pVEC uptake mechanism cannot be explained by simple passive transport. Our results suggest that LLIIL residues are key contributors to pVEC antibacterial activity because of irreversible membrane disruption.     

Detailed positron annihilation lifetime spectroscopic investigation of atrazine imprinted polymers grafted onto PE/PP non‐woven fabrics

This study presents the preparation of molecularly imprinted matrices by using radiation‐induced grafting technique onto polyethylene/polypropylene (PE/PP) non‐woven fabrics. Atrazine imprinted polymers were grafted onto PE/PP non‐woven fabrics through the use of methacrylic acid (MAA) and ethylene glycol dimethylacrylate (EGDMA) as the functional monomer and crosslinking agent, respectively. Grafted MIPs were characterized by attenuated total reflectance Fourier transform infra‐red spectroscopy (ATR‐FTIR), X‐ray photoelectron spectroscopy (XPS), elemental analysis, scanning electron microscopy (SEM), and positron annihilation lifetime spectroscopy (PALS). The average diameter of free volume holes was determined as 0.612 nm which correlates very well with the size of template molecule atrazine, 0.512 nm. Binding behaviors were investigated against various factors, such as concentration of template molecule, pH, and contact time. Furthermore, the specific selectivity of grafted MIP on non‐woven fabric was studied by using other common triazine compounds, such as simazine and metribuzine which show structural similarities to atrazine. The specific binding values for atrazine, simazine, and metribuzine were determined as 40%, 2.5%, and 1.5%, respectively.     

An integrative anatomical,morphological, micromorphological and molecular approach to Turkish epidendroid and orchidoid species (Orchidaceae)

We aimed to describe and analyse the morphological, anatomical and micromorphological traits of 36 Turkish orchids representing 12 genera (e.g. Anacamptis, Cephalanthera, Dactylorhiza, Orchis, Serapias) in detail and analyse their usability for solving phylogenetic and taxonomic issues. We applied UPGMA cluster analysis to anatomical, morphological and micromorphological characters such as root tubers, leaf and flower structures, pit, sclerenchymatic sheath, vascular bundle shape, crystal and starch, exodermis and endodermis structure, stomata type, bulliform cells in roots, shoots and leaves, surface structures like papillae, hairs and ornamentation on flower parts, leaves, fruits and seeds. Furthermore, in a phylogenetic framework, we analysed nuclear ribosomal ITS diversity in the same orchid species belonging, and in a combined Bayesian phylogenetic analysis based on anatomical, morphological, micromorphogical and ITS data we confirmed the usefulness of multiple data sets for effectively assessing taxonomically critical orchids. In the combined analysis, all genera were resolved as monophyletic with topologies congruent with recently published more thorough molecular phylogenetic reconstructions, while the trees obtained by seprately analysing the ITS and the anatomical, morphological, micromorphogical data were less resolved and partly inconclusive.