Retained binding mode of various DNA-binding molecules under molecular crowding condition

Meso-tetrakis(N-methyl pyridinium-4-yl)porphyrin (TMPyP) intercalates between the base-pairs of DNA at a low [TMPyP]/[DNA base] ratio in aqueous solutions and molecular crowding conditions, which is induced by the addition of Poly(ethylene glycol) (PEG). Studied DNA-binding drugs, including TMPyP, 9-aminoacridine, ethidium bromide, and DAPI (4′,6-diamidino-2-phenylindole) showed similar binding properties in the presence or absence of PEG molecules which is examined by circular and linear dichroism. According to the LD^r (reduced linear dichroism) results of the binding drugs examined in this work, PEG molecules induced no significant change compared to their binding properties in aqueous buffering systems. These results suggest that the transition moments are not expected to be perturbed significantly by PEG molecules. In this study, the experimental conditions of PEG 8000 were maintained at 35% (v/v) of total reaction volume, which is equal to the optimal molar concentration (0.0536 M as final concentration for PEG 8000) to maintain suitable cell-like conditions. Therefore, there was no need to focus on the conformational changes of the DNA helical structure, such as forming irregular aggregate structures, induced by large quantities of molecular crowding media itself at this stage.     

Evidence of salicylic acid pathway with EDS1 and PAD4 proteins by molecular dynamics simulation for grape improvement

Biotic stress is a major cause of heavy loss in grape productivity. In order to develop biotic stress-resistant grape varieties, the key defense genes along with its pathway have to be deciphered. In angiosperm plants, lipase-like protein phytoalexin deficient 4 (PAD4) is well known to be essential for systemic resistance against biotic stress. PAD4 functions together with its interacting partner protein enhanced disease susceptibility 1 (EDS1) to promote salicylic acid (SA)-dependent and SA-independent defense pathway. Existence and structure of key protein of systemic resistance EDS1 and PAD4 are not known in grapes. Before SA pathway studies are taken in grape, molecular evidence of EDS1: PAD4 complex is to be established. To establish this, EDS1 protein sequence was retrieved from NCBI and homologous PAD4 protein was generated using Arabidopsis thaliana as template and conserved domains were confirmed. In this study, computational methods were used to model EDS1 and PAD4 and simulated the interactions of EDS1 and PAD4. Since no structural details of the proteins were available, homology modeling was employed to construct three-dimensional structures. Further, molecular dynamic simulations were performed to study the dynamic behavior of the EDS1 and PAD4. The modeled proteins were validated and subjected to molecular docking analysis. Molecular evidence of stable complex of EDS1:PAD4 in grape supporting SA defense pathway in response to biotic stress is reported in this study. If SA defense pathway genes are explored, then markers of genes involved can play pivotal role in grape variety development especially against biotic stress leading to higher productivity.     

Multifaceted applications of nanomaterials in cell engineering and therapy

Nanomaterials with superior physiochemical properties have been rapidly developed and integrated in every aspect of cell engineering and therapy for translating their great promise to clinical success. Here we demonstrate the multifaceted roles played by innovatively-designed nanomaterials in addressing key challenges in cell engineering and therapy such as cell isolation from heterogeneous cell population, cell instruction in vitro to enable desired functionalities, and targeted cell delivery to therapeutic sites for prompting tissue repair. The emerging trends in this interdisciplinary and dynamic field are also highlighted, where the nanomaterial-engineered cells constitute the basis for establishing in vitro disease model; and nanomaterial-based in situ cell engineering are accomplished directly within the native tissue in vivo. We will witness the increasing importance of nanomaterials in revolutionizing the concept and toolset of cell engineering and therapy which will enrich our scientific understanding of diseases and ultimately fulfill the therapeutic demand in clinical medicine.     

Organization of cortical processing for facial movements during licking in cats

We proposed that cortical organization for the execution of adequate licking in cats was processed under the control of two kinds of affiliated groups for face and jaw & tongue movements (Hiraba H, Sato T. 2005A. Cerebral control of face, jaw, and tongue movements in awake cats: Changes in regional cerebral blood flow during lateral feeding Somatosens Mot Res 22:307–317). We assumed the cortical organization for face movements from changes in MRN (mastication-related neuron) activities recorded at area M (motor cortex) and orofacial behaviors after the lesion in the facial SI (facial region in the primary somatosensory cortex). Although we showed the relationship between facial SI (area 3b) and area M (area 4δ), the property of area C (area 3a) was not fully described. The aim of this present study is to investigate the functional role of area C (the anterior part of the coronal sulcus) that transfers somatosensory information in facial SI to area M, as shown in a previous paper (Hiraba H. 2004. The function of sensory information from the first somatosensory cortex for facial movements during ingestion in cats Somatosens Mot Res 21:87--97). We examined the properties of MRNs in area C and changes in orofacial behaviors after the area C or area M lesion. MRNs in area C had in common RFs in the lingual, perioral, and mandibular parts, and activity patterns of MRNs showed both post- and pre-movement types. Furthermore, cats with the area C lesion showed similar disorders to cats with the area M lesion, such as the dropping of food from the contralateral mouth, prolongation of the period of ingestion and mastication, and so on. From these results, we believe firmly the organization of unilateral cortical processing in facial SI, area C, and area M for face movements during licking.     

9-Phenanthrol and flufenamic acid inhibit calcium oscillations in HL-1 mouse cardiomyocytes

It is well established that intracellular calcium ([Ca²⁺]_i) controls the inotropic state of the myocardium, and evidence mounts that a “Ca²⁺ clock” controls the chronotropic state of the heart. Recent findings describe a calcium-activated nonselective cation channel (NSC_Ca) in various cardiac preparations sharing hallmark characteristics of the transient receptor potential melastatin 4 (TRPM4). TRPM4 is functionally expressed throughout the heart and has been implicated as a NSC_Ca that mediates membrane depolarization. However, the functional significance of TRPM4 in regards to Ca²⁺ signaling and its effects on cellular excitability and pacemaker function remains inconclusive. Here, we show by Fura2 Ca-imaging that pharmacological inhibition of TRPM4 in HL-1 mouse cardiac myocytes by 9-phenanthrol (10 μM) and flufenamic acid (10 and 100 μM) decreases Ca²⁺ oscillations followed by an overall increase in [Ca²⁺]_i. The latter occurs also in HL-1 cells in Ca²⁺-free solution and after depletion of sarcoplasmic reticulum Ca²⁺ with thapsigargin (10 μM). These pharmacologic agents also depolarize HL-1 cell mitochondrial membrane potential. Furthermore, by on-cell voltage clamp we show that 9-phenanthrol reversibly inhibits membrane current; by fluorescence immunohistochemistry we demonstrate that HL-1 cells display punctate surface labeling with TRPM4 antibody; and by immunoblotting using this antibody we show these cells express a 130–150 kDa protein, as expected for TRPM4. We conclude that 9-phenanthrol inhibits TRPM4 ion channels in HL-1 cells, which in turn decreases Ca²⁺ oscillations followed by a compensatory increase in [Ca²⁺]_i from an intracellular store other than the sarcoplasmic reticulum. We speculate that the most likely source is the mitochondrion.     

The kinetic properties of a human PPIP5K reveal that its kinase activities are protected against the consequences of a deteriorating cellular bioenergetic environment

We obtained detailed kinetic characteristics–stoichiometry, reaction rates, substrate affinities and equilibrium conditions–of human PPIP5K2 (diphosphoinositol pentakisphosphate kinase 2). This enzyme synthesizes ‘high-energy’ PP-InsPs (diphosphoinositol polyphosphates) by metabolizing InsP₆ (inositol hexakisphosphate) and 5-InsP₇ (5-diphosphoinositol 1,2,3,4,6-pentakisphosphate) to 1-InsP₇ (1-diphosphoinositol 2,3,4,5,6-pentakisphosphate) and InsP₈ (1,5-bis-diphosphoinositol 2,3,4,6-tetrakisphosphate), respectively. These data increase our insight into the PPIP5K2 reaction mechanism and clarify the interface between PPIP5K catalytic activities and cellular bioenergetic status. For example, stochiometric analysis uncovered non-productive, substrate-stimulated ATPase activity (thus, approximately 2 and 1.2 ATP molecules are utilized to synthesize each molecule of 1-InsP₇ and InsP₈, respectively). Impaired ATPase activity of a PPIP5K2-K248A mutant increased atomic-level insight into the enzyme''s reaction mechanism. We found PPIP5K2 to be fully reversible as an ATP-synthase in vitro, but our new data contradict previous perceptions that significant ‘reversibility’ occurs in vivo. PPIP5K2 was insensitive to physiological changes in either [AMP] or [ATP]/[ADP] ratios. Those data, together with adenine nucleotide kinetics (ATP K_m=20–40 μM), reveal how insulated PPIP5K2 is from cellular bioenergetic challenges. Finally, the specificity constants for PPIP5K2 revise upwards by one-to-two orders of magnitude the inherent catalytic activities of this enzyme, and we show its equilibrium point favours 80–90% depletion of InsP₆/5-InsP₇.     

Purinergic stimulation of K+-dependent Na+/Ca2+ exchanger isoform 4 requires dual activation by PKC and CaMKII

K⁺-dependent Na⁺/Ca²⁺-exchanger isoform 4 (NCXK4) is one of the most broadly expressed members of the NCKX (K⁺-dependent Na⁺/Ca²⁺-exchanger) family. Recent data indicate that NCKX4 plays a critical role in controlling normal Ca²⁺ signal dynamics in olfactory and other neurons. Synaptic Ca²⁺ dynamics are modulated by purinergic regulation, mediated by ATP released from synaptic vesicles or from neighbouring glial cells. Previous studies have focused on modulation of Ca²⁺ entry pathways that initiate signalling. Here we have investigated purinergic regulation of NCKX4, a powerful extrusion pathway that assists in terminating Ca²⁺ signals. NCKX4 activity was stimulated by ATP through activation of the P2Y receptor signalling pathway. Stimulation required dual activation of PKC (protein kinase C) and CaMKII (Ca²⁺/calmodulin-dependent protein kinase II). Mutating T312, a putative PKC phosphorylation site on NCKX4, partially prevented purinergic stimulation. These data illustrate how purinergic regulation can shape the dynamics of Ca²⁺ signalling by activating a signal damping and termination pathway.     

Enhanced anti-topoisomerase II activity by mucoadhesive 4-CBS–chitosan/poly (lactic acid) nanoparticles

In this study, the biodegradable mucoadhesive 4-carboxybenzensulfonamide chitosan (4-CBS–chitosan)/poly (lactic acid) (PLA) nanoparticles were fabricated by the electrospray ionization technique for enhancing anti-topoisomerase II (Topo II) activity. The obtained (4-CBS–chitosan/PLA)-DOX nanoparticles were characterized using SEM, particle size analyzer. We emphasis on encapsulation efficiency, in vitro drug release behavior and also performed in vitro studies of Topo II inhibitory activity using gel electrophoresis. In addition, the cytotoxicity of the 4-CBS–chitosan/PLA nanoparticles using MTT assay was also studied. The mean particle size of spherical shaped (4-CBS–chitosan/PLA)-DOX is less than 300 nm. The DOX loaded 4-CBS–chitosan/PLA composite nanoparticles produced high entrapment efficiency of 85.8% and provided the prolonged release of DOX extended to 26 days and also still had strong Topo II inhibitory activity up to 77.4%. Overall, it was shown that 4-CBS–chitosan/PLA nanoparticles could be promising carriers for controlled delivery of anticancer drugs.     

Struvite Precipitation Induced by a Novel Sulfate-Reducing Bacterium Acinetobacter calcoaceticus SRB4 Isolated from River Sediment

This article presents a study of struvite formation in liquid medium induced by the sulfate-reducing bacterium Acinetobacter calcoaceticus SRB4, a strain isolated from river sediment. We identified the bacterial strain A. calcoaceticus SRB4 and analyzed its micromorphology. The minerals formed were studied with an electroprobe microanalyzer, Fourier transform infrared spectroscopy, high-resolution transmission electron microscopy, selected-area electron diffraction, X-ray diffraction, thermogravimetry, differential thermogravimetry, and differential scanning calorimetry. Acinetobacter calcoaceticus SRB4 was found to induce struvite precipitation, whereas sterile control cultures did not. Many transparent stick-shaped struvite precipitates were distributed at the bottom of the conical flasks in the experimental group. Most bacteria were spherical and a large quantity of spherical struvite particles (less than 200 nm in diameter) adhered to the bacterial surface. An electron probe microanalysis showed that the precipitates contained C, O, P, Mg, and other elements. Fourier transformation infrared spectra showed that the precipitates contained crystalline water, NH₄⁺, and PO₄^3? groups. X-ray diffraction spectra showed that the precipitates were struvite crystals, with preferential orientation and lattice distortion. Thermogravimetry showed that the weight loss was caused by the evaporation of crystalline water at temperatures lower than 136°C and the release of ammonia from struvite at temperatures of 136–228.5°C. In this article, we discuss the possible mechanism of struvite formation and the possible role played by A. calcoaceticus SRB4. Our study extends our understanding of the phosphate biomineralization mechanism and should prove useful in recycling phosphorus in wastewater.