Chemical structure requirements and cellular targeting of microRNA-122 by peptide nucleic acids anti-miRs

Anti-miRs are oligonucleotide inhibitors complementary to miRNAs that have been used extensively as tools to gain understanding of specific miRNA functions and as potential therapeutics. We showed previously that peptide nucleic acid (PNA) anti-miRs containing a few attached Lys residues were potent miRNA inhibitors. Using miR-122 as an example, we report here the PNA sequence and attached amino acid requirements for efficient miRNA targeting and show that anti-miR activity is enhanced substantially by the presence of a terminal-free thiol group, such as a Cys residue, primarily due to better cellular uptake. We show that anti-miR activity of a Cys-containing PNA is achieved by cell uptake through both clathrin-dependent and independent routes. With the aid of two PNA analogues having intrinsic fluorescence, thiazole orange (TO)-PNA and [bis-o-(aminoethoxy)phenyl]pyrrolocytosine (BoPhpC)-PNA, we explored the subcellular localization of PNA anti-miRs and our data suggest that anti-miR targeting of miR-122 may take place in or associated with endosomal compartments. Our findings are valuable for further design of PNAs and other oligonucleotides as potent anti-miR agents.     

Polymerase incorporation of pyrene-nucleoside triphosphates

Pyrene-deoxynucleoside triphosphates (dPTPs), varying by the positioning of the aromatic system, were synthesized. Their ability to function as substrates for the Klenow fragment of Escherichia coli DNA polymerase I and the TdT polymerase was assessed. The dPTPs are all equally well tolerated by the Klenow fragment, and lead to elongation of up to 5 extra nucleotides of a ssDNA primer in a TdT-mediated reaction. The tailing efficiency of the dPTPs compares favorably to other less drastically modified dNTPs.     

Iteration model of starch hydrolysis by amylolytic enzymes.

An elaborate computer program to simulate the process of starch hydrolysis by amylolytic enzymes was been developed. It is based on the Monte Carlo method and iteration kinetic model, which predict productive and non-productive amylase complexes with substrates. It describes both multienzymatic and multisubstrate reactions simulating the "real" concentrations of all components versus the time of the depolymerization reaction the number of substrates, intermediate products, and final products are limited only by computer memory. In this work, it is assumed that the "proper" substrate for amylases is the glucoside linkages in starch molecules. Dynamic changes of substrate during the simulation adequately influence the increase or decrease of reaction velocity, as well as the kinetics of depolymerization. The presented kinetic model, can be adapted to describe most enzymatic degradations of a polymer. This computer program has been tested on experimental data obtained for alpha- and beta-amylases.     

Limb lymph node response to bone fracture

In previous clinical studies, dilation of afferent lymphatics and enlargement of inguinal lymph nodes (LN) were observed in lymphoscintigrams from patients with persistent posttraumatic edema of lower extremities after fractures and trauma of soft tissues. In this study, changes in rat popliteal and iliac lymph nodes draining lymph from the site of tibial fracture and adjacent soft tissue injury were investigated. The observed parameters were lymph node weight, cell number, phenotype frequency, cell cytokine expression, and reactivity to mitogens. The key observations included: a) increase in the weight and total cell number of the lymph nodes; b) increased autotransformation rate and responsiveness of lymph node cells to mitogen; c) decreased frequency of ED1 macrophages and activated OX8 cytotoxic cells in flow cytometry analysis; d) high expression of OX6 class II-positive, OX7 (stem cells), OX62 (migrating dendritic cells), ED1 (macrophages), and OX12 (B cells) on immunohistochemical sections of LNs with some few HIS48 (granulocytes); e) high expression of NOS3 and TGF beta by lymph node lymphocytes and endothelial cells. In summary, local lymph nodes reacted to internal wounds, such as bone fracture and injury to adjacent tissues, through mobilization of cells from the blood circulation, along with activation of cellular subsets. The molecular mechanism that provides the signal for this reaction remains unknown. The absence of major changes in the frequency of lymph node cell subpopulations indicates that lymph nodes are constitutively prepared for influx of antigens from damaged tissues and react only with increase in cell number and cell activation. The nature of the reaction, including lack of immunization against autoantigens, remains unclear. Further elucidation will require studies on the mechanism of cross-tolerance to self-antigens during wound healing.     

Ontogeny of the expression of some catecholamine synthesising enzymes in the female porcine preoptic area

Ontogeny of the catecholaminergic system of the preoptic area (PA) was studied in various animal species including mice, rats, cats and lower vertebrates. Until now, there has been no data about development of catecholaminergic structures in the porcine PA. To study this problem, hypothalami from six groups of animals were collected. Three groups of foetuses (70, 84 and 112 days old) and three groups of female pigs (1 day, 10 weeks and 7-8 months old) were used. Nerve structures immunoreactive for the studied substances: tyrosine hydroxylase (TH), dopamine beta-hydroxylase (DbetaH) and phenylethanoloamine-N-metylthransferase (PNMT) were observed in different periods. In PA, TH-IR (immunoreactive) structures appeared before 70th day of foetal life, DbetaH-IR between 70th and 84th day of foetal live and PNMT-IR only in 10-week old and adult animals. In the PA of 70-day old foetuses, single smooth and varicose nerve fibres immunoreactive only to TH were found. In PA of 84-day old foetuses, additionally, single nerve cell bodies immunoreactive to TH were shown and some of them also contained immunoreactivity to DbetaH. In PA of 1-day old piglets, moderate numbers of nerve fibres immunoreactive to TH and only single TH/DbetaH-IR nerve terminals were observed. TH-IR nerve cell bodies were also moderate in number and many of them contained simultaneously immunoreactivity to DbetaH. In PA of 10-week old pigs, a moderate number of immunopositive nerve fibres was observed. They contained mainly TH, but part of them stained also for TH/DbetaH. Only very few nerve fibres containing exclusively DbetaH were found. These nerve terminals were observed in a close vicinity of blood vessels. In PA, moderate numbers of TH-IR nerve cell bodies were found, some of them contained also immunoreactivity to DH but never to PNMT. Perikarya containing PNMT were TH-negative. In the PA of sexually mature sows, additional, single, large nerve cell bodies (about 35 microm in a diameter) containing TH only were found. In many cases, TH- and DbetaH-IR "basket-like" structures surrounding nerve cell bodies were seen, suggesting an influence of those fibres on the neuronal activity.     

Metabolic and ultrastructural responses of lupine embryo axes to sugar starvation

Embryo axes isolated from germinating lupine seeds were cultivated in vitro for 24-96 h over media containing either 60 mmol/L sucrose or no sucrose. Ultrastructural studies showed that large vacuoles were accumulating in a central region of primary parenchyma cells in sucrose starved lupine embryo axes, whereas cytoplasm along with organelles were forced to a periphery of the cells. We suggest that the autolysis of cytoplasmic proteins contributes to the accumulation of the vacuoles and this suggestion is consistent with the results of the characterisation of protein content. The level of cytosolic proteins was reduced by 50% and the activity of cytosolic marker enzyme, PEP carboxylase, was reduced by 46% in starved embryos as compared to control. The mitochondria from starved tissues were not degraded. The level of mitochondrial proteins was reduced by only 10% and the activity of mitochondrial NAD-isocitrate dehydrogenase decreased by 8% as a result of starvation. As demonstrated by the results of Percoll density gradient centrifugation, sucrose starvation caused an increase of 49% in many of the higher density mitochondria fractions, whereas many of the lower density mitochondria fractions were decreased by 33%. The samples of mitochondria from starved embryo axes were determined to have higher respiration activity in the presence of glutamate and malate as compared to control samples. EPR-based analyses of free radicals showed the presence of free radicals with a signal at g = 2.0060 in embryo axes. The level of the radical was two times higher in sucrose-starved embryo axes than in control (the level of this radical increased in senescing plant tissues as well). The results of EPR-based quantitation of Mn2+ ions revealed that the level was a few times higher in starved material than in control. Starved embryo axes, however, do possess a number of adaptive mechanisms protecting them from oxidative damage. Densitometric analyses of gels revealed an increase in the activity of SOD in sugar-starved embryos, whereas CAT and POX activities were lower in axes grown without sucrose as compared to control. Superoxide dismutase, catalase and peroxidase zymogram analyses showed that synthesis of new isoforms was not induced by sugar starvation. An accumulation of phytoferritin was found in plastids of sucrose starved embryos. These results are discussed in relation to the metabolic changes observed in senescing plant tissues.     

Molecular Architecture of Plant Thylakoids under Physiological and Light Stress Conditions: A Study of Lipid–Light-Harvesting Complex II Model Membranes

In this study, we analyzed multibilayer lipid-protein membranes composed of the photosynthetic light-harvesting complex II (LHCII; isolated from spinach [Spinacia oleracea]) and the plant lipids monogalcatosyldiacylglycerol and digalactosyldiacylglycerol. Two types of pigment-protein complexes were analyzed: those isolated from dark-adapted leaves (LHCII) and those from leaves preilluminated with high-intensity light (LHCII-HL). The LHCII-HL complexes were found to be partially phosphorylated and contained zeaxanthin. The results of the x-ray diffraction, infrared imaging microscopy, confocal laser scanning microscopy, and transmission electron microscopy revealed that lipid-LHCII membranes assemble into planar multibilayers, in contrast with the lipid-LHCII-HL membranes, which form less ordered structures. In both systems, the protein formed supramolecular structures. In the case of LHCII-HL, these structures spanned the multibilayer membranes and were perpendicular to the membrane plane, whereas in LHCII, the structures were lamellar and within the plane of the membranes. Lamellar aggregates of LHCII-HL have been shown, by fluorescence lifetime imaging microscopy, to be particularly active in excitation energy quenching. Both types of structures were stabilized by intermolecular hydrogen bonds. We conclude that the formation of trans-layer, rivet-like structures of LHCII is an important determinant underlying the spontaneous formation and stabilization of the thylakoid grana structures, since the lamellar aggregates are well suited to dissipate excess energy upon overexcitation.     

How well does cholesteryl hemisuccinate mimic cholesterol in saturated phospholipid bilayers?

Journal of Molecular Modeling - We studied the doping effects on the electronic and structural properties of graphene upon interaction with phenol. Calculations were performed within the periodic...