Quadruplexes of human telomere DNA analogs designed to contain G:A:G:A,G:G:A:A,and A:A:A:A tetrads

Replacement of two to four guanines by adenines in the human telomere DNA repeat dG₃(TTAG₃)₃ did not hinder the formation of quadruplexes if the substitutions took place in the terminal tetrad bridged by the diagonal loop of the intramolecular antiparallel three‐tetrad scaffold, as proved by CD and PAGE in both Na⁺ and K⁺ solutions. Thermodynamic data showed that, in Na⁺ solution, the dG₃(TTAG₃)₃ quadruplex was destabilized, the least by the two G:A:G:A tetrads, the most by the G:G:A:A tetrad in which the adenosines replaced syn‐guanosines. In physiological K⁺ solution, the highest destabilization was caused by the 4A tetrad. In K⁺, only the unmodified dG₃(TTAG₃)₃ quadruplex rearranged into a K⁺‐dependent quadruplex form, none of the multiple adenine‐modified structures did so. This may imply biological consequences for nonrepaired A‐for‐G mutations. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 880–886, 2010.     

Photochemistry of heteropoly electrolytes: the 1:12 tungstates

1:12 tungstates are photosensitive in near visible and ultra-violet areas at the oxygen to metal charge transfer bands, in the presence of a great variety of organic reagents. Photosensitivity results in multi- electoral reduction of tungstates with concomitant oxidation of oganic compounds. Photosensitivity follows the order PW₁₂O_4o^3? > SiW₁₂O_4o^4? > FeW₁₂O_4o^5? > H₂W₁₂O_4o^6?, which is the same order with the increasing negative redox potentials. Maximum quantum yield ～ 15% is obtained with high concentrations of organic reagents (1–10 M). The reduced heteropoly compounds (HPC) are eacily re-oxidized by atmospheirc oxygen. They are also capable of reducing hydrogen ions and this limits the extent of photoreduction.     

Dithionitronium hexachloroantimonate: A thionitrosylating reagent

The reaction of Ru(CO)₃(PPh₃)₂ with (NS₂)(SbCl₆) in acetonitrile results in the formation of [Ru(CO)₂(NS₂)(PPh₃)₂](SbCl₆) which reacts with PPh₃ to give the thionitrosyl complex [Ru(CO)₂(NS)(PPh₃)₂](SbCl₆). The NS₂-complex in CH₂Cl₂ gives Ru(CO)₂Cl₂(PPh₃)₂.     

Enkephalinase: Selective peptide inhibitors

A unique, CNS membrane bound enkephalinase is described with greatest activities being measured in the striatum of the mouse. This enzyme was resistant to inhibition by puromycin and bestatin which are potent aminopeptidase inhibitors and to the angiotensin converting enzyme inhibitors, captopril and the free acid of MK-421, which were also very weak inhibitors of aminopeptidase. However, the glycopeptide, phosphoramidon, and the hydroxamic acids, HO-NHCOCH(CH₂CH(CH₃)₂)-CO-Ala-Gly-NH₂ and HO-NHCOCH(CH₂C₆H₅)-CO-Ala-Gly-NH₂, were potent enkephalinase inhibitors with IC₅₀'s (nM) of 39, 3.1 and 8.4, respectively. These peptides remain to be tested $\text{in}$$\text{vivo}$.     

Photo and thermoluminescence of KMgSO4F: Ce and :Mn phosphors

KMgSO₄F:Ce and KMgSO₄F:Mn phosphors were prepared by a wet chemical method and studied for their photoluminescence (PL) and thermoluminescence (TL) characteristics. PL emission of KMgSO₄F:Ce peaked at around 440 nm for the excitation at 377 nm due to 5d → 4f transition, while KMgSO₄F:Mn had a peak at 540 nm for an excitation at 363 nm and 247 nm due to ⁴T_1g → ⁶A_1g transition. The phosphors also showed good thermoluminescence characteristics when they were exposed to γ‐rays at a 5 Gy dose at the rate of 0.36 kGyh^?1. KMgSO₄F:Ce exhibited a single thermoluminescence (TL) peak at around 167 °C and KMgSO₄F:Mn also exhibited a single TL peak at around 177 °C. Possible trapping parameters such as order of kinetics (b), the geometrical factor (μ_g), the frequency factor (s) and the activation energy were also evaluated by Chen's half width method. This article discusses fundamental PL and TL characteristics in inorganic fluoride material activated by Ce³⁺ and Mn²⁺ ions and prepared by a wet chemical method. Copyright © 2014 John Wiley & Sons, Ltd.     

Thematic Review Series: Phospholipases: Central Role in Lipid Signaling and Disease: A new era of secreted phospholipase A2

Among more than 30 members of the phospholipase A₂ (PLA₂) superfamily, secreted PLA₂ (sPLA₂) enzymes represent the largest family, being Ca²⁺-dependent low-molecular-weight enzymes with a His-Asp catalytic dyad. Individual sPLA₂s exhibit unique tissue and cellular distributions and enzymatic properties, suggesting their distinct biological roles. Recent studies using transgenic and knockout mice for nearly a full set of sPLA₂ subtypes, in combination with sophisticated lipidomics as well as biochemical and cell biological studies, have revealed distinct contributions of individual sPLA₂s to various pathophysiological events, including production of pro- and anti-inflammatory lipid mediators, regulation of membrane remodeling, degradation of foreign phospholipids in microbes or food, or modification of extracellular noncellular lipid components. In this review, we highlight the current understanding of the in vivo functions of sPLA₂s and the underlying lipid pathways as revealed by a series of studies over the last decade.     

Bothropstoxin-I: Amino acid sequence and function

The complete amino acid sequence of bothropstoxin-I (BthTX-I), a myotoxin isolated fromBothrops jararacussu snake venom, is reported. The results show that BthTX-I is a Lys₄₉ phospholipase A₂ (PLA₂)-like protein composed of a single polypeptide chain of 121 amino acid residues (M _r=13,720), containing one methionine and 14 half-cystines. Although deprived of any detectable PLA₂ activity, BthTX-I reveals a high degree of sequence homology with Asp₄₉-PLA_2s and with other Lys₄₉-myotoxins. Critical mutations—such as Leu₅ for Phe₅; Gln₁₁ for X₁₁; Asn₂₈ for Tyr₂₈; Leu₃₂ for Gly₃₂; Lys₄₉ for Asp₄₉; and Asp₇₁ for Asn₇₁—which are apparently involved with the decreasing or elimination of PLA₂ activity, have been detected. The same mutations occurred in myotoxin II fromBothrops asper venom, but five extra changes—namely, Pro₉₀ for Ser₉₀; Gly₁₁₁ for Asn₁₁₁; His₁₂₀ for Tyr₁₂₀; Phe₁₂₄ for Leu₁₂₄; and Pro₁₃₂ for Ala₁₃₂—have been found relative to myotoxin II.     

Photosystem II: Structure and mechanism of the water:plastoquinone oxidoreductase

This mini-review briefly summarizes our current knowledge on the reaction pattern of light-driven water splitting and the structure of Photosystem II that acts as a water:plastoquinone oxidoreductase. The overall process comprises three types of reaction sequences: (a) light-induced charge separation leading to formation of the radical ion pair P680^+•Q_A^−•; (b) reduction of plastoquinone to plastoquinol at the Q_B site via a two-step reaction sequence with Q_A^−• as reductant and (c) oxidative water splitting into O₂ and four protons at a manganese-containing catalytic site via a four-step sequence driven by P680^+• as oxidant and a redox active tyrosine Y_Z acting as mediator. Based on recent progress in X-ray diffraction crystallographic structure analysis the array of the cofactors within the protein matrix is discussed in relation to the functional pattern. Special emphasis is paid on the structure of the catalytic sites of PQH₂ formation (Q_B-site) and oxidative water splitting (Mn₄O _x Ca cluster). The energetics and kinetics of the reactions taking place at these sites are presented only in a very concise manner with reference to recent up-to-date reviews. It is illustrated that several questions on the mechanism of oxidative water splitting and the structure of the catalytic sites are far from being satisfactorily answered.     

Hierarchical Classification I: Single-Linkage Method

This is the first part of a survey of hierarchical clustering algorithms using joining methods: the Single-Linkage algorithm. Complete-Linkage and general algorithms defined by d(A_i, B) = = α,d(A_i, A_r)±α_sd(A_i, A_s)±βd(A_r, A_s) will be discussed in two subsequent papers.     

Mathematical biology of social behavior: III

A society composed of individuals each of whom can perform one of two mutually exclusive activitiesR ₁ andR ₂ is considered. The tendency toward the performance of those activities is measured by the intensities ε₁ and ε₂ of excitation of two corresponding neural centers, which cross-inhibit each other. It follows from the theory developed by H. D. Landahl that an individual with ε₁ − ε₂ = 0, that is one who has no preference for either one of the two activities, will on the average performR ₁ andR ₂ with equal probability. As ε₁ − ε₂ increases, the probabilityP ₁ ofR ₁ increases, tending to 1. As ε₂ − ε₁ increases, the probabilityP ₂ ofR ₂ increases, tending to 1. We haveP ₁+P ₂=1. The effect of imitation is now studied. The total number of individuals in the society which exhibits an activityR ₁ at a given time is considered as constituting a stimulus which increases ε₁. Similarly, the total number of individuals which exhibits activityR ₂ at a given time constitutes a stimulus which increases ε₂. Using the standard equations of the mathematical biophysics of the central nervous system, equations are established which govern the behavior of such a society and the following conclusions are reached. It the quantity ε₁ − ε₂ is distributed in the society in such a way that the distribution function is symmetric with respect to ε₁ − ε₂ = 0, then on the average one-half of the population exhibitsR ₁, the other halfR ₂. This social configuration may, however, be unstable. The slightest accidental excess of individuals exhibiting, for example,R ₁, may bring it into a stable configuration, in which most individuals exhibitR ₁, and only a smaller fraction exhibitR ₂. A slight initial deviation in favor ofR ₂ brings it into a stable configuration, in which most individuals exhibitR ₂. Thus in this case there may be two stable configurations. If the population is in one of those stable configurations, and the distribution function of ε₁ − ε₂ is made asymmetric, favoring the other activity, the population will pass into a stable configuration, in which that other activity is predominant, if the asymmetry of the distribution exceeds a threshold value. By making some drastic simplifications the equations derived here may be reduced to a form which waspostulated by the author previously in his mathematical theory of human relations.     

IRBIT: It Is Everywhere

IRBIT (IP₃Rs binding protein released with IP₃) is a protein originally identified by the Mikoshiba group as an inhibitor of IP₃ receptors function. Subsequently it was found to have multiple functions and regulate the activity of diverse proteins, including regulation of HCO₃ ⁻ transporters to coordinate epithelial HCO₃ ⁻ secretion and to determine localization of the Fip1 subunit of the CPSF complex to regulate mRNA processing. This review highlights the remarkably divers functions of IRBIT that are likely only a fraction of all the potential functions of this protein.     

Biological nitrogen fixation: A key to world protein

Summary 1. Characteristics and methodology of the C₂H₂-C₂H₄ assay forin situ measurement of N₂ fixation are outlined. 2. Electron micrographic analysis of the developmental morphology of the natural soybean symbiosis and C₂H₂-C₂H₄ analysis indicate that increasing N₂-fixing activity from 12–35 days of age is accompanied by an increase in bacteroid number per cell, bacteroid number per vesicle and inclusions per bacteroid. The mole ratio of leghemoglobin to nitrogenase also increases from 50 to a relatively constant plateau of 500 to 1500 during this period. The quantitative validity of the C₂H₂-C₂H₄ assay as a measure of N₂ fixation during a complete growth cycle of soybeans on nitrogen-free medium is demonstrated by Σ (C₂H₂→C₂H₄)×28/3 values which are 75–95% of the values determined for N₂ fixed by Kjeldahl analyses. 3. A technique for the establishment of the first callus N₂-fixing symbiosis in mixed cultures ofRhizobium legume provides a defined experimental system for exploration of legume symbiosis. N₂-fixing activity is about 1% of the natural system and is influenced by exogenous auxins and cytokinins. Morphology, including infection threads and vesicle enclosed bacteroids, is similar to the nodule system. 4. N₂-fixing activity of field-grown soybeans, including varieties which differed in flowering characteristics and maturity dates, and of peanuts was determined biweekly with the C₂H₂-C₂H₄ assay. Activity extended from nodule initiation to senescence and correlated with the nitrogen demands of the plant and in most cases >90% of the N₂ fixed during the 60–70 day period of fruit formation and maturation. A logarithmic relationship between N₂-fixing activity and age, and N₂ fixed and age was demonstrated as a fundamental characteristic of these annual symbionts,i.e. log N₂ fixed =k(t−t ₀), wheret ₀ is age at activity initiation. The resultant parameters: 1) age at activity initiation, 2) calculated rate of daily increase (7–9% for soybeans and 7–10% for peanuts), 3) age at end of logarithmic phase (about 80 days for soybeans), and 4) total N₂ fixed (about 250 mg per soybean plant) are useful bases for evaluation of environmental, bacterial and host effects on N₂ fixation. Various N fertilizers applied at planting and flowering inhibited N₂ fixation of soybeans by decreasing the rate of daily increase. 5. Physical and chemical characteristics of nitrogenase, including those of crystalline Mo-Fe protein, reactions of nitrogenase, and model studies are consistent with a proposed mechanism. 6. Potential utilities of N₂ fixation research include increased food protein production via initially enhanced N₂ fixation of legumes such as soybeans and eventually extension of N₂-fixing symbioses to non-legumes and new chemistry of N₂, including the direct incorporation of aerial N₂ into important organic compounds. Contribution No. 1748.     

IP6: A novel anti-cancer agent

Inositol hcxaphosphate (InsP₆ or IP₆) is ubiquitous. At 10 μM to 1 mM concentrations, IP₆ and its lower phosphorylated forms (IP_1–5) as well as inositol (Ins) are contained in most mammalian cells, wherein they are important in regulating vital cellular functions such as signal transduction, cell proliferation and differentiation. A striking anti-cancer action of IP₆ has been demonstrated both in vivo and in vitro, which is based on the hypotheses that exogenously administered IP₆ may be internalized, dephosphorylated to IP_1–5, and inhibit cell growth. There is additional evidence that Ins alone may further enhance the anti-cancer effect of IP₆. Besides decreasing cellular proliferation, IP₆ also causes differentiation of malignant cells often resulting in a reversion to normal phenotype. These data strongly point towards the involvement of signal transduction pathways, cell cycle regulatory genes, differentiation genes, oncogenes and perhaps, tumor suppressor genes in bringing about the observed anti-neoplastic action of IP₆.     

Nitroxide Sod-Mimics: Modes of Action

Low molecular weight superoxide dismutase mimics have been shown to afford protection from oxidative damage. Such SOD-mimics can readily permeate cell membrane achieving sufficiently high levels both inside and outside the cell to effectively detoxify intracellular O^?₂. Preliminary findings also indicated that metal-based and metal-free SOD-mimics can protect hypoxic cells from H₂O₂-induced damage. The present study explored the possibility that SOD-mimics such as desferrioxamine-Mn(III) chelate [DF-Mn] or cyclic nitroxide stable free radicals could protect from O^?₂-independent damage. Killing of monolayered V79 Chinese hamster cells was induced by H₂O₂ or by t-butyl hydroperoxide (t-BHP) and assayed clonogenically. Neither catalase nor native SOD protected the cells from t-BHP. In contrast. both DF-Mn and cyclic nitroxides protected suggesting cytotoxic processes independent of O^?₂ or of O^?₂ -derived active species. The inhibition of the damage by both metal-free and metal-based SOD mimics is attributable to either SOD-mimic reacting with reduced transition metal to block the Fenton reaction and/or intercepting and detoxifying intracellular organic free radicals.     

Photosynthesis research on yellowtops: Macroevolutionn in progress

The vast majority of angiosperms, including most of the agronomically important crop plants (wheat, etc.), assimilate CO₂ through the inefficient C₃ pathway of photosynthesis. Under ambient conditions these organisms loose about 1/3 of fixed carbon via photorespiration, an energetically wasteful process. Plants with C₄ photosynthesis (such as maize) eliminate photorespiration via a biochemical CO₂-pump and thus have a larger rate of carbon gain. The genus Flaveria (yellowtops, Asteraceae) contains not only C₃ and C₄ species, but also many C₃-C₄ intermediates, which have been interpreted as evolving from C₃ to fully expressed C₄ metabolism. However, the evolutionary significance of C₃-C₄Flaveria-intermediates has long been a matter of debate. A well-resolved phylogeny of nearly all Flaveria species has recently been published. Here, we review pertinent background information and combine this novel phylogeny with physiological data. We conclude that the Flaveria species complex provides a robust model system for the study of the transition from C₃ to C₄ photosynthesis, which is arguably a macroevolutionary event. We conclude with comments relevant to the current Intelligent Design debate.     

Stoichiometry-driven Protein Folding: A Comment

Abstract

We have found, with the aid of 2-D gel electrophoresis, that double-stranded human telomeric repeat, (T₂AG₃)₁₂·(C₃TA₂)₁₂, being cloned within a plasmid, forms a protonated superhelically-induced structure. Experiments on chemical and enzymatic probing also indicate that the human telomeric repeats adopt an unusual structure. We have proposed an eclectic model for this structure in which four different elements coexist: a non-orthodox intramolecular triplex stabilized by the canonical protonated C · G*C⁺ base-triads and highly enriched by non-canonical base-triads; the intramolecular quadruplex formed by a portion of the G-rich strand; the single-stranded region encompassing a portion of the G-rich strand and, probably, the (C,A)-hairpin formed by a portion of the C-rich strand.     

Nucleosomes and subnucleosomes: heterogeneity and composition

Previous studies (Varshavsky, Bakayev and Georgiev, 1976a) have shown that chromatin subunits (mononucleosomes) and their oligomers in a mild staphylococcal nuclease digest of chromatin display a heterogeneous content of histone H1. We now report that a mild staphylococcal nuclease digest of either chromatin or nuclei from mouse Ehrlich tumor cells contains mononucleosomes of three discrete kinds. The smallest mononucleosome (MN₁) contains all histones except H1 and a DNA fragment 140 base pairs (bp) long. The intermediate mononucleosome (MN₂) contains all five histones and a DNA fragment 170 bp long. The third mononucleosome (MN₃) also contains all five histones, but its DNA fragment is longer and more heterogeneous in size (180–200 bp). Most of the MN₃ particles are rapidly converted by nuclease into mononucleosomes MN₁ and MN₂ There exists, however, a relatively nuclease-resistant subpopulation of the MN₃ mononucleosomes. These 200 bp MN₁ particles contain not only histones but also nonhistone proteins, and are significantly more resistant to nuclease than the bulk of MN₃ particles and the smaller mononucleosomes MN₁ and MN₂.There are eight major kinds of staphylococcal nuclease-produced soluble subnucleosomes (SN). The SN₁ is a set of naked double-stranded DNA fragments ～20 bp long. The SN₂ is a complex of a specific basic nonhistone protein (molecular weight ～16,000 daltons) and a DNA fragment ～27 bp long. The SN₃ contains histone H4, the above-mentioned specific nonhistone protein and a DNA fragment ～27 bp long. The SN₄ contains histones H2a, H2b, H4 and a DNA fragment ～45 bp long. The SN₅ contains histones H2a, H2b, H3 and a DNA fragment ～55 bp long. The SN₆ is a complex of histone H1 and a DNA fragment ～35 bp long. Subnucleosomes SN₇ and SN₈ each contain all the histones except H1, and DNA fragments ～100 and ～120 bp long, respectively.Nuclease digestion of isolated mono- or dinucleosomes does not produce some of the subnucleosomes. These and related findings indicate that the cleavage required to generate these subnucleosomes result from some aspect of chromatin structure which is lost upon digestion to mono- and dinucleosomes.     

Self-assembly in tetrameric 1:1 silver(I) halide:tri-p-tolylphosphine complexes: An in-depth structural investigation

The reaction of silver(I) bromide with tri(p-tolyl)phosphine in MeCN solution in 1:1 molar ratios resulted in a complexes of the formula [AgBr{P(4-MeC₆H₄)₃}]₄. This compound has a tetrameric structure with a concave coordination polyhedron, in between a cube and a stella quadrangula. Weak silver-silver interactions were observed. The current compound is compared to the Cl and I analogs using distance-distance plots. The silver-silver interactions seem to dominate the geometry of these tetrameric type of complexes.