Organic Tracers from Asphalt in Propolis Produced by Urban Honey Bees,Apis mellifera Linn.

Propolis is a gummy material produced by honey bees to protect their hives and currently has drawn the attention of researchers due to its broad clinical use. It has been reported, based only on observations, that honey bees also collect other non-vegetation substances such as paint or asphalt/tar to make propolis. Therefore, propolis samples were collected from bee hives in Riyadh and Al-Bahah, a natural area, Saudi Arabia to determine their compositional characteristics and possible sources of the neutral organic compounds. The samples were extracted with hexane and analyzed by gas chromatography-mass spectrometry. The results showed that the major compounds were n-alkanes, n-alkenes, methyl n-alkanoates, long chain wax esters, triterpenoids and hopanes. The n-alkanes (ranging from C₁₇ to C₄₀) were significant with relative concentrations varying from 23.8 to 56.8% (mean = 44.9+9.4%) of the total extracts. Their odd carbon preference index (CPI) ranged from 3.6 to 7.7, with a maximum concentration at heptacosane indicating inputs from higher plant vegetation wax. The relative concentrations of the n-alkenes varied from 23.8 to 41.19% (mean = 35.6+5.1%), with CPI = 12.4-31.4, range from C₂₅ to C₃₅ and maximum at tritriacontane. Methyl n-alkanoates, ranged from C₁₂ to C₂₆ as acids, with concentrations from 3.11 to 33.2% (mean = 9.6+9.5%). Long chain wax esters and triterpenoids were minor. The main triterpenoids were α- and β-amyrins, amyrones and amyryl acetates. The presence of hopanes in some total extracts (up to 12.5%) indicated that the bees also collected petroleum derivatives from vicinal asphalt and used that as an additional ingredient to make propolis. Therefore, caution should be taken when considering the chemical compositions of propolis as potential sources of natural products for biological and pharmacological applications. Moreover, beekeepers should be aware of the proper source of propolis in the flight range of their bee colonies.     

Sulphated tyrosines mediate association of chemokines and Plasmodium vivax Duffy binding protein with the Duffy antigen/receptor for chemokines (DARC)

Plasmodium vivax is one of four Plasmodium species that cause human malaria. P. vivax and a related simian malaria parasite, Plasmodium knowlesi, invade erythrocytes by binding the Duffy antigen/receptor for chemokines (DARC) through their respective Duffy binding proteins. Here we show that tyrosines 30 and 41 of DARC are modified by addition of sulphate groups, and that the sulphated tyrosine 41 is essential for association of the Duffy binding proteins of P. vivax (PvDBP) and P. knowlesi (PkDaBP) with DARC-expressing cells. These sulphated tyrosines also participate in the association of DARC with each of its four known chemokine ligands. Alteration of tyrosine 41 to phenylalanine interferes with MCP-1, RANTES and MGSA association with DARC, but not with that of IL8. In contrast, alteration of tyrosine 30 to phenylalanine interferes with the association of IL8 with DARC. A soluble sulphated amino-terminal domain of DARC, but not one modified to phenylalanine at residue 41, can be used to block the association of PvDBP and PkDaBP with red blood cells, with an IC50 of approximately 5 nM. These data are consistent with a role for tyrosine sulphation in the association of many or most chemokines with their receptors, and identify a key molecular determinant of erythrocyte invasion by P. vivax.     

Lipid Formation by Aqueous Fischer-Tropsch-Type Synthesis over a Temperature Range of 100 to 400 °C

The formation of lipid compounds during anaqueous Fischer-Tropsch-type reaction was studied withsolutions of oxalic acid as the carbon and hydrogensource. The reactions were conducted in stainlesssteel vessels by heating the oxalic acid solution atdiscrete temperatures from 100 to 400 °C, atintervals of 50 °C for two days each. Themaximum lipid yield, especially for oxygenatedcompounds, is in the window of 150–250 °C. At atemperature of 100 °C only a trace amount oflipids was detected. At temperatures above150 °C the lipid components ranged from C₁₂to >C₃₃ and included n-alkanols, n-alkanoic acids, n-alkyl formates, n-alkanals, n-alkanones, n-alkanes, andn-alkenes, all with essentially no carbon numberpreference. The n-alkanes increased inconcentration over the oxygenated compounds attemperatures of 200 °C and above, with a slightreduction in their carbon number ranges due tocracking. It was also noted that the n-alkanoicacids increased while n-alkanols decreased withincreasing temperature above 200 °C. Attemperatures above 300 °C synthesis competeswith cracking and reforming reactions. At 400 °Csignificant cracking was observed and polynucleararomatic hydrocarbons and their alkylated homologswere detected. The results of this work suggest thatthe formation of lipid compounds by aqueous FTTreactions proceeds by insertion of a CO group at theterminal end of a carboxylic acid functionality toform n-oxoalkanoic acids, followed by reductionto n-alkanoic acids, to n-alkanals, thento n-alkanols. The n-alkenes areintermediate homologs for n-alkan-2-ones andn-alkanes. This proposed mechanism for aqueousFTT synthesis differs from the surface-catalyzedstepwise FT process (i.e., gaseous) of polymerization of methylene reported in the literature.     

Recent evaporite deposition associated with microbial mats,Al-Kharrar supratidal–intertidal sabkha,Rabigh area,Red Sea coastal plain of Saudi Arabia

The supratidal–intertidal sabkha of the Al-Kharrar area, Red Sea coast, Saudi Arabia, contains the evaporite minerals gypsum, anhydrite, and halite. Microbial mats flourish adjacent to the sabkha evaporites in tidal flats and pools of the Al Kharrar lagoon. Desiccation and decay of some microbial mats in tidal flat areas have led to precipitation of gypsum and halite there. The evaporite minerals have been precipitated through displacive, inclusive, and replacive growth within mud, sand, gravelly sand, and bioclastic sediment of the sabkha. Gypsum occurs as lenticular and tabular crystals whereas anhydrite occurs as nodular (individual, mosaic, and enterolithic) and pseudomorphs of lenticular gypsum crystals that grew displacively and replacively near the surface of the sabkha. Halite exists as a diagenetic cement within the sabkha sediment, or as primary rafts and skeletal crystals in desiccated tidal pools with salinity over 220‰. Microbial mats are growing on the surface of the upper tidal flat areas and in pools at a salinity range of 80–110‰, and they lead to biostabilization of the sediment. They have induced a range of sedimentary surface structures (MISS) including gas domes, reticulate patterns, tufts, pinnacles, wrinkles, and microbial shrinkage cracks. The occurrence, abundance, and association of evaporite minerals and MISS are controlled by local environmental factors such topography of the sabkha, emergence or submergence of tidal areas, surface area of the evaporite basin, contribution of meteoric water from floods from the adjoining Red Sea Mountains, and water salinity. These factors promote the growth of the microbial mats in the winter months, and deposition of evaporite minerals during summer months. Field and petrographic data indicate that the main recharge to the sabkha area is from tidal flow and water seepage from the Al-Kharrar lagoon. The results of this study indicate that within a small sabkha area of Al-Kharrar (3?×?17 km), a large variation in evaporite mineral types and morphologies grade into and are associated with MISS due to local environmental parameters. The interpretation of this association of evaporite minerals and MISS provides useful data for understanding the mechanisms responsible for precipitation of evaporite minerals and formation of MISS.     

Inhibition of retroviral Gag assembly by non-silencing miRNAs promotes autophagic viral degradation

We recently reported an unconventional mechanism by which miRNAs inhibit HIV-1 viral production. This occurs when miRNAs bind nonspecifically to the viral structural protein Gag, interfering with viral RNA-mediated Gag assembly at the plasma membrane. Consequently, misassembled viral complexes are redirected into the endocytic pathway where they are delivered to lysosomes for degradation. In this study, we demonstrate that autophagy is a critical mediator of the viral degradation pathway and that this pathway is not HIV-1 specific. Misassembled viral complexes were found to colocalize extensively with LC3 and p62 in late endosomes/lysosomes, demonstrating a convergence of autophagy with functional degradative compartments. Knocking down autophagosome formation machineries reduced this convergence, while treatment with autophagy-inducer rapamycin enhanced the convergence. Furthermore, similar autophagy-dependent nonspecific miRNA inhibition of murine leukemia virus (MLV) assembly was shown. Overall, these results reveal autophagy as a crucial regulator of the retroviral degradation pathway in host cells initiated by nonspecific miRNA-Gag interactions. These findings could have significant implications for understanding how cells may regulate retroviral complex assembly by miRNA expression and autophagy, and raise the possibility that similar regulations can occur in other biological contexts.     

Abiotic Condensation Synthesis of Glyceride Lipids and Wax Esters Under Simulated Hydrothermal Conditions

Precursor compounds for abiotic proto cellular membranes are necessary for the origin of life. Amphipathic compounds such as fatty acids and acyl glycerols are important candidates for micelle/bilayer/vesicle formation. Two sets of experiments were conducted to study dehydration reactions of model lipid precursors in aqueous media to form acyl polyols and wax esters, and to evaluate the stability and reactions of the products at elevated temperatures. In the first set, mixtures of n-nonadecanoic acid and ethylene glycol in water, with and without oxalic acid, were heated at discrete temperatures from 150 ^∘C to 300 ^∘C for 72 h. The products were typically alkyl alkanoates, ethylene glycolyl alkanoates, ethylene glycolyl bis-alkanoates and alkanols. The condensation products had maximum yields between 150 ^∘C and 250 ^∘C, and were detectable and thus stable under hydrothermal conditions to temperatures < 300 ^∘C. In the second set of experiments, mixtures of n-heptanoic acid and glycerol were heated using the same experimental conditions, with and without oxalic acid, between 100 ^∘C and 250 ^∘C. The main condensation products were two isomers each of monoacylglycerols and diacylglycerols at all temperatures, as well as minor amounts of the fatty acid anhydride and methyl ester. The yield of glyceryl monoheptanoates generally increased with increasing temperature and glyceryl diheptanoates decreased noticeably with increasing temperature. The results indicate that condensation reactions and abiotic synthesis of organic lipid compounds under hydrothermal conditions occur easily, provided precursor concentrations are sufficiently high.     

Mapping binding residues in the Plasmodium vivax domain that binds Duffy antigen during red cell invasion

Summary Plasmodium vivax depends on interaction with the Duffy antigen/receptor for chemokines (DARC) for invasion of human erythrocytes. The 140 kDa P. vivax Duffy-binding protein (PvDBP) mediates interaction with DARC. The receptor-binding domain of PvDBP maps to its N-terminal, cysteine-rich region, region II (PvRII), which contains approximately 300 amino acid residues including 12 conserved cysteines. Using surface plasmon resonance, we show that binding of PvRII to DARC is a high-affinity interaction with a binding constant (K(D)) of 8.7 nM. The minimal binding domain of PvRII has been previously mapped to a central 170-amino-acid stretch that includes cysteines 5-8. Here, we have used site-directed mutagenesis and quantitative binding assays to map amino acid residues within PvRII that make contact with DARC. Of the seven alanine replacement mutations that had an effect on binding, five were mutations in hydrophobic residues suggesting that hydrophobic interactions play a major role in the interaction of PvDBP with DARC. Genetic diversity studies have shown that six of the seven binding residues identified in PvRII are conserved in P. vivax field isolates, which provides support for their role in interaction with DARC.     

Map-invariant spectral analysis for the identification of DNA periodicities

Many signal processing based methods for finding hidden periodicities in DNA sequences have primarily focused on assigning numerical values to the symbolic DNA sequence and then applying spectral analysis tools such as the short-time discrete Fourier transform (ST-DFT) to locate these repeats. The key results pertaining to this approach are however obtained using a very specific symbolic to numerical map, namely the so-called Voss representation. An important research problem is to therefore quantify the sensitivity of these results to the choice of the symbolic to numerical map. In this article, a novel algebraic approach to the periodicity detection problem is presented and provides a natural framework for studying the role of the symbolic to numerical map in finding these repeats. More specifically, we derive a new matrix-based expression of the DNA spectrum that comprises most of the widely used mappings in the literature as special cases, shows that the DNA spectrum is in fact invariable under all these mappings, and generates a necessary and sufficient condition for the invariance of the DNA spectrum to the symbolic to numerical map. Furthermore, the new algebraic framework decomposes the periodicity detection problem into several fundamental building blocks that are totally independent of each other. Sophisticated digital filters and/or alternate fast data transforms such as the discrete cosine and sine transforms can therefore be always incorporated in the periodicity detection scheme regardless of the choice of the symbolic to numerical map. Although the newly proposed framework is matrix based, identification of these periodicities can be achieved at a low computational cost.