The application of strand invasion phenomenon,directed by peptide nucleic acid (PNA) and single‐stranded DNA binding protein (SSB) for the recognition of specific sequences of human endogenous retroviral HERV‐W family

The HERV‐W family of human endogenous retroviruses represents a group of numerous sequences that show close similarity in genetic composition. It has been documented that some members of HERV‐W–derived expression products are supposed to play significant role in humans' pathology, such as multiple sclerosis or schizophrenia. Other members of the family are necessary to orchestrate physiological processes (eg, ERVWE1 coding syncytin‐1 that is engaged in syncytiotrophoblast formation). Therefore, an assay that would allow the recognition of particular form of HERV‐W members is highly desirable. A peptide nucleic acid (PNA)–mediated technique for the discrimination between multiple sclerosis‐associated retrovirus and ERVWE1 sequence has been developed. The assay uses a PNA probe that, being fully complementary to the ERVWE1 but not to multiple sclerosis‐associated retrovirus (MSRV) template, shows high selective potential. Single‐stranded DNA binding protein facilitates the PNA‐mediated, sequence‐specific formation of strand invasion complex and, consequently, local DNA unwinding. The target DNA may be then excluded from further analysis in any downstream process such as single‐stranded DNA‐specific exonuclease action. Finally, the reaction conditions have been optimized, and several PNA probes that are targeted toward distinct loci along whole HERV‐W env sequences have been evaluated. We believe that PNA/single‐stranded DNA binding protein–based application has the potential to selectively discriminate particular HERV‐W molecules as they are at least suspected to play pathogenic role in a broad range of medical conditions, from psycho‐neurologic disorders (multiple sclerosis and schizophrenia) and cancers (breast cancer) to that of an auto‐immunologic background (psoriasis and lupus erythematosus).     

Isomeric lipid signatures reveal compartmentalized fatty acid metabolism in cancer

The cellular energy and biomass demands of cancer drive a complex dynamic between uptake of extracellular FAs and their de novo synthesis. Given that oxidation of de novo synthesized FAs for energy would result in net-energy loss, there is an implication that FAs from these two sources must have distinct metabolic fates; however, hitherto, all FAs have been considered part of a common pool. To probe potential metabolic partitioning of cellular FAs, cancer cells were supplemented with stable isotope-labeled FAs. Structural analysis of the resulting glycerophospholipids revealed that labeled FAs from uptake were largely incorporated to canonical (sn-) positions on the glycerol backbone. Surprisingly, labeled FA uptake also disrupted canonical isomer patterns of the unlabeled lipidome and induced repartitioning of n-3 and n-6 PUFAs into glycerophospholipid classes. These structural changes support the existence of differences in the metabolic fates of FAs derived from uptake or de novo sources and demonstrate unique signaling and remodeling behaviors usually hidden from conventional lipidomics.     

Environmental and genetic control of crassulacean acid metabolism in two crassulacean species and an F1 hybrid with differing biomass δ13C values

Abstract The growth, biomass δ¹³C values, and ability to accumulate titratable acidity at night were compared in eight environmental treatments for Cremnophila linguifolia, Sedum greggii, and their F₁ hybrid. In the phytotron, differences in treatment daylength, day/night temperature and water availability were all found to have effects on total plant dry weight, nocturnal accumulation of titratable acidity and biomass δ¹³C value of at least some of the genotypes. However, there were differences between the genotypes both in the magnitude and direction of response of the phenotypic properties to the treatment variables. The phytotron δ¹³C values ranged from -12.9 to -19.2‰ for C. linguifolia, from -22.2 to -33.4‰ for S. greggii, and from -19.2 to -24.9‰ for the hybrid. After with-holding water for 76 h both C. linguifolia and the hybrid had midday Ψ_leaf values of -0.23 MPa; however, S. greggii had a value of -1.05 MPa. In contrast to past observations of other species, the daily watered plants of C. linguifolia had less negative δ¹³C values than did the plants watered only weekly.     

Screening environmental samples for source-specific bacteriophage hosts using a method for the simultaneous pouring of 12 petri plates

A simple apparatus was developed to allow 12 petri plates to be poured simultaneously by hand. It was used when screening bacterial isolates from sewage and dog feces for their ability to detect phages from these sources. This was done to assess the ease with which source-specific phage hosts can be isolated from these sources of fecal pollution. Host bacteria that consistently detected phages from sewage were easily isolated from sewage. These bacterial isolates did not detect phages from dog feces. Host bacteria were not isolated from dog feces even after screening hundreds of colonies from fecal samples from six dogs. Journal of Industrial Microbiology & Biotechnology (2000) 24, 124–126. Received 06 July 1999/ Accepted in revised form 05 November 1999     

Cortinarius sarcoflammeus sp. nov, a new species of subgenus Dermocybe (Agaricales) growing in Sphagnum bogs

 Cortinarius sarcoflammeus is proposed as a new species belonging to subgenus Dermocybe, on the basis of its morphological, chemical and ecological characters. The strong red-orange colour of the context and stipe base, large spores, sphagnicolous habitat and high dermorubin content are characteristic for the new species. Holotypes of C. huronensis and C. huronensis var. olivaceus have been examined for comparison, and their differences discussed. Photographs and line drawings of C. sarcoflammeus are added. Received February 13, 2001 Accepted March 23, 2001     

Enzymatic removal of zeins from the surface of maize starch granules

Alcohol-extractable, hydrophobic zein proteins contaminate starch granule surfaces and can be removed by enzymatic digestion with thermolysin. The goal of this research was to find practical alternatives to thermolysin that might be used during the corn wet-milling process. All of the commercial thermostable alkaline proteases studied (SP 709, Neutrase, and Spezyme FAN) removed the zein proteins from various types of cornstarch, as demonstrated by the lack of protein bands below 30 kDa under the reducing conditions of SDS-PAGE gel. Each enzyme removed the zein proteins as effectively as thermolysin removed them. However, the removal of the zein protein did not reduce the quantity of free fatty acids associated with the starch. Journal of Industrial Microbiology & Biotechnology (2000) 24, 71–74. Received 27 May 1999/ Accepted in revised form 01 October 1999     

Computational Investigations of the Chalcogen-Substituted Carboxylic Acids RC(=O)XH and RC(=X)OH and their Dimers [RC(=O)XH]2 and [RC(=X)OH]2 (X=S, Se, Te)

Semiempirical and ab initio theoretical methods have been used to investigate molecular structures of the chalcogen-substituted carboxylic acid isomers RC(=O)XH (chalcogenol acid) and RC(=X)OH (chalcogenon acid). A recent experimental report suggests that the chalcogenon isomers, although less stable at room temperature, predominate at low temperature in polar solvents and that there is only a small barrier to isomerization between the isomers. Theoretical calculations have been used to locate minimum energy structures of chalcogen-substituted carboxylic acid isomers and to calculate energy differences between pairs of isomers. Carboxylic acids are well known to dimerize, especially in the gas phase and in non-polar solvents. We have, therefore, also calculated energies of dimerization of the chalcogen-substituted acids by optimizing the geometries of the symmetric dimers. We note that the PM3 level of theory is only qualitatively correct for sulfur- and selenium-containing species but fails even qualitatively for the tellurium-containing compounds. Ab initio results confirm the experimental observations and provide good estimates of both isomerization and dimerization energies. We conclude that for many functional groups with tautomers RC(=X)YH and RC(=Y)XH, the more acidic tautomer is the one with the acid proton on the smaller, more electronegative atom, although in many cases this may not be the more stable tautomer.Electronic Supplementary Material available.