Oxidation of guanine nucleosides to 4-amidinocarbamoyl-5-hydroxyimidazoles by dimethyldioxirane

Final oxidation products generated from guanosine and 2'-deoxyguanosine by reaction with dimethyldioxirane have been identified as 4-amidinocarbamoyl-5-hydroxyimidazoles.     

Type I collagen N-telopeptides adopt an ordered structure when docked to their helix receptor during fibrillogenesis

The in vitro rate and specificity of fibrillogenesis in type I collagen depends on the integrity of the amino (N)-telopeptide domain. In vivo an intact N-telopeptide domain is also required for normal fibril assembly. Although Chou-Fasman predictions and NMR studies suggested that a type I beta-turn could be induced in alpha1(I) N-telopeptide chains, computer modeling did not identify ordered structures. Nevertheless, X-ray analysis and electron tomography studies have shown that the N-telopeptide is in one of the most highly ordered fibril domains. This study was undertaken to determine if the docking of the N-telopeptide to its helix receptor domain could induce the telopeptides to take up a specific conformation. With use of molecular modeling suite of programs, a (Gly-Pro-Pro)(n) triple-helical structure was built on the basis of high-resolution X-ray crystallographic coordinates and then replaced with the actual bovine collagen residues 924-938, the triple-helical alpha1(I)-N-telopeptide-receptor sequences. Energy minimization produced a modified triple-helical conformation. The bovine alpha1(I) N-telopeptide sequence was similarly minimized and docked to this receptor. The docking induced an ordered conformation with a stabilizing hydrogen bond in the N-telopeptide and, importantly, a reciprocal reordering of the triple-helical conformation in the binding domain. This docked structure placed Lys residues in both telopeptide and helix in the correct locations for cross-link formation. The modeling has been extended to the three-chain N-telopeptide domain and finally to the construction of the Hulmes-Miller quasi-hexagonal packing structure. Each N-telopeptide domain can form linkages with two adjacent, aligned helix receptor domains. The telopeptides and the order of staggering of the three chains in the helix play crucial roles in the packing and intrafibrillar cross-linking patterns and the relative azimuthal orientations of adjacent molecules in the fibril. The models confirm the high order in the N-telopeptide 4D overlap zone.     

Direct measurement of sodium and potassium in the transpiration stream of salt-excluding and non-excluding varieties of wheat

The xylem-feeding insect Philaenus spumarius was used to analyse sodium and potassium fluxes in the xylem of intact, transpiring wheat plants. Two cultivars were compared: the salt-excluding (Chinese Spring) and the non-excluding (Langdon). Chinese Spring accumulated much less sodium in its leaves than the salt-sensitive Langdon. After 7 d in 150 mol m(-3) NaCl, the sodium concentration in the leaf sap of Langdon reached over 600 mol m(-3). This was some three-fold greater than that in Chinese Spring. Similar findings have previously been reported from these cultivars. The reduced ion accumulation was specific to sodium; accumulation of K(+) was unaffected by NaCl in Chinese Spring, such that it developed a much lower leaf Na(+)/K(+) ratio than Langdon. The spittlebug, P. spumarius was used to sample xylem sap from both cultivars. This approach showed that the leaf xylem sap of Chinese Spring had much lower levels of sodium than that of Langdon. In the 150 mol m(-3) NaCl treatment, sodium levels in the leaf xylem reached only 2-3 mol m(-3) in Chinese Spring, compared with 8-10 mol m(-3) in Langdon. Transpiration rates were found to be similar in the two varieties. The lower leaf xylem content alone was thus sufficient to account for the reduced accumulation of sodium in leaves of Chinese Spring. The mechanisms by which xylem sodium might be lowered are discussed and it is concluded that sodium is probably excluded from the xylem in the root of Chinese Spring.     

Diffusion theory in biology: a relic of mechanistic materialism

Diffusion theory explains in physical terms how materials move through a medium, e.g. water or a biological fluid. There are strong and widely acknowledged grounds for doubting the applicability of this theory in biology, although it continues to be accepted almost uncritically and taught as a basis of both biology and medicine. Our principal aim is to explore how this situation arose and has been allowed to continue seemingly unchallenged for more than 150 years. The main shortcomings of diffusion theory will be briefly reviewed to show that the entrenchment of this theory in the corpus of biological knowledge needs to be explained, especially as there are equally valid historical grounds for presuming that bulk fluid movement powered by the energy of cell metabolism plays a prominent note in the transport of molecules in the living body. First, the theory's evolution, notably from its origins in connection with the mechanistic materialist philosophy of mid nineteenth century physiology, is discussed. Following this, the entrenchment of the theory in twentieth century biology is analyzed in relation to three situations: the mechanism of oxygen transport between air and mammalian tissues; the structure and function of cell membranes; and the nature of the intermediary metabolism, with its implicit presumptions about the intracellular organization and the movement of molecules within it. In our final section, we consider several historically based alternatives to diffusion theory, all of which have their precursors in nineteenth and twentieth century philosophy of science. This revised version was published online in July 2006 with corrections to the Cover Date.     

Transfer and expression of foreign genes in mammalian cells

The transfer of foreign genes into eukaryotic cells, in particular mammalian cells, has been essential to our understanding of the functional significance of genes and regulatory sequences as well as the development of gene therapy strategies. To this end, different mammalian expression vector systems have been designed. The choice of a particular expression system depends on the nature and purpose of the study and will involve selecting particular parameters of expression systems such as the type of promoter/enhancer sequences, the type of expression (transient versus stable) and the level of desired expression. In addition, the success of the study depends on efficient gene transfer. The purification of the expression vectors, as well as the transfer method, affects transfection efficiency. Numerous approaches have been developed to facilitate the transfer of genes into cells via physical, chemical or viral strategies. While these systems have all been effective in vitro they need to be optimized for individual cell types and, in particular, for in vivo transfection.     

Record of Blue tilapia Oreochromis aureus (Steindachner, 1864) in the Eerste River catchment,Western Cape province,South Africa

Oreochromis aureus was imported from Israel into South Africa in 1959 but data on its current status in South Africa are lacking. Genomic DNA was extracted and the COI gene amplified at the South African Institute for Aquatic Biodiversity. The identity of the sequences and specimens was determined using the Barcode of Life Data Systems and GenBank. Morphological and genetic assessment demonstrated that 11 specimens collected from two farm dams in the Eerste River System, Western Cape province, were Oreochromis aureus. A MaxEnt model compiled using global distribution, rainfall and temperature data predicted that large areas of southern Africa were climatically suitable for this species, indicating considerable invasion debt in southern Africa. As a result, surveys to assess for the extent of the invasion in South Africa and eradication of existing populations, if feasible, are recommended management actions.     

Effects of simulated drought on the carbon balance of Everglades short‐hydroperiod marsh

Hydrology drives the carbon balance of wetlands by controlling the uptake and release of CO₂ and CH₄. Longer dry periods in between heavier precipitation events predicted for the Everglades region, may alter the stability of large carbon pools in this wetland's ecosystems. To determine the effects of drought on CO₂ fluxes and CH₄ emissions, we simulated changes in hydroperiod with three scenarios that differed in the onset rate of drought (gradual, intermediate, and rapid transition into drought) on 18 freshwater wetland monoliths collected from an Everglades short‐hydroperiod marsh. Simulated drought, regardless of the onset rate, resulted in higher net CO₂ losses net ecosystem exchange (NEE) over the 22‐week manipulation. Drought caused extensive vegetation dieback, increased ecosystem respiration (R_eco), and reduced carbon uptake gross ecosystem exchange (GEE). Photosynthetic potential measured by reflective indices (photochemical reflectance index, water index, normalized phaeophytinization index, and the normalized difference vegetation index) indicated that water stress limited GEE and inhibited R_eco. As a result of drought‐induced dieback, NEE did not offset methane production during periods of inundation. The average ratio of net CH₄ to NEE over the study period was 0.06, surpassing the 100‐year greenhouse warming compensation point for CH₄ (0.04). Drought‐induced diebacks of sawgrass (C₃) led to the establishment of the invasive species torpedograss (C₄) when water was resupplied. These changes in the structure and function indicate that freshwater marsh ecosystems can become a net source of CO₂ and CH₄ to the atmosphere, even following an extended drought. Future changes in precipitation patterns and drought occurrence/duration can change the carbon storage capacity of freshwater marshes from sinks to sources of carbon to the atmosphere. Therefore, climate change will impact the carbon storage capacity of freshwater marshes by influencing water availability and the potential for positive feedbacks on radiative forcing.