Structure/function analysis of the Saccharomyces cerevisiae Trf4/Pol sigma DNA polymerase

The Trf4p/Pol sigma DNA polymerase (formerly Trf4p/Pol kappa) couples DNA replication to the establishment of sister chromatid cohesion. The polymerase is encoded by two redundant homologs in Saccharomyces cerevisiae, TRF4 and TRF5, that together define a fourth essential nuclear DNA polymerase in yeast and probably in all eukaryotes. Here we present a thorough genetic analysis of the founding member of this novel family of DNA polymerases, TRF4. Analyses of mutants carrying 1 of 34 "surface-targeted" alanine scanning mutations in TRF4 have identified those regions required for Pol sigma's essential function, for its role in DNA double-strand break repair, and for its association with chromosomes. The data strongly support the importance of the regions of predicted structural similarity with the Pol beta superfamily as critical for Trf4p/Pol sigma's essential and repair functions. Surprisingly, five lethal mutations lie outside all polymerase homology in a C-terminal region. The protein possesses Mg2+-dependent 3' to 5' exonuclease activity. Cell cycle analysis reveals that Trf4p/Pol sigma associates with chromosomes in G1, S, and G2 phases, but that association is abolished coincident with dissolution of cohesion at the metaphase-to-anaphase transition.     

Growth depensation and group behaviour in juvenile hybrid striped bass Morone chrysops×Morone saxatilis: effects of group membership, feeding method, ration size and size disparity

The effects of group membership (three group sizes), feeding method (single site v. scattered), variation in ration size (low v. high) and starting size disparity (range of starting sizes) on growth, growth depensation and group behaviour of juvenile hybrid striped bass (HSB) Morone chrysops female × Morone saxatilis male were tested. Group membership, starting size disparity and ration size affected the growth, growth depensation and behaviour of juvenile HSB. Growth was higher in fish held within large group memberships and high ration treatments. Growth depensation (size variation among individuals of the same age) in group memberships of three and 12 fish per tank was minimal when compared to intermediate memberships (six fish per tank). In addition, small fish held in tanks with fish of intermediate sizes demonstrated higher growth when compared to small fish housed with large individuals. Some behaviours, specifically activity and scramble feeding, were more elevated in large group memberships when compared to groups with fewer members. Activity was also found to increase over time during size disparity testing. Results suggest that HSB are ideally suited for high-density, intensive aquaculture since they appear to thrive in high group memberships of similar starting sizes and when a sufficient amount of feed in administered.     

Molecular phylogeny of the major arthropod groups indicates polyphyly of crustaceans and a new hypothesis for the origin of hexapods

A phylogeny of the arthropods was inferred from analyses of amino acid sequences derived from the nuclear genes encoding elongation factor-1 alpha and the largest subunit of RNA polymerase II using maximum- parsimony, neighbor-joining, and maximum-likelihood methods. Analyses of elongation factor-1 alpha from 17 arthropods and 4 outgroup taxa recovered many arthropod clades supported by previous morphological studies, including Diplopoda, Myriapoda, Insecta, Hexapoda, Branchiopoda (Crustacea), Araneae, Tetrapulmonata, Arachnida, Chelicerata, and Malacostraca (Crustacea). However, counter to previous studies, elongation factor-1 alpha placed Malacostraca as sister group to the other arthropods. Branchiopod crustaceans were found to be more closely related to hexapods and myriapods than to malacostracan crustaceans. Sequences for RNA polymerase II were obtained from 11 arthropod taxa and were analyzed separately and in combination with elongation factor-1 alpha. Results from these analyses were concordant with those derived from elongation factor-1 alpha alone and provided support for a Hexapoda/Branchiopoda clade, thus arguing against the monophyly of the traditionally defined Atelocerata (Hexapoda + Myriapoda).      

Analysis of effector cell-derived lyso platelet activating factor by electron capture negative ion mass spectrometry.

Quantification of 1-O-alkyl-2-lyso-sn-3-glycero-phosphocholine (lysoPAF) and determination of the different molecular species released by cells has been hampered by the molecules's lack of intrinsic bioactivity, unavailability of a suitable internal standard, and reliance on derivatives requiring electron impact techniques. We have synthesized trideuterated internal standards (labeled on the terminal carbon of the alkyl chain) for both C16:0 and C18:0 lysoPAF. Using these standards, we isolated and quantified lysoPAF released from A23187-stimulated human neutrophils and rat alveolar macrophages. Extracted lysoPAF was purified by solid-phase extraction and thin-layer chromatography. The polar phosphorylcholine group was removed with 29 M HF or phospholipase C. The two free hydroxyl groups were derivatized with pentafluorobenzoyl chloride. The resultant bis-pentafluorobenzoyl derivative, analyzed by gas chromatography/electron capture negative ion mass spectrometry, underwent substantial fragmentation. Lowering of the ion source temperature resulted in a dramatic increase in signal-to-noise ratio, with the vast majority of the ion current carried in the molecular anion. Stimulated neutrophils released 16.3 and 10.2 ng/10(6) cells of C16:0 lysoPAF and C18:0 lysoPAF, respectively. Rat macrophages synthesized 15.9 ng/10(6) cells of C16:0 lysoPAF, but C18:0 lysoPAF was variably detected at low levels. We conclude that use of the bispentafluorobenzoyl ester derivative of lysoPAF allows facile quantification of this autacoid metabolite in biological matrices.     

Inhibition of development of characteristic indices of myeloid differentiation by a factor released from a tetraploid variant of the human promyelocytic cell line, HL-60

HL-60TR, a tetraploid variant of the human promyeloid cell line HL-60, was obtained by culturing HL-60 cells for one week with the tumor promoter 12-O-tetradecanoylphorbol-13-acetate (TPA) at 400 pM. HL-60TR cells have lost the ability to develop several common markers of maturation in response to compounds that induce monocytoid or myelocytoid differentiation of HL-60 cells. In addition, they release a factor which inhibits induction of the same markers in HL-60 cells. Medium conditioned by HL-60TR cells also inhibits colony formation by normal mouse bone marrow cells. These properties have been maintained by HL-60TR cells through more than one year of constant subculture in the absence of TPA, a finding which suggests the possibility that TPA may promote tumor formation not only through direct effects on the phenotype of initiated cells but also through induction of continued production of factors that affect differentiation of normal stem cells.     

Inhibition of DNA methyltransferase and induction of Friend erythroleukemia cell differentiation by 5-azacytidine and 5-aza-2'-deoxycytidine

Treatment of Friend erythroleukemia cells with the antileukemic drugs 5-azacytidine and 5-aza-2'-deoxycytidine leads to rapid, time-dependent, and dose-dependent decrease of DNA methyltransferase activity and synthesis of markedly undermethylated DNA. Since this DNA is at least partially methylated in vivo and serves as an excellent substrate for methylation in vitro, hypomethylation of DNA in analog-treated cells appears to result from the loss of DNA methyltransferase, rather than from an inherent inability of 5-azacytosine- substituted DNA to serve as a methyl acceptor. Inhibition of DNA synthesis blocks the loss of DNA methyltransferase activity while inhibitors of RNA synthesis do not, suggesting that the analogs must be incorporated into DNA to mediate their effect on the enzyme, and that minor substitution of 5-azacytosine for cytosine in DNA (approximately 0.3%) suffices to inactivate more than 95% of the enzyme in the cell. Several lines of evidence link changes in the pattern of DNA modification with differentiation. In this regard, it is significant that 5-azacytidine and 5-aza-2'-deoxycytidine act as weak inducers of erythroid differentiation of Friend erythroleukemia cells in the same concentration range where they affect DNA methyltransferase activity. For differentiation to proceed, the cells must be washed free of the drugs. Less than 24 h later, normal levels of DNA methyltransferase activity are restored and within 48 h, DNA isolated from the cells is not detectably undermethylated. This may in part explain why 5-azacytidine and 5-aza-2'-deoxycytidine induce differentiation in less than 15% of the population despite their initial profound effect on DNA methylation.     

On the distribution of Na+ pump sites in the frog skin

Exposure of the outside of the isolated frog skin to a Ringer's solution, made hypertonic by the addition of mannitol, causes a rapid and sustained increase in transepithelial permeability through a structural distortion-a focal blistering-of the "tight" junctions of the outermost living cell layer. [(3)H]ouabain, used as an autoradiographic marker for the Na+-pump (Na+-K+-adenosine triphosphatase), is usually unable to penetrate the frog skin from the outside solution, but when added to a hypertonic mannitol- Ringer's solution in the outside bath it readily penetrates the epithelium, presumably through the opened shunt pathway. Radioautographic analysis of [(3)H]ouabain binding sites revealed that most of ouabain enters from the outside solution binds to the sites on the cell membranes of the stratum spinosum, as was the case when it was applied from the inside bath in an earlier study. The outer living cell layer, the first to be exposed to ouabain, does not appear to be the major site for the Na+-pump, and therefore, is not likely to be responsible for most of the active pumping of Na+. This result demonstrates that previous failure to show a high density of Na+-pump sites on the cells of the outermost layer, when [(3)H]ouabain was applied from the inside solution, was not due to the inability of the marker to reach these cells at a sufficient concentration to reveal all pump sites. These results provide further support for a model of Na+-transport across the frog skin which distributes the active pump step on the inward facing membranes of all living cells.