Climate and geochemistry as drivers of eucalypt diversification in Australia

Eucalypts cover most of Australia. Here, we investigate the relative contribution of climate and geochemistry to the distribution and diversity of eucalypts. Using geostatistics, we estimate major element concentrations, pH, and electrical conductivity at sites where eucalypts have been recorded. We compare the median predicted geochemistry and reported substrate for individual species that appear associated with extreme conditions; this provides a partial evaluation of the predictions. We generate a site-by-species matrix by aggregating observations to the centroids of 100-km-wide grid cells, calculate diversity indices, and use numerical ecology methods (ordination, variation partitioning) to investigate the ecology of eucalypts and their response to climatic and geochemical gradients. We find that β-diversity coincides with variations in climatic and geochemical patterns. Climate and geochemistry together account for less than half of the variation in eucalypt species assemblages across Australia but for greater than 80% in areas of high species richness. Climate is more important than geochemistry in explaining eucalypts species distribution and change in assemblages across Australia as a whole but there are correlations between the two sets of environmental variables. Many individual eucalypt species and entire taxonomic sections (Aromatica, Longistylus of subgenus Eucalyptus, Dumaria, and Liberivalvae of subgenus Symphyomyrtus) have distributions affected strongly by geochemistry. We conclude that eucalypt diversity is driven by steep geochemical gradients that have arisen as climate patterns have fluctuated over Australia over the Cenozoic, generally aridifying since the Miocene. The diversification of eucalypts across Australia is thus an excellent example of co-evolution of landscapes and biota in space and time and challenges accepted notions of macroecology.

Bimetallic Ni–Cu alloy nanoparticles supported on silica for the water-gas shift reaction: activating surface hydroxyls via enhanced CO adsorption

Strong CO adsorption activates surface OH for enhanced WGS activity.

Shapes of a suspended curly hair

We investigate how natural curvature affects the configuration of a thin elastic rod suspended under its own weight, as when a single strand of hair hangs under gravity. We combine precision desktop experiments, numerics, and theoretical analysis to explore the equilibrium shapes set by the coupled effects of elasticity, natural curvature, nonlinear geometry, and gravity. A phase diagram is constructed in terms of the control parameters of the system, namely the dimensionless curvature and weight, where we identify three distinct regions: planar curls, localized helices, and global helices. We analyze the stability of planar configurations, and describe the localization of helical patterns for long rods, near their free end. The observed shapes and their associated phase boundaries are then rationalized based on the underlying physical ingredients.

The role of discriminative stimuli in concurrent performances

Key pecking in pigeons was examined under concurrent and parallel arrangements of two independent and simultaneously available variable-interval schedules. Pecks on the changeover key alternated the schedule of reinforcement for responses on the main key. Under concurrent schedules, discriminative stimuli were paired with the reinforcement schedule arranged in each component and changeover responses also alternated these stimuli. Under parallel schedules, changeover responses alternated the effective reinforcement schedule, but did not change the discriminative stimulus. On concurrent procedures, changeover response rate was inversely related to the difference in reinforcement rate between the two components, whereas on parallel schedules no consistent relationship was found. With both schedules, absolute response and reinforcement rates were positively related, although for a given set of reinforcement frequencies, rates were often higher on the concurrent schedules. On concurrent schedules, relative response rates and relative times were equal to relative reinforcement rates. On parallel schedules these ratios were positively related, but response and time ratios were much smaller than were obtained with comparable concurrent schedules. This inequality was most pronounced when absolute reinforcement frequencies were lowest.

An efficient homologous recombination vector pTV(I) contains a hot spot for increased recombinant protein expression in Chinese hamster ovary cells

We employed reverse genetics to clone a 5.0 kb genomic DNA hot spot HIRPE (hot spot for increased recombinant protein expression) flanking the plasmid integration site from a recombinant Chinese hamster ovary (CHO) cell line. DNA sequence analysis of the 5.0 kb fragment revealed that HIRPE is enriched for repetitive elements, Alu-like sequences and matrix-associated regions that are known to be linked with transcriptionally active regions in a number of mammalian systems. The construction of a homologous recombination vector, pTV1, containing the 5.0 kb HIRPE genomic DNA, a recombinant gene human CTLA4-Ig, and the dhfr gene as a positive selection marker is described. It was observed that the pTV1 vector targeted the CTLA4Ig gene to a preferred locus in the CHO genome contributing to high recombinant gene expression in transfected CHO cells. Preliminary studies suggest that similar to the observation with the parental cell line, pTV1-generated transfectomas that were analyzed appear to harbor an inverted duplication of the genomic DNA at the plasmid integration site.

A novel interaction of tRNA(Lys,3) with the feline immunodeficiency virus RNA genome governs initiation of minus strand DNA synthesis

Complementarity between nucleotides at the 5' terminus of tRNA(Lys,3) and the U5-IR loop of the feline immunodeficiency virus RNA genome suggests a novel intermolecular interaction controls initiation of minus strand synthesis in a manner analogous to other retroviral systems. Base pairing of this tRNA-viral RNA duplex was confirmed by nuclease mapping of the RNA genome containing full-length or 5'-deleted variants of tRNA(Lys,3) hybridized to the primer-binding site. A major pause in RNA-dependent DNA synthesis occurred 14 nucleotides ahead of the primer-binding site with natural and synthetic tRNA(Lys,3) primers, indicating it was not a consequence of tRNA base modifications. The majority of the paused complexes resulted in dissociation of the reverse transcriptase from the template/primer, as demonstrated by an assay limited to a single binding event. Hybridization of a tRNA mutant whose 5' nucleotides are deleted relieved pausing at this position and subsequently allowed high level DNA synthesis. Additional experiments with tRNA-DNA chimeric primers were used to localize the stage of minus strand synthesis at which the tRNA-viral RNA interaction was disrupted. Finally, replacing nucleotides of the feline immunodeficiency virus U5-IR loop with the (A)(4) sequence of its human immunodeficiency virus (HIV)-1 counterpart also relieved pausing, but did not induce pausing immediately downstream of the primer-binding site previously noted during initiation of HIV-1 DNA synthesis. These combined observations provide further evidence of cis-acting sequences immediately adjacent to the primer-binding site controlling initiation of minus strand DNA synthesis in retroviruses and retrotransposons.

Molecular phylogenetics of Acacia (Fabaceae: Mimosoideae) based on the chloroplast MATK coding sequence and flanking TRNK intron spacer regions

The tribe Acacieae (Fabaceae: Mimosoideae) contains two genera, the monotypic African Faidherbia and the pantropical Acacia, which comprise about 1200 species with over 950 confined to Australia. As currently recognized, the genus Acacia is subdivided into three subgenera: subg. Acacia, subg. Aculeiferum, and the predominantly Australian subg. Phyllodineae. Morphological studies have suggested the tribe Acacieae and genus Acacia are artificial and have a close affinity to the tribe Ingeae. Based on available data there is no consensus on whether Acacia should be subdivided. Sequence analysis of the chloroplast trnK intron, including the matK coding region and flanking noncoding regions, indicate that neither the tribe Acacieae nor the genus Acacia are monophyletic. Two subgenera are monophyletic; section Filicinae of subgenus Aculeiferum does not group with taxa of the subgenus. Section Filicinae, eight Ingeae genera, and Faidherbia form a weakly supported paraphyletic grade with respect to subg. Phyllodineae. Acacia subg. Aculeiferum (s. s.) is sister to the grade. These data suggest that characters currently used to differentiate taxa at the tribal, generic, and subgeneric levels are polymorphic and homoplasious in cladistic analyses.

Molecular phylogenetics of Acacia (Fabaceae: Mimosoideae) based on the chloroplast MATK coding sequence and flanking TRNK intron spacer regions

The tribe Acacieae (Fabaceae: Mimosoideae) contains two genera, the monotypic African Faidherbia and the pantropical Acacia, which comprise about 1200 species with over 950 confined to Australia. As currently recognized, the genus Acacia is subdivided into three subgenera: subg. Acacia, subg. Aculeiferum, and the predominantly Australian subg. Phyllodineae. Morphological studies have suggested the tribe Acacieae and genus Acacia are artificial and have a close affinity to the tribe Ingeae. Based on available data there is no consensus on whether Acacia should be subdivided. Sequence analysis of the chloroplast trnK intron, including the matK coding region and flanking noncoding regions, indicate that neither the tribe Acacieae nor the genus Acacia are monophyletic. Two subgenera are monophyletic; section Filicinae of subgenus Aculeiferum does not group with taxa of the subgenus. Section Filicinae, eight Ingeae genera, and Faidherbia form a weakly supported paraphyletic grade with respect to subg. Phyllodineae. Acacia subg. Aculeiferum (s. s.) is sister to the grade. These data suggest that characters currently used to differentiate taxa at the tribal, generic, and subgeneric levels are polymorphic and homoplasious in cladistic analyses.

[Phosphinic analog of methionine inhibits growth of leucosis cell L1210 and transforms to phosphinic analog of S-adenosylmethionine]

A phosphinic analogue of methionine bearing a phosphinic H(OH)(O)P fragment in place of the carboxyl group inhibited the growth of the L1210 cells and was intracellularly transformed to the phosphinic analogue of S-adenosylmethionine.

Interaction of p55 reverse transcriptase from the Saccharomyces cerevisiae retrotransposon Ty3 with conformationally distinct nucleic acid duplexes

The 55-kDa reverse transcriptase (RT) domain of the Ty3 POL3 open reading frame was purified and evaluated on conformationally distinct nucleic acid duplexes. Purified enzyme migrated as a monomer by size exclusion chromatography. Enzymatic footprinting indicate Ty3 RT protects template nucleotides +7 through -21 and primer nucleotides -1 through -24. Contrary to previous data with retroviral enzymes, a 4-base pair region of the template-primer duplex remained nuclease accessible. The C-terminal portion of Ty3 RT encodes a functional RNase H domain, although the hydrolysis profile suggests an increased spatial separation between the catalytic centers. Despite conservation of catalytically important residues in the RNase H domain, Fe(2+) fails to replace Mg(2+) in the RNase H catalytic center for localized generation of hydroxyl radicals, again suggesting this domain may be structurally distinct from its retroviral counterparts. RNase H specificity was investigated using a model system challenging the enzyme to select the polypurine tract primer from within an RNA/DNA hybrid, extend this into (+) DNA, and excise the primer from nascent DNA. Purified RT catalyzed each of these three steps but was almost inactive on a non-polypurine tract RNA primer. Our studies provide the first detailed characterization of the enzymatic activities of a retrotransposon reverse transcriptase.

Polyamine analogue induction of the p53-p21WAF1/CIP1-Rb pathway and G1 arrest in human melanoma cells

Although polyamines are well recognized for their critical involvement in cell growth, the cell cycle specificity of this requirement has not yet been characterized with respect to the newly delineated regulatory pathways. We recently reported that polyamine analogues having close structural and functional similarities to the natural polyamines produce a distinct G1 and G2-M cell cycle arrest in MALME-3M human melanoma cells. To determine a molecular basis for this observation, we examined the effects of N1,N11-diethylnorspermine on cell cycle regulatory proteins associated with G1 arrest. The analogue is known to deplete polyamine pools by suppressing biosynthetic enzymes and potently inducing the polyamine catabolic enzyme spermidine/spermine N1-acetyltransferase. Treatment of MALME-3M cells with 10 microM N1,N11-diethylnorspermine caused an increase in hypophosphorylated Rb, which correlated temporally with the onset of G1 arrest at 16-24 h. Rb hypophosphorylation was preceded by an increase in wild-type p53 (approximately 100-fold at maximum) and a concomitant increase in the cyclin-dependent kinase inhibitor, p21WAF1/CIP1 (p21; approximately 5-fold at maximum). Another cyclin-dependent kinase inhibitor, p27KIP1, and cyclin D increased slightly, whereas proliferating cell nuclear antigen and p130 remained unchanged. Induction of p21 protein was accompanied by an increase in p21 mRNA, whereas induction of p53 protein was not, suggesting transcriptional activation of the former and posttranscriptional regulation of the latter. SK-MEL-28 human melanoma cells, which contain a mutated p53, failed to induce p53 or p21 and did not arrest in G1. Rather, these cells rapidly underwent programmed cell death within 48 h. Overall, these findings provide the first indication of the cell cycle regulatory pathways by which polyamine antagonists such as analogues might inhibit growth in cells containing wild-type p53 and further suggest a mechanistic basis for differential cellular responses to these agents.

Retrotransposon-related DNA sequences in the centromeres of grass chromosomes

Several distinct DNA fragments were subcloned from a sorghum (Sorghum bicolor) bacterial artificial chromosome clone 13I16 that was derived from a centromere. Three fragments showed significant sequence identity to either Ty3/gypsy- or Ty1/copia-like retrotransposons. Fluorescence in situ hybridization (FISH) analysis revealed that the Ty1/copia-related DNA sequences are not specific to the centromeric regions. However, the Ty3/gypsy-related sequences were present exclusively in the centromeres of all sorghum chromosomes. FISH and gel-blot hybridization showed that these sequences are also conserved in the centromeric regions of all species within Gramineae. Thus, we report a new retrotransposon that is conserved in specific chromosomal regions of distantly related eukaryotic species. We propose that the Ty3/gypsy-like retrotransposons in the grass centromeres may be ancient insertions and are likely to have been amplified during centromere evolution. The possible role of centromeric retrotransposons in plant centromere function is discussed.

Rice (Oryza sativa) centromeric regions consist of complex DNA

Rice bacterial artificial chromosome clones containing centromeric DNA were isolated by using a DNA sequence (pSau3A9) that is present in the centromeres of Gramineae species. Seven distinct repetitive DNA elements were isolated from a 75-kilobase rice bacterial artificial chromosome clone. All seven DNA elements are present in every rice centromere as demonstrated by fluorescence in situ hybridization. Six of the elements are middle repetitive, and their copy numbers range from approximately 50 to approximately 300 in the rice genome. Five of these six middle repetitive DNA elements are present in all of the Gramineae species, and the other element is detected only in species within the Bambusoideae subfamily of Gramineae. All six middle repetitive DNA elements are dispersed in the centromeric regions. The seventh element, the RCS2 family, is a tandem repeat of a 168-bp sequence that is represented approximately 6,000 times in the rice genome and is detected only in Oryza species. Fiber-fluorescence in situ hybridization analysis revealed that the RCS2 family is organized into long uninterrupted arrays and resembles previously reported tandem repeats located in the centromeres of human and Arabidopsis thaliana chromosomes. We characterized a large DNA fragment derived from a plant centromere and demonstrated that rice centromeres consist of complex DNA, including both highly and middle repetitive DNA sequences.

Mutating a region of HIV-1 reverse transcriptase implicated in tRNA(Lys-3) binding and the consequences for (-)-strand DNA synthesis

Recently, tRNALys-3 was cross-linked via its anticodon loop to human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) between residues 230 and 357 (Mishima, Y., and Steitz, J. A. (1995) EMBO J. 14, 2679-2687). Scanning the surface of this region identified three basic amino acids Lys249, Arg307, and Lys311 flanking a small crevice on the p66 thumb subdomain outside the primer-template binding cleft. To assess an interaction of this region with the tRNA anticodon loop, these p66 residues were altered to Glu or Gln. p66 subunits containing K249Q, K311Q, K311E, and a dual R307E/K311E mutation formed a stable dimer with wild type p51. All mutants showed reduced affinity for tRNALys-3 and supported significantly less (-)-strand DNA synthesis from this primer than the parental heterodimer. In contrast, these variants efficiently synthesized HIV-1 (-)-strand strong-stop DNA from oligonucleotide primers and had minimal effect on RNase H activity, retaining endonucleolytic and directed cleavage of an RNA/DNA hybrid. Structural features of binary RT.tRNALys-3 complexes were examined by in situ footprinting, via susceptibility to 1, 10-phenanthroline-copper-mediated cleavage. Unlike wild type RT, mutants p66(K311Q)/p51 and p66(K311E)/p51 failed to protect the tRNA anticodon domain from chemical cleavage, indicating a significant structural alteration in the binary RT.tRNA complex. These results suggest a crevice in the p66 thumb subdomain of HIV-1 RT supports an interaction with the tRNALys-3 anticodon loop critical for efficient (-)-strand DNA synthesis.

Human prostatic carcinoma cell lines display altered regulation of polyamine transport in response to polyamine analogs and inhibitors

BACKGROUND

The possibility was investigated that complex homeostatic mechanisms which maintain polyamine pools in prostate-derived tumors may differ from those which are typically seen in other tissues and tumors.

METHODS

Growth sensitivity and various regulatory responses were investigated in three human prostate carcinoma cell lines (LNCaP, DU145, and PC-3) treated with the inhibitor of S-adenosylmethionine decarboxylase CGP-48664 or the polyamine analog N1,N11-diethylnorspermine (DENSPM), both of which are currently undergoing phase I clinical trial.

RESULTS

Prostate tumor cell lines were all similarly growth-inhibited by the inhibitor CGP-48664 (IC50 values, 1-5 microM at 72 hr), but varied considerably in their sensitivity to DENSPM. The rank-order for cell-line growth inhibition by the analog was DU145 > PC-3 > LNCaP, with IC50 values of 1, 30, and 1,000 microM, respectively. Both compounds depleted intracellular polyamine pools to levels which seemed sufficient to account for inhibition of cell growth. While polyamine enzyme regulatory responses to both CGP-48664 and DENSPM were typical of those seen in other cell types, regulation of polyamine transport differed distinctly. Based on Vmax determinations, LNCaP cells failed to upregulate transport in response to CGP-48664, while PC-3 and LNCaP cells failed to downregulate transport in response to DENSPM.

CONCLUSIONS

Relative to other cell lines, polyamine transport in prostate carcinoma cell lines was found to be uniquely insensitive to regulation by polyamines or analogs. Although this did not seem to correlate with growth sensitivity to polyamine analogs in vitro, it should be therapeutically exploitable in in vivo systems.

Multiple biological roles associated with the Rous sarcoma virus 5' untranslated RNA U5-IR stem and loop

The 5' untranslated region of Rous sarcoma virus (RSV) RNA is a highly ordered structure involved in multiple processes in the viral replication cycle. One of these structures, referred to as the U5-IR stem, is located immediately upstream of the 5' end of the primer binding site. Disruption of its base pairing results in a decrease in initiation of reverse transcription (D. Cobrinik, A. Aiyar, Z. Ge, M. Katzman, H. Huang, and J. Leis, J. Virol. 65:3864-3872, 1991). In the present study, the length of the U5-IR stem structure has been extended by insertions of different sequences which decrease the efficiency of reverse transcription, in vivo and in vitro. Reverse transcription is rescued partially by placing single-stranded bulges into the middle of the extended duplexes. Nucleotide substitutions or insertions into the loop region of the U5-IR stem also decrease the efficiency of reverse transcription, suggesting that these sequences may specifically interact with reverse transcriptase. Surprisingly, all of the extended stem mutations cause significant RNA packaging defects. In contrast, nucleotide insertions or base substitutions in the U5-IR loop do not affect RNA packaging. These data indicate that the reverse transcription initiation complex and RNA packaging apparatus are influenced by the same region of RSV RNA and that each process is differentially sensitive to changes in sequence and/or secondary structure.