Morphometric analysis and taxonomic revision of the Vriesea paraibica complex (Bromeliaceae)

The species related to Vriesea paraibica (Bromeliaceae, Tillandsioideae) have controversial taxonomic limits. For several decades, this group has been identified in herbarium collections as V. × morreniana, an artificial hybrid that does not grow in natural habitats. The aim of this study was to assess the morphological variation in the V. paraibica complex through morphometric analyses of natural populations. Two sets of analyses were performed: the first involved six natural populations (G1) and the second was carried out on taxa that emerged from the first analysis, but using material from herbarium collections (G2). Univariate ANOVA was used, as well as discriminant analysis of 16 morphometric variables in G1 and 18 in G2. The results of the analyses of the two groups were similar and led to the selection of diagnostic traits of four species. Lengths of the lower and median floral bracts were significant for the separation of red and yellow floral bracts. Vriesea paraibica and V. interrogatoria have red bracts; these two species are differentiated by the widths of the lower and median portions of the inflorescence and by scape length. These structures are larger in the former and smaller in the latter. Of the species with yellow floral bracts, V. eltoniana is distinguished by longer leaf blades and scapes and V. flava is characterized by its shorter sepal lengths. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159 , 163–181.     

Hydrologic regulation of gross methyl chloride and methyl bromide uptake from Alaskan Arctic tundra

The Arctic tundra has been shown to be a potentially significant regional sink for methyl chloride (CH₃Cl) and methyl bromide (CH₃Br), although prior field studies were spatially and temporally limited, and did not include gross flux measurements. Here we compare net and gross CH₃Cl and CH₃Br fluxes in the northern coastal plain and continental interior. As expected, both regions were net sinks for CH₃Cl and CH₃Br. Gross uptake rates (−793 nmol CH₃Cl m⁻² day⁻¹ and −20.3 nmol CH₃Br m⁻² day⁻¹) were 20–240% greater than net fluxes, suggesting that the Arctic is an even greater sink than previously believed. Hydrology was the principal regulator of methyl halide flux, with an overall trend towards increasing methyl halide uptake with decreasing soil moisture. Water table depth was one of the best predictors of net and gross uptake, with uptake increasing proportionately with water table depth. In drier areas, gross uptake was very high, averaging −1201 nmol CH₃Cl m⁻² day⁻¹ and −34.9 nmol CH₃Br m⁻² day⁻¹; in flooded areas, gross uptake was significantly lower, averaging −61 nmol CH₃Cl m⁻² day⁻¹ and −2.3 nmol CH₃Br m⁻² day⁻¹. Net and gross uptake was greater in the continental interior than in the northern coastal plain, presumably due to drier inland conditions. Within certain microtopographic features (low‐ and high‐centered polygons), uptake rates were positively correlated with soil temperature, indicating that temperature played a secondary role in methyl halide uptake. Incubations suggested that the inverse relationship between water content and methyl halide uptake was the result of mass transfer limitation in saturated soils, rather than because of reduced microbial activity under anaerobic conditions. These findings have potential regional significance, as the Arctic is expected to become warmer and drier due to anthropogenic climate forcing, potentially enhancing the Arctic sink for CH₃Cl and CH₃Br.     

DOG-SPOT database for comprehensive management of dog genetic research data

Research laboratories studying the genetics of companion animals have no database tools specifically designed to aid in the management of the many kinds of data that are generated, stored and analyzed. We have developed a relational database, "DOG-SPOT," to provide such a tool. Implemented in MS-Access, the database is easy to extend or customize to suit a lab's particular needs. With DOG-SPOT a lab can manage data relating to dogs, breeds, samples, biomaterials, phenotypes, owners, communications, amplicons, sequences, markers, genotypes and personnel. Such an integrated data structure helps ensure high quality data entry and makes it easy to track physical stocks of biomaterials and oligonucleotides.     

Understanding down-regulation of photosynthesis under water stress: future prospects and searching for physiological tools for irrigation management

Photosynthetic down-regulation and/or inhibition under water stress conditions are determinants for plant growth, survival and yield in drought-prone areas. Current knowledge about the sequence of metabolic events that leads to complete inhibition of photosynthesis under severe water stress is reviewed. An analysis of published data reveals that a key regulatory role for Rubisco in photosynthesis is improbable under water stress conditions. By contrast, the little data available for other Calvin cycle enzymes suggest the possibility of a key regulatory role for some enzymes involved in the regeneration of RuBP. There are insufficient data to determine the role of photophosphorylation. Several important gaps in our knowledge of this field are highlighted. The most important is the remarkable scarcity of data about the regulation/inhibition of photosynthetic enzymes other than Rubisco under water stress. Consequently, new experiments are urgently needed to improve our current understanding of photosynthetic down-regulation under water stress. A second gap is the lack of knowledge of photosynthetic recovery after irrigation of plants which have been subjected to different stages of water stress. This knowledge is necessary in order to match physiological down-regulation by water stress with controlled irrigation programmes.     

Molecular determinants of macrophage tropism and viral persistence: importance of single amino acid changes in the polymerase and glycoprotein of lymphocytic choriomeningitis virus.

This study documents that the immunosuppressive lymphocytic choriomeningitis virus (LCMV) variant, clone 13, shows a specific predilection for enhanced infection of macrophages both in vitro and in vivo and that single amino acid changes in the viral polymerase and glycoprotein are responsible for macrophage tropism. The growth difference seen between variant clone 13 and the parental Armstrong strain was specific for macrophages, since both clone 13 and Armstrong grew equally well in fibroblasts and neither isolate infected lymphocytes efficiently. Complete sequencing of the clone 13 genome, along with genetic analysis, showed that a single amino acid change in the polymerase (K-->Q at position 1079) was the major determinant of virus yield in macrophages. This was proven unequivocally by comparing the sequences of parental and reassortant viruses, which were identical at all loci except for the single mutation in the polymerase gene. This finding was further strengthened by showing that reversion at this site back to lysine (Q-->K) resulted in loss of macrophage tropism. In addition, an independently derived macrophage-tropic variant of LCMV, clone 28b, had a K-->N mutation at the same position. Thus, these results show that substitution of the positively charged amino acid K with a neutral amino acid (either Q or N) at residue 1079 of the polymerase resulted in enhanced viral replication in macrophages. In addition to the polymerase change, a mutation in the glycoprotein was also associated with macrophage tropism. This single amino acid change in the glycoprotein (F-->L at position 260) did not affect virus yield per macrophage but was critical in determining the number of macrophages infected. Our previous studies have shown that the same two mutations in the polymerase and glycoprotein are essential for establishing a chronic infection in adult mice. Since the same mutations confer macrophage tropism and ability to persist in vivo, these studies provide compelling evidence that infection of macrophages is a critical determinant of viral persistence and immune suppression.     

STUDY ON THE PROLIFERATIVE STATE OF HAEMOPOIETIC STEM CELLS (CFU)

Hydroxyurea was used to study the proliferation rate of haemopoietic stem cells (CFUJ in normal mice, after irradiation or transplantation into irradiated recipients. It was demonstrated that the proliferation rate of endogenous CFU_S (endo-CFU,) and exogenous CFU_S (exo-CFU_s) are identical. After irradiation (650 R) the surviving endo-CFU_s begin to proliferate immediately. By contrast exo-CFU, transplanted into the irradiated recipient mouse (850 R), begin to proliferate only after about 30 hr. However, injection of isoproterenol (which stimulates adenyl cyclase) or dibutyryl cyclic adenosine 3′,5′-monophosphate shortly after marrow cell graft, triggers the transplanted CFU_S into cell cycle as shown by an almost immediately increased sensitivity to hydroxyurea. Isoproterenol is capable of inducing DNA synthesis also in stem cells of normal mice but it takes about 20 hr before CFU, become to be increasingly sensitive to hydroxyurea.     

PHM is required for normal developmental transitions and for biosynthesis of secretory peptides in Drosophila

To understand the roles of secretory peptides in developmental signaling, we have studied Drosophila mutant for the gene peptidylglycine alpha-hydroxylating monooxygenase (PHM). PHM is the rate-limiting enzyme for C-terminal alpha-amidation, a specific and necessary modification of secretory peptides. In insects, more than 90% of known or predicted neuropeptides are amidated. PHM mutants lack PHM protein and enzyme activity; most null animals die as late embryos with few morphological defects. Natural and synthetic PHM hypomorphs revealed phenotypes that resembled those of animals with mutations in genes of the ecdysone-inducible regulatory circuit. Animals bearing a strong hypomorphic allele contain no detectable PHM enzymatic activity or protein; approximately 50% hatch and initially display normal behavior, then die as young larvae, often while attempting to molt. PHM mutants were rescued with daily induction of a PHM transgene and complete rescue was seen with induction limited to the first 4 days after egg-laying. The rescued mutant adults produced progeny which survived to various stages up through metamorphosis (synthetic hypomorphs) and displayed prepupal and pupal phenotypes resembling those of ecdysone-response gene mutations. Examination of neuropeptide biosynthesis in PHM mutants revealed specific disruptions: Amidated peptides were largely absent in strong hypomorphs, but peptide precursors, a nonamidated neuropeptide, nonpeptide transmitters, and other peptide biosynthetic enzymes were readily detected. Mutant adults that were produced by a minimal rescue schedule had lowered PHM enzyme levels and reproducibly altered patterns of amidated neuropeptides in the CNS. These deficits were partially reversed within 24 h by a single PHM induction in the adult stage. These genetic results support the hypothesis that secretory peptide signaling is critical for transitions between developmental stages, without strongly affecting morphogenetic events within a stage. Further, they show that PHM is required for peptide alpha-amidating activity throughout the life of Drosophila. Finally, they define novel methods to study neural and endocrine peptide biosynthesis and functions in vivo.     

Comparative context analysis of codon pairs on an ORFeome scale

Codon context is an important feature of gene primary structure that modulates mRNA decoding accuracy. We have developed an analytical software package and a graphical interface for comparative codon context analysis of all the open reading frames in a genome (the ORFeome). Using the complete ORFeome sequences of Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans and Escherichia coli, we show that this methodology permits large-scale codon context comparisons and provides new insight on the rules that govern the evolution of codon-pair context.