Species-specific nuclear and chloroplast single nucleotide polymorphisms to distinguish Picea glauca, P. mariana and P. rubens

 Picea rubens (red spruce) and P. mariana (black spruce) are closely related species which are difficult to differentiate morphologically. They are sympatric with P. glauca (white spruce) in the northern portion of their ranges. In order to identify potential interspecific polymorphisms, the chloroplast trnK intron and rpl33-psaJ-trnP region were sequenced, and the nuclear-encoded ITS region of the rDNA repeat was partially sequenced. Thirteen chloroplast and 12 nuclear candidate interspecific single nucleotide polymorphisms (SNPs) were identified. The species-specificity of several SNPs was determined by surveying DNAs amplified from trees representing range-wide provenance tests; these included 46 red spruce from 11 provenances, 84 black spruce from 30 provenances and 90 white spruce from 22 provenances. Two SNPs (1 chloroplast and 1 nuclear), which distinguish black spruce from red and white spruce, were consistent among 96–100% of the trees surveyed. Five SNPs (4 chloroplast and 1 nuclear), which distinguish white spruce from red and black spruce, were consistent among 100% of surveyed trees. These species-specific SNPs were used to identify anonymous spruce samples in a blind test, and their utility for small amounts of tissue, as little as single needles, was demonstrated. Scoring these SNPs is much less labor intensive than previous molecular methods for taxa differentiation (restriction fragment length polymorphisms or random amplified polymorphic DNAs), therefore they can be applied to large population studies. Received: 16 December 1998 / Accepted: 5 January 1999     

Serine Biosynthesis in Desulfovibrio desulfuricans

Cell-free extracts of Desulfovibrio desulfuricans possess enzymes which catalyze the synthesis of serine from 3-phosphoglycerate via the intermediates phosphohydroxypyruvate and phosphoserine.     

Characterization and identification of vaccine candidate proteins through analysis of the group A Streptococcus surface proteome

We describe a proteomic approach for identifying bacterial surface-exposed proteins quickly and reliably for their use as vaccine candidates. Whole cells are treated with proteases to selectively digest protruding proteins that are subsequently identified by mass spectrometry analysis of the released peptides. When applied to the sequenced M1_SF370 group A Streptococcus strain, 68 PSORT-predicted surface-associated proteins were identified, including most of the protective antigens described in the literature. The number of surface-exposed proteins varied from strain to strain, most likely as a consequence of different capsule content. The surface-exposed proteins of the highly virulent M23_DSM2071 strain included 17 proteins, 15 in common with M1_SF370. When 14 of the 17 proteins were expressed in E. coli and tested in the mouse for their capacity to confer protection against a lethal dose of M23_DSM2071, one new protective antigen (Spy0416) was identified. This strategy overcomes the difficulties so far encountered in surface protein characterization and has great potential in vaccine discovery.     

In vitro culture of Lippia dulcis (Trev.): light intensity and wavelength effects on growth,antioxidant defense,and volatile compound production

In Vitro Cellular & Developmental Biology - Plant - Plants of the Verbenaceae family are well known for having constituents with important bioactive properties. The objective of this study was...     

COPD patients with chronic bronchitis and higher sputum eosinophil counts show increased type-2 and PDE4 gene expression in sputum

Chronic obstructive pulmonary disease (COPD) patients with higher eosinophil counts are associated with increased clinical response to phosphodiesterase-4-inhibitors (PDE4i). However, the underlying inflammatory mechanisms associated with this increased response is not yet elucidated. This post hoc analysis focused on sputum gene expression in patients with chronic bronchitis who underwent 32-day treatment with two doses of the inhaled PDE4i CHF6001 (tanimilast) or placebo on top of triple therapy. Biological characterization and treatment effects were assessed between patients with different sputum eosinophil levels (eosinophil^high ≥ 3%; eosinophil^low < 3%) at baseline (primary samples) or at the end of the treatment of the placebo arm (validation samples). Forty-one genes were differentially expressed in primary samples (p-adjusted for false discovery rate < 0.05); all up-regulated in eosinophil^high patients and functionally enriched for type-2 and PDE4 inflammatory processes. Eleven out of nineteen genes having immune system biological processes annotations including IL5RA, ALOX15, IL1RL1, CLC, GATA1 and PDE4D were replicated using validation samples. The expression of a number of these inflammatory mediators was reduced by tanimilast treatment, with greater effects observed in eosinophil^high patients. These findings suggest that type-2 and PDE4 overexpression in COPD patients with higher sputum eosinophil counts contribute to the differential clinical response to PDE4i observed in previous clinical trials.     

Purification and functional analysis of recombinant Acholeplasma laidlawii histone-like HU protein

HU is a most abundant DNA-binding protein in bacteria. This protein is conserved either in its heterodimeric form or in one of its homodimeric forms in all bacteria, in plant chloroplasts, and in some viruses. HU protein non-specifically binds and bends DNA as a hetero- or homodimer and can participate in DNA supercoiling and DNA condensation. It also takes part in some DNA functions such as replication, recombination, and repair. HU does not recognize any specific sequences but shows some specificity to cruciform DNA and to repair intermediates, e.g., nick, gap, bulge, 3′-overhang, etc. To understand the features of HU binding to DNA and repair intermediates, a fast and easy HU proteins purification procedure is required. Here we report overproduction and purification of the HU homodimers. The method of HU purification allows obtaining a pure recombinant non-tagged protein cloned in Escherichia coli. We applied this method for purification of Acholeplasma laidlawii HU and demonstrated that this protein possesses a DNA - binding activity and is free of contaminating nuclease activity. Besides that we have shown that expression of A. laidlawii ihf_hu gene in a slow-growing hupAB E. coli strain restores the wild-type growth indicating that aclHU can perform the basic functions of E. coli HU in vivo.