CpG islands from the alpha-globin gene cluster increase gene expression in an integration-dependent manner.

In contrast to other globin genes, the human and rabbit alpha-globin genes are expressed in transfected erythroid and nonerythroid cells in the absence of an enhancer. This enhancer-independent expression of the alpha-globin gene requires extensive sequences not only from the 5' flanking sequence but also from the intragenic region. However, the features of these internal sequences that are responsible for their positive effect are unclear. We tested several possible determinants of this activity. One possibility is that a previously identified array of discrete binding sites for known and potential regulatory proteins within the alpha-globin gene comprise an intragenic enhancer specific for the alpha-globin promoter, but directed rearrangements of the sequences show that this is not the case. Alternatively, the promoter may extend into the gene, with the function of the discrete binding sites being dependent on maintenance of their proper positions and orientations relative to the 5' flanking sequence. However, the positive effects observed in gene fusions do not localize to a discrete region of the alpha-globin gene and the results of internal deletions and point mutations argue against a required role of the targeted discrete binding sites. A third possibility is that the CpG island, which includes both the 5' flanking and intragenic regions associated with the positive activity, may itself have a more general effect on expression in transfected cells. Indeed, we show that the size of the CpG island in constructs correlates with the level of gene expression. Furthermore, the alpha-globin promoter is more active in the context of a previously inactive CpG island than in an A+T-rich context, showing that the CpG island provides an environment more permissive for expression. These effects are seen only after integration, suggesting a possible mechanism at the level of chromatin structure.     

Rapid evolution of immunoglobulin superfamily C2 domains expressed in immune system cells

To test the hypothesis that proteins expressed in cells of the vertebrate immune system evolve unusually rapidly, 107 orthologous immunoglobulin C2 domains were compared between human and murine rodent. The analysis showed that the rate of nonsynonymous (amino-acid- altering) nucleotide substitution in these domains was correlated with factors associated with protein structure and with breadth of tissue expression, as well as with the rate of synonymous substitution. However, when such factors were controlled for statistically, there remained a strong positive association between expression in the immune system and nonsynonymous rate, with the highest rates being seen in genes expressed in the immune system only. Certain immune system genes are known to be subject to positive selection favoring diversity at the amino acid level; most of these genes encode receptors that interact directly with foreign antigens. The observed acceleration of the rate of nonsynonymous evolution in C2 domains of immune system proteins may be explained by either (1) reduced constraint at the amino acid level on molecules interacting with immune system receptors that are themselves evolving rapidly due to positive diversifying selection or (2) positive selection favoring amino acid changes correlated with changes in the immune system receptors.      

Metabolism of Diethyl Ether and Cometabolism of Methyl tert-Butyl Ether by a Filamentous Fungus, a Graphium sp

In this study, evidence for two novel metabolic processes catalyzed by a filamentous fungus, Graphium sp. strain ATCC 58400, is presented. First, our results indicate that this Graphium sp. can utilize the widely used solvent diethyl ether (DEE) as the sole source of carbon and energy for growth. The kinetics of biomass accumulation and DEE consumption closely followed each other, and the molar growth yield on DEE was indistinguishable from that with n-butane. n-Butane-grown mycelia also immediately oxidized DEE without the extracellular accumulation of organic oxidation products. This suggests a common pathway for the oxidation of both compounds. Acetylene, ethylene, and other unsaturated gaseous hydrocarbons completely inhibited the growth of this Graphium sp. on DEE and DEE oxidation by n-butane-grown mycelia. Second, our results indicate that gaseous n-alkane-grown Graphium mycelia can cometabolically degrade the gasoline oxygenate methyl tert-butyl ether (MTBE). The degradation of MTBE was also completely inhibited by acetylene, ethylene, and other unsaturated hydrocarbons and was strongly influenced by n-butane. Two products of MTBE degradation, tert-butyl formate (TBF) and tert-butyl alcohol (TBA), were detected. The kinetics of product formation suggest that TBF production temporally precedes TBA accumulation and that TBF is hydrolyzed both biotically and abiotically to yield TBA. Extracellular accumulation of TBA accounted for only a maximum of 25% of the total MTBE consumed. Our results suggest that both DEE oxidation and MTBE oxidation are initiated by cytochrome P-450-catalyzed reactions which lead to scission of the ether bonds in these compounds. Our findings also suggest a potential role for gaseous n-alkane-oxidizing fungi in the remediation of MTBE contamination.     

Constrained sequence alignment

This paper presents a dynamic programming algorithm for aligning two sequeces when the alignment is constrained to lie between two arbitrary boundary lines in the dynamic programming matrix. For affine gap penalties, the algorithm requires onlyO(F) computation time andO(M+N) space, whereF is the area of the feasible region andM andN are the sequence lengths. The result extends to concave gap penalties, with somewhat increased time and space bounds. K.-M. C. and W. M. were supported in part by grant R01 LM05110 from the National Library of Medicine. R. C. H. was supported by PHS grant R01 DK27635.     

Isolation and characterization of microsatellite loci in the sand fly Phlebotomus papatasi (Diptera: Psychodidae)

Phlebotomus papatasi is a proven vector of Leishmania major which is one of the causative agents of cutaneous leishmaniasis in the Old World. Although it has a wide geographical range, its population structure is not yet well understood. In an effort to better understand the population dynamics of this vector, we developed a panel of di‐ and trinucleotide microsatellite markers, using a magnetic bead hybridization enrichment protocol. These microsatellite loci showed three to seven alleles with an expected heterozygosity range between 0.702 and 0.876. The level of polymorphisms found in this study suggests that these microsatellite loci can be used for population analysis of P. papatasi.     

Morphology and morphogenesis of a new marine hypotrichous ciliate (Protozoa,Ciliophora, Pseudoamphisiellidae), including a report on the small subunit rRNA gene sequence

The morphology and morphogenesis of a new marine hypotrichous ciliate Pseudoamphisiella elongata sp. nov. isolated from mussel‐farming waters near Qingdao, China, are described based on living and protargol‐impregnated specimens. Morphologically, the new species can be distinguished from its known congeners by its elongate body shape, narrow oral field, having fewer dorsal kineties and caudal cirri, more marginal cirri, and differentiated pretransverse cirri. The identification as a new species is firmly supported by the sequences of the small subunit ribosomal rRNA (SSU rRNA) gene, compared with other known Pseudoamphisiella species, and the phylogenetic analysis. The morphogenetic characteristics can be summarized as follows: (1) the parental adoral zone of membranelles and undulating membranes are entirely rebuilt by the oral primordium, which develops de novo in the outermost region of the cortex; (2) the oral primordium in the opisthe and the frontoventral–transverse (FVT) anlagen in both dividers are formed independently on the cell surface; (3) an ‘extra’ marginal anlage originates to the right of the right marginal anlage, and develops into two or three ‘extra’ marginal cirri; (4) the FVT anlagen develop in the primary mode, and the last FVT streak contributes two migratory cirri (frontoterminal cirri), which are probably resorbed; (5) the right marginal anlagen in both dividers occur close together, independent of the old structure. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 231–243.     

Localization of the alpha-like globin gene cluster to region q12 of rabbit chromosome 6 by in situ hybridization

The rabbit (Oryctolagus cuniculus) alpha-like globin gene cluster (HBAC) contains several block duplications of zeta-, alpha and theta-globin genes. Using in situ hybridizations to metaphase chromosome spreads, the gene cluster has been mapped to region q12 of chromosome 6. Given that human HBAC maps to the short arm of chromosome 16, the mapping of rabbit HBAC to 6q12 confirms the assignment of homology between OCU6q and HSA16p based on similarities of chromosomal banding patterns. In both species, HBAC is in a very G + C-rich region within the most distal band of the chromosome.