Polymorphism and Gene Conversion in Mouse α-Globin Haplotypes

We have cloned and characterized three distinct alpha-globin haplotypes obtained from inbred strains of the mouse, Mus domesticus. We report here the complete nucleotide sequence of the six alpha-globin genes that the haplotypes contain. Our analysis of these genes and those from one other previously described haplotype indicates that recurrent gene conversion events have played a major role in their history. The pattern of nucleotide substitutions suggests that conversions have occurred both within and between haplotypes. Limited segments of coding and noncoding DNA have been involved in these gene conversion events. In two of the haplotypes, the nonallelic genes of each maintain DNA sequence identity over discrete intervals and encode the same alpha-globin polypeptide. On the other hand, the coding regions of some genes have accumulated replacement changes that result in distinct alpha-globins. In one instance, these changes appear to reflect positive selection of advantageous mutations.     

Gene Conversion and Functional Divergence in the β-Globin Gene Family

Different models of gene family evolution have been proposed to explain the mechanism whereby gene copies created by gene duplications are maintained and diverge in function. Ohta proposed a model which predicts a burst of nonsynonymous substitutions following gene duplication and the preservation of duplicates through positive selection. An alternative model, the duplication–degeneration–complementation (DDC) model, does not explicitly require the action of positive Darwinian selection for the maintenance of duplicated gene copies, although purifying selection is assumed to continue to act on both copies. A potential outcome of the DDC model is heterogeneity in purifying selection among the gene copies, due to partitioning of subfunctions which complement each other. By using the d_N/d_S () rate ratio to measure selection pressure, we can distinguish between these two very different evolutionary scenarios. In this study we investigated these scenarios in the -globin family of genes, a textbook example of evolution by gene duplication. We assembled a comprehensive dataset of 72 vertebrate -globin sequences. The estimated phylogeny suggested multiple gene duplication and gene conversion events. By using different programs to detect recombination, we confirmed several cases of gene conversion and detected two new cases. We tested evolutionary scenarios derived from Ohtas model and the DDC model by examining selective pressures along lineages in a phylogeny of -globin genes in eutherian mammals. We did not find significant evidence for an increase in the ratio following major duplication events in this family. However, one exception to this pattern was the duplication of -globin in simian primates, after which a few sites were identified to be under positive selection. Overall, our results suggest that following gene duplications, paralogous copies of -globin genes evolved under a nonepisodic process of functional divergence.[Reviewing Editor: Martin Kreitman]     

Synthesis and Photochemical Conversion of Oligonucleotides Containing 2-Chloro-2′-Deoxyadenosine

Abstract

The rate and velocity of the photoconversion of 2-chloro-2′-deoxyadenosine into 2′-deoxyisoguanosine within oligonucleotides was found to be sequence-specific and depends on the nearest neighbor.     

Sequence-Dependent Gene Conversion: Can Duplicated Genes Diverge Fast Enough to Escape Conversion?

Conversion between duplicated genes limits their independent evolution. Models in which conversion frequencies decrease as genes diverge are examined to determine conditions under which genes can "escape" further conversion and hence escape from a gene family. A review of results from various recombination systems suggests two classes of sequence-dependence models: (1) the "k-hit" model in which conversion is completely inactivated by a few (k) mutational events, such as the insertion of a mobile element, and (2) more general models where conversion frequency gradually declines as genes diverge through the accumulation of point mutants. Exact analysis of the k-hit model is given and an approximate analysis of a more general sequence-dependent model is developed and verified by computer simulation. If mu is the per nucleotide mutation rate, then neutral duplicated genes diverging through point mutants are likely to escape conversion provided 2 mu/lambda much greater than 0.1, where lambda is the conversion rate between identical genes. If 2 mu/lambda much less than 0.1, the expected number of conversions before escape increases exponentially so that, for biological purposes, the genes never escape conversion. For single mutational events sufficient to block further conversions, occurring at rate nu per copy per generation, many conversions are expected if 2 nu/lambda much less than 1, while the genes essentially evolve independently if 2 nu/lambda much greater than 1. Implications of these results for both models of concerted evolution and the evolution of new gene functions via gene duplication are discussed.     

Mitigation of Prion Infectivity and Conversion Capacity by a Simulated Natural Process—Repeated Cycles of Drying and Wetting

Prions enter the environment from infected hosts, bind to a wide range of soil and soil minerals, and remain highly infectious. Environmental sources of prions almost certainly contribute to the transmission of chronic wasting disease in cervids and scrapie in sheep and goats. While much is known about the introduction of prions into the environment and their interaction with soil, relatively little is known about prion degradation and inactivation by natural environmental processes. In this study, we examined the effect of repeated cycles of drying and wetting on prion fitness and determined that 10 cycles of repeated drying and wetting could reduce PrP^Sc abundance, PMCA amplification efficiency and extend the incubation period of disease. Importantly, prions bound to soil were more susceptible to inactivation by repeated cycles of drying and wetting compared to unbound prions, a result which may be due to conformational changes in soil-bound PrP^Sc or consolidation of the bonding between PrP^Sc and soil. This novel finding demonstrates that naturally-occurring environmental process can degrade prions.     

Conversion of d-Glucose into d-Oxybiotin†

2,5-Anhydro-3-azido-3-deoxy-D-xylose dimethyl acetal (XI), the key intermediate for the stereospecific synthesis of d-oxybiotin, was prepared by methanolysis of 3-azido-3-deoxy-1,2-O-isopropylidene-5-O-p-tolylsulfonyl-α-d-xylofuranose (VIIIa) or of 3-azido-3-deoxy-l,2-O-cyclohexylidene-5-0-p-tolylsulfonyl-α-d-xylofuranose (VIIIb).     

Conversion of (−)-Carvotanacetone and (+)-Carvotanacetone by Pseudomonas ovalis,Strain 6–1

As a part of series on the biochemical reduction of terpenes, the conversion of (?)-carvotanacetone (I) and (+)-carvotanacetone (II) by Pseudomonas ovalis, strain 6–1, has been studied.

By the action of the microorganism, I was reduced to give (+)-carvomenthone (III), (+)-neocarvomenthol (IV), and (?)-carvomenthol (V), whereas II was also reduced to (?)-isocarvomenthone (VI), (?)-carvomenthone (VII), (?)-isocarvomenthol (VIII), and (?)-neoisocarvomenthol (IX); of which III, VI and IX are the major products.

The metabolic pathways of I and II and mechanism of stereospecific hydrogenation are also discussed.     

Conversion of ω-terminal-acetylenic sugar derivatives into acetylenic glycosides and nucleosides,and formation of “double-headed nucleoside” analogs

3,5-Di-O-acetyl-6,7-dideoxy-1,2-O-isopropylidene-β-L-ido- and α-d-gluco-hept-6-ynofuranose were separately deacetonated, and the products acetylated, to give the 1,2,3,5-tetra-O-acetyl analogs (2 and 6). Fusion of compounds 2 and 6 with 2,6-dichloropurine under acid catalysis produced 2,6-dichloro-9-(2,3,5-tri-O-acetyl-6,7-dideoxy-α-L-ido-hept-6-ynofuranosyl)-9H-purine (3) and its β-d-gluco analog 7, respectively. Methanolic ammonia converted 3 in good yield into 2-chloro-9-(6,7-dideoxy-α-L-ido-hept-6-ynofuranosyl)-6-methoxy-9H-purine. Treatment of compound 3 with mesityl nitrile oxide gave a “double-headed nucleoside” analog. Upon treatment with phenyl azide, the d-gluco derivative 7 produced another “double-headed nucleoside”. Fusion of 2 and 6 with p-nitrophenol yielded the respective p-nitrophenyl glycosides. The stereochemistry and regiospecificity of the reactions were verified spectroscopically.     

Environmental Influences on Bovine κ-Casein: Reduction and Conversion to Fibrillar (Amyloid) Structures

The caseins of milk form a unique calcium–phosphate transport complex that provides these necessary nutrients to the neonate. The colloidal stability of these particles is primarily the result of κ-casein. As purified from milk, this protein occurs as spherical particles with a weight average molecular weight of 1.18 million. The protein exhibits a unique disulfide bonding pattern, which (in the absence of reducing agents) ranges from monomer to octamers and above on SDS-PAGE. Severe heat treatment of the κ-casein (90°C) in the absence of SDS, before electrophoresis, caused an increase in the polymeric distribution: up to 40% randomly aggregated high–molecular weight polymers, presumably promoted by free sulfhydryl groups (J. Protein Chem. 17: 73–84, 1998). To ascertain the role of the sulfhydryl groups, the protein was reduced and carboxymethylated (RCM-κ). Surprisingly, at only 37°C, the RCM-κ-casein exhibited an increase in weight average molecular weight and tendency to self-association when studied at 3000 rpm by analytical ultracentrifugation. Electron microscopy (EM) of the 37°C RCM sample showed that, in addition to the spherical particles found in the native protein, there was a high proportion of fibrillar structures. The fibrillar structures were up to 600 nm in length. Circular dichroism (CD) spectroscopy was used to investigate the temperature-induced changes in the secondary structure of the native and RCM-κ-caseins. These studies indicate that there was little change in the distribution of secondary structural elements during this transition, with extended strand and κ turns predominating. On the basis of three-dimensional molecular modeling predictions, there may exist a tyrosine-rich repeated sheet-turnsheet motif in κ-casein (residues 15–65), which may allow for the stacking of the molecules into fibrillar structures. Previous studies on amyloid proteins have suggested that such motifs promote fibril formation, and near-ultraviolet CD and thioflavin-T binding studies on RCM-κ-casein support this concept. The results are discussed with respect to the role that such fibrils may play in the synthesis and secretion of casein micelles in lactating mammary gland.     

Conversion of 4-aminobutyraldehyde to γ-aminobutyric acid in striatum treated with semicarbazide and kainic acid

4-Aminobutyraldehyde (ABAL) has been shown to cross the blood-brain barrier and to be converted rapidly to -aminobutyric acid (GABA) in various regions of the brain. In this paper, the formation of GABA from ABAL was studied with striatum that had suffered a lesion to GABA synthesis via glutamic acid decarboxylase (GAD). The GABA formation from ABAL was invariably observed in striatum in which GAD was severely inhibited by semicarbazide or kainic acid. Thus, this is another pathway for GABA formation.     

Conversion of iodine to fluorine-18 based on iodinated chalcone and evaluation for β-amyloid PET imaging

In the amyloid cascade hypothesis, β-amyloid (Aβ) plaques is one of the major pathological biomarkers in the Alzheimer’s disease (AD) brain. We report the synthesis and evaluation of novel radiofluorinated chalcones, [¹⁸F]4-dimethylamino-4′-fluoro-chalcone ([¹⁸F]DMFC) and [¹⁸F]4′-fluoro-4-methylamino-chalcone ([¹⁸F]FMC), as Aβ imaging probes. The conversion of iodine directly introduced to the chalcone backbone into fluorine was successfully carried out by ¹⁸F-labeling via the corresponding boronate precursors, achieving the direct introduction of fluorine-18 into the chalcone backbone to prepare [¹⁸F]DMFC and [¹⁸F]FMC. In a biodistribution study using normal mice, [¹⁸F]DMFC and [¹⁸F]FMC showed a higher initial uptake (4.43 and 5.47% ID/g at 2?min postinjection, respectively) into and more rapid clearance (0.52 and 0.66% ID/g at 30?min postinjection, respectively) from the brain than a Food and Drug Administration (FDA)-approved Aβ imaging agent ([¹⁸F]Florbetapir), meaning the improvement of the probability of detecting Aβ plaques and the reduction of non-specific binding in the brain. In the in vitro binding studies using aggregates of recombinant Aβ peptides, [¹⁸F]DMFC and [¹⁸F]FMC showed high binding affinity to recombinant Aβ aggregates at the K_d values of 4.47 and 6.50?nM, respectively. In the in vitro autoradiography (ARG) experiment with AD brain sections, [¹⁸F]DMFC and [¹⁸F]FMC markedly accumulated only in a region with abundant Aβ plaques, indicating that they clearly recognized human Aβ plaques in vitro. These encouraging results suggest that [¹⁸F]DMFC and [¹⁸F]FMC may be promising PET probes for the detection of an amyloid pathology and the early diagnosis of AD with marked accuracy.     

Conversion of O species by cellobiose dehydrogenase (cellobiose oxidase) and glucose oxidase – a comparison

Cellobiose dehydrogenase from Phanerochaete chrysosporium produces HO by electron transfer between cellobiose and O with a lower yield than the 1:1:1 molar ratio displayed by Aspergillus niger. glucose oxidase in the similar reaction between glucose and O. The discrepancy could best be explained if both a FentonÕs reaction and the spontaneous reactivity of the oxygen species formed were taken into account.     

Chemical Conversion of Uridine to 3′-Branched Sugar Nucleosides (Nucleosides and Nucleotides. 421.)

Abstract

Deamination of 1-(3-amino-3-deoxy-β-D-glucopyranosyl)-uracil gave a ring contracted nucleoside, 3′-deoxy-3′-formyluridine as a hemiacetal form, and uracil. Similar treatment of the 2′-deoxyderivative, 1-(3-amino-2,3-dideoxy-β-D-glucopyranosyl)uracil, gave the corresponding 2′,3′-dideoxy-3′-formyluridine in high yield. The 3′-epimerization of the 3′-formyluridine derivative was achieved and after reduction of the formyl groups, 2′,3′-dideoxy-3′(R and S)-hydroxymethyluridine were obtained.     

Conversion ofN-acetyl-o-toluidine into 4′-hydroxy-N-acetyl-o-toluidine byFusarium verticillioides

Summary Approximately 850 fungus and yeast strains were tested for their ability to hydroxylateN-acetyl-o-toluidine in the 4-position. The strain Y-1 selected as the best producer, was identified asFusarium verticilliides, and accumulated 1.5 mg of 4-hydroxy-N-acetyl-o-toluidine per ml of culture broth.     

The Inactivation of Arx in Pancreatic α-Cells Triggers Their Neogenesis and Conversion into Functional β-Like Cells

Recently, it was demonstrated that pancreatic new-born glucagon-producing cells can regenerate and convert into insulin-producing β-like cells through the ectopic expression of a single gene, Pax4. Here, combining conditional loss-of-function and lineage tracing approaches, we show that the selective inhibition of the Arx gene in α-cells is sufficient to promote the conversion of adult α-cells into β-like cells at any age. Interestingly, this conversion induces the continuous mobilization of duct-lining precursor cells to adopt an endocrine cell fate, the glucagon⁺ cells thereby generated being subsequently converted into β-like cells upon Arx inhibition. Of interest, through the generation and analysis of Arx and Pax4 conditional double-mutants, we provide evidence that Pax4 is dispensable for these regeneration processes, indicating that Arx represents the main trigger of α-cell-mediated β-like cell neogenesis. Importantly, the loss of Arx in α-cells is sufficient to regenerate a functional β-cell mass and thereby reverse diabetes following toxin-induced β-cell depletion. Our data therefore suggest that strategies aiming at inhibiting the expression of Arx, or its molecular targets/co-factors, may pave new avenues for the treatment of diabetes.     

2′-Deoxycoformycin: Biosynthesis and Enzymatic Conversion of 8-Keto-Deoxycoformycin to 2′-Deoxycoformycin by Streptomyces Antibioticus

Abstract

Studies on t h e biosynthesis o f the N-nucleoside antibiotics have established that the purine and pyrimidine nucleosides/nucleotides serve as the carbon and nitrogen skeleton, whereas with the C-nucleoside antibioticus, the C-N precursor forthe aglycon is either acetate or glutamate. With the pyrrolopyrimidine nucleoside antibiotics (toyocamycin, tubercidin, and sangi vamycin), either two or three carbons of the N-riboside/ribotide of GTP contribute to carbons 5 and 6 of the pyrrolering and the cyano or carboxamide group. With the naturally occurring nucleoside antibiotic containing the 1,3-diazepine seven-membered ring,2′-deoxycoformycin (dCF)(I), the precursor is not immediately obvious.     

Dissecting Variation in Biomass Conversion Factors across China’s Forests: Implications for Biomass and Carbon Accounting

Biomass conversion factors (BCFs, defined as the ratios of tree components (i.e. stem, branch, foliage and root), as well as aboveground and whole biomass of trees to growing stock volume, Mg m⁻³) are considered as important parameters in large-scale forest biomass carbon estimation. To date, knowledge of possible sources of the variation in BCFs is still limited at large scales. Using our compiled forest biomass dataset of China, we presented forest type-specific values of BCFs, and examined the variation in BCFs in relation to forest type, stand development and environmental factors (climate and soil fertility). BCFs exhibited remarkable variation across forest types, and also were significantly related to stand development (especially growing stock volume). BCFs (except Stem BCF) had significant relationships with mean annual temperature (MAT) and mean annual precipitation (MAP) (P<0.001). Climatic data (MAT and MAP) collectively explained 10.0–25.0% of the variation in BCFs (except Stem BCFs). Moreover, stronger climatic effects were found on BCFs for functional components (i.e. branch, foliage and root) than BCFs for combined components (i.e. aboveground section and whole trees). A general trend for BCFs was observed to decrease and then increase from low to high soil fertility. When qualitative soil fertility and climatic data (MAT and MAP) were combined, they explained 14.1–29.7% of the variation in in BCFs (except Stem BCFs), adding only 4.1–4.9% than climatic data used. Therefore, to reduce the uncertainty induced by BCFs in forest carbon estimates, we should apply values of BCFs for a specified forest type, and also consider climatic and edaphic effects, especially climatic effect, in developing predictive models of BCFs (except Stem BCF).     

Conversion of α-Terpineol to 8,9-Epoxy-p-menthan-1-ol

The complete amino acid sequence of pokeweed lectin-B (PL-B) has been analyzed by first sequencing seven lysylendopeptidase peptides derived from the reduced and S-pyridylethylated PL-B and then connecting them by analyzing the arginylendopeptidase peptides from the reduced and S-carboxymethylated PL-B. PL-B consists of 295 amino acid residues and two oligosaccharides linked to Asn96 and Asnl39, and has a molecular mass of 34,493 Da. PL-B is composed of seven repetitive chitin-binding domains having 48–79% sequence homology with each other. Twelve amino acid residues including eight cysteine residues in these domains are absolutely conserved in all other chitin-binding domains of plant lectins and class I chitinases. Also, it was strongly suggested that the extremely high hemagglutinating and mitogenic activities of PL-B may be ascribed to its seven-domain structure.     

Conversion of Methylthioadenosine Into its Naturally Occurring 3′-Isomer

Abstract

Methylthioadenosine (MTA) has been converted into its 3′ naturally occurring isomer (xylosyl-MTA) via protection at 2′-OH, oxidation, reduction and deprotection.