Codon usage in the vertebrate hemoglobins and its implications

A study of codon usage in vertebrate hemoglobins revealed an evolutionary trend toward elevated numbers of CpG codon boundary pairs in mammalian hemoglobin alpha genes. Selection for CpG codon boundaries countering the generally observed CpG suppression is strongly suggested by these data. These observations parallel recently published experimental results that indicate that constitutive expression of the human alpha-globin gene appears to be determined by regulatory information encoded within the structural gene. The possibility is raised that, in the absence of selection, CpG decay can be used to date the evolutionary origin of a mammalian alpha pseudogene from its active alpha gene.      

Evolution of crystallins: expression of lens-specific proteins in the blind mammals mole (Talpa europaea) and mole rat (Spalax ehrenbergi)

The mole (Talpa europaea; Insectivora) and the mole rat (Spalax ehrenbergi; Rodentia) both have degenerated eyes as a convergent adaptation to subterranean life. The rudimentary eye lenses of these blind mammals no longer function in a visual process. The crystallin genes, which display a lens-specific expression pattern, were studied in these blind mammals and in related species with normal eyes by hybridizing their genomic DNAs with probes obtained from cDNA clones for alpha A-, alpha B-, and beta Bp-crystallins from calf and gamma 3- crystallin from the rat. For all crystallin genes examined, the hybridization signals of mole and mole rat genomic DNA were comparable, respectively, with those of shrew and of rat and mouse, normal-vision representatives of the orders Insectivora and Rodentia. The expression of the crystallins at the protein level was tested by using antiserum specific for alpha-crystallin in immunofluorescence reactions on lens sections of mole and mole rat eyes and by using antisera against the beta- and gamma-crystallins on sections of the mole eye. All antisera gave positive fluorescence reactions exclusively with lens tissue of these blind mammals, indicating that the crystallins are still normally expressed despite the fact that these lenses have had no function in a visual process in these mammals for at least many million years. These findings apparently imply that some unknown selective advantage has conserved the crystallin genes and their expression after the loss of normal function of the lenses.      

Flavonoid Accumulation Is Correlated with Adventitious Roots Formation in Eucalyptus gunnii Hook Micropropagated through Axillary Bud Stimulation

Eucalyptus gunnii Hook microcuttings, obtained in vitro through axillary bud stimulation, show different rooting responses on the same rooting medium depending on the physiological state induced by cytokinins used in the previous multiplication medium. 6-Furfurylamino purine and 6-(4-hydroxy-3-methylbut-2-enylamino)purine induced a physiological state characterized by high sensitivity of microcuttings to the rooting stimulus exerted by the auxin 3-indolebutyric acid, but N⁶-benzyladenine did not produce the same effect. The former physiological state was characterized by an increased accumulation of two endogenous flavonoids (identified as quercetin glycosides) which may be markers of a well defined physiological state. They could have some direct influence on the rooting processes of the explants cultivated in vitro.     

The evolutionary history of the amylase multigene family in Drosophila pseudoobscura

In Drosophila pseudoobscura, the amylase (Amy) multigene family is contained within a series of inversions, or gene arrangements, on the third chromosome. The Standard (ST), Santa Cruz (SC), and Tree Line (TL) inversions are central to the phylogeny of arrangements, and have clusters of other arrangements derived from them. The gene arrangements belonging to each of these three clusters have a characteristic number of Amy genes, ranging from three in ST to two in SC to one in TL. This distribution pattern can reflect a history of either duplications or deletions, although the data available in the past did not permit a decision between these alternatives. We provide unambiguous evidence that three Amy genes were present before the divergence of the ST, SC, and TL arrangements. Thus, the current status of the Amy multigene family is the result of deletions in the TL and SC arrangements, which created three new pseudogenes: TL Amy2-psi, TL Amy3-psi, and SC Amy3- psi. Analysis of pseudogene sequences revealed that, in the SC and ST arrangements, pseudogene evolution has been retarded, most likely due to the homogenization effect of gene conversion. Finally, by determining the original copy number, we have reconstructed the evolutionary history of the Amy multigene family and linked it with the evolution of the central gene arrangements.      

Combined action of stem cell factor,leukemia inhibitory factor,and cAMP on in vitro proliferation of mouse primordial germ cells

In the present paper we investigated the effects of stem cell factor/mastocyte growth factor (SCF/MGF), leukemia inhibitory factor/differentiating inhibitory activity (LIF/DIA) (two growth factors known to affect primordial germ cell growth in vitro) and forskolin (FRSK) (an activator of adenylate cyclase in many cell types) alone or in combination on the survival and proliferation of primordial germ cells (PGCs) obtained from 8.5, 10.5, and 11.5 days post coitum (dpc) mouse embryos and cultured without pre-formed cell feeder layers. The results showed that both at 1 and 3 days of culture the addition of 100 ng/ml SCF, 20 μM FRSK, or in some instances 20 ng/ml LIF alone caused a significant increase of PGC number as compared with controls. The highest effects were obtained when SCF and/or LIF were used together with FRSK. Moreover, we found that FRSK elevated cAMP levels in purified 11.5 dpc PGCs and that this compound, but not SCF and LIF, stimulated PGC proliferation, as assessed by 5-bromo-2′-deoxyuridin (BrdU) incorporation. These results suggest a mechanism of combined action of cAMP with SCF and/or LIF in the control of proliferation of mouse PGCs in vitro. © 1993 Wiley-Liss, Inc.     

Evidence for gene conversion in the amylase multigene family of Drosophila pseudoobscura

The alpha-amylase (Amy) multigene family in Drosophila pseudoobscura is located on the third chromosome, which is polymorphic for more than 40 inverted gene arrangements. The number of copies in this family ranges from one to three, depending on the arrangement in question. A previous study of the three Amy genes from the Standard (ST) arrangement suggested either that duplicated copies (Amy2 and Amy3) are functionally constrained or that they are undergoing gene conversion with Amy1. In order to elucidate further the pattern of molecular evolution in this family, we cloned and sequenced four additional Amy genes, two from the Santa Cruz (SC) and two from the Chiricahua (CH) gene arrangement. Of the two alternatives, only the hypothesis of gene conversion is supported by the sequence analysis. The homogenization effect of gene conversion has been strongest in SC, whose copies differ by only two nucleotides, less noticeable in ST, and negligible in the CH. Furthermore, the action of gene conversion is apparently localized, occurring only in the coding region. Interestingly, these results concur with the findings of other workers for the duplicated Amy genes in the Drosophila melanogaster group. Thus, the occurrence of gene conversion in the Amy multigene family seems to be a common feature in the Drosophila species studied so far.      

The plant antifungal isoflavone genistein is metabolized by Armillaria mellea Vahl to give non-fungitoxic products

Abstract

Armillaria mellea, the causal agent of root rot, is a fungal pathogen which proved able to convert the leguminous plant antifungal compound 4′,5,7-trihydroxyisoflavone (genistein) into intermediate metabolites. After suitable periods of incubation, the metabolites were extracted and concentrated from liquid culture media, containing both the isoflavone and the fungus. After purification by column chromatography, the molecular structure of the metabolites was determined by means of mass spectrometry and nuclear magnetic resonance analyses. Five different compounds were identified: 1,3,5-trihydroxybenzene, 4-hydroxyphenylacetic acid, 2,5-dihydroxyphenylacetic acid (homogentisic acid), its lactone 5-hydroxy-2(3H)-benzofuranone, and 1,4-benzoquinone. In vitro experiments showed that while the starting compound, i.e. genistein, has some activity in inhibiting the growth of the fungal pathogen, the degradation products are devoid of any appreciable fungitoxic activity. Moreover, results show that the isoflavone metabolites can be, at least partially, utilized by A. mellea as a carbon source.     

Kaempferide triglycoside: a possible factor of resistance of carnation (Dianthus caryophyllus) to Fusarium oxysporum f. sp. dianthi

A kaempferide triglycoside has been found as a constitutive component in an uninfected carnation (Dianthus caryophyllus) of the cultivar Novada. The chemical structure has been determined mainly by the use of spectroscopic methods, including 2D NMR experiments. It showed a strong activity in restricting fungal parasite development, which could contribute to the known ability of carnation cv. Novada to resist to Fusarium oxysporum f. sp. dianthi infection.     

Detection of DNA from periodontal pathogenic bacteria in biofilm obtained from waterlines in dental units

Direct person-to-person transmission of periodontal bacteria through saliva has recently been widely reported and dental units have been demonstrated to retract saliva from patients under treatment and to release it into the mouths of subjects undergoing the next operation. In this study the presence of a group of periodontal pathogenic bacteria inside waterlines in dental units was investigated using polymerase chain reaction (PCR) based methods. Briefly, 18 dental units of three different manufacturers were studied. Dental units were divided into two groups according to their prevalent use in routine practice. The first group consisted of nine dental units characterized by the frequent use of high-speed dental hand-pieces directly inside the mouth and in contact with patients' saliva. The second group, as a control, consisted of nine dental units where high-speed dental hand-pieces were not in use. A one cm section of the waterline tubing connected to the high-speed hand-piece was removed from each dental unit to evaluate the presence of DNA of Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, Bacteroides forsythus, Treponema denticola. Two specimens were positive for Prevotella intermedia DNA. All the positive results were from samples obtained from dental units categorised in the first group. These findings clearly suggest that dental units have the potential to transmit periodontal pathogens. Manufacturers should be invited to design dental units that incorporate automated devices to disinfect DUWLs between patients with minimal effort by dental staff.     

Microbiota of the <Emphasis Type="Italic">Planalto de Bolona</Emphasis>: an artisanal cheese produced in uncommon environmental conditions in the Cape Verde Islands

The present study aimed to evaluate the dominant microbial community naturally present in the Planalto de Bolona cheese, produced in the Cape Verde Islands. Samples of milk, curd and cheese from two different producers were examined through culture-dependent and independent-methods. Traditional plating and genetic identification of lactic acid bacteria (LAB) and yeast isolates were carried out. Moreover, DNA and RNA extracted directly from samples were subjected to Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE). Concerning the LAB population, a total of 278 isolates were identified: Lactococcus lactis subsp. lactis and Enterococcus faecium represented the most isolated species. Regarding yeasts, the analysis of isolates throughout the manufacturing period showed a consistent presence of the genus Candida. Divergences in species detection between culture-dependent and culture-independent methods were observed, as well as between DNA and RNA analysis. PCR-DGGE underlined high heterogeneity among bacterial species while yeast microbiota was dominated by Aureobasidium pullulans at DNA level. The obtained results represent a first approach in the understanding of the Planalto de Bolona cheese microbial ecology and consequently may constitute a first step towards the full comprehension of the microbiota of this artisanal cheese produced in unusual environmental conditions in the Cape Verde Islands.