The evolution of long interspersed repeated DNA (L1, LINE 1) as revealed by the analysis of an ancient rodent L1 DNA family

Summary All modern mammals contain a distinctive, highly repeated (⩾50,000 members) family of long interspersed repeated DNA called the L1 (LINE 1) family. While the modern L1 families were derived from a common ancestor that predated the mammalian radiation ∼80 million years ago, most of the members of these families were generated within the last 5 million years. However, recently we demonstrated that modern murine (Old World rats and mice) genomes share an older long interspersed repeated DNA family that we called Lx. Here we report our analysis of the DNA sequence of Lx family members and the relationship of this family to the modern L1 families in mouse and rat. The extent of DNA sequence divergence between Lx members indicates that the Lx amplification occurred about 12 million years ago, around the time of the murine radiation. Parsimony analysis revealed that Lx elements were ancestral to both the modern rat and mouse L1 families. However, we found that few if any of the evolutionary intermediates between the Lx and the modern L1 families were extensively amplified. Because the modern L1 families have evolved under selective pressure, the evolutionary intermediates must have been capable of replication. Therefore, replicationcompetent L1 elements can reside in genomes without undergoing extensive amplification. We discuss the bearing of our findings on the evolution of L1 DNA elements and the mammalian genome.     

Copper association with iron sulfide magnetosomes in a magnetotactic bacterium

Greigite (Fe₃S₄) and pyrite (FeS₂) particles in the magnetosomes of a many-celled, magnetotactic prokaryote (MMP), common in brackish-to-marine, sulfidic, aquatic habitats, contained relatively high concentrations of copper which ranged from about 0.1 to 10 atomic per cent relative to iron. In contrast, the greigite particles in the magnetosomes of a curved magnetotactic bacterium collected from the same sampling site did not contain significant levels of copper. The ability of the MMP to biomineralize copper within its magnetosomes appeared to be limited to that organism and dependent upon the site from which it was collected. Although the chemical mechanism and physiological function of copper accumulation in the magnetosomes of the MMP is unclear, the presence of copper is the first evidence that another transition metal ion could be incorporated in the mineral phase of the magnetosomes of a magnetotactic bacterium.Abbreviation MMP many-celled magnetotactic prokaryote     

The differential expression of lamin epitopes during mouse spermatogenesis

The presence of lamin proteins in mouse spermatogenic cells has been examined by using an anti-lamin AC and an anti-lamin B antisera which recognize somatic lamins A and C, and somatic lamin B, respectively. Anti-lamin B binds to the nuclear periphery of all cell types examined, including Sertoli cells, primitive type A spermatogonia, preleptotene, leptotene, zygotene and pachytene spermatocytes, and round spermatids. In sperm nuclei, the antigenic determinants are localized to a narrow domain of the nucleus. However, after removing the perinuclear theca, anti-lamin B localizes to the entire nuclear periphery in a punctate pattern, suggesting that it is binding to determinants previously covered by the theca constituents. On immunoblots anti-lamin B reacts with a ～ 68 kD polypeptide in all germ cells and, to a lesser extent, with four additional polypeptides present only in meiotic and post-meiotic nuclear matrices. Anti-lamin AC also reacts with the perinuclear region of the somatic cells in the testes, in particular, those of the interstitium and also the Sertoli cells of the seminiferous epithelium. In contrast to anti-lamin B, anti-lamin AC does not bind to the germ cells at any stage of spermatogenesis. In addition, nuclear matrix proteins from isolated spermatogenic cells do not bind anti-lamin AC on immunoblots, suggesting the lack of reactivity is not due to the masking of any antigenic sites. These data demonstrate that germ cells contain lamin B throughout spermatogenesis, even during meiosis and spermiogenesis when the nuclear periphery lacks a distinct fibrous lamina. © 1993 Wiley-Liss, Inc.     

Generation of the benthic foraminiferal assemblage: Theory and preliminary data

The production of benthic foraminiferal communities is filtered through taphonomic (mainly destructive) processes within the sediments to generate the fossil assemblage. Both the production and the taphonomy depend on bottom water oxygen content and flux of organic carbon to the seabed. An examination of the relationships of processes generating the fossil assemblage to oxygen and organic carbon supply is made using pore water geochemical measurements to estimate carbon flux for locations in the Gulf of Mexico and the central California margin. The locations are plotted in a three dimensional field with bottom water oxygen content, organic carbon flux, and sediment depth as the axes. Then the response of foraminiferal standing stock, taphonomic processes and the developing fossil assemblage to the field is investigated. Variation in the vertical stratification of foraminiferal standing stock and test production, species' stratification, taphonomic process intensity and stratification, and sediment bioturbation lead to marked differences in the way the fossil assemblage is generated across the oxygen content-organic carbon flux field. The result is that the oxygen-carbon flux field has a significant impact on the fossil assemblage through the interaction of biological and biogeochemical processes in the sediments. A model of this interaction is investigated to show how its elements change across the oxygen-carbon flux field and how these affect the generation of the fossil assemblage.     

Comparison of European and US biological indicators for ethylene oxide sterilization

Summary Biological indicators (BIs) are used to monitor ethylene oxide (EO) gas sterilization processes for medical devices. Several European and United States BIs for EO sterilization were evaluated for resistance according to both United States Pharmacopeia (USP) XXI and United Kingdom's (UK) tests for D-values. US BIs areB. subtilis var. niger spores on paper strips or disc carriers while European BIs use aluminum strips, quartz sand, or cotton yarn. Numerous BIs per run and runs per lot, as well as 2–3 different lots of BIs from each manufacturer, were examined. Both British and US BIs met their respective label claims for rates of inactivation when tested against British and USP EO test parameters, respectively. However, Danish BIs, on cotton yarn or quartz sand, were not inactivated following USP specifications during the exposure dwell times tested (600 mg L^–1 EO, 54°C, 60% RH, 0–110 min). The Danish BIs will require further testing in order for us to determine if theirB. subtilis spores are unusually resistant to EO or if the spore carrier substrates protect the spores from the sterilizing gas. In conclusion, the British and American BIs for EO sterilization are equivalent in resistance despite differences in carrier substrate, recovery conditions, calculation methods for D-values, and the labeled sterilization conditions for use.     

The interaction between coumarin drugs and DNA gyrase

The coumarin group of antibiotics have as their target the bacterial enzyme DNA gyrase. The drugs bind to the B subunit of gyrase and inhibit DNA supercoiling by blocking the ATPase activity. Recent data show that the binding site for the drugs lies within the N-terminal part of the B protein, and individual amino acids involved in coumarin interaction are being identified. The mode of inhibition of the gyrase ATPase reaction by coumarins is unlikely to be simple competitive inhibition, and the drugs may act by stabilizing a conformation of the enzyme with low affinity for ATP.     

Glycosylation sites identified by solid-phase Edman degradation: O-linked glycosylation motifs on human glycophorin A

The human red blood cell sialoglycoprotein, glycophorin A (GpA),contains a ‘mucin-like’ extensively O-glycosylatedextracellular domain which carries the MN blood group antigens.We have revised the sites of O-glyccsylation in the extracellulardomain of GpA by automated solid-phase Edman degradation, whichallowed positive identification and quantitation of O-glycosylatedSer and Thr residues, as well as the single N-glycosylationsite. One N-linked and 16 O-linked sites were identified. Carbohydratewas absent on Ser 1, Ser14, Ser15, Ser23, Thr28 and Thr58 inGpA. We propose that the glycosyltransferases present in erythrocytesrecognize specific flanking sequences around potential O-glycosylationsites. All 16 O-glycosylation sites are explained on the basisof four motifs. Three motifs are associated with Thr-glycosylation:Xaa—Pro—Xaa—Xaa where at least one Xaa = Thr;Thr—Xaa—Xaa—Xaa where at least one Xaa = Thr;Xaa—Xaa—Thr—Xaa where at least one X = Argor Lys. The fourth motif is associated with Ser-glycosylation:Ser—Xaa—Xaa—Xaa where at least one Xaa = Ser.These simple rules explain the glycosylation (or lack of it)on 21 of 22 Ser/Thr in the extracellular domain of GpA. glycophorin A O-glycosylation motif solid-phase Edman degradation     

Selective incorporation of 5-hydroxytryptophan blocks long range electron transfer in oxalate decarboxylase

Oxalate decarboxylase from Bacillus subtilis is a binuclear Mn-dependent acid stress response enzyme that converts the mono-anion of oxalic acid into formate and carbon dioxide in a redox neutral unimolecular disproportionation reaction. A π-stacked tryptophan dimer, W96 and W274, at the interface between two monomer subunits facilitates long-range electron transfer between the two Mn ions and plays an important role in the catalytic mechanism. Substitution of W96 with the unnatural amino acid 5-hydroxytryptophan leads to a persistent EPR signal which can be traced back to the neutral radical of 5-hydroxytryptophan with its hydroxyl proton removed. 5-Hydroxytryptophan acts as a hole sink preventing the formation of Mn(III) at the N-terminal active site and strongly suppresses enzymatic activity. The lower boundary of the standard reduction potential for the active site Mn(II)/Mn(III) couple can therefore be estimated as 740 mV against the normal hydrogen electrode at pH 4, the pH of maximum catalytic efficiency. Our results support the catalytic importance of long-range electron transfer in oxalate decarboxylase while at the same time highlighting the utility of unnatural amino acid incorporation and specifically the use of 5-hydroxytryptophan as an energetic sink for hole hopping to probe electron transfer in redox proteins.     

Interaction between the black yeast Aureobasidium pullulans and the gall midge Lasioptera ephedricola in gall formation on the desert shrub Ephedra trifurca

Galls produced by the cecidomynd Lastoptera ephedncola on Ephedia trifurca always have a black ring associated with them while galls produced by the congener L ephedrae never do Black ring material after microscopic examination and culture proved to be Aureobasidium pullulans In addition to lacking black ring material neither L ephedrae galls nor healthy stems consistently yielded Aureobasidium on culture Gall and larva size measurements indicated that continued larval presence is not necessary for gall development, suggesting fungus initiated gall formation However inoculation of healthy stems with Aureobasidium caused lesions hut not galls The mycelium m galls did not appear grazed and neither larvae nor pupae contained Aureobasidium propagules suggesting that larvae do not feed directly on fungi These data also suggest that there is no trans-pupal passage of fungus from larvae or pupae to adults Newly emerged females do not carry fungal propagules suggesting that thcy are not inoculated upon exiting the gall Gall position leaf culture and stem culture data suggest that the fungus is picked up from leaves prior to oviposition