Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria

Speciation involves the establishment of genetic barriers between closely related organisms. The extent of genetic recombination is a key determinant and a measure of genetic isolation. The results reported here reveal that genetic barriers can be established, eliminated, or modified by manipulating two systems which control genetic recombination, SOS and mismatch repair. The extent of genetic isolation between enterobacteria is a simple mathematical function of DNA sequence divergence. The function does not depend on hybrid DNA stability, but rather on the number of blocks of sequences identical in the two mating partners and sufficiently large to allow the initiation of recombination. Further, there is no obvious discontinuity in the function that could be used to define a level of divergence for distinguishing species.

Long-term potentiation activates the GAP-43 promoter: Selective participation of hippocampal mossy cells

Perforant path long-term potentiation (LTP) in intact mouse hippocampal dentate gyrus increased the neuron-specific, growth-associated protein GAP-43 mRNA in hilar cells 3 days after tetanus, but surprisingly not in granule cells, the perforant path target. This increase was positively correlated with level of enhancement and restricted to central hilar cells on the side of stimulation. Blockade of LTP by puffing dl-aminophosphonovalerate (APV), an N-methyl-d-aspartate (NMDA) receptor blocker into the molecular layer, eliminated LTP-induced GAP-43 mRNA elevation in hilar cells. To determine whether the mRNA elevation was mediated by transcription, LTP was studied in transgenic mice bearing a GAP-43 promoter-lacZ reporter gene. Promoter activity as indexed by Transgene expression (PATE) increased as indicated by blue staining of the lacZ gene product, β-galactosidase. Potentiation induced a blue band bilaterally in the inner molecular layer of the dentate gyrus along the entire septotemporal axis. Because mossy cells are the only neurons in the central hilar zone that project to the inner molecular layer bilaterally along the entire septotemporal axis and LTP-induced activation of PATE in this zone was confined to the side of stimulation, we concluded that mossy cells were unilaterally activated, increasing synthesis of β-galactosidase, which was transported bilaterally. Neither granule cells nor pyramidal cells demonstrated increased PATE or increased GAP-43 mRNA levels. These results and recent evidence indicating the necessity of hilar neurons for LTP point to previously unheralded mossy cells as potentially critical for perforant path LTP and the GAP-43 in these cells as important for LTP persistence lasting days.

Long-range disruption of gene expression by a selectable marker cassette

Recent studies have suggested that the retention of selectable marker cassettes (like PGK–Neo, in which a hybrid gene consisting of the phosphoglycerate kinase I promoter drives the neomycin phosphotransferase gene) in targeted loci can cause unexpected phenotypes in “knockout” mice due to disruption of expression of neighboring genes within a locus. We have studied targeted mutations in two multigene clusters, the granzyme B locus and the β-like globin gene cluster. The insertion of PGK–Neo into the granzyme B gene, the most 5′ gene in the granzyme B gene cluster, severely reduced the normal expression of multiple genes within the locus, even at distances greater than 100 kb from the mutation. Similarly, the insertion of a PGK–Neo cassette into the β-globin locus control region (LCR) abrogates the expression of multiple globin genes downstream from the cassette. In contrast, a targeted mutation of the promyelocyte-specific cathepsin G gene (which lies just 3′ to the granzyme genes in the same cluster) had minimal effects on upstream granzyme gene expression. Although the mechanism of these long distance effects are unknown, the expression of PGK–Neo can be “captured” by the regulatory domain into which it is inserted. These results suggest that the PGK–Neo cassette can interact productively with locus control regions and thereby disrupt normal interactions between local and long-distance regulatory regions within a tissue-specific domain.

Peptide nucleic acid–DNA duplexes: Long range hole migration from an internally linked anthraquinone

The discovery that peptide nucleic acids (PNA) mimic DNA and RNA by forming complementary duplex structures following Watson–Crick base pairing rules opens fields in biochemistry, diagnostics, and medicine for exploration. Progress requires the development of modified PNA duplexes having unique and well defined properties. We find that anthraquinone groups bound to internal positions of a PNA oligomer intercalate in the PNA–DNA hybrid. Their irradiation with near-UV light leads to electron transfer and oxidative damage at remote GG doublets on the complementary DNA strand. This behavior mimics that observed in related DNA duplexes and provides the first evidence for long range electron (hole) transport in PNA–DNA hybrid. Analysis of the mechanism for electron transport supports hole hopping.

A common polymorphism associated with antibiotic-induced cardiac arrhythmia

Drug-induced long QT syndrome (LQTS) is a prevalent disorder of uncertain etiology that predisposes to sudden death. KCNE2 encodes MinK-related peptide 1 (MiRP1), a subunit of the cardiac potassium channel IKr that has been associated previously with inherited LQTS. Here, we examine KCNE2 in 98 patients with drug-induced LQTS, identifying three individuals with sporadic mutations and a patient with sulfamethoxazole-associated LQTS who carried a single-nucleotide polymorphism (SNP) found in ≈1.6% of the general population. While mutant channels showed diminished potassium flux at baseline and wild-type drug sensitivity, channels with the SNP were normal at baseline but inhibited by sulfamethoxazole at therapeutic levels that did not affect wild-type channels. We conclude that allelic variants of MiRP1 contribute to a significant fraction of cases of drug-induced LQTS through multiple mechanisms and that common sequence variations that increase the risk of life-threatening drug reactions can be clinically silent before drug exposure.

Hybrid vigor, fetal overgrowth, and viability of mice derived by nuclear cloning and tetraploid embryo complementation

To assess whether heterozygosity of the donor cell genome was a general parameter crucial for long-term survival of cloned animals, we tested the ability of embryonic stem (ES) cells with either an inbred or F1 genetic background to generate cloned mice by nuclear transfer. Most clones derived from five F1 ES cell lines survived to adulthood. In contrast, clones from three inbred ES cell lines invariably died shortly after birth due to respiratory failure. Comparison of mice derived from nuclear cloning, in which a complete blastocyst is derived from a single ES cell, and tetraploid blastocyst complementation, in which only the inner cell mass is formed from a few injected ES cells, allows us to determine which phenotypes depend on the technique or on the characteristics of the ES cell line. Neonatal lethality also has been reported in mice entirely derived from inbred ES cells that had been injected into tetraploid blastocysts (ES cell-tetraploids). Like inbred clones, ES cell-tetraploid pups derived from inbred ES cell lines died shortly after delivery with signs of respiratory distress. In contrast, most ES cell-tetraploid neonates, derived from six F1 ES cell lines, developed into fertile adults. Cloned pups obtained from both inbred and F1 ES cell nuclei frequently displayed increased placental and birth weights whereas ES cell-tetraploid pups were of normal weight. The potency of F1 ES cells to generate live, fertile adults was not lost after either long-term in vitro culture or serial gene targeting events. We conclude that genetic heterozygosity is a crucial parameter for postnatal survival of mice that are entirely derived from ES cells by either nuclear cloning or tetraploid embryo complementation. In addition, our results demonstrate that tetraploid embryo complementation using F1 ES cells represents a simple, efficient procedure for deriving animals with complex genetic alterations without the need for a chimeric intermediate.

Induction of long-term potentiation is associated with major ultrastructural changes of activated synapses.

Long-term potentiation (LTP), an increase in synaptic efficacy believed to underlie learning and memory mechanisms, has been proposed to involve structural modifications of synapses. Precise identification of the morphological changes associated with LTP has however been hindered by the difficulty in distinguishing potentiated or activated from nonstimulated synapses. Here we used a cytochemical method that allowed detection in CA1 hippocampus at the electron microscopy level of a stimulation-specific, D-AP5-sensitive accumulation of calcium in postsynaptic spines and presynaptic terminals following application of high-frequency trains. Morphometric analyses carried out 30-40 min after LTP induction revealed dramatic ultrastructural differences between labeled and nonlabeled synapses. The majority of labeled synapses (60%) exhibited perforated postsynaptic densities, whereas this proportion was only 20% in nonlabeled synaptic contacts. Labeled synaptic profiles were also characterized by a larger apposition zone between pre- and postsynaptic structures, longer postsynaptic densities, and enlarged spine profiles. These results add strong support to the idea that ultrastructural modifications and specifically an increase in perforated synapses are associated with LTP induction in field CA1 of hippocampus and they suggest that a majority of activated contacts may exhibit such changes.

Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain.

A long-term goal in the field of restriction-modification enzymes has been to generate restriction endonucleases with novel sequence specificities by mutating or engineering existing enzymes. This will avoid the increasingly arduous task of extensive screening of bacteria and other microorganisms for new enzymes. Here, we report the deliberate creation of novel site-specific endonucleases by linking two different zinc finger proteins to the cleavage domain of Fok I endonuclease. Both fusion proteins are active and under optimal conditions cleave DNA in a sequence-specific manner. Thus, the modular structure of Fok I endonuclease and the zinc finger motifs makes it possible to create "artificial" nucleases that will cut DNA near a predetermined site. This opens the way to generate many new enzymes with tailor-made sequence specificities desirable for various applications.

Long Island, New York & Connecticut, 1863 (Raster Image)

This layer is a georeferenced raster image of the historic paper map entitled: Map of Long Island and the southern part of Connecticut. It was published by J.H. Colton in 1863. Scale [ca. 1:165,000]. The image inside the map neatline is georeferenced to the surface of the earth and fit to the North American Datum 1983, Universal Transverse Mercator (UTM) Zone 18N projected coordinate system. All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, index maps, legends, or other information associated with the principal map. This map shows features such as drainage, cities and other human settlements, shoreline features, roads, railroads, canals, post offices, churches, mills and factories, township and county boundaries, and more. Relief shown by hachures. Depths shown by soundings. Includes also inset of Greater New York.This layer is part of a selection of digitally scanned and georeferenced historic maps from the Harvard Map Collection. These maps typically portray both natural and manmade features. The selection represents a range of originators, ground condition dates, scales, and map purposes.

Distribution of planktonic foraminifera and paleotemperature reconstruction for the Subantarctic Zone of the South Atlantic

Pleistocene summer sea-surface temperatures (SSST) have been reconstructed on a composite core section recovered in the Subantarctic Zone of the Southern Ocean from planktonic foraminifers applying the Modern Analog Technique. The composite consists of Core PS2489-2 and the sections recovered at ODP Site 1090, and documents the last 1.83 Ma. Three distinct climatic periods can be identified that mirror the Pleistocene development of the Southern Ocean hydrography. Cold climatic conditions prevailed at 43°S during glacial as well as during interglacial periods during the early Pleistocene (1.83-0.87 Ma), indicating a northward shift of isotherms that characterize the present-day Polar Front Zone by about 7° of latitude. Evidence shows a strong linkage between Southern Ocean and low latitude climate during that interval time. Between the Mid-Pleistocene Revolution (ca. 0.9 Ma) and the Mid-Brunhes Event (ca. 0.4 Ma), we observe higher amplitude fluctuations in the SSST between glacial and interglacial periods, corresponding to the temperature range between the present Polar Front and Subantarctic Front. These climatic variations have been related to changes in the northern hemisphere ice sheets. The past 0.4 Ma are characterized by strong SSST variations, of up to 8°C, between glacials and interglacials. Only during the climatic optima (stages 11.3, 9.3, 7.5, 7.1, 5.5, and the early Holocene), SSST exceeded present SSST at the core locality (10.2°C). Although the carbonate dissolution record exhibits high variability during the Pleistocene, it can be shown that SSST estimates were not significantly biased. The Mid-Brunhes dissolution cycle as well as the Mid-Pleistocene enhanced carbonate preservation appear to belong to a global long-term variability in carbonate preservation.

(Table 1) Mean sizes of Hydrobia ulvae juveniles in the littoral zone of the Chernaya Inlet (Kandalaksha Bay, White Sea) in July-September 1995

Based on observations and experiments carried out within the White Sea silty-sandy littoral zone in 1994-1997 data on biology of development and behavior of Hydrobia ulvae juveniles over water column and in sediments were obtained. Hydrobiid juveniles 0.125-0.150 mm in size appear in plankton during the second half of June and in two to three weeks they precipitate on sediments reaching 0.300-0.350 mm in size. Specific biological features of the White Sea hydrobiids are a short reproductive period and a short period of juvenile growth related to long under-ice time and decelerated warming of shallow waters. Distribution of juvenile individuals of H. ulvae is primarily determined by hydrodynamics and microtopography of the littoral zone. Redistribution of the juveniles permanently takes place, since all size groups of the juveniles are equally subjected to migration. During the first few weeks after settling mortality of juvenile mudsnails is 85%.

Long-term effects of beach nourishment on the benthic fauna of Panama City Beach, Florida /

The long-term effects of beach nourishment on the benthic infauna and surface sediments of Panama City beaches were investigated. Forty-seven stations located on nine transects between West Pass and Philips Inlet, and two nourishment borrow sites were sampled in November-December 1979 and May 1980. The data collected were compared to prenourishment base-line information collected by Saloman (1976). Abiotic parameters, water temperature, dissolved oxygen and salinity were measured. Sediments were analyzed for particle-size distribution, percent organic carbon and percent carbonate. Benthic macroinvertebrates were represented by 162 taxa of 14 major animal phyla. Species composition and faunal densities varied seasonally. Polychaetes and amphipods were the most abundant animal groups; a small number of species were dominant at nearly all stations. Species diversity was lowest in the swash zone and sandbar stations and highest offshore. Sediment composition was similar to that of Saloman's (1976) study within limits of sampling and processing errors. Faunal composition was found to be different from 1976 but was attributed to normal seasonal and spatial variations. Based on benthic community analyses and sediment parameters, no significant differences were found between nourishment borrow sites and surrounding areas and in the nearshore areas where beach nourishment was conducted. No long-term adverse effects of beach nourishment were detected. (Author).

Leached zone : dissolution of values using heat treated feeds /

"U.S. AEC Contract AT(49-1)-545."

Long chain alkyl diol distribution in Arabian Sea surface sediments

Oxygen exposure has a large impact on lipid biomarker preservation in surface sediments and may affect the application of organic proxies used for reconstructing past environmental conditions. To determine its effect on long chain alkyl diol and keto-ol based proxies, the distributions of these lipids was studied in nine surface sediments from the Murray Ridge in the Arabian Sea obtained from varying water depths (900 to 3000 m) but in close lateral proximity and, therefore, likely receiving a similar particle flux. Due to substantial differences in bottom water oxygen concentration (<3 to 77 µmol/L) and sedimentation rate, substantial differences exist in the time the biomarker lipids are exposed to oxygen in the sediment. Long chain alkyl diol and keto-ol concentrations in the surface sediments (0-0.5 cm) decreased progressively with increasing oxygen exposure time, suggesting increased oxic degradation. The 1,15-keto-ol/diol ratio (DOXI) increased slightly with oxygen exposure time as diols had apparently slightly higher degradation rates than keto-ols. The ratio of 1,14- vs. 1,13- or 1,15-diols, used as upwelling proxies, did not show substantial changes. However, the C30 1,15-diol exhibited a slightly higher degradation rate than C28 and C30 1,13-diols, and thus the Long chain Diol Index (LDI), used as sea surface temperature proxy, showed a negative correlation with the maximum residence time in the oxic zone of the sediment, resulting in ca. 2-3.5 °C change, when translated to temperature. The UK'37 index did not show significant changes with increasing oxygen exposure. This suggests that oxic degradation may affect temperature reconstructions using the LDI in oxic settings and where oxygen concentrations have varied substantially over time.

Controlling Long-Range Ordered Self-assembly of Solid-Binding Peptide Monolayers on Atomically Flat Layered Materials

Thesis (Master's)--University of Washington, 2016-06