Nonlinearity in genetic decoding: Homologous DNA replicase genes use alternatives of transcriptional slippage or translational frameshifting

The τ and γ subunits of DNA polymerase III are both encoded by a single gene in Escherichia coli and Thermus thermophilus. γ is two-thirds the size of τ and shares virtually all its amino acid sequence with τ. E. coli and T. thermophilus have evolved very different mechanisms for setting the approximate 1:1 ratio between τ and γ. Both mechanisms put ribosomes into alternate reading frames so that stop codons in the new frame serve to make the smaller γ protein. In E. coli, ≈50% of initiating ribosomes translate the dnaX mRNA conventionally to give τ, but the other 50% shift into the −1 reading frame at a specific site (A AAA AAG) in the mRNA to produce γ. In T. thermophilus ribosomal frameshifting is not required: the dnaX mRNA is a heterogeneous population of molecules with different numbers of A residues arising from transcriptional slippage on a run of nine T residues in the DNA template. Translation of the subpopulation containing nine As (or +/− multiples of three As) yields τ. The rest of the population of mRNAs (containing nine +/− nonmultiples of three As) puts ribosomes into the alternate reading frames to produce the γ protein(s). It is surprising that two rather similar dnaX sequences in E. coli and T. thermophilus lead to very different mechanisms of expression.

The virion glycoproteins of Ebola viruses are encoded in two reading frames and are expressed through transcriptional editing.

In late 1994 and early 1995, Ebola (EBO) virus dramatically reemerged in Africa, causing human disease in the Ivory Coast and Zaire. Analysis of the entire glycoprotein genes of these viruses and those of other EBO virus subtypes has shown that the virion glycoprotein (130 kDa) is encoded in two reading frames, which are linked by transcriptional editing. This editing results in the addition of an extra nontemplated adenosine within a run of seven adenosines near the middle of the coding region. The primary gene product is a smaller (50-70 kDa), nonstructural, secreted glycoprotein, which is produced in large amounts and has an unknown function. Phylogenetic analysis indicates that EBO virus subtypes are genetically diverse and that the recent Ivory Coast isolate represents a new (fourth) subtype of EBO virus. In contrast, the EBO virus isolate from the 1995 outbreak in Kikwit, Zaire, is virtually identical to the virus that caused a similar epidemic in Yambuku, Zaire, almost 20 years earlier. This genetic stability may indicate that EBO viruses have coevolved with their natural reservoirs and do not change appreciably in the wild.

Transcription termination at intrinsic terminators: the role of the RNA hairpin.

Intrinsic termination of transcription in Escherichia coli involves the formation of an RNA hairpin in the nascent RNA. This hairpin plays a central role in the release of the transcript and polymerase at intrinsic termination sites on the DNA template. We have created variants of the lambda tR2 terminator hairpin and examined the relationship between the structure and stability of this hairpin and the template positions and efficiencies of termination. The results were used to test the simple nucleic acid destabilization model of Yager and von Hippel and showed that this model must be modified to provide a distinct role for the rU-rich sequence in the nascent RNA, since a perfect palindromic sequence that is sufficiently long to form an RNA hairpin that could destabilize the entire putative 12-bp RNA-DNA hybrid does not trigger termination at the expected positions. Rather, our results show that both a stable terminator hairpin and the run of 6-8 rU residues that immediately follows are required for effective intrinsic termination and that termination occurs at specific and invariant template positions relative to these two components. Possible structural or kinetic modifications of the simple model are proposed in the light of these findings and of recent results implicating "inchworming" and possible conformational heterogeneity of transcription complexes in intrinsic termination. Thus, these findings argue that the structure and dimensions of the hairpin are important determinants of the termination-elongation decision and suggest that a complete mechanism is likely to involve specific interactions of the polymerase, the RNA terminator hairpin, and, perhaps, the dT-rich template sequence that codes for the run of rU residues at the 3' end of the nascent transcript.

Limnologia, balneabilidade e impactos ambientais: uma análise temporal e espacial na represa do Lobo (Broa), Itirapina/Brotas - SP

Considerando a importância da represa do Lobo, os indícios de eutrofização encontrados na área e tendo a recreação como seu principal uso, buscou-se, neste trabalho, avaliar a qualidade da água nos rios tributários e na represa, e sua adequação a balneabilidade. Para os afluentes do sistema, estimando-se, ainda, a contribuição dos mesmos ao aporte de materiais à represa, foram amostrados o córrego do Geraldo, a confluência dos córregos Água Branca e Limoeiro, o rio Itaqueri (antes da mineradora), o ribeirão do Lobo, o córrego das Perdizes, avaliando-se parâmetros físicos, químicos e biológicos da água e a vazão dos rios, em dois períodos (agosto/setembro e dezembro) de 2002. Os resultados, com base no índice de estado trófico, indicam que a maioria dos tributários, com exceção do córrego Água Branca (eutrófico), é oligotrófico. Na represa o estudo teve avaliações mensais para alguns parâmetros (nutrientes totais e dissolvidos, clorofila total e material em suspensão) e semanais para outros (pH, condutividade elétrica, temperatura da água, oxigênio dissolvido e coliformes fecais) ao longo de um ano (dezembro de 2001 a dezembro de 2002), em nove pontos, abrangendo a região de foz do rio Itaqueri, córrego do Geraldo e ribeirão do Lobo, quatro pontos distribuídos na praia do balneário Santo Antônio e um ponto a jusante da represa. A foz do rio Itaqueri apresentou-se meso-eutrófica no período, enquanto os outros pontos avaliados, oligotróficos. Apesar da condição favorável apresentada, a análise temporal dos dados (com estudos realizados nos últimos 30 anos), mostra uma evidente e preocupante alteração nas condições originárias desse sistema, indicando um evidente processo de eutrofização do reservatório, associado aos usos e ocupação da bacia hidrográfica (resíduos domiciliares, turismo, agricultura e pecuária). Em relação a balneabilidade os principais pontos de contaminação fecal na represa são as entradas dos tributários, enquanto o corpo da represa foi considerado excelente em todo o período amostrado. O córrego Água Branca, como corpo receptor do esgoto de Itirapina, é o mais comprometido dos corpos de água avaliados, além de ser o principal contribuinte de nutrientes e coliformes fecais para a represa do Lobo, através do rio Itaqueri.

Nile River Delta, Egypt, 1785 (Raster Image)

This layer is a georeferenced raster image of the untitled historic paper map: Basse Egypte, E. Giraud, sculp. It was published by Onfroi in 1785. Scale [ca. 1:550,000]. Covers the Nile River Delta, Egypt. Map in French. The image inside the map neatline is georeferenced to the surface of the earth and fit to the Africa Lambert Conformal Conic 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, canals, ancient branches of river and canals, cities and other human settlements, monasteries, shoreline features, and more. Relief shown by hachures. 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.

Analysis of Hyporheic Flow Induced by a Bar in a Gravel Stream: an Experimental Study

Thesis (Master, Civil Engineering) -- Queen's University, 2016-06-01 00:03:02.939

Effects of climate change on fisheries : from a global to a regional perspective

Tese de doutoramento, Biologia (Biologia Marinha e Aquacultura), Universidade de Lisboa, Faculdade de Ciências, 2016

Petrophysical measurement of ODP Leg 122 and 123 samples (Tables 1, 2)

The capillary-pressure characteristics of 22 samples of lithified post-Paleozoic Indian-Ocean carbonates were compared to published data from older carbonate rocks (lower Paleozoic Hunton Group of Texas and Oklahoma). The Indian-Ocean samples are considerably more porous than are the Paleozoic samples, yet all of the Indian-Ocean samples fit readily into a descriptive petrofacies scheme previously established for the Hunton Group. The Indian-Ocean samples may be assigned to four petrophysical facies (petrofacies) based on the shapes of their capillary-pressure curves, their pore-throat-size distributions, their estimated recovery efficiency values (for nonwetting fluids), and the visual characteristics of their pore systems, as observed with a scanning-electron microscope. Petrofacies assignments for the Indian-Ocean samples are as follows. Petrofacies I includes six samples collected from the coarse basal portions of event deposits (primarily turbidites). These samples have large throats, leptokurtic throat-size distributions, low- to moderate recovery efficiency values, concave cumulative-intrusion capillary-pressure curves, and high porosity values. Petrofacies II includes two sedimentologically dissimilar samples that have medium-size throats, platykurtic throat-size distributions, moderate- to-high recovery efficiency values, gently sloping cumulative-intrusion capillary-pressure curves, and high porosity values. Petrofacies III includes two polymictic sandstones and a skeletal packstone that have small throats, polymodal throat-size distributions, moderate recovery efficiency values, gently sloping cumulative-intrusion capillary-pressure curves, and high porosity values. Petrofacies IV includes 11 samples, mostly recrystallized neritic carbonates, that have small throats, leptokurtic throat-size distributions, high recovery efficiency values, convex cumulative-intrusion capillary-pressure curves, and low porosity values. Comparison of petrofacies assignment to core-, thin-section-, and smear-slide data, and to inferred depositional setting, suggests that pore systems in most samples from Holes 765C and 766A result from primary depositional features, whereas pore systems in samples from Hole 761C and one sample from Hole 765C have been strongly influenced by diagenetic processes. For Hole 761C, prediction of petrophysical parameters should be most successful if based on diagenetic facies patterns. By contrast, the distribution of favorable reservoir facies and of permeability barriers in less highly altered rocks collected from Holes 765C and 766A is related to depositional patterns. Recovery efficiency is inversely related to both porosity and median throat size for the present data set. This relationship is similar to that observed for carbonates of the lower Paleozoic Hunton Group and the Ordovician Ellenburger dolomite, but opposite of that observed for some other ancient carbonates. The coarse deposits of the massive basal units of turbidites are petrophysically distinct and form a coherent petrophysical group (Petrofacies I) with substantial reservoir potential. Two samples assigned to Petrofacies I have extremely large throats (median throat size at least 4 ?m, and at least six times that of any other sample) and therefore high permeability values. These two samples come from thin, coarse turbidites that lack or have poorly developed fine divisions and are interpreted to have been deposited on channeled suprafan lobes in a proximal mid-fan setting. The restriction of extremely high permeability values to a single depositional facies suggests that careful facies mapping of deep-sea fans in a deliberate search for such coarse turbidites could dramatically enhance the success of exploration for aquifers or hydrocarbon reservoirs. Such reservoirs should have substantial vertical heterogeneity. They should have high lateral permeability values but low vertical permeability values, and reservoir sections should include numerous thin units having widely differing petrophysical characteristics.

Clay mineralogy and organic carbon content of sediment core GeoB1401-4

Late Quaternary sediments recovered in a core from the area of the Zaire Fan, Central Africa, were analyzed for clay mineral composition in order to reconstruct fluctuations in the sediment input and freshwater discharge of the Zaire River. Clay mineral assemblages are dominated by kaolinite and smectite, which both originate mainly from the Zaire River and contain only minor contributions of eolian dust. Smectite crystallinity and chemical character of illites (Fe, Mg- or Al-rich) are used to track sediment input from the Zaire River and assess fluctuations in the freshwater discharge. Both parameters record a high-latitude forcing of river runoff at 100 ka periodicities reflecting glacial aridity and increased runoff during interglacials 1, 5 and 7. This signal is also observed in kaolinite/smectite ratios which represent the extension and intensity of the freshwater plume of the Zaire River. Clay mineral proxies reveal that river discharge and associated sediment input fluctuated in tune with precessional cycles of African monsoon intensity. Increased eolian input of kaolinite-rich dust with intensified northeast trades during glacials flattens the precessional signal in kaolinite/smectite ratios.

Proxy calibration on two sedimentary sequences off Lisbon

High-resolution proxy data analyzed on two high-sedimentation shallow water sedimentary sequences (PO287-26B and PO287-28B) recovered off Lisbon (Portugal) provide the means for comparison to long-term instrumental time series of marine and atmospheric parameters (sea surface temperature (SST), precipitation, total river flow, and upwelling intensity computed from sea level pressure) and the possibility to do the necessary calibration for the quantification of past climate conditions. XRF Fe is used as proxy for river flow, and the upwelling-related diatom genus Chaetoceros is our upwelling proxy. SST is estimated from the coccolithophore-synthesized alkenones and Uk'37 index. Comparison of the Fe record to the instrumental data reveals its similarity to a mean average run of the instrumentally measured winter (JFMA) river flow on both sites. The upwelling diatom record concurs with the upwelling indices at both sites; however, high opal dissolution, below 20-25 cm, prevents its use for quantitative reconstructions. Alkenone-derived SST at site 28B does not show interannual variation; it has a mean value around 16°C and compares quite well with the instrumental winter/spring temperature. At site 26B the mean SST is the same, but a high degree of interannual variability (up to 4°C) appears to be determined by summer upwelling conditions. Stepwise regression analyses of the instrumental and proxy data sets provided regressions that explain from 65 to 94% of the variability contained in the original data, and reflect spring and summer river flow, as well as summer and winter upwelling indices, substantiating the relevance of seasons to the interpretation of the different proxy signals. The lack of analogs and the small data set available do not allow quantitative reconstructions at this time, but this might be a powerful tool for reconstructing past North Atlantic Oscillation conditions, should we be able to find continuous high-resolution records and overcome the analog problem.

Proglacial river dataset from the Akuliarusiarsuup Kuua River northern tributary, Southwest Greenland, 2008 - 2010, version 1.0

Pressing scientific questions concerning the Greenland ice sheet's climatic sensitivity, hydrology, and contributions to current and future sea level rise require hydrological datasets to resolve. While direct observations of ice sheet meltwater losses can be obtained in terrestrial rivers draining the ice sheet and from lake levels, few such datasets exist. We present a new dataset of meltwater river discharge for the vicinity of Kangerlussuaq, Southwest Greenland. The dataset contains measurements of river stage and discharge for three sites along the Akuliarusiarsuup Kuua (Watson) River's northern tributary, with 30 minute temporal resolution between June 2008 and August 2010. Additional data of water temperature, air pressure, and lake water depth and temperature are also provided. Discharge data were measured at sites with near-ideal properties for such data collection. Regardless, high water bedload and turbulent flow introduce considerable uncertainty. These were constrained and quantified using statistical techniques, thereby providing a high quality dataset from this important site. The greatest data uncertainties are associated with streambed elevation change and measurements. Large portions of stream channels deepened according to statistical tests, but poor precision of streambed depth measurements also added uncertainty. Quality checked data are freely available for scientific use as supplementary online material.

The charter of the Albany and Greenbush Bridge Company : and a statement of its claims on the public interest in connection with the Boston, Hoosac Tunnel and Albany Railroad.

"J.W. Gascoigne, secretary."

Village of Rosemont special project report : Willow-Higgins Creek Flood Mitigation Project phases III & IV, Cook County, Illinois.

Report by the Illinois Office of Water Resources on Phases III & IV of a flood hazard mitigation project in Rosemont, Illinois. Phase III of the Willow-Higgins Flood Mitigation Project consists of widening and improving a 340-foot reach of Willow-Higgins Creek upstream of River Road. The improvement will include the replacement of 340 lineal feet of vertical floodwall along both sides of Willow-Higgins Creek. Phase IV of the Willow-Higgins Flood Mitigation Project consists of widening and improving a reach of Willow-Higgins Creek between the downstream end of Phase II, which is 2565 feet downstream of Higgins Road, and Granville Road; and also between Willow Creek Road and a point 160 feet downstream of Willow Creek Road. The improvement will include placement of 2200 lineal feet of vertical floodwall along the north side of Willow-Higgins Creek and 160 feet of vertical floodwall along both sides of Willow-Higgins Creek downstream of Willow Creek Road.

The Literary examiner: consisting of the Indicator, a review of books, and miscellaneous pieces in prose and verse.

Brewer: p.117, but rebound in polished calf by Root & Son.

Plan of playground ... Pyott Playground. Oak Park, Illinois. Post-1918

Black, red, blue ink, pencil; location of proposed reservoir and embankment; unsigned. 88x52 cm. Scale: 1"=30' [from photographic copy by Lance Burgharrdt]