Nitrogen recycling in coastal waters of southeastern U.S. during summer 1986

Summer-time pelagic nitrogen recycling using an 15NH4+ tracer technique was studied for important biological pathways, sinks, and residence times in the microbial food web of coastal Georgia, U.S.A. Results showed that estimated rates of NH4+ regeneration by a variety of microheterotrophs and microzooplankton balanced rates of NH4+ assimilation by the microbial community, i.e., phytoplankton, bacteria and other microheterotrophs, in surface waters. In bottom water below the 1% light level, NH4+ regeneration exceeded community NH4+ assimilation by 3.5 times. However, over a period of 2 weeks, high NH4+ concentrations rarely occurred in bottom waters, and this was attributed to rapid mixing of the water column by winds and tides. Estimated mixing times from time-dependent numerical models were on the order of NH4+ turnover times of 5 to 10 hours. Overall, rates of community NH4+ assimilation exceeded rate estimates of phytoplankton N demand by 1.8 to 2.7 fold, which were made from rates of 14CO2 incorporation into proteins. In bottom samples where phytoplankton were light limited, rates of NH4+ assimilation exceeded the phytoplankton N demand by 3.6 to 11.1 fold. Calculations concerning the role of dissolved organic nitrogen in N cycling suggest that only 10% is recycled to NH4+ daily. This N could support 12 to 29% of the estimated phytoplankton N demand. Residence times of particulate nitrogen pools, based on rates of NH4+ regeneration, were on the order of 3–10 days. During summer-time hydrographic conditions and despite other losses, particulate nitrogen could recycle as often as 100 times before autumn removal processes occur off southeastern U.S

MOLECULAR APPROACHES FOR IN SITU IDENTIFCIATION OF NITRATE UTILIZATION BY MARINE BACTERIA AND PHYTOPLANKTON

Traditionally, the importance of inorganic nitrogen (N) for the nutrition and growth of marine phytoplankton has been recognized, while inorganic N utilization by bacteria has received less attention. Likewise, organic N has been thought to be important for heterotrophic organisms but not for phytoplankton. However, accumulating evidence suggests that bacteria compete with phytoplankton for nitrate (NO3-) and other N species. The consequences of this competition may have a profound effect on the flux of N, and therefore carbon (C), in ocean margins. Because it has been difficult to differentiate between N uptake by heterotrophic bacterioplankton versus autotrophic phytoplankton, the processes that control N utilization, and the consequences of these competitive interactions, have traditionally been difficult to study. Significant bacterial utilization of DIN may have a profound effect on the flux of N and C in the water column because sinks for dissolved N that do not incorporate inorganic C represent mechanisms that reduce the atmospheric CO2 drawdown via the ?biological pump? and limit the flux of POC from the euphotic zone. This project was active over the period of 1998-2007 with support from the DOE Biotechnology Investigations ? Ocean Margins Program (BI-OMP). Over this period we developed a tool kit of molecular methods (PCR, RT-PCR, Q-PCR, QRT-PCR, and TRFLP) and combined isotope mass spectrometry and flow-cytometric approaches that allow selective isolation, characterization, and study of the diversity and genetic expression (mRNA) of the structural gene responsible for the assimilation of NO3- by heterotrophic bacteria (nasA). As a result of these studies we discovered that bacteria capable of assimilating NO3- are ubiquitous in marine waters, that the nasA gene is expressed in these environments, that heterotrophic bacteria can account for a significant fraction of total DIN uptake in different ocean margin systems, that the expression of nasA is differentially regulated in genetically distinct NO3- assimilating bacteria, and that the best predictors of nasA gene expression are either NO3- concentration or NO3- uptake rates. These studies provide convincing evidence of the importance of bacterial utilization of NO3-, insight into controlling processes, and provide a rich dataset that are being used to develop linked C and N modeling components necessary to evaluate the significance of bacterial DIN utilization to global C cycling. Furthermore, as a result of BI-OMP funding we made exciting strides towards institutionalizing a research and education based collaboration between the Skidaway Institute of Oceanography (SkIO) and Savannah State University (SSU), an historically black university within the University System of Georgia with undergraduate and now graduate programs in marine science. The BI-OMP program, in addition to supporting undergraduate (24) graduate (10) and postdoctoral (2) students, contributed to the development of a new graduate program in Marine Sciences at SSU that remains an important legacy of this project. The long-term goals of these collaborations are to increase the capacity for marine biotechnology research and to increase representation of minorities in marine, environmental and biotechnological sciences

Influences of physical oceanographic processes on chlorophyll distributions in coastal and estuarine waters of the South Atlantic Bight

Coastal and estuarine waters of the South Atlantic Bight are highly productive, with primary production of 600-700 gC/m2/y. While controls and fate of this production are conceptually well understood, the importance of meteorology and physical circulation processes on phytoplankton has not received equivalent attention. Here, we describe the effects of wind stress and tidal currents on temporal and spatial distributions of phytoplankton biomass represented as chlorophyll a (chl a). Moored instruments were deployed and shipboard sampling was conducted in the North Edisto estuary (South Carolina) and adjacent inner shelf waters during four, two-week field studies in May and August 1993, and June and September 1994. Local wind regimes induced upwelling- and downwelling-favorable conditions which strengthened or reduced vertical density stratification in the coastal frontal zone, respectively, and shifted the location of the front. Chl a in shelf waters was more or less homogenous independent of the wind regime, while chl a on the estuary delta was generally vertically stratified. Within the estuary, chl a concentrations were positively correlated with the alongshore component of wind stress; chl a was not correlated with the weaker cross-shelf component of wind stress. Highest chl a occurred during strong downwelling-favorable events. The quick response time to wind forcing (6-12 hrs) implied a direct effect on chl a distributions and not a stimulation of growth processes. The source of the elevated chl a in response to wind forcing was apparently resuspension of settled and epibenthic algal cells. Tidal currents also influenced the vertical distribution and concentration of chl a. Time series sampling on the estuary delta showed that, with increasing velocity of ebb and flood tide currents, the relative contributions of pennate and centric diatoms with attached detritus and sand grains also increased, indicating that tidal resuspension of settled and epibenthic microalgae also occurred. Vertical stratification of chl a (highest concentrations near the bottom) began to degrade upon mixing by tidal currents with velocities as low as 10 cm/sec. Homogenization of 5-7 m water columns was fully achieved at velocities of 20-30 cm/sec. The data document the direct and comparatively immediate (timescales of minuteshours) impact of tidal and wind energy on concentrations and distribution patterns of phytoplankton in coastal and estuarine waters of the South Atlantic Bight

The Butterfly Fauna Of The Italian Maritime Alps:Results Of The «Edit» Project

Bonelli, Simona, Barbero, Francesca, Casacci, Luca Pietro, Cerrato, Cristiana, Balletto, Emilio (2015): The butterfly fauna of the Italian Maritime Alps: results of the EDIT project. Zoosystema 37 (1): 139-167, DOI: 10.5252/z2015n1a6, URL: http://dx.doi.org/10.5252/z2015n1a

Widespread Aberrant Alternative Splicing despite Molecular Remission in Chronic Myeloid Leukaemia Patients

Vast transcriptomics and epigenomics changes are characteristic of human cancers, including leukaemia. At remission, we assume that these changes normalise so that omics-profiles resemble those of healthy individuals. However, an in-depth transcriptomic and epigenomic analysis of cancer remission has not been undertaken. A striking exemplar of targeted remission induction occurs in chronic myeloid leukaemia (CML) following tyrosine kinase inhibitor (TKI) therapy. Using RNA sequencing and whole-genome bisulfite sequencing, we profiled samples from chronic-phase CML patients at diagnosis and remission and compared these to healthy donors. Remarkably, our analyses revealed that abnormal splicing distinguishes remission samples from normal controls. This phenomenon is independent of the TKI drug used and in striking contrast to the normalisation of gene expression and DNA methylation patterns. Most remarkable are the high intron retention (IR) levels that even exceed those observed in the diagnosis samples. Increased IR affects cell cycle regulators at diagnosis and splicing regulators at remission. We show that aberrant splicing in CML is associated with reduced expression of specific splicing factors, histone modifications and reduced DNA methylation. Our results provide novel insights into the changing transcriptomic and epigenomic landscapes of CML patients during remission. The conceptually unanticipated observation of widespread aberrant alternative splicing after remission induction warrants further exploration. These results have broad implications for studying CML relapse and treating minimal residual disease

Biomass burning and anthropogenic sources of CO over New England in the summer 2004

During the summer of 2004 large wildfires were burning in Alaska and Canada, and part of the emissions were transported toward the northeast United States, where they were measured during the NEAQS-ITCT 2k4 (New England Air Quality Study-Intercontinental Transport and Chemical Transformation) study on board the NOAA WP-3 aircraft and the NOAA research vessel Ronald H. Brown. Using acetonitrile and chloroform as tracers the biomass burning and the anthropogenic fraction of the carbon monoxide (CO) enhancement are determined. As much as 30% of the measured enhancement is attributed to the forest fires in Alaska and Canada transported into the region, and 70% is attributed to the urban emissions of mainly New York and Boston. On some days the forest fire emissions were mixed down to the surface and dominated the CO enhancement. The results compare well with the FLEXPART transport model, indicating that the total emissions during the measurement campaign for biomass burning might be about 22 Tg. The total U.S. anthropogenic CO sources used in FLEXPART are 25 Tg. FLEXPART model, using the U.S. EPA NEI-99 data, overpredicts the CO mixing ratio around Boston and New York in 2004 by about 50%. Copyright 2006 by the American Geophysical Union

Isomorphisms of types in the presence of higher-order references (extended version)

We investigate the problem of type isomorphisms in the presence of higher-order references. We first introduce a finitary programming language with sum types and higher-order references, for which we build a fully abstract games model following the work of Abramsky, Honda and McCusker. Solving an open problem by Laurent, we show that two finitely branching arenas are isomorphic if and only if they are geometrically the same, up to renaming of moves (Laurent's forest isomorphism). We deduce from this an equational theory characterizing isomorphisms of types in our language. We show however that Laurent's conjecture does not hold on infinitely branching arenas, yielding new non-trivial type isomorphisms in a variant of our language with natural numbers

Pristup procjeni zdravstvenoga rizika za ljude prilikom izgradnje gradskoga parka

A Human Health Risk Assessment (HHRA) was undertaken for a proposed park development “River Landing”, to be constructed along the north bank of the South Saskatchewan River in the City of Saskatoon, Saskatchewan, Canada. The purpose of the HHRA was to determine whether chemical constituents identified at the site, including polycyclic aromatic hydrocarbons (PAHs), petroleum hydrocarbons (PHCs), and toxic and heavy metals, would adversely affect the health of construction workers and potential park users. Although more traditional remediation options were considered, the risk assessment approach was chosen since it represented the best available technology. The HHRA was undertaken using protocols and methodologies proposed and readily accepted by the Canadian Council of Ministers of the Environment (CCME), Health Canada, and the United States Environmental Protection Agency (US EPA). Results of the risk assessment revealed that the magnitude and distribution of the chemicals at the site were such that extensive remediation was not required, and that the site could be developed without any significant restrictions on the proposed use. The assessment revealed that potential exposure to soil constituents would not result in adverse health risk to construction workers involved in park development or future park users.Napravljena je procjena zdravstvenoga rizika za ljude (izv. human health risk assessment, HHRA) za projekt gradskoga parka “River Landing” koji bi se trebao izgraditi duž sjeverne obale rijeke South Saskatchewan u Saskatoonu, saveznoj državi Saskatchewan u Kanadi. Svrha je procjene bila utvrditi mogu li kemijski spojevi zatečeni na gradilištu, uključujući policikličke aromatske ugljikovodike, naftne ugljikovodike te toksične i teške metale, štetno utjecati na zdravlje građevinskih radnika i korisnika parka. Premda je razmotrena i uporaba tradicionalnijih metoda sanacije, izabran je ovaj pristup procjeni rizika zbog toga što rabi najbolju dostupnu tehnologiju. Procjena rizika provedena je prema protokolima i metodama koje je odmah usvojio Kanadski savjet ministara za zaštitu okoliša (izv. Canadian Council of Ministers of the Environment, CCME), savezni ured za zdravlje Health Canada te Agencija za zaštitu okoliša Sjedinjenih Država (izv. United States Environmental Protection Agency, US EPA). Procjena rizika pokazala je da količina i rasprostranjenost kemikalija na gradilištu nisu takvi da zahtijevaju opsežniju sanaciju, te da se lokacija može izgraditi bez značajnih ograničenja u namjeni. Procjenom je također utvrđeno da eventualno izlaganje sastavnicama tla neće dovesti do štetnih posljedica za zdravlje građevinskih radnika koji rade na parku, a niti za buduće korisnike parka

Scans for signatures of selection in Russian cattle breed genomes reveal new candidate genes for environmental adaptation and acclimation

Domestication and selective breeding has resulted in over 1000 extant cattle breeds. Many of these breeds do not excel in important traits but are adapted to local environments. These adaptations are a valuable source of genetic material for efforts to improve commercial breeds. As a step toward this goal we identified candidate regions to be under selection in genomes of nine Russian native cattle breeds adapted to survive in harsh climates. After comparing our data to other breeds of European and Asian origins we found known and novel candidate genes that could potentially be related to domestication, economically important traits and environmental adaptations in cattle. The Russian cattle breed genomes contained regions under putative selection with genes that may be related to adaptations to harsh environments (e.g., AQP5, RAD50, and RETREG1). We found genomic signatures of selective sweeps near key genes related to economically important traits, such as the milk production (e.g., DGAT1, ABCG2), growth (e.g., XKR4), and reproduction (e.g., CSF2). Our data point to candidate genes which should be included in future studies attempting to identify genes to improve the extant breeds and facilitate generation of commercial breeds that fit better into the environments of Russia and other countries with similar climates