Ground-water status report, Pearl Harbor area, Hawaii, 1978

USGS Publications Warehouse

Soroos, Ronald L.; Ewart, Charles J.

1979-01-01

Increasing demand for freshwater in Hawaii has placed heavy stress on many of the State 's basal aquifer systems. The most heavily stressed of these systems is the Pearl Harbor on Oahu. The Pearl Harbor basal aquifer supplies as much as 277 million gallons per day. Since early in this century, spring discharge has been declining while pumpage has been increasing. Total ground-water discharge has remained steady despite short-term fluctuations. Some wells show general increases in chloride concentration while others remain steady. Chloride concentrations throughout the area show no apparent increase since 1970. Basal water head maps of the Pearl Harbor area clearly reflect the natural discharge points, which are the springs located along the shore near the center of Pearl Harbor. Basal-water hydrographs show a general decline of about 0.09 foot per year. This implies depletion of storage at a rate of about 25 million gallons per day. (USGS).

The War on Cancer: Cold Spring Harbor Laboratory Is Fighting the Good Fight.

PubMed

Mertz, Leslie

2017-01-01

Located on the north shore of Long Island in New York, Cold Spring Harbor Laboratory (Figure 1) started out with a marine biology emphasis at the end of the 19th century, but it soon established itself as a prominent cancer research facility. That strong emphasis on cancer work continues today as this private, not-for-profit research institution enters its 127th year (Figure 2).

Comparison of benthos and plankton for Waukegan Harbor Area of Concern, Illinois, and Burns Harbor-Port of Indiana non-Area of Concern, Indiana, in 2015

USGS Publications Warehouse

Eikenberry, Barbara C. Scudder; Olds, Hayley T.; Burns, Daniel J.; Dobrowolski, Edward G.; Schmude, Kurt L.

2017-06-06

During two seasonal sampling events in spring (June) and fall (August) of 2015, the U.S. Geological Survey collected benthos (benthic invertebrates) and plankton (zooplankton and phytoplankton) at three sites each in the Waukegan Harbor Area of Concern (AOC) in Illinois and in Burns Harbor-Port of Indiana, a non-AOC comparison site in Indiana. The study was done in cooperation with the U.S. Environmental Protection Agency and the Illinois Department of Natural Resources. Samples were collected concurrently for physical and chemical parameters (specific conductance, temperature, pH, dissolved oxygen, chlorophyll-a, total and volatile suspended solids in water samples; particle size and volatile-on-ignition solids of sediment in dredge samples). The purpose of the study was to assess whether or not aquatic communities at the AOC were degraded in comparison to communities at the non-AOC, which was presumed to be less impaired than the AOC. Benthos were collected by using Hester-Dendy artificial substrate samplers and a Ponar® dredge sampler to collect composited grabs of bottom sediment; zooplankton were collected by using tows from depth to the surface with a 63-micrometer mesh plankton net; phytoplankton were collected by using whole water samples composited from set depth intervals. Aquatic communities at the AOC and the non-AOC were compared by use of univariate statistical analyses with metrics such as taxa richness (number of unique taxa), diversity, and a multimetric Index of Biotic Integrity (IBI, for artificial-substrate samples only) as well as by use of multivariate statistical analyses of taxa relative abundances.Although benthos communities at Waukegan Harbor AOC were not rated as degraded in comparison to the non-AOC, metrics for zooplankton and phytoplankton communities did show some impairment for the 2015 sampling. Across seasons, benthos richness and diversity were significantly higher and rated as less degraded at the AOC compared to the non-AOC; however, benthos IBIs were not significantly different. Multivariate comparisons revealed that the benthos communities in the AOC and non-AOC were significantly different, but these comparisons do not address current degradation in either harbor. The dominant taxa in dredge samples were oligochaete worms in both harbors, but there were differences in the relative abundances of Dreissena as well as oligochaete and midge taxa. Although zooplankton richness and diversity in the AOC were lower and rated as more degraded in spring, these metrics were rated as less degraded in fall compared to the non-AOC, effectively balancing out so that there was no difference across seasons. Multivariate comparisons also indicated that zooplankton communities in the AOC were significantly different from those in the non-AOC for spring only but not across seasons, possibly because of lower water temperatures in spring at Waukegan Harbor than at the non-AOC site. The spring zooplankton community in Waukegan Harbor was dominated in density and biomass by the rotifer Synchaeta. Across seasons, diatom richness was significantly higher and rated as less degraded in the AOC than the non-AOC because of spring values, whereas soft algae richness was significantly lower and rated as more degraded in the AOC because of fall values. Spring richness of combined phytoplankton (soft algae and diatoms) was significantly higher in the AOC than in the non-AOC. Neither diatom diversity nor soft algae diversity differed significantly between the harbors, but combined phytoplankton diversity across seasons, if replicates were included, was significantly lower and rated as more degraded in the AOC than in the non-AOC. Multivariate tests indicated that the combined phytoplankton communities in the harbors were not significantly different across seasons. Significant differences were not found between harbors for chlorophyll-a, suspended solids, algal densities, or biomass.

Homogenization of Mammalian Cells.

PubMed

de Araújo, Mariana E G; Lamberti, Giorgia; Huber, Lukas A

2015-11-02

Homogenization is the name given to the methodological steps necessary for releasing organelles and other cellular constituents as a free suspension of intact individual components. Most homogenization procedures used for mammalian cells (e.g., cavitation pump and Dounce homogenizer) rely on mechanical force to break the plasma membrane and may be supplemented with osmotic or temperature alterations to facilitate membrane disruption. In this protocol, we describe a syringe-based homogenization method that does not require specialized equipment, is easy to handle, and gives reproducible results. The method may be adapted for cells that require hypotonic shock before homogenization. We routinely use it as part of our workflow to isolate endocytic organelles from mammalian cells. © 2015 Cold Spring Harbor Laboratory Press.

Preparation of Single-Stranded Bacteriophage M13 DNA by Precipitation with Polyethylene Glycol.

PubMed

Green, Michael R; Sambrook, Joseph

2017-11-01

Bacteriophage M13 single-stranded DNA is prepared from virus particles secreted by infected bacteria into the surrounding medium. Several methods are available to purify the polymorphic filamentous particles. In this protocol, the particles are concentrated by precipitation with polyethylene glycol (PEG) in the presence of high salt. Subsequent extraction with phenol releases the single-stranded DNA, which is then collected by precipitation with ethanol. The resulting preparation is pure enough to be used as a template for DNA sequencing. A yield of 5-10 µg of single-stranded DNA/mL of infected cells may be expected from recombinant bacteriophages bearing inserts of 300-1000 nt. © 2017 Cold Spring Harbor Laboratory Press.

Genetic Interaction Mapping in Schizosaccharomyces pombe Using the Pombe Epistasis Mapper (PEM) System and a ROTOR HDA Colony Replicating Robot in a 1536 Array Format.

PubMed

Roguev, Assen; Xu, Jiewei; Krogan, Nevan

2018-02-01

This protocol describes an optimized high-throughput procedure for generating double deletion mutants in Schizosaccharomyces pombe using the colony replicating robot ROTOR HDA and the PEM (pombe epistasis mapper) system. The method is based on generating high-density colony arrays (1536 colonies per agar plate) and passaging them through a series of antidiploid and mating-type selection (ADS-MTS) and double-mutant selection (DMS) steps. Detailed program parameters for each individual replication step are provided. Using this procedure, batches of 25 or more screens can be routinely performed. © 2018 Cold Spring Harbor Laboratory Press.

Genetic and Molecular Analysis of the Mechanisms by which TSC Regulates Neuronal Differentiation

DTIC Science & Technology

2009-03-01

2004 Programmed autophagy in the Drosophila fat body is in- duced by ecdysone through regulation of the PI3K pathway. Dev. Cell 7: 179–192. Sarbassov...embryonic Drosophila CNS. Mech. Dev. 64: 137–151. Scott, R. C., O. Schuldiner and T. P. Neufeld, 2004 Role and reg- ulation of starvation-induced autophagy ...in The Development of Drosophila melanogaster , edited by M. Bates and A. Martinez-Arias. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY

Binding of Helocobacter pyori to Human Gastric Mucose: Identification and Characterization of a Lewis b Bingind Protein.

DTIC Science & Technology

1995-06-01

putative virulence factors of H. pylori have been identified to date. These factors include a urease , flagella, a mucinase, a cytotoxin, and two adhesins...The urease is believed to aid in bacterial survival of the harsh gastric environment by generating ammonia from urea to neutralize the low pH (Segal...A Laboratory Manual. Cold Spring Harbor, New York. Cold Spring Harbor Laboratory Press. Hazell, S., A. Lee. 1986. Campylobacter pyloridis urease

Sulphur Spring: Busy Intersection and Possible Martian Analogue

NASA Technical Reports Server (NTRS)

Nankivell, A.; Andre, N.; Thomas-Keprta, K.; Allen, C.; McKay, D.

2000-01-01

Life in extreme environments exhibiting conditions similar to early Earth and Mars, such as Sulphur Spring, may harbor microbiota serving as both relics from the past as well as present day Martian analogues.

Exchange of nitrogen and phosphorus between a shallow lagoon and coastal waters

USGS Publications Warehouse

Hayn, Melanie; Howarth, Robert W.; Ganju, Neil K.; Berg, Peter; Foreman, Kenneth H.; Giblin, Anne E.; McGlathery, Karen

2014-01-01

West Falmouth Harbor, a shallow lagoon on Cape Cod, has experienced a threefold increase in nitrogen load since the mid- to late 1990s due to input from a groundwater plume contaminated by a municipal wastewater treatment plant. We measured the exchange of nitrogen and phosphorus between the harbor and the coastal waters of Buzzards Bay over several years when the harbor was experiencing this elevated nitrogen load. During summer months, the harbor not only retained the entire watershed nitrogen load but also had a net import of nitrogen from Buzzards Bay. During the spring and fall, the harbor had a net export of nitrogen to Buzzards Bay. We did not measure the export in winter, but assuming the winter net export was less than 112 % of the load, the harbor exported less than half of the watershed nitrogen load on an annual basis. For phosphorus, the harbor had a net import from coastal waters in the spring and summer months and a net export in the fall. Despite the large increase in nitrogen load to the harbor, the summertime import of phosphorus from Buzzards Bay was sufficient to maintain nitrogen limitation of primary productivity during the summer. Our findings illustrate that shallow systems dominated by benthic producers have the potential to retain large terrestrial nitrogen loads when there is sufficient supply of phosphorus from exchange with coastal waters.

Preparation of Double-Stranded (Replicative Form) Bacteriophage M13 DNA.

PubMed

Green, Michael R; Sambrook, Joseph

2017-11-01

The double-stranded, closed-circular, replicative form (RF) of M13 DNA is present in high copy numbers in infected cells, and its physical characteristics are essentially identical to those of closed-circular plasmid DNAs. Any of the methods commonly used to purify plasmid DNA can therefore be used to isolate M13 RF DNA. This protocol describes the isolation of M13 RF DNA by alkaline lysis from small volumes (1-2 mL) of infected bacterial cultures. The yield of DNA (1-4 mg, depending on the size of the M13 clone) is more than enough for most purposes in molecular cloning. However, should more DNA be needed, the procedure can easily be scaled up. © 2017 Cold Spring Harbor Laboratory Press.

Plating Bacteriophage M13.

PubMed

Green, Michael R; Sambrook, Joseph

2017-10-03

A plaque of bacteriophage M13 derives from infection of a single bacterium by a single virus particle. The progeny particles infect neighboring bacteria, which, in turn, release another generation of daughter virus particles. If the bacteria are growing in semisolid medium (e.g., containing agar or agarose), then the diffusion of the progeny particles is limited. Cells infected with bacteriophage M13 are not killed, but have a longer generation time than uninfected Escherichia coli In consequence, plaques appear as areas of slower-growing cells on a faster-growing lawn of bacterial cells. This protocol describes plating of bacteriophage M13 stocks. Plaques are readily detectable on top agar after 4-8 h of incubation at 37°C. © 2017 Cold Spring Harbor Laboratory Press.

ChIP-seq.

PubMed

Kim, Tae Hoon; Dekker, Job

2018-05-01

Owing to its digital nature, ChIP-seq has become the standard method for genome-wide ChIP analysis. Using next-generation sequencing platforms (notably the Illumina Genome Analyzer), millions of short sequence reads can be obtained. The densities of recovered ChIP sequence reads along the genome are used to determine the binding sites of the protein. Although a relatively small amount of ChIP DNA is required for ChIP-seq, the current sequencing platforms still require amplification of the ChIP DNA by ligation-mediated PCR (LM-PCR). This protocol, which involves linker ligation followed by size selection, is the standard ChIP-seq protocol using an Illumina Genome Analyzer. The size-selected ChIP DNA is amplified by LM-PCR and size-selected for the second time. The purified ChIP DNA is then loaded into the Genome Analyzer. The ChIP DNA can also be processed in parallel for ChIP-chip results. © 2018 Cold Spring Harbor Laboratory Press.

An analysis of geothermal and carbonic springs in the western United States sustained by deep fluid inputs.

PubMed

Colman, D R; Garcia, J R; Crossey, L J; Karlstrom, K; Jackson-Weaver, O; Takacs-Vesbach, C

2014-01-01

Hydrothermal springs harbor unique microbial communities that have provided insight into the early evolution of life, expanded known microbial diversity, and documented a deep Earth biosphere. Mesothermal (cool but above ambient temperature) continental springs, however, have largely been ignored although they may also harbor unique populations of micro-organisms influenced by deep subsurface fluid mixing with near surface fluids. We investigated the microbial communities of 28 mesothermal springs in diverse geologic provinces of the western United States that demonstrate differential mixing of deeply and shallowly circulated water. Culture-independent analysis of the communities yielded 1966 bacterial and 283 archaeal 16S rRNA gene sequences. The springs harbored diverse taxa and shared few operational taxonomic units (OTUs) across sites. The Proteobacteria phylum accounted for most of the dataset (81.2% of all 16S rRNA genes), with 31 other phyla/candidate divisions comprising the remainder. A small percentage (~6%) of bacterial 16S rRNA genes could not be classified at the phylum level, but were mostly distributed in those springs with greatest inputs of deeply sourced fluids. Archaeal diversity was limited to only four springs and was primarily composed of well-characterized Thaumarchaeota. Geochemistry across the dataset was varied, but statistical analyses suggested that greater input of deeply sourced fluids was correlated with community structure. Those with lesser input contained genera typical of surficial waters, while some of the springs with greater input may contain putatively chemolithotrophic communities. The results reported here expand our understanding of microbial diversity of continental geothermal systems and suggest that these communities are influenced by the geochemical and hydrologic characteristics arising from deeply sourced (mantle-derived) fluid mixing. The springs and communities we report here provide evidence for opportunities to understand new dimensions of continental geobiological processes where warm, highly reduced fluids are mixing with more oxidized surficial waters. © 2013 John Wiley & Sons Ltd.

Preparation of Total RNA from Fission Yeast.

PubMed

Bähler, Jürg; Wise, Jo Ann

2017-04-03

Treatment with hot phenol breaks open fission yeast cells and begins to strip away bound proteins from RNA. Deproteinization is completed by multiple extractions with chloroform/isoamyl alcohol and separation of the aqueous and organic phases using MaXtract gel, an inert material that acts as a physical barrier between the phases. The final step is concentration of the RNA by ethanol precipitation. The protocol can be used to prepare RNA from several cultures grown in parallel, but it is important not to process too many samples at once because delays can be detrimental to RNA quality. A reasonable number of samples to process at once would be three to four for microarray or RNA sequencing analyses and six for preliminary investigations of mutants implicated in RNA metabolism. © 2017 Cold Spring Harbor Laboratory Press.

2011 Annual Report: Monitoring and evaluation for conserving biological resources of the Spring Mountains National Recreation Area

Treesearch

Stephen J. Solem; Burton K. Pendleton; Julie A. Woldow; Marc Coles-Ritchie; Jeri Ledbetter; Kevin S. McKelvey; Joy Berg; Amy Gilboy; Jim Menlove; Carly K. Woodlief

2012-01-01

The Spring Mountains National Recreation Area (SMNRA) includes approximately 316,000 acres of National Forest System lands managed by the Humboldt-Toiyabe National Forest in Clark and Nye Counties, Nevada (see Figure 1-1). The Spring Mountains have long been recognized as an island of endemism, harboring flora and fauna found nowhere else in the world. Conservation of...

2010 Annual Report: Monitoring and evaluation for conserving biological resources of the Spring Mountains National Recreation Area

Treesearch

Stephen J. Solem; Burton K. Pendleton; Marc Coles-Ritchie; Jeri Ledbetter; Kevin S. McKelvey; Joy Berg; Kellen Nelson; James Menlove

2011-01-01

The Spring Mountains National Recreation Area (SMNRA) includes approximately 316,000 acres of National Forest System lands managed by the Humboldt-Toiyabe National Forest in Clark and Nye Counties, Nevada (see Figure 1-1). The Spring Mountains have long been recognized as an island of endemism, harboring flora and fauna found nowhere else in the world. Conservation of...

Mouse Embryo Cryopreservation by Rapid Cooling.

PubMed

Shaw, Jillian

2018-05-01

Embryo cryopreservation has been used to archive mouse strains. Protocols have evolved over this time and now vary considerably in terms of cryoprotectant solution, cooling and warming rates, methods to add and remove cryoprotectant, container or carrier type, volume of cryoprotectant, the stage of preimplantation development, and the use of additional treatments such as blastocyst puncture and microinjection. The rapid cooling methods use concentrated solutions of cryoprotectants to reduce the water content of the cell before cooling commences, thus preventing the formation of ice crystals. Embryos are equilibrated with the cryoprotectants, loaded into a carrier, and then rapidly cooled (e.g., by being plunged directly into LN 2 or onto a surface cooled in LN 2 ). The rapid cooling methods eliminate the need for controlled-rate freezers and seeding procedures. However, they are much more sensitive to minor variations when performing the steps. The rapid-cooling protocol described here is suitable for use with plastic insemination straws. Because it uses relatively large volumes, it is less technically demanding than some other methods that use minivolume devices. © 2018 Cold Spring Harbor Laboratory Press.

Distribution of suspended sediment in a partially mixed estuary, Charleston Harbor, South Carolina, U.S.A.

NASA Astrophysics Data System (ADS)

Althausen, J. D.; Kjerfve, Björn

1992-11-01

A well-defined turbidity maximum zone (TMZ) exists 15-45 km upstream of the entrance to Charleston Harbor, South Carolina, on the Cooper River, where the salinity varies between 5-15 ppt. The TMZ is characterized by less than 60% light transmission over a 5 cm path-length near the bottom, as compared to 70-90% light transmission elsewhere. The TMZ oscillates along the Cooper River 3-13 km during a tidal cycle. The range of total suspended sediment (TSS) concentration is 40-100 mg l -1 in the TMZ, while 10-30 mg l -1 is the most common TSS concentration elsewhere in the estuarine portion of Charleston Harbor and the Cooper River. Transmissivity is well-correlated with TSS ( r2 = 0·77) throughout the estuary. TSS concentration depends largely on tidal stage and varies significantly from spring to neap tide. Spring tide TSS concentrations are 2-3 times greater than concentrations during neap tides. The net downstream transport of suspended sediment is primarily a function of fresh water discharge, but is particularly large when flood events coincide with spring tides as was evident during the sampling of the TMZ following Hurricane Hugo (22 September 1989).

Final Program Report for 2010-2012: Monitoring and evaluation for conserving biological resources of the Spring Mountains National Recreation Area

Treesearch

Stephen J. Solem; Burton K. Pendleton; Casey Giffen; Marc Coles-Ritchie; Jeri Ledbetter; Kevin S. McKelvey; Joy Berg; Jim Menlove; Carly K. Woodlief; Luke A. Boehnke

2013-01-01

The Spring Mountains National Recreation Area (SMNRA) includes approximately 316,000 acres of National Forest System (NFS) lands managed by the Humboldt-Toiyabe National Forest in Clark and Nye Counties, Nevada (see fig. 1-1). The Spring Mountains have long been recognized as an island of endemism, harboring flora and fauna found nowhere else in the world. Conservation...

Electroporation of Postimplantation Mouse Embryos In Utero.

PubMed

Huang, Cheng-Chiu; Carcagno, Abel

2018-02-01

Gene transfer by electroporation is possible in mouse fetuses within the uterus. As described in this protocol, the pregnant female is anesthetized, the abdominal cavity is opened, and the uterus with the fetuses is exteriorized. A solution of plasmid DNA is injected through the uterine wall directly into the fetus, typically into a cavity like the brain ventricle, guided by fiber optic illumination. Electrodes are positioned on the uterus around the region of the fetus that was injected, and electrical pulses are delivered. The uterus is returned to the abdominal cavity, the body wall is sutured closed, and the female is allowed to recover. The manipulated fetuses can then be collected and analyzed at various times after the electroporation. This method allows experimental access to later-stage developing mouse embryos. © 2018 Cold Spring Harbor Laboratory Press.

76 FR 79209 - Proposed Safe Harbor Agreement for the Shasta Crayfish in Cassel, Shasta County, CA

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-21

... occur in the future during routine maintenance of a water intake pipe on the south side of the pond.... Background Under a safe harbor agreement, participating landowners voluntarily undertake management... flow. The water from the spring is ponded by a levee that was originally built in the early 20th...

Diagnostic Approach to Acute Diarrheal Illness in a Military Population on Training Exercises in Thailand, a Region of Campylobacter Hyperendemicity

DTIC Science & Technology

2008-04-01

Center (Silver Spring, MD) and the Armed Forces Research Institute FIG. 1. Posttest probability of Campylobacter-associated illness based on the...Sanders5 Enteric Diseases Department, Naval Medical Research Center, Silver Spring, Maryland1; Armed Forces Research Institute of Medical Sciences, Bangkok...Thailand2; Walter Reed Army Institute of Research , Silver Spring, Maryland3; Naval Environmental Preventive Medicine Unit 6, Pearl Harbor, Hawaii4

Mapping protein-protein interactions using yeast two-hybrid assays.

PubMed

Mehla, Jitender; Caufield, J Harry; Uetz, Peter

2015-05-01

Yeast two-hybrid (Y2H) screens are an efficient system for mapping protein-protein interactions and whole interactomes. The screens can be performed using random libraries or collections of defined open reading frames (ORFs) called ORFeomes. This protocol describes both library and array-based Y2H screening, with an emphasis on array-based assays. Array-based Y2H is commonly used to test a number of "prey" proteins for interactions with a single "bait" (target) protein or pool of proteins. The advantage of this approach is the direct identification of interacting protein pairs without further downstream experiments: The identity of the preys is known and does not require further confirmation. In contrast, constructing and screening a random prey library requires identification of individual prey clones and systematic retesting. Retesting is typically performed in an array format. © 2015 Cold Spring Harbor Laboratory Press.

Culturing primary mouse pancreatic ductal cells.

PubMed

Reichert, Maximilian; Rhim, Andrew D; Rustgi, Anil K

2015-06-01

The most common subtype of pancreatic cancer is pancreatic ductal adenocarcinoma (PDAC). PDAC resembles ductal cells morphologically. To study pancreatic ductal cell (PDC) and pancreatic intraepithelial neoplasia (PanIN)/PDAC biology, it is essential to have reliable in vitro culture conditions. Here we describe a methodology to isolate, culture, and passage PDCs and duct-like cells from the mouse pancreas. It can be used to isolate cells from genetically engineered mouse models (GEMMs), providing a valuable tool to study disease models in vitro to complement in vivo findings. The culture conditions allow epithelial cells to outgrow fibroblast and other "contaminating" cell types within a few passages. However, the resulting cultures, although mostly epithelial, are not completely devoid of fibroblasts. Regardless, this protocol provides guidelines for a robust in vitro culture system to isolate, maintain, and expand primary pancreatic ductal epithelial cells. It can be applied to virtually all GEMMs of pancreatic disease and other diseases and cancers that arise from ductal structures. Because most carcinomas resemble ductal structures, this protocol has utility in the study of other cancers in addition to PDAC, such as breast and prostate cancers. © 2015 Cold Spring Harbor Laboratory Press.

Assessment of sediment quality based on acid-volatile sulfide and simultaneously extracted metals in heavily industrialized area of Asaluyeh, Persian Gulf: concentrations, spatial distributions, and sediment bioavailability/toxicity.

PubMed

Arfaeinia, Hossein; Nabipour, Iraj; Ostovar, Afshin; Asadgol, Zahra; Abuee, Ehsan; Keshtkar, Mozhgan; Dobaradaran, Sina

2016-05-01

Sediment samples from the coastal area of Asaluyeh harbor were collected during autumn and spring 2015. The acid-volatile sulfide (AVS) and simultaneously extracted metals (SEMs) were measured to assess the sediment quality and potential ecological risks. The average concentrations (and relative standard deviation (RSD)) of AVS in the industrial sediments were 12.32 μmol/g (36.91) and 6.34 μmol/g (80.05) in autumn and spring, respectively, while in the urban area, these values were 0.44 μmol/g (123.50) and 0.31 μmol/g (160.0) in autumn and spring, respectively. The average concentrations of SEM (and RSD) in the industrial sediments were 15.02 μmol/g (14.38) and 12.34 μmol/g (20.65) in autumn and spring, respectively, while in the urban area, these values were 1.10 μmol/g (43.03) and 1.06 μmol/g (55.59) in autumn and spring, respectively. Zn was the predominant component (34.25-86.24 %) of SEM, while the corresponding value for Cd, much more toxic ingredient, was less than 1 %. Some of the coastal sediments in the harbor of Asaluyeh (20 and 47 % in autumn and spring, respectively) had expected adverse biological effects based on the suggested criterion by United States Environmental Protection Agency (USEPA), while most stations (80 and 53 % in autumn and spring, respectively) had uncertain adverse effects.

Tracing submarine groundwater discharge flux in Tolo Harbor, Hong Kong (China)

NASA Astrophysics Data System (ADS)

Liu, Yi; Jiao, Jiu Jimmy; Cheng, Ho Kwan

2018-02-01

Submarine groundwater discharge (SGD) is an important pathway for groundwater and associated chemicals to discharge to the sea. Groundwater levels monitored along a transect perpendicular to the shoreline are used to calculate SGD flux from the nearshore aquifer to Tolo Harbor, Hong Kong (China). The calculated SGD flux—recharge/discharge measured with Darcy's Law methods—agrees well with estimates based on geo-tracer techniques and seepage meter in Tolo Harbor during previous studies. The estimated freshwater SGD is 1.69-2.0 m2/d at the study site and 0.3 ± 0.04 cm/d for the whole of Tolo Harbor, which is comparable to the river discharge (0.25 ± 0.07 cm/d) and precipitation (0.45 ± 0.15 cm/d). The tide-driven SGD in the intertidal zone is 13.98-17.59 m2/d at the study site and 2.42 ± 0.56 cm/d for the whole of Tolo Harbor. The SGD occurring in the subtidal zone and the bottom of Tolo Harbor is 3.12 ± 4.63 cm/d. Fresh SGD accounts for 5% of the total SGD, while the rest ( 95%) is contributed by saline SGD driven by various forces. About 96% of the tide-driven SGD in the intertidal zone occurs in the ebbing tide period because the head difference between the groundwater level and sea level is great during this period. Tide-driven SGD in the spring tide is 1.2 times that during neap tide. The tidal fluctuation amplitude and tide-driven SGD in the intertidal zone are positively correlated to each other; thus, a spring neap variation of the tide-driven SGD is observed.

Ambient air metallic pollutant study at HAF areas during 2013-2014

NASA Astrophysics Data System (ADS)

Fang, Guor-Cheng; Kuo, Yu-Chen; Zhuang, Yuan-Jie

2015-05-01

This study characterized diurnal variations of the total suspended particulate (TSP) concentrations, dry deposition flux and dry deposition velocity of metallic elements at Taichung Harbor (Harbor), Gong Ming Junior High School (Airport) and Sha lu Farmland (Farmland) sampling sites in central Taiwan between August, 2013 and July, 2014 in this study. The result indicated that: 1) the ambient air particulate concentrations, dry depositions were displayed as Harbor > Farmland > Airport during the day time sampling period. However, dry deposition velocities were shown as Airport > Harbor > Farmland for this study. 2) The ambient air particulate concentrations, dry depositions were displayed as Airport > Harbor > Farmland during the night time sampling period. However, dry deposition velocities were shown as Farmland > Harbor > Airport for this study. 3) The metallic element Zn has the average highest concentrations at Airport, Harbor and Farmland among all the metallic elements during the day time sampling period in this study. 4) There were significant differences for the metallic elements (Cr, Cu, Zn and Pb) in dry depositions at these three characteristic sampling sites (HAF) for the night time sampling period. The only exception is metallic element Cd. It displayed that there were no significant differences for the metallic element Cd at the Airport and Farmland sampling sites during the night time sampling period. 5) The average highest values for the metallic element Cu in TSP among the three characteristic sampling sites occurred during the fall and winter seasons for this study. As for the dry depositions, the average highest values in dry deposition among the three characteristic sampling sites occurred during the spring and summer seasons for this study. 6) The average highest values for the metallic element Cd in TSP among the three characteristic sampling sites occurred during the spring and summer seasons for this study. As for the dry depositions, the average highest values in dry deposition among the three characteristic sampling sites occurred during fall and winter for this study.

Functional Profiling Using the Saccharomyces Genome Deletion Project Collections.

PubMed

Nislow, Corey; Wong, Lai Hong; Lee, Amy Huei-Yi; Giaever, Guri

2016-09-01

The ability to measure and quantify the fitness of an entire organism requires considerably more complex approaches than simply using traditional "omic" methods that examine, for example, the abundance of RNA transcripts, proteins, or metabolites. The yeast deletion collections represent the only systematic, comprehensive set of null alleles for any organism in which such fitness measurements can be assayed. Generated by the Saccharomyces Genome Deletion Project, these collections allow the systematic and parallel analysis of gene functions using any measurable phenotype. The unique 20-bp molecular barcodes engineered into the genome of each deletion strain facilitate the massively parallel analysis of individual fitness. Here, we present functional genomic protocols for use with the yeast deletion collections. We describe how to maintain, propagate, and store the deletion collections and how to perform growth fitness assays on single and parallel screening platforms. Phenotypic fitness analyses of the yeast mutants, described in brief here, provide important insights into biological functions, mechanisms of drug action, and response to environmental stresses. It is important to bear in mind that the specific assays described in this protocol represent some of the many ways in which these collections can be assayed, and in this description particular attention is paid to maximizing throughput using growth as the phenotypic measure. © 2016 Cold Spring Harbor Laboratory Press.

Dissecting and Culturing Animal Cap Explants.

PubMed

Dingwell, Kevin S; Smith, James C

2018-05-16

The animal cap explant is a simple but adaptable tool available to developmental biologists. The use of animal cap explants in demonstrating the presence of mesoderm-inducting activity in the Xenopus embryo vegetal pole is one of many elegant examples of their worth. Animal caps respond to a range of growth factors (e.g., Wnts, FGF, TGF-β), making them especially useful for studying signal transduction pathways and gene regulatory networks. Explants are also suitable for examining cell behavior and have provided key insights into the molecular mechanisms controlling vertebrate morphogenesis. In this protocol, we outline two methods to isolate animal cap explants from Xenopus laevis , both of which can be applied easily to Xenopus tropicalis The first method is a standard manual method that can be used in any laboratory equipped with a standard dissecting microscope. For labs planning on dissecting large numbers of explants on a regular basis, a second, high throughput method is described that uses a specialized microcautery surgical instrument. © 2018 Cold Spring Harbor Laboratory Press.

Northern blots: capillary transfer of RNA from agarose gels and filter hybridization using standard stringency conditions.

PubMed

Rio, Donald C

2015-03-02

In this protocol, an RNA sample, fractionated by gel electrophoresis, is transferred from the gel onto a membrane by capillary transfer. Short-wave UV light is used to fix the transferred RNA to the membrane. The membrane is then pretreated to block nonspecific probe-binding sites, and hybridization of the immobilized RNA to a (32)P-labeled DNA or RNA probe specific for the mRNA of interest is performed. Finally, the membrane is washed and subjected to autoradiography or phosphorimaging. Because exposure to UV cross-links the RNA to the membrane, the membrane can be stripped and hybridized with other probes. The procedure is suitable for detecting poly(A)(+)-selected mRNA or mRNA in total cellular RNA if the target transcript is relatively abundant. Using DNA or RNA probes labeled to 1 × 10(8)-10 × 10(8) cpm/µg, it should be possible to detect ∼5 pg of a specific RNA. © 2015 Cold Spring Harbor Laboratory Press.

Generating an Open Reading Frame (ORF) Entry Clone and Destination Clone.

PubMed

Reece-Hoyes, John S; Walhout, Albertha J M

2018-01-02

This protocol describes using the Gateway recombinatorial cloning system to create an Entry clone carrying an open reading frame (ORF) and then to transfer the ORF into a Destination vector. In this example, BP recombination is used to clone an ORF from a cDNA source into the Donor vector pDONR 221. The ORF from the resulting Entry clone is then transferred into the Destination vector pDEST-15; the product (the Destination clone) will express the ORF as an amino-terminal GST-fusion. The technique can be used as a guide for cloning any other DNA fragment of interest-a promoter sequence or 3' untranslated region (UTR), for example-with substitutions of different genetic material such as genomic DNA, att sites, and vectors as required. The series of constructions and transformations requires 9-15 d, not including time that may be required for sequence confirmation, if desired/necessary. © 2018 Cold Spring Harbor Laboratory Press.

Mouse Sperm Cryopreservation Using Cryoprotectant Containing l-Glutamine.

PubMed

Takeo, Toru; Nakagata, Naomi

2018-06-01

Efforts to advance sperm cryopreservation are ongoing and include modifications in the cryoprotective agents. The addition of l-glutamine maintains post-thaw motility and reduces plasma membrane damage to sperm. © 2018 Cold Spring Harbor Laboratory Press.

Recombinant DNA Paper Model Simulation: The Genetic Engineer.

ERIC Educational Resources Information Center

Wagner, Joan

1998-01-01

Describes a course for talented high school students that focuses on DNA science and technology. Employs Cold Spring Harbor's DNA Science laboratory manual. Engages students in performing sickle-cell anemia and thalassemia tests in rabbits. (DDR)

Isolation of High-Molecular-Weight DNA from Mammalian Tissues Using Proteinase K and Phenol.

PubMed

Green, Michael R; Sambrook, Joseph

2017-03-01

This procedure is the method of choice for purification of genomic DNA from mammalian tissues when large amounts of DNA are required, for example, for Southern blotting. © 2017 Cold Spring Harbor Laboratory Press.

Adapting a rapid assessment protocol to environmentally assess palm swamp (Veredas) springs in the Cerrado biome, Brazil.

PubMed

Guimarães, Ariane; de Lima Rodrigues, Aline Sueli; Malafaia, Guilherme

2017-10-30

The exploitation and degradation of natural environments exert intense pressure on important ecosystems worldwide. Thus, it is necessary developing or adapting assessment methods to monitor environmental changes and to generate results to be applied to environmental management programs. The Brazilian Veredas (phytophysiognomies typical to the Cerrado biome) are threatened by several human activities; thus, the aim of the present study is to adapt a rapid assessment protocol (RAP) to be applied to Veredas springs, by using the upper course of the Vai-e-Vem stream watershed (Ipameri County, Goiás State, Brazil). Therefore, several springs in the study site were visited and 11 of them were considered Veredas springs. After the RAP was adapted, the instrument was validated and used to environmentally assess the springs in order to demonstrate its applicability. The present study has provided an instrument of option to monitor Veredas springs.

Microbial and Chemical Characterization of Underwater Fresh Water Springs in the Dead Sea

PubMed Central

Ionescu, Danny; Siebert, Christian; Polerecky, Lubos; Munwes, Yaniv Y.; Lott, Christian; Häusler, Stefan; Bižić-Ionescu, Mina; Quast, Christian; Peplies, Jörg; Glöckner, Frank Oliver; Ramette, Alban; Rödiger, Tino; Dittmar, Thorsten; Oren, Aharon; Geyer, Stefan; Stärk, Hans-Joachim; Sauter, Martin; Licha, Tobias; Laronne, Jonathan B.; de Beer, Dirk

2012-01-01

Due to its extreme salinity and high Mg concentration the Dead Sea is characterized by a very low density of cells most of which are Archaea. We discovered several underwater fresh to brackish water springs in the Dead Sea harboring dense microbial communities. We provide the first characterization of these communities, discuss their possible origin, hydrochemical environment, energetic resources and the putative biogeochemical pathways they are mediating. Pyrosequencing of the 16S rRNA gene and community fingerprinting methods showed that the spring community originates from the Dead Sea sediments and not from the aquifer. Furthermore, it suggested that there is a dense Archaeal community in the shoreline pore water of the lake. Sequences of bacterial sulfate reducers, nitrifiers iron oxidizers and iron reducers were identified as well. Analysis of white and green biofilms suggested that sulfide oxidation through chemolitotrophy and phototrophy is highly significant. Hyperspectral analysis showed a tight association between abundant green sulfur bacteria and cyanobacteria in the green biofilms. Together, our findings show that the Dead Sea floor harbors diverse microbial communities, part of which is not known from other hypersaline environments. Analysis of the water’s chemistry shows evidence of microbial activity along the path and suggests that the springs supply nitrogen, phosphorus and organic matter to the microbial communities in the Dead Sea. The underwater springs are a newly recognized water source for the Dead Sea. Their input of microorganisms and nutrients needs to be considered in the assessment of possible impact of dilution events of the lake surface waters, such as those that will occur in the future due to the intended establishment of the Red Sea−Dead Sea water conduit. PMID:22679498

The ecology and diversity of microbial eukaryotes in geothermal springs.

PubMed

Oliverio, Angela M; Power, Jean F; Washburne, Alex; Cary, S Craig; Stott, Matthew B; Fierer, Noah

2018-04-16

Decades of research into the Bacteria and Archaea living in geothermal spring ecosystems have yielded great insight into the diversity of life and organismal adaptations to extreme environmental conditions. Surprisingly, while microbial eukaryotes (protists) are also ubiquitous in many environments, their diversity across geothermal springs has mostly been ignored. We used high-throughput sequencing to illuminate the diversity and structure of microbial eukaryotic communities found in 160 geothermal springs with broad ranges in temperature and pH across the Taupō Volcanic Zone in New Zealand. Protistan communities were moderately predictable in composition and varied most strongly across gradients in pH and temperature. Moreover, this variation mirrored patterns observed for bacterial and archaeal communities across the same spring samples, highlighting that there are similar ecological constraints across the tree of life. While extreme pH values were associated with declining protist diversity, high temperature springs harbored substantial amounts of protist diversity. Although protists are often overlooked in geothermal springs and other extreme environments, our results indicate that such environments can host distinct and diverse protistan communities.

Building Whales in Sand and Mind.

ERIC Educational Resources Information Center

Warner, Carolyn

1980-01-01

Describes two-week summer workshops on evolution, adaptation, and behavior of whales, conducted for children by Cold Spring Harbor Whaling Museum (New York), and culminating in creation of life-size sand sculptures of whales. Provides selected list of periodicals, teaching materials, identification guides, records, and societies devoted to whales…

Measuring the steady-state properties of Ca²⁺ indicators with a set of calibrated [Ca²⁺] solutions.

PubMed

Faas, Guido C; Mody, Istvan

2014-07-01

Fluorescent Ca(2+) indicators are widely used to measure the concentration of free Ca(2+) ([Ca(2+)]free) in biological processes. By calibrating the dye under the same experimental conditions as employed during its planned use, the actual [Ca(2+)] can be calculated from the measured fluorescence. When using non ratiometric dyes, such as the Oregon Green BAPTA (OGB) family of dyes or the Fluo dyes, the steady-state affinity (K(d)) and the ratio between the maximal and minimal fluorescence (F(ratio) = F(max)/F(min)) of the particular dye are needed for this conversion. Although these values are usually given by the manufacturer, we consistently find that the actual values can differ between various batches delivered by the companies that make the dyes. In this protocol, we provide the recipe for a series of solutions with a known and tightly buffered [Ca(2+)](free) and describe how to use these mixtures to determine the exact K(d) and F(ratio) of a fluorescent Ca(2+) dye. © 2014 Cold Spring Harbor Laboratory Press.

77 FR 27041 - Combined Notice of Filings # 1

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-08

... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings 1 Take notice...-161-003; ER12-164-002. Applicants: Forward Energy LLC, Sheldon Energy LLC, Invenergy Cannon Falls LLC, Spindle Hill Energy LLC, Spring Canyon Energy LLC, Grays Harbor Energy LLC, Grand Ridge Energy LLC, Willow...

Accurate typing of short tandem repeats from genome-wide sequencing data and its applications.

PubMed

Fungtammasan, Arkarachai; Ananda, Guruprasad; Hile, Suzanne E; Su, Marcia Shu-Wei; Sun, Chen; Harris, Robert; Medvedev, Paul; Eckert, Kristin; Makova, Kateryna D

2015-05-01

Short tandem repeats (STRs) are implicated in dozens of human genetic diseases and contribute significantly to genome variation and instability. Yet profiling STRs from short-read sequencing data is challenging because of their high sequencing error rates. Here, we developed STR-FM, short tandem repeat profiling using flank-based mapping, a computational pipeline that can detect the full spectrum of STR alleles from short-read data, can adapt to emerging read-mapping algorithms, and can be applied to heterogeneous genetic samples (e.g., tumors, viruses, and genomes of organelles). We used STR-FM to study STR error rates and patterns in publicly available human and in-house generated ultradeep plasmid sequencing data sets. We discovered that STRs sequenced with a PCR-free protocol have up to ninefold fewer errors than those sequenced with a PCR-containing protocol. We constructed an error correction model for genotyping STRs that can distinguish heterozygous alleles containing STRs with consecutive repeat numbers. Applying our model and pipeline to Illumina sequencing data with 100-bp reads, we could confidently genotype several disease-related long trinucleotide STRs. Utilizing this pipeline, for the first time we determined the genome-wide STR germline mutation rate from a deeply sequenced human pedigree. Additionally, we built a tool that recommends minimal sequencing depth for accurate STR genotyping, depending on repeat length and sequencing read length. The required read depth increases with STR length and is lower for a PCR-free protocol. This suite of tools addresses the pressing challenges surrounding STR genotyping, and thus is of wide interest to researchers investigating disease-related STRs and STR evolution. © 2015 Fungtammasan et al.; Published by Cold Spring Harbor Laboratory Press.

All Hands Online : Official Magazine of the U.S. Navy

Science.gov Websites

Hands logo Search Departments Advancements and Promotions Around The Fleet Diversity Focus on Service Health and Fitness History and Heritage Pay and Benefits Talking with Sailors Training and Education , mid-spring afternoon in Port Hueneme, California, at the Navy Safe Harbor Wounded Warrior Training

How Partners are Producing Science and Addressing Issues of Scale for Springs Management in the Desert Southwest

NASA Astrophysics Data System (ADS)

Johnson, G.; Springer, A. E.; Misztal, L.; Grabau, M.

2017-12-01

Climate changes in the arid Southwest are expected to further stress critical water sources, such as springs, in the near future. Springs are abundant features in the Southwest, providing habitat for listed species and water for wildlife, agricultural, cities, recreation, and the base flow for many rivers. But springs occupy a small fraction of the land area and, as a result, they have not been significantly studied or mapped. Managers recognize that effective stewardship of these critical resources requires a landscape-scale understanding of distribution, ecological integrity, and risks; access to comprehensive inventory, assessment and restoration protocols; and local implementation. They need easy access to information at varying scales to respond to stressors like climate change. The Desert Landscape Conservation Cooperative, Sky Island Alliance, and Springs Stewardship Institute worked with scientists, resource managers, and conservationists to develop and increase access to data by involving them in the entire research process through field surveys, workshops, trainings, and development of products needed to solve critical management challenges. We built on and connected existing efforts underway in the Southwest, including developing: 1) Springs Inventory Protocol, 2) an online geospatial database, 3) methodologies for climate-savvy monitoring and 4) a springs restoration handbook. We also worked with partners to evaluate the condition and risk of springs' resources at the local scale to create products used in site-specific management planning. Our results indicate that coproduction resulted in more understanding of common issues, more focus on solving management challenges, and increased use of the science and protocols produced. Information developed through this project assists managers in understanding how their springs contribute at local and landscape scales. New information developed through this project is being used in support of planning and decisions that address resource protection at the regional level and in climate change adaptation planning for natural resources. This work highlights the need to increase collaboration and coproduction of information tailored for management issues at different spatial and temporal scales.

NIH Courts Younger Researchers, Even as It Debates How Far to Go

ERIC Educational Resources Information Center

Basken, Paul

2012-01-01

On the surface, a gathering held for young research faculty last week at Cold Spring Harbor Laboratory was a clear expression of determination by the National Institutes of Health (NIH) to help them compete for grants. The agency fears that continued Congressional budget cuts, combined with the growing number of scientists who work later into…

Web-Based Analysis for Student-Generated Complex Genetic Profiles

ERIC Educational Resources Information Center

Kass, David H.; LaRoe, Robert

2007-01-01

A simple, rapid method for generating complex genetic profiles using Alu-based markers was recently developed for students primarily at the undergraduate level to learn more about forensics and paternity analysis. On the basis of the Cold Spring Harbor Allele Server, which provides an excellent tool for analyzing a single Alu variant, we present a…

An Innovative Plant Genomics and Gene Annotation Program for High School, Community College, and University Faculty

ERIC Educational Resources Information Center

Hacisalihoglu, Gokhan; Hilgert, Uwe; Nash, E. Bruce; Micklos, David A.

2008-01-01

Today's biology educators face the challenge of training their students in modern molecular biology techniques including genomics and bioinformatics. The Dolan DNA Learning Center (DNALC) of Cold Spring Harbor Laboratory has developed and disseminated a bench- and computer-based plant genomics curriculum for biology faculty. In 2007, a five-day…

Differentiating Mouse Embryonic Stem Cells into Embryoid Bodies by Hanging-Drop Cultures.

PubMed

Behringer, Richard; Gertsenstein, Marina; Nagy, Kristina Vintersten; Nagy, Andras

2016-12-01

Embryonic stem (ES) cells can develop into many types of differentiated tissues if they are placed into a differentiating environment. This can occur in vivo when the ES cells are injected into or aggregated with an embryo, or in vitro if their culture conditions are modified to induce differentiation. There are an increasing number of differentiating culture conditions that can bias the differentiation of ES cells into desired cell types. Determining the mechanisms that control ES cell differentiation into therapeutically important cell types is a quickly growing area of research. Knowledge gained from these studies may eventually lead to the use of stem cells to repair specific damaged tissues. Many times ES cell differentiation proceeds through an intermediate stage called the embryoid body (EB). EBs are round structures composed of ES cells that have undergone some of the initial stages of differentiation. EBs can then be manipulated further to generate more specific cell types. This protocol describes a method to differentiate ES cells into EBs. It produces EBs of comparable size. This aspect is important because the differentiation processes taking place inside an EB are influenced by its size. © 2016 Cold Spring Harbor Laboratory Press.

Assessment of general health of fishes collected at selected sites in the Great Lakes Basin In 2012

USGS Publications Warehouse

Mazik, Patricia M.; Braham, Ryan P.; Hahn, Cassidy M.; Blazer, Vicki

2015-01-01

The U. S. Fish and Wildlife Service received funding through the Great Lakes Restoration Initiative (GLRI) for an Early Warning Program to detect and identify emerging contaminants and to evaluate the effects of these contaminants on fish and wildlife. The U.S. Geological Survey (WV Cooperative Fish and Wildlife Research Unit and National Fish Health Research Laboratory, Leetown Science Center) developed and implemented a biological effects monitoring protocol to assist in this program. Fish collections and measurements of biomarkers of exposure in Fall 2010 and Spring 2011 occurred at individual sites within select Areas of Concern (AOCs). They provided an assessment of the utility of the suite of biomarkers and also identified sites for more in-depth analyses. Selected areas are characterized as areas with known emerging contaminants, sensitive or listed species, areas downstream from municipal wastewater discharges or receiving waters for industrial facilities, and/or areas susceptible to agricultural or urban contamination, or harbors or ports. The results of the 2010- 2011 studies were summarized in Blazer et al. 2014 a, b, c; Braham et al. in review and Blazer et al. in review.

ChIP-chip.

PubMed

Kim, Tae Hoon; Dekker, Job

2018-05-01

ChIP-chip can be used to analyze protein-DNA interactions in a region-wide and genome-wide manner. DNA microarrays contain PCR products or oligonucleotide probes that are designed to represent genomic sequences. Identification of genomic sites that interact with a specific protein is based on competitive hybridization of the ChIP-enriched DNA and the input DNA to DNA microarrays. The ChIP-chip protocol can be divided into two main sections: Amplification of ChIP DNA and hybridization of ChIP DNA to arrays. A large amount of DNA is required to hybridize to DNA arrays, and hybridization to a set of multiple commercial arrays that represent the entire human genome requires two rounds of PCR amplifications. The relative hybridization intensity of ChIP DNA and that of the input DNA is used to determine whether the probe sequence is a potential site of protein-DNA interaction. Resolution of actual genomic sites bound by the protein is dependent on the size of the chromatin and on the genomic distance between the probes on the array. As with expression profiling using gene chips, ChIP-chip experiments require multiple replicates for reliable statistical measure of protein-DNA interactions. © 2018 Cold Spring Harbor Laboratory Press.

Identification of Chemical-Genetic Interactions via Parallel Analysis of Barcoded Yeast Strains.

PubMed

Suresh, Sundari; Schlecht, Ulrich; Xu, Weihong; Miranda, Molly; Davis, Ronald W; Nislow, Corey; Giaever, Guri; St Onge, Robert P

2016-09-01

The Yeast Knockout Collection is a complete set of gene deletion strains for the budding yeast, Saccharomyces cerevisiae In each strain, one of approximately 6000 open-reading frames is replaced with a dominant selectable marker flanked by two DNA barcodes. These barcodes, which are unique to each gene, allow the growth of thousands of strains to be individually measured from a single pooled culture. The collection, and other resources that followed, has ushered in a new era in chemical biology, enabling unbiased and systematic identification of chemical-genetic interactions (CGIs) with remarkable ease. CGIs link bioactive compounds to biological processes, and hence can reveal the mechanism of action of growth-inhibitory compounds in vivo, including those of antifungal, antibiotic, and anticancer drugs. The chemogenomic profiling method described here measures the sensitivity induced in yeast heterozygous and homozygous deletion strains in the presence of a chemical inhibitor of growth (termed haploinsufficiency profiling and homozygous profiling, respectively, or HIPHOP). The protocol is both scalable and amenable to automation. After competitive growth of yeast knockout collection cultures, with and without chemical inhibitors, CGIs can be identified and quantified using either array- or sequencing-based approaches as described here. © 2016 Cold Spring Harbor Laboratory Press.

PCoD Lite - Using an Interim PCoD Protocol to Assess the Effects of Disturbance Associated with US Navy Exercises on Marine Mammal Populations

DTIC Science & Technology

2014-09-30

1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. PCoD Lite - Using an Interim PCoD Protocol to Assess...Skookum Tom Road Friday Harbor, WA, USA phone: 1-360-370-5493 email: jw@smrullc.com Award Number: N000141410406 http://www.smrumarine.com/ pcod ...DATE 30 SEP 2014 2. REPORT TYPE 3. DATES COVERED 00-00-2014 to 00-00-2014 4. TITLE AND SUBTITLE PCoD Lite - Using an Interim PCoD Protocol to

Washington, D.C.'s vanishing springs and waterways

USGS Publications Warehouse

Williams, Garnett P.

1977-01-01

This paper traces the disappearance or reduction of the many prominent springs and waterways that existed in Washington, D.C. , 200 years ago. The best known springs were the Smith Springs (now under the McMillan Reservoir), the Franklin Park Springs (13th and I Streets, NW.), Gibson 's Spring (15th and E Streets, NE.), Caffrey 's Spring (Ninth and F Streets, NW.), and the City Spring (C Street between Four and One-Half and Sixth Streets, NW.). Tiber Creek, flowing south to the Capitol and thence westward along Consititution Avenue, joined the Potomac River at 17th Street and Constitution Avenue. In the 1800's, the Constitution Avenue reach was made into a canal which was used by scows and steamboats up to about 1850. The canal was changed into a covered sewer in the 1870's, and the only remaining visible surface remnant is the lock-keeper 's little stone house at 17th and Constitution Avenue, NW. Because of sedimentation problems and reclamation projects, Rock Creek, the Potomac River , and the Anacostia River are considerably narrower and shallower today than they were in colonial times. For example, the mouth of Rock Creek at one time was a wide, busy ship harbor , which Georgetown used for an extensive foreign trade, and the Potomac River shore originally extended to 17th and Constitution Avenue, NW. (Woodard-USGS)

Alzheimer's Disease and Related Disorders: The Government's Response. Hearing before the Select Committee on Aging. House of Representatives, Ninety-Ninth Congress, Second Session (Cold Spring Harbor, NY).

ERIC Educational Resources Information Center

Congress of the U.S., Washington, DC. House Select Committee on Aging.

This document presents witness testimonies and prepared statements from the Congressional hearing called to examine questions surrounding Alzheimer's disease, its treatment, funding for research, legal aspects, and support for families of Alzheimer's victims. Opening statements are included from Congressmen Downey, Mrazek, and Manton. Testimonies…

Data files from the Grays Harbor Sediment Transport Experiment Spring 2001

USGS Publications Warehouse

Landerman, Laura A.; Sherwood, Christopher R.; Gelfenbaum, Guy; Lacy, Jessica; Ruggiero, Peter; Wilson, Douglas; Chisholm, Tom; Kurrus, Keith

2005-01-01

This publication consists of two DVD-ROMs, both of which are presented here. This report describes data collected during the Spring 2001 Grays Harbor Sediment Transport Experiment, and provides additional information needed to interpret the data. Two DVDs accompany this report; both contain documentation in html format that assist the user in navigating through the data. DVD-ROM-1 contains a digital version of this report in .pdf format, raw Aquatec acoustic backscatter (ABS) data in .zip format, Sonar data files in .avi format, and coastal processes and morphology data in ASCII format. ASCII data files are provided in .zip format; bundled coastal processes ASCII files are separated by deployment and instrument; bundled morphology ASCII files are separated into monthly data collection efforts containing the beach profiles collected (or extracted from the surface map) at that time; weekly surface maps are also bundled together. DVD-ROM-2 contains a digital version of this report in .pdf format, the binary data files collected by the SonTek instrumentation, calibration files for the pressure sensors, and Matlab m-files for loading the ABS data into Matlab and cleaning-up the optical backscatter (OBS) burst time-series data.

Spring Meeting sail-in

NASA Astrophysics Data System (ADS)

Hanshaw, Bruce B.

In May 1986, Ian MacGregor and I sailed into Baltimore's Inner Harbor to live aboard my boat while we attended the AGU Spring Meeting. During our stay at the Marina, which is only 400-500 m from the Convention Center, we ran into AGU members from several other boats. From these chance encounters an idea was born: Why not have a more coordinated sail-in for the meeting in 1987!! I have offered to act as the commodore/coordinator for this informal event. I'm willing to keep track of the boats that wish dock space and make arrangements with the marina so that boats associated with the sail-in will be together on one “finger” pier.

Origins of DNA Replication and Amplification in the Breast Cancer Genome

DTIC Science & Technology

2011-09-01

AD_________________ Award Number: W81XWH-10-1-0463 TITLE: Origins of DNA Replication and...hypothesis we need to map origins of DNA replication in the genome and ask which of these coincide with sites of DNA amplification and with ER...Spring Harbor DNA Replication meetings this summer/earlyfall. Figures from the posters and also the abstracts are attached. The samples have been

'Big bang' of B-cell development revealed.

PubMed

Murre, Cornelis

2018-01-15

Earlier studies have identified transcription factors that specify B-cell fate, but the underlying mechanisms remain to be revealed. Two new studies by Miyai and colleagues (pp. 112-126) and Li and colleagues (pp. 96-111) in this issue of Genes & Development provide new and unprecedented insights into the genetic and epigenetic mechanisms that establish B-cell identity. © 2018 Murre; Published by Cold Spring Harbor Laboratory Press.

Subcellular evidences of redox imbalance in well-established populations of an endangered limpet. Reasons for alarm?

PubMed

Espinosa, Free; Rivera-Ingraham, Georgina A

2016-08-15

Intertidal species are more vulnerable to anthropogenic disturbances than others inhabiting subtidal and offshore habitats. Coastal development frequently results in trace-metal pollution. For endangered species such as Patella ferruginea it can be a high risk that leads local populations to extinction. Three localities were surveyed, one within a natural and unpolluted area and the other two within the harbor of Ceuta (Strait of Gibraltar), on breakwaters outside and inside. The specimens collected inside the harbor reached 3-fold higher Hg content than for those incoming from the natural area. PERMANOVA test indicated that metal composition of the specimens from inside the harbor was different from the rest. In addition, evidence of cell damage was detected in the specimens from the harbor area. This highlights the urgency of undertaking a physiological evaluation of some of the most vulnerable populations, establishing eco-physiological protocols for monitoring and managing populations settled on artificial substrata. Copyright © 2016 Elsevier Ltd. All rights reserved.

PHYTOREMEDIATING DREDGED SEDIMENTS: A BENEFICIAL REUSE PROTOCOL

EPA Science Inventory

The Jones Island Confined Disposal Facility (CDF) located in Milwaukee Harbor Wisconsin, receives dredged materials from normal maintenance of Milwaukee's waterways. Like many CDFs they face the dilemma of steady inputs and no feasible alternative for expansion. The Army Corps of...

Agrobacterium-mediated transformation of Fraxinus pennsylvanica hypocotyls and plant regeneration

Treesearch

Ningxia Du; Paula M. Pijut

2009-01-01

A genetic transformation protocol for green ash (Fraxinus pennsylvanica) hypocotyl explants was developed. Green ash hypocotyls were transformed using Agrobacterium tumefaciens strain EHA105 harboring binary vector pq35GR containing the neomycin phosphotransferase (nptII) and β-glucuronidase (GUS) fusion...

The Protein Data Bank at 40: Reflecting on the Past to Prepare for the Future

PubMed Central

Berman, Helen M.; Kleywegt, Gerard J.; Nakamura, Haruki; Markley, John L.

2012-01-01

A symposium celebrating the 40th anniversary of the Protein Data Bank archive (PDB), organized by the Worldwide Protein Data Bank, was held at Cold Spring Harbor Laboratory (CSHL) October 28–30, 2011. PDB40’s distinguished speakers highlighted four decades of innovation in structural biology, from the early era of structural determination to future directions for the field. PMID:22404998

Isolation of High-Molecular-Weight DNA from Monolayer Cultures of Mammalian Cells Using Proteinase K and Phenol.

PubMed

Green, Michael R; Sambrook, Joseph

2017-07-05

This procedure is the method of choice for purification of mammalian genomic DNA from monolayer cultures when large amounts of DNA are required, for example, for Southern blotting. Approximately 200 µg of mammalian DNA, 100-150 kb in length, is obtained from 5 × 10 7 cultured aneuploid cells (e.g., HeLa cells). © 2017 Cold Spring Harbor Laboratory Press.

Nutrition Frontiers - Spring 2018 | Division of Cancer Prevention

Cancer.gov

Dear Colleague, The spring issue of Nutrition Frontiers showcases the association of gut microbial communities in premenopausal women, how high-fat, high-calorie-diet-induced obesity may increase pancreatic cancer, and the effects of calorie restriction protocols on pro-inflammatory cytokines. Meet our spotlight investigator, Dr. Purnima Kumar, and her research on black

Human heredity and politics: A comparative institutional study of the Eugenics Record Office at Cold Spring Harbor (United States), the Kaiser Wilhelm Institute for Anthropology, Human Heredity, and Eugenics (Germany), and the Maxim Gorky Medical Genetics Institute (USSR).

PubMed

Adams, Mark B; Allen, Garland E; Weiss, Sheila Faith

2005-01-01

Despite the fact that much has been written in recent years about the science of heredity under the Third Reich, there is as yet no satisfying analysis of two central questions: What, if anything, was peculiarly "Nazi" about human genetics under National Socialism? How, under whatever set of causes, did at least some of Germany's most well-known and leading biomedical practioners become engaged in entgrenzte Wissenschaft (science without moral boundaries)? This paper attempts to provide some answers to these two questions comparing three institutes that studied eugenics and human heredity in the 1920s and 1930s: the Eugenics Record Office at Cold Spring Harbor, New York, directed by Charles B. Davenport; the Kaiser Wilhelm Institute for Anthropology, Human Heredity and Eugenics, in Berlin, directed by Eugen Fischer; and the Maxim Gorky Medical Genetics Institute in Moscow, directed by Solomon G. Levit. The institutes are compared on the basis of the kind and quality of their research in eugenics and medical genetics, organizational structure, leadership, patronage (private or state), and the economic-social-political context in which they functioned.

Adenylylation of small RNA sequencing adapters using the TS2126 RNA ligase I.

PubMed

Lama, Lodoe; Ryan, Kevin

2016-01-01

Many high-throughput small RNA next-generation sequencing protocols use 5' preadenylylated DNA oligonucleotide adapters during cDNA library preparation. Preadenylylation of the DNA adapter's 5' end frees from ATP-dependence the ligation of the adapter to RNA collections, thereby avoiding ATP-dependent side reactions. However, preadenylylation of the DNA adapters can be costly and difficult. The currently available method for chemical adenylylation of DNA adapters is inefficient and uses techniques not typically practiced in laboratories profiling cellular RNA expression. An alternative enzymatic method using a commercial RNA ligase was recently introduced, but this enzyme works best as a stoichiometric adenylylating reagent rather than a catalyst and can therefore prove costly when several variant adapters are needed or during scale-up or high-throughput adenylylation procedures. Here, we describe a simple, scalable, and highly efficient method for the 5' adenylylation of DNA oligonucleotides using the thermostable RNA ligase 1 from bacteriophage TS2126. Adapters with 3' blocking groups are adenylylated at >95% yield at catalytic enzyme-to-adapter ratios and need not be gel purified before ligation to RNA acceptors. Experimental conditions are also reported that enable DNA adapters with free 3' ends to be 5' adenylylated at >90% efficiency. © 2015 Lama and Ryan; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Cloning Mice.

PubMed

Ogura, Atsuo

2017-08-01

Viable and fertile mice can be generated by somatic nuclear transfer into enucleated oocytes, presumably because the transplanted somatic cell genome becomes reprogrammed by factors in the oocyte. The first somatic cloned offspring of mice were obtained by directly injecting donor nuclei into recipient enucleated oocytes. When this method is used (the so-called Honolulu method of somatic cell nuclear transfer [SCNT]), the donor nuclei readily and completely condense within the enucleated metaphase II-arrested oocytes, which contain high levels of M-phase-promoting factor (MPF). It is believed that the condensation of the donor chromosomes promotes complete reprogramming of the donor genome within the mouse oocytes. Another key to the success of mouse cloning is the use of blunt micropipettes attached to a piezo impact-driving micromanipulation device. This system saves a significant amount of time during the micromanipulation of oocytes and thus minimizes the loss of oocyte viability in vitro. For example, a group of 20 oocytes can be enucleated within 10 min by an experienced operator. This protocol is composed of seven parts: (1) preparing micropipettes, (2) setting up the enucleation and injection micropipettes, (3) collecting and enucleating oocytes, (4) preparing nucleus donor cells, (5) injecting donor nuclei, (6) activating embryos and culturing, and (7) transferring cloned embryos. © 2017 Cold Spring Harbor Laboratory Press.

Preparation of the Nuclear Matrix for Parallel Microscopy and Biochemical Analyses.

PubMed

Wilson, Rosemary H C; Hesketh, Emma L; Coverley, Dawn

2016-01-04

Immobilized proteins within the nucleus are usually identified by treating cells with detergent. The detergent-resistant fraction is often assumed to be chromatin and is described as such in many studies. However, this fraction consists of both chromatin-bound and nuclear-matrix-bound proteins. To investigate nuclear-matrix-bound proteins alone, further separation of these fractions is required; the DNA must be removed so that the remaining proteins can be compared with those from untreated cells. This protocol uses a nonionic detergent (Triton X-100) to remove membranes and soluble proteins from cells under physiologically relevant salt concentrations, followed by extraction with 0.5 m NaCl, digestion with DNase I, and removal of fragmented DNA. It uses a specialized buffer (cytoskeletal buffer) to stabilize the cytoskeleton and nuclear matrix in relatively gentle conditions. Nuclear matrix proteins can then be assessed by either immunofluorescence (IF) and immunoblotting (IB). IB has the advantage of resolving different forms of a protein of interest, and the soluble fractions can be analyzed. The major advantage of IF analysis is that individual cells (rather than homogenized populations) can be monitored, and the spatial arrangement of proteins bound to residual nuclear structures can be revealed. © 2016 Cold Spring Harbor Laboratory Press.

Metatranscriptomic analysis of a high-sulfide aquatic spring reveals insights into sulfur cycling and unexpected aerobic metabolism.

PubMed

Spain, Anne M; Elshahed, Mostafa S; Najar, Fares Z; Krumholz, Lee R

2015-01-01

Zodletone spring is a sulfide-rich spring in southwestern Oklahoma characterized by shallow, microoxic, light-exposed spring water overlaying anoxic sediments. Previously, culture-independent 16S rRNA gene based diversity surveys have revealed that Zodletone spring source sediments harbor a highly diverse microbial community, with multiple lineages putatively involved in various sulfur-cycling processes. Here, we conducted a metatranscriptomic survey of microbial populations in Zodletone spring source sediments to characterize the relative prevalence and importance of putative phototrophic, chemolithotrophic, and heterotrophic microorganisms in the sulfur cycle, the identity of lineages actively involved in various sulfur cycling processes, and the interaction between sulfur cycling and other geochemical processes at the spring source. Sediment samples at the spring's source were taken at three different times within a 24-h period for geochemical analyses and RNA sequencing. In depth mining of datasets for sulfur cycling transcripts revealed major sulfur cycling pathways and taxa involved, including an unexpected potential role of Actinobacteria in sulfide oxidation and thiosulfate transformation. Surprisingly, transcripts coding for the cyanobacterial Photosystem II D1 protein, methane monooxygenase, and terminal cytochrome oxidases were encountered, indicating that genes for oxygen production and aerobic modes of metabolism are actively being transcribed, despite below-detectable levels (<1 µM) of oxygen in source sediment. Results highlight transcripts involved in sulfur, methane, and oxygen cycles, propose that oxygenic photosynthesis could support aerobic methane and sulfide oxidation in anoxic sediments exposed to sunlight, and provide a viewpoint of microbial metabolic lifestyles under conditions similar to those seen during late Archaean and Proterozoic eons.

EPIGEN-Brazil Initiative resources: a Latin American imputation panel and the Scientific Workflow.

PubMed

Magalhães, Wagner C S; Araujo, Nathalia M; Leal, Thiago P; Araujo, Gilderlanio S; Viriato, Paula J S; Kehdy, Fernanda S; Costa, Gustavo N; Barreto, Mauricio L; Horta, Bernardo L; Lima-Costa, Maria Fernanda; Pereira, Alexandre C; Tarazona-Santos, Eduardo; Rodrigues, Maíra R

2018-06-14

EPIGEN-Brazil is one of the largest Latin American initiatives at the interface of human genomics, public health, and computational biology. Here, we present two resources to address two challenges to the global dissemination of precision medicine and the development of the bioinformatics know-how to support it. To address the underrepresentation of non-European individuals in human genome diversity studies, we present the EPIGEN-5M+1KGP imputation panel-the fusion of the public 1000 Genomes Project (1KGP) Phase 3 imputation panel with haplotypes derived from the EPIGEN-5M data set (a product of the genotyping of 4.3 million SNPs in 265 admixed individuals from the EPIGEN-Brazil Initiative). When we imputed a target SNPs data set (6487 admixed individuals genotyped for 2.2 million SNPs from the EPIGEN-Brazil project) with the EPIGEN-5M+1KGP panel, we gained 140,452 more SNPs in total than when using the 1KGP Phase 3 panel alone and 788,873 additional high confidence SNPs ( info score ≥ 0.8). Thus, the major effect of the inclusion of the EPIGEN-5M data set in this new imputation panel is not only to gain more SNPs but also to improve the quality of imputation. To address the lack of transparency and reproducibility of bioinformatics protocols, we present a conceptual Scientific Workflow in the form of a website that models the scientific process (by including publications, flowcharts, masterscripts, documents, and bioinformatics protocols), making it accessible and interactive. Its applicability is shown in the context of the development of our EPIGEN-5M+1KGP imputation panel. The Scientific Workflow also serves as a repository of bioinformatics resources. © 2018 Magalhães et al.; Published by Cold Spring Harbor Laboratory Press.

Development of a Design Protocol : Sustainable Stabilization of Slope Using Recycled Plastic Pin in Mississippi

DOT National Transportation Integrated Search

2017-10-14

The maritime and multimodal system is an integral part of the efficient movement of the nations freight, which includes around 25,000 miles of commercially navigable harbors, channels, and waterways; 4 million miles of public highways and roads; a...

Agrobacterium-medicated transformation of mature Prunus serotina (black cherry) and regeneration of trangenic shoots

Treesearch

Xiaomei Liu; Paula Pijut

2010-01-01

A protocol for Agrobacterium-mediated transformation was developed for in vitro leaf explants of an elite, mature Prunus serotina tree. Agrobacterium tumefaciens strain EHA105 harboring an RNAi plasmid with the black cherry AGAMOUS (AG) gene was used. Bacteria were induced...

Biogeographic patterns of desert springs in the Great Basin with an emphasis on regional aquifer thermal springs as refugia for vulnerable crenobiotic species

NASA Astrophysics Data System (ADS)

Forrest, M.; Sada, D. W.; Norris, R. D.

2013-12-01

The desert springs of the Great Basin Region in western North America provide ideal systems to study biogeographic and evolutionary patterns. In arid regions, springs are biodiversity hotspots because they often provide the sole source of water for the biota within and around them. In the Great Basin, springs provide critical habitat for diverse and extensive crenobiotic flora and fauna comprising over 125 endemic species. These aquatic environments represent island ecosystems surrounded by seas of desert, and researchers have compiled large databases of their biota and chemistry. Consequently, desert springs are excellent systems for biogeographic studies and multivariate statistical analyses of relationships between the chemical and physical characteristics of the springs and the biological communities that they support. The purpose of this study is to elucidate the relationships between the physicochemical characteristics of springs and their biota using multivariate statistical analyses to characterize 1325 springs, including regional aquifer springs, local aquifer cold springs and geothermal springs. The analyses reveal that regional aquifer thermal springs harbor disproportionate numbers of crenobiotic species including endemic gastropods, fishes, and aquatic insects. However, these regional aquifer springs also contain significantly more introduced species than cold and geothermal local aquifer springs. Springs are threatened by anthropogenic impacts including groundwater depletion and pollution, alteration of flow regimes, and the introduction of exotic species. In this study, one of the major factors that distinguished regional aquifer thermal springs from cold and geothermal local aquifer springs was the higher number of introduced species found in regional aquifer springs. This may be due to the influences of the same physicochemical characteristics that allow regional aquifer springs to serve as refugia for endemic species--species that are able to gain access to these environments and cope with their extreme physicochemical characteristics may be provided with refuge from extinction. The disproportionate number of endemic crenobiotic species found in regional aquifer thermal springs, as well as in some local aquifer geothermal springs, within the Great Basin strongly suggests that these hydrothermal habitats represent important biodiversity hotspots, and efforts to conserve and restore these unique ecosystems should be a major priority to ensure that the valuable information that these species can provide is not lost forever.

Influence of the Tumor Microenvironment on Genomic Changes Conferring Chemoresistance in Breast Cancer

DTIC Science & Technology

2013-04-01

tumor microenvironment on clonal selection using intravital microscopy Jae-Hyun Park 1 , Miriam R. Fein 1 , Mikala Egeblad 1 1 Cold Spring Harbor...used surgically implanted mammary imaging windows in immunocompetent mice and injected “brainbow” expressing, syngeneic 4T1 breast carcinoma cells...under the windows. This allowed us to acquire multiple time- lapse imaging series by spinning disk confocal microscopy of the same tumor, done about 3

Seroprevalence of Antibodies against Seal Influenza A(H10N7) Virus in Harbor Seals and Gray Seals from the Netherlands.

PubMed

Bodewes, Rogier; Rubio García, Ana; Brasseur, Sophie M; Sanchez Conteras, Guillermo J; van de Bildt, Marco W G; Koopmans, Marion P G; Osterhaus, Albert D M E; Kuiken, Thijs

2015-01-01

In the spring and summer 2014, an outbreak of seal influenza A(H10N7) virus infection occurred among harbor seals (Phoca vitulina) off the coasts of Sweden and Denmark. This virus subsequently spread to harbor seals off the coasts of Germany and the Netherlands. While thousands of seals were reported dead in Sweden, Denmark and Germany, only a limited number of seals were found dead in the Netherlands. To determine the extent of exposure of seals in the Netherlands to influenza A/H10N7 virus, we measured specific antibody titers in serum samples from live-captured seals and seals admitted for rehabilitation in the Netherlands by use of a hemagglutination inhibition assay and an ELISA. In harbor seals in 2015, antibodies against seal influenza A(H10N7) virus were detected in 41% (32 out of 78) pups, 10% (5 out of 52) weaners, and 58% (7 out of 12) subadults or adults. In gray seals (Halichoerus grypus) in 2015, specific antibodies were not found in the pups (n = 26), but in 26% (5 out of 19) of the older animals. These findings indicate that, despite apparent low mortality, infection with seal influenza A(H10N7) virus was geographically widespread and also occurred in grey seals.

Finger millet [Eleusine coracana (L.) Gaertn].

PubMed

Ceasar, Stanislaus Antony; Ignacimuthu, Savarimuthu

2015-01-01

Millets are the primary food source for millions of people in tropical regions of the world supplying mineral nutrition and protein. In this chapter, we describe an optimized protocol for the Agrobacterium-mediated transformation of finger millet variety GPU 45. Agrobacterium strain LBA4404 harboring plasmid pCAMBIA1301 which contains hygromycin phosphotransferase (hph) as selectable marker gene and β-glucuronidase (GUS) as reporter gene has been used. This protocol utilizes the shoot apex explants for the somatic embryogenesis and regeneration of finger millet after the transformation by Agrobacterium. Desiccation of explants during cocultivation helps for the better recovery of transgenic plants. This protocol is very useful for the efficient production of transgenic plants in finger millet through Agrobacterium-mediated transformation.

Metatranscriptomic analysis of a high-sulfide aquatic spring reveals insights into sulfur cycling and unexpected aerobic metabolism

PubMed Central

Elshahed, Mostafa S.; Najar, Fares Z.; Krumholz, Lee R.

2015-01-01

Zodletone spring is a sulfide-rich spring in southwestern Oklahoma characterized by shallow, microoxic, light-exposed spring water overlaying anoxic sediments. Previously, culture-independent 16S rRNA gene based diversity surveys have revealed that Zodletone spring source sediments harbor a highly diverse microbial community, with multiple lineages putatively involved in various sulfur-cycling processes. Here, we conducted a metatranscriptomic survey of microbial populations in Zodletone spring source sediments to characterize the relative prevalence and importance of putative phototrophic, chemolithotrophic, and heterotrophic microorganisms in the sulfur cycle, the identity of lineages actively involved in various sulfur cycling processes, and the interaction between sulfur cycling and other geochemical processes at the spring source. Sediment samples at the spring’s source were taken at three different times within a 24-h period for geochemical analyses and RNA sequencing. In depth mining of datasets for sulfur cycling transcripts revealed major sulfur cycling pathways and taxa involved, including an unexpected potential role of Actinobacteria in sulfide oxidation and thiosulfate transformation. Surprisingly, transcripts coding for the cyanobacterial Photosystem II D1 protein, methane monooxygenase, and terminal cytochrome oxidases were encountered, indicating that genes for oxygen production and aerobic modes of metabolism are actively being transcribed, despite below-detectable levels (<1 µM) of oxygen in source sediment. Results highlight transcripts involved in sulfur, methane, and oxygen cycles, propose that oxygenic photosynthesis could support aerobic methane and sulfide oxidation in anoxic sediments exposed to sunlight, and provide a viewpoint of microbial metabolic lifestyles under conditions similar to those seen during late Archaean and Proterozoic eons. PMID:26417542

Fidelity of DNA Replication in Normal and Malignant Human Breast Cells.

DTIC Science & Technology

1997-08-01

enzyme) into the multiple cloning site (MCS). This template will not only replicate inside a mammalian cell (utilizing the E-B virus origin), and...Maniatis, T. Commonly used techniques in molecular cloning . In: Molecular cloning : REFERENCES a laboratory manual, 2nd edition. Cold Spring Harbor...A vatit"Y Of DNA synthesis and the typt of DNA replica~tion Products " celular prca including DNA rsplicatlon. DNA repsair. R~NA formed in experiments

Introduction to Chronobiology.

PubMed

Kuhlman, Sandra J; Craig, L Michon; Duffy, Jeanne F

2017-10-16

A diverse range of species, from cyanobacteria to humans, evolved endogenous biological clocks that allow for the anticipation of daily variations in light and temperature. The ability to anticipate regular environmental rhythms promotes optimal performance and survival. Herein we present a brief historical timeline of how circadian concepts and terminology have emerged since the early observation of daily leaf movement in plants made by an astronomer in the 1700s. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

Moving beyond Bermuda: sharing data to build a medical information commons.

PubMed

Cook-Deegan, Robert; McGuire, Amy L

2017-06-01

The ubiquity of DNA sequencing and the advent of medical imaging, electronic health records, and "omics" technologies have produced a deluge of data. Making meaning of those data-creating scientific knowledge and useful clinical information-will vastly exceed the capacity of even the largest institutions. Data must be shared to achieve the promises of genomic science and precision medicine. © 2017 Cook-Deegan and McGuire; Published by Cold Spring Harbor Laboratory Press.

Identification and Manipulation of Memory Engram Cells.

PubMed

Liu, Xu; Ramirez, Steve; Redondo, Roger L; Tonegawa, Susumu

2014-01-01

How memories are formed and stored in the brain remains a fascinating question in neuroscience. Here we discuss the memory engram theory, our recent attempt to identify and manipulate memory engram cells in the brain with optogenetics, and how these methods are used to address questions such as how false memory is formed and how the valence of a memory can be changed in the brain. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

Microbial community analysis of a coastal hot spring in Kagoshima, Japan, using molecular- and culture-based approaches.

PubMed

Nishiyama, Minako; Yamamoto, Shuichi; Kurosawa, Norio

2013-08-01

Ibusuki hot spring is located on the coastline of Kagoshima Bay, Japan. The hot spring water is characterized by high salinity, high temperature, and neutral pH. The hot spring is covered by the sea during high tide, which leads to severe fluctuations in several environmental variables. A combination of molecular- and culture-based techniques was used to determine the bacterial and archaeal diversity of the hot spring. A total of 48 thermophilic bacterial strains were isolated from two sites (Site 1: 55.6°C; Site 2: 83.1°C) and they were categorized into six groups based on their 16S rRNA gene sequence similarity. Two groups (including 32 isolates) demonstrated low sequence similarity with published species, suggesting that they might represent novel taxa. The 148 clones from the Site 1 bacterial library included 76 operational taxonomy units (OTUs; 97% threshold), while 132 clones from the Site 2 bacterial library included 31 OTUs. Proteobacteria, Bacteroidetes, and Firmicutes were frequently detected in both clone libraries. The clones were related to thermophilic, mesophilic and psychrophilic bacteria. Approximately half of the sequences in bacterial clone libraries shared <92% sequence similarity with their closest sequences in a public database, suggesting that the Ibusuki hot spring may harbor a unique and novel bacterial community. By contrast, 77 clones from the Site 2 archaeal library contained only three OTUs, most of which were affiliated with Thaumarchaeota.

Constitutive properties of adult mammalian cardiac muscle cells

NASA Technical Reports Server (NTRS)

Zile, M. R.; Richardson, K.; Cowles, M. K.; Buckley, J. M.; Koide, M.; Cowles, B. A.; Gharpuray, V.; Cooper, G. 4th

1998-01-01

BACKGROUND: The purpose of this study was to determine whether changes in the constitutive properties of the cardiac muscle cell play a causative role in the development of diastolic dysfunction. METHODS AND RESULTS: Cardiocytes from normal and pressure-hypertrophied cats were embedded in an agarose gel, placed on a stretching device, and subjected to a change in stress (sigma), and resultant changes in cell strain (epsilon) were measured. These measurements were used to examine the passive elastic spring, viscous damping, and myofilament activation. The passive elastic spring was assessed in protocol A by increasing the sigma on the agarose gel at a constant rate to define the cardiocyte sigma-versus-epsilon relationship. Viscous damping was assessed in protocol B from the loop area between the cardiocyte sigma-versus-epsilon relationship during an increase and then a decrease in sigma. In both protocols, myofilament activation was minimized by a reduction in [Ca2+]i. Myofilament activation effects were assessed in protocol C by defining cardiocyte sigma versus epsilon during an increase in sigma with physiological [Ca2+]i. In protocol A, the cardiocyte sigma-versus-epsilon relationship was similar in normal and hypertrophied cells. In protocol B, the loop area was greater in hypertrophied than normal cardiocytes. In protocol C, the sigma-versus-epsilon relation in hypertrophied cardiocytes was shifted to the left compared with normal cells. CONCLUSIONS: Changes in viscous damping and myofilament activation in combination may cause pressure-hypertrophied cardiocytes to resist changes in shape during diastole and contribute to diastolic dysfunction.

Land use, water use, streamflow characteristics, and water-quality characteristics of the Charlotte Harbor inflow area, Florida

USGS Publications Warehouse

Hammett, K.M.

1990-01-01

Charlotte Harbor is a 270-square-mile estuarine system in west-central Florida. It is being subjected to increasing environmental stress by rapid population growth and development. By 2020, population in the inflow area may double, which will result in increased demands for freshwater and increased waste loads. The Charlotte Harbor inflow area includes about 4,685 square miles. The Myakka, the Peace, and the Caloosahatchee are the major rivers emptying into the harbor. About 70 percent of the land in these three river basins is used for agriculture and range. In the coastal basin around Charlotte Harbor, about 50 percent of the total land area is devoted to commercial or residential uses. Water use in the inflow area is about 565 million gallons per day, of which 59 percent is used for irrigation, 26 percent for industry, 11 percent for public supply, and 4 percent for rural supply. Total freshwater inflow from the three major rivers, the coastal area, and rainfall directly into Charlotte Harbor averages between 5,700 and 6,100 cubic feet per second, which is more than 3,500 million gallons per day. A trend analysis of about 50 years of streamflow data shows a statistically significant decreasing trend for the Peace River stations at Bartow, Zolfo Springs, and Arcadia. No significant trend has been observed in the Myakka or the Caloosahatchee River data. In the Peace River, the decrease in flow may be related to a long-term decline in the potentiometric surface of the underlying Floridan aquifer system, which resulted from ground-water withdrawals. It is not possible to determine whether the trend will continue. However, if it does continue at the same rate, then, except for brief periods of storm runoff, the Peace River at Zolfo Springs could be dry year-round in about 100 years. Of the 114 facilities permitted to discharge domestic or industrial effluent to waters tributary to Charlotte Harbor, 88 are in the Peace River basin. Phosphate ore and citrus processing account for most of the industrial effluent. Several locations in the headwaters of the Peace River have been significantly affected as a result of receiving wastewater effluent. The Peace, the Myakka, and the Caloosahatchee Rivers transport more than 2,000 tons per day of dissolved solids, more than 17 tons per day of nitrogen, and about 6 tons per day of phosphorus. By 2020, the population in the inflow area is expected to increase by more than 500,000 people. They will require an additional 76 million gallons per day for water supply. The increased population will produce an additional 60 million gallons per day of domestic wastewater, which could result in an additional 3 tons per day of nitrogen and 0.65 ton per day of phosphorus. More than 150 square miles of land will be converted to urban uses, which will produce another 0.25 ton per day of nitrogen from urban runoff. These increased nutrient loads can be expected to occur concurrently with decreased freshwater inflow.

A germline FANCA alteration that is associated with increased sensitivity to DNA damaging agents.

PubMed

Wilkes, David C; Sailer, Verena; Xue, Hui; Cheng, Hongwei; Collins, Colin C; Gleave, Martin; Wang, Yuzhuo; Demichelis, Francesca; Beltran, Himisha; Rubin, Mark A; Rickman, David S

2017-09-01

Defects in genes involved in DNA damage repair (DDR) pathway are emerging as novel biomarkers and targets for new prostate cancer drug therapies. A previous report revealed an association between an exceptional response to cisplatin treatment and a somatic loss of heterozygosity (LOH) of FANCA in a patient with metastatic prostate cancer who also harbored a germline FANCA variant (S1088F). Although germline FANCA mutations are the most frequent alterations in patients with Fanconi anemia, germline alterations are less common in prostate cancer. We hypothesized that the germline S1088F FANCA variant in combination with FANCA LOH was deleterious for FANCA function and contributed to the patient's exceptional response to cisplatin. We show that although it properly localizes to the nucleus, the S1088F FANCA mutant protein disrupts the FANC protein complex resulting in increased sensitivity to DNA damaging agents. Because molecular stratification is emerging as a strategy for treating men with metastatic, castrate-resistant prostate cancer harboring specific DDR gene defects, our findings suggest that more biomarker studies are needed to better define clinically relevant germline and somatic alterations. © 2017 Wilkes et al.; Published by Cold Spring Harbor Laboratory Press.

Effects of dredging operations on soft bottom macrofauna in a harbor in the Patos Lagoon estuarine region of southern Brazil.

PubMed

Bemvenuti, C E; Angonesi, L G; Gandra, M S

2005-11-01

An evaluation was made of the effects of dredging on the soft bottom community in the channel of the Rio Grande harbor in the Patos Lagoon estuarine region of southern Brazil. During four seasonal cruises, samples were collected from nine biological stations, one of which was located outside the dredged area. Three macrobenthic samples were collected on each cruise from each station, using a 0.08 m2 van Veen grab. A cluster analysis was applied to group summer and autumn cruise stations before the dredging period, revealing larger numbers of species (35-36 spp.) and higher densities of organisms. The station located outside the dredging area was always included in this group, regardless of the sampling period or conditions of salinity. Another group comprised the winter and spring stations during the dredging period. This group was characterized by stations with the fewest species (20-18 spp.) and the lowest and most variable organism densities. The efficient strategies of resilience of the dominant estuarine species may minimize the effects of dredging on the biota through the rapid recolonization of the soft bottom of the harbor channel.

The impact of post-exercise hydration with deep-ocean mineral water on rehydration and exercise performance.

PubMed

Keen, Douglas A; Constantopoulos, Eleni; Konhilas, John P

2016-01-01

Dehydration caused by prolonged exercise impairs thermoregulation, endurance and exercise performance. Evidence from animal and human studies validates the potential of desalinated deep-ocean mineral water to positively impact physiological and pathophysiological conditions. Here, we hypothesize that deep-ocean mineral water drawn from a depth of 915 m off the Kona, HI coast enhances recovery of hydration and exercise performance following a dehydrating exercise protocol compared to mountain spring water and a carbohydrate-based sports drink. Subjects (n = 8) were exposed to an exercise-dehydration protocol (stationary biking) under warm conditions (30 °C) to achieve a body mass loss of 3 % (93.4 ± 21.7 total exercise time). During the post-exercise recovery period, subjects received deep-ocean mineral water (Kona), mountain spring water (Spring) or a carbohydrate-based sports drink (Sports) at a volume (in L) equivalent to body mass loss (in Kg). Salivary samples were collected at regular intervals during exercise and post-exercise rehydration. Additionally, each participant performed peak torque knee extension as a measure of lower body muscle performance. Subjects who received Kona during the rehydrating period showed a significantly more rapid return to pre-exercise (baseline) hydration state, measured as the rate of decline in peak to baseline salivary osmolality, compared to Sports and Spring groups. In addition, subjects demonstrated significantly improved recovery of lower body muscle performance following rehydration with Kona versus Sports or Spring groups. Deep-ocean mineral water shows promise as an optimal rehydrating source over spring water and/or sports drink.

Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments.

PubMed

Saxena, Rituja; Dhakan, Darshan B; Mittal, Parul; Waiker, Prashant; Chowdhury, Anirban; Ghatak, Arundhuti; Sharma, Vineet K

2016-01-01

Extreme ecosystems such as hot springs are of great interest as a source of novel extremophilic species, enzymes, metabolic functions for survival and biotechnological products. India harbors hundreds of hot springs, the majority of which are not yet explored and require comprehensive studies to unravel their unknown and untapped phylogenetic and functional diversity. The aim of this study was to perform a large-scale metagenomic analysis of three major hot springs located in central India namely, Badi Anhoni, Chhoti Anhoni, and Tattapani at two geographically distinct regions (Anhoni and Tattapani), to uncover the resident microbial community and their metabolic traits. Samples were collected from seven distinct sites of the three hot spring locations with temperature ranging from 43.5 to 98°C. The 16S rRNA gene amplicon sequencing of V3 hypervariable region and shotgun metagenome sequencing uncovered a unique taxonomic and metabolic diversity of the resident thermophilic microbial community in these hot springs. Genes associated with hydrocarbon degradation pathways, such as benzoate, xylene, toluene, and benzene were observed to be abundant in the Anhoni hot springs (43.5-55°C), dominated by Pseudomonas stutzeri and Acidovorax sp., suggesting the presence of chemoorganotrophic thermophilic community with the ability to utilize complex hydrocarbons as a source of energy. A high abundance of genes belonging to methane metabolism pathway was observed at Chhoti Anhoni hot spring, where methane is reported to constitute >80% of all the emitted gases, which was marked by the high abundance of Methylococcus capsulatus . The Tattapani hot spring, with a high-temperature range (61.5-98°C), displayed a lower microbial diversity and was primarily dominated by a nitrate-reducing archaeal species Pyrobaculum aerophilum . A higher abundance of cell metabolism pathways essential for the microbial survival in extreme conditions was observed at Tattapani. Taken together, the results of this study reveal a novel consortium of microbes, genes, and pathways associated with the hot spring environment.

Comparison of sediments and organisms in identifying sources of biologically available trace metal contamination

USGS Publications Warehouse

Thomson, E.A.; Luoma, S.N.; Johansson, C.E.; Cain, D.J.

1984-01-01

Sediments and an indicator organism (Macoma balthica, a deposit-feeding bivalve) were used to assess the relative importance of secondary sewage, urban runoff, a landfill containing metal-enriched ash wastes and a yacht harbor in contributing to Ag, Cu and Zn enrichment in South San Francisco Bay. Spatial gradients in sediments and organisms showed Cu and Ag enrichment originated from sewage discharge, whereas Zn enrichment originated from both sewage and urban runoff. Elevated concentrations of Cu in the sediments of the yacht harbor resulted from a high abundance of fine particles. The biological availability of Cu, Ag and Zn did not coincide with metal enrichment in sediments. The availability of Cu and Ag was greatest nearest the sewage outfall and greater in winter and spring than in summer. The availability of Zn in urban runoff appeared to be lower than the availability of Zn associated with sewage.

Distribution and Abundance of Dungeness Crab and Crangon Shrimp and Dredging-Related Mortality of Invertebrates and Fish in Grays Harbor, Washington,

DTIC Science & Technology

1982-01-01

Cont’d). salinity . Crabs were most abundant in spring and least abundant in summer. Diel migrations were evident and dependent upon tidal level, light...driving cycles include: 1. Density- dependent mechanisms based on compensatory influences such as competition for food between young and older crabs...and salinity . Annual mean crab density was greater in the channel than on the flats. Crabs generally changed their diet with age from one consisting

Psoriasis.

PubMed

Di Meglio, Paola; Villanova, Federica; Nestle, Frank O

2014-08-01

Psoriasis is a common chronic inflammatory skin disease with a spectrum of clinical phenotypes and results from the interplay of genetic, environmental, and immunological factors. Four decades of clinical and basic research on psoriasis have elucidated many of the pathogenic mechanisms underlying disease and paved the way to effective targeted therapies. Here, we review this progress and identify future directions of study that are supported by a more integrative research approach and aim at further improving the patients' life. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

Baltimore Harbor and Channels Deepening Study; Chesapeake Bay Hydraulic Model Investigation.

DTIC Science & Technology

1982-02-01

neap-spring salinity vari- ability. Stations within the Patapsco River (Plates 78-90), and the Magothy River station (MA-I-1, Plate 74), immediately...to-base salinity variations are found at upper bay stations above the constriction at range CB-4. Only Magothy River sta MA-l, and sta CB-7-1 have...Across the bay at the western shore Magothy River sta MA-I-I (Plate 74) no appreciable plan-to-base salinity differences are found, although during

Anatomy and Histology of the Human and Murine Prostate.

PubMed

Ittmann, Michael

2018-05-01

The human and murine prostate glands have similar functional roles in the generation of seminal fluid to assist in reproduction. There are significant differences in the anatomy and histology of murine and human prostate and knowledge of the normal anatomy and histology of the murine prostate is essential to interpreting changes in genetically engineered mouse models. In this review, the normal anatomy and histology of both human and mouse prostate will be described. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

12. VIEW OF TYPICAL CELL LOCKING MECHANISM, BUILDING 220 CELL ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

12. VIEW OF TYPICAL CELL LOCKING MECHANISM, BUILDING 220 CELL BLOCK 'A'. THE FACE PLATE OF THE CELL LOCK IS SHOWN REMOVED, EXPOSING THE ELECTROMAGNETIC LOCKING MECHANISM COMPRISING OF 2 MICROSWITCHES FOR LOCK POSITION INDICATION (FRONT LEFT CENTER AND REAR RIGHT CENTER OF PANEL); KEY SLOT MECHANICAL LOCK; LOCK SPRING (UPPER RIGHT OF PANEL); ELECTRIC SOLENOID (BOTTOM RIGHT CORNER OF PANEL); AND MISCELLANEOUS MECHANICAL LINKAGES. - U.S. Naval Base, Pearl Harbor, Brig, Neville Way near Ninth Street at Marine Barracks, Pearl City, Honolulu County, HI

Airpower as a Tool of Foreign Policy, Two Case Studies of Airpower’s Use: The Philippines in 1941 and Berlin in 1948

DTIC Science & Technology

1993-05-01

Vallance , RAF, ed., Air Power Doctrine (United Kingdom: Crown Copyright, 1990). Group Captain Vallance provides a comprehensive discussion of The...Spring 1964): 1-7. Current, Richard N. �How Stimson Meant to �Manuever� the Japanese.� The Mississippi Valley Historical Review, 11 (June 1953...War II, the Pacific War. New York: Marshall Cavendish, 1992. Collier, Richard . The Road to Pearl Harbor: 1941. New York: Atheneum, 1981

Small but Mighty: Cell Size and Bacteria.

PubMed

Levin, Petra Anne; Angert, Esther R

2015-06-08

Our view of bacteria is overwhelmingly shaped by their diminutive nature. The most ancient of organisms, their very presence was not appreciated until the 17th century with the invention of the microscope. Initially, viewed as "bags of enzymes," recent advances in imaging, molecular phylogeny, and, most recently, genomics have revealed incredible diversity within this previously invisible realm of life. Here, we review the impact of size on bacterial evolution, physiology, and morphogenesis. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

Empowering Children to Lead Change: Incorporating Preparedness Curricula in the K-12 Educational System

DTIC Science & Technology

2009-03-01

Japanese attack on Pearl Harbor is commonly credited for the re-stimulation of civil defense, President Roosevelt, in fact, reactivated the Council...Britain used advertising in the form of print media, short films on the BBC and in cinemas , as well as exercises and demonstrations to educate the...During the spring of 1942, “a Japanese submarine surfaced near the coast of southern California and fired a salvo of shells that exploded on an oil

History of the Discovery of Hepatitis A Virus.

PubMed

Feinstone, Stephen M

2018-04-30

Disease outbreaks resembling hepatitis A have been known since antiquity. However, it was not until World War II when two forms of viral hepatitis were clearly differentiated. After the discovery of Australia antigen and its association with hepatitis B, similar methodologies were used to find the hepatitis A virus. The virus was ultimately identified when investigators changed the focus of their search from serum to feces and applied appropriate technology. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

Characteristics of PM2.5 from ship emissions and their impacts on the ambient air: A case study in Yangshan Harbor, Shanghai.

PubMed

Mamoudou, Issoufou; Zhang, Fan; Chen, Qi; Wang, Panpan; Chen, Yingjun

2018-05-30

The rapid development of ports in China over the last two decades has had inevitable consequences on the ambient air quality in coastal areas and harbors. For mitigation strategies and monitoring aims, the contributions of ship emissions should be identified, especially in these specific areas. Therefore, in this study, fine particulate matters (PM 2.5 ) samples were collected at Yangshan Harbor in 2016 to characterize ship emissions and estimate their impacts on the ambient air. The results showed that the average annual PM 2.5 concentration was 44.02 μg/m 3 at Yangshan Harbor. The mean seasonal PM 2.5 concentrations reached a maximum in the spring (60.28 μg/m 3 ) and a minimum in the summer (28.04 μg/m 3 ). Two methods were used in this study to estimate the contributions of ship emissions to the ambient air. When a V-based method was used, the primary estimated daily contributions of ship emissions to the ambient air at Yangshan Harbor ranged from 0.02 to 0.73 μg/m 3 with an annual average of 0.10 μg/m 3 . When a PMF-based method was used, the contributions ranged from 0.02 to 9.15 μg/m 3 with an annual average of 1.02 μg/m 3 . In fact, there was a significant underestimation of the true influences of ship emissions when only the primary contribution was considered. In accordance with this evidence, there was a main average underestimation of 1.84 μg/m 3 . Copyright © 2018 Elsevier B.V. All rights reserved.

Plague dynamics are driven by climate variation.

PubMed

Stenseth, Nils Chr; Samia, Noelle I; Viljugrein, Hildegunn; Kausrud, Kyrre Linné; Begon, Mike; Davis, Stephen; Leirs, Herwig; Dubyanskiy, V M; Esper, Jan; Ageyev, Vladimir S; Klassovskiy, Nikolay L; Pole, Sergey B; Chan, Kung-Sik

2006-08-29

The bacterium Yersinia pestis causes bubonic plague. In Central Asia, where human plague is still reported regularly, the bacterium is common in natural populations of great gerbils. By using field data from 1949-1995 and previously undescribed statistical techniques, we show that Y. pestis prevalence in gerbils increases with warmer springs and wetter summers: A 1 degrees C increase in spring is predicted to lead to a >50% increase in prevalence. Climatic conditions favoring plague apparently existed in this region at the onset of the Black Death as well as when the most recent plague pandemic arose in the same region, and they are expected to continue or become more favorable as a result of climate change. Threats of outbreaks may thus be increasing where humans live in close contact with rodents and fleas (or other wildlife) harboring endemic plague.

Novelty and fear conditioning induced gene expression in high and low states of anxiety.

PubMed

Donley, Melanie P; Rosen, Jeffrey B

2017-09-01

Emotional states influence how stimuli are interpreted. High anxiety states in humans lead to more negative, threatening interpretations of novel information, typically accompanied by activation of the amygdala. We developed a handling protocol that induces long-lasting high and low anxiety-like states in rats to explore the role of state anxiety on brain activation during exposure to a novel environment and fear conditioning. In situ hybridization of the inducible transcription factor Egr-1 found increased gene expression in the lateral nucleus of the amygdala (LA) following exposure to a novel environment and contextual fear conditioning in high anxiety-like rats. In contrast, low state anxiety-like rats did not generate Egr-1 increases in LA when placed in a novel chamber. Egr-1 expression was also examined in the dorsal hippocampus and prefrontal cortex. In CA1 of the hippocampus and medial prefrontal cortex (mPFC), Egr-1 expression increased in response to novel context exposure and fear conditioning, independent of state anxiety level. Furthermore, in mPFC, Egr-1 in low anxiety-like rats was increased more with fear conditioning than novel exposure. The current series of experiments show that brain areas involved in fear and anxiety-like states do not respond uniformly to novelty during high and low states of anxiety. © 2017 Donley and Rosen; Published by Cold Spring Harbor Laboratory Press.

Methods for processing high-throughput RNA sequencing data.

PubMed

Ares, Manuel

2014-11-03

High-throughput sequencing (HTS) methods for analyzing RNA populations (RNA-Seq) are gaining rapid application to many experimental situations. The steps in an RNA-Seq experiment require thought and planning, especially because the expense in time and materials is currently higher and the protocols are far less routine than those used for other high-throughput methods, such as microarrays. As always, good experimental design will make analysis and interpretation easier. Having a clear biological question, an idea about the best way to do the experiment, and an understanding of the number of replicates needed will make the entire process more satisfying. Whether the goal is capturing transcriptome complexity from a tissue or identifying small fragments of RNA cross-linked to a protein of interest, conversion of the RNA to cDNA followed by direct sequencing using the latest methods is a developing practice, with new technical modifications and applications appearing every day. Even more rapid are the development and improvement of methods for analysis of the very large amounts of data that arrive at the end of an RNA-Seq experiment, making considerations regarding reproducibility, validation, visualization, and interpretation increasingly important. This introduction is designed to review and emphasize a pathway of analysis from experimental design through data presentation that is likely to be successful, with the recognition that better methods are right around the corner. © 2014 Cold Spring Harbor Laboratory Press.

Larval fish dynamics in spring pools in middle Tennessee

USGS Publications Warehouse

Bettoli, Phillip William; Goldsworthy, C.A.

2011-01-01

We used lighted larval traps to assess reproduction by fishes inhabiting nine spring pools in the Barrens Plateau region of middle Tennessee between May and September 2004. The traps (n = 162 deployments) captured the larval or juvenile forms of Etheostoma crossopterum (Fringed Darter) (n = 188), Gambusia affinis (Western Mosquitofish) (n = 139), Hemitremia flammea (Flame Chub) (n = 55), the imperiled Fundulus julisia (Barrens Topminnow) (n = 10), and Forbesichthys agassizii (Spring Cavefish) (n = 1). The larval forms of four other species (Families Centrarchidae, Cyprinidae, and Cottidae) were not collected, despite the presence of adults. Larval Barrens Topminnow hatched over a protracted period (early June through late September); in contrast, hatching intervals were much shorter for Fringed Darter (mid-May through early June). Flame Chub hatching began before our first samples in early May and concluded by late-May. Juvenile Western Mosquitofish were collected between early June and late August. Our sampling revealed that at least two species (Flame Chub and Fringed Darter) were able to reproduce and recruit in habitats harboring the invasive Western Mosquitofish, while Barrens Topminnow could not.

Ecohydrology of seepage springs in an urban National Park

NASA Astrophysics Data System (ADS)

Knee, K.; Melone, J.; Friedel, B.; Fong, D.

2014-12-01

Shallow groundwater-fed seepage springs, also known as hypotelminorheic habitats, are found around the Washington, DC area, including in the George Washington Parkway, a National Park unit in northern Virginia. These springs differ from better-known vernal pools both in their hydrology and their ecology: because they are groundwater-fed, they are more resistant to drying out than vernal pools, and they harbor cave-adapted arthropod species including amphipods of the genus Stygobroumus. This project seeks to understand the ecohydrology of the hypotelminorheic habitats that support these species, some of which are endangered, and which comprise an important but underappreciated component of biodiversity in DC-area National Parks. Our study focuses on two hypotelminorheic habitats in the GW Parkway area and consists of three main components: (1) a weekly population census of Stygobroumus using multiple mark-recapture methodology, (2) weekly monitoring of dissolved radon, a tracer of groundwater discharge, as well as conductivity, dissolved oxygen, and pH, and (3) continuous logging of spring water temperature. This poster presents preliminary data from the Stygobroumus population census and explores how these animals may be affected by spring hydrology. Specifically, we use temperature, conductivity, radon activity and precipitation data from a nearby weather station to understand how the springs respond to episodic and seasonal variation in temperature, precipitation and groundwater seepage and how this affects Stygobromus populations. We also explore whether variations in Stygobromus counts reflect (1) active migration between the surficial spring and the larger subterranean habitat, or (2) passive flushing driven by groundwater discharge. Our results provide basic hydrologic data about a little-understood habitat type and will help managers protect Stygobromus in the urban park environment.

Tales of some ancient harbors in the Aegean back-arc region: Earthquakes, coastal changes, historical impacts

NASA Astrophysics Data System (ADS)

Stiros, Stathis; Saltogianni, Vasso

2017-04-01

Tectonically active terrains are characterized by seismic transient ground motions (shaking) and by permanent ground motions in the vicinity of activated faults, with both effects occasionally leaving their signature on human constructions and the landscape. Especially in coastal areas marked by small tidal ranges and normal water salinity, as is the case with most parts of the Eastern Mediterranean, even small-amplitude tectonic motions can be derived from observations on coastal constructions, mainly harbors, but also on spring chambers in nearly arid environments, sewers, etc. Such observations, if coupled with well-dated observations of destructions and repairs and of changes in the occupation style of ancient sites can permit precious information conveyed from archaeology to tectonics/seismology and vice versa. A transect with harbor remains from Rhodes to the Gulf of Corinth and then till the Ionian Islands provides some excellent examples. The military harbor of Rhodes, in an area of long term uplift, a coded report of which seems to be provided by ancient poet Pindar, was subject to seismic subsidence and destruction, but with major international support, it was repaired, till renewed uplift brought it several meters above the water. In the Corinth area, the Kenchreai harbor was abruptly submerged during a major repair of a temple, as revealed by precious stained glass panels, ready to use but abandoned in shallow water beneath ruins, while radiometric dating of the uplift in the western Lechaion harbor, constrains its excavation in swampy environment not in Roman times, but to the period of flourishing of Corinth in circa 600BC and the colonization of Italy. Farther west, the sea-level mark of the harbor of Aigeira, at Mavra Litharia (Derveni/Akrata) indicates 4m uplift since the Roman period, at least partly seismic, correlating with an exposed reef and the abandonment of the repairs of the theatre of Aigeira. Seismic land uplift explains the demise of this ancient town since approximately AD200 as a result of loss of the only significant harbor along the southern coast of the Gulf of Corinth. Farther west, in the south part of the Greek mainland, rising of the level of the dock shortly after its construction may imply response to seismic land subsidence, while at the nearby harbor of Palairos, remains of a submerged breakwater, offset by several meters, testify to strike slip faulting with seismic offset amplified by liquefaction.

Multi-faceted monitoring of estuarine turbidity and particulate matter provenance: Case study from Salem Harbor, USA.

PubMed

Hubeny, J Bradford; Kenney, Melanie; Warren, Barbara; Louisos, Jeremy

2017-01-01

Turbidity is a water quality parameter that is known to adversely affect aquatic systems, however the causes of turbid water are often elusive. We present results of a study designed to constrain the source of particulate matter in a coastal embayment that has suffered from increased turbidity over past decades. Our approach utilized monitoring buoys to quantify turbidity at high temporal resolution complemented by geochemical isotope analysis of suspended sediment samples and meteorological data. Results reveal a complex system in which multiple sources are associated with particulate matter. Weight of evidence demonstrates that phytoplankton productivity in the water column, however, is the dominant source of particulate matter associated with elevated turbidity in Salem Harbor, Massachusetts. Allochthonous matter from the watershed was observed to mix into the pool of suspended particulate matter near river mouths, especially in spring and summer. Resuspension of harbor surface sediments likely provides additional particulates in the regions of boat moorings, especially during summer when recreational boats are attached to moorings. Our approach allows us to constrain the causes of turbidity events in this embayment, is helping with conservation efforts of environmental quality in the region, and can be used as a template for other locations. Copyright © 2016 Elsevier B.V. All rights reserved.

Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments

PubMed Central

Saxena, Rituja; Dhakan, Darshan B.; Mittal, Parul; Waiker, Prashant; Chowdhury, Anirban; Ghatak, Arundhuti; Sharma, Vineet K.

2017-01-01

Extreme ecosystems such as hot springs are of great interest as a source of novel extremophilic species, enzymes, metabolic functions for survival and biotechnological products. India harbors hundreds of hot springs, the majority of which are not yet explored and require comprehensive studies to unravel their unknown and untapped phylogenetic and functional diversity. The aim of this study was to perform a large-scale metagenomic analysis of three major hot springs located in central India namely, Badi Anhoni, Chhoti Anhoni, and Tattapani at two geographically distinct regions (Anhoni and Tattapani), to uncover the resident microbial community and their metabolic traits. Samples were collected from seven distinct sites of the three hot spring locations with temperature ranging from 43.5 to 98°C. The 16S rRNA gene amplicon sequencing of V3 hypervariable region and shotgun metagenome sequencing uncovered a unique taxonomic and metabolic diversity of the resident thermophilic microbial community in these hot springs. Genes associated with hydrocarbon degradation pathways, such as benzoate, xylene, toluene, and benzene were observed to be abundant in the Anhoni hot springs (43.5–55°C), dominated by Pseudomonas stutzeri and Acidovorax sp., suggesting the presence of chemoorganotrophic thermophilic community with the ability to utilize complex hydrocarbons as a source of energy. A high abundance of genes belonging to methane metabolism pathway was observed at Chhoti Anhoni hot spring, where methane is reported to constitute >80% of all the emitted gases, which was marked by the high abundance of Methylococcus capsulatus. The Tattapani hot spring, with a high-temperature range (61.5–98°C), displayed a lower microbial diversity and was primarily dominated by a nitrate-reducing archaeal species Pyrobaculum aerophilum. A higher abundance of cell metabolism pathways essential for the microbial survival in extreme conditions was observed at Tattapani. Taken together, the results of this study reveal a novel consortium of microbes, genes, and pathways associated with the hot spring environment. PMID:28105025

Fluorescence microscopy.

PubMed

Sanderson, Michael J; Smith, Ian; Parker, Ian; Bootman, Martin D

2014-10-01

Fluorescence microscopy is a major tool with which to monitor cell physiology. Although the concepts of fluorescence and its optical separation using filters remain similar, microscope design varies with the aim of increasing image contrast and spatial resolution. The basics of wide-field microscopy are outlined to emphasize the selection, advantages, and correct use of laser scanning confocal microscopy, two-photon microscopy, scanning disk confocal microscopy, total internal reflection, and super-resolution microscopy. In addition, the principles of how these microscopes form images are reviewed to appreciate their capabilities, limitations, and constraints for operation. © 2014 Cold Spring Harbor Laboratory Press.

Role of Human DNA Polymerase and Its Accessory Proteins in Breast Cancer

DTIC Science & Technology

2002-04-01

the POLD1 gene in breast cancer tissues using a Non-Isotopic RNase Cleavage Assay (NIRCA) and DNA sequencing techniques. Four novel mutations , P327L...M.Y.W.T. Mutational Analysis of the Exo Motif of POLD1 gene in human Breast Cancer cells (in preparation) 9. Jaime, C., Mazloum N., and Lee, M.Y.W. T...Cold Spring Harbor 1999 8. Xu, H., and Lee, M.Y.W.T. Analyzes of POLD1 gene mutation and study of its transcriptional regulation in Breast Cancer Cells

Gene Therapy for the Retinal Degeneration of Usher Syndrome Caused by Mutations in MYO7A.

PubMed

Lopes, Vanda S; Williams, David S

2015-01-20

Usher syndrome is a deaf-blindness disorder. One of the subtypes, Usher 1B, is caused by loss of function of the gene encoding the unconventional myosin, MYO7A. A variety of different viral-based delivery approaches have been tested for retinal gene therapy to prevent the blindness of Usher 1B, and a clinical trial based on one of these approaches has begun. This review evaluates the different approaches. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

Puget Sound Dredged Disposal Analysis (PSDDA). Final Environmental Impact Statement Unconfined Open-Water Disposal for Dredged Material, Phase 2. (North and South Puget Sound)

DTIC Science & Technology

1989-09-01

flathead sole, rex sole, and rock sole all showed indications of blood worm infestations. One liver tumor was found in a rex sole during spring in the ZSF...concentrations Hainly in invertebrates; some trations (.01 ppb) in waters (from lOx to 42Ox reference) in fish livers ; rarely in fish of Puget Sound central...Eagle Harbor, and Sinclair fish livers , and birds in Inlet. Highest elevation industrialized ’-ban areas. along Ruston-Point Defiance Copper is a natural

High-throughput and site-specific identification of 2'-O-methylation sites using ribose oxidation sequencing (RibOxi-seq).

PubMed

Zhu, Yinzhou; Pirnie, Stephan P; Carmichael, Gordon G

2017-08-01

Ribose methylation (2'- O -methylation, 2'- O Me) occurs at high frequencies in rRNAs and other small RNAs and is carried out using a shared mechanism across eukaryotes and archaea. As RNA modifications are important for ribosome maturation, and alterations in these modifications are associated with cellular defects and diseases, it is important to characterize the landscape of 2'- O -methylation. Here we report the development of a highly sensitive and accurate method for ribose methylation detection using next-generation sequencing. A key feature of this method is the generation of RNA fragments with random 3'-ends, followed by periodate oxidation of all molecules terminating in 2',3'-OH groups. This allows only RNAs harboring 2'-OMe groups at their 3'-ends to be sequenced. Although currently requiring microgram amounts of starting material, this method is robust for the analysis of rRNAs even at low sequencing depth. © 2017 Zhu et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Life Beneath Glacial Ice - Earth(!) Mars(?) Europa(?)

NASA Technical Reports Server (NTRS)

Allen, Carlton C.; Grasby, Stephen E.; Longazo, Teresa G.; Lisle, John T.; Beauchamp, Benoit

2002-01-01

We are investigating a set of cold springs that deposit sulfur and carbonate minerals on the surface of a Canadian arctic glacier. The spring waters and mineral deposits contain microorganisms, as well as clear evidence that biological processes mediate subglacial chemistry, mineralogy, and isotope fractionation . The formation of native sulphur and associated deposits are related to bacterially mediated reduction and oxidation of sulphur below the glacier. A non-volcanic, topography driven geothermal system, harboring a microbiological community, operates in an extremely cold environment and discharges through solid ice. Microbial life can thus exist in isolated geothermal refuges despite long-term subfreezing surface conditions. Earth history includes several periods of essentially total glaciation. lee in the near subsurface of Mars may have discharged liquid water in the recent past Cracks in the ice crust of Europa have apparently allowed the release of water to the surface. Chemolithotrophic bacteria, such as those in the Canadian springs, could have survived beneath the ice of "Snowball Earth", and life forms with similar characteristics might exist beneath the ice of Mars or Europa. Discharges of water from such refuges may have brought to the surface living microbes, as well as longlasting chemical, mineralogical, and isotopic indications of subsurface life.

Opening the black box of spring water microbiology from alpine karst aquifers to support proactive drinking water resource management

PubMed Central

Savio, Domenico; Stadler, Philipp; Reischer, Georg H.; Kirschner, Alexander K.T.; Demeter, Katalin; Linke, Rita; Blaschke, Alfred P.; Sommer, Regina; Szewzyk, Ulrich; Wilhartitz, Inés C.; Mach, Robert L.; Stadler, Hermann

2018-01-01

Over the past 15 years, pioneering interdisciplinary research has been performed on the microbiology of hydrogeologically well‐defined alpine karst springs located in the Northern Calcareous Alps (NCA) of Austria. This article gives an overview on these activities and links them to other relevant research. Results from the NCA springs and comparable sites revealed that spring water harbors abundant natural microbial communities even in aquifers with high water residence times and the absence of immediate surface influence. Apparently, hydrogeology has a strong impact on the concentration and size of the observed microbes, and total cell counts (TCC) were suggested as a useful means for spring type classification. Measurement of microbial activities at the NCA springs revealed extremely low microbial growth rates in the base flow component of the studied spring waters and indicated the importance of biofilm‐associated microbial activities in sediments and on rock surfaces. Based on genetic analysis, the autochthonous microbial endokarst community (AMEC) versus transient microbial endokarst community (TMEC) concept was proposed for the NCA springs, and further details within this overview article are given to prompt its future evaluation. In this regard, it is well known that during high‐discharge situations, surface‐associated microbes and nutrients such as from soil habitats or human settlements—potentially containing fecal‐associated pathogens as the most critical water‐quality hazard—may be rapidly flushed into vulnerable karst aquifers. In this context, a framework for the comprehensive analysis of microbial pollution has been proposed for the NCA springs to support the sustainable management of drinking water safety in accordance with recent World Health Organization guidelines. Near‐real‐time online water quality monitoring, microbial source tracking (MST) and MST‐guided quantitative microbial‐risk assessment (QMRA) are examples of the proposed analytical tools. In this context, this overview article also provides a short introduction to recently emerging methodologies in microbiological diagnostics to support reading for the practitioner. Finally, the article highlights future research and development needs. This article is categorized under: 1Engineering Water > Water, Health, and Sanitation2Science of Water > Water Extremes3Water and Life > Nature of Freshwater Ecosystems PMID:29780584

Opening the black box of spring water microbiology from alpine karst aquifers to support proactive drinking water resource management.

PubMed

Savio, Domenico; Stadler, Philipp; Reischer, Georg H; Kirschner, Alexander K T; Demeter, Katalin; Linke, Rita; Blaschke, Alfred P; Sommer, Regina; Szewzyk, Ulrich; Wilhartitz, Inés C; Mach, Robert L; Stadler, Hermann; Farnleitner, Andreas H

2018-01-01

Over the past 15 years, pioneering interdisciplinary research has been performed on the microbiology of hydrogeologically well-defined alpine karst springs located in the Northern Calcareous Alps (NCA) of Austria. This article gives an overview on these activities and links them to other relevant research. Results from the NCA springs and comparable sites revealed that spring water harbors abundant natural microbial communities even in aquifers with high water residence times and the absence of immediate surface influence. Apparently, hydrogeology has a strong impact on the concentration and size of the observed microbes, and total cell counts (TCC) were suggested as a useful means for spring type classification. Measurement of microbial activities at the NCA springs revealed extremely low microbial growth rates in the base flow component of the studied spring waters and indicated the importance of biofilm-associated microbial activities in sediments and on rock surfaces. Based on genetic analysis, the autochthonous microbial endokarst community (AMEC) versus transient microbial endokarst community (TMEC) concept was proposed for the NCA springs, and further details within this overview article are given to prompt its future evaluation. In this regard, it is well known that during high-discharge situations, surface-associated microbes and nutrients such as from soil habitats or human settlements-potentially containing fecal-associated pathogens as the most critical water-quality hazard-may be rapidly flushed into vulnerable karst aquifers. In this context, a framework for the comprehensive analysis of microbial pollution has been proposed for the NCA springs to support the sustainable management of drinking water safety in accordance with recent World Health Organization guidelines. Near-real-time online water quality monitoring, microbial source tracking (MST) and MST-guided quantitative microbial-risk assessment (QMRA) are examples of the proposed analytical tools. In this context, this overview article also provides a short introduction to recently emerging methodologies in microbiological diagnostics to support reading for the practitioner. Finally, the article highlights future research and development needs. This article is categorized under: 1Engineering Water > Water, Health, and Sanitation2Science of Water > Water Extremes3Water and Life > Nature of Freshwater Ecosystems.

Using Phage Display to Create Recombinant Antibodies.

PubMed

Dasch, James R; Dasch, Amy L

2017-09-01

A variety of phage display technologies have been developed since the approach was first described for antibodies. The most widely used approaches incorporate antibody sequences into the minor coat protein pIII of the nonlytic filamentous phage fd or M13. Libraries of variable gene sequences, encoding either scFv or Fab fragments, are made by incorporating sequences into phagemid vectors. The phagemid is packaged into phage particles with the assistance of a helper phage to produce the antibody display phage. This protocol describes a method for creating a phagemid library. The multiple cloning site (MCS) of the pBluescript KS(-) phagemid vector is replaced by digestion with the restriction enzyme BssHII, followed by the insertion of four overlapping oligonucleotides to create a new MCS within the vector. Next, the 3' portion of gene III (from M13mp18) is amplified and combined with an antibody sequence using overlap extension PCR. This product is inserted into the phagemid vector to create pPDS. Two helper plasmids are also created from the modified pBluescript vector: pLINK provides the linker between the heavy and light chains, and pFABC provides the CH1 domain of the heavy chain. An antibody cDNA library is constructed from the RNA of interest and ligated into pPDS. The phagemid library is electroporated into Escherichia coli cells along with the VCS-M13 helper phage. © 2017 Cold Spring Harbor Laboratory Press.

Read clouds uncover variation in complex regions of the human genome.

PubMed

Bishara, Alex; Liu, Yuling; Weng, Ziming; Kashef-Haghighi, Dorna; Newburger, Daniel E; West, Robert; Sidow, Arend; Batzoglou, Serafim

2015-10-01

Although an increasing amount of human genetic variation is being identified and recorded, determining variants within repeated sequences of the human genome remains a challenge. Most population and genome-wide association studies have therefore been unable to consider variation in these regions. Core to the problem is the lack of a sequencing technology that produces reads with sufficient length and accuracy to enable unique mapping. Here, we present a novel methodology of using read clouds, obtained by accurate short-read sequencing of DNA derived from long fragment libraries, to confidently align short reads within repeat regions and enable accurate variant discovery. Our novel algorithm, Random Field Aligner (RFA), captures the relationships among the short reads governed by the long read process via a Markov Random Field. We utilized a modified version of the Illumina TruSeq synthetic long-read protocol, which yielded shallow-sequenced read clouds. We test RFA through extensive simulations and apply it to discover variants on the NA12878 human sample, for which shallow TruSeq read cloud sequencing data are available, and on an invasive breast carcinoma genome that we sequenced using the same method. We demonstrate that RFA facilitates accurate recovery of variation in 155 Mb of the human genome, including 94% of 67 Mb of segmental duplication sequence and 96% of 11 Mb of transcribed sequence, that are currently hidden from short-read technologies. © 2015 Bishara et al.; Published by Cold Spring Harbor Laboratory Press.

Basic quantitative polymerase chain reaction using real-time fluorescence measurements.

PubMed

Ares, Manuel

2014-10-01

This protocol uses quantitative polymerase chain reaction (qPCR) to measure the number of DNA molecules containing a specific contiguous sequence in a sample of interest (e.g., genomic DNA or cDNA generated by reverse transcription). The sample is subjected to fluorescence-based PCR amplification and, theoretically, during each cycle, two new duplex DNA molecules are produced for each duplex DNA molecule present in the sample. The progress of the reaction during PCR is evaluated by measuring the fluorescence of dsDNA-dye complexes in real time. In the early cycles, DNA duplication is not detected because inadequate amounts of DNA are made. At a certain threshold cycle, DNA-dye complexes double each cycle for 8-10 cycles, until the DNA concentration becomes so high and the primer concentration so low that the reassociation of the product strands blocks efficient synthesis of new DNA and the reaction plateaus. There are two types of measurements: (1) the relative change of the target sequence compared to a reference sequence and (2) the determination of molecule number in the starting sample. The first requires a reference sequence, and the second requires a sample of the target sequence with known numbers of the molecules of sequence to generate a standard curve. By identifying the threshold cycle at which a sample first begins to accumulate DNA-dye complexes exponentially, an estimation of the numbers of starting molecules in the sample can be extrapolated. © 2014 Cold Spring Harbor Laboratory Press.

RNA-seq of 272 gliomas revealed a novel, recurrent PTPRZ1-MET fusion transcript in secondary glioblastomas.

PubMed

Bao, Zhao-Shi; Chen, Hui-Min; Yang, Ming-Yu; Zhang, Chuan-Bao; Yu, Kai; Ye, Wan-Lu; Hu, Bo-Qiang; Yan, Wei; Zhang, Wei; Akers, Johnny; Ramakrishnan, Valya; Li, Jie; Carter, Bob; Liu, Yan-Wei; Hu, Hui-Min; Wang, Zheng; Li, Ming-Yang; Yao, Kun; Qiu, Xiao-Guang; Kang, Chun-Sheng; You, Yong-Ping; Fan, Xiao-Long; Song, Wei Sonya; Li, Rui-Qiang; Su, Xiao-Dong; Chen, Clark C; Jiang, Tao

2014-11-01

Studies of gene rearrangements and the consequent oncogenic fusion proteins have laid the foundation for targeted cancer therapy. To identify oncogenic fusions associated with glioma progression, we catalogued fusion transcripts by RNA-seq of 272 gliomas. Fusion transcripts were more frequently found in high-grade gliomas, in the classical subtype of gliomas, and in gliomas treated with radiation/temozolomide. Sixty-seven in-frame fusion transcripts were identified, including three recurrent fusion transcripts: FGFR3-TACC3, RNF213-SLC26A11, and PTPRZ1-MET (ZM). Interestingly, the ZM fusion was found only in grade III astrocytomas (1/13; 7.7%) or secondary GBMs (sGBMs, 3/20; 15.0%). In an independent cohort of sGBMs, the ZM fusion was found in three of 20 (15%) specimens. Genomic analysis revealed that the fusion arose from translocation events involving introns 3 or 8 of PTPRZ and intron 1 of MET. ZM fusion transcripts were found in GBMs irrespective of isocitrate dehydrogenase 1 (IDH1) mutation status. sGBMs harboring ZM fusion showed higher expression of genes required for PIK3CA signaling and lowered expression of genes that suppressed RB1 or TP53 function. Expression of the ZM fusion was mutually exclusive with EGFR overexpression in sGBMs. Exogenous expression of the ZM fusion in the U87MG glioblastoma line enhanced cell migration and invasion. Clinically, patients afflicted with ZM fusion harboring glioblastomas survived poorly relative to those afflicted with non-ZM-harboring sGBMs (P < 0.001). Our study profiles the shifting RNA landscape of gliomas during progression and reveled ZM as a novel, recurrent fusion transcript in sGBMs. © 2014 Bao et al.; Published by Cold Spring Harbor Laboratory Press.

Recovery and validation of historical sediment quality data from coastal and estuarine areas: An integrated approach

USGS Publications Warehouse

Manheim, F.T.; Buchholtz ten Brink, Marilyn R.; Mecray, E.L.

1998-01-01

A comprehensive database of sediment chemistry and environmental parameters has been compiled for Boston Harbor and Massachusetts Bay. This work illustrates methodologies for rescuing and validating sediment data from heterogeneous historical sources. It greatly expands spatial and temporal data coverage of estuarine and coastal sediments. The database contains about 3500 samples containing inorganic chemical, organic, texture and other environmental data dating from 1955 to 1994. Cooperation with local and federal agencies as well as universities was essential in locating and screening documents for the database. More than 80% of references utilized came from sources with limited distribution (gray literature). Task sharing was facilitated by a comprehensive and clearly defined data dictionary for sediments. It also served as a data entry template and flat file format for data processing and as a basis for interpretation and graphical illustration. Standard QA/QC protocols are usually inapplicable to historical sediment data. In this work outliers and data quality problems were identified by batch screening techniques that also provide visualizations of data relationships and geochemical affinities. No data were excluded, but qualifying comments warn users of problem data. For Boston Harbor, the proportion of irreparable or seriously questioned data was remarkably small (<5%), although concentration values for metals and organic contaminants spanned 3 orders of magnitude for many elements or compounds. Data from the historical database provide alternatives to dated cores for measuring changes in surficial sediment contamination level with time. The data indicate that spatial inhomogeneity in harbor environments can be large with respect to sediment-hosted contaminants. Boston Inner Harbor surficial sediments showed decreases in concentrations of Cu, Hg, and Zn of 40 to 60% over a 17-year period.A comprehensive database of sediment chemistry and environmental parameters has been compiled for Boston Harbor and Massachusetts Bay. This work illustrates methodologies for rescuing and validating sediment data from heterogeneous historical sources. It greatly expands spatial and temporal data coverage of estuarine and coastal sediments. The database contains about 3500 samples containing inorganic chemical, organic, texture and other environmental data dating from 1995 to 1994. Cooperation with local and federal agencies as well as universities was essential in locating and screening documents for the database. More than 80% of references utilized came from sources with limited distribution (gray Task sharing was facilitated by a comprehensive and clearly defined data dictionary for sediments. It also served as a data entry template and flat file format for data processing and as a basis for interpretation and graphical illustration. Standard QA/QC protocols are usually inapplicable to historical sediment data. In this work outliers and data quality problems were identified by batch screening techniques that also provide visualizations of data relationships and geochemical affinities. No data were excluded, but qualifying comments warn users of problem data. For Boston Harbor, the proportion of irreparable or seriously questioned data was remarkably small (<5%), although concentration values for metals and organic contaminants spanned 3 orders of magnitude for many elements or compounds. Data from the historical database provide alternatives to dated cores for measuring changes in surficial sediment contamination level with time. The data indicate that spatial inhomogeneity in harbor environments can be large with respect to sediment-hosted contaminants. Boston Inner Harbor surficial sediments showed decreases in concentrations Cu, Hg, and Zn of 40 to 60% over a 17-year period.

Patenting the life sciences at the European Patent Office.

PubMed

Gates, Christina

2014-10-23

The European patent system is very much like those of the United States and other major countries. Patent applications can be filed as a first filing, as a priority application, or as a national phase of a Patent Cooperation Treaty application. The applications are searched, rigorously examined, and ultimately granted, with the time periods varying somewhat depending on the application type. The object of this article is to highlight some of the differences between the U.S. and European systems, particularly as they relate to life sciences. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

FGFR1 tyrosine kinase domain duplication in pilocytic astrocytoma with anaplasia.

PubMed

Ballester, Leomar Y; Penas-Prado, Marta; Leeds, Norman E; Huse, Jason T; Fuller, Gregory N

2018-04-01

We report the case of a 27-yr-old male with visual field loss who had a 4.9-cm complex cystic mass in the right occipital lobe. Histologic examination showed pilocytic astrocytoma (PA) with anaplasia, and molecular characterization revealed FGFR1 duplication with additional variants of unknown significance in several genes ( ARID1A, ARID1B, CHEK2, EPHA5, and MLL2 ). This is one of only a very few reported cases of anaplastic PA with characterization of molecular alterations. © 2018 Ballester et al.; Published by Cold Spring Harbor Laboratory Press.

Human telomerase: biogenesis, trafficking, recruitment, and activation.

PubMed

Schmidt, Jens C; Cech, Thomas R

2015-06-01

Telomerase is the ribonucleoprotein enzyme that catalyzes the extension of telomeric DNA in eukaryotes. Recent work has begun to reveal key aspects of the assembly of the human telomerase complex, its intracellular trafficking involving Cajal bodies, and its recruitment to telomeres. Once telomerase has been recruited to the telomere, it appears to undergo a separate activation step, which may include an increase in its repeat addition processivity. This review covers human telomerase biogenesis, trafficking, and activation, comparing key aspects with the analogous events in other species. © 2015 Schmidt and Cech Published by Cold Spring Harbor Laboratory Press.

Cross-β Polymerization of Low Complexity Sequence Domains.

PubMed

Kato, Masato; McKnight, Steven L

2017-03-01

Most transcription factors and RNA regulatory proteins encoded by eukaryotic genomes ranging from yeast to humans contain polypeptide domains variously described as intrinsically disordered, prion-like, or of low complexity (LC). These LC domains exist in an unfolded state when DNA and RNA regulatory proteins are studied in biochemical isolation from cells. Upon incubation in the purified state, many of these LC domains polymerize into homogeneous, labile amyloid-like fibers. Here, we consider several lines of evidence that may favor biologic utility for LC domain polymers. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

Sexual conflict, life span, and aging.

PubMed

Adler, Margo I; Bonduriansky, Russell

2014-06-17

The potential for sexual conflict to influence the evolution of life span and aging has been recognized for more than a decade, and recent work also suggests that variation in life span and aging can influence sexually antagonistic coevolution. However, empirical exploration of these ideas is only beginning. Here, we provide an overview of the ideas and evidence linking inter- and intralocus sexual conflicts with life span and aging. We aim to clarify the conceptual basis of this research program, examine the current state of knowledge, and suggest key questions for further investigation. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

The impact of long-term hydrocarbon exposure on the structure, activity, and biogeochemical functioning of microbial mats.

PubMed

Aubé, Johanne; Senin, Pavel; Pringault, Olivier; Bonin, Patricia; Deflandre, Bruno; Bouchez, Olivier; Bru, Noëlle; Biritxinaga-Etchart, Edurne; Klopp, Christophe; Guyoneaud, Rémy; Goñi-Urriza, Marisol

2016-10-15

Photosynthetic microbial mats are metabolically structured systems driven by solar light. They are ubiquitous and can grow in hydrocarbon-polluted sites. Our aim is to determine the impact of chronic hydrocarbon contamination on the structure, activity, and functioning of a microbial mat. We compared it to an uncontaminated mat harboring similar geochemical characteristics. The mats were sampled in spring and fall for 2years. Seasonal variations were observed for the reference mat: sulfur cycle-related bacteria dominated spring samples, while Cyanobacteria dominated in autumn. The contaminated mat showed minor seasonal variation; a progressive increase of Cyanobacteria was noticed, indicating a perturbation of the classical seasonal behavior. Hydrocarbon content was the main factor explaining the differences in the microbial community structure; however, hydrocarbonoclastic bacteria were among rare or transient Operational Taxonomic Units (OTUs) in the contaminated mat. We suggest that in long-term contaminated systems, hydrocarbonoclastic bacteria cannot be considered a sentinel of contamination. Copyright © 2016 Elsevier Ltd. All rights reserved.

Metagenomic and Biochemical Characterizations of Sulfur Oxidation Metabolism in Uncultured Large Sausage-Shaped Bacterium in Hot Spring Microbial Mats

PubMed Central

Tamaki, Hideyuki; Kamagata, Yoichi; Hanada, Satoshi

2012-01-01

So-called “sulfur-turf” microbial mats in sulfide containing hot springs (55–70°C, pH 7.3–8.3) in Japan were dominated by a large sausage-shaped bacterium (LSSB) that is closely related to the genus Sulfurihydrogenibium. Several previous reports proposed that the LSSB would be involved in sulfide oxidation in hot spring. However, the LSSB has not been isolated yet, thus there has been no clear evidence showing whether it possesses any genes and enzymes responsible for sulfide oxidation. To verify this, we investigated sulfide oxidation potential in the LSSB using a metagenomic approach and subsequent biochemical analysis. Genome fragments of the LSSB (a total of 3.7 Mb sequence including overlapping fragments) were obtained from the metagenomic fosmid library constructed from genomic DNA of the sulfur-turf mats. The sequence annotation clearly revealed that the LSSB possesses sulfur oxidation-related genes coding sulfide dehydrogenase (SD), sulfide-quinone reductase and sulfite dehydrogenase. The gene encoding SD, the key enzyme for sulfide oxidation, was successfully cloned and heterologously expressed in Escherichia coli. The purified recombinant enzyme clearly showed SD activity with optimum temperature and pH of 60°C and 8.0, respectively, which were consistent with the environmental conditions in the hot spring where the sulfur-turf thrives. Furthermore, the affinity of SD to sulfide was relatively high, which also reflected the environment where the sulfide could be continuously supplied. This is the first report showing that the LSSB harbors sulfide oxidizing metabolism adapted to the hot spring environment and can be involved in sulfide oxidation in the sulfur-turf microbial mats. PMID:23185438

Journal of Special Operations Medicine, Spring 2008, Training Supplement

DTIC Science & Technology

2008-01-01

Tactical Combat Casualty Care (CoTCCC), have been changed in the TME Protocols. (2007) • The Fentanyl oral dosage of 800 mcg, as recommended by the...14aTMEP Behavioral Changes (Includes Psychosis, Depression, Suicidal Impulses)------------------------- 15 aTMEP Bronchitis/ Pneumonia

Year 1 Field Work Report: Utah Bat Monitoring Protocol

DTIC Science & Technology

2010-01-28

Plateau shrublands, Great Basin shrub steppe, Wasatch and Uinta montane forests, Mojave Desert and Wyoming Basin shrub steppe. A total 65, 20 x 20 km... Basin shrub steppe, Wasatch and Uinta montane forests) each harbored 20 sampling cells, while the limited size of the Mojave Desert and Wyoming Basin ...Wasatch and Uinta montane forest and Wyoming Basin shrub steppe). Site # A unique identifier between 1 and 20 within each ecoregion. UTM The

Size distributions of ambient air particles and enrichment factor analyses of metallic elements at Taichung Harbor near the Taiwan Strait

NASA Astrophysics Data System (ADS)

Fang, Guor-Cheng; Wu, Yuh-Shen; Chang, Shih-Yu; Huang, Shih-Han; Rau, Jui-Yeh

2006-10-01

This work attempts to characterize metallic elements associated with atmospheric particulate matter on a dry deposition plate, a TE-PUF high-volume air sampler and a universal air sampler. Dry deposition fluxes of particulates and concentrations of total suspended particulate, fine (PM 2.5) and coarse (PM 2.5-10) particulate matters were collected at Taichung harbor sampling sites from August 2004 to January 2005. Chemical analyses of metallic elements were made using a flame atomic absorption spectrophotometer coupled with hollow cathode lamps. Concentrations of metal elements in the forms of coarse particles and fine particles as well as the coarse/fine particulate ratios were presented. Statistical methods such as correlation analysis, principal component analysis and enrichment factor analysis were performed to compare the chemical components and identify possible emission sources at the sampling sites. Metallic elements of Cu, Zn, Pb, Cr, Ni and Mg had higher EF crust ratios in winter and spring than in summer and autumn. Diurnal and nocturnal variations of metallic element concentrations in fine and coarse particles were also discussed.

Tributary loading of mercury to Lake Michigan: Importance of seasonal events and phase partitioning

USGS Publications Warehouse

Hurley, J.P.; Cowell, S.E.; Shafer, M.M.; Hughes, P.E.

1998-01-01

As a component of a lakewide mass balance study for Lake Michigan, we measured total mercury (Hg(T)) concentrations and fluxes in 11 selected tributaries. Unfiltered Hg(T) concentrations ranged from 0.56 ng l-61 at the Pete Marquette River to 182 ng l-1 at the Fox River. Highest mean Hg(T) concentrations were observed in the Fox R., Indiana Harbor Ship Canal, Grand R. and the Kalamazoo R. Mean particulate matter Hg(T) content ranged from about 0.1 to 1.5 ??g g-1, with highest levels from the industrialized basins of the Indiana Harbor and Fox River. Highest tributary loading rates (g day-1) were observed from the Fox, Grand, Kalamazoo and St. Joseph Rivers. Increased loading rates during spring melt and summer/fall storm events in these tributaries were generally associated with particulate loading from either sediment resuspension or erosional processes. In contrast, filtered Hg(T) represented 80% of the Hg(T) flux in the Manistique R., whose watershed is comprised almost entirely of wetlands and forest.

Microbial diversity in an Armenian geothermal spring assessed by molecular and culture-based methods.

PubMed

Panosyan, Hovik; Birkeland, Nils-Kåre

2014-11-01

The phylogenetic diversity of the prokaryotic community thriving in the Arzakan hot spring in Armenia was studied using molecular and culture-based methods. A sequence analysis of 16S rRNA gene clone libraries demonstrated the presence of a diversity of microorganisms belonging to the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Epsilonproteobacteria, Firmicutes, Bacteroidetes phyla, and Cyanobacteria. Proteobacteria was the dominant group, representing 52% of the bacterial clones. Denaturing gradient gel electrophoresis profiles of the bacterial 16S rRNA gene fragments also indicated the abundance of Proteobacteria, Bacteroidetes, and Cyanobacteria populations. Most of the sequences were most closely related to uncultivated microorganisms and shared less than 96% similarity with their closest matches in GenBank, indicating that this spring harbors a unique community of novel microbial species or genera. The majority of the sequences of an archaeal 16S rRNA gene library, generated from a methanogenic enrichment, were close relatives of members of the genus Methanoculleus. Aerobic endospore-forming bacteria mainly belonging to Bacillus and Geobacillus were detected only by culture-dependent methods. Three isolates were successfully obtained having 99, 96, and 96% 16S rRNA gene sequence similarities to Arcobacter sp., Methylocaldum sp., and Methanoculleus sp., respectively. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Microbial ecology of two hot springs of Sikkim: Predominate population and geochemistry.

PubMed

Najar, Ishfaq Nabi; Sherpa, Mingma Thundu; Das, Sayak; Das, Saurav; Thakur, Nagendra

2018-10-01

Northeastern regions of India are known for their floral and faunal biodiversity. Especially the state of Sikkim lies in the eastern Himalayan ecological hotspot region. The state harbors many sulfur rich hot springs which have therapeutic and spiritual values. However, these hot springs are yet to be explored for their microbial ecology. The development of neo generation techniques such as metagenomics has provided an opportunity for inclusive study of microbial community of different environment. The present study describes the microbial diversity in two hot springs of Sikkim that is Polok and Borong with the assist of culture dependent and culture independent approaches. The culture independent techniques used in this study were next generation sequencing (NGS) and Phospholipid Fatty Acid Analysis (PLFA). Having relatively distinct geochemistry both the hot springs are thermophilic environments with the temperature range of 50-77 °C and pH range of 5-8. Metagenomic data revealed the dominance of bacteria over archaea. The most abundant phyla were Proteobacteria and Bacteroidetes although other phyla were also present such as Acidobacteria, Nitrospirae, Firmicutes, Proteobacteria, Parcubacteria and Spirochaetes. The PLFA studies have shown the abundance of Gram Positive bacteria followed by Gram negative bacteria. The culture dependent technique was correlative with PLFA studies. Most abundant bacteria as isolated and identified were Gram-positive genus Geobacillus and Anoxybacillus. The genus Geobacillus has been reported for the first time in North-Eastern states of India. The Geobacillus species obtained from the concerned hot springs were Geobacillus toebii, Geobacillus lituanicus, Geobacillus Kaustophillus and the Anoxybacillus species includes Anoxybacillus gonensis and Anoxybacillus Caldiproteolyticus. The distribution of major genera and their statistical correlation analyses with the geochemistry of the springs predicted that the temperature, pH, alkalinity, Ca 2+ , Mg 2+ , Cl 2+ , and sulfur were main environmental variables influencing the microbial community composition and diversity. Also the piper diagram suggested that the water of both the hot springs are Ca-HCO 3- type and can be predicted as shallow fresh ground waters. This study has provided an insight into the ecological interaction of the diverse microbial communities and associated physicochemical parameters, which will help in determining the future studies on different biogeochemical pathways in these hot springs. Copyright © 2018. Published by Elsevier B.V.

Membrane Transport across Polarized Epithelia.

PubMed

Garcia-Castillo, Maria Daniela; Chinnapen, Daniel J-F; Lencer, Wayne I

2017-09-01

Polarized epithelial cells line diverse surfaces throughout the body forming selective barriers between the external environment and the internal milieu. To cross these epithelial barriers, large solutes and other cargoes must undergo transcytosis, an endocytic pathway unique to polarized cell types, and significant for the development of cell polarity, uptake of viral and bacterial pathogens, transepithelial signaling, and immunoglobulin transport. Here, we review recent advances in our knowledge of the transcytotic pathway for proteins and lipids. We also discuss briefly the promise of harnessing the molecules that undergo transcytosis as vehicles for clinical applications in drug delivery. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

Ambiguity produces attention shifts in category learning.

PubMed

Vadillo, Miguel A; Orgaz, Cristina; Luque, David; Nelson, James Byron

2016-04-01

It has been suggested that people and nonhuman animals protect their knowledge from interference by shifting attention toward the context when presented with information that contradicts their previous beliefs. Despite that suggestion, no studies have directly measured changes in attention while participants are exposed to an interference treatment. In the present experiments, we adapted a dot-probe task to track participants' attention to cues and contexts while they were completing a simple category learning task. The results support the hypothesis that interference produces a change in the allocation of attention to cues and contexts. © 2016 Vadillo et al.; Published by Cold Spring Harbor Laboratory Press.

Neurodegenerative Disease Transmission and Transgenesis in Mice.

PubMed

Dugger, Brittany N; Perl, Daniel P; Carlson, George A

2017-11-01

Although the discovery of the prion protein (PrP) resulted from its co-purification with scrapie infectivity in Syrian hamsters, work with genetically defined and genetically modified mice proved crucial for understanding the fundamental processes involved not only in prion diseases caused by PrP misfolding, aggregation, and spread but also in other, much more common, neurodegenerative brain diseases. In this review, we focus on methodological and conceptual approaches used to study scrapie and related PrP misfolding diseases in mice and how these approaches have advanced our understanding of related disorders including Alzheimer's and Parkinson's disease. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

How natural a kind is "eukaryote?".

PubMed

Doolittle, W Ford

2014-06-02

Systematics balances uneasily between realism and nominalism, uncommitted as to whether biological taxa are discoveries or inventions. If the former, they might be taken as natural kinds. I briefly review some philosophers' concepts of natural kinds and then argue that several of these apply well enough to "eukaryote." Although there are some sticky issues around genomic chimerism and when eukaryotes first appeared, if we allow for degrees in the naturalness of kinds, existing eukaryotes rank highly, higher than prokaryotes. Most biologists feel this intuitively: All I attempt to do here is provide some conceptual justification. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

Molecular Mechanisms of Preeclampsia.

PubMed

Hod, Tammy; Cerdeira, Ana Sofia; Karumanchi, S Ananth

2015-08-20

Preeclampsia is a pregnancy-specific disease characterized by new onset hypertension and proteinuria after 20 wk of gestation. It is a leading cause of maternal and fetal morbidity and mortality worldwide. Exciting discoveries in the last decade have contributed to a better understanding of the molecular basis of this disease. Epidemiological, experimental, and therapeutic studies from several laboratories have provided compelling evidence that an antiangiogenic state owing to alterations in circulating angiogenic factors leads to preeclampsia. In this review, we highlight the role of key circulating antiangiogenic factors as pathogenic biomarkers and in the development of novel therapies for preeclampsia. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

Design Automation in Synthetic Biology.

PubMed

Appleton, Evan; Madsen, Curtis; Roehner, Nicholas; Densmore, Douglas

2017-04-03

Design automation refers to a category of software tools for designing systems that work together in a workflow for designing, building, testing, and analyzing systems with a target behavior. In synthetic biology, these tools are called bio-design automation (BDA) tools. In this review, we discuss the BDA tools areas-specify, design, build, test, and learn-and introduce the existing software tools designed to solve problems in these areas. We then detail the functionality of some of these tools and show how they can be used together to create the desired behavior of two types of modern synthetic genetic regulatory networks. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

Potential Uses and Inherent Challenges of Using Genome-Scale Sequencing to Augment Current Newborn Screening.

PubMed

Berg, Jonathan S; Powell, Cynthia M

2015-10-05

Since newborn screening (NBS) began in the 1960s, technological advances have enabled its expansion to include an increasing number of disorders. Recent developments now make it possible to sequence an infant's genome relatively quickly and economically. Clinical application of whole-exome and whole-genome sequencing is expanding at a rapid pace but presents many challenges. Its utility in NBS has yet to be demonstrated and its application in the pediatric population requires examination, not only for potential clinical benefits, but also for the unique ethical challenges it presents. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

Plasmodium Sporozoite Biology.

PubMed

Frischknecht, Friedrich; Matuschewski, Kai

2017-05-01

Plasmodium sporozoite transmission is a critical population bottleneck in parasite life-cycle progression and, hence, a target for prophylactic drugs and vaccines. The recent progress of a candidate antisporozoite subunit vaccine formulation to licensure highlights the importance of sporozoite transmission intervention in the malaria control portfolio. Sporozoites colonize mosquito salivary glands, migrate through the skin, penetrate blood vessels, breach the liver sinusoid, and invade hepatocytes. Understanding the molecular and cellular mechanisms that mediate the remarkable sporozoite journey in the invertebrate vector and the vertebrate host can inform evidence-based next-generation drug development programs and immune intervention strategies. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

p53 as an Effector or Inhibitor of Therapy Response.

PubMed

Ablain, Julien; Poirot, Brigitte; Esnault, Cécile; Lehmann-Che, Jacqueline; de Thé, Hugues

2015-12-04

Although integrity of the p53 signaling pathway in a given tumor was expected to be a critical determinant of response to therapies, most clinical studies failed to link p53 status and treatment outcome. Here, we present two opposite situations: one in which p53 is an essential effector of cure by targeted leukemia therapies and another one in advanced breast cancers in which p53 inactivation is required for the clinical efficacy of dose-dense chemotherapy. If p53 promotes or blocks therapy response, therapies must be tailored on its status in individual tumors. Copyright © 2016 Cold Spring Harbor Laboratory Press; all rights reserved.

Reactive Behavior Patterns Go Online.

ERIC Educational Resources Information Center

Dziuban, Charles D.; Moskal, Patsy D.; Dziuban, Emily K.

2000-01-01

Surveys of all online students at the University of Central Florida during summer 1997 and spring 1998 provided 381 useable survey instruments assessing learner reactive behavior patterns with the Long-Dziuban Reactive Behavior Protocol. Results indicated that students in online courses tended not to be the independent learners. (PGS)

Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data.

PubMed

Teng, Mingxiang; Irizarry, Rafael A

2017-11-01

The main application of ChIP-seq technology is the detection of genomic regions that bind to a protein of interest. A large part of functional genomics' public catalogs is based on ChIP-seq data. These catalogs rely on peak calling algorithms that infer protein-binding sites by detecting genomic regions associated with more mapped reads (coverage) than expected by chance, as a result of the experimental protocol's lack of perfect specificity. We find that GC-content bias accounts for substantial variability in the observed coverage for ChIP-seq experiments and that this variability leads to false-positive peak calls. More concerning is that the GC effect varies across experiments, with the effect strong enough to result in a substantial number of peaks called differently when different laboratories perform experiments on the same cell line. However, accounting for GC content bias in ChIP-seq is challenging because the binding sites of interest tend to be more common in high GC-content regions, which confounds real biological signals with unwanted variability. To account for this challenge, we introduce a statistical approach that accounts for GC effects on both nonspecific noise and signal induced by the binding site. The method can be used to account for this bias in binding quantification as well to improve existing peak calling algorithms. We use this approach to show a reduction in false-positive peaks as well as improved consistency across laboratories. © 2017 Teng and Irizarry; Published by Cold Spring Harbor Laboratory Press.

A historical reflection on the discovery of human retroviruses.

PubMed

Vahlne, Anders

2009-05-01

The discovery of HIV-1 as the cause of AIDS was one of the major scientific achievements during the last century. Here the events leading to this discovery are reviewed with particular attention to priority and actual contributions by those involved. Since I would argue that discovering HIV was dependent on the previous discovery of the first human retrovirus HTLV-I, the history of this discovery is also re-examined. The first human retroviruses (HTLV-I) was first reported by Robert C. Gallo and coworkers in 1980 and reconfirmed by Yorio Hinuma and coworkers in 1981. These discoveries were in turn dependent on the previous discovery by Gallo and coworkers in 1976 of interleukin 2 or T-cell growth factor as it was called then. HTLV-II was described by Gallo's group in 1982. A human retrovirus distinct from HTLV-I and HTLV-II in that it was shown to have the morphology of a lentivirus was in my mind described for the first time by Luc Montagnier in an oral presentation at Cold Spring Harbor in September of 1983. This virus was isolated from a patient with lymphadenopathy using the protocol previously described for HTLV by Gallo. The first peer reviewed paper by Montagnier's group of such a retrovirus, isolated from two siblings of whom one with AIDS, appeared in Lancet in April of 1984. However, the proof that a new human retrovirus (HIV-1) was the cause of AIDS was first established in four publications by Gallo's group in the May 4th issue of Science in 1984.

Seasonal use of shallow water habitat in the Lower Snake River reservoirs by juvenile fall Chinook salmon

USGS Publications Warehouse

Tiffan, Kenneth F.; Connor, William P.

2012-01-01

The U.S. Army Corps of Engineers (COE) is preparing a long term management plan for sediments that affect the authorized project purposes of the Lower Granite, Little Goose, Lower Monumental, and Ice Harbor reservoirs (hereafter, the lower Snake River reservoirs), and the area from the mouth of the Snake River to Ice Harbor Dam. We conducted a study from spring 2010 through winter 2011 to describe the habitat use by juvenile Chinook salmon within a selected group of shallow water habitat complexes (< 6 m deep) in the lower Snake River reservoirs to help inform the long-term plan. Natural fry and parr were present within all four shallow water habitat complexes that we studied from early spring through early summer, and parr ( = 40,345 ± 18,800 [error bound]) were more abundant than fry ( = 24,615 ± 5,701). Water < 2 m deep was highly used for rearing by natural fall Chinook salmon subyearlings (fry and parr combined; hereafter natural subyearlings) based on duration of use and relative group abundances during spring and summer, whereas the 2–6 m depth interval was more highly used by migratory hatchery fall Chinook salmon subyearlings and spring, summer, and fall Chinook salmon yearlings. Overall mean spring-summer apparent density of natural subyearlings was 15.5 times higher within the < 2 m depth interval than within the 2–6 m depth interval. Density of natural subyearlings also decreased as the distance a given shallow water habitat complex was located from the riverine spawning areas increased. Reservoir-type juveniles (or fish likely destined to become reservoir-type juveniles) were present in the lower Snake River reservoirs from fall 2010 through winter 2011; however, use of shallow water habitat by reservoir-type juveniles was limited during our study. We only collected 38 reservoir-type juveniles in shallow water habitat sites in beach and lampara seines during the fall. Radiotelemetry data revealed that though many tagged fish passed shallow water habitat sites, relatively few fish entered them and the median time fish spent within a given site was less than 1.4 h. Fish located by mobile tracking away from study sites were pelagically oriented, and generally not found over shallow water or close to shore. The findings in this report: (1) support the selection of natural fall Chinook subyearlings as the indicator group for determining the potential benefits of using dredge spoils to create shallow water habitat, (2) provide evidence for shallow water habitat use by natural subyearlings, (3) provide evidence against large-scale use of shallow water habitat by reservoir-type juveniles, (4) suggest that the depth criterion for defining shallow water habitat (i.e., < 6 m deep) warrants reconsideration, and (5) provide guidance for when to dredge and create shallow water habitat. Future research on habitat preference, feeding ecology, the food web, and intra-specific competition would help to better inform the long-term management plan.

Diversity and abundance of the arsenite oxidase gene aioA in geothermal areas of Tengchong, Yunnan, China.

PubMed

Jiang, Zhou; Li, Ping; Jiang, Dawei; Wu, Geng; Dong, Hailiang; Wang, Yanhong; Li, Bing; Wang, Yanxin; Guo, Qinghai

2014-01-01

A total of 12 samples were collected from the Tengchong geothermal areas of Yunnan, China, with the goal to assess the arsenite (AsIII) oxidation potential of the extant microbial communities as inferred by the abundance and diversity of the AsIII oxidase large subunit gene aioA relative to geochemical context. Arsenic concentrations were higher (on average 251.68 μg/L) in neutral or alkaline springs than in acidic springs (on average 30.88 μg/L). aioA abundance ranged from 1.63 × 10(1) to 7.08 × 10(3) per ng of DNA and positively correlated with sulfide and the ratios of arsenate (AsV):total dissolved arsenic (AsTot). Based on qPCR estimates of bacterial and archaeal 16S rRNA gene abundance, aioA-harboring organisms comprised as much as ~15% of the total community. Phylogenetically, the major aioA sequences (270 total) in the acidic hot springs (pH 3.3-4.4) were affiliated with Aquificales and Rhizobiales, while those in neutral or alkaline springs (pH 6.6-9.1) were inferred to be primarily bacteria related to Thermales and Burkholderiales. Interestingly, aioA abundance at one site greatly exceeded bacterial 16S rRNA gene abundance, suggesting these aioA genes were archaeal even though phylogenetically these aioA sequences were most similar to the Aquificales. In summary, this study described novel aioA sequences in geothermal features geographically far removed from those in the heavily studied Yellowstone geothermal complex.

Agrobacterium-Mediated Transformation of Bread and Durum Wheat Using Freshly Isolated Immature Embryos

NASA Astrophysics Data System (ADS)

Huixia, Wu; Angela, Doherty; Jones, Huw D.

Agrobacterium-mediated transformation of wheat is becoming a viable alternative to the more established biolistic protocols. It offers advantages in terms of simple, low-copy-number integrations and can be applied with similar efficiencies to specific durum wheat and spring and winter bread wheat types varieties.

Harmonization of Bordetella pertussis real-time PCR diagnostics in the United States in 2012.

PubMed

Williams, Margaret M; Taylor, Thomas H; Warshauer, David M; Martin, Monte D; Valley, Ann M; Tondella, M Lucia

2015-01-01

Real-time PCR (rt-PCR) is an important diagnostic tool for the identification of Bordetella pertussis, Bordetella holmesii, and Bordetella parapertussis. Most U.S. public health laboratories (USPHLs) target IS481, present in 218 to 238 copies in the B. pertussis genome and 32 to 65 copies in B. holmesii. The CDC developed a multitarget PCR assay to differentiate B. pertussis, B. holmesii, and B. parapertussis and provided protocols and training to 19 USPHLs. The 2012 performance exercise (PE) assessed the capability of USPHLs to detect these three Bordetella species in clinical samples. Laboratories were recruited by the Wisconsin State Proficiency Testing program through the Association of Public Health Laboratories, in partnership with the CDC. Spring and fall PE panels contained 12 samples each of viable Bordetella and non-Bordetella species in saline. Fifty and 53 USPHLs participated in the spring and fall PEs, respectively, using a variety of nucleic acid extraction methods, PCR platforms, and assays. Ninety-six percent and 94% of laboratories targeted IS481 in spring and fall, respectively, in either singleplex or multiplex assays. In spring and fall, respectively, 72% and 79% of USPHLs differentiated B. pertussis and B. holmesii and 68% and 72% identified B. parapertussis. IS481 cycle threshold (CT) values for B. pertussis samples had coefficients of variation (CV) ranging from 10% to 28%. Of the USPHLs that differentiated B. pertussis and B. holmesii, sensitivity was 96% and specificity was 95% for the combined panels. The 2012 PE demonstrated increased harmonization of rt-PCR Bordetella diagnostic protocols in USPHLs compared to that of the previous survey. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Host specificity and coevolution of Flavobacteriaceae endosymbionts within the siphonous green seaweed Bryopsis.

PubMed

Hollants, Joke; Leliaert, Frederik; Verbruggen, Heroen; De Clerck, Olivier; Willems, Anne

2013-06-01

The siphonous green seaweed Bryopsis harbors complex intracellular bacterial communities. Previous studies demonstrated that certain species form close, obligate associations with Flavobacteriaceae. A predominant imprint of host evolutionary history on the presence of these bacteria suggests a highly specialized association. In this study we elaborate on previous results by expanding the taxon sampling and testing for host-symbiont coevolution Therefore, we optimized a PCR protocol to directly and specifically amplify Flavobacteriaceae endosymbiont 16S rRNA gene sequences, which allowed us to screen a large number of algal samples without the need for cultivation or surface sterilization. We analyzed 146 Bryopsis samples, and 92 additional samples belonging to the Bryopsidales and other orders within the class Ulvophyceae. Results indicate that the Flavobacteriaceae endosymbionts are restricted to Bryopsis, and only occur within specific, warm-temperate and tropical clades of the genus. Statistical analyses (AMOVA) demonstrate a significant non-random host-symbiont association. Comparison of bacterial 16S rRNA and Bryopsis rbcL phylogenies, however, reveal complex host-symbiont evolutionary associations, whereby closely related hosts predominantly harbor genetically similar endosymbionts. Bacterial genotypes are rarely confined to a single Bryopsis species and most Bryopsis species harbored several Flavobacteriaceae, obscuring a clear pattern of coevolution. Copyright © 2013 Elsevier Inc. All rights reserved.

Marine Ship Automatic Identification System (AIS) for Enhanced Coastal Security Capabilities: An Oil Spill Tracking Application

DTIC Science & Technology

2007-09-01

in port, harbor or waterway incidents; and, oil or oily wastes illegally dumped at sea, including illegal discharge of oily bilge or ballast waters ...quantities of oily waste and oily bilge water and sludge at sea using specially installed pipes, which they were careful to have removed and hidden...detailing specifics for oil and bilge water handling equipment, oil hold washing protocols, and a 15 part per million discharge limit of oil content in

A GMP-compliant protocol to expand and transfect cancer patient T cells with mRNA encoding a tumor-specific chimeric antigen receptor.

PubMed

Krug, Christian; Wiesinger, Manuel; Abken, Hinrich; Schuler-Thurner, Beatrice; Schuler, Gerold; Dörrie, Jan; Schaft, Niels

2014-10-01

Chimeric antigen receptors (CARs), which combine an antibody-derived binding domain (single chain fragment variable) with T-cell-activating signaling domains, have become a promising tool in the adoptive cellular therapy of cancer. Retro- and lenti-viral transductions are currently the standard methods to equip T cells with a CAR; permanent CAR expression, however, harbors several risks like uncontrolled auto-reactivity. Modification of T cells by electroporation with CAR-encoding RNA to achieve transient expression likely circumvents these difficulties. We here present a GMP-compliant protocol to activate and expand T cells for clinical application. The protocol is optimized in particular to produce CAR-modified T cells in clinically sufficient numbers under full GMP-compliance from late-stage cancer patients. This protocol allows the generation of 6.7 × 10(8) CAR-expressing T cells from one patient leukapheresis. The CAR-engineered T cells produced pro-inflammatory cytokines after stimulation with antigen-bearing tumor cells and lysed tumor cells in an antigen-specific manner. This functional capacity was maintained after cryopreservation. Taken together, we provide a clinically applicable protocol to transiently engineer sufficient numbers of antigen-specific patient T cells for use in adoptive cell therapy of cancer.

Seasonal monitoring of blue mussel (Mytilus spp.) populations in a harbor area: A focus on responses to environmental factors and chronic contamination.

PubMed

Lacroix, C; Duvieilbourg, E; Guillou, N; Guyomarch, J; Bassoulet, C; Moraga, D; Chapalain, G; Auffret, M

2017-08-01

Coastal waters corresponding to macrotidal systems are among the most variable marine biotopes. Sessile animals as bivalve mollusks may however be found forming intertidal beds at high densities, as allowed by full adaptation to local conditions. A better knowledge of adaptive responses to environmental factors is required to foresee possible adverse effects of global change. At the sub-cellular level, transcriptional responses are among the earliest signals of environmental disturbances and they can reveal subtle and meaningful changes in organism exposed to stress. Three blue mussel (Mytilus spp.) populations inhabiting the Bay of Brest (France) in sites exposed to different levels of chronic pollution, from low to moderate, were surveyed upon a seasonal schedule, with special attention to the reproductive cycle. Major seawater parameters were monitored over a full-year in the framework of the S!RANO project, based on an automatic high frequency acquisition system installed aboard a ship of opportunity. The health status of mussels has been assessed by measuring a condition index and gametogenesis has been followed by histology. Selected biological responses to environmental stress were detected using a multimarker approach including expression of genes involved in chemical stress response and energetic metabolism, and cellular immune parameters. Environmental parameters showed deep seasonal variations which differed among sites. Most biological responses followed a seasonal pattern. Late winter and spring corresponded to an active reproduction period in the Bay of Brest. Earlier spawning was observed in harbor areas compared to the oceanic site and an altered physiological state was assumed in commercial harbor mussels during the reproductive period, suggesting that their health is compromised at this time of year. However, no signs of severe chemical stress were detected in both harbor mussel populations, which could reflect adaptive responses to adverse environmental conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Environmental parameters influence on the dynamics of total and pathogenic Vibrio parahaemolyticus densities in Crassostrea virginica harvested from Mexico's Gulf coast.

PubMed

López-Hernández, Karla M; Pardío-Sedas, Violeta T; Lizárraga-Partida, Leonardo; Williams, José de J; Martínez-Herrera, David; Flores-Primo, Argel; Uscanga-Serrano, Roxana; Rendón-Castro, Karla

2015-02-15

The influence of environmental parameters on the total and pathogenic Vibrio parahaemolyticus seasonal densities in American oysters (Crassostrea virginica) was evaluated for 1 year. Harvesting site A yielded the highest mean densities of V. parahaemolyticus tlh+, tdh+/trh-, tdh-/trh+ and tdh+/trh+ during spring season at 2.57, 1.74, 0.36, and -0.40 log10 MPN/g, respectively, and tdh+/orf8+ during winter season (0.90 log10 MPN/g). V. parahaemolyticus tlh+ densities were associated to salinity (R(2)=0.372, P<0.022), tdh+/trh+ to turbidity (R(2)=0.597, P<0.035), and orf8+ to temperature, salinity, and pH (R(2)=0.964, P<0.001). The exposure to salinity and temperature conditions during winter and spring seasons regulated the dynamics of V. parahaemolyticus harboring potentially pathogenic genotypes within the oyster. The adaptive response of V. parahaemolyticus to seasonal environmental changes may lead to an increase in survival and virulence, threatening the seafood safety and increasing the risk of illness. Copyright © 2014 Elsevier Ltd. All rights reserved.

Sustainable Management of Springs and Associated Wetlands in Aridland Regions: A Water Quality Perspective for Cibola National Forest, NM

NASA Astrophysics Data System (ADS)

Paffett, K.; Crossey, L. J.; Crowley, L.; Karlstrom, K. E.

2010-12-01

In the arid southwestern U.S., springs and their associated wetlands provide an opportunity for diverse ecosystems to flourish. With increasing encroachment, multiple-use requirements and increasing groundwater depletion, a better understanding of how the springs function is needed in order to properly manage the springs as a resource. Critical data on spring status (discharge patterns across seasons and water quality) are lacking for most springs. New strategies and environmental sensors can be employed to provide baseline information, as well as continuous data. We report here on systematic evaluation of a suite of springs of the Cibola National Forest in central New Mexico, including characteristics of discharge and water quality. The work is prompted by concerns on preservation of vital habitat for the Zuni Bluehead Sucker in portions of the Cibola National Forest. Spring occurrence includes a range of elevation (2000-2500m), vegetation type (arid grasslands to alpine wilderness), impact (livestock use, increased groundwater withdrawal, species of concern, and increased recreational use), and water quality (potable to saline). Many of the springs occur along fault structures, and are fed by groundwater from confined aquifer systems. Two levels of protocols are described: Level One for developing a baseline survey for water quality in managed lands (geospatial data, geologic map, systematic photography, discharge estimate and field-determined water quality parameters); and Level Two Impact Evaluation Monitoring (includes high-resolution geologic mapping, major ion chemistry, multiple sampling dates, and real-time autonomous logging of several parameters including temperature, pH, conductance and dissolved oxygen). Data collected from the surveys are stored in a geospatial repository to serve as background for future monitoring of the water resources in the area.

Comparison of benthos and plankton for selected areas of concern and non-areas of concern in western Lake Michigan Rivers and Harbors in 2012

USGS Publications Warehouse

Eikenberry, Barbara C. Scudder; Bell, Amanda H.; Olds, Hayley T.; Burns, Daniel J.

2016-07-25

Recent data are lacking to assess whether impairments still exist at four of Wisconsin’s largest Lake Michigan harbors that were designated as Areas of Concern (AOCs) in the late 1980s due to sediment contamination and multiple Beneficial Use Impairments (BUIs), such as those affecting benthos (macroinvertebrates) and plankton (zooplankton and phytoplankton) communities. During three seasonal sampling events (“seasons”) in May through August 2012, the U.S. Geological Survey collected sediment benthos and water plankton at the four AOCs as well as six less-degraded non-AOCs along the western Lake Michigan shoreline to assess whether AOC communities were degraded in comparison to non-AOC communities. The four AOCs are the Lower Menominee River, the Lower Green Bay and Fox River, the Sheboygan River, and the Milwaukee Estuary. Due to their size and complexity, multiple locations or “subsites” were sampled within the Lower Green Bay and Fox River AOC (Lower Green Bay, the Fox River near Allouez, and the Fox River near De Pere) and within the Milwaukee Estuary AOC (the Milwaukee River, the Menomonee River, and the Milwaukee Harbor) and single locations were sampled at the other AOCs and non-AOCs. The six non-AOCs are the Escanaba River in Michigan, and the Oconto River, Ahnapee River, Kewaunee River, Manitowoc River, and Root River in Wisconsin. Benthos samples were collected by using Hester-Dendy artificial substrates deployed for 30 days and by using a dredge sampler; zooplankton were collected by net and phytoplankton by whole-water sampler. Except for the Lower Green Bay and Milwaukee Harbor locations, communities at each AOC were compared to all non-AOCs as a group and to paired non-AOCs using taxa relative abundances and metrics, including richness, diversity, and an Index of Biotic Integrity (IBI, for Hester-Dendy samples only). Benthos samples collected during one or more seasons were rated as degraded for at least one metric at all AOCs. In the Milwaukee Estuary, benthos richness was lower in the Milwaukee River subsite spring and summer samples and in the Menomonee River subsite spring sample relative to the paired non-AOCs. Benthos diversity and IBIs at the Menomonee River subsite and IBIs at the Milwaukee River subsite and Sheboygan River were significantly lower than at all non-AOCs as a group across all seasons and therefore were rated as degraded. In addition, IBIs at the Lower Menominee River were significantly lower than those at the paired non-AOCs during all seasons and were therefore rated degraded. Benthos at both Fox River subsites and the Milwaukee River subsite were significantly different from their paired non-AOCs during all three seasons, based on a comparison of the relative abundances of taxa using multivariate testing. Metrics for plankton at AOCs were not significantly lower than those at the paired or group non-AOCs during all seasons; however, zooplankton richness in spring at the Sheboygan River and in fall at the Menomonee River subsite was rated as degraded in comparison to paired non-AOCs. Also, zooplankton richness in fall at the Fox River near Allouez subsite and in spring at the Milwaukee River subsite was rated degraded overall because values were lower than at all non-AOCs as a group and lower than at the paired non-AOCs. Zooplankton diversity in fall at the Fox River near Allouez subsite and the Lower Menominee River was rated degraded in comparison to paired non-AOC comparison sites. Zooplankton communities at the Fox River near Allouez subsite were significantly different from the paired non-AOCs when multivariate comparisons were made without rotifers other than A. priodonta. Overall, benthos and zooplankton BUIs remained at the AOCs in 2012 but no AOCs with a phytoplankton BUI were rated degraded in comparison to non-AOCs. The use of a multiple ecological measures, structural and functional, and multiple statistical analyses, biological metrics and multivariate statistics, provided assessments that defined 2012 status of communities relative to less-impaired non-AOCs in the Great Lakes area.

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data.

PubMed

Ha, Gavin; Roth, Andrew; Khattra, Jaswinder; Ho, Julie; Yap, Damian; Prentice, Leah M; Melnyk, Nataliya; McPherson, Andrew; Bashashati, Ali; Laks, Emma; Biele, Justina; Ding, Jiarui; Le, Alan; Rosner, Jamie; Shumansky, Karey; Marra, Marco A; Gilks, C Blake; Huntsman, David G; McAlpine, Jessica N; Aparicio, Samuel; Shah, Sohrab P

2014-11-01

The evolution of cancer genomes within a single tumor creates mixed cell populations with divergent somatic mutational landscapes. Inference of tumor subpopulations has been disproportionately focused on the assessment of somatic point mutations, whereas computational methods targeting evolutionary dynamics of copy number alterations (CNA) and loss of heterozygosity (LOH) in whole-genome sequencing data remain underdeveloped. We present a novel probabilistic model, TITAN, to infer CNA and LOH events while accounting for mixtures of cell populations, thereby estimating the proportion of cells harboring each event. We evaluate TITAN on idealized mixtures, simulating clonal populations from whole-genome sequences taken from genomically heterogeneous ovarian tumor sites collected from the same patient. In addition, we show in 23 whole genomes of breast tumors that the inference of CNA and LOH using TITAN critically informs population structure and the nature of the evolving cancer genome. Finally, we experimentally validated subclonal predictions using fluorescence in situ hybridization (FISH) and single-cell sequencing from an ovarian cancer patient sample, thereby recapitulating the key modeling assumptions of TITAN. © 2014 Ha et al.; Published by Cold Spring Harbor Laboratory Press.

Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia.

PubMed

Bhattacharya, Sanchita; Li, Jian; Sockell, Alexandra; Kan, Matthew J; Bava, Felice A; Chen, Shann-Ching; Ávila-Arcos, María C; Ji, Xuhuai; Smith, Emery; Asadi, Narges B; Lachman, Ralph S; Lam, Hugo Y K; Bustamante, Carlos D; Butte, Atul J; Nolan, Garry P

2018-04-01

Over a decade ago, the Atacama humanoid skeleton (Ata) was discovered in the Atacama region of Chile. The Ata specimen carried a strange phenotype-6-in stature, fewer than expected ribs, elongated cranium, and accelerated bone age-leading to speculation that this was a preserved nonhuman primate, human fetus harboring genetic mutations, or even an extraterrestrial. We previously reported that it was human by DNA analysis with an estimated bone age of about 6-8 yr at the time of demise. To determine the possible genetic drivers of the observed morphology, DNA from the specimen was subjected to whole-genome sequencing using the Illumina HiSeq platform with an average 11.5× coverage of 101-bp, paired-end reads. In total, 3,356,569 single nucleotide variations (SNVs) were found as compared to the human reference genome, 518,365 insertions and deletions (indels), and 1047 structural variations (SVs) were detected. Here, we present the detailed whole-genome analysis showing that Ata is a female of human origin, likely of Chilean descent, and its genome harbors mutations in genes ( COL1A1 , COL2A1 , KMT2D , FLNB , ATR , TRIP11 , PCNT ) previously linked with diseases of small stature, rib anomalies, cranial malformations, premature joint fusion, and osteochondrodysplasia (also known as skeletal dysplasia). Together, these findings provide a molecular characterization of Ata's peculiar phenotype, which likely results from multiple known and novel putative gene mutations affecting bone development and ossification. © 2018 Bhattacharya et al.; Published by Cold Spring Harbor Laboratory Press.

The Need for Integrated Approaches in Metabolic Engineering.

PubMed

Lechner, Anna; Brunk, Elizabeth; Keasling, Jay D

2016-11-01

This review highlights state-of-the-art procedures for heterologous small-molecule biosynthesis, the associated bottlenecks, and new strategies that have the potential to accelerate future accomplishments in metabolic engineering. We emphasize that a combination of different approaches over multiple time and size scales must be considered for successful pathway engineering in a heterologous host. We have classified these optimization procedures based on the "system" that is being manipulated: transcriptome, translatome, proteome, or reactome. By bridging multiple disciplines, including molecular biology, biochemistry, biophysics, and computational sciences, we can create an integral framework for the discovery and implementation of novel biosynthetic production routes. Copyright © 2016 Cold Spring Harbor Laboratory Press; all rights reserved.

Uncoupling neurogenic gene networks in the Drosophila embryo.

PubMed

Rogers, William A; Goyal, Yogesh; Yamaya, Kei; Shvartsman, Stanislav Y; Levine, Michael S

2017-04-01

The EGF signaling pathway specifies neuronal identities in the Drosophila embryo by regulating developmental patterning genes such as intermediate neuroblasts defective ( ind ). EGFR is activated in the ventral midline and neurogenic ectoderm by the Spitz ligand, which is processed by the Rhomboid protease. CRISPR/Cas9 was used to delete defined rhomboid enhancers mediating expression at each site of Spitz processing. Surprisingly, the neurogenic ectoderm, not the ventral midline, was found to be the dominant source of EGF patterning activity. We suggest that Drosophila is undergoing an evolutionary transition in central nervous system (CNS)-organizing activity from the ventral midline to the neurogenic ectoderm. © 2017 Rogers et al.; Published by Cold Spring Harbor Laboratory Press.

Binding among select episodic elements is altered via active short-term retrieval.

PubMed

Bridge, Donna J; Voss, Joel L

2015-08-01

Of the many elements that comprise an episode, are any disproportionately bound to the others? We tested whether active short-term retrieval selectively increases binding. Individual objects from multiobject displays were retrieved after brief delays. Memory was later tested for the other objects. Cueing with actively retrieved objects facilitated memory of associated objects, which was associated with unique patterns of viewing behavior during study and enhanced ERP correlates of retrieval during test, relative to other reminder cues that were not actively retrieved. Active short-term retrieval therefore enhanced binding of retrieved elements with others, thus creating powerful memory cues for entire episodes. © 2015 Bridge and Voss; Published by Cold Spring Harbor Laboratory Press.

Negative reinforcement impairs overnight memory consolidation.

PubMed

Stamm, Andrew W; Nguyen, Nam D; Seicol, Benjamin J; Fagan, Abigail; Oh, Angela; Drumm, Michael; Lundt, Maureen; Stickgold, Robert; Wamsley, Erin J

2014-11-01

Post-learning sleep is beneficial for human memory. However, it may be that not all memories benefit equally from sleep. Here, we manipulated a spatial learning task using monetary reward and performance feedback, asking whether enhancing the salience of the task would augment overnight memory consolidation and alter its incorporation into dreaming. Contrary to our hypothesis, we found that the addition of reward impaired overnight consolidation of spatial memory. Our findings seemingly contradict prior reports that enhancing the reward value of learned information augments sleep-dependent memory processing. Given that the reward followed a negative reinforcement paradigm, consolidation may have been impaired via a stress-related mechanism. © 2014 Stamm et al.; Published by Cold Spring Harbor Laboratory Press.

Is There Natural Killer Cell Memory and Can It Be Harnessed by Vaccination? Vaccination Strategies Based on NK Cell and ILC Memory.

PubMed

Cooper, Megan A; Fehniger, Todd A; Colonna, Marco

2017-12-18

Studies over the last decade have decisively shown that innate immune natural killer (NK) cells exhibit enhanced long-lasting functional responses following a single activation event. With the increased recognition of memory and memory-like properties of NK cells, questions have arisen with regard to their ability to effectively mediate vaccination responses in humans. Moreover, recently discovered innate lymphoid cells (ILCs) could also potentially exhibit memory-like functions. Here, we review different forms of NK cell memory, and speculate about the ability of these cells and ILCs to meaningfully contribute to vaccination responses. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

Cellular and Synaptic Properties of Local Inhibitory Circuits.

PubMed

Hull, Court

2017-05-01

Inhibitory interneurons play a key role in sculpting the information processed by neural circuits. Despite the wide range of physiologically and morphologically distinct types of interneurons that have been identified, common principles have emerged that have shed light on how synaptic inhibition operates, both mechanistically and functionally, across cell types and circuits. This introduction summarizes how electrophysiological approaches have been used to illuminate these key principles, including basic interneuron circuit motifs, the functional properties of inhibitory synapses, and the main roles for synaptic inhibition in regulating neural circuit function. It also highlights how some key electrophysiological methods and experiments have advanced our understanding of inhibitory synapse function. © 2017 Cold Spring Harbor Laboratory Press.

Canada's Patented Medicines (Notice of Compliance) Proceedings and Intellectual Property.

PubMed

Bian, Henry; McCourt, Conor

2015-01-08

Canada's Patent Register is a tool created by the Patented Medicines (Notice of Compliance) Regulations to help innovators protect their inventions relating to pharmaceuticals. This tool exists at the intersection between the intellectual property and drug approval regimes. By listing a patent on the Patent Register, an innovator can prevent a generic manufacturer from entering the marketplace rather than having to wait for his or her patent to be infringed. This article provides information on the requirements for listing a patent on the Patent Register and an overview of how the Patent Medicines (Notice of Compliance) Regulations affect the drug approval process. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

Do Memory CD4 T Cells Keep Their Cell-Type Programming: Plasticity versus Fate Commitment? Epigenome: A Dynamic Vehicle for Transmitting and Recording Cytokine Signaling.

PubMed

Johnson, John L; Vahedi, Golnaz

2018-03-01

CD4 + T cells are critical for the elimination of an immense array of microbial pathogens. Although there are aspects of helper T-cell differentiation that can be modeled as a classic cell-fate commitment, CD4 + T cells also maintain considerable flexibility in their transcriptional program. Here, we present an overview of chromatin biology during cellular reprogramming and, within this context, envision how the scope of cellular reprogramming may be expanded to further our understanding of the controversy surrounding CD4 + T lymphocyte plasticity or determinism. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

Sex differences in fear discrimination do not manifest as differences in conditioned inhibition.

PubMed

Foilb, Allison R; Bals, Julia; Sarlitto, Mary C; Christianson, John P

2018-01-01

Distinguishing safety from danger is necessary for survival, but is aberrant in individuals with post-traumatic stress disorder (PTSD). While PTSD is more prevalent in women than men, research on sex differences in safety learning is limited. Here, female rats demonstrated greater fear discrimination than males in a CS+/CS- paradigm. To determine if this sex difference transferred to fear inhibition, rats were tested for conditioned inhibition in a summation test with the CS+ and CS- presented in compound; no sex difference emerged. The results suggest sex differences in the neural mechanisms of discrimination learning but not recall of a fear inhibitor. © 2018 Foilb et al.; Published by Cold Spring Harbor Laboratory Press.

Primary auditory cortex regulates threat memory specificity.

PubMed

Wigestrand, Mattis B; Schiff, Hillary C; Fyhn, Marianne; LeDoux, Joseph E; Sears, Robert M

2017-01-01

Distinguishing threatening from nonthreatening stimuli is essential for survival and stimulus generalization is a hallmark of anxiety disorders. While auditory threat learning produces long-lasting plasticity in primary auditory cortex (Au1), it is not clear whether such Au1 plasticity regulates memory specificity or generalization. We used muscimol infusions in rats to show that discriminatory threat learning requires Au1 activity specifically during memory acquisition and retrieval, but not during consolidation. Memory specificity was similarly disrupted by infusion of PKMζ inhibitor peptide (ZIP) during memory storage. Our findings show that Au1 is required at critical memory phases and suggest that Au1 plasticity enables stimulus discrimination. © 2016 Wigestrand et al.; Published by Cold Spring Harbor Laboratory Press.

Mitosis-associated repression in development.

PubMed

Esposito, Emilia; Lim, Bomyi; Guessous, Ghita; Falahati, Hanieh; Levine, Michael

2016-07-01

Transcriptional repression is a pervasive feature of animal development. Here, we employ live-imaging methods to visualize the Snail repressor, which establishes the boundary between the presumptive mesoderm and neurogenic ectoderm of early Drosophila embryos. Snail target enhancers were attached to an MS2 reporter gene, permitting detection of nascent transcripts in living embryos. The transgenes exhibit initially broad patterns of transcription but are refined by repression in the mesoderm following mitosis. These observations reveal a correlation between mitotic silencing and Snail repression. We propose that mitosis and other inherent discontinuities in transcription boost the activities of sequence-specific repressors, such as Snail. © 2016 Esposito et al.; Published by Cold Spring Harbor Laboratory Press.

From structure to mechanism-understanding initiation of DNA replication.

PubMed

Riera, Alberto; Barbon, Marta; Noguchi, Yasunori; Reuter, L Maximilian; Schneider, Sarah; Speck, Christian

2017-06-01

DNA replication results in the doubling of the genome prior to cell division. This process requires the assembly of 50 or more protein factors into a replication fork. Here, we review recent structural and biochemical insights that start to explain how specific proteins recognize DNA replication origins, load the replicative helicase on DNA, unwind DNA, synthesize new DNA strands, and reassemble chromatin. We focus on the minichromosome maintenance (MCM2-7) proteins, which form the core of the eukaryotic replication fork, as this complex undergoes major structural rearrangements in order to engage with DNA, regulate its DNA-unwinding activity, and maintain genome stability. © 2017 Riera et al.; Published by Cold Spring Harbor Laboratory Press.

Wound healing and skin regeneration.

PubMed

Takeo, Makoto; Lee, Wendy; Ito, Mayumi

2015-01-05

The skin is a complex organ consisting of the epidermis, dermis, and skin appendages, including the hair follicle and sebaceous gland. Wound healing in adult mammals results in scar formation without any skin appendages. Studies have reported remarkable examples of scarless healing in fetal skin and appendage regeneration in adult skin following the infliction of large wounds. The models used in these studies have offered a new platform for investigations of the cellular and molecular mechanisms underlying wound healing and skin regeneration in mammals. In this article, we will focus on the contribution of skin appendages to wound healing and, conversely, skin appendage regeneration following injuries. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

Subsecond fear discrimination in rats: adult impairment in adolescent heavy alcohol drinkers.

PubMed

DiLeo, Alyssa; Wright, Kristina M; McDannald, Michael A

2016-11-01

Discriminating safety from danger must be accurate and rapid. Yet, the rapidity with which fear discrimination emerges remains unknown. Rapid fear discrimination in adulthood may be susceptible to impairment by adolescent heavy alcohol drinking, which increases incidence of anxiety disorders. Rats were given voluntary, adolescent alcohol access, and heavy drinkers were identified. In adulthood, rapid fear discrimination of safety, uncertainty, and danger cues was assessed. Normal rats, but not heavy drinkers, showed discriminative fear <1 sec following cue onset. This provides the first demonstration of subsecond fear discrimination and its adult impairment in adolescent heavy alcohol drinkers. © 2016 DiLeo et al.; Published by Cold Spring Harbor Laboratory Press.

Molecular Regulation of Exercise-Induced Muscle Fiber Hypertrophy.

PubMed

Bamman, Marcas M; Roberts, Brandon M; Adams, Gregory R

2018-06-01

Skeletal muscle hypertrophy is a widely sought exercise adaptation to counteract the muscle atrophy of aging and disease, or to improve athletic performance. While this desired muscle enlargement is a well-known adaptation to resistance exercise training (RT), the mechanistic underpinnings are not fully understood. The purpose of this review is thus to provide the reader with a summary of recent advances in molecular mechanisms-based on the most current literature-that are thought to promote RT-induced muscle hypertrophy. We have therefore focused this discussion on the following areas of fertile investigation: ribosomal function and biogenesis, muscle stem (satellite) cell activity, transcriptional regulation, mechanotransduction, and myokine signaling. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

Biology of Bone: The Vasculature of the Skeletal System.

PubMed

Watson, Emma C; Adams, Ralf H

2017-09-11

Blood vessels are essential for the distribution of oxygen, nutrients, and immune cells, as well as the removal of waste products. In addition to this conventional role as a versatile conduit system, the endothelial cells forming the innermost layer of the vessel wall also possess important signaling capabilities and can control growth, patterning, homeostasis, and regeneration of the surrounding organ. In the skeletal system, blood vessels regulate developmental and regenerative bone formation as well as hematopoiesis by providing vascular niches for hematopoietic stem cells. Here we provide an overview of blood vessel architecture, growth and properties in the healthy, aging, and diseased skeletal system. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

What is your reasonable expectation of success in obtaining pharmaceutical or biotechnology patents having nonobvious claimed inventions that the courts will uphold? An overview of obviousness court decisions.

PubMed

Pereira, Daniel J; Kunin, Stephen G

2014-12-04

This article explores the legal basis for establishing the nonobviousness of patent claims in the life sciences fields of technology drawn from the guidance provided in published decisions of the U.S. Patent and Trademark Office's Patent Trial and Appeal Board, federal district courts, the Federal Circuit Court of Appeals, and the U.S. Supreme Court. Our analysis, although equally applicable to all disciplines and technologies, focuses primarily on decisions of greatest import affecting patents in the fields of pharmaceutical chemistry and biotechnology. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

Improved Agrobacterium-mediated transformation and high efficiency of root formation from hypocotyl meristem of spring Brassica napus 'Precocity' cultivar.

PubMed

Liu, X X; Lang, S R; Su, L Q; Liu, X; Wang, X F

2015-12-14

Rape seed (Brassica napus L.) is one of the most important oil seed crops in the world. Genetic manipulation of rapeseed requires a suitable tissue culture system and an efficient method for plant regeneration, as well as an efficient transformation procedure. However, development of transgenic B. napus has been problematic, and current studies are limited to cultivated varieties. In this study, we report a protocol for regeneration of transgenic rape after Agrobacterium-mediated transformation of hypocotyls from the spring B. napus 'Precocity' cultivar. We analyzed the effects of plant growth regulators in the medium on regeneration. Additionally, factors affecting the transformation efficiency, including seedling age, Agrobacterium concentration, infection time, and co-cultivation time, were assessed by monitoring GUS expression. Results from these experiments revealed that transformation was optimized when the meristematic parts of the hypocotyls were taken from 8 day-old seedlings, cultured on Murashinge and Skoog basal media containing 0.1 mg/L 1-naphthaleneacetic acid and 2.5 mg/L 6-benzylaminopurine, and incubated in Agrobacterium suspension (OD600 = 0.5) for 3 to 5 min, followed by 2 days of co-cultivation. Integration of T-DNA into the plant genome was confirmed by polymerase chain reaction (PCR), b-glucuronidase histochemical staining, and quantitative real-time PCR. The protocols developed for regeneration, transformation, and rooting described in this study could help to accelerate the development of transgenic spring rape varieties with novel features.

A Comprehensive Census of Microbial Diversity in Hot Springs of Tengchong, Yunnan Province China Using 16S rRNA Gene Pyrosequencing

PubMed Central

Dong, Hailiang; Jiang, Hongchen; Briggs, Brandon R.; Peacock, Joseph P.; Huang, Qiuyuan; Huang, Liuqin; Wu, Geng; Zhi, Xiaoyang; Li, Wenjun; Dodsworth, Jeremy A.; Hedlund, Brian P.; Zhang, Chuanlun; Hartnett, Hilairy E.; Dijkstra, Paul; Hungate, Bruce A.

2013-01-01

The Rehai and Ruidian geothermal fields, located in Tengchong County, Yunnan Province, China, host a variety of geochemically distinct hot springs. In this study, we report a comprehensive, cultivation-independent census of microbial communities in 37 samples collected from these geothermal fields, encompassing sites ranging in temperature from 55.1 to 93.6°C, in pH from 2.5 to 9.4, and in mineralogy from silicates in Rehai to carbonates in Ruidian. Richness was low in all samples, with 21–123 species-level OTUs detected. The bacterial phylum Aquificae or archaeal phylum Crenarchaeota were dominant in Rehai samples, yet the dominant taxa within those phyla depended on temperature, pH, and geochemistry. Rehai springs with low pH (2.5–2.6), high temperature (85.1–89.1°C), and high sulfur contents favored the crenarchaeal order Sulfolobales, whereas those with low pH (2.6–4.8) and cooler temperature (55.1–64.5°C) favored the Aquificae genus Hydrogenobaculum. Rehai springs with neutral-alkaline pH (7.2–9.4) and high temperature (>80°C) with high concentrations of silica and salt ions (Na, K, and Cl) favored the Aquificae genus Hydrogenobacter and crenarchaeal orders Desulfurococcales and Thermoproteales. Desulfurococcales and Thermoproteales became predominant in springs with pH much higher than the optimum and even the maximum pH known for these orders. Ruidian water samples harbored a single Aquificae genus Hydrogenobacter, whereas microbial communities in Ruidian sediment samples were more diverse at the phylum level and distinctly different from those in Rehai and Ruidian water samples, with a higher abundance of uncultivated lineages, close relatives of the ammonia-oxidizing archaeon “Candidatus Nitrosocaldus yellowstonii”, and candidate division O1aA90 and OP1. These differences between Ruidian sediments and Rehai samples were likely caused by temperature, pH, and sediment mineralogy. The results of this study significantly expand the current understanding of the microbiology in Tengchong hot springs and provide a basis for comparison with other geothermal systems around the world. PMID:23326417

A comprehensive census of microbial diversity in hot springs of Tengchong, Yunnan Province China using 16S rRNA gene pyrosequencing.

PubMed

Hou, Weiguo; Wang, Shang; Dong, Hailiang; Jiang, Hongchen; Briggs, Brandon R; Peacock, Joseph P; Huang, Qiuyuan; Huang, Liuqin; Wu, Geng; Zhi, Xiaoyang; Li, Wenjun; Dodsworth, Jeremy A; Hedlund, Brian P; Zhang, Chuanlun; Hartnett, Hilairy E; Dijkstra, Paul; Hungate, Bruce A

2013-01-01

The Rehai and Ruidian geothermal fields, located in Tengchong County, Yunnan Province, China, host a variety of geochemically distinct hot springs. In this study, we report a comprehensive, cultivation-independent census of microbial communities in 37 samples collected from these geothermal fields, encompassing sites ranging in temperature from 55.1 to 93.6°C, in pH from 2.5 to 9.4, and in mineralogy from silicates in Rehai to carbonates in Ruidian. Richness was low in all samples, with 21-123 species-level OTUs detected. The bacterial phylum Aquificae or archaeal phylum Crenarchaeota were dominant in Rehai samples, yet the dominant taxa within those phyla depended on temperature, pH, and geochemistry. Rehai springs with low pH (2.5-2.6), high temperature (85.1-89.1°C), and high sulfur contents favored the crenarchaeal order Sulfolobales, whereas those with low pH (2.6-4.8) and cooler temperature (55.1-64.5°C) favored the Aquificae genus Hydrogenobaculum. Rehai springs with neutral-alkaline pH (7.2-9.4) and high temperature (>80°C) with high concentrations of silica and salt ions (Na, K, and Cl) favored the Aquificae genus Hydrogenobacter and crenarchaeal orders Desulfurococcales and Thermoproteales. Desulfurococcales and Thermoproteales became predominant in springs with pH much higher than the optimum and even the maximum pH known for these orders. Ruidian water samples harbored a single Aquificae genus Hydrogenobacter, whereas microbial communities in Ruidian sediment samples were more diverse at the phylum level and distinctly different from those in Rehai and Ruidian water samples, with a higher abundance of uncultivated lineages, close relatives of the ammonia-oxidizing archaeon "Candidatus Nitrosocaldus yellowstonii", and candidate division O1aA90 and OP1. These differences between Ruidian sediments and Rehai samples were likely caused by temperature, pH, and sediment mineralogy. The results of this study significantly expand the current understanding of the microbiology in Tengchong hot springs and provide a basis for comparison with other geothermal systems around the world.

Water- versus land-based exercise in elderly subjects: effects on physical performance and body composition

PubMed Central

Bergamin, Marco; Ermolao, Andrea; Tolomio, Silvia; Berton, Linda; Sergi, Giuseppe; Zaccaria, Marco

2013-01-01

The aim of this study was to assess the effectiveness of a 24-week exercise protocol carried out in geothermal spring water to improve overall physical function and muscle mass in a group of healthy elderly subjects. A further aim was to compare this water-based protocol with a land-based protocol and a control group. For this purpose, 59 subjects were recruited and randomly allocated to three groups: aquatic group (AG), land group (LG), and control group (CG). AG and LG followed a 6-month, twice-weekly, multimodality exercise intervention. AG underwent the protocol in hot-spring water (36°C) while LG did it in a land-based environment. After the intervention, knee-extension strength was maintained in AG and LG. The 8-foot up-and-go test showed a reduction in both exercise groups (AG −19.3%, P < 0.05; LG −12.6%, P < 0.05), with a significantly greater decrease in AG. The back-scratch test revealed an improvement only in AG (25.8%; P < 0.05), while the sit-and-reach test improved in all groups. Finally, AG reduced fat mass by 4% (P < 0.05), and dominant forearm fat decreased by 9.2% (P < 0.05). In addition, calf muscle density increased by 1.8% (P < 0.05). In summary, both water- and land-based activities were beneficial in maintaining strength and in improving lower-body flexibility. Aquatic exercise appeared a better activity to improve dynamic balance. Thermal swimming pools and the use of rating of perceived exertion as a method of exercise monitoring should be considered potentially useful tools to enhance physical performance and body composition in healthy elderly. PMID:24009416

Springs as Ecosystems: Clarifying Groundwater Dependence and Wetland Status (Invited)

NASA Astrophysics Data System (ADS)

Stevens, L.; Springer, A. E.; Ledbetter, J. D.

2013-12-01

Springs ecosystems are among the most productive, biologically diverse and culturally important ecosystems on Earth. Net annual productivity of some springs exceeds 5 kg/m^2/yr. Springs support an estimated 19% of the endangered species and numerous rare taxa in the United States. Springs serve as keystone ecosystems in arid regions, and as cornerstones of indigenous cultural well-being, history, economics, and aesthetics. Despite their significance, the ecosystem ecology and stewardship of springs have received scant scientific and public attention, resulting in loss or impairment of 50-90% of the springs in many regions, both arid and temperate. Six reasons contribute to the lack of attention to springs. Springs are poorly mapped because: 1) their generally small size is less than the pixel area of most remote sensing analyses and they are overlooked; and 2) springs detection is often limited by emergence on cliff faces, beneath heavy vegetation cover, or under water. In addition, 3) high levels of ecosystem complexity at springs require multidisciplinary team approaches for inventory, assessment, and research, but collaboration between the fields of hydrogeology and ecology has been limited. 4) Protectionism by land owners and organizations that manage springs limits the availability information, preventing regional assessment of status. 5) Prior to recent efforts, the absence of a descriptive lexicon of springs types has limited discussion about variation in ecological characteristics and processes. 6) Neither regarded entirely as groundwater or as surface water, springs fall 'between jurisdictional cracks' and are not subject to clear legal and regulatory oversight. With regards to the latter point, two jurisdictional phrases have reduced scientific understanding and stewardship of springs ecosystems: 'jurisdictional wetlands' and 'groundwater-dependent ecosystems' (GDEs). Most springs have insufficient monitoring data to establish perenniality or the range of natural variation in flow, and many of the 12 springs types do not develop hydric soils or wetland vegetation. These factors and their normally small size preclude springs as jurisdictional wetlands by U.S. Environmental Protection Agency and Army Corps of Engineers criteria. Helocrenes (springfed wet meadows, cienegas, and some fens) are considered as wetlands, but the other 11 types of terrestrial springs often are not. The use of the phrase 'GDE' applies to any aquatic ecosystem supported by groundwater, and the utility of this phrase as a descriptor of springs is diluted by its application to all subterranean and surface aquatic habitats. The failure to recognize the importance of springs ecosystems has become a quiet but global crisis, in part due to inappropriate conceptual understanding and poor jurisdictional terminology. We clarify relationships between these concepts and terms to establish effective, consistent monitoring, assessment, restoration, management, and monitoring goals and protocols for improving springs stewardship.

What's Slithering around on Your School Grounds? Transforming Student Awareness of Reptile & Amphibian Diversity

ERIC Educational Resources Information Center

Tomasek, Terry M.; Matthews, Catherine E.; Hall, Jeff

2005-01-01

The protocols used in a research project on amphibian and reptile diversity at Cool Springs Environmental Education Center near New Bern, North Carolina is described. An increasing or stable number of amphibians and reptiles would indicate that the forest has a balance of invertebrates, leaf litter, moisture, pH, debris, burrows and habitat…

Occupancy modeling of ruffed grouse in the Black Hills National Forest

Treesearch

Christopher P. Hansen; Joshua J. Millspaugh; Mark A. Rumble

2011-01-01

Ruffed grouse (Bonasa umbellus) are a popular game bird and the management indicator species for quaking aspen (Populus tremuloides) in the Black Hills National Forest (BHNF), which requires development of a robust monitoring protocol to evaluate trends in ruffed grouse populations. We used roadside drumming surveys in spring 2007 and 2008 to estimate ruffed grouse...

Molecular Detection of Vertebrates in Stream Water: A Demonstration Using Rocky Mountain Tailed Frogs and Idaho Giant Salamanders

PubMed Central

Goldberg, Caren S.; Pilliod, David S.; Arkle, Robert S.; Waits, Lisette P.

2011-01-01

Stream ecosystems harbor many secretive and imperiled species, and studies of vertebrates in these systems face the challenges of relatively low detection rates and high costs. Environmental DNA (eDNA) has recently been confirmed as a sensitive and efficient tool for documenting aquatic vertebrates in wetlands and in a large river and canal system. However, it was unclear whether this tool could be used to detect low-density vertebrates in fast-moving streams where shed cells may travel rapidly away from their source. To evaluate the potential utility of eDNA techniques in stream systems, we designed targeted primers to amplify a short, species-specific DNA fragment for two secretive stream amphibian species in the northwestern region of the United States (Rocky Mountain tailed frogs, Ascaphus montanus, and Idaho giant salamanders, Dicamptodon aterrimus). We tested three DNA extraction and five PCR protocols to determine whether we could detect eDNA of these species in filtered water samples from five streams with varying densities of these species in central Idaho, USA. We successfully amplified and sequenced the targeted DNA regions for both species from stream water filter samples. We detected Idaho giant salamanders in all samples and Rocky Mountain tailed frogs in four of five streams and found some indication that these species are more difficult to detect using eDNA in early spring than in early fall. While the sensitivity of this method across taxa remains to be determined, the use of eDNA could revolutionize surveys for rare and invasive stream species. With this study, the utility of eDNA techniques for detecting aquatic vertebrates has been demonstrated across the majority of freshwater systems, setting the stage for an innovative transformation in approaches for aquatic research. PMID:21818382

Molecular detection of vertebrates in stream water: a demonstration using Rocky Mountain tailed frogs and Idaho giant salamanders.

PubMed

Goldberg, Caren S; Pilliod, David S; Arkle, Robert S; Waits, Lisette P

2011-01-01

Stream ecosystems harbor many secretive and imperiled species, and studies of vertebrates in these systems face the challenges of relatively low detection rates and high costs. Environmental DNA (eDNA) has recently been confirmed as a sensitive and efficient tool for documenting aquatic vertebrates in wetlands and in a large river and canal system. However, it was unclear whether this tool could be used to detect low-density vertebrates in fast-moving streams where shed cells may travel rapidly away from their source. To evaluate the potential utility of eDNA techniques in stream systems, we designed targeted primers to amplify a short, species-specific DNA fragment for two secretive stream amphibian species in the northwestern region of the United States (Rocky Mountain tailed frogs, Ascaphus montanus, and Idaho giant salamanders, Dicamptodon aterrimus). We tested three DNA extraction and five PCR protocols to determine whether we could detect eDNA of these species in filtered water samples from five streams with varying densities of these species in central Idaho, USA. We successfully amplified and sequenced the targeted DNA regions for both species from stream water filter samples. We detected Idaho giant salamanders in all samples and Rocky Mountain tailed frogs in four of five streams and found some indication that these species are more difficult to detect using eDNA in early spring than in early fall. While the sensitivity of this method across taxa remains to be determined, the use of eDNA could revolutionize surveys for rare and invasive stream species. With this study, the utility of eDNA techniques for detecting aquatic vertebrates has been demonstrated across the majority of freshwater systems, setting the stage for an innovative transformation in approaches for aquatic research.

Molecular detection of vertebrates in stream water: A demonstration using rocky mountain tailed frogs and Idaho giant salamanders

USGS Publications Warehouse

Goldberg, C.S.; Pilliod, D.S.; Arkle, R.S.; Waits, L.P.

2011-01-01

Stream ecosystems harbor many secretive and imperiled species, and studies of vertebrates in these systems face the challenges of relatively low detection rates and high costs. Environmental DNA (eDNA) has recently been confirmed as a sensitive and efficient tool for documenting aquatic vertebrates in wetlands and in a large river and canal system. However, it was unclear whether this tool could be used to detect low-density vertebrates in fast-moving streams where shed cells may travel rapidly away from their source. To evaluate the potential utility of eDNA techniques in stream systems, we designed targeted primers to amplify a short, species-specific DNA fragment for two secretive stream amphibian species in the northwestern region of the United States (Rocky Mountain tailed frogs, Ascaphus montanus, and Idaho giant salamanders, Dicamptodon aterrimus). We tested three DNA extraction and five PCR protocols to determine whether we could detect eDNA of these species in filtered water samples from five streams with varying densities of these species in central Idaho, USA. We successfully amplified and sequenced the targeted DNA regions for both species from stream water filter samples. We detected Idaho giant salamanders in all samples and Rocky Mountain tailed frogs in four of five streams and found some indication that these species are more difficult to detect using eDNA in early spring than in early fall. While the sensitivity of this method across taxa remains to be determined, the use of eDNA could revolutionize surveys for rare and invasive stream species. With this study, the utility of eDNA techniques for detecting aquatic vertebrates has been demonstrated across the majority of freshwater systems, setting the stage for an innovative transformation in approaches for aquatic research.

DNA Extraction Protocols for Whole-Genome Sequencing in Marine Organisms.

PubMed

Panova, Marina; Aronsson, Henrik; Cameron, R Andrew; Dahl, Peter; Godhe, Anna; Lind, Ulrika; Ortega-Martinez, Olga; Pereyra, Ricardo; Tesson, Sylvie V M; Wrange, Anna-Lisa; Blomberg, Anders; Johannesson, Kerstin

2016-01-01

The marine environment harbors a large proportion of the total biodiversity on this planet, including the majority of the earths' different phyla and classes. Studying the genomes of marine organisms can bring interesting insights into genome evolution. Today, almost all marine organismal groups are understudied with respect to their genomes. One potential reason is that extraction of high-quality DNA in sufficient amounts is challenging for many marine species. This is due to high polysaccharide content, polyphenols and other secondary metabolites that will inhibit downstream DNA library preparations. Consequently, protocols developed for vertebrates and plants do not always perform well for invertebrates and algae. In addition, many marine species have large population sizes and, as a consequence, highly variable genomes. Thus, to facilitate the sequence read assembly process during genome sequencing, it is desirable to obtain enough DNA from a single individual, which is a challenge in many species of invertebrates and algae. Here, we present DNA extraction protocols for seven marine species (four invertebrates, two algae, and a marine yeast), optimized to provide sufficient DNA quality and yield for de novo genome sequencing projects.

A quantitative PCR approach for quantification of functional genes involved in the degradation of polycyclic aromatic hydrocarbons in contaminated soils.

PubMed

Shahsavari, Esmaeil; Aburto-Medina, Arturo; Taha, Mohamed; Ball, Andrew S

2016-01-01

Polycyclic aromatic hydrocarbons (PAHs) are major pollutants globally and due to their carcinogenic and mutagenic properties their clean-up is paramount. Bioremediation or using PAH degrading microorganisms (mainly bacteria) to degrade the pollutants represents cheap, effective methods. These PAH degraders harbor functional genes which help microorganisms use PAHs as source of food and energy. Most probable number (MPN) and plate counting methods are widely used for counting PAHs degraders; however, as culture based methods only count a small fraction (<1%) of microorganisms capable of carrying out PAH degradation, the use of culture-independent methodologies is desirable.•This protocol presents a robust, rapid and sensitive qPCR method for the quantification of the functional genes involved in the degradation of PAHs in soil samples.•This protocol enables us to screen a vast number of PAH contaminated soil samples in few hours.•This protocol provides valuable information about the natural attenuation potential of contaminated soil and can be used to monitor the bioremediation process.

Population structure and life history of Hemimysis lamornae mediterranea (Malacostraca: Mysida) in the Ebro Delta (NW Mediterranean)

NASA Astrophysics Data System (ADS)

Delgado, L.; Guerao, G.; Vicente, C. San; Ribera, C.

2013-10-01

Hemimysis lamornae mediterraneaBacescu, 1936 has been recently reported in the Ebro Delta (Spain, NW Mediterranean). Little is known about the biology and ecology of this mysid and we provide the first information about its population biology. H. l. mediterranea were collected from Sant Carles de la Ràpita harbor from June 2010 to March 2012 at night. The H. l. mediterranea population was composed of two main individual size categories: larger-sized winter/spring individuals and smaller-sized spring/summer individuals. The overall sex ratio is highly skewed; mature females are 2.5 times more abundant than mature males. Reproductive activity was higher during late winter and spring but was almost continuous throughout the year. The intra-marsupial development and growth of juveniles has been studied in the laboratory. The mean duration of incubation period (intra-marsupial stages) in laboratory conditions was 11 days (20 °C) and the age at first maturity ranged from14 to 20 days. The growth rate was faster in early juveniles and declined with age, showing a maximum of 0.152 mm d- 1. The laboratory results and demographic data suggest that H. l. mediterranea will produce several generations per year in the Ebro Delta. H. l. mediterranea was characterized by a combination of early maturation of individuals (short juvenile period), rapid growth, small adult size, a continuous reproduction all year round, iteroparous females, a relatively high fecundity and a high number of generations per year.

Iron-Tolerant Cyanobacteria: Ecophysiology and Fingerprinting

NASA Technical Reports Server (NTRS)

Brown, I. I.; Mummey, D.; Lindsey, J.; McKay, D. S.

2006-01-01

Although the iron-dependent physiology of marine and freshwater cyanobacterial strains has been the focus of extensive study, very few studies dedicated to the physiology and diversity of cyanobacteria inhabiting iron-depositing hot springs have been conducted. One of the few studies that have been conducted [B. Pierson, 1999] found that cyanobacterial members of iron depositing bacterial mat communities might increase the rate of iron oxidation in situ and that ferrous iron concentrations up to 1 mM significantly stimulated light dependent consumption of bicarbonate, suggesting a specific role for elevated iron in photosynthesis of cyanobacteria inhabiting iron-depositing hot springs. Our recent studies pertaining to the diversity and physiology of cyanobacteria populating iron-depositing hot springs in Great Yellowstone area (Western USA) indicated a number of different isolates exhibiting elevated tolerance to Fe(3+) (up to 1 mM). Moreover, stimulation of growth was observed with increased Fe(3+) (0.02-0.4 mM). Molecular fingerprinting of unialgal isolates revealed a new cyanobacterial genus and species Chroogloeocystis siderophila, an unicellular cyanobacterium with significant EPS sheath harboring colloidal Fe(3+) from iron enriched media. Our preliminary data suggest that some filamentous species of iron-tolerant cyanobacteria are capable of exocytosis of iron precipitated in cytoplasm. Prior to 2.4 Ga global oceans were likely significantly enriched in soluble iron [Lindsay et al, 2003], conditions which are not conducive to growth of most contemporary oxygenic cyanobacteria. Thus, iron-tolerant CB may have played important physiological and evolutionary roles in Earths history.

Iron Homeostasis in Yellowstone National Park Hot Spring Microbial Communities

NASA Technical Reports Server (NTRS)

Brown, I.; Tringe, S. G.; Franklin, H.; Bryant, D. A.; Klatt, C. G.; Sarkisova, S. A.; Guevara, M.

2010-01-01

It has been postulated that life may have originated on Earth, and possibly on Mars, in association with hydrothermal activity and high concentrations of ferrous iron. However, it is not clear how an iron-rich thermal hydrosphere could be hospitable to microbes, since reduced iron appears to stimulate oxidative stress in all domains of life and particularly in oxygenic phototrophs. Therefore, the study of microbial diversity in iron-depositing hot springs (IDHS) and the mechanisms of iron homeostasis and suppression of oxidative stress may help elucidate how Precambrian organisms could withstand the extremely high concentrations of reactive oxygen species (ROS) produced by interaction between environmental Fe(2+) and O2. Proteins and clusters of orthologous groups (COGs) involved in the maintenance of Fe homeostasis found in cyanobacteria (CB) inhabiting environments with high and low [Fe] were main target of this analysis. Preliminary results of the analysis suggest that the Chocolate Pots (CP) microbial community is heavily dominated by phototrophs from the cyanobacteria (CB), Chloroflexi and Chlorobi phyla, while the Mushroom Spring (MS) effluent channel harbors a more diverse community in which Chloroflexi are the dominant phototrophs. It is speculated that CB inhabiting IDHS have an increased tolerance to both high concentrations of Fe(2+) and ROS produced in the Fenton reaction. This hypothesis was explored via a comparative analysis of the diversity of proteins and COGs involved in Fe and redox homeostasis in the CP and MS microbiomes.

McNary Dam, Ice Harbor Dam, and Lower Monumental Dam Smolt Monitoring Program; 1996 Annual Report.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hillson, Todd; Lind, Sharon; Price, William

1997-07-01

The Washington Department of Fish & Wildlife (WDFW) assumed responsibility for the Smolt Monitoring Program at McNary Dam on the Columbia River in 1990 and at the new juvenile collection facility at Lower Monumental Dam on the Snake River in 1993. In 1996, Smolt Monitoring Program activities also began at the new juvenile collection facility located at Ice Harbor Dam. This report summarizes the 1996 Smolt Monitoring work at all three sites. The work at Ice Harbor consisted of Gas Bubble Trauma (GBT) monitoring only. In general, the 1996 passage season at both the McNary and Lower Monumental sites canmore » be characterized by reduced passage of juveniles through the collection systems due to elevated river flows and spill, and low (<1%) overall facility mortality rates most likely resulting from cooler water temperatures. In accordance with the National Marine Fisheries Service recommendations (NMFS, 1995) all spring migrants were bypassed at McNary Dam in 1996. Mechanical problems within the McNary collection system resulted in collection and sampling activities being delayed until April 18 at this site, while sampling and collection began on the scheduled starting date of April 1 at Lower Monumental Dam. Monitoring operations were conducted through December 14 at McNary Dam and through October 28 at Lower Monumental Dam. An ongoing transportation evaluation summer migrant marking program was conducted at McNary Dam in 1996 by the NMFS. This necessitated the sampling of 394,211 additional fish beyond the recommended sampling guidelines. All total, 509,237 and 31,219 juvenile salmonids were anesthetized and individually counted, examined for scale loss, injuries, and brands by WDFW Smolt Monitoring personnel in 1996 at McNary Dam and Lower Monumental Dam, respectively.« less

Determination of in vivo RNA kinetics using RATE-seq.

PubMed

Neymotin, Benjamin; Athanasiadou, Rodoniki; Gresham, David

2014-10-01

The abundance of a transcript is determined by its rate of synthesis and its rate of degradation; however, global methods for quantifying RNA abundance cannot distinguish variation in these two processes. Here, we introduce RNA approach to equilibrium sequencing (RATE-seq), which uses in vivo metabolic labeling of RNA and approach to equilibrium kinetics, to determine absolute RNA degradation and synthesis rates. RATE-seq does not disturb cellular physiology, uses straightforward normalization with exogenous spike-ins, and can be readily adapted for studies in most organisms. We demonstrate the use of RATE-seq to estimate genome-wide kinetic parameters for coding and noncoding transcripts in Saccharomyces cerevisiae. © 2014 Neymotin et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Insufficient chunk concatenation may underlie changes in sleep-dependent consolidation of motor sequence learning in older adults.

PubMed

Bottary, Ryan; Sonni, Akshata; Wright, David; Spencer, Rebecca M C

2016-09-01

Sleep enhances motor sequence learning (MSL) in young adults by concatenating subsequences ("chunks") formed during skill acquisition. To examine whether this process is reduced in aging, we assessed performance changes on the MSL task following overnight sleep or daytime wake in healthy young and older adults. Young adult performance enhancement was correlated with nREM2 sleep, and facilitated by preferential improvement of slowest within-sequence transitions. This effect was markedly reduced in older adults, and accompanied by diminished sigma power density (12-15 Hz) during nREM2 sleep, suggesting that diminished chunk concatenation following sleep may underlie reduced consolidation of MSL in older adults. © 2016 Bottary et al.; Published by Cold Spring Harbor Laboratory Press.

The prelimbic cortex directs attention toward predictive cues during fear learning.

PubMed

Sharpe, Melissa J; Killcross, Simon

2015-06-01

The prelimbic cortex is argued to promote conditioned fear expression, at odds with appetitive research implicating this region in attentional processing. Consistent with an attentional account, we report that the effect of prelimbic lesions on fear expression depends on the degree of competition between contextual and discrete cues. Further, when competition from contextual cues is low, we found that PL inactivation resulted in animals expressing fear toward irrelevant discrete cues; an effect selective to inactivation during the learning phase and not during retrieval. These data demonstrate that the prelimbic cortex modulates attention toward cues to preferentially direct fear responding on the basis of their predictive value. © 2015 Sharpe and Killcross; Published by Cold Spring Harbor Laboratory Press.

The effects of extinction-aroused attention on context conditioning.

PubMed

Nelson, James Byron; Fabiano, Andrew M; Lamoureux, Jeffrey A

2018-04-01

Two experiments assessed the effects of extinguishing a conditioned cue on subsequent context conditioning. Each experiment used a different video-game method where sensors predicted attacking spaceships and participants responded to the sensor in a way that prepared them for the upcoming attack. In Experiment 1 extinction of a cue which signaled a spaceship-attack outcome facilitated subsequent learning when the attack occurred unsignaled. In Experiment 2 extinction of a cue facilitated subsequent learning, regardless of whether the spaceship outcome was the same or different as used in the earlier training. In neither experiment did the extinction context become inhibitory. Results are discussed in terms of current associative theories of attention and conditioning. © 2018 Nelson et al.; Published by Cold Spring Harbor Laboratory Press.

Analyzing and Understanding Lipids of Yeast: A Challenging Endeavor.

PubMed

Kohlwein, Sepp D

2017-05-01

Lipids are essential biomolecules with diverse biological functions, ranging from building blocks for all biological membranes to energy substrates, signaling molecules, and protein modifiers. Despite advances in lipid analytics by mass spectrometry, the extraction and quantitative analysis of the diverse classes of lipids are still an experimental challenge. Yeast is a model organism that provides several advantages for studying lipid metabolism, because most biosynthetic pathways are well described and a great deal of information is available on the regulatory mechanisms that control lipid homeostasis. In addition, the composition of yeast lipids is much less complex than that of mammalian lipids, making yeast an excellent reference system for studying lipid-associated cell functions. © 2017 Cold Spring Harbor Laboratory Press.

Schizosaccharomyces pombe Polysome Profile Analysis and RNA Purification.

PubMed

Wolf, Dieter A; Bähler, Jürg; Wise, Jo Ann

2017-04-03

Polysome profile analysis is widely used by investigators studying the mechanism and regulation of translation. The method described here uses high-velocity centrifugation of whole cell extracts on linear sucrose gradients to separate 40S and 60S ribosomal subunits from 80S monosomes and polysomes. Cycloheximide is included in the lysis buffer to "freeze" polysomes by blocking translation. After centrifugation, the gradient is fractionated and RNA (and/or protein) is prepared from each fraction for subsequent analysis of individual species using northern or western blots. The entire RNA population in each fraction can be analyzed by hybridization to microarrays or by high-throughput RNA sequencing, and the proteins present can be identified by mass spectrometry analysis. © 2017 Cold Spring Harbor Laboratory Press.

Patentability of Stem Cells in the United States.

PubMed

Fendrick, Sarah E; Zuhn, Donald L

2015-08-20

Until recently, the patentability of stem cells was well established within the judicial and statutory framework in the United States. However, the shifting landscape of patent law, particularly with regard to patent-eligible subject matter under 35 U.S.C. §101, presents new challenges to the patentability of stem cells. In this paper, we discuss the legal precedent that paved the way for stem cell patents, including Diamond v. Chakrabarty and In re Bergy. Additionally, we review recent Supreme Court cases and recent guidance issued by the U.S. Patent and Trademark Office that impose new limitations on patent-eligible subject matter and thereby threaten the patentability of stem cells in the United States. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

Comparative Pathology of Hepatitis A Virus and Hepatitis E Virus Infection.

PubMed

Cullen, John M; Lemon, Stanley M

2018-04-30

Hepatitis A virus (HAV) and hepatitis E virus (HEV) cause acute, self-limiting hepatic infections that are usually spread by the fecal-oral route in humans. Naturally occurring and experimental infections are possible in a variety of nonhuman primates and, in the case of HEV, a number of other species. Many advances in understanding the pathogenesis of these viruses have come from studies in experimental animals. In general, animals infected with these viruses recapitulate the histologic lesions seen in infected humans, but typically with less severe clinical and histopathological manifestations. This review describes the histopathologic changes associated with HAV and HEV infection in humans and experimental animals. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

AMPA receptors control fear extinction through an Arc-dependent mechanism.

PubMed

Trent, Simon; Barnes, Philip; Hall, Jeremy; Thomas, Kerrie L

2017-08-01

Activity-regulated cytoskeleton-associated protein (Arc) supports fear memory through synaptic plasticity events requiring actin cytoskeleton rearrangements. We have previously shown that reducing hippocampal Arc levels through antisense knockdown leads to the premature extinction of contextual fear. Here we show that the AMPA receptor antagonist CNQX elevates hippocampal Arc levels during extinction and blocks extinction that can be rescued by reducing Arc. Increasing Arc levels with CNQX also overcomes the actin-destabilizing properties of cytochalasin D and promotes extinction. Therefore, extinction is dependent on AMPA-mediated reductions of Arc via a mechanism consistent with a role for Arc in stabilizing the actin cytoskeleton to constrain extinction. © 2017 Trent et al.; Published by Cold Spring Harbor Laboratory Press.

Licensing biotech intellectual property in university-industry partnerships.

PubMed

Drozdoff, Vladimir; Fairbairn, Daryl

2015-01-20

Appropriate negotiation and drafting of license agreements are critical to successfully establishing and managing the expansive and complex relationships that are becoming more common between industry and universities. More often than not, the resulting licensing agreements become quite lengthy and complex, and the key principles become difficult to discern among all the details. This summary provides a short, nonexhaustive introduction to some of the essential components of these licenses with the intent of providing the non-licensing professional a better appreciation of some of the key commercial and legal terms from both an academic and company perspective, keeping in mind some of the considerations that particularly apply to biotechnology deals. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

Treatment principles for the management of mold infections.

PubMed

Kontoyiannis, Dimitrios P; Lewis, Russell E

2014-11-06

Survival rates among immunocompromised patients with invasive mold infections have markedly improved over the last decade with earlier diagnosis and new antifungal treatment options. Yet, increasing antifungal resistance, breakthrough infections with intrinsically resistant fungi, and potentially life-threatening adverse effects and drug interactions are becoming more problematic, especially with prolonged therapy. Evidence-based recommendations for treating invasive aspergillosis and mucormycosis provide excellent guidance on the initial workup and treatment of these molds, but they cannot address all of the key management issues. Herein, we discuss 10 general treatment principles in the management of invasive mold disease in immunocompromised patients and discuss how these principles can be integrated to develop an effective, individualized treatment plan. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

Differential development of retroactive and proactive interference during post-learning wakefulness.

PubMed

Brawn, Timothy P; Nusbaum, Howard C; Margoliash, Daniel

2018-07-01

Newly encoded, labile memories are prone to disruption during post-learning wakefulness. Here we examine the contributions of retroactive and proactive interference to daytime forgetting on an auditory classification task in a songbird. While both types of interference impair performance, they do not develop concurrently. The retroactive interference of task-B on task-A developed during the learning of task-B, whereas the proactive interference of task-A on task-B emerged during subsequent waking retention. These different time courses indicate an asymmetry in the emergence of retroactive and proactive interference and suggest a mechanistic framework for how different types of interference between new memories develop. © 2018 Brawn et al.; Published by Cold Spring Harbor Laboratory Press.

Practice makes perfect in memory recall.

PubMed

Romani, Sandro; Katkov, Mikhail; Tsodyks, Misha

2016-04-01

A large variability in performance is observed when participants recall briefly presented lists of words. The sources of such variability are not known. Our analysis of a large data set of free recall revealed a small fraction of participants that reached an extremely high performance, including many trials with the recall of complete lists. Moreover, some of them developed a number of consistent input-position-dependent recall strategies, in particular recalling words consecutively ("chaining") or in groups of consecutively presented words ("chunking"). The time course of acquisition and particular choice of positional grouping were variable among participants. Our results show that acquiring positional strategies plays a crucial role in improvement of recall performance. © 2016 Romani et al.; Published by Cold Spring Harbor Laboratory Press.

Transcriptional integration of mitogenic and mechanical signals by Myc and YAP.

PubMed

Croci, Ottavio; De Fazio, Serena; Biagioni, Francesca; Donato, Elisa; Caganova, Marieta; Curti, Laura; Doni, Mirko; Sberna, Silvia; Aldeghi, Deborah; Biancotto, Chiara; Verrecchia, Alessandro; Olivero, Daniela; Amati, Bruno; Campaner, Stefano

2017-10-15

Mammalian cells must integrate environmental cues to determine coherent physiological responses. The transcription factors Myc and YAP-TEAD act downstream from mitogenic signals, with the latter responding also to mechanical cues. Here, we show that these factors coordinately regulate genes required for cell proliferation. Activation of Myc led to extensive association with its genomic targets, most of which were prebound by TEAD. At these loci, recruitment of YAP was Myc-dependent and led to full transcriptional activation. This cooperation was critical for cell cycle entry, organ growth, and tumorigenesis. Thus, Myc and YAP-TEAD integrate mitogenic and mechanical cues at the transcriptional level to provide multifactorial control of cell proliferation. © 2017 Croci et al.; Published by Cold Spring Harbor Laboratory Press.

Sleep supports inhibitory operant conditioning memory in Aplysia.

PubMed

Vorster, Albrecht P A; Born, Jan

2017-06-01

Sleep supports memory consolidation as shown in mammals and invertebrates such as bees and Drosophila. Here, we show that sleep's memory function is preserved in Aplysia californica with an even simpler nervous system. Animals performed on an inhibitory conditioning task ("learning that a food is inedible") three times, at Training, Retrieval 1, and Retrieval 2, with 17-h intervals between tests. Compared with Wake animals, remaining awake between Training and Retrieval 1, Sleep animals with undisturbed post-training sleep, performed significantly better at Retrieval 1 and 2. Control experiments testing retrieval only after ∼34 h, confirmed the consolidating effect of sleep occurring within 17 h after training. © 2017 Vorster and Born; Published by Cold Spring Harbor Laboratory Press.

The Prehistory of Antibiotic Resistance.

PubMed

Perry, Julie; Waglechner, Nicholas; Wright, Gerard

2016-06-01

Antibiotic resistance is a global problem that is reaching crisis levels. The global collection of resistance genes in clinical and environmental samples is the antibiotic "resistome," and is subject to the selective pressure of human activity. The origin of many modern resistance genes in pathogens is likely environmental bacteria, including antibiotic producing organisms that have existed for millennia. Recent work has uncovered resistance in ancient permafrost, isolated caves, and in human specimens preserved for hundreds of years. Together with bioinformatic analyses on modern-day sequences, these studies predict an ancient origin of resistance that long precedes the use of antibiotics in the clinic. Understanding the history of antibiotic resistance is important in predicting its future evolution. Copyright © 2016 Cold Spring Harbor Laboratory Press; all rights reserved.

Humans and monkeys use different strategies to solve the same short-term memory tasks.

PubMed

Wittig, John H; Morgan, Barak; Masseau, Evan; Richmond, Barry J

2016-11-01

The neural mechanisms underlying human working memory are often inferred from studies using old-world monkeys. Humans use working memory to selectively memorize important information. We recently reported that monkeys do not seem to use selective memorization under experimental conditions that are common in monkey research, but less common in human research. Here we compare the performance of humans and monkeys under the same experimental conditions. Humans selectively remember important images whereas monkeys largely rely on recency information from nonselective memorization. Working memory studies in old-world monkeys must be interpreted cautiously when making inferences about the mechanisms underlying human working memory. © 2016 Wittig, et al.; Published by Cold Spring Harbor Laboratory Press.

Inherent Anticipation in the Pharmaceutical and Biotechnology Industries.

PubMed

Goldman, Michael; Evans, Georgia; Zappia, Andrew

2015-04-15

Pharmaceutical and biotech research often involves discovering new properties of, or new methods to use, existing compositions. The doctrine of inherent anticipation, however, prevents the issuance and/or validity of a patent for discoveries deemed to have been implicitly disclosed in the prior art. This can be a barrier to patent rights in these technologies. Inherent anticipation therefore creates uncertainty for patent protection in the pharmaceutical and biotech sciences. Despite this uncertainty, Federal Circuit jurisprudence provides guidance on the boundaries of the inherent anticipation doctrine. In view of the case law, certain strategies may be employed to protect inventions that may potentially be viewed as inherent in the prior art. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

Careers in Science Journalism and Writing.

PubMed

Pearson, Helen

2017-09-01

Science journalists cover some of the most complex, exciting, and important issues of our day, ranging from the impacts of climate change to emerging infectious diseases. They use words, sounds, images, and graphics to create compelling stories about science that appear in newspapers and magazines, in print and online, on the radio and TV, and in podcasts and videos. The field is undergoing rapid change, which presents both challenges and opportunities. The migration of readers and advertising to the internet and digital platforms has led to declining sales of print publications. This means that jobs are now scarce in traditional print media, but that there are growing opportunities to produce digital content. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

Agrobacterium- and Biolistic-Mediated Transformation of Maize B104 Inbred.

PubMed

Raji, Jennifer A; Frame, Bronwyn; Little, Daniel; Santoso, Tri Joko; Wang, Kan

2018-01-01

Genetic transformation of maize inbred genotypes remains non-routine for many laboratories due to variations in cell competency to induce embryogenic callus, as well as the cell's ability to receive and incorporate transgenes into the genome. This chapter describes two transformation protocols using Agrobacterium- and biolistic-mediated methods for gene delivery. Immature zygotic embryos of maize inbred B104, excised from ears harvested 10-14 days post pollination, are used as starting explant material. Disarmed Agrobacterium strains harboring standard binary vectors and the biolistic gun system Bio-Rad PDS-1000/He are used as gene delivery systems. The herbicide resistant bar gene and selection agent bialaphos are used for identifying putative transgenic type I callus events. Using the step-by-step protocols described here, average transformation frequencies (number of bialaphos resistant T 0 callus events per 100 explants infected or bombarded) of 4% and 8% can be achieved using the Agrobacterium- and biolistic-mediated methods, respectively. An estimated duration of 16-21 weeks is needed using either protocol from the start of transformation experiments to obtaining putative transgenic plantlets with established roots. In addition to laboratory in vitro procedures, detailed greenhouse protocols for producing immature ears as transformation starting material and caring for transgenic plants for seed production are also described.

Connecting the Force from Space: The IRIS Joint Capability Technology Demonstration

DTIC Science & Technology

2010-01-01

the Joint in Joint Capability Technology Demonstration, we have two sponsors, both U.S. Strategic Command and the Defense Information Systems...Capability Technology Demonstration will provide an excellent source of data on space-based Internet Protocol net- working. Operational... Internet Routing in Space Joint Capability Technology Demonstration Operational Manager, Space and Missile Defense Battle Lab, Colorado Springs

Accelerated Growth and Initial Flowering of S2 Pinus Banksiana Selected for Precocious Flowering

Treesearch

Hyun Kang; Robert A. Cecich

1999-01-01

An accelerated growth protocol was applied in a greenhouse to hasten flowering in 13 S2 lines of jack pine (Pinus banksiana Lamb.) selected for precocious flowering. Seeds were sown on October 1. After the artificial "summer, fall, winter, and spring," seedlings were placed outdoors between June 20 and November 1. Ovulate strobili were...

RBFOX and PTBP1 proteins regulate the alternative splicing of micro-exons in human brain transcripts.

PubMed

Li, Yang I; Sanchez-Pulido, Luis; Haerty, Wilfried; Ponting, Chris P

2015-01-01

Ninety-four percent of mammalian protein-coding exons exceed 51 nucleotides (nt) in length. The paucity of micro-exons (≤ 51 nt) suggests that their recognition and correct processing by the splicing machinery present greater challenges than for longer exons. Yet, because thousands of human genes harbor processed micro-exons, specialized mechanisms may be in place to promote their splicing. Here, we survey deep genomic data sets to define 13,085 micro-exons and to study their splicing mechanisms and molecular functions. More than 60% of annotated human micro-exons exhibit a high level of sequence conservation, an indicator of functionality. While most human micro-exons require splicing-enhancing genomic features to be processed, the splicing of hundreds of micro-exons is enhanced by the adjacent binding of splice factors in the introns of pre-messenger RNAs. Notably, splicing of a significant number of micro-exons was found to be facilitated by the binding of RBFOX proteins, which promote their inclusion in the brain, muscle, and heart. Our analyses suggest that accurate regulation of micro-exon inclusion by RBFOX proteins and PTBP1 plays an important role in the maintenance of tissue-specific protein-protein interactions. © 2015 Li et al.; Published by Cold Spring Harbor Laboratory Press.

Investigating passage of ESA-listed juvenile fall Chinook salmon at Lower Granite Dam during winter when the fish bypass system is not operated

USGS Publications Warehouse

Kock, Tobias J.; Tiffan, Kenneth F.; Connor, William P.

2007-01-01

During the winter of 2006-07, we radio and passive integrated transponder (PIT) tagged, and released 99 juvenile fall Chinook salmon to evaluate over-wintering behavior and dam passage in the lower Snake River, Washington. All fish were released 10 km upstream of Lower Granite Dam at Granite Point in early November, 2006. Fixed radio telemetry detection sites located in the forebay and tailrace areas of Lower Granite, Little Goose, Lower Monumental, Ice Harbor, Bonneville dams, and at Lyle, Washington were used to monitor fish movements and dam passage through early-May 2007. Of the 99 fish released during our study, 80 passed Lower Granite Dam and were detected at downstream detection sites, 37 passed Little Goose Dam, 41 passed Lower Monumental Dam, 31 passed Ice Harbor Dam, 18 passed Lyle, WA, and 13 passed Bonneville Dam. Of the fish that passed Lower Granite Dam in the fall, 63 fish did so during the extended bypass period from November 1 through December 16. Of these fish, 53 were also detected by the PIT-tag interrogation system. Fifteen of the fish that passed Lower Granite Dam in the fall continued to pass lower Snake River dams and exit the system by the end of January. The remaining fish either died, their tags failed, or they resided in Little Goose Reservoir until spring when relatively few continued their seaward migration. Passage of tagged fish past lower Snake River dams generally declined during the winter as temperatures decreased, but increased again in the spring as temperatures and flows increased. Fish residence times in reservoirs and forebays was lengthy during the winter (up to 160 d), and varied by reservoir and time of year. We observed no diel trends in fish passage. Very few fish were detected at PIT-tag interrogation sites in the spring compared to detection by radio telemetry detection sites indicating that fish may have passed via spill. We believe that passage of overwintering juvenile fall Chinook salmon during winter is due more to chance than directed downstream movement. Since the primary route of passage during the winter is through powerhouse turbines, the potential exists for increased mortality for over-wintering juvenile fall Chinook salmon in the Snake River. Our findings that some fish can pass undetected during the winter likely bias traditional smolt-to-adult return rate calculations that are typically used to measure the success of juvenile transportation studies.

Beach Erosion and Accretion: Comparison of the Seasonal Influence of Suspended- and Bedload-Sediment Transport at Grays Harbor, Washington, U. S. A.

NASA Astrophysics Data System (ADS)

Sherwood, C. R.; Lacy, J. R.; Ruggiero, P.; Kerr, L. A.; Gelfenbaum, G.; Wilson, D. J.

2001-12-01

We conducted field studies on the ebb-tidal delta near the entrance to Grays Harbor, Washington in Autumn, 1999 and Spring 2001, with the objectives of 1) providing directional wave data to validate a shoaling and refraction model for the ebb-tidal delta, and 2) measuring forcing (wave- and current-induced near-bottom velocities, accelerations, and shear stresses) and responses (bedforms, suspended-sediment profiles, and sediment fluxes) associated with intervals of beach erosion and accretion. In the Autumn experiment (October - December), tripods were deployed at shallow ( ~14-m) and deep ( ~24-m) sites on the northern, middle, and southern flanks of the ebb tidal. In the Spring experiment (May - mid-July), tripods were redeployed at four sites and a new inshore site ( ~9-m depth), and pressures, current velocities, and suspended-sediment concentrations were measured with 5-MHz acoustic Doppler velocimeters (ADVs), optical backscatterance sensors, upward-looking acoustic Doppler current profilers (ADCPs), a downward-looking pulse-coherent acoustic Doppler profiler (PCADP), and an acoustic backscatterance sensor (ABS). We also measured bedforms with profiling and imaging sonars and estimated Reynolds stresses with a pair of 10-MHz ADVs at the inshore site. Incident waves, nearshore circulation patterns, statistics of near-bottom wave- and current-induced velocities, and sediment fluxes were distinctly different in the two experiments. During the Autumn measurements, the general direction of wave approach shifted from WNW to WSW as the North Pacific weather pattern shifted from summer to winter, and we observed a large storm (offshore significant wave heights Hs of ~8 m) and a sequence of about 8 smaller events with ~4 to 5-m waves. Sediment transport was dominated by storm-induced, downwelling-favorable circulation that transported suspended sediments northward and offshore. Inferred bedload fluxes were directed shoreward, but were much smaller. In contrast, Spring wave conditions were much milder (maximum Hs of ~4 m), and waves approached mostly from the WNW. There were long periods of upwelling-favorable circulation interrupted by intervals of storm-induced northward flow. Net suspended-sediment transport was directed northward at the deeper sites and southward at the inshore sites. Near-bottom transport remained offshore at the deeper sites, but was lower, with negligible net cross-shore component at the shallow sites. The relative contribution of shoreward bedload transport was much larger. These changes in sediment transport outside the breaker zone are consistent with measured changes in beach and bar morphology.

Results of bulk sediment analysis and bioassay testing on selected sediments from Oakland Inner Harbor and Alcatraz disposal site, San Francisco, California

DOE Office of Scientific and Technical Information (OSTI.GOV)

Word, J Q; Ward, J A; Woodruff, D L

1990-09-01

The Battelle/Marine Sciences Laboratory (MSL) was contracted by the US Army Corps of Engineers, San Francisco District, to perform bulk sediment analysis and oyster larvae bioassays (elutriate) on sediments from Inner Oakland Harbor, California. Analysis of sediment characteristics by MSL indicated elevated priority pollutants, PAHs, pesticides, metals, organotins, and oil and grease concentrations, when compared to Alcatraz Island Dredged Material Disposal Site sediment concentrations. Larvae of the Pacific oyster, Crassostrea gigas, were exposed to seawater collected from the Alcatraz Island Site water, and a series of controls using water and sediments collected from Sequim Bay, Washington. Exposure of larvae tomore » the Alcatraz seawater and the 50% and 100% elutriate concentrations from each Oakland sediment resulted in low survival and a high proportion of abnormal larvae compared to Sequim Bay control exposures. MSL identified that field sample collection, preservation, and storage protocols used by Port of Oakland contractors were inconsistent with standard accepted practices. 23 refs., 10 figs., 40 tabs.« less

Team Faces Tough Odds to Implement New Phone Network | Poster

Cancer.gov

It was a Saturday, in the final stretch of winter in late February, and the temperature peaked to a pleasant 66 degrees. Many people were outside enjoying the spring-like weather; however, the Voice over Internet Protocol (VoIP) Deployment Team was hard at work at Industry Lane. The team of 10 was installing the new voice-only network, including deploying 145 phones, switching

Effects of post-encoding stress on performance in the DRM false memory paradigm.

PubMed

Pardilla-Delgado, Enmanuelle; Alger, Sara E; Cunningham, Tony J; Kinealy, Brian; Payne, Jessica D

2016-01-01

Numerous studies have investigated how stress impacts veridical memory, but how stress influences false memory formation remains poorly understood. In order to target memory consolidation specifically, a psychosocial stress (TSST) or control manipulation was administered following encoding of 15 neutral, semantically related word lists (DRM false memory task) and memory was tested 24 h later. Stress decreased recognition of studied words, while increasing false recognition of semantically related lure words. Moreover, while control subjects remembered true and false words equivalently, stressed subjects remembered more false than true words. These results suggest that stress supports gist memory formation in the DRM task, perhaps by hindering detail-specific processing in the hippocampus. © 2015 Pardilla-Delgado et al.; Published by Cold Spring Harbor Laboratory Press.

Experience during early adulthood shapes the learning capacities and the number of synaptic boutons in the mushroom bodies of honey bees (Apis mellifera).

PubMed

Cabirol, Amélie; Brooks, Rufus; Groh, Claudia; Barron, Andrew B; Devaud, Jean-Marc

2017-10-01

The honey bee mushroom bodies (MBs) are brain centers required for specific learning tasks. Here, we show that environmental conditions experienced as young adults affect the maturation of MB neuropil and performance in a MB-dependent learning task. Specifically, olfactory reversal learning was selectively impaired following early exposure to an impoverished environment lacking some of the sensory and social interactions present in the hive. In parallel, the overall number of synaptic boutons increased within the MB olfactory neuropil, whose volume remained unaffected. This suggests that experience of the rich in-hive environment promotes MB maturation and the development of MB-dependent learning capacities. © 2017 Cabirol et al.; Published by Cold Spring Harbor Laboratory Press.

Synthetic Morphogenesis.

PubMed

Teague, Brian P; Guye, Patrick; Weiss, Ron

2016-09-01

Throughout biology, function is intimately linked with form. Across scales ranging from subcellular to multiorganismal, the identity and organization of a biological structure's subunits dictate its properties. The field of molecular morphogenesis has traditionally been concerned with describing these links, decoding the molecular mechanisms that give rise to the shape and structure of cells, tissues, organs, and organisms. Recent advances in synthetic biology promise unprecedented control over these molecular mechanisms; this opens the path to not just probing morphogenesis but directing it. This review explores several frontiers in the nascent field of synthetic morphogenesis, including programmable tissues and organs, synthetic biomaterials and programmable matter, and engineering complex morphogenic systems de novo. We will discuss each frontier's objectives, current approaches, constraints and challenges, and future potential. Copyright © 2016 Cold Spring Harbor Laboratory Press; all rights reserved.

Synthetic Biology in Cell and Organ Transplantation.

PubMed

Stevens, Sean

2017-02-01

The transplantation of cells and organs has an extensive history, with blood transfusion and skin grafts described as some of the earliest medical interventions. The speed and efficiency of the human immune system evolved to rapidly recognize and remove pathogens; the human immune system also serves as a barrier against the transplant of cells and organs from even highly related donors. Although this shows the remarkable effectiveness of the immune system, the engineering of cells and organs that will survive in a host patient over the long term remains a steep challenge. Progress in the understanding of host immune responses to donor cells and organs, combined with the rapid advancement in synthetic biology applications, allows the rational engineering of more effective solutions for transplantation. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

The adrenal capsule is a signaling center controlling cell renewal and zonation through Rspo3.

PubMed

Vidal, Valerie; Sacco, Sonia; Rocha, Ana Sofia; da Silva, Fabio; Panzolini, Clara; Dumontet, Typhanie; Doan, Thi Mai Phuong; Shan, Jingdong; Rak-Raszewska, Aleksandra; Bird, Tom; Vainio, Seppo; Martinez, Antoine; Schedl, Andreas

2016-06-15

Adrenal glands are zonated endocrine organs that are essential in controlling body homeostasis. How zonation is induced and maintained and how renewal of the adrenal cortex is ensured remain a mystery. Here we show that capsular RSPO3 signals to the underlying steroidogenic compartment to induce β-catenin signaling and imprint glomerulosa cell fate. Deletion of RSPO3 leads to loss of SHH signaling and impaired organ growth. Importantly, Rspo3 function remains essential in adult life to ensure replenishment of lost cells and maintain the properties of the zona glomerulosa. Thus, the adrenal capsule acts as a central signaling center that ensures replacement of damaged cells and is required to maintain zonation throughout life. © 2016 Vidal et al.; Published by Cold Spring Harbor Laboratory Press.

Which Dengue Vaccine Approach Is the Most Promising, and Should We Be Concerned about Enhanced Disease after Vaccination? The Challenges of a Dengue Vaccine.

PubMed

Screaton, Gavin; Mongkolsapaya, Juthathip

2017-07-17

A dengue vaccine has been pursued for more than 50 years and, unlike other flaviviral vaccines such as that against yellow fever, progress has been slow. In this review, we describe progress toward the first licensed dengue vaccine Dengvaxia, which does not give complete protection against disease. The antibody response to the dengue virion is reviewed, highlighting immunodominant yet poorly neutralizing responses in the context of a highly dynamic structurally flexible dengue virus particle. Finally, we review recent evidence for cross-reactivity between antibody responses to Zika and dengue viruses, which may further complicate the development of broadly protective dengue virus vaccines. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

Nonhuman Primate Models of Hepatitis A Virus and Hepatitis E Virus Infections.

PubMed

Lanford, Robert E; Walker, Christopher M; Lemon, Stanley M

2018-04-23

Although phylogenetically unrelated, human hepatitis viruses share an exclusive or near exclusive tropism for replication in differentiated hepatocytes. This narrow tissue tropism may contribute to the restriction of the host ranges of these viruses to relatively few host species, mostly nonhuman primates. Nonhuman primate models thus figure prominently in our current understanding of the replication and pathogenesis of these viruses, including the enterically transmitted hepatitis A virus (HAV) and hepatitis E virus (HEV), and have also played major roles in vaccine development. This review draws comparisons of HAV and HEV infection from studies conducted in nonhuman primates, and describes how such studies have contributed to our current understanding of the biology of these viruses. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

New Insights into Ribosome Structure and Function.

PubMed

Jobe, Amy; Liu, Zheng; Gutierrez-Vargas, Cristina; Frank, Joachim

2018-06-14

In the past 4 years, because of the advent of new cameras, many ribosome structures have been solved by cryoelectron microscopy (cryo-EM) at high, often near-atomic resolution, bringing new mechanistic insights into the processes of translation initiation, peptide elongation, termination, and recycling. Thus, cryo-EM has joined X-ray crystallography as a powerful technique in structural studies of translation. The significance of this new development is that structures of ribosomes in complex with their functional binding partners can now be determined to high resolution in multiple states as they perform their work. The aim of this article is to provide an overview of these new studies and assess the contributions they have made toward an understanding of translation and translational control. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

FIND: difFerential chromatin INteractions Detection using a spatial Poisson process.

PubMed

Djekidel, Mohamed Nadhir; Chen, Yang; Zhang, Michael Q

2018-02-12

Polymer-based simulations and experimental studies indicate the existence of a spatial dependency between the adjacent DNA fibers involved in the formation of chromatin loops. However, the existing strategies for detecting differential chromatin interactions assume that the interacting segments are spatially independent from the other segments nearby. To resolve this issue, we developed a new computational method, FIND, which considers the local spatial dependency between interacting loci. FIND uses a spatial Poisson process to detect differential chromatin interactions that show a significant difference in their interaction frequency and the interaction frequency of their neighbors. Simulation and biological data analysis show that FIND outperforms the widely used count-based methods and has a better signal-to-noise ratio. © 2018 Djekidel et al.; Published by Cold Spring Harbor Laboratory Press.

Fibroblast growth factor signaling in skeletal development and disease.

PubMed

Ornitz, David M; Marie, Pierre J

2015-07-15

Fibroblast growth factor (FGF) signaling pathways are essential regulators of vertebrate skeletal development. FGF signaling regulates development of the limb bud and formation of the mesenchymal condensation and has key roles in regulating chondrogenesis, osteogenesis, and bone and mineral homeostasis. This review updates our review on FGFs in skeletal development published in Genes & Development in 2002, examines progress made on understanding the functions of the FGF signaling pathway during critical stages of skeletogenesis, and explores the mechanisms by which mutations in FGF signaling molecules cause skeletal malformations in humans. Links between FGF signaling pathways and other interacting pathways that are critical for skeletal development and could be exploited to treat genetic diseases and repair bone are also explored. © 2015 Ornitz and Marie; Published by Cold Spring Harbor Laboratory Press.

Fixed-Cell Imaging of Schizosaccharomyces pombe.

PubMed

Hagan, Iain M; Bagley, Steven

2016-07-01

The acknowledged genetic malleability of fission yeast has been matched by impressive cytology to drive major advances in our understanding of basic molecular cell biological processes. In many of the more recent studies, traditional approaches of fixation followed by processing to accommodate classical staining procedures have been superseded by live-cell imaging approaches that monitor the distribution of fusion proteins between a molecule of interest and a fluorescent protein. Although such live-cell imaging is uniquely informative for many questions, fixed-cell imaging remains the better option for others and is an important-sometimes critical-complement to the analysis of fluorescent fusion proteins by live-cell imaging. Here, we discuss the merits of fixed- and live-cell imaging as well as specific issues for fluorescence microscopy imaging of fission yeast. © 2016 Cold Spring Harbor Laboratory Press.

New genes often acquire male-specific functions but rarely become essential in Drosophila.

PubMed

Kondo, Shu; Vedanayagam, Jeffrey; Mohammed, Jaaved; Eizadshenass, Sogol; Kan, Lijuan; Pang, Nan; Aradhya, Rajaguru; Siepel, Adam; Steinhauer, Josefa; Lai, Eric C

2017-09-15

Relatively little is known about the in vivo functions of newly emerging genes, especially in metazoans. Although prior RNAi studies reported prevalent lethality among young gene knockdowns, our phylogenomic analyses reveal that young Drosophila genes are frequently restricted to the nonessential male reproductive system. We performed large-scale CRISPR/Cas9 mutagenesis of "conserved, essential" and "young, RNAi-lethal" genes and broadly confirmed the lethality of the former but the viability of the latter. Nevertheless, certain young gene mutants exhibit defective spermatogenesis and/or male sterility. Moreover, we detected widespread signatures of positive selection on young male-biased genes. Thus, young genes have a preferential impact on male reproductive system function. © 2017 Kondo et al.; Published by Cold Spring Harbor Laboratory Press.

Sex chromosome drive.

PubMed

Helleu, Quentin; Gérard, Pierre R; Montchamp-Moreau, Catherine

2014-12-18

Sex chromosome drivers are selfish elements that subvert Mendel's first law of segregation and therefore are overrepresented among the products of meiosis. The sex-biased progeny produced then fuels an extended genetic conflict between the driver and the rest of the genome. Many examples of sex chromosome drive are known, but the occurrence of this phenomenon is probably largely underestimated because of the difficulty to detect it. Remarkably, nearly all sex chromosome drivers are found in two clades, Rodentia and Diptera. Although very little is known about the molecular and cellular mechanisms of drive, epigenetic processes such as chromatin regulation could be involved in many instances. Yet, its evolutionary consequences are far-reaching, from the evolution of mating systems and sex determination to the emergence of new species. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

Desmosomes and Intermediate Filaments: Their Consequences for Tissue Mechanics.

PubMed

Hatzfeld, Mechthild; Keil, René; Magin, Thomas M

2017-06-01

Adherens junctions (AJs) and desmosomes connect the actin and keratin filament networks of adjacent cells into a mechanical unit. Whereas AJs function in mechanosensing and in transducing mechanical forces between the plasma membrane and the actomyosin cytoskeleton, desmosomes and intermediate filaments (IFs) provide mechanical stability required to maintain tissue architecture and integrity when the tissues are exposed to mechanical stress. Desmosomes are essential for stable intercellular cohesion, whereas keratins determine cell mechanics but are not involved in generating tension. Here, we summarize the current knowledge of the role of IFs and desmosomes in tissue mechanics and discuss whether the desmosome-keratin scaffold might be actively involved in mechanosensing and in the conversion of chemical signals into mechanical strength. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

Genetic analysis of multi-environmental spring wheat trials identifies genomic regions for locus-specific trade-offs for grain weight and grain number.

PubMed

Sukumaran, Sivakumar; Lopes, Marta; Dreisigacker, Susanne; Reynolds, Matthew

2018-04-01

GWAS on multi-environment data identified genomic regions associated with trade-offs for grain weight and grain number. Grain yield (GY) can be dissected into its components thousand grain weight (TGW) and grain number (GN), but little has been achieved in assessing the trade-off between them in spring wheat. In the present study, the Wheat Association Mapping Initiative (WAMI) panel of 287 elite spring bread wheat lines was phenotyped for GY, GN, and TGW in ten environments across different wheat growing regions in Mexico, South Asia, and North Africa. The panel genotyped with the 90 K Illumina Infinitum SNP array resulted in 26,814 SNPs for genome-wide association study (GWAS). Statistical analysis of the multi-environmental data for GY, GN, and TGW observed repeatability estimates of 0.76, 0.62, and 0.95, respectively. GWAS on BLUPs of combined environment analysis identified 38 loci associated with the traits. Among them four loci-6A (85 cM), 5A (98 cM), 3B (99 cM), and 2B (96 cM)-were associated with multiple traits. The study identified two loci that showed positive association between GY and TGW, with allelic substitution effects of 4% (GY) and 1.7% (TGW) for 6A locus and 0.2% (GY) and 7.2% (TGW) for 2B locus. The locus in chromosome 6A (79-85 cM) harbored a gene TaGW2-6A. We also identified that a combination of markers associated with GY, TGW, and GN together explained higher variation for GY (32%), than the markers associated with GY alone (27%). The marker-trait associations from the present study can be used for marker-assisted selection (MAS) and to discover the underlying genes for these traits in spring wheat.

Effect of light wavelength on hot spring microbial mat biodiversity

PubMed Central

Nishida, Akifumi; Thiel, Vera; Nakagawa, Mayuko; Ayukawa, Shotaro

2018-01-01

Hot spring associated phototrophic microbial mats are purely microbial communities, in which phototrophic bacteria function as primary producers and thus shape the community. The microbial mats at Nakabusa hot springs in Japan harbor diverse photosynthetic bacteria, mainly Thermosynechococcus, Chloroflexus, and Roseiflexus, which use light of different wavelength for energy conversion. The aim of this study was to investigate the effect of the phototrophs on biodiversity and community composition in hot spring microbial mats. For this, we specifically activated the different phototrophs by irradiating the mats with different wavelengths in situ. We used 625, 730, and 890 nm wavelength LEDs alone or in combination and confirmed the hypothesized increase in relative abundance of different phototrophs by 16S rRNA gene sequencing. In addition to the increase of the targeted phototrophs, we studied the effect of the different treatments on chemotrophic members. The specific activation of Thermosynechococcus led to increased abundance of several other bacteria, whereas wavelengths specific to Chloroflexus and Roseiflexus induced a decrease in >50% of the community members as compared to the dark conditions. This suggests that the growth of Thermosynechococcus at the surface layer benefits many community members, whereas less benefit is obtained from an increase in filamentous anoxygenic phototrophs Chloroflexus and Roseiflexus. The increases in relative abundance of chemotrophs under different light conditions suggest a relationship between the two groups. Aerobic chemoheterotrophs such as Thermus sp. and Meiothermus sp. are thought to benefit from aerobic conditions and organic carbon in the form of photosynthates by Thermosynechococcus, while the oxidation of sulfide and production of elemental sulfur by filamentous anoxygenic phototrophs benefit the sulfur-disproportionating Caldimicrobium thiodismutans. In this study, we used an experimental approach under controlled environmental conditions for the analysis of natural microbial communities, which proved to be a powerful tool to study interspecies relationships in the microbiome. PMID:29381713

Effect of light wavelength on hot spring microbial mat biodiversity.

PubMed

Nishida, Akifumi; Thiel, Vera; Nakagawa, Mayuko; Ayukawa, Shotaro; Yamamura, Masayuki

2018-01-01

Hot spring associated phototrophic microbial mats are purely microbial communities, in which phototrophic bacteria function as primary producers and thus shape the community. The microbial mats at Nakabusa hot springs in Japan harbor diverse photosynthetic bacteria, mainly Thermosynechococcus, Chloroflexus, and Roseiflexus, which use light of different wavelength for energy conversion. The aim of this study was to investigate the effect of the phototrophs on biodiversity and community composition in hot spring microbial mats. For this, we specifically activated the different phototrophs by irradiating the mats with different wavelengths in situ. We used 625, 730, and 890 nm wavelength LEDs alone or in combination and confirmed the hypothesized increase in relative abundance of different phototrophs by 16S rRNA gene sequencing. In addition to the increase of the targeted phototrophs, we studied the effect of the different treatments on chemotrophic members. The specific activation of Thermosynechococcus led to increased abundance of several other bacteria, whereas wavelengths specific to Chloroflexus and Roseiflexus induced a decrease in >50% of the community members as compared to the dark conditions. This suggests that the growth of Thermosynechococcus at the surface layer benefits many community members, whereas less benefit is obtained from an increase in filamentous anoxygenic phototrophs Chloroflexus and Roseiflexus. The increases in relative abundance of chemotrophs under different light conditions suggest a relationship between the two groups. Aerobic chemoheterotrophs such as Thermus sp. and Meiothermus sp. are thought to benefit from aerobic conditions and organic carbon in the form of photosynthates by Thermosynechococcus, while the oxidation of sulfide and production of elemental sulfur by filamentous anoxygenic phototrophs benefit the sulfur-disproportionating Caldimicrobium thiodismutans. In this study, we used an experimental approach under controlled environmental conditions for the analysis of natural microbial communities, which proved to be a powerful tool to study interspecies relationships in the microbiome.

CLINICAL AND EPIDEMIOLOGIC CONSIDERATIONS OF CLOSTRIDIUM DIFFICILE IN HARBOR SEALS (PHOCA VITULINA) AT A MARINE MAMMAL REHABILITATION CENTER.

PubMed

Anderson, Chelsea E; Haulena, Martin; Zabek, Erin; Habing, Gregory; Raverty, Stephen

2015-06-01

Between 1998 and 2008, 15 cases of segmental to diffuse hemorrhagic to necrohemorrhagic enterocolitis were diagnosed in neonatal and weaned juvenile harbor seals (Phoca vitulina) presented from the Vancouver Aquarium Marine Mammal Rescue Centre for rehabilitation. Based on a combination of gross pathology, histopathology, bacterial isolation, and toxin testing, Clostridium difficile enterocolitis was diagnosed. Most pups were anorexic or inappetant and died acutely with few other premonitory signs. Due to ongoing clinical concerns and possible emergence of this pathogen at the facility, efforts to better characterize the disease and understand the epidemiology of C. difficile was initiated in 95 harbor seal pups presented for rehabilitation in a single stranding season. Fecal samples were collected on admission, following completion of antibiotic treatment, and also prerelease or postmortem. All samples were collected fresh and submitted either directly or stored frozen. Fecal samples were inoculated into selective media for culture and screened by enzyme-linked immunosorbant assay (ELISA) for C. difficile toxins A, B, or both. Results of the 95 seals in the study were as follows: on hospital admit 72 seals were sampled, 10 were culture positive, 12 were ELISA positive; following antibiotic therapy 46 seals were sampled noting three culture positive and nine ELISA positive; prior to release 58 seals were sampled noting zero culture positive and one ELISA positive; and on postmortem exam seven seals were sampled noting zero culture positive and two ELISA positive. Clostridium difficile was not deemed to be the cause of death in any of the animals. Although the exact mechanism of disease is unknown, this study suggests that C. difficile infection is not a significant cause of mortality and may be part of the normal flora in harbor seals undergoing rehabilitation. Morbidity and mortality from this bacterium can likely be minimized by judicious use of antibiotics, effective biosecurity-biocontainment protocols, and clean husbandry practices.

Riparian buffer design guidelines for water quality and wildlife habitat functions on agricultural landscapes in the Intermountain West: Case Study

Treesearch

Craig W. Johnson; Susan Buffler

2008-01-01

This hypothetical case study illustrates how the riparian buffer planning protocol described in the RB handbook is used to plan a buffer for both water quality and wildlife conservation on a specific project site. The case study site includes riparian buffer characteristics typical of the study area-variable topography and soils, flood plain wetlands, seeps, springs,...

Multiple protein-protein interactions converging on the Prp38 protein during activation of the human spliceosome.

PubMed

Schütze, Tonio; Ulrich, Alexander K C; Apelt, Luise; Will, Cindy L; Bartlick, Natascha; Seeger, Martin; Weber, Gert; Lührmann, Reinhard; Stelzl, Ulrich; Wahl, Markus C

2016-02-01

Spliceosomal Prp38 proteins contain a conserved amino-terminal domain, but only higher eukaryotic orthologs also harbor a carboxy-terminal RS domain, a hallmark of splicing regulatory SR proteins. We show by crystal structure analysis that the amino-terminal domain of human Prp38 is organized around three pairs of antiparallel α-helices and lacks similarities to RNA-binding domains found in canonical SR proteins. Instead, yeast two-hybrid analyses suggest that the amino-terminal domain is a versatile protein-protein interaction hub that possibly binds 12 other spliceosomal proteins, most of which are recruited at the same stage as Prp38. By quantitative, alanine surface-scanning two-hybrid screens and biochemical analyses we delineated four distinct interfaces on the Prp38 amino-terminal domain. In vitro interaction assays using recombinant proteins showed that Prp38 can bind at least two proteins simultaneously via two different interfaces. Addition of excess Prp38 amino-terminal domain to in vitro splicing assays, but not of an interaction-deficient mutant, stalled splicing at a precatalytic stage. Our results show that human Prp38 is an unusual SR protein, whose amino-terminal domain is a multi-interface protein-protein interaction platform that might organize the relative positioning of other proteins during splicing. © 2016 Schütze et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Testing a new hypothesis on the persistence of Calanus finmarchicus in the Gulf of Maine: Coastal Amplification of Supply and Transport (CAST)

NASA Astrophysics Data System (ADS)

Ji, R.; Feng, Z.; Jones, B.; Chen, C.; Record, N.; Runge, J. A.

2016-02-01

The lipid-rich calanoid copepod, Calanus finmarchicus, plays a critical role in the pelagic food web of the North Atlantic ecosystem. Deep basins along the continental shelf, such as Wilkinson Basin (WB) in the Gulf of Maine, harbor high abundance of diapausing C. finmarchicus during the summer and fall that have persisted despite predictions to the contrary. Identifying the major source of diapausing individuals is critical to the understanding of mechanisms that allow population persistence. This is especially true for a shelf system such as the the Gulf of Maine, which has recently experienced significant warming that could potentially threaten the existence of the population in the region. In this study, we conduct a series of Lagrangian tracking experiments using a copepod life history individual-based model. Model results suggest that coastal waters are the major upstream source for individuals entering dormancy in WB over summertime, although pathways and distribution patterns vary with vertical positioning and release timing of particles. By linking these model results and the observed high springtime egg production rate in the coastal Gulf of Maine, we propose a new mechanism for population persistence that involves coastal amplification of supply (spring reproduction/summer growth in the food-rich coastal region) and transport to receiving basins (e.g. WB) capable of harboring the overwintering stock.

Development of a new method for the determination of residues of the neonictinoid insecticide imidacloprid in juvenile Chinook (Oncorhynchus tyshawytscha) using ELISA detection

USGS Publications Warehouse

Frew, John A.; Grue, Christian E.

2012-01-01

The neonicotinoid insecticide imidacloprid (IMI) has been proposed as an alternative to carbaryl for controlling indigenous burrowing shrimp on commercial oyster beds in Willapa Bay and Grays Harbor, Washington. A focus of concern over the use of this insecticide in an aquatic environment is the potential for adverse effects from exposure to non-target species residing in the Bay, such as juvenile Chinook (Oncorhynchus tshawytscha) and cutthroat trout (O. clarki). Federal registration and State permiting approval for the use of IMI will require confirmation that the compound does not adversely impact these salmonids following field applications. This will necessitate an environmental monitoring program for evaluating exposure in salmonids following the treatment of beds. Quantification of IMI residues in tissue can be used for determining salmonid exposure to the insecticide. Refinement of an existing protocol using liquid-chromatography mass spectrometry (LC-MS) detection would provide the low limits of quantification, given the relatively small tissue sample sizes, necessary for determining exposure in individual fish. Such an approach would not be viable for the environmental monitoring effort in Willapa Bay and Grays Harbor due to the high costs associated with running multiple analyses, however. A new sample preparation protocol was developed for use with a commercially available enzyme-linked immunosorbent assay (ELISA) for the quantification of IMI, thereby providing a low-cost alternative to LC-MS for environmental monitoring in Willapa Bay and Grays Harbor. Extraction of the analyte from the salmonid brain tissue was achieved by Dounce homogenization in 4.0 mL of 20.0 mM Triton X-100, followed by a 6 h incubation at 50–55 °C. Centrifugal ultrafiltration and reversed phase solid phase extraction were used for sample cleanup. The limit of quantification for an average 77.0 mg whole brain sample was calculated at 18.2 μg kg-1 (ppb) with an average recovery of 79%. This relatively low limit of quantification allows for the analysis of individual fish. Using controlled laboratory studies, a curvelinear relationship was found between the measured IMI residue concentrations in brain tissue and exposure concentrations in seawater. Additonally, a range of IMI brain residue concentrations was associated with an overt effect; illustrating the utility of the IMI tissue residue quantification approach for linking exposure with defined effects.

Efficient, footprint-free human iPSC genome editing by consolidation of Cas9/CRISPR and piggyBac technologies.

PubMed

Wang, Gang; Yang, Luhan; Grishin, Dennis; Rios, Xavier; Ye, Lillian Y; Hu, Yong; Li, Kai; Zhang, Donghui; Church, George M; Pu, William T

2017-01-01

Genome editing of human induced pluripotent stem cells (hiPSCs) offers unprecedented opportunities for in vitro disease modeling and personalized cell replacement therapy. The introduction of Cas9-directed genome editing has expanded adoption of this approach. However, marker-free genome editing using standard protocols remains inefficient, yielding desired targeted alleles at a rate of ∼1-5%. We developed a protocol based on a doxycycline-inducible Cas9 transgene carried on a piggyBac transposon to enable robust and highly efficient Cas9-directed genome editing, so that a parental line can be expeditiously engineered to harbor many separate mutations. Treatment with doxycycline and transfection with guide RNA (gRNA), donor DNA and piggyBac transposase resulted in efficient, targeted genome editing and concurrent scarless transgene excision. Using this approach, in 7 weeks it is possible to efficiently obtain genome-edited clones with minimal off-target mutagenesis and with indel mutation frequencies of 40-50% and homology-directed repair (HDR) frequencies of 10-20%.

Extraction of Total Nucleic Acids From Ticks for the Detection of Bacterial and Viral Pathogens

PubMed Central

Crowder, Chris D.; Rounds, Megan A.; Phillipson, Curtis A.; Picuri, John M.; Matthews, Heather E.; Halverson, Justina; Schutzer, Steven E.; Ecker, David J.; Eshoo, Mark W.

2010-01-01

Ticks harbor numerous bacterial, protozoal, and viral pathogens that can cause serious infections in humans and domestic animals. Active surveillance of the tick vector can provide insight into the frequency and distribution of important pathogens in the environment. Nucleic-acid based detection of tick-borne bacterial, protozoan, and viral pathogens requires the extraction of both DNA and RNA (total nucleic acids) from ticks. Traditional methods for nucleic acid extraction are limited to extraction of either DNA or the RNA from a sample. Here we present a simple bead-beating based protocol for extraction of DNA and RNA from a single tick and show detection of Borrelia burgdorferi and Powassan virus from individual, infected Ixodes scapularis ticks. We determined expected yields for total nucleic acids by this protocol for a variety of adult tick species. The method is applicable to a variety of arthropod vectors, including fleas and mosquitoes, and was partially automated on a liquid handling robot. PMID:20180313

Marine optical characterizations

NASA Technical Reports Server (NTRS)

Clark, Dennis K.; Ge, Yuntao; Hovey, Phil; King, ED; Stengel, Eric; Yuen, Marilyn; Koval, Larisa

1995-01-01

During the past three months, the MOCE Team conducted two field experiments in Mill Creek,Chesapeake Bay, from July 24 to August 4, and at the MOBY operations site at Snug Harbor, Honolulu, Hawaii, from August 15-30, prepared two technical memoranda, and continued MOCE-2 and MOCE-3 data reduction. The primary purposes of the experiments were to test the SeaWiFS 'remote sensing reflectance' protocol, obtain turbid water data for ocean color satellite algorithm development, perform calibration for both Near Infrared (NIR) and Visible Rainbow Spectrometer system, continue assembling the operational Marine Optical Buoy, and to test the MOBY cellular phone communications link at the Lanai mooring site.

Army Communicator. Volume 28, Number 1, Spring 2003

DTIC Science & Technology

2003-01-01

SUBJECT TERMS 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT Same as Report (SAR) 18. NUMBER OF PAGES 72 19a. NAME OF RESPONSIBLE PERSON ...does business to meet these requirements and the growing expectations from the president and his staff for instantaneous, global, secure , reliable and...by COL Tim Gibson Do you have access to a secure Internet-protocol router network terminal on a regular basis? If you answered yes, you’re wrong

Isolation of sphere-forming stem cells from the mouse inner ear.

PubMed

Oshima, Kazuo; Senn, Pascal; Heller, Stefan

2009-01-01

The mammalian inner ear has very limited ability to regenerate lost sensory hair cells. This deficiency becomes apparent when hair cell loss leads to hearing loss as a result of either ototoxic insult or the aging process. Coincidently, with this inability to regenerate lost hair cells, the adult cochlea does not appear to harbor cells with a proliferative capacity that could serve as progenitor cells for lost cells. In contrast, adult mammalian vestibular sensory epithelia display a limited ability for hair cell regeneration, and sphere-forming cells with stem cell features can be isolated from the adult murine vestibular system. The neonatal inner ear, however, does harbor sphere-forming stem cells residing in cochlear and vestibular tissues. Here, we provide protocols to isolate sphere-forming stem cells from neonatal vestibular and cochlear sensory epithelia as well as from the spiral ganglion. We further describe procedures for sphere propagation, cell differentiation, and characterization of inner ear cell types derived from spheres. Sphere-forming stem cells from the mouse inner ear are an important tool for the development of cellular replacement strategies of damaged inner ears and are a bona fide progenitor cell source for transplantation studies.

Metformin: A Hopeful Promise in Aging Research.

PubMed

Novelle, Marta G; Ali, Ahmed; Diéguez, Carlos; Bernier, Michel; de Cabo, Rafael

2016-03-01

Even though the inevitable process of aging by itself cannot be considered a disease, it is directly linked to life span and is the driving force behind all age-related diseases. It is an undisputable fact that age-associated diseases are among the leading causes of death in the world, primarily in industrialized countries. During the last several years, an intensive search of antiaging treatments has led to the discovery of a variety of drugs that promote health span and/or life extension. The biguanide compound metformin is widely used for treating people with type 2 diabetes and appears to show protection against cancer, inflammation, and age-related pathologies. Here, we summarize the recent developments about metformin use in translational aging research and discuss its role as a potential geroprotector. Copyright © 2016 Cold Spring Harbor Laboratory Press; all rights reserved.

Fungi on the skin: dermatophytes and Malassezia.

PubMed

White, Theodore C; Findley, Keisha; Dawson, Thomas L; Scheynius, Annika; Boekhout, Teun; Cuomo, Christina A; Xu, Jun; Saunders, Charles W

2014-08-01

Several human skin diseases and disorders are associated with two groups of fungi, the dermatophytes and Malassezia. Although these skin-related problems are not generally life threatening, they are among the most common diseases and disorders of mankind. These fungi are phylogenetically divergent, with the dermatophytes within the Ascomycota and Malassezia within Basidiomycota. Genome analysis indicates that the adaptations to the skin environment are different in these two groups of fungi. Malassezia are dependent on host lipids and secrete lipases and phospholipases that likely release host fatty acids. The dermatophytes encode multiple enzymes with potential roles in modulating host interactions: polyketide synthases, nonribosomal peptide synthetases, LysM, proteases, kinases, and pseudokinases. These two fungal groups have maximized their interactions with the host using two very different mechanisms. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

Protecting Traditional Knowledge Related to Biological Resources: Is Scientific Research Going to Become More Bureaucratized?

PubMed

Reddy, Prashant; Lakshmikumaran, Malathi

2015-06-22

For the past several decades, there has been a world debate on the need for protecting traditional knowledge. A global treaty appears to be a distant reality. Of more immediate concern are the steps taken by the global community to protect access to biological resources in the name of protecting traditional knowledge. The Indian experience with implementing the Convention on Biological Diversity has created substantial legal uncertainty in collaborative scientific research between Indians and foreigners apart from bureaucratizing the entire process of scientific research, especially with regard to filing of applications for intellectual property rights. The issue therefore is whether the world needs to better balance the needs of the scientific community with the rights of those who have access to traditional knowledge. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

What Is the Predictive Value of Animal Models for Vaccine Efficacy in Humans? Reevaluating the Potential of Mouse Models for the Human Immune System.

PubMed

Jameson, Stephen C; Masopust, David

2018-04-02

Much of what we understand about immunology, including the response to vaccines, come from studies in mice because they provide many practical advantages compared with research in higher mammals and humans. Nevertheless, modalities for preventing or treating disease do not always translate from mouse to humans, which has led to increasing scrutiny of the continued merits of mouse research. Here, we summarize the pros and cons of current laboratory mouse models for immunology research and discuss whether overreliance on nonphysiological, ultra-hygienic animal husbandry approaches has limited the ultimate translation potential of mouse-derived data to humans. Alternative approaches are discussed that may extend the use of the mouse model for preclinical studies. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

OutKnocker: a web tool for rapid and simple genotyping of designer nuclease edited cell lines.

PubMed

Schmid-Burgk, Jonathan L; Schmidt, Tobias; Gaidt, Moritz M; Pelka, Karin; Latz, Eicke; Ebert, Thomas S; Hornung, Veit

2014-10-01

The application of designer nucleases allows the induction of DNA double-strand breaks (DSBs) at user-defined genomic loci. Due to imperfect DNA repair mechanisms, DSBs can lead to alterations in the genomic architecture, such as the disruption of the reading frame of a critical exon. This can be exploited to generate somatic knockout cell lines. While high genome editing activities can be achieved in various cellular systems, obtaining cell clones that contain all-allelic frameshift mutations at the target locus of interest remains a laborious task. To this end, we have developed an easy-to-follow deep sequencing workflow and the evaluation tool OutKnocker (www.OutKnocker.org), which allows convenient, reliable, and cost-effective identification of knockout cell lines. © 2014 Schmid-Burgk et al.; Published by Cold Spring Harbor Laboratory Press.

Globalization and the Changing Epidemiology of Hepatitis A Virus.

PubMed

Jacobsen, Kathryn H

2018-03-02

Increased economic interdependence, social integration, and other aspects of globalization are contributing to significant changes in hepatitis A epidemiology. Globally, the incidence of hepatitis A virus (HAV) infection is decreasing, the age at midpoint of population immunity (AMPI) is increasing, and the proportion of symptomatic cases is increasing as the average age at infection increases. In low-income countries, HAV remains endemic but improved water and sanitation systems are reducing transmission rates among young children. In high-income countries, most adults remain susceptible to HAV and foodborne outbreaks are becoming more frequent. Middle-income countries have diverse epidemiological profiles, and they play important roles in the global spread of HAV through international trade and travel. Future changes in the epidemiology of hepatitis A will be heavily influenced by globalization processes. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

Sexual cannibalism as a manifestation of sexual conflict.

PubMed

Schneider, Jutta M

2014-09-11

Sexual cannibalism is a well-known example for sexual conflict and has many facets that determine the costs and benefits for the cannibal and the victim. Here, I focus on species in which sexual cannibalism is a general component of a mating system in which males invest maximally in mating with a single (monogyny) or two (bigyny) females. Sexual cannibalism can be a male strategy to maximize paternity and a female strategy to prevent paternity monopolization by any or a particular male. Considerable variation exists between species (1) in the potential of males to monopolize females, and (2) in the success of females in preventing monopolization by males. This opens up exciting future possibilities to investigate sexually antagonistic coevolution in a largely unstudied mating system. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

Big Bang Tumor Growth and Clonal Evolution.

PubMed

Sun, Ruping; Hu, Zheng; Curtis, Christina

2018-05-01

The advent and application of next-generation sequencing (NGS) technologies to tumor genomes has reinvigorated efforts to understand clonal evolution. Although tumor progression has traditionally been viewed as a gradual stepwise process, recent studies suggest that evolutionary rates in tumors can be variable with periods of punctuated mutational bursts and relative stasis. For example, Big Bang dynamics have been reported, wherein after transformation, growth occurs in the absence of stringent selection, consistent with effectively neutral evolution. Although first noted in colorectal tumors, effective neutrality may be relatively common. Additionally, punctuated evolution resulting from mutational bursts and cataclysmic genomic alterations have been described. In this review, we contrast these findings with the conventional gradualist view of clonal evolution and describe potential clinical and therapeutic implications of different evolutionary modes and tempos. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

Which Dengue Vaccine Approach Is the Most Promising, and Should We Be Concerned about Enhanced Disease after Vaccination? Questions Raised by the Development and Implementation of Dengue Vaccines: Example of the Sanofi Pasteur Tetravalent Dengue Vaccine.

PubMed

Guy, Bruno

2018-06-01

Dengue is a still-growing public health concern in many tropical and subtropical regions of the world. The development and implementation of an effective dengue vaccine in these regions is a high priority. This insight focuses on the expected characteristics of a safe and efficacious vaccine, referring to the clinical experience obtained during the development of the first tetravalent dengue vaccine from Sanofi Pasteur, now licensed in several endemic countries. Safety and efficacy data from both short- and long-term follow-up of large-scale efficacy studies will be discussed, as well as the next steps following vaccine introduction. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

Which Dengue Vaccine Approach Is the Most Promising, and Should We Be Concerned about Enhanced Disease after Vaccination? The Path to a Dengue Vaccine: Learning from Human Natural Dengue Infection Studies and Vaccine Trials.

PubMed

de Silva, Aravinda M; Harris, Eva

2018-06-01

Dengue virus (DENV) is the most common arthropod-borne viral disease of humans. Although effective vaccines exist against other flaviviral diseases like yellow fever and Japanese encephalitis, dengue vaccine development is complicated by the presence of four virus serotypes and the possibility of partial immunity enhancing dengue disease severity. Several live attenuated dengue vaccines are being tested in human clinical trials. Initial results are mixed, with variable efficacy depending on DENV serotype and previous DENV exposure. Here, we highlight recent discoveries about the human antibody response to DENV and propose guidelines for advancing development of safe and effective dengue vaccines. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

Perspectives on Human Variation through the Lens of Diversity and Race.

PubMed

Chakravarti, Aravinda

2015-09-01

Human populations, however defined, differ in the distribution and frequency of traits they display and diseases to which individuals are susceptible. These need to be understood with respect to three recent advances. First, these differences are multicausal and a result of not only genetic but also epigenetic and environmental factors. Second, the actions of genes, although crucial, turn out to be quite dynamic and modifiable, which contrasts with the classical view that they are inflexible machines. Third, the diverse human populations across the globe have spent too little time apart from our common origin 50,000 years ago to have developed many individually adapted traits. Human trait and disease differences by continental ancestry are thus as much the result of nongenetic as genetic forces. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

Control of Cell Survival in Adult Mammalian Neurogenesis.

PubMed

Kuhn, H Georg

2015-10-28

The fact that continuous proliferation of stem cells and progenitors, as well as the production of new neurons, occurs in the adult mammalian central nervous system (CNS) raises several basic questions concerning the number of neurons required in a particular system. Can we observe continued growth of brain regions that sustain neurogenesis? Or does an elimination mechanism exist to maintain a constant number of cells? If so, are old neurons replaced, or are the new neurons competing for limited network access among each other? What signals support their survival and integration and what factors are responsible for their elimination? This review will address these and other questions regarding regulatory mechanisms that control cell-death and cell-survival mechanisms during neurogenesis in the intact adult mammalian brain. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

Temporal and Spatial Diversity of Bacterial Communities in Coastal Waters of the South China Sea

PubMed Central

Du, Jikun; Xiao, Kai; Li, Li; Ding, Xian; Liu, Helu; Lu, Yongjun; Zhou, Shining

2013-01-01

Bacteria are recognized as important drivers of biogeochemical processes in all aquatic ecosystems. Temporal and geographical patterns in ocean bacterial communities have been observed in many studies, but the temporal and spatial patterns in the bacterial communities from the South China Sea remained unexplored. To determine the spatiotemporal patterns, we generated 16S rRNA datasets for 15 samples collected from the five regularly distributed sites of the South China Sea in three seasons (spring, summer, winter). A total of 491 representative sequences were analyzed by MOTHUR, yielding 282 operational taxonomic units (OTUs) grouped at 97% stringency. Significant temporal variations of bacterial diversity were observed. Richness and diversity indices indicated that summer samples were the most diverse. The main bacterial group in spring and summer samples was Alphaproteobacteria, followed by Cyanobacteria and Gammaproteobacteria, whereas Cyanobacteria dominated the winter samples. Spatial patterns in the samples were observed that samples collected from the coastal (D151, D221) waters and offshore (D157, D1512, D224) waters clustered separately, the coastal samples harbored more diverse bacterial communities. However, the temporal pattern of the coastal site D151 was contrary to that of the coastal site D221. The LIBSHUFF statistics revealed noticeable differences among the spring, summer and winter libraries collected at five sites. The UPGMA tree showed there were temporal and spatial heterogeneity of bacterial community composition in coastal waters of the South China Sea. The water salinity (P=0.001) contributed significantly to the bacteria-environment relationship. Our results revealed that bacterial community structures were influenced by environmental factors and community-level changes in 16S-based diversity were better explained by spatial patterns than by temporal patterns. PMID:23785512

Spatial and Seasonal Calcification in Corals and Calcareous Crusts in a Naturally Warm Coral Reef Region

NASA Astrophysics Data System (ADS)

Roik, A.; Roder, C.; Roethig, T.; Voolstra, C. R.

2016-02-01

The Red Sea harbors highly diverse and structurally complex coral reefs and is of interest for ocean warming studies. In the central and southern part, water temperatures rise above 30°C during summer, constituting one of the warmest coral reef environments worldwide. Additionally, seasonal variability of temperatures allows studying changes of environmental conditions and their effects on coral reef processes. To explore the influence of these warm and seasonally variable habitats on reef calcification, we measured in situ calcification of primary and secondary reef-builders in the central Red Sea. We collected calcification rates on the major habitat-forming coral genera Porites, Acropora, and Pocillopora, and also on calcareous crusts (CC). The study comprised forereef and backreef environments of three reefs along a cross-shelf gradient assessed over four seasons of the year. Calcification patterns of all coral genera were consistent across the shelf and highest in spring. In contrast to the corals, CC calcification strongly increased with distance from shore, but varied to a lesser extend over the seasons demonstrating lower calcification rates during spring and summer. Interestingly, reef calcification rates in the central Red Sea were on average in the range of data reported from the Caribbean and Indo-Pacific. For Acropora, annual average calcification rates were even at the lower end in comparison to studies from other locations. While coral calcification maxima typically have been observed during summer in many reef locations worldwide, we observed calcification maxima during spring in the central Red Sea indicating that summer temperatures may exceed the optima of reef calcifiers. Our study provides a baseline of calcification data for the region and serves as a foundation for comparative efforts to quantify the impact of future environmental change.

Coupling Genetic and Chemical Microbiome Profiling Reveals Heterogeneity of Archaeome and Bacteriome in Subsurface Biofilms That Are Dominated by the Same Archaeal Species

PubMed Central

Holman, Hoi-Ying N.; DeSantis, Todd Z.; Wanner, Gerhard; Andersen, Gary L.; Perras, Alexandra K.; Meck, Sandra; Völkel, Jörg; Bechtel, Hans A.; Wirth, Reinhard; Moissl-Eichinger, Christine

2014-01-01

Earth harbors an enormous portion of subsurface microbial life, whose microbiome flux across geographical locations remains mainly unexplored due to difficult access to samples. Here, we investigated the microbiome relatedness of subsurface biofilms of two sulfidic springs in southeast Germany that have similar physical and chemical parameters and are fed by one deep groundwater current. Due to their unique hydrogeological setting these springs provide accessible windows to subsurface biofilms dominated by the same uncultivated archaeal species, called SM1 Euryarchaeon. Comparative analysis of infrared imaging spectra demonstrated great variations in archaeal membrane composition between biofilms of the two springs, suggesting different SM1 euryarchaeal strains of the same species at both aquifer outlets. This strain variation was supported by ultrastructural and metagenomic analyses of the archaeal biofilms, which included intergenic spacer region sequencing of the rRNA gene operon. At 16S rRNA gene level, PhyloChip G3 DNA microarray detected similar biofilm communities for archaea, but site-specific communities for bacteria. Both biofilms showed an enrichment of different deltaproteobacterial operational taxonomic units, whose families were, however, congruent as were their lipid spectra. Consequently, the function of the major proportion of the bacteriome appeared to be conserved across the geographic locations studied, which was confirmed by dsrB-directed quantitative PCR. Consequently, microbiome differences of these subsurface biofilms exist at subtle nuances for archaea (strain level variation) and at higher taxonomic levels for predominant bacteria without a substantial perturbation in bacteriome function. The results of this communication provide deep insight into the dynamics of subsurface microbial life and warrant its future investigation with regard to metabolic and genomic analyses. PMID:24971452

The New York Brain Bank of Columbia University: practical highlights of 35 years of experience.

PubMed

Ramirez, Etty Paola Cortes; Keller, Christian Ernst; Vonsattel, Jean Paul

2018-01-01

The New York Brain Bank processes brains and organs of clinically well-characterized patients with age-related neurodegenerative diseases, and for comparison, from individuals without neurologic or psychiatric impairments. The donors, either patients or individuals, were evaluated at healthcare facilities of the Columbia University of New York. Each source brain yields four categories of samples: fresh frozen blocks and crushed parenchyma, and formalin-fixed wet blocks and histology sections. A source brain is thoroughly evaluated to determine qualitatively and quantitatively any changes it might harbor using conventional neuropathologic techniques. The clinical and pathologic diagnoses are integrated to determine the distributive diagnosis assigned to the samples obtained from a source brain. The gradual standardization of the protocol was developed in 1981 in response to the evolving requirements of basic investigations on neurodegeneration. The methods assimilate long-standing experience from multiple centers. The resulting and current protocol includes a constant central core applied to all brains with conditional flexibility around it. The New York Brain Bank is an integral part of the department of pathology, where the expertise, teaching duties, and hardware are shared. Since details of the protocols are available online, this chapter focuses on practical issues in professionalizing brain banking. Copyright © 2018 Elsevier B.V. All rights reserved.

Generation of polyhormonal and multipotent pancreatic progenitor lineages from human pluripotent stem cells.

PubMed

Korytnikov, Roman; Nostro, Maria Cristina

2016-05-15

Generation of pancreatic β-cells from human pluripotent stem cells (hPSCs) has enormous importance in type 1 diabetes (T1D), as it is fundamental to a treatment strategy based on cellular therapeutics. Being able to generate β-cells, as well as other mature pancreatic cells, from human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs) will also enable the development of platforms that can be used for disease modeling and drug testing for a variety of pancreas-associated diseases, including cystic fibrosis. For this to occur, it is crucial to develop differentiation strategies that are robust and reproducible across cell lines and laboratories. In this article we describe two serum-free differentiation protocols designed to generate specific pancreatic lineages from hPSCs. Our approach employs a variety of cytokines and small molecules to mimic developmental pathways active during pancreatic organogenesis and allows for the in vitro generation of distinct pancreatic populations. The first protocol is designed to give rise to polyhormonal cells that have the potential to differentiate into glucagon-producing cells. The second protocol is geared to generate multipotent pancreatic progenitor cells, which harbor the potential to generate all pancreatic lineages including: monohormonal endocrine cells, acinar, and ductal cells. Copyright © 2016 Elsevier Inc. All rights reserved.

Mount Rainier National Park and Olympic National Park Elk Monitoring Program Annual Report 2010

USGS Publications Warehouse

Griffin, Paul; Happe, Patricia J.; Jenkins, Kurt J.; Reid, Mason; Vales, David J.; Moeller, Barbara J.; Tirhi, Michelle; McCorquodale, Scott; Miller, Pat

2010-01-01

Fiscal year 2010 was the third year of gathering data needed for protocol development while simultaneously implementing what is expected to be the elk monitoring protocol at Mount Rainier (MORA) and Olympic (OLYM) national parks in the North Coast and Cascades Network (NCCN). Elk monitoring in these large wilderness parks relies on aerial surveys from a helicopter. Summer surveys are planned for both parks and are intended to provide quantitative estimates of abundance, sex and age composition, and distribution of migratory elk in high elevation trend count areas. Spring surveys are planned at Olympic National Park and are intended to provide quantitative estimates of abundance of resident and migratory elk on low-elevation winter ranges within surveyed trend count areas. An unknown number of elk is not detected during surveys. The protocol under development aims to estimate the number of missed elk by applying a model that accounts for detection bias. Detection bias in elk surveys in MORA will be estimated using a double-observer sightability model that was developed based on data from surveys conducted in 2008-2010. The model was developed using elk that were previously equipped with radio collars by cooperating tribes. That model is currently in peer review. At the onset of protocol development in OLYM there were no existing radio- collars on elk. Consequently double-observer sightability models have not yet been developed for elk surveys in OLYM; the majority of the effort in OLYM has been focused on capturing and radio collaring elk to permit the development of sightability models for application in OLYM. As a result, no estimates of abundance or composition are included in this annual report, only raw counts of the numbers of elk seen in surveys. At MORA each of the two trend count areas (North Rainier herd, and South Rainier herd) were surveyed twice. 290 and 380 elk were counted on the two replicates in the North Rainier herd, and 621 and 327 elk counted on the two replicate South Rainier counts. At Olympic National Park, each of three spring trend count areas was surveyed once in March 2010. 27 elk were observed in the South Fork Hoh trend count area, 137 elk were observed in the Hoh trend count area, and 131 elk were observed in the Queets trend count area. In September 2010, 18 elk were captured and fitted with radio collars as part of a contracted animal capture, eradication and tagging of animals (ACETA) operation. These animals will be available to contribute double-observer sightability data in future spring and summer surveys. There were no summer surveys for elk in OLYM in 2010.

A dangerous context changes the way that rats learn about and discriminate between innocuous events in sensory preconditioning.

PubMed

Holmes, Nathan M; Westbrook, R Frederick

2017-09-01

Four experiments used a sensory preconditioning protocol to examine how a dangerous context influences learning about innocuous events. In Experiments 1, 2, and 3, rats were exposed to presentations of a tone followed immediately or 20-sec later by presentations of a light. These tone-light pairings occurred in a context that was either familiar and safe, or equally familiar but dangerous, that is, it was a context in which rats had been exposed to footshock. Rats were next exposed to parings of the light and shock and then tested with the tone (and light). The experiments showed that a dangerous context permits formation of a tone-light association under circumstances that preclude formation of that same association in a safe context (Experiments 1 and 2), and that this facilitative effect on associative formation depends on the content being currently dangerous rather than having been dangerous in the past (Experiment 3). Experiment 4 examined whether a dangerous context facilitates discrimination between two innocuous events. In a safe or dangerous context, rats were exposed to a tone that signaled the light and then to a white noise presented alone. Subsequent to conditioning of the light, the tests revealed that rats that had been exposed to these tone-light and white noise alone presentations in a dangerous context froze to the tone but not to the noise, whereas those exposed in a safe context froze to both the tone and the white noise. The results were related to previous evidence that the amygdala is critical for processing information about innocuous stimuli in a dangerous but not a safe context. They were attributed to an amygdala-based enhancement of arousal and/or attention in a dangerous context, hence the facilitation of associative formation and enhanced discriminability in this context. © 2017 Holmes and Westbrook; Published by Cold Spring Harbor Laboratory Press.

33 CFR 125.15 - Access to waterfront facilities, and port and harbor areas, including vessels and harbor craft...

Code of Federal Regulations, 2010 CFR

2010-07-01

..., and port and harbor areas, including vessels and harbor craft therein. 125.15 Section 125.15....15 Access to waterfront facilities, and port and harbor areas, including vessels and harbor craft....09 to those waterfront facilities, and port and harbor areas, including vessels and harbor craft...

Temporal Epidemiology of Sudden Oak Death in Oregon.

PubMed

Peterson, Ebba K; Hansen, Everett M; Kanaskie, Alan

2015-07-01

An effort to eradicate Phytophthora ramorum, causal agent of sudden oak death, has been underway since its discovery in Oregon forests. Using an information-theoretical approach, we sought to model yearly variation in the size of newly infested areas and dispersal distance. Maximum dispersal distances were best modeled by spring and winter precipitation 2 years before detection, and infestation size the year prior. Infestation size was best modeled by infestation size and spring precipitation the year prior. In our interpretation, there is a 2-year delay between the introduction of inoculum and onset of mortality for a majority of sites. The year-long gap in between allows ample time for the production of inoculum contributing to the spread of P. ramorum. This is supported by epidemic development following changes in eradication protocols precipitated by an outbreak in 2011, attributable to a 2009 treatment delay and an uncharacteristically wet spring in 2010. Posteradication, we have observed an increase in the total area of new outbreaks and increased frequency in dispersal distances greater than 4 km. Although the eradication program has not eliminated P. ramorum from Oregon forests, it has likely moderated this epidemic, emphasizing the need for prompt treatment of future invasive forest pathogens.

The potential for facilitating spring discharge from continental climate waste stabilisation ponds by carry-over of treated wastewater: concepts and experimental findings.

PubMed

Whalley, C; Pak, L N; Heaven, S

2007-01-01

The research investigated some factors influencing the rate of stabilisation of wastewater in the spring period in continental climate waste stabilisation ponds, and in particular the potential for bringing forward the discharge date by optimising storage capacity and dilution. Experiments using pilot and modelscale ponds were set up in Almaty, Kazakhstan. These simulated operating regimes for a facultative and storage/maturation pond system subject to ice cover from late November until late March. Two pilot-scale facultative ponds were operated at hydraulic retention times (HRT) of 20 and 30 days, with surface loading rates of 100 and 67 kg BOD ha(-1) day(-1). Effluent from the 20-day HRT facultative pond was then fed to two pilot-scale storage/maturation ponds which had been partially emptied and allowed to refill over the winter period with no removal of effluent. The paper discusses the results of the experiments with respect to selection of an operating regime to make treated wastewater available early in the spring. Preliminary results indicate that there may be potential for alternative operating protocols designed to maximise their performance and economic potential.

Spatial distribution, temporal variability, and chemistry of the salt wedge in the lower Charles River, Massachusetts, June 1998 to July 1999

USGS Publications Warehouse

Breault, R.F.; Barlow, L.K.; Reisig, K.D.; Parker, G.W.

2000-01-01

The Charles River is of great recreational and ecological value to the Boston metropolitan region and the Commonwealth of Massachusetts. It is also the focus of the U.S. Environmental Protection Agency (USEPA) Region I, Clean Charles 2005 Task Force. The main goal of the Task Force is to make the Charles River 'fishable and swimmable' by the year 2005. Achieving 'fishable and swimmable' conditions will require continued progress in addressing a range of environmental conditions now degrading water quality, including the infiltration of saltwater from Boston Harbor into the freshwater Charles River.To better understand the pattern of saltwater intrusion, the U.S. Geological Survey (USGS), in cooperation with the U.S. Environmental Protection Agency (USEPA), Massachusetts Department of Environmental Management (MADEM), and New England Interstate Water Pollution Control Commission (NEIWPCC), collected data on the spatial distribution, temporal variability, and chemistry of the saltwater that entered the lower Charles River from June 1998 to July 1999. The purpose of this investigation is to extend and complement a regional-scale study of Charles River water quality conducted in 1996 (T. Faber, U.S. Environmental Protection Agency, written commun., 1997), and the ongoing water monitoring activities of the Massachusetts Water Resources Authority (MWRA) and the Charles River Watershed Association (CRWA). The data collected by this investigation supports the Clean Charles 2005 Task Force by providing detailed information concerning a major factor limiting 'fishable and swimmable' conditions in the lower Charles River. Finally, the study will be used to assist current planning efforts of the Metropolitan District Commission (MDC) to restore the historic parklands of the lower Charles River.The 'Basin' is the local term for the reach of the Charles River that begins at the Watertown Dam in Watertown, Mass., and extends about 8 mi through suburban and urban areas to Boston Harbor. Discharge to the harbor is controlled by the 'new' Charles River Dam in Boston (fig. 1). The Basin was created by construction of the 'old' Charles River Dam in 1908 to solve Boston's sanitary problems. Prior to the building of the old Charles River Dam, the lower Charles River was a tidal estuary in which the water levels rose and fell twice daily with the tidal cycle. Low tide would expose untreated sewage that was discharged directly into the river. Exposed sewage created noxious odors and served as a breeding ground for mosquitoes that caused sporadic epidemics of malaria and yellow fever (Jobin, 1998). Damming of the river interrupted the normal tidal cycle and flooded the estuary by creating a freshwater pool (the Basin) that had a constant water elevation of about 0.8 meters (m) above mean sea level. Flooding of the estuary initially improved sanitary conditions and the Basin became a source of enjoyment for the local population and the focus of a large waterfront park in Boston and Cambridge (Jobin, 1998).Although the infiltration of saltwater from the harbor into the Basin was anticipated when the old Charles River Dam was built, neither the magnitude nor the consequences of the infiltration was considered. By 1975, the Metropolitan District Commission (MDC) determined that harbor water covered about 80 percent of the river bottom within the Basin and composed about 50 percent of its depth. The MDC also concluded that fish kills and odors in the spring of 1975 were likely the result of the sulfide-rich saltwater mixing with the overlying freshwater (Metropolitan District Commission, 1975).Saltwater from Boston Harbor that enters the Basin is known as the 'salt wedge' because of the shape it assumes as it moves upstream. Freshwater discharge from upstream pushes against the intruding harbor water until the density differences cause stratification to occur; the freshwater then overrides the denser harbor water (Fischer and others, 1979). The depth from

Restoration Science in New York Harbor: It takes a (large, diverse and engaged) village

NASA Astrophysics Data System (ADS)

Newton, R.; Birney, L.; Janis, S.; Groome, M.; Palmer, M.; Bone, E.; O'Neil, J. M.; Hill, J.; Dennison, W.; Malinowski, P.; Kohne, L.; Molina, M.; Moore, G.; Woods, N.

2015-12-01

The Curriculum + Community Enterprise for Restoration Science (CCE-RS) facilitates partnerships between scientists and middle school educators on ecological restoration and environmental monitoring projects. The educational model is designed to wrap around the student, including classroom instruction, field science, after-school programs and engagement with the student's community. Its pillars include: a teacher training fellowship at Pace University, student curriculum, a digital platform, afterschool and summer mentoring, and community exhibits. The digital platform includes a tablet app tailored to the project's field protocols and linked to a database shared across schools and partnering institutions. Through the digital platform, data is integrated into a single citizen-science monitoring project, teachers share curriculum and best practices, and students link directly to their peers at other schools. Curriculum development has been collaborative between scientists, science education specialists, and secondary school teachers. The CCE-RS is rooted in project-based learning: the New York Harbor School has engaged high school students in environmental monitoring and oyster restoration in the Harbor for about the last decade. The science partners (U. of Maryland and Columbia) have been working with students and other citizen scientists in outdoor science over about the last decade. Local partners in outside-the-classroom education include the New York Academy of Sciences, The River Project, which will provide field education services, and Good Shepherd Services, which provides after-school programming in schools serving primarily poor families. Scientists on the project engage directly with teachers and informal educators in curriculum development and citizen-science outreach. We present the lessons learned from our first cohort of Fellows, the pedagogical model, and the digital platform, which is extensible to other ecological restoration settings.

Protocol Design for the Bench to Bed Trial in Alectinib-Refractory Non-Small-Cell Lung Cancer Patients Harboring the EML4-ALK Fusion Gene (ALRIGHT/OLCSG1405).

PubMed

Isozaki, Hideko; Hotta, Katsuyuki; Ichihara, Eiki; Takigawa, Nagio; Ohashi, Kadoaki; Kubo, Toshio; Ninomiya, Takashi; Ninomiya, Kiichiro; Oda, Naohiro; Yoshioka, Hiroshige; Ichikawa, Hirohisa; Inoue, Masaaki; Takata, Ichiro; Shibayama, Takuo; Kuyama, Shoichi; Sugimoto, Keisuke; Harada, Daijiro; Harita, Shingo; Sendo, Toshiaki; Tanimoto, Mitsune; Kiura, Katsuyuki

2016-11-01

Based on our preclinical study results, which showed that the activation of the hepatocyte growth factor/MET pathway is a potential mechanism of acquired resistance to alectinib, we launched the ALRIGHT (OLCSG1405 [alectinib-refractory non-small-cell lung cancer patients harboring the EML4-ALK fusion gene]), a phase II trial of the anaplastic lymphoma kinase (ALK)/MET inhibitor crizotinib in patients with non-small-cell lung cancer refractory to alectinib and harboring the echinoderm microtubule-associated protein-like 4 (EML4)-ALK fusion gene. Patients with ALK-rearranged tumors who have developed disease progression during alectinib treatment will receive crizotinib monotherapy until disease progression or the occurrence of unacceptable toxicity. The primary endpoint is set as the objective response rate, assuming that a response in 50% of eligible patients will indicate potential usefulness and that 15% would be the lower limit of interest (1-sided α of 0.05, β of 0.20). The estimated accrual number of patients is 9. The secondary endpoints include progression-free survival, overall survival, adverse events, and patient-reported outcomes. We will also take tissue samples before crizotinib monotherapy to conduct an exploratory analysis of ALK and hepatocyte growth factor/MET expression levels and gene alterations (eg, mutations, amplifications, and translocations). We will obtain information regarding whether crizotinib, which targets not only ALK, but also MET, can truly produce efficacy with acceptable safety profiles in ALK + non-small-cell lung cancer even in the alectinib-refractory setting. Copyright © 2016 Elsevier Inc. All rights reserved.

Investigation of Bartonella infection in ixodid ticks from California.

PubMed

Chang, Chao-chin; Hayashidani, Hideki; Pusterla, Nicola; Kasten, Rickie W; Madigan, John E; Chomel, Bruno B

2002-07-01

A total of 1253 ixodid ticks (254 tick pools) collected between the end of 1995 and the spring of 1997 from six California counties (El Dorado, Los Angeles, Orange, Santa Cruz, Shasta and Sonoma) were examined for the presence of Bartonella DNA by PCR of the citrate synthase gene. Of 1,119 adult Ixodes pacificus ticks tested, 26 (11.6%) of 224 pools, each containing five ticks, were positive (minimum percentage of ticks harboring detectable Bartonella DNA, 2.3%). Bartonella PCR-positive ticks were identified in five counties but none of the ticks from Los Angeles County was positive. Among 47 nymphal I. pacificus ticks collected in Sonoma County, one (10%) positive pool out of 10 pools was identified (minimum percentage of ticks harboring detectable Bartonella DNA, 2.1%). Among the 54 Dermacentor occidentalis grouped in 12 pools from Orange County, one pool (8.3%) was PCR positive for Bartonella and similarly one pool (14.3%) was positive among the 30 Dermacentor variabilis ticks grouped in seven pools. None of the three D. occidentalis from El Dorado County were positive. None of the nine tick pools positive for Ehrlichia phagocytophila were positive for Bartonella. Following our previous findings of Bartonella PCR-positive adult I. pacificus ticks in central coastal California, this is the first preliminary report of the presence of Bartonella DNA in I. pacificus nymphs and in Dermacentor sp. ticks. Distribution of Bartonella among ixodid ticks appears widespread in California.

Generation of a neuro-specific microarray reveals novel differentially expressed noncoding RNAs in mouse models for neurodegenerative diseases.

PubMed

Gstir, Ronald; Schafferer, Simon; Scheideler, Marcel; Misslinger, Matthias; Griehl, Matthias; Daschil, Nina; Humpel, Christian; Obermair, Gerald J; Schmuckermair, Claudia; Striessnig, Joerg; Flucher, Bernhard E; Hüttenhofer, Alexander

2014-12-01

We have generated a novel, neuro-specific ncRNA microarray, covering 1472 ncRNA species, to investigate their expression in different mouse models for central nervous system diseases. Thereby, we analyzed ncRNA expression in two mouse models with impaired calcium channel activity, implicated in Epilepsy or Parkinson's disease, respectively, as well as in a mouse model mimicking pathophysiological aspects of Alzheimer's disease. We identified well over a hundred differentially expressed ncRNAs, either from known classes of ncRNAs, such as miRNAs or snoRNAs or which represented entirely novel ncRNA species. Several differentially expressed ncRNAs in the calcium channel mouse models were assigned as miRNAs and target genes involved in calcium signaling, thus suggesting feedback regulation of miRNAs by calcium signaling. In the Alzheimer mouse model, we identified two snoRNAs, whose expression was deregulated prior to amyloid plaque formation. Interestingly, the presence of snoRNAs could be detected in cerebral spine fluid samples in humans, thus potentially serving as early diagnostic markers for Alzheimer's disease. In addition to known ncRNAs species, we also identified 63 differentially expressed, entirely novel ncRNA candidates, located in intronic or intergenic regions of the mouse genome, genomic locations, which previously have been shown to harbor the majority of functional ncRNAs. © 2014 Gstir et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Murine Stem Cell-Based Retrovirus Production for Marking Primary Mouse Mammary Cells for Metastasis Studies.

PubMed

Beverly, Levi J; Podsypanina, Katrina

2016-02-01

Since the introduction of retroviral vector technology, permanent genetic marking of cells has considerably contributed to the understanding of different physiological and disease processes in vivo. Recent marking strategies aim to elucidate the contribution of cells on the clonal level, and the advent of fluorescent proteins has opened new avenues for the in vivo analysis of gene-marked cells. Gene-modified cells are easily identifiable (e.g., via the introduced fluorescent protein) within whole organ structures, allowing one to measure the contribution of transduced cells to malignant outgrowth. In our laboratory, we use the tetracycline-inducible system to study oncogene cooperation in metastatic progression. We use bicistronic retroviruses expressing the tetracycline transactivator (tTA) and the candidate gene (MIT-gene) or the tTA alone (MIT-Rx) to infect primary mammary cells from mice harboring tetracycline-inducible transgenes. This allows for constitutive expression of the candidate gene and tTA-dependent expression of the inducible oncogene. We also use MIG-based vectors, which allow for constitutive expression of the candidate gene and a green fluorescent protein. Here we describe how to produce retroviral particles carrying both MIT- and MIG-based vectors. Because of the fragility of the retroviral envelope, we do not attempt to concentrate the virus, and we directly use packaging cell media to infect primary epithelial cells (either normal or tumor). Infected cells can be transplanted into recipient mice to investigate metastatic colonization. © 2016 Cold Spring Harbor Laboratory Press.

Bermudagrass (Cynodon spp.).

PubMed

Ge, Yaxin; Wang, Zeng-Yu

2006-01-01

Bermudagrass is an important warm-season forage and turf species widely grown in the southern United States. This chapter describes a rapid and efficient protocol that allows for the generation of a large number of transgenic bermudagrass plants, bypassing the callus formation phase. Stolon nodes are infected and co-cultivated with Agrobacterium tumefaciens harboring pCAMBIA binary vectors. Hygromycin phosphotransferase gene (hph) is used as the selectable marker and hygromycin is used as the selection agent. Green shoots are directly produced from infected stolon nodes 4 to 5 wk after hygromycin selection. Without callus formation and with minimum tissue culture, this procedure allowed us to obtain well-rooted transgenic plantlets in only 7 wk and greenhouse-grown plants in only 9 wk.

Petunia (Petunia hybrida).

PubMed

Lutke, W Kevin

2006-01-01

Petunia hybrida genetic transformation continues to be a valuable tool for genetic research into biochemical pathways and gene expression, as well as generating commercial products with varying floral colors. In this chapter, we describe a simple and reproducible genetic transformation protocol for generating transgenic petunia plants harboring a gene of interest and selectable marker. The system utilizes Agrobacterium tumefaciens for transgene integration with plant recovery via shoot organogenesis from leaf explant material. Selection for transgenic plants is achieved using the bar gene conferring resistance to glufosinate or nptII gene for resistance to kanamycin. Transformation efficiencies of around 10% are achievable with shoots being recovered about 8 wk after transgene insertion and rooted plants transferred to the greenhouse about twelve weeks after inoculation.

Variant discovery in the sheep milk transcriptome using RNA sequencing.

PubMed

Suárez-Vega, Aroa; Gutiérrez-Gil, Beatriz; Klopp, Christophe; Tosser-Klopp, Gwenola; Arranz, Juan José

2017-02-15

The identification of genetic variation underlying desired phenotypes is one of the main challenges of current livestock genetic research. High-throughput transcriptome sequencing (RNA-Seq) offers new opportunities for the detection of transcriptome variants (SNPs and short indels) in different tissues and species. In this study, we used RNA-Seq on Milk Sheep Somatic Cells (MSCs) with the goal of characterizing the genetic variation within the coding regions of the milk transcriptome in Churra and Assaf sheep, two common dairy sheep breeds farmed in Spain. A total of 216,637 variants were detected in the MSCs transcriptome of the eight ewes analyzed. Among them, a total of 57,795 variants were detected in the regions harboring Quantitative Trait Loci (QTL) for milk yield, protein percentage and fat percentage, of which 21.44% were novel variants. Among the total variants detected, 561 (2.52%) and 1,649 (7.42%) were predicted to produce high or moderate impact changes in the corresponding transcriptional unit, respectively. In the functional enrichment analysis of the genes positioned within selected QTL regions harboring novel relevant functional variants (high and moderate impact), the KEGG pathway with the highest enrichment was "protein processing in endoplasmic reticulum". Additionally, a total of 504 and 1,063 variants were identified in the genes encoding principal milk proteins and molecules involved in the lipid metabolism, respectively. Of these variants, 20 mutations were found to have putative relevant effects on the encoded proteins. We present herein the first transcriptomic approach aimed at identifying genetic variants of the genes expressed in the lactating mammary gland of sheep. Through the transcriptome analysis of variability within regions harboring QTL for milk yield, protein percentage and fat percentage, we have found several pathways and genes that harbor mutations that could affect dairy production traits. Moreover, remarkable variants were also found in candidate genes coding for major milk proteins and proteins related to milk fat metabolism. Several of the SNPs found in this study could be included as suitable markers in genotyping platforms or custom SNP arrays to perform association analyses in commercial populations and apply genomic selection protocols in the dairy production industry.

Curing color blindness--mice and nonhuman primates.

PubMed

Neitz, Maureen; Neitz, Jay

2014-08-21

It has been possible to use viral-mediated gene therapy to transform dichromatic (red-green color-blind) primates to trichromatic. Even though the third cone type was added after the end of developmental critical periods, treated animals acquired red-green color vision. What happened in the treated animals may represent a recapitulation of the evolution of trichromacy, which seems to have evolved with the acquisition of a third cone type without the need for subsequent modification to the circuitry. Some transgenic mice in which a third cone type was added also acquired trichromacy. However, compared with treated primates, red-green color vision in mice is poor, indicating large differences between mice and monkeys in their ability to take advantage of the new input. These results have implications for understanding the limits and opportunities for using gene therapy to treat vision disorders caused by defects in cone function. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

Circular RNAs: diversity of form and function.

PubMed

Lasda, Erika; Parker, Roy

2014-12-01

It is now clear that there is a diversity of circular RNAs in biological systems. Circular RNAs can be produced by the direct ligation of 5' and 3' ends of linear RNAs, as intermediates in RNA processing reactions, or by "backsplicing," wherein a downstream 5' splice site (splice donor) is joined to an upstream 3' splice site (splice acceptor). Circular RNAs have unique properties including the potential for rolling circle amplification of RNA, the ability to rearrange the order of genomic information, protection from exonucleases, and constraints on RNA folding. Circular RNAs can function as templates for viroid and viral replication, as intermediates in RNA processing reactions, as regulators of transcription in cis, as snoRNAs, and as miRNA sponges. Herein, we review the breadth of circular RNAs, their biogenesis and metabolism, and their known and anticipated functions. © 2014 Lasda and Parker; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Metazoan tRNA introns generate stable circular RNAs in vivo.

PubMed

Lu, Zhipeng; Filonov, Grigory S; Noto, John J; Schmidt, Casey A; Hatkevich, Talia L; Wen, Ying; Jaffrey, Samie R; Matera, A Gregory

2015-09-01

We report the discovery of a class of abundant circular noncoding RNAs that are produced during metazoan tRNA splicing. These transcripts, termed tRNA intronic circular (tric)RNAs, are conserved features of animal transcriptomes. Biogenesis of tricRNAs requires anciently conserved tRNA sequence motifs and processing enzymes, and their expression is regulated in an age-dependent and tissue-specific manner. Furthermore, we exploited this biogenesis pathway to develop an in vivo expression system for generating "designer" circular RNAs in human cells. Reporter constructs expressing RNA aptamers such as Spinach and Broccoli can be used to follow the transcription and subcellular localization of tricRNAs in living cells. Owing to the superior stability of circular vs. linear RNA isoforms, this expression system has a wide range of potential applications, from basic research to pharmaceutical science. © 2015 Lu et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Muscle Contraction.

PubMed

Sweeney, H Lee; Hammers, David W

2018-02-01

SUMMARYMuscle cells are designed to generate force and movement. There are three types of mammalian muscles-skeletal, cardiac, and smooth. Skeletal muscles are attached to bones and move them relative to each other. Cardiac muscle comprises the heart, which pumps blood through the vasculature. Skeletal and cardiac muscles are known as striated muscles, because the filaments of actin and myosin that power their contraction are organized into repeating arrays, called sarcomeres, that have a striated microscopic appearance. Smooth muscle does not contain sarcomeres but uses the contraction of filaments of actin and myosin to constrict blood vessels and move the contents of hollow organs in the body. Here, we review the principal molecular organization of the three types of muscle and their contractile regulation through signaling mechanisms and discuss their major structural and functional similarities that hint at the possible evolutionary relationships between the cell types. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

Essays in the Non-Science Major Astrobiology Course

NASA Astrophysics Data System (ADS)

D'Cruz, Noella L.

2014-06-01

The non-science major "Life in the Universe" class offers students many opportunities to explore topics such as whether or not to send manned missions to Mars, which jovian moon is a suitable candidate for harboring life, etc. Some of these topics are suited to being offered as projects. At Joliet Junior College, Joliet, IL, we offer this general education class every semester to around 40 students. We expect our students to complete three short essays in a semester, instead of doing one or two large projects. The essays enable students to be engaged more deeply with some aspects of the course than is usually possible in the classroom. Some of our essay topics are based on suggestions in the textbook, others have been developed by us. In this poster, we will report on the essay topics and the attitudes of our Fall 2013 and Spring 2014 students to such essays.

PI3K: A Crucial Piece in the RAS Signaling Puzzle.

PubMed

Krygowska, Agata Adelajda; Castellano, Esther

2018-06-01

RAS proteins are key signaling switches essential for control of proliferation, differentiation, and survival of eukaryotic cells. RAS proteins are mutated in 30% of human cancers. In addition, mutations in upstream or downstream signaling components also contribute to oncogenic activation of the pathway. RAS proteins exert their functions through activation of several signaling pathways and dissecting the contributions of these effectors in normal cells and in cancer is an ongoing challenge. In this review, we summarize our current knowledge about how RAS regulates type I phosphatidylinositol 3-kinase (PI3K), one of the main RAS effectors. RAS signaling through PI3K is necessary for normal lymphatic vasculature development and for RAS-induced transformation in vitro and in vivo, especially in lung cancer, where it is essential for tumor initiation and necessary for tumor maintenance. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

IL-6 in inflammation, immunity, and disease.

PubMed

Tanaka, Toshio; Narazaki, Masashi; Kishimoto, Tadamitsu

2014-09-04

Interleukin 6 (IL-6), promptly and transiently produced in response to infections and tissue injuries, contributes to host defense through the stimulation of acute phase responses, hematopoiesis, and immune reactions. Although its expression is strictly controlled by transcriptional and posttranscriptional mechanisms, dysregulated continual synthesis of IL-6 plays a pathological effect on chronic inflammation and autoimmunity. For this reason, tocilizumab, a humanized anti-IL-6 receptor antibody was developed. Various clinical trials have since shown the exceptional efficacy of tocilizumab, which resulted in its approval for the treatment of rheumatoid arthritis and juvenile idiopathic arthritis. Moreover, tocilizumab is expected to be effective for other intractable immune-mediated diseases. In this context, the mechanism for the continual synthesis of IL-6 needs to be elucidated to facilitate the development of more specific therapeutic approaches and analysis of the pathogenesis of specific diseases. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

Origin and evolution of the self-organizing cytoskeleton in the network of eukaryotic organelles.

PubMed

Jékely, Gáspár

2014-09-02

The eukaryotic cytoskeleton evolved from prokaryotic cytomotive filaments. Prokaryotic filament systems show bewildering structural and dynamic complexity and, in many aspects, prefigure the self-organizing properties of the eukaryotic cytoskeleton. Here, the dynamic properties of the prokaryotic and eukaryotic cytoskeleton are compared, and how these relate to function and evolution of organellar networks is discussed. The evolution of new aspects of filament dynamics in eukaryotes, including severing and branching, and the advent of molecular motors converted the eukaryotic cytoskeleton into a self-organizing "active gel," the dynamics of which can only be described with computational models. Advances in modeling and comparative genomics hold promise of a better understanding of the evolution of the self-organizing cytoskeleton in early eukaryotes, and its role in the evolution of novel eukaryotic functions, such as amoeboid motility, mitosis, and ciliary swimming. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

Genetic considerations in recurrent pregnancy loss.

PubMed

Hyde, Kassie J; Schust, Danny J

2015-02-06

Human reproduction is remarkably inefficient; nearly 70% of human conceptions do not survive to live birth. Spontaneous fetal aneuploidy is the most common cause for spontaneous loss, particularly in the first trimester of pregnancy. Although losses owing to de novo fetal aneuploidy occur at similar frequencies among women with sporadic and recurrent losses, some couples with recurrent pregnancy loss have additional associated genetic factors and some have nongenetic etiologies. Genetic testing of the products of conception from couples experiencing two or more losses may aid in defining the underlying etiology and in counseling patients about prognosis in a subsequent pregnancy. Parental karyotyping of couples who have experienced recurrent pregnancy loss (RPL) will detect some couples with an increased likelihood of recurrent fetal aneuploidy; this may direct interventions. The utility of preimplantation genetic analysis in couples with RPL is unproven, but new approaches to this testing show great promise. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

Epidemiology and Transmission of Hepatitis A Virus and Hepatitis E Virus Infections in the United States.

PubMed

Hofmeister, Megan G; Foster, Monique A; Teshale, Eyasu H

2018-04-30

There are many similarities in the epidemiology and transmission of hepatitis A virus (HAV) and hepatitis E virus (HEV) genotype (gt)3 infections in the United States. Both viruses are enterically transmitted, although specific routes of transmission are more clearly established for HAV than for HEV: HAV is restricted to humans and primarily spread through the fecal-oral route, while HEV is zoonotic with poorly understood modes of transmission in the United States. New cases of HAV infection have decreased dramatically in the United States since infant vaccination was recommended in 1996. In recent years, however, outbreaks have occurred among an increasingly susceptible adult population. Although HEV is the most common cause of acute viral hepatitis in developing countries, it is rarely diagnosed in the United States. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

7SL RNA in Vertebrate Red Blood Cells.

PubMed

Talhouarne, Gaëlle J S; Gall, Joseph G

2018-04-23

We report that 7SL, the RNA component of the signal recognition particle (SRP), is an abundant ncRNA in mature red blood cells (RBCs) of human, mouse, and the frog Xenopus. 7SL RNA in RBCs is not associated with the canonical proteins of the SRP. Instead, it co-immunoprecipitates from a lysate of RBCs with a number of membrane-binding proteins. Human and mouse RBCs also contain a previously undescribed 68 nt RNA, sRN7SL, derived from the "S domain" of 7SL RNA. We discuss the possibility that 7SL RNA is selectively protected from nucleases by association with the RBC membrane. Because 7SL is not associated with the canonical proteins of the SRP, it could represent a non-functional remnant of the protein synthetic machinery. Alternatively, it could play a new, as yet undefined role in RBC metabolism. Published by Cold Spring Harbor Laboratory Press for the RNA Society.

The Biology of Bone Metastasis.

PubMed

Esposito, Mark; Guise, Theresa; Kang, Yibin

2018-06-01

Bone metastasis, or the development of secondary tumors within the bone of cancer patients, is a debilitating and incurable disease. Despite its morbidity, the biology of bone metastasis represents one of the most complex and intriguing of all oncogenic processes. This complexity derives from the intricately organized bone microenvironment in which the various stages of hematopoiesis, osteogenesis, and osteolysis are jointly regulated but spatially restricted. Disseminated tumor cells (DTCs) from various common malignancies such as breast, prostate, lung, and kidney cancers or myeloma are uniquely primed to subvert these endogenous bone stromal elements to grow into pathological osteolytic or osteoblastic lesions. This colonization process can be separated into three key steps: seeding, dormancy, and outgrowth. Targeting the processes of dormancy and initial outgrowth offers the most therapeutic promise. Here, we discuss the concepts of the bone metastasis niche, from controlling tumor-cell survival to growth into clinically detectable disease. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

Functions and regulation of the multitasking FANCM family of DNA motor proteins.

PubMed

Xue, Xiaoyu; Sung, Patrick; Zhao, Xiaolan

2015-09-01

Members of the conserved FANCM family of DNA motor proteins play key roles in genome maintenance processes. FANCM supports genome duplication and repair under different circumstances and also functions in the ATR-mediated DNA damage checkpoint. Some of these roles are shared among lower eukaryotic family members. Human FANCM has been linked to Fanconi anemia, a syndrome characterized by cancer predisposition, developmental disorder, and bone marrow failure. Recent studies on human FANCM and its orthologs from other organisms have provided insights into their biological functions, regulation, and collaboration with other genome maintenance factors. This review summarizes the progress made, with the goal of providing an integrated view of the functions and regulation of these enzymes in humans and model organisms and how they advance our understanding of genome maintenance processes. © 2015 Xue et al.; Published by Cold Spring Harbor Laboratory Press.

De novo variants in EBF3 are associated with hypotonia, developmental delay, intellectual disability, and autism.

PubMed

Tanaka, Akemi J; Cho, Megan T; Willaert, Rebecca; Retterer, Kyle; Zarate, Yuri A; Bosanko, Katie; Stefans, Vikki; Oishi, Kimihiko; Williamson, Amy; Wilson, Golder N; Basinger, Alice; Barbaro-Dieber, Tina; Ortega, Lucia; Sorrentino, Susanna; Gabriel, Melissa K; Anderson, Ilse J; Sacoto, Maria J Guillen; Schnur, Rhonda E; Chung, Wendy K

2017-11-01

Using whole-exome sequencing, we identified seven unrelated individuals with global developmental delay, hypotonia, dysmorphic facial features, and an increased frequency of short stature, ataxia, and autism with de novo heterozygous frameshift, nonsense, splice, and missense variants in the Early B-cell Transcription Factor Family Member 3 ( EBF3 ) gene. EBF3 is a member of the collier/olfactory-1/early B-cell factor (COE) family of proteins, which are required for central nervous system (CNS) development. COE proteins are highly evolutionarily conserved and regulate neuronal specification, migration, axon guidance, and dendritogenesis during development and are essential for maintaining neuronal identity in adult neurons. Haploinsufficiency of EBF3 may affect brain development and function, resulting in developmental delay, intellectual disability, and behavioral differences observed in individuals with a deleterious variant in EBF3 . © 2017 Tanaka et al.; Published by Cold Spring Harbor Laboratory Press.

Production of systemically circulating Hedgehog by the intestine couples nutrition to growth and development.

PubMed

Rodenfels, Jonathan; Lavrynenko, Oksana; Ayciriex, Sophie; Sampaio, Julio L; Carvalho, Maria; Shevchenko, Andrej; Eaton, Suzanne

2014-12-01

In Drosophila larvae, growth and developmental timing are regulated by nutrition in a tightly coordinated fashion. The networks that couple these processes are far from understood. Here, we show that the intestine responds to nutrient availability by regulating production of a circulating lipoprotein-associated form of the signaling protein Hedgehog (Hh). Levels of circulating Hh tune the rates of growth and developmental timing in a coordinated fashion. Circulating Hh signals to the fat body to control larval growth. It regulates developmental timing by controlling ecdysteroid production in the prothoracic gland. Circulating Hh is especially important during starvation, when it is also required for mobilization of fat body triacylglycerol (TAG) stores. Thus, we demonstrate that Hh, previously known only for its local morphogenetic functions, also acts as a lipoprotein-associated endocrine hormone, coordinating the response of multiple tissues to nutrient availability. © 2014 Rodenfels et al.; Published by Cold Spring Harbor Laboratory Press.

The Role of Hox Genes in Female Reproductive Tract Development, Adult Function, and Fertility.

PubMed

Du, Hongling; Taylor, Hugh S

2015-11-09

HOX genes convey positional identity that leads to the proper partitioning and adult identity of the female reproductive track. Abnormalities in reproductive tract development can be caused by HOX gene mutations or altered HOX gene expression. Diethylstilbestrol (DES) and other endocrine disruptors cause Müllerian defects by changing HOX gene expression. HOX genes are also essential regulators of adult endometrial development. Regulated HOXA10 and HOXA11 expression is necessary for endometrial receptivity; decreased HOXA10 or HOXA11 expression leads to decreased implantation rates. Alternation of HOXA10 and HOXA11 expression has been identified as a mechanism of the decreased implantation associated with endometriosis, polycystic ovarian syndrome, leiomyoma, polyps, adenomyosis, and hydrosalpinx. Alteration of HOX gene expression causes both uterine developmental abnormalities and impaired adult endometrial development that prevent implantation and lead to female infertility. Copyright © 2016 Cold Spring Harbor Laboratory Press; all rights reserved.

Cell of Origin and Cancer Stem Cells in Tumor Suppressor Mouse Models of Glioblastoma.

PubMed

Alcantara Llaguno, Sheila R; Xie, Xuanhua; Parada, Luis F

2016-01-01

The cellular origins and the mechanisms of progression, maintenance of tumorigenicity, and therapeutic resistance are central questions in the glioblastoma multiforme (GBM) field. Using tumor suppressor mouse models, our group recently reported two independent populations of adult GBM-initiating central nervous system progenitors. We found different functional and molecular subtypes depending on the tumor-initiating cell lineage, indicating that the cell of origin is a driver of GBM subtype diversity. Using an in vivo model, we also showed that GBM cancer stem cells (CSCs) or glioma stem cells (GSCs) contribute to resistance to chemotherapeutic agents and that genetic ablation of GSCs leads to a delay in tumor progression. These studies are consistent with the cell of origin and CSCs as critical regulators of the pathogenesis of GBM. © 2016 Alcantara Llaguno et al; Published by Cold Spring Harbor Laboratory Press.

Hepatitis A Virus Genome Organization and Replication Strategy.

PubMed

McKnight, Kevin L; Lemon, Stanley M

2018-04-02

Hepatitis A virus (HAV) is a positive-strand RNA virus classified in the genus Hepatovirus of the family Picornaviridae It is an ancient virus with a long evolutionary history and multiple features of its capsid structure, genome organization, and replication cycle that distinguish it from other mammalian picornaviruses. HAV proteins are produced by cap-independent translation of a single, long open reading frame under direction of an inefficient, upstream internal ribosome entry site (IRES). Genome replication occurs slowly and is noncytopathic, with transcription likely primed by a uridylated protein primer as in other picornaviruses. Newly produced quasi-enveloped virions (eHAV) are released from cells in a nonlytic fashion in a unique process mediated by interactions of capsid proteins with components of the host cell endosomal sorting complexes required for transport (ESCRT) system. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

Vaccines to Accelerate Malaria Elimination and Eventual Eradication.

PubMed

Healer, Julie; Cowman, Alan F; Kaslow, David C; Birkett, Ashley J

2017-09-01

Remarkable progress has been made in coordinated malaria control efforts with substantial reductions in malaria-associated deaths and morbidity achieved through mass administration of drugs and vector control measures including distribution of long-lasting insecticide-impregnated bednets and indoor residual spraying. However, emerging resistance poses a significant threat to the sustainability of these interventions. In this light, the malaria research community has been charged with the development of a highly efficacious vaccine to complement existing malaria elimination measures. As the past 40 years of investment in this goal attests, this is no small feat. The malaria parasite is a highly complex organism, exquisitely adapted for survival under hostile conditions within human and mosquito hosts. Here we review current vaccine strategies to accelerate elimination and the potential for novel and innovative approaches to vaccine design through a better understanding of the host-parasite interaction. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

Post-training reversible disconnection of the ventral hippocampal-basolateral amygdaloid circuits impairs consolidation of inhibitory avoidance memory in rats.

PubMed

Wang, Gong-Wu; Liu, Jian; Wang, Xiao-Qin

2017-11-01

The ventral hippocampus (VH) and the basolateral amygdala (BLA) are both crucial in inhibitory avoidance (IA) memory. However, the exact role of the VH-BLA circuit in IA memory consolidation is unclear. This study investigated the effect of post-training reversible disconnection of the VH-BLA circuit in IA memory consolidation. Male Wistar rats with implanted guide cannulae were trained with a one-trial IA task, then received immediate intracerebral injections of muscimol or saline, and were tested 24 h later. Muscimol injection into the bilateral BLA, or the unilateral VH and contralateral BLA, but not the unilateral VH and ipsilateral BLA, significantly decreased the retention latencies (versus saline treatment). The results suggest that the VH-BLA circuit could be an important circuit to modulate consolidation of IA memory in rats. © 2017 Wang et al.; Published by Cold Spring Harbor Laboratory Press.

Transcription and recombination: when RNA meets DNA.

PubMed

Aguilera, Andrés; Gaillard, Hélène

2014-08-01

A particularly relevant phenomenon in cell physiology and proliferation is the fact that spontaneous mitotic recombination is strongly enhanced by transcription. The most accepted view is that transcription increases the occurrence of double-strand breaks and/or single-stranded DNA gaps that are repaired by recombination. Most breaks would arise as a consequence of the impact that transcription has on replication fork progression, provoking its stalling and/or breakage. Here, we discuss the mechanisms responsible for the cross talk between transcription and recombination, with emphasis on (1) the transcription-replication conflicts as the main source of recombinogenic DNA breaks, and (2) the formation of cotranscriptional R-loops as a major cause of such breaks. The new emerging questions and perspectives are discussed on the basis of the interference between transcription and replication, as well as the way RNA influences genome dynamics. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

Topologically Associating Domains in Chromosome Architecture and Gene Regulatory Landscapes during Development, Disease, and Evolution.

PubMed

Galupa, Rafael; Heard, Edith

2018-04-23

The packaging of genetic material into chromatin and chromosomes has been recognized for more than a century, thanks to microscopy and biochemical approaches. This was followed by the progressive realization that chromatin organization is critical for genome functions such as transcription and DNA replication and repair. The recent discovery that chromosomes are partitioned at the submegabase scale into topologically associating domains (TADs) has implications for our understanding of gene regulation during developmental processes such as X-chromosome inactivation, as well as for evolution and for the search for disease-associated loci. Here we discuss our current knowledge about this recently recognized level of mammalian chromosome organization, with a special emphasis on the potential role of TADs as a structural basis for the function and evolution of mammalian regulatory landscapes. © 2017 Galupa and Heard; Published by Cold Spring Harbor Laboratory Press.

Analysis of Schizosaccharomyces pombe Meiosis.

PubMed

Yamashita, Akira; Sakuno, Takeshi; Watanabe, Yoshinori; Yamamoto, Masayuki

2017-09-01

Meiosis is a specialized cell cycle that generates haploid gametes from diploid cells. The fission yeast Schizosaccharomyces pombe is one of the best model organisms for studying the regulatory mechanisms of meiosis. S. pombe cells, which normally grow in the haploid state, diploidize by conjugation and initiate meiosis when starved for nutrients, especially nitrogen. Following two rounds of chromosome segregation, spore formation takes place. The switch from mitosis to meiosis is controlled by a kinase, Pat1, and an RNA-binding protein, Mei2. Mei2 is also a key factor for meiosis-specific gene expression. Studies on S. pombe have offered insights into cell cycle regulation and chromosome segregation during meiosis. Here we outline the current understanding of the molecular mechanisms regulating the initiation and progression of meiosis, and introduce methods for the study of meiosis in fission yeast. © 2017 Cold Spring Harbor Laboratory Press.

MYC association with cancer risk and a new model of MYC-mediated repression.

PubMed

Cole, Michael D

2014-07-01

MYC is one of the most frequently mutated and overexpressed genes in human cancer but the regulation of MYC expression and the ability of MYC protein to repress cellular genes (including itself) have remained mysterious. Recent genome-wide association studies show that many genetic polymorphisms associated with disease risk map to distal regulatory elements that regulate the MYC promoter through large chromatin loops. Cancer risk-associated single-nucleotide polymorphisms (SNPs) contain more potent enhancer activity, promoting higher MYC levels and a greater risk of disease. The MYC promoter is also subject to complex regulatory circuits and limits its own expression by a feedback loop. A model for MYC autoregulation is discussed which involves a signaling pathway between the PTEN (phosphatase and tensin homolog) tumor suppressor and repressive histone modifications laid down by the EZH2 methyltransferase. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

In vitro reconstitution of chaperone-mediated human RISC assembly.

PubMed

Naruse, Ken; Matsuura-Suzuki, Eriko; Watanabe, Mariko; Iwasaki, Shintaro; Tomari, Yukihide

2018-01-01

To silence target mRNAs, small RNAs and Argonaute (Ago) proteins need to be assembled into RNA-induced silencing complexes (RISCs). Although the assembly of Drosophila melanogaster RISC was recently reconstituted by Ago2, the Dicer-2/R2D2 heterodimer, and five chaperone proteins, the absence of a reconstitution system for mammalian RISC assembly has posed analytical challenges. Here we describe reconstitution of human RISC assembly using Ago2 and five recombinant chaperone proteins: Hsp90β, Hsc70, Hop, Dnaja2, and p23. Our data show that ATP hydrolysis by both Hsp90β and Hsc70 is required for RISC assembly of small RNA duplexes but not for that of single-stranded RNAs. The reconstitution system lays the groundwork for further studies of small RNA-mediated gene silencing in mammals. © 2018 Naruse et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Food-derived sensory cues modulate longevity via distinct neuroendocrine insulin-like peptides.

PubMed

Artan, Murat; Jeong, Dae-Eun; Lee, Dongyeop; Kim, Young-Il; Son, Heehwa G; Husain, Zahabiya; Kim, Jinmahn; Altintas, Ozlem; Kim, Kyuhyung; Alcedo, Joy; Lee, Seung-Jae V

2016-05-01

Environmental fluctuations influence organismal aging by affecting various regulatory systems. One such system involves sensory neurons, which affect life span in many species. However, how sensory neurons coordinate organismal aging in response to changes in environmental signals remains elusive. Here, we found that a subset of sensory neurons shortens Caenorhabditis elegans' life span by differentially regulating the expression of a specific insulin-like peptide (ILP), INS-6. Notably, treatment with food-derived cues or optogenetic activation of sensory neurons significantly increases ins-6 expression and decreases life span. INS-6 in turn relays the longevity signals to nonneuronal tissues by decreasing the activity of the transcription factor DAF-16/FOXO. Together, our study delineates a mechanism through which environmental sensory cues regulate aging rates by modulating the activities of specific sensory neurons and ILPs. © 2016 Artan et al.; Published by Cold Spring Harbor Laboratory Press.

Introduction to Intellectual Property: A U.S. Perspective.

PubMed

Murphy, Amanda; Stramiello, Michael; Lewis, Stacy; Irving, Tom

2015-03-27

This review introduces patents and trade secrets, the two mechanisms that U.S. law provides inventors to protect their inventions. These mechanisms are mutually exclusive: One demands disclosure and the other calls for concealment. Many biotechnology innovators opt for patents, which grant legal, time-limited monopolies to eligible inventions.To obtain a patent in the United States, an invention must be useful to the public and made or altered by the hand of man. It must then clear the hurdles of novelty and nonobviousness. If an invention can do that, obtaining a patent becomes a matter of form: Who qualifies as an inventor? Does the application demonstrate possession, stake a clear claim to the protection sought, and enable "ordinary" colleagues to replicate it? Has the inventor purposely withheld anything? This review addresses each of these hurdles as they apply to biotech inventions. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

Novel transcriptional networks regulated by CLOCK in human neurons.

PubMed

Fontenot, Miles R; Berto, Stefano; Liu, Yuxiang; Werthmann, Gordon; Douglas, Connor; Usui, Noriyoshi; Gleason, Kelly; Tamminga, Carol A; Takahashi, Joseph S; Konopka, Genevieve

2017-11-01

The molecular mechanisms underlying human brain evolution are not fully understood; however, previous work suggested that expression of the transcription factor CLOCK in the human cortex might be relevant to human cognition and disease. In this study, we investigated this novel transcriptional role for CLOCK in human neurons by performing chromatin immunoprecipitation sequencing for endogenous CLOCK in adult neocortices and RNA sequencing following CLOCK knockdown in differentiated human neurons in vitro. These data suggested that CLOCK regulates the expression of genes involved in neuronal migration, and a functional assay showed that CLOCK knockdown increased neuronal migratory distance. Furthermore, dysregulation of CLOCK disrupts coexpressed networks of genes implicated in neuropsychiatric disorders, and the expression of these networks is driven by hub genes with human-specific patterns of expression. These data support a role for CLOCK-regulated transcriptional cascades involved in human brain evolution and function. © 2017 Fontenot et al.; Published by Cold Spring Harbor Laboratory Press.

Microprocessor dynamics shows co- and post-transcriptional processing of pri-miRNAs.

PubMed

Louloupi, Annita; Ntini, Evgenia; Liz, Julia; Ørom, Ulf Andersson

2017-06-01

miRNAs are small regulatory RNAs involved in the regulation of translation of target transcripts. miRNA biogenesis is a multistep process starting with the cleavage of the primary miRNA transcript in the nucleus by the Microprocessor complex. Endogenous processing of pri-miRNAs is challenging to study and the in vivo kinetics of this process is not known. Here, we present a method for determining the processing kinetics of pri-miRNAs within intact cells over time, using a pulse-chase approach to label transcribed RNA during 15 min, and follow the processing within a 1-hour window after labeling with bromouridine. We show that pri-miRNAs exhibit different processing kinetics ranging from fast over intermediate to slow processing, and we provide evidence that pri-miRNA processing can occur both cotranscriptionally and post-transcriptionally. © 2017 Louloupi et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

REC-1 and HIM-5 distribute meiotic crossovers and function redundantly in meiotic double-strand break formation in Caenorhabditis elegans.

PubMed

Chung, George; Rose, Ann M; Petalcorin, Mark I R; Martin, Julie S; Kessler, Zebulin; Sanchez-Pulido, Luis; Ponting, Chris P; Yanowitz, Judith L; Boulton, Simon J

2015-09-15

The Caenorhabditis elegans gene rec-1 was the first genetic locus identified in metazoa to affect the distribution of meiotic crossovers along the chromosome. We report that rec-1 encodes a distant paralog of HIM-5, which was discovered by whole-genome sequencing and confirmed by multiple genome-edited alleles. REC-1 is phosphorylated by cyclin-dependent kinase (CDK) in vitro, and mutation of the CDK consensus sites in REC-1 compromises meiotic crossover distribution in vivo. Unexpectedly, rec-1; him-5 double mutants are synthetic-lethal due to a defect in meiotic double-strand break formation. Thus, we uncovered an unexpected robustness to meiotic DSB formation and crossover positioning that is executed by HIM-5 and REC-1 and regulated by phosphorylation. © 2015 Chung et al.; Published by Cold Spring Harbor Laboratory Press.

Molecular Regulation of Parturition: The Role of the Decidual Clock.

PubMed

Norwitz, Errol R; Bonney, Elizabeth A; Snegovskikh, Victoria V; Williams, Michelle A; Phillippe, Mark; Park, Joong Shin; Abrahams, Vikki M

2015-04-27

The timing of birth is a critical determinant of perinatal outcome. Despite intensive research, the molecular mechanisms responsible for the onset of labor both at term and preterm remain unclear. It is likely that a "parturition cascade" exists that triggers labor at term, that preterm labor results from mechanisms that either prematurely stimulate or short-circuit this cascade, and that these mechanisms involve the activation of proinflammatory pathways within the uterus. It has long been postulated that the fetoplacental unit is in control of the timing of birth through a "placental clock." We suggest that it is not a placental clock that regulates the timing of birth, but rather a "decidual clock." Here, we review the evidence in support of the endometrium/decidua as the organ primarily responsible for the timing of birth and discuss the molecular mechanisms that prime this decidual clock. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

The role of model organisms in the history of mitosis research.

PubMed

Yanagida, Mitsuhiro

2014-09-02

Mitosis is a cell-cycle stage during which condensed chromosomes migrate to the middle of the cell and segregate into two daughter nuclei before cytokinesis (cell division) with the aid of a dynamic mitotic spindle. The history of mitosis research is quite long, commencing well before the discovery of DNA as the repository of genetic information. However, great and rapid progress has been made since the introduction of recombinant DNA technology and discovery of universal cell-cycle control. A large number of conserved eukaryotic genes required for the progression from early to late mitotic stages have been discovered, confirming that DNA replication and mitosis are the two main events in the cell-division cycle. In this article, a historical overview of mitosis is given, emphasizing the importance of diverse model organisms that have been used to solve fundamental questions about mitosis. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

Fear memory consolidation in sleep requires protein kinase A.

PubMed

Cho, Jiyeon; Sypniewski, Krzysztof A; Arai, Shoko; Yamada, Kazuo; Ogawa, Sonoko; Pavlides, Constantine

2018-05-01

It is well established that protein kinase A (PKA) is involved in hippocampal dependent memory consolidation. Sleep is also known to play an important role in this process. However, whether sleep-dependent memory consolidation involves PKA activation has not been clearly determined. Using behavioral observation, animals were categorized into sleep and awake groups. We show that intrahippocampal injections of the PKA inhibitor Rp-cAMPs in post-contextual fear conditioning sleep produced a suppression of long-term fear memory, while injections of Rp-cAMPs during an awake state, at a similar time point, had no effect. In contrast, injections of the PKA activator Sp-cAMPs in awake state, rescued sleep deprivation-induced memory impairments. These results suggest that following learning, PKA activation specifically in sleep is required for the consolidation of long-term memory. © 2018 Cho et al.; Published by Cold Spring Harbor Laboratory Press.

Role of eIF2α Kinases in Translational Control and Adaptation to Cellular Stress.

PubMed

Wek, Ronald C

2018-02-12

A central mechanism regulating translation initiation in response to environmental stress involves phosphorylation of the α subunit of eukaryotic initiation factor 2 (eIF2α). Phosphorylation of eIF2α causes inhibition of global translation, which conserves energy and facilitates reprogramming of gene expression and signaling pathways that help to restore protein homeostasis. Coincident with repression of protein synthesis, many gene transcripts involved in the stress response are not affected or are even preferentially translated in response to increased eIF2α phosphorylation by mechanisms involving upstream open reading frames (uORFs). This review highlights the mechanisms regulating eIF2α kinases, the role that uORFs play in translational control, and the impact that alteration of eIF2α phosphorylation by gene mutations or small molecule inhibitors can have on health and disease. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

Enabling functional genomics with genome engineering.

PubMed

Hilton, Isaac B; Gersbach, Charles A

2015-10-01

Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunities for therapeutic designs. The rapid evolution of these methods has also catalyzed a new era of genomics that includes multiple approaches to functionally characterize and manipulate the regulation of genomic information. Here, we review the recent advances of the most widely adopted genome engineering platforms and their application to functional genomics. This includes engineered zinc finger proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances. © 2015 Hilton and Gersbach; Published by Cold Spring Harbor Laboratory Press.

New York City, Hudson River, NY, USA

NASA Image and Video Library

1991-05-06

STS039-88-054 (28 April-6 May 1991) --- The dense urban development of the New York City metropolitan area in downstate New York, Long Island and New Jersey shows up as gray and white on this color Infrared photograph. The scene was taken on a remarkably clear spring day. Almost all the major man-made structures of the area are obvious, including ship traffic in and out of New York Harbor, the piers, all of the bridges spanning the area rivers and connecting Manhattan Island with New Jersey, the Bronx, Brooklyn and Queens, the three major airports (Newark, La Guardia and JFK), the New York State thruway, as well as Shea Stadium and Yankee Stadium. The reds and pinks are vegetated areas. Central Park clearly shows up on Manhattan, as do the string of parks along the cliffs (formed by the Palisades sill) along the west side of the Hudson north of the George Washington Bridge.

Enzymatic production of single-molecule FISH and RNA capture probes.

PubMed

Gaspar, Imre; Wippich, Frank; Ephrussi, Anne

2017-10-01

Arrays of singly labeled short oligonucleotides that hybridize to a specific target revolutionized RNA biology, enabling quantitative, single-molecule microscopy analysis and high-efficiency RNA/RNP capture. Here, we describe a simple and efficient method that allows flexible functionalization of inexpensive DNA oligonucleotides by different fluorescent dyes or biotin using terminal deoxynucleotidyl transferase and custom-made functional group conjugated dideoxy-UTP. We show that (i) all steps of the oligonucleotide labeling-including conjugation, enzymatic synthesis, and product purification-can be performed in a standard biology laboratory, (ii) the process yields >90%, often >95% labeled product with minimal carryover of impurities, and (iii) the oligonucleotides can be labeled with different dyes or biotin, allowing single-molecule FISH, RNA affinity purification, and Northern blot analysis to be performed. © 2017 Gaspar et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Synthetic Botany.

PubMed

Boehm, Christian R; Pollak, Bernardo; Purswani, Nuri; Patron, Nicola; Haseloff, Jim

2017-07-05

Plants are attractive platforms for synthetic biology and metabolic engineering. Plants' modular and plastic body plans, capacity for photosynthesis, extensive secondary metabolism, and agronomic systems for large-scale production make them ideal targets for genetic reprogramming. However, efforts in this area have been constrained by slow growth, long life cycles, the requirement for specialized facilities, a paucity of efficient tools for genetic manipulation, and the complexity of multicellularity. There is a need for better experimental and theoretical frameworks to understand the way genetic networks, cellular populations, and tissue-wide physical processes interact at different scales. We highlight new approaches to the DNA-based manipulation of plants and the use of advanced quantitative imaging techniques in simple plant models such as Marchantia polymorpha. These offer the prospects of improved understanding of plant dynamics and new approaches to rational engineering of plant traits. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

Neurobiology of fear and specific phobias.

PubMed

Garcia, René

2017-09-01

Fear, which can be expressed innately or after conditioning, is triggered when a danger or a stimulus predicting immediate danger is perceived. Its role is to prepare the body to face this danger. However, dysfunction in fear processing can lead to psychiatric disorders in which fear outweighs the danger or possibility of harm. Although recognized as highly debilitating, pathological fear remains insufficiently treated, indicating the importance of research on fear processing. The neurobiological basis of normal and pathological fear reactions is reviewed in this article. Innate and learned fear mechanisms, particularly those involving the amygdala, are considered. These fear mechanisms are also distinguished in specific phobias, which can indeed be nonexperiential (implicating innate, learning-independent mechanisms) or experiential (implicating learning-dependent mechanisms). Poor habituation and poor extinction are presented as dysfunctional mechanisms contributing to persistence of nonexperiential and experiential phobias, respectively. © 2017 Garcia; Published by Cold Spring Harbor Laboratory Press.

Modification of Antibody Function by Mutagenesis.

PubMed

Dasch, James R; Dasch, Amy L

2017-09-01

The ability to "fine-tune" recombinant antibodies by mutagenesis separates recombinant antibodies from hybridoma-derived antibodies because the latter are locked with respect to their properties. Recombinant antibodies can be modified to suit the application: Changes in isotype, format (e.g., scFv, Fab, bispecific antibodies), and specificity can be made once the heavy- and light-chain sequences are available. After immunoglobulin heavy and light chains for a particular antibody have been cloned, the binding site-namely, the complementarity determining regions (CDR)-can be manipulated by mutagenesis to obtain antibody variants with improved properties. The method described here is relatively simple, uses commercially available reagents, and is effective. Using the pComb3H vector, a commercial mutagenesis kit, PfuTurbo polymerase (Agilent), and two mutagenic primers, a library of phage with mutagenized heavy and light CDR3 can be obtained. © 2017 Cold Spring Harbor Laboratory Press.

Team Faces Tough Odds to Implement New Phone Network | Poster

Cancer.gov

It was a Saturday, in the final stretch of winter in late February, and the temperature peaked to a pleasant 66 degrees. Many people were outside enjoying the spring-like weather; however, the Voice over Internet Protocol (VoIP) Deployment Team was hard at work at Industry Lane. The team of 10 was installing the new voice-only network, including deploying 145 phones, switching and testing the 911 feature, connecting wall mounts, and verifying each phone... Read more

A Standardized Shift Handover Protocol: Improving Nurses’ Safe Practice in Intensive Care Units

PubMed Central

Malekzadeh, Javad; Mazluom, Seyed Reza; Etezadi, Toktam; Tasseri, Alireza

2013-01-01

Introduction: For maintaining the continuity of care and improving the quality of care, effective inter-shift information communication is necessary. Any handover error can endanger patient safety. Despite the importance of shift handover, there is no standard handover protocol in our healthcare settings. Methods: In this one-group pretest-posttest quasi-experimental study conducted in spring and summer of 2011, we recruited a convenience sample of 56 ICU nurses. The Nurses’ Safe Practice Evaluation Checklist was used for data collection. The Content Validity Index and the inter-rater correlation coefficient of the checklist was 0.92 and 89, respectively. We employed the SPSS 11.5 software and the Mc Nemar and paired-samples t test for data analysis. Results: Study findings revealed that nurses’ mean score on the Safe Practice Evaluation Checklist increased significantly from 11.6 (2.7) to 17.0 (1.8) (P < 0.001). Conclusion: using a standard handover protocol for communicating patient’s needs and information improves nurses’ safe practice in the area of basic nursing care. PMID:25276725

77 FR 41441 - Federal Property Suitable as Facilities To Assist the Homeless

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-13

...; need repairs Land Hawaii 3.15 Acres Joint Base Pearl Harbor Hickam Pearl Harbor HI 96818 Landholding... Harbor Hickam Pearl Harbor HI 96818 Landholding Agency: Navy Property Number: 77201220013 Status... is still in use by the Navy 2.77 Acres Joint Base Pearl Harbor Hickam Pearl Harbor HI 96818...

Temporal and spatial variations in nutrient stoichiometry and regulation of phytoplankton biomass in Hong Kong waters: influence of the Pearl River outflow and sewage inputs.

PubMed

Xu, Jie; Ho, Alvin Y T; Yin, Kedong; Yuan, Xiangcheng; Anderson, Donald M; Lee, Joseph H W; Harrison, Paul J

2008-01-01

In 2001, the Hong Kong government implemented the Harbor Area Treatment Scheme (HATS) under which 70% of the sewage that had been formerly discharged into Victoria Harbor is now collected and sent to Stonecutters Island Sewage Works where it receives chemically enhanced primary treatment (CEPT), and is then discharged into waters west of the Harbor. The relocation of the sewage discharge will possibly change the nutrient dynamics and phytoplankton biomass in this area. Therefore, there is a need to examine the factors that regulate phytoplankton growth in Hong Kong waters in order to understand future impacts. Based on a historic nutrient data set (1986-2001), a comparison of ambient nutrient ratios with the Redfield ratio (N:P:Si=16:1:16) showed clear spatial variations in the factors that regulate phytoplankton biomass along a west (estuary) to east (coastal/oceanic) transect through Hong Kong waters. Algal biomass was constrained by a combination of low light conditions, a rapid change in salinity, and strong turbulent mixing in western waters throughout the year. Potential stoichiometric Si limitation (up to 94% of the cases in winter) occurred in Victoria Harbor due to the contribution of sewage effluent with high N and P enrichment all year, except for summer when the frequency of stoichiometric Si limitation (48%) was the same as P, owing to the influence of the high Si in the Pearl River discharge. In the eastern waters, potential N limitation and N and P co-limitation occurred in autumn and winter respectively, because of the dominance of coastal/oceanic water with low nutrients and low N:P ratios. In contrast, potential Si limitation occurred in spring and a switch to potential N, P and Si limitation occurred in eastern waters in summer. In southern waters, there was a shift from P limitation (80%) in summer due to the influence of the N-rich Pearl River discharge, to N limitation (68%) in autumn, and to N and P co-limitation in winter due to the dominance of N-poor oceanic water from the oligotrophic South China Sea. Our results show clear temporal and spatial variations in the nutrient stoichiometry which indicates potential regulation of phytoplankton biomass in HK waters due to the combination of the seasonal exchange of the Pearl River discharge and oceanic water, sewage effluent inputs, and strong hydrodynamic mixing from SW monsoon winds in summer and the NE monsoon winds in winter.

Temporal and Spatial Variations in Nutrient Stoichiometry and Regulation of Phytoplankton Biomass in Hong Kong waters: Influence of the Pearl River Outflow and Sewage Inputs

PubMed Central

Xu, Jie; Ho, Alvin Y. T.; Yin, Kedong; Yuan, Xiangcheng; Anderson, Donald M.; Lee, Joseph H.W.; Harrison, Paul J.

2017-01-01

In 2001, the Hong Kong government implemented the Harbor Area Treatment Scheme (HATS) under which 70% of the sewage that had been formerly discharged into Victoria Harbor is now collected and sent to Stonecutters Island Sewage Works where it receives chemically enhanced primary treatment (CEPT), and is then discharged into waters west of the Harbor. The relocation of the sewage discharge will possibly change the nutrient dynamics and phytoplankton biomass in this area. Therefore, there is a need to examine the factors that regulate phytoplankton growth in Hong Kong waters in order to understand future impacts. Based on a historic nutrient data set (1986–2001), a comparison of ambient nutrient ratios with the Redfield ratio (N:P:Si=16:1:16) showed clear spatial variations in the factors that regulate phytoplankton biomass along a west (estuary) to east (coastal/oceanic) transect through Hong Kong waters. Algal biomass was constrained by a combination of low light conditions, a rapid change in salinity, and strong turbulent mixing in western waters throughout the year. Potential stoichiometric Si limitation (up to 94% of the cases in winter) occurred in Victoria Harbor due to the contribution of sewage effluent with high N and P enrichment all year, except for summer when the frequency of stoichiometric Si limitation (48%) was the same as P, owing to the influence of the high Si in the Pearl River discharge. In the eastern waters, potential N limitation and N and P co-limitation occurred in autumn and winter respectively, because of the dominance of coastal/oceanic water with low nutrients and low N:P ratios. In contrast, potential Si limitation occurred in spring and a switch to potential N, P and Si limitation occurred in eastern waters in summer. In southern waters, there was a shift from P limitation (80%) in summer due to the influence of the N-rich Pearl River discharge, to N limitation (68%) in autumn, and to N and P co-limitation in winter due to the dominance of N-poor oceanic water from the oligotrophic South China Sea. Our results show clear temporal and spatial variations in the nutrient stoichiometry which indicates potential regulation of phytoplankton biomass in HK waters due to the combination of the seasonal exchange of the Pearl River discharge and oceanic water, sewage effluent inputs, and strong hydrodynamic mixing from SW monsoon winds in summer and the NE monsoon winds in winter. PMID:18313698

77 FR 50916 - Safety Zone; Boston Harbor's Rock Removal Project, Boston Inner Harbor, Boston, MA

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-23

... DEPARTMENT OF HOMELAND SECURITY Coast Guard 33 CFR Part 165 [Docket No. USCG-2012-0767] RIN 1625-AA00 Safety Zone; Boston Harbor's Rock Removal Project, Boston Inner Harbor, Boston, MA AGENCY: Coast.... 165.T01-0767 Safety Zone; Boston Harbor's Rock Removal Project, Boston Inner Harbor, Boston, MA. (a...

Cetacean distributions relative to ocean processes in the northern California Current System

NASA Astrophysics Data System (ADS)

Tynan, Cynthia T.; Ainley, David G.; Barth, John A.; Cowles, Timothy J.; Pierce, Stephen D.; Spear, Larry B.

2005-01-01

Associations between cetacean distributions, oceanographic features, and bioacoustic backscatter were examined during two process cruises in the northern California Current System (CCS) during late spring and summer 2000. Line-transect surveys of cetaceans were conducted across the shelf and slope, out to 150 km offshore from Newport, Oregon (44.6°N) to Crescent City, California (41.9°N), in conjunction with multidisciplinary mesoscale and fine-scale surveys of ocean and ecosystem structure. Occurrence patterns (presence/absence) of cetaceans were compared with hydrographic and ecological variables (e.g., sea surface salinity, sea surface temperature, thermocline depth, halocline depth, chlorophyll maximum, distance to the center of the equatorward jet, distance to the shoreward edge of the upwelling front, and acoustic backscatter at 38, 120, 200 and 420 kHz) derived from a towed, undulating array and a bioacoustic system. Using a multiple logistic regression model, 60.2% and 94.4% of the variation in occurrence patterns of humpback whales Megaptera novaeangliae during late spring and summer, respectively, were explained. Sea surface temperature, depth, and distance to the alongshore upwelling front were the most important environmental variables during June, when humpbacks occurred over the slope (200-2000 m). During August, when humpbacks concentrated over a submarine bank (Heceta Bank) and off Cape Blanco, sea surface salinity was the most important variable, followed by latitude and depth. Humpbacks did not occur in the lowest salinity water of the Columbia River plume. For harbor porpoise Phocoena phocoena, the model explained 79.2% and 70.1% of the variation in their occurrence patterns during June and August, respectively. During spring, latitude, sea surface salinity, and thermocline gradient were the most important predictors. During summer, latitude and distance to the inshore edge of the upwelling front were the most important variables. Typically a coastal species, harbor porpoises extended their distribution farther offshore at Heceta Bank and at Cape Blanco, where they were associated with the higher chlorophyll concentrations in these regions. Pacific white-sided dolphin Lagenorhynchus obliquidens was the most numerous small cetacean in early June, but was rare during August. The model explained 44.5% of the variation in their occurrence pattern, which was best described by distance to the upwelling front and acoustic backscatter at 38 kHz. The model of the occurrence pattern of Dall's porpoise Phocoenoides dalli was more successful when mesoscale variability in the CCS was higher during summer. Thus, the responses of cetaceans to biophysical features and upwelling processes in the northern CCS were both seasonally and spatially specific. Heceta Bank and associated flow-topography interactions were very important to a cascade of trophic dynamics that ultimately influenced the distribution of foraging cetaceans. The higher productivity associated with upwelling near Cape Blanco also had a strong influence on the distribution of cetaceans.

Assessment of levels of bacterial contamination of large wild game meat in Europe.

PubMed

Membré, Jeanne-Marie; Laroche, Michel; Magras, Catherine

2011-08-01

The variations in prevalence and levels of pathogens and fecal contamination indicators in large wild game meat were studied to assess their potential impact on consumers. This analysis was based on hazard analysis, data generation and statistical analysis. A total of 2919 meat samples from three species (red deer, roe deer, wild boar) were collected at French game meat traders' facilities using two sampling protocols. Information was gathered on the types of meat cuts (forequarter or haunch; first sampling protocol) or type of retail-ready meat (stewing meat or roasting meat; second protocol), and also on the meat storage conditions (frozen or chilled), country of origin (eight countries) and shooting season (autumn, winter, spring). The samples were analyzed in both protocols for detection and enumeration of Escherichia coli, coagulase+staphylococci and Clostridium perfringens. In addition, detection and enumeration of thermotolerant coliforms and Listeria monocytogenes were performed for samples collected in the first and second protocols, respectively. The levels of bacterial contamination of the raw meat were determined by performing statistical analysis involving probabilistic techniques and Bayesian inference. C. perfringens was found in the highest numbers for the three indicators of microbial quality, hygiene and good handling, and L. monocytogenes in the lowest. Differences in contamination levels between game species and between meats distributed as chilled or frozen products were not significant. These results might be included in quantitative exposure assessments. Copyright © 2011 Elsevier Ltd. All rights reserved.

Modulating the Levels of Plant Hormone Cytokinins at the Host-Pathogen Interface.

PubMed

Naseem, Muhammad; Shams, Shabana; Roitsch, Thomas

2017-01-01

Cytokinins are adenine and non-adenine derived heterogeneous class of regulatory molecules that participate in almost every aspect of plant biology. They also affect plant defense responses as well as help microbial pathogens to establish pathogenesis. The functional approaches that ensure desired and subtle modulations in the levels of plant cytokinins are highly instrumental in assessing their functions in plant immunity. Here, we describe a detailed working protocol regarding the enhanced production of cytokinins from plants that harbor isopentenyltransferase (IPT) enzyme gene under the control of 4xJERE (jasmonic acid and elicitor-responsive element) pathogen-inducible promoter. Our devised expression system is a context-dependent solution when it comes to investigating host-pathogen interactions under the modulated conditions of plant cytokinins.

Microbial Metabolic Diversity Study of the Kuantzuling Mud Hot Spring in the Southwestern Taiwan

NASA Astrophysics Data System (ADS)

Lin, Y.; Wang, P.; Lin, L.

2009-12-01

Organic carbon, sulfate, methane, and hydrogen are available for microorganisms to carry on diverse metabolisms in the Kuantzuling mud hot spring, southwestern Taiwan. On the basis of bioenergetic evaluations and environmental DNA analyses, previous studies have inferred diverse metabolic capabilities, including methanogenesis, sulfate reduction, fermentation, aerobic heterotrophy and methanotrophy. However, active metabolisms have never been confirmed by cultivation-based analysis. Due to the temperature fluctuation of the Kuantzuling mud spring, this study performed a set of enrichment experiments at temperatures ranging from 25oC to 80oC to understand the activity and interaction among microorganisms at various temperatures. Pure stains were also isolated along with their physiological tests to reveal their possible roles in this terrestrial hot spring ecosystem. According to the geochemical and molecular data, nine types of media were designed to enrich different kinds of metabolisms in the slurry. Positive enrichments were obtained in all types of media, but not at all investigated temperatures. Methanogens using acetate, methanol, and hydrogen and carbon dioxide, sulfate reducers, thiosulfate reducers, fermenters, aerobic heterotrophs could be enriched at temperatures higher than 50oC and even 80oC. Methanogen using methylamine and aerobic methanotroph can only be enriched at temperatures lower than 50 oC. This result is generally consistent with previous energetic evaluation and molecular analysis. It also inferred that microbial assemblages possessing diverse metabolisms were either competitive or collaborative to each other for degradation of organic carbon or carbon cycling. Two strains were isolated from aerobic heterotrophic media. The 16S rDNA gene sequence of one strain exhibited a very close affiliation (at a similarity of 99%) with Meiothermus ruber strain SPS242 and that of the other showed an affiliation to that of Rhodobacter vinaykumarii JA123 at the similarity of 95%. The former grew at the pH values between 5 and 9, at the temperatures ranging from 20 to 70oC with the optimal growth temperature at 60oC, while the later can grow at the pH values between 6 and 9, at the temperatures ranging from 20 to 60oC with the optimal growth temperature at 50oC. The Kuantzuling mud spring harbors diverse microorganisms. Such a wide range of physiological capability might represent an unstable ecosystem constantly exposed to the substantial environmental fluctuations, such as temperature, oxygen content and fluid source.

Investigating passage of ESA-listed juvenile fall Chinook salmon at Lower Granite Dam during winter when the fish bypass system is not operated. 2006 Annual Report

USGS Publications Warehouse

Tiffan, Kenneth F.; Kock, Tobias J.; Connor, William P.

2007-01-01

During the winter of 2005-06, we radio and PIT tagged and released 48 juvenile fall Chinook salmon to evaluate over-wintering behavior and dam passage in the lower Snake River, Washington. Fish were released at the upstream end of the Lower Granite Dam forebay in November and December 2005. Fixed radio telemetry detection sites located in forebay and tailrace areas of Lower Granite, Little Goose, Lower Monumental and Ice Harbor dams were used to monitor fish movements and dam passage through early-May 2006. Of the 48 fish released during our study, 39 (81 %) passed Lower Granite Dam and were detected at downstream detection sites, 29 (60%) passed Little Goose Dam, 25 (52%) passed Lower Monumental Dam, and 15 (31%) passed Ice Harbor Dam. Thirty-seven (95%), 23 (79%), 16 (64%), and 9 (60%) of the fish that passed Lower Granite, Little Goose, Lower Monumental, and Ice Harbor dams respectively, did so when the fish bypass system was not operated. Passage of tagged fish past lower Snake River dams generally declined during the winter, but increased again after bypass began in April. Fish residence times in reservoirs and forebays was lengthy during the winter (up to 118 d), and varied by reservoir and time of year. We observed no diel passage trends. Only 15 of the 48 fish were subsequently detected at a PIT-tag interrogation site the following spring. We believe that passage of overwintering juvenile fall Chinook salmon during winter is due more to chance than directed downstream movement. Since the primary route of passage during the winter is through powerhouse turbines, the potential exists for increased mortality for over-wintering juvenile fall Chinook salmon in the Snake River. Our findings also have implications for transportation studies of subyearling fall Chinook salmon in the Snake River. Specifically, the finding that some fish can pass undetected during the winter may bias smolt-to-adult return rate calculations that are typically used to measure the success of the aforementioned management actions.

Relative Sea Level, Tidal Range, and Extreme Water Levels in Boston Harbor from 1825 to 2016

NASA Astrophysics Data System (ADS)

Talke, S. A.; Kemp, A.; Woodruff, J. D.

2017-12-01

Long time series of water-level measurements made by tide gauges provide a rich and valuable observational history of relative sea-level change, the frequency and height of extreme water levels and evolving tidal regimes. However, relatively few locations have available tide-gauge records longer than 100 years and most of these places are in northern Europe. This spatio-temporal distribution hinders efforts to understand global-, regional- and local-scale trends. Using newly-discovered archival measurements, we constructed a 200 year, instrumental record of water levels, tides, and storm surges in Boston Harbor. We detail the recovery, datum reconstruction, digitization, quality assurance, and analysis of this extended observational record. Local, decadally-averaged relative sea-level rose by 0.28 ± 0.05 m since the 1820s, with an acceleration of 0.023 ±0.009 mm/yr2. Approximately 0.13 ± 0.02 m of the observed RSL rise occurred due to ongoing glacial isostatic adjustment, and the remainder occurred due to changes in ocean mass and volume associated with the onset of modern mean sea-level rise. Change-point analysis of the new relative sea level record confirms that anthropogenic rise began in 1924-1932, which is in agreement with global mean sea level estimates from the global tide gauge network. Tide range decreased by 5.5% between 1830 and 1910, likely due in large part to anthropogenic development. Storm tides in Boston Harbor are produced primarily by extratropical storms during the November-April time frame. The three largest storm tides occurred in 1851, 1909, and 1978. Because 90% of the top 20 storm tides since 1825 occurred during a spring tide, the secular change in tide range contributes to a slight reduction in storm tide magnitudes. However, non-stationarity in storm hazard was historically driven primarily by local relative sea-level rise; a modest 0.2 m increase in relative sea level reduces the 100 year high water mark to a once-in-10 year event.

Manila clams from Hg polluted sediments of Marano and Grado lagoons (Italy) harbor detoxifying Hg resistant bacteria in soft tissues

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baldi, Franco, E-mail: baldi@unive.it; Gallo, Michele; Marchetto, Davide

2013-08-15

A mechanism of mercury detoxification has been suggested by a previous study on Hg bioaccumulation in Manila clams (Ruditapes philippinarum) in the polluted Marano and Grado lagoons and in this study we demonstrate that this event could be partly related to the detoxifying activities of Hg-resistant bacteria (MRB) harbored in clam soft tissues. Therefore, natural clams were collected in six stations during two different periods (winter and spring) from Marano and Grado Lagoons. Siphons, gills and hepatopancreas from acclimatized clams were sterile dissected to isolate MRB. These anatomical parts were glass homogenized or used for whole, and they were lyingmore » on a solid medium containing 5 mg l{sup −1} HgCl{sub 2} and incubated at 30 °C. A total of fourteen bacterial strains were isolated and were identified by 16S rDNA sequencing and analysis, revealing that strains were representative of eight bacterial genera, four of which were Gram-positive (Enterococcus, Bacillus, Jeotgalicoccus and Staphylococcus) and other four were Gram-negative (Stenotrophomonas, Vibrio, Raoultella and Enterobacter). Plasmids and merA genes were found and their sequences determined. Fluorescence in situ hybridization (FISH) technique shows the presence of Firmicutes, Actinobacteria and Gammaproteobacteria by using different molecular probes in siphon and gills. Bacterial clumps inside clam flesh were observed and even a Gram-negative endosymbiont was disclosed by transmission electronic microscope inside clam cells. Bacteria harbored in cavities of soft tissue have mercury detoxifying activity. This feature was confirmed by the determination of mercuric reductase in glass-homogenized siphons and gills. -- Highlights: ► We isolated Gram-positive and Gram-negative Hg resistant strains from soft tissues of Ruditapes philippinarum. ► We identify 14 mercury resistant strains by 16S rRNA gene sequences. ► Bacteria in siphon and gill tissues of clams were observed by TEM and identified with different FISH probes. ► Hg-reductase (MerA) activity in glass homogenized clam tissues was also determined.« less

Second metrology round-robin of APS, ESRF and SPring-8 laboratories of elliptical and spherical hard-x-ray mirrors.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rommeveaux, A.; Assoufid, L.; Ohashi, H.

2007-01-01

The first series of metrology round-robin measurements carried out in 2005 at the APS, ESRF and SPring-8 metrology laboratories involving two flat x-ray mirrors and a cylindrical x-ray mirror has shown excellent agreement among the three facilities Long Trace Profilers (LTP) despite their architectural differences. Because of the growing interest in diffraction-limited hard x-ray K-B focusing mirrors, it was decided to extend the round robin measurements to spherical and aspheric x-ray mirrors. The strong surface slope variation of these mirrors presents a real challenge to LTP. As a result, new LTP measurement protocol has to be developed and implemented tomore » ensure measurement accuracy and consistency. In this paper, different measurement techniques and procedures will be described, the results will be discussed, and comparison will be extended to micro-stitching interferometry measurements performed at Osaka University, Japan.« less

Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome

PubMed Central

Abby, Sophie S.; Melcher, Michael; Kerou, Melina; Krupovic, Mart; Stieglmeier, Michaela; Rossel, Claudia; Pfeifer, Kevin; Schleper, Christa

2018-01-01

Ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread in moderate environments but their occurrence and activity has also been demonstrated in hot springs. Here we present the first enrichment of a thermophilic representative with a sequenced genome, which facilitates the search for adaptive strategies and for traits that shape the evolution of Thaumarchaeota. Candidatus Nitrosocaldus cavascurensis has been enriched from a hot spring in Ischia, Italy. It grows optimally at 68°C under chemolithoautotrophic conditions on ammonia or urea converting ammonia stoichiometrically into nitrite with a generation time of approximately 23 h. Phylogenetic analyses based on ribosomal proteins place the organism as a sister group to all known mesophilic AOA. The 1.58 Mb genome of Ca. N. cavascurensis harbors an amoAXCB gene cluster encoding ammonia monooxygenase and genes for a 3-hydroxypropionate/4-hydroxybutyrate pathway for autotrophic carbon fixation, but also genes that indicate potential alternative energy metabolisms. Although a bona fide gene for nitrite reductase is missing, the organism is sensitive to NO-scavenging, underlining the potential importance of this compound for AOA metabolism. Ca. N. cavascurensis is distinct from all other AOA in its gene repertoire for replication, cell division and repair. Its genome has an impressive array of mobile genetic elements and other recently acquired gene sets, including conjugative systems, a provirus, transposons and cell appendages. Some of these elements indicate recent exchange with the environment, whereas others seem to have been domesticated and might convey crucial metabolic traits. PMID:29434576

Loci associated with resistance to stripe rust (Puccinia striiformis f. sp. tritici) in a core collection of spring wheat (Triticum aestivum).

PubMed

Muleta, Kebede T; Bulli, Peter; Rynearson, Sheri; Chen, Xianming; Pumphrey, Michael

2017-01-01

Stripe rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst) remains one of the most significant diseases of wheat worldwide. We investigated stripe rust resistance by genome-wide association analysis (GWAS) in 959 spring wheat accessions from the United States Department of Agriculture-Agricultural Research Service National Small Grains Collection, representing major global production environments. The panel was characterized for field resistance in multi-environment field trials and seedling resistance under greenhouse conditions. A genome-wide set of 5,619 informative SNP markers were used to examine the population structure, linkage disequilibrium and marker-trait associations in the germplasm panel. Based on model-based analysis of population structure and hierarchical Ward clustering algorithm, the accessions were clustered into two major subgroups. These subgroups were largely separated according to geographic origin and improvement status of the accessions. A significant correlation was observed between the population sub-clusters and response to stripe rust infection. We identified 11 and 7 genomic regions with significant associations with stripe rust resistance at adult plant and seedling stages, respectively, based on a false discovery rate multiple correction method. The regions harboring all, except three, of the QTL identified from the field and greenhouse studies overlap with positions of previously reported QTL. Further work should aim at validating the identified QTL using proper germplasm and populations to enhance their utility in marker assisted breeding.

Loci associated with resistance to stripe rust (Puccinia striiformis f. sp. tritici) in a core collection of spring wheat (Triticum aestivum)

PubMed Central

Bulli, Peter; Rynearson, Sheri; Chen, Xianming; Pumphrey, Michael

2017-01-01

Stripe rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst) remains one of the most significant diseases of wheat worldwide. We investigated stripe rust resistance by genome-wide association analysis (GWAS) in 959 spring wheat accessions from the United States Department of Agriculture-Agricultural Research Service National Small Grains Collection, representing major global production environments. The panel was characterized for field resistance in multi-environment field trials and seedling resistance under greenhouse conditions. A genome-wide set of 5,619 informative SNP markers were used to examine the population structure, linkage disequilibrium and marker-trait associations in the germplasm panel. Based on model-based analysis of population structure and hierarchical Ward clustering algorithm, the accessions were clustered into two major subgroups. These subgroups were largely separated according to geographic origin and improvement status of the accessions. A significant correlation was observed between the population sub-clusters and response to stripe rust infection. We identified 11 and 7 genomic regions with significant associations with stripe rust resistance at adult plant and seedling stages, respectively, based on a false discovery rate multiple correction method. The regions harboring all, except three, of the QTL identified from the field and greenhouse studies overlap with positions of previously reported QTL. Further work should aim at validating the identified QTL using proper germplasm and populations to enhance their utility in marker assisted breeding. PMID:28591221

Suspended Sediment in the Indiana Harbor Canal and the Grand Calumet River, Northwestern Indiana, May 1996-June 1998

USGS Publications Warehouse

Renn, Danny E.

2000-01-01

Suspended-sediment samples and streamflow data were collected from May 1996 through June 1998 at three sites in the Grand Calumet River Basin - Indiana Harbor Canal at East Chicago, the east branch of the Grand Calumet River at Gary, and the west branch of the Grand Calumet River at Hammond. Sample analysis allowed for retention of sediments of 0.0015 millimeters or larger. At Indiana Harbor Canal at East Chicago, an automated sampler collected 2,005 suspended-sediment samples from the canal and, of these, 1,856 had associated streamflow values. To evaluate any bias between instream concentrations of suspended sediment and samples collected by the automated sampler, 27 sets of suspended-sediment samples were collected manually in the canal at the same time samples were collected by the automated sampler. There was no consistent bias between the samples collected manually instream and the samples collected by the automated sampler; therefore, no correction factor was applied to the concentrations of suspended sedment for the samples collected by the automated sampler. For the 2,005 and 1,856 samples, the mean suspended-sediment concentrations were the same, 15 milligrams per liter (mg/L), and the range in suspended-sediment concentrations were the same, from less than 1 mg/L to 97 mg/L. No apparent relation between the concentration of suspended sediment measured in samples from the Indiana Harbor Canal and streamflow was indicated, probably because of complex hydraulic conditions in the study area; most of the streamflow is from industrial and municipal discharges, and streamflow is affected by changes in water levels in Lake Michigan. There did appear to be a seasonal trend in the concentrations of suspended sediment, however, in that the largest concentrations generally were measured during the spring. During the study, four substantial rainfall events were recorded. Only for a rainfall event of 4.20 inches was there a substantial increase in the concentrations of suspended sediment and streamflow in the Indiana Harbor Canal. Six sets of samples were collected from the canal for determination of the percentage of organic material in the suspended sediment. Organic material in these samples averaged 26 percent. Bedload-sediment samples were collected three times in the canal with a bedload-sediment sampler; the collection-bag mesh size was 0.25 millimeter. No bedload sediments were collected in the sampler for any of the sample collections. Seven suspended-sediment samples were collected from the Grand Calumet River at Gary and at Hammond. The mean suspended sediment concentration measured in samples collected at Gary was 13 mg/L, and the mean suspended-sediment concentration measured in samples collected at Hammond was 6 mg/L. For both sites, there was no apparent relation between the concentration of suspended sediment and streamflow. Four suspended sediment samples were collected from the Grand Calumet River at Gary and at Hammond for determination of the percentage of organic material. The amount of organic material at Gary averaged 35 percent, and the amount of organic material at Hammond averaged 34 percent. The concentrations of suspended sediment determined for samples collected from the Indiana Harbor Canal and from the Grand Calumet River are less than concentrations of suspended sediment in samples collected from other streams in northwestern Indiana and in other parts of the State. Loads of suspended sediment were computed as the product of the weekly mean suspended-sediment concentration and the daily average streamflow for the Indiana Harbor Canal at East Chicago. The average suspended-sediment load computed for the canal was 29 tons per day for the first year of the study (June 1996 through May 1997) and 23 tons per day for the second year of the study (June 1997 through May 1998). Loads of suspended sediment for the Grand Calumet River at Gary and at Hammond were estimated by use of the ratin

33 CFR 80.1122 - Channel Islands Harbor, CA.

Code of Federal Regulations, 2012 CFR

2012-07-01

... INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1122 Channel Islands Harbor, CA. (a) A line drawn from Channel Islands Harbor South Jetty Light 2 to Channel Islands Harbor Breakwater... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Channel Islands Harbor, CA. 80...

33 CFR 80.1122 - Channel Islands Harbor, CA.

Code of Federal Regulations, 2010 CFR

2010-07-01

... INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1122 Channel Islands Harbor, CA. (a) A line drawn from Channel Islands Harbor South Jetty Light 2 to Channel Islands Harbor Breakwater... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Channel Islands Harbor, CA. 80...

33 CFR 80.1122 - Channel Islands Harbor, CA.

Code of Federal Regulations, 2014 CFR

2014-07-01

... INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1122 Channel Islands Harbor, CA. (a) A line drawn from Channel Islands Harbor South Jetty Light 2 to Channel Islands Harbor Breakwater... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Channel Islands Harbor, CA. 80...

33 CFR 80.1122 - Channel Islands Harbor, CA.

Code of Federal Regulations, 2013 CFR

2013-07-01

... INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1122 Channel Islands Harbor, CA. (a) A line drawn from Channel Islands Harbor South Jetty Light 2 to Channel Islands Harbor Breakwater... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Channel Islands Harbor, CA. 80...

33 CFR 80.1122 - Channel Islands Harbor, CA.

Code of Federal Regulations, 2011 CFR

2011-07-01

... INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1122 Channel Islands Harbor, CA. (a) A line drawn from Channel Islands Harbor South Jetty Light 2 to Channel Islands Harbor Breakwater... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Channel Islands Harbor, CA. 80...

33 CFR 110.250 - St. Thomas Harbor, Charlotte Amalie, V.I.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false St. Thomas Harbor, Charlotte... SECURITY ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.250 St. Thomas Harbor, Charlotte Amalie... move promptly upon notification by the Harbor Master. (4) The harbor regulations for the Port of St...

33 CFR 100.109 - Winter Harbor Lobster Boat Race, Winter Harbor, ME.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Winter Harbor Lobster Boat Race, Winter Harbor, ME. 100.109 Section 100.109 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF... Lobster Boat Race, Winter Harbor, ME. (a) Regulated area. The regulated area includes all waters of Winter...

Assessing Juvenile Salmonid Passage Through Culverts: Field Research in Support of Protocol Development

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williams, Greg D.; Evans, Nathan R.; Pearson, Walter H.

2001-10-30

The primary goal of our research this spring/ summer was to refine techniques and examine scenarios under which a standardized protocol could be applied to assess juvenile coho salmon (O. kisutch) passage through road culverts. Field evaluations focused on capture-mark- recapture methods that allowed analysis of fish movement patterns, estimates of culvert passability, and potential identification of cues inducing these movements. At this stage, 0+ age coho salmon fry 30 mm to 65 mm long (fork length) were the species and age class of interest. Ultimately, the protocol will provide rapid, statistically rigorous methods for trained personnel to perform standardizedmore » biological assessments of culvert passability to a number of juvenile salmon species. Questions to be addressed by the research include the following: ? Do hydraulic structures such as culverts restrict habitat for juvenile salmonids? ? How do existing culverts and retrofits perform relative to juvenile salmonid passage? ? Do some culvert characteristics and hydraulic conditions provide better passage than others? ? Does the culvert represent a barrier to certain size classes of fish? Recommendations addressed issues of study site selection, initial capture, marking, recapture/observations, and estimating movement.« less

Speciation and Bioavailability Measurements of Environmental Plutonium Using Diffusion in Thin Films.

PubMed

Cusnir, Ruslan; Steinmann, Philipp; Christl, Marcus; Bochud, François; Froidevaux, Pascal

2015-11-09

The biological uptake of plutonium (Pu) in aquatic ecosystems is of particular concern since it is an alpha-particle emitter with long half-life which can potentially contribute to the exposure of biota and humans. The diffusive gradients in thin films technique is introduced here for in-situ measurements of Pu bioavailability and speciation. A diffusion cell constructed for laboratory experiments with Pu and the newly developed protocol make it possible to simulate the environmental behavior of Pu in model solutions of various chemical compositions. Adjustment of the oxidation states to Pu(IV) and Pu(V) described in this protocol is essential in order to investigate the complex redox chemistry of plutonium in the environment. The calibration of this technique and the results obtained in the laboratory experiments enable to develop a specific DGT device for in-situ Pu measurements in freshwaters. Accelerator-based mass-spectrometry measurements of Pu accumulated by DGTs in a karst spring allowed determining the bioavailability of Pu in a mineral freshwater environment. Application of this protocol for Pu measurements using DGT devices has a large potential to improve our understanding of the speciation and the biological transfer of Pu in aquatic ecosystems.

Hydraulic modeling of stream channels and structures in Harbor and Crow Hollow Brooks, Meriden, Connecticut

USGS Publications Warehouse

Weiss, Lawrence A.; Sears, Michael P.; Cervione, Michael A.

1994-01-01

Effects of urbanization have increased the frequency and size of floods along certain reaches of Harbor Brook and Crow Hollow Brook in Meriden, Conn. A floodprofile-modeling study was conducted to model the effects of selected channel and structural modifications on flood elevations and inundated areas. The study covered the reach of Harbor Brook downstream from Interstate 691 and the reach of Crow Hollow Brook downstream from Johnson Avenue. Proposed modifications, which include changes to bank heights, channel geometry, structural geometry, and streambed armoring on Harbor Brook and changes to bank heights on Crow Hollow Brook, significantly lower flood elevations. Results of the modeling indicate a significant reduction of flood elevations for the 10-year, 25-year, 35-year, 50-year, and 100-year flood frequencies using proposed modifications to (1 ) bank heights between Harbor Brook Towers and Interstate 691 on Harbor Brook, and between Centennial Avenue and Johnson Avenue on Crow Hollow Brook; (2) channel geometry between Coe Avenue and Interstate 69 1 on Harbor Brook; (3) bridge and culvert opening geometry between Harbor Brook Towers and Interstate 691 on Harbor Brook; and (4) channel streambed armoring between Harbor Brook Towers and Interstate 691 on Harbor Brook. The proposed modifications were developed without consideration of cost-benefit ratios.

Efficient generation of dopaminergic-like neurons by overexpression of Nurr1 and Pitx3 in mouse induced Pluripotent Stem Cells.

PubMed

Salemi, Salemeh; Baktash, Parvaneh; Rajaei, Bahareh; Noori, Mehri; Amini, Hossein; Shamsara, Mehdi; Massumi, Mohammad

2016-07-28

Parkinson's disease (PD) is a neurodegenerative disorder, in which the nigro-striatal Dopaminergic (DAergic) neurons are selectively lost. Treatment of neurodegenerative diseases with Pluripotent Stem Cells (PSCs) is a big interest in cell therapy. Here, we used induced Pluripotent Stem Cells (iPSCs) expressing two master Dopaminergic (DAergic) transcription factors, i.e. Nurr1 and Pitx3, to generate functional in vitro DAergic-like neurons. After establishment and characterization of Doxycycline-inducible iPSCs from mouse fibroblasts, the cells were transduced by NURR1- and PITX3-harboring lentiviruses. The Nurr1/Pitx3 -iPSCs were differentiated through a five-stage protocol to generate DAergic-like neurons. The results confirmed the efficient expression of DAergic neuron markers in the end of protocol. Beside, the generated cells could exclusively synthesize and secrete Dopamine in response to secretagogues. In conclusion, overexpression of Nurr1 and Pitx3 in iPSCs could efficiently program iPSCs into functional DAergic-like neurons. This finding may have an impact on future stem cell therapy of PD. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Clinical Management and Tumor Surveillance Recommendations of Inherited Mismatch Repair Deficiency in Childhood.

PubMed

Tabori, Uri; Hansford, Jordan R; Achatz, Maria Isabel; Kratz, Christian P; Plon, Sharon E; Frebourg, Thierry; Brugières, Laurence

2017-06-01

Replication proofreading is crucial to avoid mutation accumulation in dividing cells. In humans, proofreading and replication repair is maintained by the exonuclease domains of DNA polymerases and the mismatch repair system. Individuals harboring germline mutations in genes involved in this process are at increased risk of early cancers from multiple organs. Biallelic mutations in any of the four mismatch repair genes MSH2, MSH6, MLH1 , and PMS2 result in one of the most aggressive childhood cancer predisposition syndromes, termed constitutional mismatch repair deficiency or constitutional mismatch repair deficiency syndrome (CMMRD). Data gathered in the last decade allow us to better define the clinical manifestations, tumor spectrum, and diagnostic algorithms for CMMRD. In this article, we summarize this information and present a comprehensive consensus surveillance protocol for these individuals. Ongoing research will allow for further definition of replication repair-deficient cancer syndromes, assessing the cost-effectiveness of such surveillance protocols and potential therapeutic interventions for these children and families. Clin Cancer Res; 23(11); e32-e37. ©2017 AACR See all articles in the online-only CCR Pediatric Oncology Series. ©2017 American Association for Cancer Research.

Sexually mature transgenic American chestnut trees via embryogenic suspension-based transformation.

PubMed

Andrade, Gisele M; Nairn, Campbell J; Le, Huong T; Merkle, Scott A

2009-09-01

The availability of a system for direct transfer of anti-fungal candidate genes into American chestnut (Castanea dentata), devastated by a fungal blight in the last century, would offer an alternative or supplemental approach to conventional breeding for production of chestnut trees resistant to the blight fungus and other pathogens. By taking advantage of the strong ability of embryogenic American chestnut cultures to proliferate in suspension, a high-throughput Agrobacterium tumefaciens-mediated transformation protocol for stable integration of foreign genes into the tree was established. Proembryogenic masses (PEMs) were co-cultivated with A. tumefaciens strain AGL1 harboring the plasmid pCAMBIA 2301, followed by stringent selection with 50 or 100 mg/l Geneticin. A protocol employing size-fractionation to enrich for small PEMs to use as target material and selection in suspension culture was applied to rapidly produce transgenic events with an average efficiency of four independent transformation events per 50 mg of target tissue and minimal escapes. Mature somatic embryos, representing 18 transgenic events and derived from multiple American chestnut target genotypes, were germinated and over 100 transgenic somatic seedlings were produced and acclimatized to greenhouse conditions. Multiple vigorous transgenic somatic seedlings produced functional staminate flowers within 3 years following regeneration.

33 CFR 165.904 - Lake Michigan at Chicago Harbor & Burnham Park Harbor-Safety and Security Zone.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Harbor, to the northwest point. (b) Effective times and dates. This safety and security zone will be in... & Burnham Park Harbor-Safety and Security Zone. 165.904 Section 165.904 Navigation and Navigable Waters... Guard District § 165.904 Lake Michigan at Chicago Harbor & Burnham Park Harbor—Safety and Security Zone...

Tech Talk for Social Studies Teachers Lest We Forget: Remembering Pearl Harbor.

ERIC Educational Resources Information Center

Green, Tim

2001-01-01

Presents an annotated bibliography that provides Web sites about Pearl Harbor (Hawaii). Includes Web sites that cover Pearl Harbor history, a live view of Pearl Harbor, stories from people who remember where they were during the attack, information on the naval station at Pearl Harbor, and a virtual tour of the USS Arizona. (CMK)

An efficient Agrobacterium-mediated transformation method for aflatoxin generation fungus Aspergillus flavus.

PubMed

Han, Guomin; Shao, Qian; Li, Cuiping; Zhao, Kai; Jiang, Li; Fan, Jun; Jiang, Haiyang; Tao, Fang

2018-05-01

Aspergillus flavus often invade many important corps and produce harmful aflatoxins both in preharvest and during storage stages. The regulation mechanism of aflatoxin biosynthesis in this fungus has not been well explored mainly due to the lack of an efficient transformation method for constructing a genome-wide gene mutant library. This challenge was resolved in this study, where a reliable and efficient Agrobacterium tumefaciens-mediated transformation (ATMT) protocol for A. flavus NRRL 3357 was established. The results showed that removal of multinucleate conidia, to collect a homogenous sample of uninucleate conidia for use as the transformation material, is the key step in this procedure. A. tumefaciens strain AGL-1 harboring the ble gene for zeocin resistance under the control of the gpdA promoter from A. nidulans is suitable for genetic transformation of this fungus. We successfully generated A. flavus transformants with an efficiency of ∼ 60 positive transformants per 10 6 conidia using our protocol. A small-scale insertional mutant library (∼ 1,000 mutants) was constructed using this method and the resulting several mutants lacked both production of conidia and aflatoxin biosynthesis capacity. Southern blotting analysis demonstrated that the majority of the transformants contained a single T-DNA insert on the genome. To the best of our knowledge, this is the first report of genetic transformation of A. flavus via ATMT and our protocol provides an effective tool for construction of genome-wide gene mutant libraries for functional analysis of important genes in A. flavus.

An improved protocol for optical projection tomography imaging reveals lobular heterogeneities in pancreatic islet and β-cell mass distribution

PubMed Central

2011-01-01

Optical projection tomography (OPT) imaging is a powerful tool for three-dimensional imaging of gene and protein distribution patterns in biomedical specimens. We have previously demonstrated the possibility, by this technique, to extract information of the spatial and quantitative distribution of the islets of Langerhans in the intact mouse pancreas. In order to further increase the sensitivity of OPT imaging for this type of assessment, we have developed a protocol implementing a computational statistical approach: contrast limited adaptive histogram equalization (CLAHE). We demonstrate that this protocol significantly increases the sensitivity of OPT imaging for islet detection, helps preserve islet morphology and diminish subjectivity in thresholding for tomographic reconstruction. When applied to studies of the pancreas from healthy C57BL/6 mice, our data reveal that, at least in this strain, the pancreas harbors substantially more islets than has previously been reported. Further, we provide evidence that the gastric, duodenal and splenic lobes of the pancreas display dramatic differences in total and relative islet and β-cell mass distribution. This includes a 75% higher islet density in the gastric lobe as compared to the splenic lobe and a higher relative volume of insulin producing cells in the duodenal lobe as compared to the other lobes. Altogether, our data show that CLAHE substantially improves OPT based assessments of the islets of Langerhans and that lobular origin must be taken into careful consideration in quantitative and spatial assessments of the pancreas. PMID:21633198

Seasonal abundance of total and pathogenic Vibrio parahaemolyticus isolated from American oysters harvested in the Mandinga Lagoon System, Veracruz, Mexico: implications for food safety.

PubMed

Flores-Primo, Argel; Pardío-Sedas, Violeta; Lizárraga-Partida, Leonardo; López-Hernández, Karla; Uscanga-Serrano, Roxana; Flores-Hernández, Reyna

2014-07-01

The abundance of total and pathogenic Vibrio parahaemolyticus (Vp) strains in American oysters (Crassostrea virginica) harvested in two different harvest sites from the Mandinga lagoon System was evaluated monthly for 1 year (January through December 2012). Frequencies of species-specific genes and pathogenic genes exhibited a seasonal distribution. The annual occurrence of Vp with the species-specific tlh gene (tlh(+)) was significantly higher during the winter windy season (32.50%) and spring dry season (15.0%), with the highest densities observed during spring dry season at 283.50 most probable number (MPN)/g (lagoon bank A, near human settlements), indicating the highest risk of infection during warmer months. Pathogenic Vp tlh(+)/tdh(+) frequency was significantly higher during the winter windy and the spring dry seasons at 22.50 and 10.00%, respectively, with highest densities of 16.22 and 41.05 MPN/g (bank A), respectively. The tlh/trh and tdh/trh gene combinations were also found in Vp isolates during the spring dry season at 1.25 and 1.3%, respectively, with densities of 1.79 and 0.4 MPN/g (bank A), respectively. The orf8 genes were detected during the winter windy season (1.25%) with highest densities of 5.96 MPN/g (bank A) and 3.21 MPN/g (bank B, near mangrove islands and a heron nesting area). Densities of Vp tdh(+) were correlated (R(2) = 0.245, P < 0.015) with those of Vp orf8(+). The seasonal dynamics of Vp harboring pathogenic genes varied with seasonal changes, with very high proportions of Vp tdh(+) and Vp orf8(+) isolates in the winter windy season at 46.2 and 17.0%, respectively, which suggests that environmental factors may differentially affect the abundance of pathogenic subpopulations. Although all densities of total Vp (Vp tlh(+)) were lower than 10(4) MPN/g, thus complying with Mexican regulations, the presence of pathogenic strains is a public health concern. Our results suggest that total Vp densities may not be appropriate for assessing oyster contamination and predicting the risk of infection. Evaluation of the presence of pathogenic strains would be a better approach to protecting public health.

33 CFR 162.155 - Sandusky and Huron Harbors, Ohio.

Code of Federal Regulations, 2011 CFR

2011-07-01

... Harbors, Ohio. (a) In Sandusky Harbor, no vessel greater than 40 feet in length may exceed 10 miles per hour. (b) In Huron Harbor, no vessel greater than 40 feet in length may exceed 6 miles per hour, except in the outer harbor where no vessel greater than 40 feet in length may exceed 10 miles per hour. Note...

33 CFR 162.155 - Sandusky and Huron Harbors, Ohio.

Code of Federal Regulations, 2014 CFR

2014-07-01

... Harbors, Ohio. (a) In Sandusky Harbor, no vessel greater than 40 feet in length may exceed 10 miles per hour. (b) In Huron Harbor, no vessel greater than 40 feet in length may exceed 6 miles per hour, except in the outer harbor where no vessel greater than 40 feet in length may exceed 10 miles per hour. Note...

33 CFR 162.155 - Sandusky and Huron Harbors, Ohio.

Code of Federal Regulations, 2013 CFR

2013-07-01

... Harbors, Ohio. (a) In Sandusky Harbor, no vessel greater than 40 feet in length may exceed 10 miles per hour. (b) In Huron Harbor, no vessel greater than 40 feet in length may exceed 6 miles per hour, except in the outer harbor where no vessel greater than 40 feet in length may exceed 10 miles per hour. Note...

33 CFR 162.155 - Sandusky and Huron Harbors, Ohio.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Harbors, Ohio. (a) In Sandusky Harbor, no vessel greater than 40 feet in length may exceed 10 miles per hour. (b) In Huron Harbor, no vessel greater than 40 feet in length may exceed 6 miles per hour, except in the outer harbor where no vessel greater than 40 feet in length may exceed 10 miles per hour. Note...

33 CFR 162.155 - Sandusky and Huron Harbors, Ohio.

Code of Federal Regulations, 2012 CFR

2012-07-01

... Harbors, Ohio. (a) In Sandusky Harbor, no vessel greater than 40 feet in length may exceed 10 miles per hour. (b) In Huron Harbor, no vessel greater than 40 feet in length may exceed 6 miles per hour, except in the outer harbor where no vessel greater than 40 feet in length may exceed 10 miles per hour. Note...

33 CFR 207.610 - St. Lawrence River, Cape Vincent Harbor, N.Y.; use, administration, and navigation of the harbor...

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false St. Lawrence River, Cape Vincent Harbor, N.Y.; use, administration, and navigation of the harbor and U.S. breakwater. 207.610 Section 207... NAVIGATION REGULATIONS § 207.610 St. Lawrence River, Cape Vincent Harbor, N.Y.; use, administration, and...

Caffeine in Boston Harbor past and present, assessing its utility as a tracer of wastewater contamination in an urban estuary

EPA Science Inventory

Sites throughout Boston Harbor were analyzed for caffeine to assess its utility as a tracer in identifying sources of sanitary wastewater. Caffeine ranged from 15 ng/L in the outer harbor to a high of 185 ng/L in the inner harbor. Inner harbor concentrations were a result of comb...

Cloth-covered chiropractic treatment tables as a source of allergens and pathogenic microbes.

PubMed

Evans, Marion W; Campbell, Alan; Husbands, Chris; Breshears, Jennell; Ndetan, Harrison; Rupert, Ronald

2008-03-01

Vinyl chiropractic tables have been found to harbor pathogenic bacteria, but wiping with a simple disinfection agent can significantly reduce the risk of bacteria. The aim of this study was to assess the presence of microbes and other allergens or pathogens on cloth chiropractic tables. Cloth-covered tables in a chiropractic college teaching clinic were selected. Samples were taken from the facial piece and hand rests with RODAC plates containing nutrient agar, followed by confirmatory testing when indicated. Numerous microbacteria strains were found, including Staphylococcus aureus and Propionibacterium. Allergen-producing molds, including Candida, were also found. Cloth tables were shown to contain pathogenic microbacteria and allergens. The chiropractic profession should establish an infection control protocol relevant to treatment tables and discard use of cloth-covered treatment tables in this process.

Centrifuge: rapid and sensitive classification of metagenomic sequences.

PubMed

Kim, Daehwan; Song, Li; Breitwieser, Florian P; Salzberg, Steven L

2016-12-01

Centrifuge is a novel microbial classification engine that enables rapid, accurate, and sensitive labeling of reads and quantification of species on desktop computers. The system uses an indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.2 GB for 4078 bacterial and 200 archaeal genomes) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together, these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers. Because of its space-optimized indexing schemes, Centrifuge also makes it possible to index the entire NCBI nonredundant nucleotide sequence database (a total of 109 billion bases) with an index size of 69 GB, in contrast to k-mer-based indexing schemes, which require far more extensive space. © 2016 Kim et al.; Published by Cold Spring Harbor Laboratory Press.

Exploring cell apoptosis and senescence to understand and treat cancer: an interview with Scott Lowe

PubMed Central

2015-01-01

ABSTRACT Scott W. Lowe is currently principal investigator at the Memorial Sloan-Kettering Cancer Center. After beginning his studies in chemical engineering, he decided to take another path and became fascinated by biochemistry, genetics and molecular biology, which ultimately led to an interest in human disease, particularly cancer. During his PhD at the Massachusetts Institute of Technology (MIT), Scott had the opportunity to benefit from the exceptional mentorship of Earl Ruley, David Housman and Tyler Jacks, and contributed to elucidating how the p53 (TP53) tumor suppressor gene limits oncogenic transformation and modulates the cytotoxic response to conventional chemotherapy. This important work earned him a fellowship from the Cold Spring Harbor Laboratory, which helped to launch his independent career. Scott is now a leading scientist in the cancer field and his work has helped to shed light on mechanisms of cell apoptosis and senescence to better understand and treat cancer. In this interview, he talks about this incredible scientific journey. PMID:26512122

Mapping Neurodegenerative Disease Onset and Progression.

PubMed

Seeley, William W

2017-08-01

Brain networks have been of long-standing interest to neurodegeneration researchers, including but not limited to investigators focusing on conventional prion diseases, which are known to propagate along neural pathways. Tools for human network mapping, however, remained inadequate, limiting our understanding of human brain network architecture and preventing clinical research applications. Until recently, neuropathological studies were the only viable approach to mapping disease onset and progression in humans but required large autopsy cohorts and laborious methods for whole-brain sectioning and staining. Despite important advantages, postmortem studies cannot address in vivo, physiological, or longitudinal questions and have limited potential to explore early-stage disease except for the most common disorders. Emerging in vivo network-based neuroimaging strategies have begun to address these issues, providing data that complement the neuropathological tradition. Overall, findings to date highlight several fundamental principles of neurodegenerative disease anatomy and pathogenesis, as well as some enduring mysteries. These principles and mysteries provide a road map for future research. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

Trade secrets in life science and pharmaceutical companies.

PubMed

Nealey, Tara; Daignault, Ronald M; Cai, Yu

2014-11-20

Trade secret protection arises under state common law and state statutes. In general, a trade secret is information that is not generally known to the public and is maintained as a secret, and it provides a competitive advantage or economic benefit to the trade secret holder. Trade secrets can be worth tens or hundreds of millions of dollars, and damage awards in trade secret litigation have been high; often, there is a lot at stake. Obtaining a trade secret through "improper means" is misappropriation. If the alleged trade secret, however, was developed independently, known publicly, or not maintained as a secret, then those defenses may successfully overcome a claim for trade secret misappropriation. With today's interconnectedness in the biotechnology and pharmaceutical fields, more collaborations, joint ventures, and outsourcing arrangements among firms, and increased mobility of employees' careers, life science companies need to not only understand how to protect their trade secrets, but also know how to defend against a claim for trade secret theft. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans.

PubMed

Cenik, Can; Cenik, Elif Sarinay; Byeon, Gun W; Grubert, Fabian; Candille, Sophie I; Spacek, Damek; Alsallakh, Bilal; Tilgner, Hagen; Araya, Carlos L; Tang, Hua; Ricci, Emiliano; Snyder, Michael P

2015-11-01

Elucidating the consequences of genetic differences between humans is essential for understanding phenotypic diversity and personalized medicine. Although variation in RNA levels, transcription factor binding, and chromatin have been explored, little is known about global variation in translation and its genetic determinants. We used ribosome profiling, RNA sequencing, and mass spectrometry to perform an integrated analysis in lymphoblastoid cell lines from a diverse group of individuals. We find significant differences in RNA, translation, and protein levels suggesting diverse mechanisms of personalized gene expression control. Combined analysis of RNA expression and ribosome occupancy improves the identification of individual protein level differences. Finally, we identify genetic differences that specifically modulate ribosome occupancy--many of these differences lie close to start codons and upstream ORFs. Our results reveal a new level of gene expression variation among humans and indicate that genetic variants can cause changes in protein levels through effects on translation. © 2015 Cenik et al.; Published by Cold Spring Harbor Laboratory Press.

Long-range RNA pairings contribute to mutually exclusive splicing.

PubMed

Yue, Yuan; Yang, Yun; Dai, Lanzhi; Cao, Guozheng; Chen, Ran; Hong, Weiling; Liu, Baoping; Shi, Yang; Meng, Yijun; Shi, Feng; Xiao, Mu; Jin, Yongfeng

2016-01-01

Mutually exclusive splicing is an important means of increasing the protein repertoire, by which the Down's syndrome cell adhesion molecule (Dscam) gene potentially generates 38,016 different isoforms in Drosophila melanogaster. However, the regulatory mechanisms remain obscure due to the complexity of the Dscam exon cluster. Here, we reveal a molecular model for the regulation of the mutually exclusive splicing of the serpent pre-mRNA based on competition between upstream and downstream RNA pairings. Such dual RNA pairings confer fine tuning of the inclusion of alternative exons. Moreover, we demonstrate that the splicing outcome of alternative exons is mediated in relative pairing strength-correlated mode. Combined comparative genomics analysis and experimental evidence revealed similar bidirectional structural architectures in exon clusters 4 and 9 of the Dscam gene. Our findings provide a novel mechanistic framework for the regulation of mutually exclusive splicing and may offer potentially applicable insights into long-range RNA-RNA interactions in gene regulatory networks. © 2015 Yue et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Principles of quasi-equivalence and Euclidean geometry govern the assembly of cubic and dodecahedral cores of pyruvate dehydrogenase complexes.

PubMed

Izard, T; Aevarsson, A; Allen, M D; Westphal, A H; Perham, R N; de Kok, A; Hol, W G

1999-02-16

The pyruvate dehydrogenase multienzyme complex (Mr of 5-10 million) is assembled around a structural core formed of multiple copies of dihydrolipoyl acetyltransferase (E2p), which exhibits the shape of either a cube or a dodecahedron, depending on the source. The crystal structures of the 60-meric dihydrolipoyl acyltransferase cores of Bacillus stearothermophilus and Enterococcus faecalis pyruvate dehydrogenase complexes were determined and revealed a remarkably hollow dodecahedron with an outer diameter of approximately 237 A, 12 large openings of approximately 52 A diameter across the fivefold axes, and an inner cavity with a diameter of approximately 118 A. Comparison of cubic and dodecahedral E2p assemblies shows that combining the principles of quasi-equivalence formulated by Caspar and Klug [Caspar, D. L. & Klug, A. (1962) Cold Spring Harbor Symp. Quant. Biol. 27, 1-4] with strict Euclidean geometric considerations results in predictions of the major features of the E2p dodecahedron matching the observed features almost exactly.

Oral Therapies for Multiple Sclerosis.

PubMed

Faissner, Simon; Gold, Ralf

2018-03-02

Multiple sclerosis treatment faces tremendous changes owing to the approval of new medications, some of which are available as oral formulations. Until now, the four orally available medications, fingolimod, dimethylfumarate (BG-12), teriflunomide, and cladribine have received market authorization, whereas laquinimod is still under development. Fingolimod is a sphingosine-1-phosphate inhibitor, which is typically used as escalation therapy and leads to up to 60% reduction of the annualized relapse rate, but might also have neuroprotective properties. In addition, there are three more specific S1P agonists in late stages of development: siponimod, ponesimod, and ozanimod. Dimethylfumarate has immunomodulatory and cytoprotective functions and is used as baseline therapy. Teriflunomide, the active metabolite of the rheumatoid arthritis medication leflunomide, targets the dihydroorotate dehydrogenase, thus inhibiting the proliferation of lymphocytes by depletion of pyrimidines. Here we will review the mechanisms of action, clinical trial data, as well as data about safety and tolerability of the compounds. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

Responses to Cytokines and Interferons that Depend upon JAKs and STATs.

PubMed

Stark, George R; Cheon, HyeonJoo; Wang, Yuxin

2018-01-02

Many cytokines and all interferons activate members of a small family of kinases (the Janus kinases [JAKs]) and a slightly larger family of transcription factors (the signal transducers and activators of transcription [STATs]), which are essential components of pathways that induce the expression of specific sets of genes in susceptible cells. JAK-STAT pathways are required for many innate and acquired immune responses, and the activities of these pathways must be finely regulated to avoid major immune dysfunctions. Regulation is achieved through mechanisms that include the activation or induction of potent negative regulatory proteins, posttranslational modification of the STATs, and other modulatory effects that are cell-type specific. Mutations of JAKs and STATs can result in gains or losses of function and can predispose affected individuals to autoimmune disease, susceptibility to a variety of infections, or cancer. Here we review recent developments in the biochemistry, genetics, and biology of JAKs and STATs. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

Clinical characteristics and current treatment of glaucoma.

PubMed

Cohen, Laura P; Pasquale, Louis R

2014-06-02

Glaucoma is a neurodegenerative disorder in which degenerating retinal ganglion cells (RGC) produce significant visual disability. Clinically, glaucoma refers to an array of conditions associated with variably elevated intraocular pressure (IOP) that contributes to RGC loss via mechanical stress, vascular abnormalities, and other mechanisms, such as immune phenomena. The clinical diagnosis of glaucoma requires assessment of the ocular anterior segment with slit lamp biomicroscopy, which allows the clinician to recognize signs of conditions that can produce elevated IOP. After measurement of IOP, a specialized prismatic lens called a gonioscope is used to determine whether the angle is physically open or closed. The structural manifestation of RGC loss is optic nerve head atrophy and excavation of the neuroretinal rim tissue. Treatment is guided by addressing secondary causes for elevated IOP (such as inflammation, infection, and ischemia) whenever possible. Subsequently, a variety of medical, laser, and surgical options are used to achieve a target IOP. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

The neomuran revolution and phagotrophic origin of eukaryotes and cilia in the light of intracellular coevolution and a revised tree of life.

PubMed

Cavalier-Smith, Thomas

2014-09-02

Three kinds of cells exist with increasingly complex membrane-protein targeting: Unibacteria (Archaebacteria, Posibacteria) with one cytoplasmic membrane (CM); Negibacteria with a two-membrane envelope (inner CM; outer membrane [OM]); eukaryotes with a plasma membrane and topologically distinct endomembranes and peroxisomes. I combine evidence from multigene trees, palaeontology, and cell biology to show that eukaryotes and archaebacteria are sisters, forming the clade neomura that evolved ~1.2 Gy ago from a posibacterium, whose DNA segregation and cell division were destabilized by murein wall loss and rescued by the evolving novel neomuran endoskeleton, histones, cytokinesis, and glycoproteins. Phagotrophy then induced coevolving serial major changes making eukaryote cells, culminating in two dissimilar cilia via a novel gliding-fishing-swimming scenario. I transfer Chloroflexi to Posibacteria, root the universal tree between them and Heliobacteria, and argue that Negibacteria are a clade whose OM, evolving in a green posibacterium, was never lost. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

MRAS: A Close but Understudied Member of the RAS Family.

PubMed

Young, Lucy C; Rodriguez-Viciana, Pablo

2018-01-08

MRAS is the closest relative to the classical RAS oncoproteins and shares most regulatory and effector interactions. However, it also has unique functions, including its ability to function as a phosphatase regulatory subunit when in complex with SHOC2 and protein phosphatase 1 (PP1). This phosphatase complex regulates a crucial step in the activation cycle of RAF kinases and provides a key coordinate input required for efficient ERK pathway activation and transformation by RAS. MRAS mutations rarely occur in cancer but deregulated expression may play a role in tumorigenesis in some settings. Activating mutations in MRAS (as well as SHOC2 and PP1) do occur in the RASopathy Noonan syndrome, underscoring a key role for MRAS within the RAS-ERK pathway. MRAS also has unique roles in cell migration and differentiation and has properties consistent with a key role in the regulation of cell polarity. Further investigations should shed light on what remains a relatively understudied RAS family member. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

Alternative Watson-Crick Synthetic Genetic Systems.

PubMed

Benner, Steven A; Karalkar, Nilesh B; Hoshika, Shuichi; Laos, Roberto; Shaw, Ryan W; Matsuura, Mariko; Fajardo, Diego; Moussatche, Patricia

2016-11-01

In its "grand challenge" format in chemistry, "synthesis" as an activity sets out a goal that is substantially beyond current theoretical and technological capabilities. In pursuit of this goal, scientists are forced across uncharted territory, where they must answer unscripted questions and solve unscripted problems, creating new theories and new technologies in ways that would not be created by hypothesis-directed research. Thus, synthesis drives discovery and paradigm changes in ways that analysis cannot. Described here are the products that have arisen so far through the pursuit of one grand challenge in synthetic biology: Recreate the genetics, catalysis, evolution, and adaptation that we value in life, but using genetic and catalytic biopolymers different from those that have been delivered to us by natural history on Earth. The outcomes in technology include new diagnostic tools that have helped personalize the care of hundreds of thousands of patients worldwide. In science, the effort has generated a fundamentally different view of DNA, RNA, and how they work. Copyright © 2016 Cold Spring Harbor Laboratory Press; all rights reserved.

Mutations in genes encoding condensin complex proteins cause microcephaly through decatenation failure at mitosis.

PubMed

Martin, Carol-Anne; Murray, Jennie E; Carroll, Paula; Leitch, Andrea; Mackenzie, Karen J; Halachev, Mihail; Fetit, Ahmed E; Keith, Charlotte; Bicknell, Louise S; Fluteau, Adeline; Gautier, Philippe; Hall, Emma A; Joss, Shelagh; Soares, Gabriela; Silva, João; Bober, Michael B; Duker, Angela; Wise, Carol A; Quigley, Alan J; Phadke, Shubha R; Wood, Andrew J; Vagnarelli, Paola; Jackson, Andrew P

2016-10-01

Compaction of chromosomes is essential for accurate segregation of the genome during mitosis. In vertebrates, two condensin complexes ensure timely chromosome condensation, sister chromatid disentanglement, and maintenance of mitotic chromosome structure. Here, we report that biallelic mutations in NCAPD2, NCAPH, or NCAPD3, encoding subunits of these complexes, cause microcephaly. In addition, hypomorphic Ncaph2 mice have significantly reduced brain size, with frequent anaphase chromatin bridge formation observed in apical neural progenitors during neurogenesis. Such DNA bridges also arise in condensin-deficient patient cells, where they are the consequence of failed sister chromatid disentanglement during chromosome compaction. This results in chromosome segregation errors, leading to micronucleus formation and increased aneuploidy in daughter cells. These findings establish "condensinopathies" as microcephalic disorders, with decatenation failure as an additional disease mechanism for microcephaly, implicating mitotic chromosome condensation as a key process ensuring mammalian cerebral cortex size. © 2016 Martin et al.; Published by Cold Spring Harbor Laboratory Press.

FANCJ suppresses microsatellite instability and lymphomagenesis independent of the Fanconi anemia pathway.

PubMed

Matsuzaki, Kenichiro; Borel, Valerie; Adelman, Carrie A; Schindler, Detlev; Boulton, Simon J

2015-12-15

Microsatellites are short tandem repeat sequences that are highly prone to expansion/contraction due to their propensity to form non-B-form DNA structures, which hinder DNA polymerases and provoke template slippage. Although error correction by mismatch repair plays a key role in preventing microsatellite instability (MSI), which is a hallmark of Lynch syndrome, activities must also exist that unwind secondary structures to facilitate replication fidelity. Here, we report that Fancj helicase-deficient mice, while phenotypically resembling Fanconi anemia (FA), are also hypersensitive to replication inhibitors and predisposed to lymphoma. Whereas metabolism of G4-DNA structures is largely unaffected in Fancj(-/-) mice, high levels of spontaneous MSI occur, which is exacerbated by replication inhibition. In contrast, MSI is not observed in Fancd2(-/-) mice but is prevalent in human FA-J patients. Together, these data implicate FANCJ as a key factor required to counteract MSI, which is functionally distinct from its role in the FA pathway. © 2015 Matsuzaki et al.; Published by Cold Spring Harbor Laboratory Press.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Breo, D.L.

The best-selling The Double Helix, published 20 years ago, describes the events that had led to the discovery by James Watson and Francis Crick in 1953 of the structure of deoxyribonucleic acid (DNA), the building block of genes and heredity. At the time, the 25-year-old Watson was widely perceived as arrogant, brash, gawky, and intense. Subsequent events did little to change that impression. Today, at age 61, James Dewey Watson is still an angry young man. As director since 1968 of the Cold Spring Harbor Laboratory on Long Island, NY, and as director since 1988 of the National Center formore » Human Genome Research at the National Institutes of Health (NIH), he is coordinating the attempt to decipher biology's deepest secrets: the mapping, sequencing, and defining of the estimated 50,000 to 100,000 human genes arranged over the 23 pairs of chromosomes. The results, expected by early next century, may reveal the chemical script of life and help solve the riddles of inherited genetic diseases and certain cancers.« less

Protein and DNA modifications: evolutionary imprints of bacterial biochemical diversification and geochemistry on the provenance of eukaryotic epigenetics.

PubMed

Aravind, L; Burroughs, A Maxwell; Zhang, Dapeng; Iyer, Lakshminarayan M

2014-07-01

Epigenetic information, which plays a major role in eukaryotic biology, is transmitted by covalent modifications of nuclear proteins (e.g., histones) and DNA, along with poorly understood processes involving cytoplasmic/secreted proteins and RNAs. The origin of eukaryotes was accompanied by emergence of a highly developed biochemical apparatus for encoding, resetting, and reading covalent epigenetic marks in proteins such as histones and tubulins. The provenance of this apparatus remained unclear until recently. Developments in comparative genomics show that key components of eukaryotic epigenetics emerged as part of the extensive biochemical innovation of secondary metabolism and intergenomic/interorganismal conflict systems in prokaryotes, particularly bacteria. These supplied not only enzymatic components for encoding and removing epigenetic modifications, but also readers of some of these marks. Diversification of these prokaryotic systems and subsequently eukaryotic epigenetics appear to have been considerably influenced by the great oxygenation event in the Earth's history. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

Wild birds and urban ecology of ticks and tick-borne pathogens, Chicago, Illinois, USA, 2005-2010.

PubMed

Hamer, Sarah A; Goldberg, Tony L; Kitron, Uriel D; Brawn, Jeffrey D; Anderson, Tavis K; Loss, Scott R; Walker, Edward D; Hamer, Gabriel L

2012-10-01

Bird-facilitated introduction of ticks and associated pathogens is postulated to promote invasion of tick-borne zoonotic diseases into urban areas. Results of a longitudinal study conducted in suburban Chicago, Illinois, USA, during 2005-2010 show that 1.6% of 6,180 wild birds captured in mist nets harbored ticks. Tick species in order of abundance were Haemaphysalis leporispalustris, Ixodes dentatus, and I. scapularis, but 2 neotropical tick species of the genus Amblyomma were sampled during the spring migration. I. scapularis ticks were absent at the beginning of the study but constituted the majority of ticks by study end and were found predominantly on birds captured in areas designated as urban green spaces. Of 120 ticks, 5 were infected with Borrelia burgdorferi, spanning 3 ribotypes, but none were infected with Anaplasma phagocytophilum. Results allow inferences about propagule pressure for introduction of tick-borne diseases and emphasize the large sample sizes required to estimate this pressure.

Wild Birds and Urban Ecology of Ticks and Tick-borne Pathogens, Chicago, Illinois, USA, 2005–2010

PubMed Central

Goldberg, Tony L.; Kitron, Uriel D.; Brawn, Jeffrey D.; Anderson, Tavis K.; Loss, Scott R.; Walker, Edward D.; Hamer, Gabriel L.

2012-01-01

Bird-facilitated introduction of ticks and associated pathogens is postulated to promote invasion of tick-borne zoonotic diseases into urban areas. Results of a longitudinal study conducted in suburban Chicago, Illinois, USA, during 2005–2010 show that 1.6% of 6,180 wild birds captured in mist nets harbored ticks. Tick species in order of abundance were Haemaphysalis leporispalustris, Ixodes dentatus, and I. scapularis, but 2 neotropical tick species of the genus Amblyomma were sampled during the spring migration. I. scapularis ticks were absent at the beginning of the study but constituted the majority of ticks by study end and were found predominantly on birds captured in areas designated as urban green spaces. Of 120 ticks, 5 were infected with Borrelia burgdorferi, spanning 3 ribotypes, but none were infected with Anaplasma phagocytophilum. Results allow inferences about propagule pressure for introduction of tick-borne diseases and emphasize the large sample sizes required to estimate this pressure. PMID:23017244

Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells.

PubMed

Ju, Young Seok; Tubio, Jose M C; Mifsud, William; Fu, Beiyuan; Davies, Helen R; Ramakrishna, Manasa; Li, Yilong; Yates, Lucy; Gundem, Gunes; Tarpey, Patrick S; Behjati, Sam; Papaemmanuil, Elli; Martin, Sancha; Fullam, Anthony; Gerstung, Moritz; Nangalia, Jyoti; Green, Anthony R; Caldas, Carlos; Borg, Åke; Tutt, Andrew; Lee, Ming Ta Michael; van't Veer, Laura J; Tan, Benita K T; Aparicio, Samuel; Span, Paul N; Martens, John W M; Knappskog, Stian; Vincent-Salomon, Anne; Børresen-Dale, Anne-Lise; Eyfjörd, Jórunn Erla; Myklebost, Ola; Flanagan, Adrienne M; Foster, Christopher; Neal, David E; Cooper, Colin; Eeles, Rosalind; Bova, Steven G; Lakhani, Sunil R; Desmedt, Christine; Thomas, Gilles; Richardson, Andrea L; Purdie, Colin A; Thompson, Alastair M; McDermott, Ultan; Yang, Fengtang; Nik-Zainal, Serena; Campbell, Peter J; Stratton, Michael R

2015-06-01

Mitochondrial genomes are separated from the nuclear genome for most of the cell cycle by the nuclear double membrane, intervening cytoplasm, and the mitochondrial double membrane. Despite these physical barriers, we show that somatically acquired mitochondrial-nuclear genome fusion sequences are present in cancer cells. Most occur in conjunction with intranuclear genomic rearrangements, and the features of the fusion fragments indicate that nonhomologous end joining and/or replication-dependent DNA double-strand break repair are the dominant mechanisms involved. Remarkably, mitochondrial-nuclear genome fusions occur at a similar rate per base pair of DNA as interchromosomal nuclear rearrangements, indicating the presence of a high frequency of contact between mitochondrial and nuclear DNA in some somatic cells. Transmission of mitochondrial DNA to the nuclear genome occurs in neoplastically transformed cells, but we do not exclude the possibility that some mitochondrial-nuclear DNA fusions observed in cancer occurred years earlier in normal somatic cells. © 2015 Ju et al.; Published by Cold Spring Harbor Laboratory Press.

The relationship between sexual selection and sexual conflict.

PubMed

Kokko, Hanna; Jennions, Michael D

2014-07-18

Evolutionary conflicts of interest arise whenever genetically different individuals interact and their routes to fitness maximization differ. Sexual selection favors traits that increase an individual's competitiveness to acquire mates and fertilizations. Sexual conflict occurs if an individual of sex A's relative fitness would increase if it had a "tool" that could alter what an individual of sex B does (including the parental genes transferred), at a cost to B's fitness. This definition clarifies several issues: Conflict is very common and, although it extends outside traits under sexual selection, sexual selection is a ready source of sexual conflict. Sexual conflict and sexual selection should not be presented as alternative explanations for trait evolution. Conflict is closely linked to the concept of a lag load, which is context-dependent and sex-specific. This makes it possible to ask if one sex can "win." We expect higher population fitness if females win. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

Trafficking Ion Transporters to the Apical Membrane of Polarized Intestinal Enterocytes.

PubMed

Engevik, Amy Christine; Goldenring, James R

2018-01-02

Epithelial cells lining the gastrointestinal tract require distinct apical and basolateral domains to function properly. Trafficking and insertion of enzymes and transporters into the apical brush border of intestinal epithelial cells is essential for effective digestion and absorption of nutrients. Specific critical ion transporters are delivered to the apical brush border to facilitate fluid and electrolyte uptake. Maintenance of these apical transporters requires both targeted delivery and regulated membrane recycling. Examination of altered apical trafficking in patients with Microvillus Inclusion disease caused by inactivating mutations in MYO5B has led to insights into the regulation of apical trafficking by elements of the apical recycling system. Modeling of MYO5B loss in cell culture and animal models has led to recognition of Rab11a and Rab8a as critical regulators of apical brush border function. All of these studies show the importance of apical membrane trafficking dynamics in maintenance of polarized epithelial cell function. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

Identification of hair shaft progenitors that create a niche for hair pigmentation.

PubMed

Liao, Chung-Ping; Booker, Reid C; Morrison, Sean J; Le, Lu Q

2017-04-15

Hair differentiates from follicle stem cells through progenitor cells in the matrix. In contrast to stem cells in the bulge, the identities of the progenitors and the mechanisms by which they regulate hair shaft components are poorly understood. Hair is also pigmented by melanocytes in the follicle. However, the niche that regulates follicular melanocytes is not well characterized. Here, we report the identification of hair shaft progenitors in the matrix that are differentiated from follicular epithelial cells expressing transcription factor KROX20. Depletion of Krox20 lineage cells results in arrest of hair growth, confirming the critical role of KROX20 + cells as antecedents of structural cells found in hair. Expression of stem cell factor (SCF) by these cells is necessary for the maintenance of differentiated melanocytes and for hair pigmentation. Our findings reveal the identities of hair matrix progenitors that regulate hair growth and pigmentation, partly by creating an SCF-dependent niche for follicular melanocytes. © 2017 Liao et al.; Published by Cold Spring Harbor Laboratory Press.

Clinical characteristics and current therapies for inherited retinal degenerations.

PubMed

Sahel, José-Alain; Marazova, Katia; Audo, Isabelle

2014-10-16

Inherited retinal degenerations (IRDs) encompass a large group of clinically and genetically heterogeneous diseases that affect approximately 1 in 3000 people (>2 million people worldwide) (Bessant DA, Ali RR, Bhattacharya SS. 2001. Molecular genetics and prospects for therapy of the inherited retinal dystrophies. Curr Opin Genet Dev 11: 307-316.). IRDs may be inherited as Mendelian traits or through mitochondrial DNA, and may affect the entire retina (e.g., rod-cone dystrophy, also known as retinitis pigmentosa, cone dystrophy, cone-rod dystrophy, choroideremia, Usher syndrome, and Bardet-Bidel syndrome) or be restricted to the macula (e.g., Stargardt disease, Best disease, and Sorsby fundus dystrophy), ultimately leading to blindness. IRDs are a major cause of severe vision loss, with profound impact on patients and society. Although IRDs remain untreatable today, significant progress toward therapeutic strategies for IRDs has marked the past two decades. This progress has been based on better understanding of the pathophysiological pathways of these diseases and on technological advances. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

Microbial Communities and Chemosynthesis in Yellowstone Lake Sublacustrine Hydrothermal Vent Waters

PubMed Central

Yang, Tingting; Lyons, Shawn; Aguilar, Carmen; Cuhel, Russell; Teske, Andreas

2011-01-01

Five sublacustrine thermal spring locations from 1 to 109 m water depth in Yellowstone Lake were surveyed by 16S ribosomal RNA gene sequencing in relation to their chemical composition and dark CO2 fixation rates. They harbor distinct chemosynthetic bacterial communities, depending on temperature (16–110°C) and electron donor supply (H2S <1 to >100 μM; NH3 <0.5 to >10 μM). Members of the Aquificales, most closely affiliated with the genus Sulfurihydrogenibium, are the most frequently recovered bacterial 16S rRNA gene phylotypes in the hottest samples; the detection of these thermophilic sulfur-oxidizing autotrophs coincided with maximal dark CO2 fixation rates reaching near 9 μM C h−1 at temperatures of 50–60°C. Vents at lower temperatures yielded mostly phylotypes related to the mesophilic gammaproteobacterial sulfur oxidizer Thiovirga. In contrast, cool vent water with low chemosynthetic activity yielded predominantly phylotypes related to freshwater Actinobacterial clusters with a cosmopolitan distribution. PMID:21716640

Different requirements of functional telomeres in neural stem cells and terminally differentiated neurons.

PubMed

Lobanova, Anastasia; She, Robert; Pieraut, Simon; Clapp, Charlie; Maximov, Anton; Denchi, Eros Lazzerini

2017-04-01

Telomeres have been studied extensively in peripheral tissues, but their relevance in the nervous system remains poorly understood. Here, we examine the roles of telomeres at distinct stages of murine brain development by using lineage-specific genetic ablation of TRF2, an essential component of the shelterin complex that protects chromosome ends from the DNA damage response machinery. We found that functional telomeres are required for embryonic and adult neurogenesis, but their uncapping has surprisingly no detectable consequences on terminally differentiated neurons. Conditional knockout of TRF2 in post-mitotic immature neurons had virtually no detectable effect on circuit assembly, neuronal gene expression, and the behavior of adult animals despite triggering massive end-to-end chromosome fusions across the brain. These results suggest that telomeres are dispensable in terminally differentiated neurons and provide mechanistic insight into cognitive abnormalities associated with aberrant telomere length in humans. © 2017 Lobanova et al.; Published by Cold Spring Harbor Laboratory Press.

Detecting Single-Nucleotide Substitutions Induced by Genome Editing.

PubMed

Miyaoka, Yuichiro; Chan, Amanda H; Conklin, Bruce R

2016-08-01

The detection of genome editing is critical in evaluating genome-editing tools or conditions, but it is not an easy task to detect genome-editing events-especially single-nucleotide substitutions-without a surrogate marker. Here we introduce a procedure that significantly contributes to the advancement of genome-editing technologies. It uses droplet digital polymerase chain reaction (ddPCR) and allele-specific hydrolysis probes to detect single-nucleotide substitutions generated by genome editing (via homology-directed repair, or HDR). HDR events that introduce substitutions using donor DNA are generally infrequent, even with genome-editing tools, and the outcome is only one base pair difference in 3 billion base pairs of the human genome. This task is particularly difficult in induced pluripotent stem (iPS) cells, in which editing events can be very rare. Therefore, the technological advances described here have implications for therapeutic genome editing and experimental approaches to disease modeling with iPS cells. © 2016 Cold Spring Harbor Laboratory Press.

Growing Bacteriophage M13 in Liquid Culture.

PubMed

Green, Michael R; Sambrook, Joseph

2017-11-01

Stocks of bacteriophage M13 are usually grown in liquid culture. The infected bacteria do not lyse but, instead, grow at a slower than normal rate to form a dilute suspension. The inoculum of bacteriophage is almost always a freshly picked plaque or a suspension of bacteriophage particles obtained from a single plaque, as described here. Infected cells contain up to 200 copies of double-stranded, replicative-form DNA and extrude several hundred bacteriophage particles per generation. Thus, a 1-mL culture of infected cells can produce enough double-stranded viral DNA (1-2 mg) for restriction mapping and recovery of cloned DNA inserts and sufficient single-stranded DNA (∼5-10 mg) for site-directed mutagenesis, DNA sequencing, or synthesis of radiolabeled probes. The titer of bacteriophages in the supernatant from infected cells is so high (∼10 12 pfu/mL) that a small aliquot serves as a permanent stock of the starting plaque. © 2017 Cold Spring Harbor Laboratory Press.

A cellular, molecular, and pharmacological basis for appendage regeneration in mice.

PubMed

Leung, Thomas H; Snyder, Emily R; Liu, Yinghua; Wang, Jing; Kim, Seung K

2015-10-15

Regenerative medicine aims to restore normal tissue architecture and function. However, the basis of tissue regeneration in mammalian solid organs remains undefined. Remarkably, mice lacking p21 fully regenerate injured ears without discernable scarring. Here we show that, in wild-type mice following tissue injury, stromal-derived factor-1 (Sdf1) is up-regulated in the wound epidermis and recruits Cxcr4-expressing leukocytes to the injury site. In p21-deficient mice, Sdf1 up-regulation and the subsequent recruitment of Cxcr4-expressing leukocytes are significantly diminished, thereby permitting scarless appendage regeneration. Lineage tracing demonstrates that this regeneration derives from fate-restricted progenitor cells. Pharmacological or genetic disruption of Sdf1-Cxcr4 signaling enhances tissue repair, including full reconstitution of tissue architecture and all cell types. Our findings identify signaling and cellular mechanisms underlying appendage regeneration in mice and suggest new therapeutic approaches for regenerative medicine. © 2015 Leung et al.; Published by Cold Spring Harbor Laboratory Press.

Actin-Based Adhesion Modules Mediate Cell Interactions with the Extracellular Matrix and Neighboring Cells.

PubMed

Bachir, Alexia I; Horwitz, Alan Rick; Nelson, W James; Bianchini, Julie M

2017-07-05

Cell adhesions link cells to the extracellular matrix (ECM) and to each other and depend on interactions with the actin cytoskeleton. Both cell-ECM and cell-cell adhesion sites contain discrete, yet overlapping, functional modules. These modules establish physical associations with the actin cytoskeleton, locally modulate actin organization and dynamics, and trigger intracellular signaling pathways. Interplay between these modules generates distinct actin architectures that underlie different stages, types, and functions of cell-ECM and cell-cell adhesions. Actomyosin contractility is required to generate mature, stable adhesions, as well as to sense and translate the mechanical properties of the cellular environment into changes in cell organization and behavior. Here, we review the organization and function of different adhesion modules and how they interact with the actin cytoskeleton. We highlight the molecular mechanisms of mechanotransduction in adhesions and how adhesion molecules mediate cross talk between cell-ECM and cell-cell adhesion sites. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

Structural Basis of Intracellular TGF-β Signaling: Receptors and Smads.

PubMed

Chaikuad, Apirat; Bullock, Alex N

2016-11-01

Stimulation of the transforming growth factor β (TGF-β) family receptors activates an intracellular phosphorylation-dependent signaling cascade that culminates in Smad transcriptional activation and turnover. Structural studies have identified a number of allosteric mechanisms that control the localization, conformation, and oligomeric state of the receptors and Smads. Such mechanisms dictate the ordered binding of substrate and adaptor proteins that determine the directionality of the signaling process. Activation of the pathway has been illustrated by the various structures of the receptor-activated Smads (R-Smads) with SARA, Smad4, and YAP, respectively, whereas mechanisms of down-regulation have been elucidated by the structural complexes of FKBP12, Ski, and Smurf1. Interesting parallels have emerged between the R-Smads and the Forkhead-associated (FHA) and interferon regulatory factor (IRF)-associated domains, as well as the Hippo pathway. However, important questions remain as to the mechanism of Smad-independent signaling. Copyright © 2016 Cold Spring Harbor Laboratory Press; all rights reserved.

Protein-Fragment Complementation Assays for Large-Scale Analysis, Functional Dissection, and Spatiotemporal Dynamic Studies of Protein-Protein Interactions in Living Cells.

PubMed

Michnick, Stephen W; Landry, Christian R; Levy, Emmanuel D; Diss, Guillaume; Ear, Po Hien; Kowarzyk, Jacqueline; Malleshaiah, Mohan K; Messier, Vincent; Tchekanda, Emmanuelle

2016-11-01

Protein-fragment complementation assays (PCAs) comprise a family of assays that can be used to study protein-protein interactions (PPIs), conformation changes, and protein complex dimensions. We developed PCAs to provide simple and direct methods for the study of PPIs in any living cell, subcellular compartments or membranes, multicellular organisms, or in vitro. Because they are complete assays, requiring no cell-specific components other than reporter fragments, they can be applied in any context. PCAs provide a general strategy for the detection of proteins expressed at endogenous levels within appropriate subcellular compartments and with normal posttranslational modifications, in virtually any cell type or organism under any conditions. Here we introduce a number of applications of PCAs in budding yeast, Saccharomyces cerevisiae These applications represent the full range of PPI characteristics that might be studied, from simple detection on a large scale to visualization of spatiotemporal dynamics. © 2016 Cold Spring Harbor Laboratory Press.

A recent bottleneck of Y chromosome diversity coincides with a global change in culture.

PubMed

Karmin, Monika; Saag, Lauri; Vicente, Mário; Wilson Sayres, Melissa A; Järve, Mari; Talas, Ulvi Gerst; Rootsi, Siiri; Ilumäe, Anne-Mai; Mägi, Reedik; Mitt, Mario; Pagani, Luca; Puurand, Tarmo; Faltyskova, Zuzana; Clemente, Florian; Cardona, Alexia; Metspalu, Ene; Sahakyan, Hovhannes; Yunusbayev, Bayazit; Hudjashov, Georgi; DeGiorgio, Michael; Loogväli, Eva-Liis; Eichstaedt, Christina; Eelmets, Mikk; Chaubey, Gyaneshwer; Tambets, Kristiina; Litvinov, Sergei; Mormina, Maru; Xue, Yali; Ayub, Qasim; Zoraqi, Grigor; Korneliussen, Thorfinn Sand; Akhatova, Farida; Lachance, Joseph; Tishkoff, Sarah; Momynaliev, Kuvat; Ricaut, François-Xavier; Kusuma, Pradiptajati; Razafindrazaka, Harilanto; Pierron, Denis; Cox, Murray P; Sultana, Gazi Nurun Nahar; Willerslev, Rane; Muller, Craig; Westaway, Michael; Lambert, David; Skaro, Vedrana; Kovačevic, Lejla; Turdikulova, Shahlo; Dalimova, Dilbar; Khusainova, Rita; Trofimova, Natalya; Akhmetova, Vita; Khidiyatova, Irina; Lichman, Daria V; Isakova, Jainagul; Pocheshkhova, Elvira; Sabitov, Zhaxylyk; Barashkov, Nikolay A; Nymadawa, Pagbajabyn; Mihailov, Evelin; Seng, Joseph Wee Tien; Evseeva, Irina; Migliano, Andrea Bamberg; Abdullah, Syafiq; Andriadze, George; Primorac, Dragan; Atramentova, Lubov; Utevska, Olga; Yepiskoposyan, Levon; Marjanovic, Damir; Kushniarevich, Alena; Behar, Doron M; Gilissen, Christian; Vissers, Lisenka; Veltman, Joris A; Balanovska, Elena; Derenko, Miroslava; Malyarchuk, Boris; Metspalu, Andres; Fedorova, Sardana; Eriksson, Anders; Manica, Andrea; Mendez, Fernando L; Karafet, Tatiana M; Veeramah, Krishna R; Bradman, Neil; Hammer, Michael F; Osipova, Ludmila P; Balanovsky, Oleg; Khusnutdinova, Elza K; Johnsen, Knut; Remm, Maido; Thomas, Mark G; Tyler-Smith, Chris; Underhill, Peter A; Willerslev, Eske; Nielsen, Rasmus; Metspalu, Mait; Villems, Richard; Kivisild, Toomas

2015-04-01

It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males. © 2015 Karmin et al.; Published by Cold Spring Harbor Laboratory Press.

Application of histone modification-specific interaction domains as an alternative to antibodies.

PubMed

Kungulovski, Goran; Kycia, Ina; Tamas, Raluca; Jurkowska, Renata Z; Kudithipudi, Srikanth; Henry, Chisato; Reinhardt, Richard; Labhart, Paul; Jeltsch, Albert

2014-11-01

Post-translational modifications (PTMs) of histones constitute a major chromatin indexing mechanism, and their proper characterization is of highest biological importance. So far, PTM-specific antibodies have been the standard reagent for studying histone PTMs despite caveats such as lot-to-lot variability of specificity and binding affinity. Herein, we successfully employed naturally occurring and engineered histone modification interacting domains for detection and identification of histone PTMs and ChIP-like enrichment of different types of chromatin. Our results demonstrate that histone interacting domains are robust and highly specific reagents that can replace or complement histone modification antibodies. These domains can be produced recombinantly in Escherichia coli at low cost and constant quality. Protein design of reading domains allows for generation of novel specificities, addition of affinity tags, and preparation of PTM binding pocket variants as matching negative controls, which is not possible with antibodies. © 2014 Kungulovski et al.; Published by Cold Spring Harbor Laboratory Press.

Functional interplay between Mediator and TFIIB in preinitiation complex assembly in relation to promoter architecture.

PubMed

Eychenne, Thomas; Novikova, Elizaveta; Barrault, Marie-Bénédicte; Alibert, Olivier; Boschiero, Claire; Peixeiro, Nuno; Cornu, David; Redeker, Virginie; Kuras, Laurent; Nicolas, Pierre; Werner, Michel; Soutourina, Julie

2016-09-15

Mediator is a large coregulator complex conserved from yeast to humans and involved in many human diseases, including cancers. Together with general transcription factors, it stimulates preinitiation complex (PIC) formation and activates RNA polymerase II (Pol II) transcription. In this study, we analyzed how Mediator acts in PIC assembly using in vivo, in vitro, and in silico approaches. We revealed an essential function of the Mediator middle module exerted through its Med10 subunit, implicating a key interaction between Mediator and TFIIB. We showed that this Mediator-TFIIB link has a global role on PIC assembly genome-wide. Moreover, the amplitude of Mediator's effect on PIC formation is gene-dependent and is related to the promoter architecture in terms of TATA elements, nucleosome occupancy, and dynamics. This study thus provides mechanistic insights into the coordinated function of Mediator and TFIIB in PIC assembly in different chromatin contexts. © 2016 Eychenne et al.; Published by Cold Spring Harbor Laboratory Press.

PDGFRβ regulates craniofacial development through homodimers and functional heterodimers with PDGFRα.

PubMed

Fantauzzo, Katherine A; Soriano, Philippe

2016-11-01

Craniofacial development is a complex morphogenetic process, disruptions in which result in highly prevalent human birth defects. While platelet-derived growth factor (PDGF) receptor α (PDGFRα) has well-documented functions in this process, the role of PDGFRβ in murine craniofacial development is not well established. We demonstrate that PDGFRα and PDGFRβ are coexpressed in the craniofacial mesenchyme of mid-gestation mouse embryos and that ablation of Pdgfrb in the neural crest lineage results in increased nasal septum width, delayed palatal shelf development, and subepidermal blebbing. Furthermore, we show that the two receptors genetically interact in this lineage, as double-homozygous mutant embryos exhibit an overt facial clefting phenotype more severe than that observed in either single-mutant embryo. We reveal a physical interaction between PDGFRα and PDGFRβ in the craniofacial mesenchyme and demonstrate that the receptors form functional heterodimers with distinct signaling properties. Our studies thus uncover a novel mode of signaling for the PDGF family during vertebrate development. © 2016 Fantauzzo and Soriano; Published by Cold Spring Harbor Laboratory Press.

Systems Chronobiology: Global Analysis of Gene Regulation in a 24-Hour Periodic World.

PubMed

Mermet, Jérôme; Yeung, Jake; Naef, Felix

2017-03-01

Mammals have evolved an internal timing system, the circadian clock, which synchronizes physiology and behavior to the daily light and dark cycles of the Earth. The master clock, located in the suprachiasmatic nucleus (SCN) of the brain, takes fluctuating light input from the retina and synchronizes other tissues to the same internal rhythm. The molecular clocks that drive these circadian rhythms are ticking in nearly all cells in the body. Efforts in systems chronobiology are now being directed at understanding, on a comprehensive scale, how the circadian clock controls different layers of gene regulation to provide robust timing cues at the cellular and tissue level. In this review, we introduce some basic concepts underlying periodicity of gene regulation, and then highlight recent genome-wide investigations on the propagation of rhythms across multiple regulatory layers in mammals, all the way from chromatin conformation to protein accumulation. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

A Career at a Small Liberal Arts College.

PubMed

Punt, Jennifer

2017-10-03

A career as a tenure-track professor at a liberal arts college provides the opportunity to combine serious interests in teaching with research. The basic goals of the liberal arts institution are to educate the student broadly while encouraging mastery of a particular area of interest. Preparing for such a career requires not only a commitment to teaching but also a productive PhD and postdoctoral experience, regardless of the expectations for active research within the job. The application and interview processes require one to be informed, flexible, energetic, and clear-in writing and in speaking. Establishing an invigorating teaching and research program will allow you to balance realism and ambition as you find a way to bring the best science to the undergraduate setting. The exposure to students whose thinking is often more unfettered and creative, and to colleagues whose scholarships span many disciplines, makes a position at a liberal arts college one of the most intellectually stimulating careers available to a scientist. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

Anopheline Reproductive Biology: Impacts on Vectorial Capacity and Potential Avenues for Malaria Control.

PubMed

Mitchell, Sara N; Catteruccia, Flaminia

2017-12-01

Vectorial capacity is a mathematical approximation of the efficiency of vector-borne disease transmission, measured as the number of new infections disseminated per case per day by an insect vector. Multiple elements of mosquito biology govern their vectorial capacity, including survival, population densities, feeding preferences, and vector competence. Intriguingly, biological pathways essential to mosquito reproductive fitness directly or indirectly influence a number of these elements. Here, we explore this complex interaction, focusing on how the interplay between mating and blood feeding in female Anopheles not only shapes their reproductive success but also influences their ability to sustain Plasmodium parasite development. Central to malaria transmission, mosquito reproductive biology has recently become the focus of research strategies aimed at malaria control, and we discuss promising new methods based on the manipulation of key reproductive steps. In light of widespread resistance to all public health-approved insecticides targeting mosquito reproduction may prove crucial to the success of malaria-eradication campaigns. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

Individual differences in fear extinction and anxiety-like behavior.

PubMed

King, Gabrielle; Scott, Elliot; Graham, Bronwyn M; Richardson, Rick

2017-05-01

There is growing appreciation for the substantial individual differences in the acquisition and inhibition of aversive associations, and the insights this might give into identifying individuals particularly vulnerable to stress and psychopathology. We examined whether animals that differed in rate of extinction (i.e., Fast versus Slow) were different in their response to an acute stress in adulthood or following a chronic stress that occurred either early or later in life. We found that Slow Extinguishers had significantly poorer extinction retention than Fast Extinguishers, but an acute stressor did not differentially affect anxiety-like behavior in the two groups. Further, while exposure to chronic stress in adulthood did not impact on the extinction phenotypes or anxiety-like behavior, exposure to chronic stress early in life affected both extinction retention and anxiety-like behavior. These findings have implications for the development of a more nuanced approach to identifying those most at risk of anxiety disorders. © 2017 King et al.; Published by Cold Spring Harbor Laboratory Press.

Can genetics help us understand Indian social history?

PubMed

Thapar, Romila

2014-06-26

Attempts have been made recently to determine the identity of the so-called "Aryans" as components of the Indian population by using DNA analysis. This is largely to ascertain whether they were indigenous to India or were foreign arrivals. Similar attempts have been made to trace the origins of caste groups on the basis of varna identities and record their distribution. The results so far have been contradictory and, therefore, not of much help to social historians. There are problems in the defining of categories and the techniques of analysis. Aryan is a linguistic and cultural category and not a biological one. Caste groups have no well-defined and invariable boundaries despite marriage codes. Various other categories have been assimilated into particular castes as part of the evolution of social history on the subcontinent. A few examples of these are discussed. The problems with using DNA analysis are also touched on. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

Control of fluxes in metabolic networks.

PubMed

Basler, Georg; Nikoloski, Zoran; Larhlimi, Abdelhalim; Barabási, Albert-László; Liu, Yang-Yu

2016-07-01

Understanding the control of large-scale metabolic networks is central to biology and medicine. However, existing approaches either require specifying a cellular objective or can only be used for small networks. We introduce new coupling types describing the relations between reaction activities, and develop an efficient computational framework, which does not require any cellular objective for systematic studies of large-scale metabolism. We identify the driver reactions facilitating control of 23 metabolic networks from all kingdoms of life. We find that unicellular organisms require a smaller degree of control than multicellular organisms. Driver reactions are under complex cellular regulation in Escherichia coli, indicating their preeminent role in facilitating cellular control. In human cancer cells, driver reactions play pivotal roles in malignancy and represent potential therapeutic targets. The developed framework helps us gain insights into regulatory principles of diseases and facilitates design of engineering strategies at the interface of gene regulation, signaling, and metabolism. © 2016 Basler et al.; Published by Cold Spring Harbor Laboratory Press.

Role of the β Common (βc) Family of Cytokines in Health and Disease.

PubMed

Hercus, Timothy R; Kan, Winnie L T; Broughton, Sophie E; Tvorogov, Denis; Ramshaw, Hayley S; Sandow, Jarrod J; Nero, Tracy L; Dhagat, Urmi; Thompson, Emma J; Shing, Karen S Cheung Tung; McKenzie, Duncan R; Wilson, Nicholas J; Owczarek, Catherine M; Vairo, Gino; Nash, Andrew D; Tergaonkar, Vinay; Hughes, Timothy; Ekert, Paul G; Samuel, Michael S; Bonder, Claudine S; Grimbaldeston, Michele A; Parker, Michael W; Lopez, Angel F

2018-06-01

The β common ([βc]/CD131) family of cytokines comprises granulocyte macrophage colony-stimulating factor (GM-CSF), interleukin (IL)-3, and IL-5, all of which use βc as their key signaling receptor subunit. This is a prototypic signaling subunit-sharing cytokine family that has unveiled many biological paradigms and structural principles applicable to the IL-2, IL-4, and IL-6 receptor families, all of which also share one or more signaling subunits. Originally identified for their functions in the hematopoietic system, the βc cytokines are now known to be truly pleiotropic, impacting on multiple cell types, organs, and biological systems, and thereby controlling the balance between health and disease. This review will focus on the emerging biological roles for the βc cytokines, our progress toward understanding the mechanisms of receptor assembly and signaling, and the application of this knowledge to develop exciting new therapeutic approaches against human disease. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

Internal States and Behavioral Decision-Making: Toward an Integration of Emotion and Cognition.

PubMed

Kennedy, Ann; Asahina, Kenta; Hoopfer, Eric; Inagaki, Hidehiko; Jung, Yonil; Lee, Hyosang; Remedios, Ryan; Anderson, David J

2014-01-01

Social interactions, such as an aggressive encounter between two conspecific males or a mating encounter between a male and a female, typically progress from an initial appetitive or motivational phase, to a final consummatory phase. This progression involves both changes in the intensity of the animals' internal state of arousal or motivation and sequential changes in their behavior. How are these internal states, and their escalating intensity, encoded in the brain? Does this escalation drive the progression from the appetitive/motivational to the consummatory phase of a social interaction and, if so, how are appropriate behaviors chosen during this progression? Recent work on social behaviors in flies and mice suggests possible ways in which changes in internal state intensity during a social encounter may be encoded and coupled to appropriate behavioral decisions at appropriate phases of the interaction. These studies may have relevance to understanding how emotion states influence cognitive behavioral decisions at higher levels of brain function. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

Tracking the fear memory engram: discrete populations of neurons within amygdala, hypothalamus, and lateral septum are specifically activated by auditory fear conditioning.

PubMed

Butler, Christopher W; Wilson, Yvette M; Gunnersen, Jenny M; Murphy, Mark

2015-08-01

Memory formation is thought to occur via enhanced synaptic connectivity between populations of neurons in the brain. However, it has been difficult to localize and identify the neurons that are directly involved in the formation of any specific memory. We have previously used fos-tau-lacZ (FTL) transgenic mice to identify discrete populations of neurons in amygdala and hypothalamus, which were specifically activated by fear conditioning to a context. Here we have examined neuronal activation due to fear conditioning to a more specific auditory cue. Discrete populations of learning-specific neurons were identified in only a small number of locations in the brain, including those previously found to be activated in amygdala and hypothalamus by context fear conditioning. These populations, each containing only a relatively small number of neurons, may be directly involved in fear learning and memory. © 2015 Butler et al.; Published by Cold Spring Harbor Laboratory Press.

The landscape of genomic imprinting across diverse adult human tissues.

PubMed

Baran, Yael; Subramaniam, Meena; Biton, Anne; Tukiainen, Taru; Tsang, Emily K; Rivas, Manuel A; Pirinen, Matti; Gutierrez-Arcelus, Maria; Smith, Kevin S; Kukurba, Kim R; Zhang, Rui; Eng, Celeste; Torgerson, Dara G; Urbanek, Cydney; Li, Jin Billy; Rodriguez-Santana, Jose R; Burchard, Esteban G; Seibold, Max A; MacArthur, Daniel G; Montgomery, Stephen B; Zaitlen, Noah A; Lappalainen, Tuuli

2015-07-01

Genomic imprinting is an important regulatory mechanism that silences one of the parental copies of a gene. To systematically characterize this phenomenon, we analyze tissue specificity of imprinting from allelic expression data in 1582 primary tissue samples from 178 individuals from the Genotype-Tissue Expression (GTEx) project. We characterize imprinting in 42 genes, including both novel and previously identified genes. Tissue specificity of imprinting is widespread, and gender-specific effects are revealed in a small number of genes in muscle with stronger imprinting in males. IGF2 shows maternal expression in the brain instead of the canonical paternal expression elsewhere. Imprinting appears to have only a subtle impact on tissue-specific expression levels, with genes lacking a systematic expression difference between tissues with imprinted and biallelic expression. In summary, our systematic characterization of imprinting in adult tissues highlights variation in imprinting between genes, individuals, and tissues. © 2015 Baran et al.; Published by Cold Spring Harbor Laboratory Press.

Mechanical efficiency of two commercial lever-propulsion mechanisms for manual wheelchair locomotion.

PubMed

Lui, Jordon; MacGillivray, Megan K; Sheel, A William; Jeyasurya, Jeswin; Sadeghi, Mahsa; Sawatzky, Bonita Jean

2013-01-01

The purpose of this study was to (1) evaluate the mechanical efficiency (ME) of two commercially available lever-propulsion mechanisms for wheelchairs and (2) compare the ME of lever propulsion with hand rim propulsion within the same wheelchair. Of the two mechanisms, one contained a torsion spring while the other used a roller clutch design. We hypothesized that the torsion spring mechanism would increase the ME of propulsion due to a passive recovery stroke enabled by the mechanism. Ten nondisabled male participants with no prior manual wheeling experience performed submaximal exercise tests using both lever-propulsion mechanisms and hand rim propulsion on two different wheelchairs. Cardiopulmonary parameters including oxygen uptake (VO2), heart rate (HR), and energy expenditure (En) were determined. Total external power (Pext) was measured using a drag test protocol. ME was determined by the ratio of Pext to En. Results indicated no significant effect of lever-propulsion mechanism for all physiological measures tested. This suggests that the torsion spring did not result in a physiological benefit compared with the roller clutch mechanism. However, both lever-propulsion mechanisms showed decreased VO2 and HR and increased ME (as a function of slope) compared with hand rim propulsion (p < 0.001). This indicates that both lever-propulsion mechanisms tested are more mechanically efficient than conventional hand rim propulsion, especially when slopes are encountered.

Rise in prostate-specific antigen in men with untreated low-grade prostate cancer is slower during spring-summer.

PubMed

Vieth, R; Choo, R; Deboer, L; Danjoux, C; Morton, G C; Klotz, L

2006-01-01

To test the hypothesis that the rate of rise in prostate-specific antigen (PSA) is slower during the spring-summer than during the rest of the year, we used PSA data from a prospective single-arm cohort study of men who had been followed to characterize a watchful observation protocol with selective delayed intervention for clinically localized, low-to-intermediate grade prostate adenocarcinoma. The rate of PSA increase was calculated as the visit-to-visit slope of log (PSA) against time, from 1 calendar-quarter visit to the next. The nonparametric Friedman test confirmed differences in rate of PSA rise among the calendar quarters (P = 0.041). Post hoc analysis showed the rate of PSA increase during Q2 was significantly slower than in each one of the other calendar quarters (Q1 versus Q2, P = 0.025; Q3 versus Q2, P = 0.002; Q4 versus Q2, P = 0.013), with no differences among quarters Q1, Q3, and Q4. These results are consistent with the vitamin D hypothesis that the higher 25-hydroxyvitamin D levels associated with spring and summer have a desirable effect on prostate biology. The therapeutic implication is that vitamin D supplementation in the range of 2000 IU/d, a dose comparable to the effect of summer, can benefit men monitored for rising PSA.

The key to commercial-scale geological CO2 sequestration: Displaced fluid management

USGS Publications Warehouse

Surdam, R.C.; Jiao, Z.; Stauffer, P.; Miller, T.

2011-01-01

The Wyoming State Geological Survey has completed a thorough inventory and prioritization of all Wyoming stratigraphic units and geologic sites capable of sequestering commercial quantities of CO2 (5-15 Mt CO 2/year). This multi-year study identified the Paleozoic Tensleep/Weber Sandstone and Madison Limestone (and stratigraphic equivalent units) as the leading clastic and carbonate reservoir candidates for commercial-scale geological CO2 sequestration in Wyoming. This conclusion was based on unit thickness, overlying low permeability lithofacies, reservoir storage and continuity properties, regional distribution patterns, formation fluid chemistry characteristics, and preliminary fluid-flow modeling. This study also identified the Rock Springs Uplift in southwestern Wyoming as the most promising geological CO2 sequestration site in Wyoming and probably in any Rocky Mountain basin. The results of the WSGS CO2 geological sequestration inventory led the agency and colleagues at the UW School of Energy Resources Carbon Management Institute (CMI) to collect available geologic, petrophysical, geochemical, and geophysical data on the Rock Springs Uplift, and to build a regional 3-D geologic framework model of the Uplift. From the results of these tasks and using the FutureGen protocol, the WSGS showed that on the Rock Springs Uplift, the Weber Sandstone has sufficient pore space to sequester 18 billion tons (Gt) of CO2, and the Madison Limestone has sufficient pore space to sequester 8 Gt of CO2. ?? 2011 Published by Elsevier Ltd.

How important is hydrotherapy? Effects of dynamic action of hot spring water as a rehabilitative treatment for burn patients in Switzerland.

PubMed

Moufarrij, S; Deghayli, L; Raffoul, W; Hirt-Burri, N; Michetti, M; de Buys Roessingh, A; Norberg, M; Applegate, L A

2014-12-31

Burn rehabilitation using hydrotherapy can have multiple benefits for the burn patient. The therapy uses specific mineral enriched hot spring water and water jets with varied hydro-pressure to combat hypertrophy, inflammatory reaction signs, abnormal pigmentation, and, more specifically, redness and scarring. Standard operating procedures for burn rehabilitation have been developed and integrated into the Standard of Care at the CHUV hospital using localized hydro-mechanical stimulation of burn sites (20 minutes of alternating anatomical sites) followed by constant pressure large-bore and filiform showers targeting specific scarred areas. These therapeutic regimens are repeated daily for 2 to 3 weeks. Patients showed lasting effects from this regimen (up to 3-6 months), the results becoming permanent with more uniform skin structure, color and visco-elasticity in addition to a decrease in pruritus. The specifications of clinical protocols are described herein along with the virtues of hot spring hydro-pressure therapy for burn rehabilitation. The use of hydrotherapy, which has been a controversial topic among burn units across the world, is also discussed. In North America, hydrotherapy is defined only within the scope of in-patient wound cleansing and is thought to lead to microbial auto-contamination and bacterial resistance. In Switzerland and France the emphasis of hydrotherapy is on rehabilitation after the wound has closed.

How important is hydrotherapy? Effects of dynamic action of hot spring water as a rehabilitative treatment for burn patients in Switzerland

PubMed Central

Moufarrij, S.; Deghayli, L.; Raffoul, W.; Hirt-Burri, N.; Michetti, M.; de Buys Roessingh, A.; Norberg, M.; Applegate, L.A.

2014-01-01

Summary Burn rehabilitation using hydrotherapy can have multiple benefits for the burn patient. The therapy uses specific mineral enriched hot spring water and water jets with varied hydro-pressure to combat hypertrophy, inflammatory reaction signs, abnormal pigmentation, and, more specifically, redness and scarring. Standard operating procedures for burn rehabilitation have been developed and integrated into the Standard of Care at the CHUV hospital using localized hydro-mechanical stimulation of burn sites (20 minutes of alternating anatomical sites) followed by constant pressure large-bore and filiform showers targeting specific scarred areas. These therapeutic regimens are repeated daily for 2 to 3 weeks. Patients showed lasting effects from this regimen (up to 3-6 months), the results becoming permanent with more uniform skin structure, color and visco-elasticity in addition to a decrease in pruritus. The specifications of clinical protocols are described herein along with the virtues of hot spring hydro-pressure therapy for burn rehabilitation. The use of hydrotherapy, which has been a controversial topic among burn units across the world, is also discussed. In North America, hydrotherapy is defined only within the scope of in-patient wound cleansing and is thought to lead to microbial auto-contamination and bacterial resistance. In Switzerland and France the emphasis of hydrotherapy is on rehabilitation after the wound has closed. PMID:26336365

Seten: a tool for systematic identification and comparison of processes, phenotypes, and diseases associated with RNA-binding proteins from condition-specific CLIP-seq profiles.

PubMed

Budak, Gungor; Srivastava, Rajneesh; Janga, Sarath Chandra

2017-06-01

RNA-binding proteins (RBPs) control the regulation of gene expression in eukaryotic genomes at post-transcriptional level by binding to their cognate RNAs. Although several variants of CLIP (crosslinking and immunoprecipitation) protocols are currently available to study the global protein-RNA interaction landscape at single-nucleotide resolution in a cell, currently there are very few tools that can facilitate understanding and dissecting the functional associations of RBPs from the resulting binding maps. Here, we present Seten, a web-based and command line tool, which can identify and compare processes, phenotypes, and diseases associated with RBPs from condition-specific CLIP-seq profiles. Seten uses BED files resulting from most peak calling algorithms, which include scores reflecting the extent of binding of an RBP on the target transcript, to provide both traditional functional enrichment as well as gene set enrichment results for a number of gene set collections including BioCarta, KEGG, Reactome, Gene Ontology (GO), Human Phenotype Ontology (HPO), and MalaCards Disease Ontology for several organisms including fruit fly, human, mouse, rat, worm, and yeast. It also provides an option to dynamically compare the associated gene sets across data sets as bubble charts, to facilitate comparative analysis. Benchmarking of Seten using eCLIP data for IGF2BP1, SRSF7, and PTBP1 against their corresponding CRISPR RNA-seq in K562 cells as well as randomized negative controls, demonstrated that its gene set enrichment method outperforms functional enrichment, with scores significantly contributing to the discovery of true annotations. Comparative performance analysis using these CRISPR control data sets revealed significantly higher precision and comparable recall to that observed using ChIP-Enrich. Seten's web interface currently provides precomputed results for about 200 CLIP-seq data sets and both command line as well as web interfaces can be used to analyze CLIP-seq data sets. We highlight several examples to show the utility of Seten for rapid profiling of various CLIP-seq data sets. Seten is available on http://www.iupui.edu/∼sysbio/seten/. © 2017 Budak et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Lorain Harbor, Ohio. Preliminary Feasibility Study (Stage 2). Review of Reports. Volume II. Appendices.

DTIC Science & Technology

1980-10-01

looked all the way from the west to all the way down to Erie , Pennsylvania . We made some initial cuts and got it down to five different ports...Harbor, MN Presque Isle :Two Harbors, MN :Gary, IN 1,721,920 25 (Litton Great Lakes):Two Harbors, MN :Calumet Harbor, IN 178,080 3 :Two Harbors, MN...WI : 2 :11 : 0: 0 : 0: 2: 3 Silver Bay, MN : 82 :67 : 96 :87 : 85 : 88: 89 Taconite, MN : 0 : 0 : 0: 0 : 0: 4: 0 Presque Isle , MI : 6 2 : 1 0.5: 2 1

Planning through Partnerships : Alternative Transportation at Boston Harbor Islands National Park Area

DOT National Transportation Integrated Search

2004-07-31

This case study tells the story of a successful and collaborative transportation planning process at Boston Harbor Islands National Park Area (Boston Harbor Islands). By using an innovative approach to planning, Boston Harbor Islands has been able to...

Disposal of Vessel Wastes: Shipboard and Shoreside Facilities. Phase 2. Graywater

DTIC Science & Technology

1979-07-01

Increase in Concentration Resulting from Daily Loadings and Vessel-Induced Mixing 45 3-7 Annual Loadings to Presque Isle - Marquette Harbor from...in port for 24 hours (Upper Lakes Reference Group, 1977a). Two harbors were considered for case studies. The first harbor, Presque Isle -Marquette...harbor. Presque Isle -Marquette The existing conditions of the harbor are considered to be of high quality with respect to coastal waters, the open waters

Super-lncRNAs: identification of lncRNAs that target super-enhancers via RNA:DNA:DNA triplex formation.

PubMed

Soibam, Benjamin

2017-11-01

Super-enhancers are characterized by high levels of Mediator binding and are major contributors to the expression of their associated genes. They exhibit high levels of local chromatin interactions and a higher order of local chromatin organization. On the other hand, lncRNAs can localize to specific DNA sites by forming a RNA:DNA:DNA triplex, which in turn can contribute to local chromatin organization. In this paper, we characterize a new class of lncRNAs called super-lncRNAs that target super-enhancers and which can contribute to the local chromatin organization of the super-enhancers. Using a logistic regression model based on the number of RNA:DNA:DNA triplex sites a lncRNA forms within the super-enhancer, we identify 442 unique super-lncRNA transcripts in 27 different human cell and tissue types; 70% of these super-lncRNAs were tissue restricted. They primarily harbor a single triplex-forming repeat domain, which forms an RNA:DNA:DNA triplex with multiple anchor DNA sites (originating from transposable elements) within the super-enhancers. Super-lncRNAs can be grouped into 17 different clusters based on the tissue or cell lines they target. Super-lncRNAs in a particular cluster share common short structural motifs and their corresponding super-enhancer targets are associated with gene ontology terms pertaining to the tissue or cell line. Super-lncRNAs may use these structural motifs to recruit and transport necessary regulators (such as transcription factors and Mediator complexes) to super-enhancers, influence chromatin organization, and act as spatial amplifiers for key tissue-specific genes associated with super-enhancers. © 2017 Soibam; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

In situ Dynamics of O2, pH, Light, and Photosynthesis in Ikaite Tufa Columns (Ikka Fjord, Greenland)-A Unique Microbial Habitat.

PubMed

Trampe, Erik C L; Larsen, Jens E N; Glaring, Mikkel A; Stougaard, Peter; Kühl, Michael

2016-01-01

The Ikka Fjord (SW Greenland) harbors a unique microbial habitat in the form of several hundred submarine tufa columns composed of ikaite, a special hexahydrate form of calcium carbonate that precipitates when alkaline phosphate- and carbonate-enriched spring water seeping out of the sea floor meets cold seawater. While several unique heterotrophic microbes have been isolated from the tufa columns, the microbial activity, and the boundary conditions for microbial growth in ikaite have remained unexplored. We present the first detailed in situ characterization of the physico-chemical microenvironment and activity of oxygenic phototrophs thriving within the ikaite columns. In situ underwater microsensor measurements of pH, temperature, and irradiance in the porous ikaite crystal matrix, revealed an extreme microenvironment characterized by low temperatures, strong light attenuation, and gradients of pH changing from pH 9 at the outer column surface to above pH 10 over the first 1-2 cm of the ikaite. This outer layer of the freshly deposited ikaite matrix contained densely pigmented yellow and green zones harboring a diverse phototrophic community dominated by diatoms and cyanobacteria, respectively, as shown by amplicon sequencing. In situ O2 measurements, as well as underwater variable chlorophyll fluorescence measurements of photosynthetic activity, demonstrated high levels of oxygenic photosynthesis in this extreme gradient environment with strong irradiance-driven O2 dynamics ranging from anoxia to hyperoxic conditions in the ikaite matrix, albeit the local formation of gas bubbles buffered the day-night dynamics of O2 in the tufa columns. The microbial phototrophs in the ikaite matrix are embedded in exopolymers forming endolithic biofilms that may interact with mineral formation and cementing of ikaite crystals.

In situ Dynamics of O2, pH, Light, and Photosynthesis in Ikaite Tufa Columns (Ikka Fjord, Greenland)—A Unique Microbial Habitat

PubMed Central

Trampe, Erik C. L.; Larsen, Jens E. N.; Glaring, Mikkel A.; Stougaard, Peter; Kühl, Michael

2016-01-01

The Ikka Fjord (SW Greenland) harbors a unique microbial habitat in the form of several hundred submarine tufa columns composed of ikaite, a special hexahydrate form of calcium carbonate that precipitates when alkaline phosphate- and carbonate-enriched spring water seeping out of the sea floor meets cold seawater. While several unique heterotrophic microbes have been isolated from the tufa columns, the microbial activity, and the boundary conditions for microbial growth in ikaite have remained unexplored. We present the first detailed in situ characterization of the physico-chemical microenvironment and activity of oxygenic phototrophs thriving within the ikaite columns. In situ underwater microsensor measurements of pH, temperature, and irradiance in the porous ikaite crystal matrix, revealed an extreme microenvironment characterized by low temperatures, strong light attenuation, and gradients of pH changing from pH 9 at the outer column surface to above pH 10 over the first 1–2 cm of the ikaite. This outer layer of the freshly deposited ikaite matrix contained densely pigmented yellow and green zones harboring a diverse phototrophic community dominated by diatoms and cyanobacteria, respectively, as shown by amplicon sequencing. In situ O2 measurements, as well as underwater variable chlorophyll fluorescence measurements of photosynthetic activity, demonstrated high levels of oxygenic photosynthesis in this extreme gradient environment with strong irradiance-driven O2 dynamics ranging from anoxia to hyperoxic conditions in the ikaite matrix, albeit the local formation of gas bubbles buffered the day-night dynamics of O2 in the tufa columns. The microbial phototrophs in the ikaite matrix are embedded in exopolymers forming endolithic biofilms that may interact with mineral formation and cementing of ikaite crystals. PMID:27242741

The Bamboo-Eating Giant Panda Harbors a Carnivore-Like Gut Microbiota, with Excessive Seasonal Variations

PubMed Central

Xue, Zhengsheng; Zhang, Wenping; Wang, Linghua; Hou, Rong; Zhang, Menghui; Fei, Lisong; Zhang, Xiaojun; Huang, He; Bridgewater, Laura C.; Jiang, Yi; Jiang, Chenglin; Zhao, Liping

2015-01-01

ABSTRACT The giant panda evolved from omnivorous bears. It lives on a bamboo-dominated diet at present, but it still retains a typical carnivorous digestive system and is genetically deficient in cellulose-digesting enzymes. To find out whether this endangered mammalian species, like other herbivores, has successfully developed a gut microbiota adapted to its fiber-rich diet, we conducted a 16S rRNA gene-based large-scale structural profiling of the giant panda fecal microbiota. Forty-five captive individuals were sampled in spring, summer, and late autumn within 1 year. Significant intraindividual variations in the diversity and structure of gut microbiota across seasons were observed in this population, which were even greater than the variations between individuals. Compared with published data sets involving 124 gut microbiota profiles from 54 mammalian species, these giant pandas, together with 9 captive and 7 wild individuals investigated previously, showed extremely low gut microbiota diversity and an overall structure that diverged from those of nonpanda herbivores but converged with those of carnivorous and omnivorous bears. The giant panda did not harbor putative cellulose-degrading phylotypes such as Ruminococcaceae and Bacteroides bacteria that are typically enriched in other herbivores, but instead, its microbiota was dominated by Escherichia/Shigella and Streptococcus bacteria. Members of the class Clostridia were common and abundant in the giant panda gut microbiota, but most of the members present were absent in other herbivores and were not phylogenetically related with known cellulolytic lineages. Therefore, the giant panda appears not to have evolved a gut microbiota compatible with its newly adopted diet, which may adversely influence the coevolutionary fitness of this herbivore. PMID:25991678

Transcription elongation rate has a tissue-specific impact on alternative cleavage and polyadenylation in Drosophila melanogaster.

PubMed

Liu, Xiaochuan; Freitas, Jaime; Zheng, Dinghai; Oliveira, Marta S; Hoque, Mainul; Martins, Torcato; Henriques, Telmo; Tian, Bin; Moreira, Alexandra

2017-12-01

Alternative polyadenylation (APA) is a mechanism that generates multiple mRNA isoforms with different 3'UTRs and/or coding sequences from a single gene. Here, using 3' region extraction and deep sequencing (3'READS), we have systematically mapped cleavage and polyadenylation sites (PASs) in Drosophila melanogaster , expanding the total repertoire of PASs previously identified for the species, especially those located in A-rich genomic sequences. Cis -element analysis revealed distinct sequence motifs around fly PASs when compared to mammalian ones, including the greater enrichment of upstream UAUA elements and the less prominent presence of downstream UGUG elements. We found that over 75% of mRNA genes in Drosophila melanogaster undergo APA. The head tissue tends to use distal PASs when compared to the body, leading to preferential expression of APA isoforms with long 3'UTRs as well as with distal terminal exons. The distance between the APA sites and intron location of PAS are important parameters for APA difference between body and head, suggesting distinct PAS selection contexts. APA analysis of the RpII215 C4 mutant strain, which harbors a mutant RNA polymerase II (RNAPII) with a slower elongation rate, revealed that a 50% decrease in transcriptional elongation rate leads to a mild trend of more usage of proximal, weaker PASs, both in 3'UTRs and in introns, consistent with the "first come, first served" model of APA regulation. However, this trend was not observed in the head, suggesting a different regulatory context in neuronal cells. Together, our data expand the PAS collection for Drosophila melanogaster and reveal a tissue-specific effect of APA regulation by RNAPII elongation rate. © 2017 Liu et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

A common class of transcripts with 5'-intron depletion, distinct early coding sequence features, and N1-methyladenosine modification.

PubMed

Cenik, Can; Chua, Hon Nian; Singh, Guramrit; Akef, Abdalla; Snyder, Michael P; Palazzo, Alexander F; Moore, Melissa J; Roth, Frederick P

2017-03-01

Introns are found in 5' untranslated regions (5'UTRs) for 35% of all human transcripts. These 5'UTR introns are not randomly distributed: Genes that encode secreted, membrane-bound and mitochondrial proteins are less likely to have them. Curiously, transcripts lacking 5'UTR introns tend to harbor specific RNA sequence elements in their early coding regions. To model and understand the connection between coding-region sequence and 5'UTR intron status, we developed a classifier that can predict 5'UTR intron status with >80% accuracy using only sequence features in the early coding region. Thus, the classifier identifies transcripts with 5 ' proximal- i ntron- m inus-like-coding regions ("5IM" transcripts). Unexpectedly, we found that the early coding sequence features defining 5IM transcripts are widespread, appearing in 21% of all human RefSeq transcripts. The 5IM class of transcripts is enriched for non-AUG start codons, more extensive secondary structure both preceding the start codon and near the 5' cap, greater dependence on eIF4E for translation, and association with ER-proximal ribosomes. 5IM transcripts are bound by the exon junction complex (EJC) at noncanonical 5' proximal positions. Finally, N 1 -methyladenosines are specifically enriched in the early coding regions of 5IM transcripts. Taken together, our analyses point to the existence of a distinct 5IM class comprising ∼20% of human transcripts. This class is defined by depletion of 5' proximal introns, presence of specific RNA sequence features associated with low translation efficiency, N 1 -methyladenosines in the early coding region, and enrichment for noncanonical binding by the EJC. © 2017 Cenik et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

QTLs associated with agronomic traits in the Attila × CDC Go spring wheat population evaluated under conventional management

PubMed Central

Zou, Jun; Iqbal, Muhammad; Chen, Hua; Asif, Mohammad; N’Diaye, Amidou; Navabi, Alireza; Perez-Lara, Enid; Pozniak, Curtis; Yang, Rong-Cai; Randhawa, Harpinder; Spaner, Dean

2017-01-01

Recently, we investigated the effect of the wheat 90K single nucleotide polymorphic (SNP) array and three gene-specific (Ppd-D1, Vrn-A1 and Rht-B1) markers on quantitative trait loci (QTL) detection in a recombinant inbred lines (RILs) population derived from a cross between two spring wheat (Triticum aestivum L.) cultivars, ‘Attila’ and ‘CDC Go’, and evaluated for eight agronomic traits at three environments under organic management. The objectives of the present study were to investigate the effect of conventional management on QTL detection in the same mapping population using the same set of markers as the organic management and compare the results with organic management. Here, we evaluated 167 RILs for number of tillers (tillering), flowering time, maturity, plant height, test weight (grain volume weight), 1000 kernel weight, grain yield, and grain protein content at seven conventionally managed environments from 2008 to 2014. Using inclusive composite interval mapping (ICIM) on phenotypic data averaged across seven environments and a subset of 1203 informative markers (1200 SNPs and 3 gene specific markers), we identified a total of 14 QTLs associated with flowering time (1), maturity (2), plant height (1), grain yield (1), test weight (2), kernel weight (4), tillering (1) and grain protein content (2). Each QTL individually explained from 6.1 to 18.4% of the phenotypic variance. Overall, the QTLs associated with each trait explained from 9.7 to 35.4% of the phenotypic and from 22.1 to 90.8% of the genetic variance. Three chromosomal regions on chromosomes 2D (61–66 cM), 4B (80–82 cM) and 5A (296–297 cM) harbored clusters of QTLs associated with two to three traits. The coincidental region on chromosome 5A harbored QTL clusters for both flowering and maturity time, and mapped about 2 cM proximal to the Vrn-A1 gene, which was in high linkage disequilibrium (0.70 ≤ r2 ≤ 0.75) with SNP markers that mapped within the QTL confidence interval. Six of the 14 QTLs (one for flowering time and plant height each, and two for maturity and kernel weight each) were common between the conventional and organic management systems, which suggests issues in directly utilizing gene discovery results based on conventional management to make in detail selection (decision) for organic management. PMID:28158253

Decadal Changes In Benthic Community Measures In New York Harbor

EPA Science Inventory

Monitoring in New York Harbor, NY, as part of the Regional Environmental Monitoring and Assessment Program has spanned a decade, and includes habitat and water quality measures and sediment contaminant levels from four sub-basins (Upper NY Harbor, Lower NY Harbor, Newark Bay, and...

Annual Report Fiscal Year 2002 of the Secretary of the Army on Civil Works Activities (1 October 2001 - 30 September 2002)

DTIC Science & Technology

2003-08-04

WI........................................21-2 2. Alpena Harbor, MI .........................................21-3 3. Arcadia Harbor, MI...DISTRICT $292,010 was for new work and $1,701,185 for maintenance. 2. ALPENA HARBOR, MI Location. At mouth of Thunder Bay River which empties into...Thunder Bay, Lake Huron. Harbor is 100 miles southeast of Cheboygan Harbor, MI. River has its source in Montmorency and Alpena Counties, MI. (See

33 CFR 165.904 - Lake Michigan at Chicago Harbor & Burnham Park Harbor-Safety and Security Zone.

Code of Federal Regulations, 2012 CFR

2012-07-01

... & Burnham Park Harbor-Safety and Security Zone. 165.904 Section 165.904 Navigation and Navigable Waters... Guard District § 165.904 Lake Michigan at Chicago Harbor & Burnham Park Harbor—Safety and Security Zone... entrance of the harbor connecting coordinates 41°51′09″ N, 087°36′36″W and 41°51′11″ N, 087°36′22″ W. (b...

33 CFR 165.904 - Lake Michigan at Chicago Harbor & Burnham Park Harbor-Safety and Security Zone.

Code of Federal Regulations, 2014 CFR

2014-07-01

... & Burnham Park Harbor-Safety and Security Zone. 165.904 Section 165.904 Navigation and Navigable Waters... Guard District § 165.904 Lake Michigan at Chicago Harbor & Burnham Park Harbor—Safety and Security Zone... entrance of the harbor connecting coordinates 41°51′09″ N, 087°36′36″ W and 41°51′11″ N, 087°36′22″ W. (b...

33 CFR 165.904 - Lake Michigan at Chicago Harbor & Burnham Park Harbor-Safety and Security Zone.

Code of Federal Regulations, 2013 CFR

2013-07-01

... & Burnham Park Harbor-Safety and Security Zone. 165.904 Section 165.904 Navigation and Navigable Waters... Guard District § 165.904 Lake Michigan at Chicago Harbor & Burnham Park Harbor—Safety and Security Zone... entrance of the harbor connecting coordinates 41°51′09″ N, 087°36′36″W and 41°51′11″ N, 087°36′22″ W. (b...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zodtner, H. H.

There is an interest in discovering the various peace time uses of nuclear explosives. One of the proposals is the building of harbors. There are several ports along the west coast of South America where lighterage is necessary. This implies a need for expanded harbor facilities. The problem is to find a good location for creating a harbor, and the feasibility of accomplishing this with the use of nuclear force. Feasibility includes blast effects, radiation hazards, the number of weapons needed, and economic considerations. Economic considerations include the cost of treating a harbor of sufficient depth and area, the buildingmore » of harbor facilities, and the estimated savings and advantages of the new harbor. Several meetings were held with naval personnel of the Military Liaison group at UCRL to discuss the general problems of harbors. Thirty-three different ports were given a preliminary investigation.« less

Exploring the Impacts of Anthropogenic Disturbance on Seawater and Sediment Microbial Communities in Korean Coastal Waters Using Metagenomics Analysis

PubMed Central

Won, Nam-Il; Kim, Ki-Hwan; Kang, Ji Hyoun; Park, Sang Rul; Lee, Hyuk Je

2017-01-01

The coastal ecosystems are considered as one of the most dynamic and vulnerable environments under various anthropogenic developments and the effects of climate change. Variations in the composition and diversity of microbial communities may be a good indicator for determining whether the marine ecosystems are affected by complex forcing stressors. DNA sequence-based metagenomics has recently emerged as a promising tool for analyzing the structure and diversity of microbial communities based on environmental DNA (eDNA). However, few studies have so far been performed using this approach to assess the impacts of human activities on the microbial communities in marine systems. In this study, using metagenomic DNA sequencing (16S ribosomal RNA gene), we analyzed and compared seawater and sediment communities between sand mining and control (natural) sites in southern coastal waters of Korea to assess whether anthropogenic activities have significantly affected the microbial communities. The sand mining sites harbored considerably lower levels of microbial diversities in the surface seawater community during spring compared with control sites. Moreover, the sand mining areas had distinct microbial taxonomic group compositions, particularly during spring season. The microbial groups detected solely in the sediment load/dredging areas (e.g., Marinobacter, Alcanivorax, Novosphingobium) are known to be involved in degradation of toxic chemicals such as hydrocarbon, oil, and aromatic compounds, and they also contain potential pathogens. This study highlights the versatility of metagenomics in monitoring and diagnosing the impacts of human disturbance on the environmental health of marine ecosystems from eDNA. PMID:28134828

Exploring the Impacts of Anthropogenic Disturbance on Seawater and Sediment Microbial Communities in Korean Coastal Waters Using Metagenomics Analysis.

PubMed

Won, Nam-Il; Kim, Ki-Hwan; Kang, Ji Hyoun; Park, Sang Rul; Lee, Hyuk Je

2017-01-27

The coastal ecosystems are considered as one of the most dynamic and vulnerable environments under various anthropogenic developments and the effects of climate change. Variations in the composition and diversity of microbial communities may be a good indicator for determining whether the marine ecosystems are affected by complex forcing stressors. DNA sequence-based metagenomics has recently emerged as a promising tool for analyzing the structure and diversity of microbial communities based on environmental DNA (eDNA). However, few studies have so far been performed using this approach to assess the impacts of human activities on the microbial communities in marine systems. In this study, using metagenomic DNA sequencing (16S ribosomal RNA gene), we analyzed and compared seawater and sediment communities between sand mining and control (natural) sites in southern coastal waters of Korea to assess whether anthropogenic activities have significantly affected the microbial communities. The sand mining sites harbored considerably lower levels of microbial diversities in the surface seawater community during spring compared with control sites. Moreover, the sand mining areas had distinct microbial taxonomic group compositions, particularly during spring season. The microbial groups detected solely in the sediment load/dredging areas (e.g., Marinobacter, Alcanivorax, Novosphingobium) are known to be involved in degradation of toxic chemicals such as hydrocarbon, oil, and aromatic compounds, and they also contain potential pathogens. This study highlights the versatility of metagenomics in monitoring and diagnosing the impacts of human disturbance on the environmental health of marine ecosystems from eDNA.

33 CFR 110.130 - Bar Harbor, Maine.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Bar Harbor, Maine. 110.130... ANCHORAGE REGULATIONS Anchorage Grounds § 110.130 Bar Harbor, Maine. (a) Anchorage grounds. (1) Anchorage “A” is that portion of Frenchman Bay, Bar Harbor, ME enclosed by a rhumb line connecting the following...

33 CFR 110.38 - Edgartown Harbor, Mass.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Edgartown Harbor, Mass. 110.38 Section 110.38 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.38 Edgartown Harbor, Mass. An area in the inner harbor...

33 CFR 110.38 - Edgartown Harbor, Mass.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Edgartown Harbor, Mass. 110.38 Section 110.38 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.38 Edgartown Harbor, Mass. An area in the inner harbor...

33 CFR 110.38 - Edgartown Harbor, Mass.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Edgartown Harbor, Mass. 110.38 Section 110.38 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.38 Edgartown Harbor, Mass. An area in the inner harbor...

33 CFR 110.38 - Edgartown Harbor, Mass.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Edgartown Harbor, Mass. 110.38 Section 110.38 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.38 Edgartown Harbor, Mass. An area in the inner harbor...

33 CFR 110.38 - Edgartown Harbor, Mass.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Edgartown Harbor, Mass. 110.38 Section 110.38 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.38 Edgartown Harbor, Mass. An area in the inner harbor...

76 FR 32071 - Safety Zone; Conneaut Festival Fireworks, Conneaut Harbor, Conneaut, OH

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-03

...-AA00 Safety Zone; Conneaut Festival Fireworks, Conneaut Harbor, Conneaut, OH AGENCY: Coast Guard, DHS... Conneaut Harbor, Conneaut, OH for the Conneaut Festival Fireworks. This zone is intended to restrict vessels from a portion of Conneaut Harbor, Conneaut, OH during the Conneaut Festival Fireworks on July 3...

76 FR 34865 - Safety Zone; Rochester Harbor Festival, Genesee River, Rochester, NY

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-15

...-AA00 Safety Zone; Rochester Harbor Festival, Genesee River, Rochester, NY AGENCY: Coast Guard, DHS... Genesee River, Rochester, NY for the Rochester Harbor Festival fireworks. This zone is intended to restrict vessels from the mouth of the Genesee River in Rochester during the Rochester Harbor Festival...

75 FR 52023 - Boston Harbor Islands National Recreation Area Advisory Council; Notice of Public Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-24

... DEPARTMENT OF THE INTERIOR National Park Service Boston Harbor Islands National Recreation Area..., Boston Harbor Islands National Recreation Area. ACTION: Notice of meeting. SUMMARY: Notice is hereby given that a meeting of the Boston Harbor Islands National Recreation Area Advisory Council will be held...

75 FR 78601 - Drawbridge Operation Regulation; Gulf Intracoastal Waterway, New Orleans Harbor, Inner Harbor...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-16

... Operation Regulation; Gulf Intracoastal Waterway, New Orleans Harbor, Inner Harbor Navigation Canal, New Orleans, Orleans Parish, LA AGENCY: Coast Guard, DHS. ACTION: Notice of temporary deviation from... Harvey Lock), at New Orleans, Orleans Parish, Louisiana. This deviation is necessary to adjust the...

78 FR 18479 - Drawbridge Operation Regulations; Inner Harbor Navigation Canal, New Orleans, LA

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-27

... Operation Regulations; Inner Harbor Navigation Canal, New Orleans, LA AGENCY: Coast Guard, DHS. ACTION... across the Inner Harbor Navigation Canal, mile 4.6, at New Orleans, Louisiana. This deviation is... Seabrook Highway crossing the Inner Harbor Navigation Canal, mile 4.6, in New Orleans, Louisiana. The...

32 CFR 765.6 - Regulations for Pearl Harbor, Hawaii.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 32 National Defense 5 2010-07-01 2010-07-01 false Regulations for Pearl Harbor, Hawaii. 765.6... RULES RULES APPLICABLE TO THE PUBLIC § 765.6 Regulations for Pearl Harbor, Hawaii. The Commander, U.S. Naval Base, Pearl Harbor, Hawaii, is responsible for prescribing and enforcing such rules and...

78 FR 42016 - Safety Zone; Discovery World Fireworks, Milwaukee Harbor, Milwaukee, WI

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-15

...-AA00 Safety Zone; Discovery World Fireworks, Milwaukee Harbor, Milwaukee, WI AGENCY: Coast Guard, DHS... Milwaukee Harbor due to 4 fireworks displays at Discovery World Pier. This safety zone is necessary to... entitled, ``Safety Zone; Discovery World Fireworks, Milwaukee Harbor, Milwaukee, Wisconsin'' in the Federal...

Lethal and sublethal effects, and incomplete clearance of ingested imidacloprid in honey bees (Apis mellifera).

PubMed

Sánchez-Bayo, Francisco; Belzunces, Luc; Bonmatin, Jean-Marc

2017-11-01

A previous study claimed a differential behavioural resilience between spring or summer honey bees (Apis mellifera) and bumble bees (Bombus terrestris) after exposure to syrup contaminated with 125 µg L -1 imidacloprid for 8 days. The authors of that study based their assertion on the lack of body residues and toxic effects in honey bees, whereas bumble bees showed body residues of imidacloprid and impaired locomotion during the exposure. We have reproduced their experiment using winter honey bees subject to the same protocol. After exposure to syrup contaminated with 125 µg L -1 imidacloprid, honey bees experienced high mortality rates (up to 45%), had body residues of imidacloprid in the range 2.7-5.7 ng g -1 and exhibited abnormal behaviours (restless, apathetic, trembling and falling over) that were significantly different from the controls. There was incomplete clearance of the insecticide during the 10-day exposure period. Our results contrast with the findings reported in the previous study for spring or summer honey bees, but are consistent with the results reported for the other bee species.

Short communication: Chemical and sensory characteristics of Canestrato di Moliterno cheese manufactured in spring.

PubMed

Trani, A; Gambacorta, G; Loizzo, P; Cassone, A; Faccia, M

2016-08-01

Canestrato di Moliterno is an Italian Protected Geographical Indication hard cheese, made in winter and spring from a mixture of ewe and goat milks, that has been poorly investigated. The present study was aimed at characterizing the cheese made in the warm season. Two series of samples, ripened in traditional rooms called fondaco as indicated in the official protocol of production, were taken from the main certified producers. The cheeses were analyzed for gross composition; proteolysis and lipolysis; volatile fraction; and organoleptic features. Gross composition was not completely homogeneous among the samples, but primary proteolysis and lipolysis were quite uniform. We observed variations in secondary proteolysis, likely caused by fluctuations in environmental conditions in the fondaco. The sensory profiles of the samples were homogeneous: the cheese was soluble, greasy, and adhesive, with a sheepfold and buttery odor. The main taste attributes were fermented, pungent, and bitter. Overall, the results of this study provide an initial contribution to the characterization of Canestrato di Moliterno, and could be used to improve marketing strategies. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Intraosseous vascular access in the treatment of chemical warfare casualties assessed by advanced simulation: proposed alteration of treatment protocol.

PubMed

Vardi, Amir; Berkenstadt, Haim; Levin, Inbal; Bentencur, Ariel; Ziv, Amitai

2004-06-01

Current treatment protocols for chemical warfare casualties assume no IV access during the early treatment stages. Time constraints in mass casualty scenarios, impaired manual dexterity of medical personnel wearing protective gear, and victims' complex clinical presentations render standard IV access techniques impractical. A newly developed spring-driven, trigger-operated intraosseous infusion device may offer an effective solution. Sophisticated simulators were developed and used to mimic scenarios of chemical warfare casualties for assessing the feasibility of intraosseous infusion delivery. We evaluated the clinical performance of medical teams in full protective gear. The success rate in intraosseous insertion, time to completion of treatment goals, and outcome were measured in a simulated setting. Medical teams from major hospitals in Israel, designated for emergency response in a real chemical warfare mass casualty scenario, were trained in a simulated setting. All 94 participating physicians were supplied with conventional treatment modalities: only the 64 study group physicians received intraosseous devices. The simulated survival rate was 73.4% for the study group and 3.3% for the controls (P < 0.001). Treatment goals were achieved within 3.5 min (range, 1-9 min) in the study group and within >10 min for controls (P < 0.001), and the complication rate for intraosseous use was 13.8%. Personnel satisfaction with the intraosseous device was unanimous and high. New-generation intraosseous infusions have great potential value in the early treatment stages of chemical warfare casualties. In a chemical warfare mass casualty scenario, the protective gear worn by medical personnel, the time constraints, and the casualties' medical condition impose limitations on the establishment of IV access during early treatment of the victims. A spring-driven, trigger-operated intraosseous infusion delivery system may offer an effective solution.

33 CFR 162.165 - Buffalo and Rochester Harbors, New York.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Buffalo and Rochester Harbors, New York. 162.165 Section 162.165 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND... and Rochester Harbors, New York. In Buffalo and Rochester Harbors, no vessel may exceed 6 miles per...

33 CFR 100.113 - Provincetown Harbor Swim for Life, Provincetown, MA.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Provincetown Harbor Swim for Life... SECURITY REGATTAS AND MARINE PARADES SAFETY OF LIFE ON NAVIGABLE WATERS § 100.113 Provincetown Harbor Swim for Life, Provincetown, MA. (a) Regulated Area. All waters of Provincetown Harbor within 200 feet of...

77 FR 27666 - Proposed Amendment of Class E Airspace; Bar Harbor, ME

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-11

...-1366; Airspace Docket No. 11-ANE-13] Proposed Amendment of Class E Airspace; Bar Harbor, ME AGENCY... action proposes to amend Class E Airspace at Bar Harbor, ME, as the Surry Non-Directional Radio Beacon... Airport, Bar Harbor, ME. Airspace reconfiguration is necessary due to the decommissioning of the Surry NDB...

33 CFR 80.1136 - Moss Landing Harbor, CA.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Moss Landing Harbor, CA. 80.1136... NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1136 Moss Landing Harbor, CA. A line drawn from the seaward extremity of the pier located 0.3 mile south of Moss Landing Harbor Entrance to the...

33 CFR 80.1136 - Moss Landing Harbor, CA.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Moss Landing Harbor, CA. 80.1136... NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1136 Moss Landing Harbor, CA. A line drawn from the seaward extremity of the pier located 0.3 mile south of Moss Landing Harbor Entrance to the...

33 CFR 165.14-1414 - Safety Zones; Hawaiian Islands Commercial Harbors; HI.

Code of Federal Regulations, 2014 CFR

2014-07-01

... harbors, or all of these harbors, dependent upon details in the tsunami warning. These safety zones extend... period. Paragraph (b) of this section will be enforced when a tsunami warning has been issued for the... Coast Guard's Homeport Web site. Following the passage of the tsunami or tsunami threat and harbor...

33 CFR 110.9 - Wells Harbor, Maine.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Wells Harbor, Maine. 110.9... ANCHORAGE REGULATIONS Special Anchorage Areas § 110.9 Wells Harbor, Maine. (a) Anchorage “A”. All of the... approximately 5,800 sq. yards, encompassing the central portion of Wells Harbor. (b) Anchorage “B”. All of the...

33 CFR 110.9 - Wells Harbor, Maine.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Wells Harbor, Maine. 110.9... ANCHORAGE REGULATIONS Special Anchorage Areas § 110.9 Wells Harbor, Maine. Link to an amendment published at..., encompassing the central portion of Wells Harbor. (b) Anchorage “B”. All of the waters enclosed by a line...

33 CFR 117.272 - Boot Key Harbor.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Boot Key Harbor. 117.272 Section 117.272 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements Florida § 117.272 Boot Key Harbor. The draw of the Boot Key Harbor drawbridge, mile 0.13, between...

46 CFR 45.181 - Load line exemption requirements for the Burns Harbor and Milwaukee routes.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 2 2014-10-01 2014-10-01 false Load line exemption requirements for the Burns Harbor... line exemption requirements for the Burns Harbor and Milwaukee routes. Barges operating on the Burns... addresses and telephone numbers); (3) Service route (Milwaukee and/or Burns Harbor); (4) Design type...

46 CFR 45.181 - Load line exemption requirements for the Burns Harbor and Milwaukee routes.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 46 Shipping 2 2013-10-01 2013-10-01 false Load line exemption requirements for the Burns Harbor... line exemption requirements for the Burns Harbor and Milwaukee routes. Barges operating on the Burns... addresses and telephone numbers); (3) Service route (Milwaukee and/or Burns Harbor); (4) Design type...

46 CFR 45.181 - Load line exemption requirements for the Burns Harbor and Milwaukee routes.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 46 Shipping 2 2012-10-01 2012-10-01 false Load line exemption requirements for the Burns Harbor... line exemption requirements for the Burns Harbor and Milwaukee routes. Barges operating on the Burns... addresses and telephone numbers); (3) Service route (Milwaukee and/or Burns Harbor); (4) Design type...

46 CFR 45.181 - Load line exemption requirements for the Burns Harbor and Milwaukee routes.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 2 2011-10-01 2011-10-01 false Load line exemption requirements for the Burns Harbor... line exemption requirements for the Burns Harbor and Milwaukee routes. Barges operating on the Burns... addresses and telephone numbers); (3) Service route (Milwaukee and/or Burns Harbor); (4) Design type...

46 CFR 45.181 - Load line exemption requirements for the Burns Harbor and Milwaukee routes.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 2 2010-10-01 2010-10-01 false Load line exemption requirements for the Burns Harbor... line exemption requirements for the Burns Harbor and Milwaukee routes. Barges operating on the Burns... (Milwaukee and/or Burns Harbor); (4) Design type (covered/uncovered hopper, deck, etc.); (5) External...

Summary of oceanographic and water–quality measurements in West Falmouth Harbor and Buzzards Bay, Massachusetts, 2009–2010

USGS Publications Warehouse

Ganju, Neil K.; Dickhudt, Patrick J.; Thomas, Jennifer A.; Borden, Jonathan; Sherwood, Christopher R.; Montgomery, Ellyn T.; Twomey, Erin R.; Martini, Marinna A.

2011-01-01

This data report presents oceanographic and water-quality observations made at six locations in West Falmouth Harbor and Buzzards Bay, Massachusetts, from August 2009 to September 2010. Both Buzzards Bay and West Falmouth Harbor are estuarine embayments; the input of freshwater on the eastern margin of Buzzards Bay adjacent to Cape Cod and West Falmouth Harbor is largely due to groundwater. In West Falmouth Harbor, the groundwater that seeps into the harbor is characterized by relatively high levels of nitrate. This high nitrate load has modified the ecology of the harbor (Howes and others, 2006) and may be a significant source of nitrate to Buzzards Bay during seasons with low biological nitrate uptake. The U.S. Geological Survey undertook these measurements to improve understanding of circulation, residence time, and water quality in the harbor and bay. We set up and monitored multiple sites in both Buzzards Bay and West Falmouth Harbor, measuring depth, water velocity,salinity, pH, dissolved oxygen, chlorophyll-a, and nitrate concentration. In this report we present the processed time-series data at these locations and provide access to the data and metadata. The results will be used to understand circulation mechanisms and verify numerical models of hydrodynamics and biogeochemistry.

The ARAC-RODOS-WSPEEDI Information Exchange Project

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sullivan, T J

1999-09-01

Under the auspices of a US DOE-JAPAN Memorandum of Understanding JAERI and LLNL agreed to develop and evaluate a prototype information exchange protocol for nuclear accident emergency situations. This project received some interest from the US DOS and FEMA as it fits nicely under the umbrella of the G-7's GEMINI (Global Emergency Management Information Network Initiative) project. Because of LLNL/ARAC and JAERV WSPEEDI interest in nuclear accident consequence assessment and hazard prediction on all scales, to include global, we were happy to participate. Subsequent to the Spring 1997 RODOS-ARAC Workshop a Memorandum of Agreement was developed to enhance mutual collaborationmore » on matters of emergency systems development. In the summer of 1998 the project leaders of RODOS, WSPEEDI and ARAC met at FZK and agreed to join in a triangular collaboration on the development and demonstration of an emergency information exchange protocol. JAERI and FZK are engaged in developing a formal cooperation agreement. The purpose of this project is to evaluate the prototype information protocol application for technical feasibility and mutual benefit through simulated (real) event; quick exchange of atmospheric modeling products and environmental data during emergencies, distribution of predicted results to other countries having no prediction capabilities, and utilization of the link for collaborative studies.« less

The effects of Low Level LASER Therapy (LLLT) on blood glucose levels in patients with Diabetes Mellitus type I : a case report

NASA Astrophysics Data System (ADS)

Longo, Leonardo; Postiglione, Marco; Buccioni, Tommaso; Longo, Diego

2009-06-01

Diabetes Mellitus (DM) is a widespread disease and a serious public health problem. Low Level LASER Therapy (LLLT) has been found to reduce glycaemia on DM type 1 patients, an observation requiring further research especially as regards characteristics of treatment protocol. The purpose of this work is to continue the line of research and propose a specific protocol for LLLT use. In spring 2008 a 48 year old man, DM type 1 insulin dependent patient has been submitted to 810 nm wavelength LLLT treatment in specific body areas daily for 3 weeks and then once a week for 4 weeks until normalization of glycaemia. Medical supervision was present before, during and after application. Insulin was reduced progressively and then stopped. A gradual reduction of glycaemia was noted during the course of treatment. In successive follow-ups a reduction in HbA1c was noted. Results confirm previous observations and need for further research on large cohorts. The indication that LASER may become a valuable addition to DM type 1 treatment is confirmed and the proposed protocol appears to be effective. The case presented merits review since it reports a therapeutic challenge, contributes to advance in medical science and spawns research.

Identifying best practices for "Safe Harbor" legislation to protect child sex trafficking victims: Decriminalization alone is not sufficient.

PubMed

Barnert, Elizabeth S; Abrams, Susan; Azzi, Veronica F; Ryan, Gery; Brook, Robert; Chung, Paul J

2016-01-01

Several states have recently enacted "Safe Harbor" laws to redirect child victims of commercial sexual exploitation and child sex trafficking from the criminal justice system and into the child welfare system. No comprehensive studies of Safe Harbor law implementation exist. The nine state Safe Harbor laws enacted by 2012 were analyzed to guide state legislators, health professionals, law enforcement agents, child welfare providers, and other responders to the commercial sexual exploitation of children on the development and implementation of state Safe Harbor laws. The authors conducted 32 semi-structured interviews with Safe Harbor experts in these states. Participants conveyed that Safe Harbor legislation signified a critical paradigm shift, treating commercially sexually exploited youth not as criminals but as vulnerable children in need of services. However, Safe Harbor legislation varied widely and significant gaps in laws exist. Such laws alone were considered insufficient without adequate funding for necessary services. As a result, many well-meaning providers were going around the Safe Harbor laws by continuing to incarcerate commercially sexually exploited youth in the juvenile justice system regardless of Safe Harbor laws in place. This was done, to act, in their view, in what was the best interest of the victimized children. With imperfect laws and implementation, these findings suggest an important role for local and state responders to act together to protect victims from unnecessary criminalization and potential further traumatization. Published by Elsevier Ltd.

A Life Cycle Based Approach to Multi-Hazard Risk Assessment

NASA Astrophysics Data System (ADS)

Keen, A. S.; Lynett, P. J.

2017-12-01

Small craft harbors are important facets to many coastal communities providing a transition from land to ocean. Because of the damage resulting from the 2010 Chile and 2011 Japanese tele-tsunamis, the tsunami risk to the small craft marinas in California has become an important concern. However, tsunamis represent only one of many hazards a harbor is likely to see in California. Other natural hazards including tsunamis, wave attack, storm surge and sea level rise all can damage a harbor but are not typically addressed in traditional risk studies. Existing approaches to assess small craft harbor vulnerably typically look at single events assigning likely damage levels to each event. However, a harbor will likely experience damage from several different types of hazards over its service life with each event contributing proportionally to the total damage state. A new, fully probabilistic risk method will be presented which considers the distribution of return period for various hazards over a harbor's service life. The likelihood of failure is connected to each hazard via vulnerability curves. By simply tabulating the expected damage levels from each event, the method provides a quantitative measure of a harbor's risk to various types of hazards as well as the likelihood of failure (i.e. cumulative risk) during the service life. Crescent City Harbor in Northern California and Kings Harbor in Southern California have been chosen as case studies. Each harbor is dynamically different and were chosen to highlight the strengths and weaknesses of the method. Findings of each study will focus on assisting the stakeholders and decision makers to better understand the relative risk to each harbor with the goal of providing them with a tool to better plan for the future maritime environment.

Cloth-covered chiropractic treatment tables as a source of allergens and pathogenic microbes☆

PubMed Central

Evans, Marion W.; Campbell, Alan; Husbands, Chris; Breshears, Jennell; Ndetan, Harrison; Rupert, Ronald

2008-01-01

Abstract Objective Vinyl chiropractic tables have been found to harbor pathogenic bacteria, but wiping with a simple disinfection agent can significantly reduce the risk of bacteria. The aim of this study was to assess the presence of microbes and other allergens or pathogens on cloth chiropractic tables. Methods Cloth-covered tables in a chiropractic college teaching clinic were selected. Samples were taken from the facial piece and hand rests with RODAC plates containing nutrient agar, followed by confirmatory testing when indicated. Results Numerous microbacteria strains were found, including Staphylococcus aureus and Propionibacterium. Allergen-producing molds, including Candida, were also found. Conclusion Cloth tables were shown to contain pathogenic microbacteria and allergens. The chiropractic profession should establish an infection control protocol relevant to treatment tables and discard use of cloth-covered treatment tables in this process. PMID:19674718

Human Cells as Platform to Produce Gamma-Carboxylated Proteins.

PubMed

de Sousa Bomfim, Aline; de Freitas, Marcela Cristina Corrêa; Covas, Dimas Tadeu; de Sousa Russo, Elisa Maria

2018-01-01

The gamma-carboxylated proteins belong to a family of proteins that depend on vitamin K for normal biosynthesis. The major representative gamma-carboxylated proteins are the coagulation system proteins, for example, factor VII, factor IX, factor X, prothrombin, and proteins C, S, and Z. These molecules have harbored posttranslational modifications, such as glycosylation and gamma-carboxylation, and for this reason they need to be produced in mammalian cell lines. Human cells lines have emerged as the most promising alternative to the production of gamma-carboxylated proteins. In this chapter, the methods to generate human cells as a platform to produce gamma-carboxylated proteins, for example the coagulation factors VII and IX, are presented. From the cell line modification up to the vitamin K adaptation of the produced cells is described in the protocols presented in this chapter.

Genetic transformation of carnation (Dianthus caryophylus L.).

PubMed

Nontaswatsri, Chalermsri; Fukai, Seiichi

2010-01-01

This chapter describes a rapid and efficient protocol for explant preparation and genetic transformation of carnation. Node explants from greenhouse-grown plants and leaf explants from in vitro plants are infected with Agrobacterium tumefaciens AGL0 harboring pKT3 plasmid, consisting of GUS and NPTII genes. Explant preparation is an important factor to obtain the transformed plants. The GUS-staining area was located only on the cut end of explants and only explants with a cut end close to the connecting area between node and leaf, produced transformed shoots. The cocultivation medium is also an important factor for the successful genetic transformation of carnation node and leaf explants. High genetic transformation efficiency of node and leaf explants cocultured with Agrobacterium tumefaciens was achieved when the explants were cocultivated on a filter paper soaked with water or water and acetosyringone mixture (AS).

Self-administered topical imiquimod treatment of vulvar intraepithelial neoplasia. A report of four cases.

PubMed

Davis, G; Wentworth, J; Richard, J

2000-08-01

Vulvar intraepithelial neoplasia (VIN) generally can be classified into viral and nonviral etiologies. The histopathologic diagnosis is often separable into basaloid and warty types. A large percentage of VIN lesions have been shown to harbor human papillomavirus (HPV), principally type 16. Imiquimod, an immune response modifier, has been shown to be safe and effective for the treatment of external and perianal genital warts caused by HPV. Four cases occurred of clinical and histopathologically diagnosed viral VIN 3. An imiquimod treatment protocol, previously used in a study of this drug for the treatment of external genital warts, was followed. Imiquimod 5% cream was patient applied three times per week until all lesions cleared, for a maximum of 16 weeks. Imiquimod may be an effective treatment modality for viral VIN 3 in the future.

Seasonal prevalence of Shiga toxin-producing Escherichia coli, including O157:H7 and non-O157 serotypes, and Salmonella in commercial beef processing plants.

PubMed

Barkocy-Gallagher, Genevieve A; Arthur, Terrance M; Rivera-Betancourt, Mildred; Nou, Xiangwu; Shackelford, Steven D; Wheeler, Tommy L; Koohmaraie, Mohammad

2003-11-01

The seasonal prevalence of Escherichia coli O157:H7, Salmonella, non-O157 E. coli (STEC), and stx-harboring cells was monitored at three Midwestern fed-beef processing plants. Overall, E. coli O157:H7 was recovered from 5.9% of fecal samples, 60.6% of hide samples, and 26.7% of carcasses sampled before the preevisceration wash. This pathogen also was recovered from 1.2% (15 of 1,232) of carcasses sampled at chilling (postintervention) at approximate levels of <3.0 cells per 100 cm2. In one case, the E. coli O157:H7 concentration dropped from ca. 1,100 cells per 320 cm2 at the preevisceration stage to a level that was undetectable on ca. 2,500 cm2 at the postintervention stage. The prevalence of E. coli O157:H7 in feces peaked in the summer, whereas its prevalence on hide was high from the spring through the fall. Overall, Salmonella was recovered from 4.4, 71.0, and 12.7% of fecal, hide, and preevisceration carcass samples, respectively. Salmonella was recovered from one postintervention carcass (of 1,016 sampled). Salmonella prevalence peaked in feces in the summer and was highest on hide and preevisceration carcasses in the summer and the fall. Non-O157 STEC prevalence also appeared to vary by season, but the efficiency in the recovery of isolates from stx-positive samples ranged from 37.5 to 83.8% and could have influenced these results. Cells harboring stx genes were detected by PCR in 34.3, 92.0, 96.6, and 16.2% of fecal, hide, preevisceration carcass, and postintervention carcass samples, respectively. The approximate level of non-O157 STEC and stx-harboring cells on postintervention carcasses was > or = 3.0 cells per 100 cm2 for only 8 of 199 carcasses (4.0%). Overall, the prevalence of E. coli O157:H7, Salmonella, and non-O157 STEC varied by season, was higher on hides than in feces, and decreased dramatically, along with pathogen levels, during processing and during the application of antimicrobial interventions. These results demonstrate the effectiveness of the current interventions used by the industry and highlight the significance of hides as a major source of pathogens on beef carcasses.

77 FR 59551 - Safety Zone, Changes to Original Rule; Boston Harbor's Rock Removal Project, Boston Inner Harbor...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-28

... DEPARTMENT OF HOMELAND SECURITY Coast Guard 33 CFR Part 165 [Docket No. USCG-2012-0767] RIN 1625-AA00 Safety Zone, Changes to Original Rule; Boston Harbor's Rock Removal Project, Boston Inner Harbor... original provisions of that temporary final rule, but adds two additional safety zones necessary for the...

78 FR 38577 - Special Local Regulations; Red Bull Flugtag National Harbor Event, Potomac River; National Harbor...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-27

...-AA08 Special Local Regulations; Red Bull Flugtag National Harbor Event, Potomac River; National Harbor... waters of the Potomac River on September 21, 2013. These special local regulations are necessary to... temporarily restrict vessel traffic in a portion of the Potomac River during the event. DATES: This rule is...

78 FR 18274 - Special Local Regulations; Red Bull Flugtag National Harbor Event, Potomac River; National Harbor...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-26

...-AA08 Special Local Regulations; Red Bull Flugtag National Harbor Event, Potomac River; National Harbor... event,'' to be held on the waters of the Potomac River on September 21, 2013. These special local... representative. This action is intended to temporarily restrict vessel traffic in a portion of the Potomac River...

77 FR 42464 - Special Local Regulations for Marine Events; Potomac River, National Harbor Access Channel, MD

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-19

...--AA08 Special Local Regulations for Marine Events; Potomac River, National Harbor Access Channel, MD... Harbor'' triathlon, a marine event to be held on the waters of the Potomac River in Prince George's...; Potomac River, National Harbor Access Channel, MD'' in the Federal Register (77 FR 20750). The rulemaking...

77 FR 19573 - Safety Zone; Wedding Fireworks Display, Boston Inner Harbor, Boston, MA

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-02

...-AA00 Safety Zone; Wedding Fireworks Display, Boston Inner Harbor, Boston, MA AGENCY: Coast Guard, DHS... zone on the navigable waters of the Boston Inner Harbor in the vicinity of Anthony's Pier 4, Boston, MA... Boston Inner Harbor in the vicinity of Anthony's Pier 4, Boston, MA. The Captain of the Port (COTP...

77 FR 45239 - Amendment of Class E Airspace; Bar Harbor, ME

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-31

...-1366; Airspace Docket No. 11-ANE-13] Amendment of Class E Airspace; Bar Harbor, ME AGENCY: Federal... area at Bar Harbor, ME, as the Surry Non-Directional Radio Beacon (NDB) has been decommissioned and new... airspace at Bar Harbor, ME (77 FR 27666) Docket No. FAA-2011-1366. Interested parties were invited to...

77 FR 40628 - Draft Safe Harbor Agreement and Application for an Enhancement of Survival Permit for the Tres...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-10

...-FF02ENEH00] Draft Safe Harbor Agreement and Application for an Enhancement of Survival Permit for the Tres... permit application and the associated draft Safe Harbor Agreement (SHA). DATES: Comment Period: To ensure... . SUPPLEMENTARY INFORMATION: Under a Safe Harbor Agreement, participating property owners voluntarily undertake...

75 FR 26198 - Foreign-Trade Zone 152 - Burns Harbor, Indiana, Application for Reorganization under Alternative...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-11

... DEPARTMENT OF COMMERCE Foreign-Trade Zones Board [Docket 32-2010] Foreign-Trade Zone 152 - Burns... six sites in the Burns Harbor/Gary, Indiana area: Site 1: (533,288 sq. ft.) located at 201 Mississippi... of Indiana/Burns International Harbor, Burns Harbor (Porter County); Site 3: (330 acres) within the...

77 FR 43513 - Olympia Harbor Days Tug Boat Races, Budd Inlet, WA

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-25

... Harbor Days Tug Boat Races, Budd Inlet, WA AGENCY: Coast Guard, DHS. ACTION: Notice of enforcement of regulation. SUMMARY: The Coast Guard will enforce the Special Local Regulation, Olympia Harbor Days Tug Boat... Special Local Regulation for Olympia Harbor Days Tug Boat Races, Budd Inlet, WA in 33 CFR 100.1309 on...

Teaching about Pearl Harbor. Curriculum Enhancement Series #1.

ERIC Educational Resources Information Center

Shields, Anna Marshall

These materials consist of sample lesson plans for teaching about the Japanese attack on Pearl Harbor on December 7, 1941, in both U.S. and world history classes. The lesson plans challenge students to examine how current attitudes toward the Japanese may be rooted in World War II and Pearl Harbor. Selected bibliographies on Pearl Harbor, World…