Modeling the Seasonal Cycle of Iron and Carbon Fluxes in the Amundsen Sea Polynya, Antarctica.

The Amundsen Sea Polynya (ASP) is distinguished by having the highest net primary production per unit area in the coastal Antarctic. Recent studies have related this high productivity to the presence of fast-melting ice shelves, but the mechanisms involved are not well understood. In this study we describe the first numerical model of the ASP to represent explicitly the ocean-ice interactions, nitrogen and iron cycles, and the coastal circulation at high resolution. The study focuses on the seasonal cycle of iron and carbon, and the results are broadly consistent with field observations collected during the summer of 2010-2011. The simulated biogeochemical cycle is strongly controlled by light availability(dictated by sea ice, phytoplankton self-shading, and variable sunlight). The micronutrient iron exhibits strong seasonality, where scavenging by biogenic particles and remineralization play large compensating roles. Lateral fluxes of iron are also important to the iron budget, and our results confirm the key role played by inputs of dissolved iron from the buoyancy-driven circulation of melting ice shelf cavities (the "meltwater pump"). The model suggests that westward flowing coastal circulation plays two important roles: it provides additional iron to the ASP and it collects particulate organic matter generated by the bloom and transports it to the west of the ASP. As a result, maps of vertical particulate organic matter fluxes show highest fluxes in shelf regions located west of the productive central ASP. Overall, these model results improve our mechanistic understanding of the ASP bloom, while suggesting testable hypotheses for future field efforts.

Ocean biogeochemistry modeled with emergent trait-based genomics.

Marine ecosystem models have advanced to incorporate metabolic pathways discovered with genomic sequencing, but direct comparisons between models and "omics" data are lacking. We developed a model that directly simulates metagenomes and metatranscriptomes for comparison with observations. Model microbes were randomly assigned genes for specialized functions, and communities of 68 species were simulated in the Atlantic Ocean. Unfit organisms were replaced, and the model self-organized to develop community genomes and transcriptomes. Emergent communities from simulations that were initialized with different cohorts of randomly generated microbes all produced realistic vertical and horizontal ocean nutrient, genome, and transcriptome gradients. Thus, the library of gene functions available to the community, rather than the distribution of functions among specific organisms, drove community assembly and biogeochemical gradients in the model ocean.

A disposable chemical heater and dry enzyme preparation for lysis and extraction of DNA and RNA from microorganisms.

Sample preparation, including bacterial lysis, remains a hurdle in the realization of complete point-of-care tests for many pathogens. Here, we developed a sample preparation methodology for enzymatic lysis and sample heating for low-resource, point-of-care applications. We show an instrument-free chemical heater system for rapid lysis of a gram-positive bacterium (Staphylococcus aureus) and an RNA virus (human respiratory syncytial virus) using a dried lysis enzyme mixture (achromopeptidase) for S. aureus. After a lysis step (<1 minute), lysis enzymes are heat deactivated (<5 minutes) using a simple disposable chemical heater. We demonstrated that both DNA and RNA in the heat-treated sample could be directly amplified without purification, even in the presence of a clinically-obtained human nasal sample. This simple approach to dry enzyme storage and sample heating is adaptable to many applications where samples need to be lysed, including use in low-resource laboratories and in single-use or cartridge-based point-of-care diagnostic devices.

Precision chemical heating for diagnostic devices.

Decoupling nucleic acid amplification assays from infrastructure requirements such as grid electricity is critical for providing effective diagnosis and treatment at the point of care in low-resource settings. Here, we outline a complete strategy for the design of electricity-free precision heaters compatible with medical diagnostic applications requiring isothermal conditions, including nucleic acid amplification and lysis. Low-cost, highly energy dense components with better end-of-life disposal options than conventional batteries are proposed as an alternative to conventional heating methods to satisfy the unique needs of point of care use.

One-step purification and concentration of DNA in porous membranes for point-of-care applications.

The emergence of rapid, user-friendly, point-of-care (POC) diagnostic systems is paving the way for better disease diagnosis and control. Lately, there has been a strong emphasis on developing molecular-based diagnostics due to their potential for greatly increased sensitivity and specificity. One of the most critical steps in developing practical diagnostic systems is the ability to perform sample preparation, especially the purification of nucleic acids (NA), at the POC. As such, we have developed a simple-to-use, inexpensive, and disposable sample preparation system for in-membrane purification and concentration of NAs. This system couples lateral flow in a porous membrane with chitosan, a linear polysaccharide that captures NAs via anion exchange chromatography. The system can also substantially concentrate the NAs. The combination of these capabilities can be used on a wide range of sample types, which are prepared for use in downstream processes, such as qPCR, without further purification.

Clinical management and humoral immune responses to rabies post-exposure prophylaxis among three patients who received solid organs from a donor with rabies.

BACKGROUND: The rabies virus causes a fatal encephalitis and can be transmitted through organ transplantation. In 2013, a man developed rabies 18 months after receiving a kidney from a donor with rabies, who was not known to have been infected when the organs were procured. Three additional persons who received organs from the same donor (liver, kidney, heart), all of whom were not vaccinated for rabies before transplantation, received rabies post-exposure prophylaxis (PEP) with rabies immune globulin and 5 doses of rabies vaccine as soon as the diagnosis of rabies was made in the donor (18 months after their transplant surgeries). We describe their clinical management. METHODS: As the 3 recipients were all on immunosuppressive medications, post-vaccination serologic testing was performed using the rapid fluorescent focus inhibition test to measure rabies virus neutralizing antibodies (RVNAs). An acceptable antibody response to administration of rabies vaccine was defined as detection of RVNAs at a concentration ≥0.1 IU/mL from a serum specimen collected ≥7 days after the fifth vaccine dose. RESULTS: All 3 recipients demonstrated an acceptable antibody response despite their immunosuppressed states. More than 36 months have passed since their transplant surgeries, and all 3 recipients have no evidence of rabies. CONCLUSIONS: The survival of 3 previously unvaccinated recipients of solid organs from a donor with rabies is unexpected. Although the precise factors that led to their survival remain unclear, our data suggest that PEP can possibly enhance transplant safety in settings in which donors are retrospectively diagnosed with rabies.

Electromechanical cell lysis using a portable audio device: enabling challenging sample preparation at the point-of-care.

Audio sources are ubiquitously available on portable electronic devices, including cell phones. Here we demonstrate lysis of Mycobacterium marinum and Staphylococcus epidermidis bacteria utilizing a portable audio device coupled with a simple and inexpensive electromagnetic coil. The resulting alternating magnetic field rotates a magnet in a tube with the sample and glass beads, lysing the cells and enabling sample preparation for these bacteria anywhere there is a cell phone, mp3 player, laptop, or other device with a headphone jack.

A low cost point-of-care viscous sample preparation device for molecular diagnosis in the developing world; an example of microfluidic origami.

The lab-on-a-chip concept has led to several point-of-care (POC) diagnostic microfluidic platforms. However, few of these can process raw samples for molecular diagnosis and fewer yet are suited for use in a resource-limited setting without permanent electrical infrastructure. We present here a very low cost paper microfluidic device for POC extraction of bacterial DNA from raw viscous samples--a challenge for conventional microfluidic platforms. This is an example of "microfluidic origami" in that the system is activated by folding; demonstrated here is room temperature cell lysis and DNA extraction from pig mucin (simulating sputum) spiked with E. coli without the use of external power. The microfluidic origami device features dry reagent storage and rehydration of the lysis buffer. We demonstrate DNA extraction from samples with a bacterial load as low as 33 CFU ml(-1). Extraction times, starting from the raw sample, have been optimized to about 1.5 h without the use of external power, or to within 1 h using an oven or a heater block. The fabrication of this paper microfluidic device can be translated into high volume production in the developing world without the need for a semiconductor clean room or a microfabrication facility. The sample preparation can be performed with the addition of just the sample, water, ethanol and elute buffer to the device, thus reducing chemical hazards during transport and handling.

Amazon River enhances diazotrophy and carbon sequestration in the tropical North Atlantic Ocean.

The fresh water discharged by large rivers such as the Amazon is transported hundreds to thousands of kilometers away from the coast by surface plumes. The nutrients delivered by these river plumes contribute to enhanced primary production in the ocean, and the sinking flux of this new production results in carbon sequestration. Here, we report that the Amazon River plume supports N(2) fixation far from the mouth and provides important pathways for sequestration of atmospheric CO(2) in the western tropical North Atlantic (WTNA). We calculate that the sinking of carbon fixed by diazotrophs in the plume sequesters 1.7 Tmol of C annually, in addition to the sequestration of 0.6 Tmol of C yr(-1) of the new production supported by NO(3) delivered by the river. These processes revise our current understanding that the tropical North Atlantic is a source of 2.5 Tmol of C to the atmosphere [Mikaloff-Fletcher SE, et al. (2007) Inverse estimates of the oceanic sources and sinks of natural CO(2) and the implied oceanic carbon transport. Global Biogeochem Cycles 21, doi:10.1029/2006GB002751]. The enhancement of N(2) fixation and consequent C sequestration by tropical rivers appears to be a global phenomenon that is likely to be influenced by anthropogenic activity and climate change.

Measurement of the D(s)+ lifetime.

A high statistics measurement of the D(s)+ lifetime from the Fermilab fixed-target FOCUS photoproduction experiment is presented. We describe the analysis of the two decay modes, D(s)+ --> phi(1020)pi+ and D(s)+ -->K*(892)0K+, used for the measurement. The measured lifetime is 507.4 +/- 5.5(stat) +/- 5.1(syst) fs using 8961 +/- 105 D(s)+ --> phi(1020)pi+ and 4680 +/- 90 D(s)+ --> K*(892)0K+ decays. This is a significant improvement over the present world average.

Inhaled nitric oxide in neurogenic cardiopulmonary dysfunction: implications for organ donation.

UNLABELLED: Many cadaveric organs for transplantation come from patients dying of sudden intracranial catastrophes. Cardiopulmonary dysfunction after such neurogenic insults is a well-recognized entity. The pulmonary dysfunction usually presents as florid pulmonary edema within minutes to hours after the initial intracranial insult and may occur in isolation or co-exist with overt or subclinical myocardial dysfunction. This may result in severe hypoxia, which threatens survival and outcomes in salvageable cases and organ preservation in patients who would be potential organ donors. Thus, rapid initiation of strategies aimed at ameliorating hypoxia after an acute neurogenic insult is paramount. Strategies aimed at improving acute hypoxia include maximizing ventilator support, diuretics, and volume resuscitation. Cardiac dysfunction may require use of ionotropes. We report the case of a 16-year-old female who developed catastrophic acute posterior fossa intracranial bleeding with resulting intractable hypoxia due to neurogenic cardiopulmonary dysfunction that responded dramatically to inhaled nitric oxide (INO). The patient went on to successfully donate organs following a non-heart-beating donor protocol. This therapy, to our knowledge, has never been described previously for use in patients with hypoxia secondary to neurogenic cardiopulmonary dysfunction. CONCLUSIONS: We document for the first time a dramatic response of hypoxia to INO in neurogenic cardiopulmonary dysfunction. This therapy ameliorates hypoxia, which may have vital implications in minimizing secondary brain injury in salvageable cases and optimizing organ preservation in potential organ donors with catastrophic intracranial insults.

A comparison of DNA vaccines for the rabies-related virus, Mokola.

Mokola virus, a rabies-related virus, has been reported to date from the African continent only. Like rabies virus, it is highly pathogenic, causes acute encephalitis, and zoonotic events have been documented. Although believed to be rare, there has been an unexplained increase in the number of isolations of the virus in South Africa in recent years. We have cloned and sequenced the glycoprotein (G) and nucleoprotein (N) genes from a South African Mokola virus, and used these in the construction of different DNA vaccines for immunization against Mokola virus. Four vaccines, utilizing different promoters and DNA backbone compositions, were generated and compared for efficacy in protection against Mokola virus. In one of these, both the Mokola virus G and N genes were co-expressed. Two of the single G-expressing DNA vaccines (based on pSG5 and pCI-neo, respectively) protected laboratory mice against lethal challenge, despite major differences in their promoters. However, neither vaccine was fully protective in a single immunization only. Serological assays confirmed titers of virus-neutralizing antibodies after immunization, which increased upon booster vaccine administration. A third construct (based on pBudCE4) was less effective in inducing a protective immune response, despite employing a strong CMV enhancer/promoter also used in the pCI-neo plasmid. Dual expression of Mokola virus G and N genes in pBudCE4 did not enhance its efficacy, under the conditions described. In addition, no significant utility could be demonstrated for a combined prime-boost approach, as no cross-protective immunity was observed against rabies or Mokola viruses from the use of pSG5-mokG or vaccinia-rabies glycoprotein recombinant virus vaccines, respectively, even though both vaccines provided 60-100% protection against homologous virus challenge.

A high statistics measurement of the Lambda(+)(c) lifetime.

A high statistics measurement of the Lambda(+)(c) lifetime from the Fermilab fixed-target FOCUS photoproduction experiment is presented. We describe the analysis technique with particular attention to the determination of the systematic uncertainty. The measured value of 204.6 +/- 3.4 (stat) +/- 2.5 (syst) fs from 8034 +/- 122 Lambda(+)(c)-->pK(-)pi(+) decays represents a significant improvement over the present world average.

Search for CP violation in the decays D+--> K(S)pi+ and D+-->K(S)K+.

A high-statistics sample of photoproduced charm from the FOCUS experiment has been used to search for direct CP violation in the decay rates for D+-->K(S)pi+ and D+-->K(S)K+. We have measured the following asymmetry parameters relative to D+-->K-pi+pi+: A(CP)(K(S)pi+) = (-1.6+/-1.5+/-0.9)%, A(CP)(K(S)K+) = (+6.9+/-6.0+/-1.5)%, and A(CP)(K(S)K+) = (+7.1+/-6.1+/-1.2)% relative to D+-->K(S)pi+. We have also measured the relative branching ratios and found Gamma(D+-->K(0)pi+)/Gamma(D+-->K-pi+pi+) = (30.60+/-0.46+/-0.32)%, Gamma(D+-->K(0)K+)/Gamma(D+-->K-pi+pi+) = (6.04+/-0.35+/-0.30)%, and Gamma(D+-->K(0)K+)/Gamma(D+-->K(0)pi+) = (19.96+/-1.19+/-0.96)%.

Measurement of the branching ratios of D(+) and D(+)(s) hadronic decays to four-body final states containing a K(S).

We have studied hadronic four-body decays of D(+) and D(+)(s) mesons with a K(S) in the final state using data recorded during the 1996-1997 fixed-target run of the Fermilab high energy photoproduction experiment FOCUS. We report a new branching ratio measurement of gamma(D(+)-->K(S)K-pi(+)pi(+))/gamma(D(+)-->K(S)pi(+)pi(+)pi(-)) = 0.0768+/-0.0041+/-0.0032. We make the first observation of three new decay modes with branching ratios gamma(D(+)-->K(S)K+pi(+)pi(-))/gamma(D(+)-->K(S)pi(+)pi(+)pi(-)) = 0.0562+/-0.0039+/-0.0040, gamma(D(+)-->K(S)K+K-pi(+))/gamma(D(+)-->K(S)pi(+)pi(+)pi(-)) = 0.0077+/-0.0015+/-0.0009, and gamma(D(+)(s)-->K(S)K+pi(+)pi(-))/gamma(D(+)(s)-->K(S)K-pi(+)pi(+)) = 0.586+/-0.052+/-0.043, where in each case the first error is statistical and the second error is systematic.

Testosterone delivery using glutamide-based complex high axial ratio microstructures.

Complex high axial ratio microstructures (CHARMs) were evaluated for delivery of testosterone in vivo. Methods to incorporate testosterone included noncovalent mixing and covalent attachment of testosterone to the lipid to form a prodrug monomer. When prepared by covalent attachment, testosterone-loaded CHARMs were resistant to in vitro spontaneous hydrolysis; when injected into rats, testosterone was released with biphasic kinetics consisting of a burst followed by a much slower phase. Some CHARM material associated with testosterone persisted at the site of injection for at least 9 days.

Rapid clearance of SAG-2 rabies virus from dogs after oral vaccination.

This study investigated the safety, efficacy, and clearance of SAG-2, an attentuated rabies virus, after oral vaccination in dogs. Nineteen dogs consumed baits containing lyophilized vaccine, but residual SAG-2 virus was recovered in only one of 57 oral swabs, collected one hour post-vaccination. Seven vaccinates were euthanized between 24 and 96 h after consuming a bait. Rabies virus RNA was detected in tonsils from all seven dogs by nested RT-PCR, with primers to the viral glycoprotein. Genomic, sense-transcripts, and m-RNAs were detected in five of seven tonsil samples using primers to the rabies virus nucleoprotein gene, as well as in four of seven samples from the buccal mucosa and one of seven from the tongue. Rabies virus antigen was detected in all tonsils by an immunohistochemistry test, confirming the RT-PCR results. In addition, virus was isolated from one tonsil sample collected at 96 h, providing supportive evidence of viral replication. Ten of 12 (83%) of the vaccinated dogs demonstrated an anamnestic response, with viral neutralizing antibody titers (> or =0.5 IU/ml), after rabies virus challenge. These ten dogs survived, whereas all control dogs succumbed to rabies. Attenuated rabies viruses, such as SAG-2, replicate in local tissues of the oral cavity and can be cleared relatively quickly, without viral excretion, leading to protective immunity against the disease.

Epidemiologic characteristics of rabies virus variants in dogs and cats in the United States, 1999.

OBJECTIVE: To evaluate epidemiologic features of rabies virus variants in dogs and cats in the United States during 1999 and assess the role of bat-associated variants. DESIGN: Epidemiologic survey. SAMPLE POPULATION: Rabies viruses from 78 dogs and 230 cats. PROCEDURE: Brain specimens from rabid dogs and cats were submitted for typing of rabies virus. Historical information, including ownership and vaccination status, was obtained for each animal. Specimens were typed by use of indirect fluorescent antibody assay or reverse transcriptase polymerase chain reaction assay and nucleotide sequence analysis. RESULTS: Nearly all animals were infected with the predicted terrestrial rabies virus variant associated with the geographic location of the submission. A bat-associated variant of rabies virus was found in a single cat from Maryland. More than half (53%) of submitted animals were classified as owned animals, and most had no known history of vaccination. One vaccination failure was reported in a dog that did not receive a booster dose of rabies vaccine after exposure to a possibly rabid animal. CONCLUSIONS AND CLINICAL RELEVANCE: Bat-associated rabies virus variants were not a common cause of rabies in dogs and cats during 1999. Vaccine failures were uncommon during the study period. Because most rabid dogs and cats were unvaccinated and were owned animals rather than strays, educational campaigns targeting owners may be useful.

A rapid diffusion immunoassay in a T-sensor.

We have developed a rapid diffusion immunoassay that allows measurement of small molecules down to subnanomolar concentrations in <1 min. This competitive assay is based on measuring the distribution of a labeled probe molecule after it diffuses for a short time from one region into another region containing antigen-specific antibodies. The assay was demonstrated in the T-sensor, a simple microfluidic device that places two fluid streams in contact and allows interdiffusion of their components. The model analyte was phenytoin, a typical small drug molecule. Clinically relevant levels were measured in blood diluted from 10- to 400-fold in buffer containing the labeled antigen. Removal of cells from blood samples was not necessary. This assay compared favorably with fluorescence polarization immunoassay (FPIA) measurements. Numerical simulations agree well with experimental results and provide insight for predicting assay performance and limitations. The assay is homogeneous, requires <1 microl of reagents and sample, and is applicable to a wide range of analytes.

Concentration and separation of proteins in microfluidic channels on the basis of transverse IEF.

The use of microfluidic channels formed by two electrodes made of gold or palladium to perform transverse isoelectric focusing (IEF) is presented as a means for continuous concentration and fractionation of proteins. The microchannels were 40 mm long with an electrode gap of 1.27 mm and a depth of 0.354 mm. The properties of pH gradients formed as a result of the electrolysis of water were influenced by variation of parameters such as the initial pH, ionic strength, and flow rate. Transverse IEF in pressure-driven flow is demonstrated using bovine serum albumin in a single ampholyte buffer as well as in multiple-component buffers. Experimental results of protein focusing compare well to predictions of a mathematical model. Optimal conditions for efficient continuous fractionation of a protein mixture are summarized and discussed.