A robotics platform for automated batch fabrication of high density, microfluidics-based DNA microarrays, with applications to single cell, multiplex assays of secreted proteins

Microfluidics flow-patterning has been utilized for the construction of chip-scale miniaturized DNA and protein barcode arrays. Such arrays have been used for specific clinical and fundamental investigations in which many proteins are assayed from single cells or other small sample sizes. However, flow-patterned arrays are hand-prepared, and so are impractical for broad applications. We describe an integrated robotics/microfluidics platform for the automated preparation of such arrays, and we apply it to the batch fabrication of up to eighteen chips of flow-patterned DNA barcodes. The resulting substrates are comparable in quality with hand-made arrays and exhibit excellent substrate-to-substrate consistency. We demonstrate the utility and reproducibility of robotics-patterned barcodes by utilizing two flow-patterned chips for highly parallel assays of a panel of secreted proteins from single macrophage cells

Atmospheric input of nitrogen and phosphorus to the Southeast Mediterranean: Sources, fluxes, and possible impact

Estimates of the sources and wet deposition fluxes of inorganic nutrients (PO43-, NO3-, NO2-, NH4+) have been made using a long-term wet atmospheric deposition measurement at three sites along the Mediterranean coast of Israel. The nutrient composition in rainwater indicated a dominant anthropogenic source for NO, and NH: and a continental, natural, and anthropogenic, rock/soil source for PO43-. The calculated long-term dissolved inorganic N (IN) and inorganic P (IP) fluxes were 0.28 and 0.009 g m(-2) yr(-1) to the coastal zone and estimated as 0.24 and 0.008 g m(-2) yr(-1) to the Southeast (SE) Mediterranean, with a possible increasing pattern of the annual dissolved IN fluxes. Concentration of total and seawater leachable LP (LIP) from dust was examined on 20 Whatman 41 filters collected during 1996. The mean total IP concentration in dust was 0.13 +/- 0.11% (geomean = 0.09%), with a mean of 387 +/- 205 mu g IP per g of dust leached by seawater. LIP from dust varies between 6 and 85% (mean of 38%) of the dry total IF. Dust of desert-type (Saharan) events exhibited lower LIP solubility in seawater (similar to 25%, median) than air masses of European origin (similar to 45%, median). The calculated ratio of wet deposition to total (wet and dry) deposition here of 0.2 showed the importance of dry deposition of P in the SE Mediterranean basin compared to atmospheric inputs into the northwestern basin. The total IP and seawater LIP fluxes from dry deposition were estimated as 0.04 and 0.01 g m(-2) yr(-1), respectively. Atmospheric inputs of bioavailable N and P represent an imbalanced contribution to the new production of 8-20 and 4-11%, respectively, and reinforce the unusual N: P ratios (similar to 27) and possible P limitation in the SE Mediterranean

Nutrient Cycling in the Mediterranean Sea: The Key to Understanding How the Unique Marine Ecosystem Functions and Responds to Anthropogenic Pressures

The Mediterranean Sea is a marine desert: although it receives large nutrient inputs from a rapidly growing coastal population, its offshore waters exhibit extremely low biological productivity. Here, we use a mass balance modelling approach to analyse the sources and fate of the two main nutrients that support marine biomass production: phosphorus (P) and nitrogen (N). Surprisingly, the main source of P and N to the Mediterranean Sea is North Atlantic surface water entering through the Strait of Gibraltar, not emissions from surrounding land. The low biological productivity of the Mediterranean Sea is linked to the switch from less bioavailable nutrients entering the basin to highly bioavailable nutrients leaving it although similar amounts of total P and N enter and leave the Mediterranean Sea. This unique feature is a direct consequence of its unusual anti-estuarine circulation. An important environmental implication of the anti-estuarine circulation is that it efficiently removes excess anthropogenic nutrients entering the Mediterranean Sea, thus protecting offshore waters against eutrophication contrary to other semi-enclosed marine basins. In a similar vein, the “self-cleaning” nature of the Mediterranean Sea may prevent severe oxygen depletion of Mediterranean deep waters should ongoing climate warming lead to a weakening of the thermohaline circulation

Development of a modified SEDEX phosphorus speciation method for ancient rocks and modern iron-rich sediments

We report the development of a modified method for evaluating different reservoirs of sedimentary phosphorus (P) in ancient marine sedimentary rocks and in modern Fe-rich sediments. Utilising the existing SEDEX scheme for P partitioning in modern sediments, we initially demonstrate limitations in the application of the original scheme to sediments and rocks containing crystalline hematite and magnetite. We tested additional extractions for these crystalline Fe phases, using both synthetic minerals, and modern and ancient sediments. The addition of 6 h oxalate and 6 h citrate-dithionate-acetate extractions considerably enhanced the total recovery of synthetic magnetite and hematite to 88.7 ± 1.1% and 76.9 ± 3.8%, respectively. In addition, application of the 6 h oxalate extraction to synthetic P-containing magnetite recovered 93.9 ± 1.7% of the Fe present and 88.2 ± 12.8% of the co-precipitated P. Based upon these results we developed a modified SEDEX extraction scheme. The modified scheme was applied to modern Fe-rich sediments from Golfo Dulce, Costa Rica, which resulted in 16% higher Fe-bound P recovery. Application of the scheme to a variety of ancient marine rocks increased the recovery of Fe-bound P by up to 22%. We also highlight the potential for authigenic carbonate fluorapatite to convert to more crystalline apatite in ancient rocks during deep burial and metamorphism. We suggest that in such systems minimum and maximum estimates of the total reactive P pool may be calculated with and without the inclusion of crystalline P. It is noted that the application of the revised method may have important implications for understanding the cycling of P in ancient marine environments

Should the Ruptured Renal Allograft Be Removed?

During a 16-month period when 93 renal transplants were performed, eight kidney graft ruptures were detected within 18 days of transplantation, without evidence of venous obstruction. Six grafts were removed at the time of an exploratory operation for rupture and only one showed signs of probable irreversible rejection when examined by microscopy. Two graft ruptures were repaired and one of these grafts has had good long-term function 22 months later. These observations suggest that if bleeding at the site of graft rupture can be securely controlled and if the conditions of the patient and of the graft are favorable except for the rupture, it may be possible to save more than one of eight grafts. © 1979, American Medical Association. All rights reserved

Potentially bioavailable iron delivery by iceberg-hosted sediments and atmospheric dust to the polar oceans

Iceberg-hosted sediments and atmospheric dust transport potentially bioavailable iron to the Arctic and Southern oceans as ferrihydrite. Ferrihydrite is nanoparticulate and more soluble, as well as potentially more bioavailable, than other iron (oxyhydr)oxide minerals (lepidocrocite, goethite, and hematite). A suite of more than 50 iceberghosted sediments contain a mean content of 0.076 wt% Fe as ferrihydrite, which produces iceberg-hosted Fe fluxes ranging from 0.7 to 5.5 and 3.2 to 25 Gmoles yr 1 to the Arctic and Southern oceans respectively. Atmospheric dust (with little or no combustion products) contains a mean ferrihydrite Fe content of 0.038 wt% (corresponding to a fractional solubility of 1 %) and delivers much smaller Fe fluxes (0.02–0.07 Gmoles yr 1 to the Arctic Ocean and 0.0– 0.02 Gmoles yr 1 to the Southern Ocean). New dust flux data show that most atmospheric dust is delivered to sea ice where exposure to melting/re-freezing cycles may enhance fractional solubility, and thus fluxes, by a factor of approximately 2.5. Improved estimates for these particulate sources require additional data for the iceberg losses during fjord transit, the sediment content of icebergs, and samples of atmospheric dust delivered to the polar regions

Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency

Citation: Serba, D. D., Uppalapati, S. R., Krom, N., Mukherjee, S., Tang, Y. H., Mysore, K. S., & Saha, M. C. (2016). Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency. Bmc Genomics, 17, 14. doi:10.1186/s12864-016-3377-8Background: Switchgrass, a warm-season perennial grass studied as a potential dedicated biofuel feedstock, is classified into two main taxa - lowland and upland ecotypes - that differ in morphology and habitat of adaptation. But there is limited information on their inherent molecular variations. Results: Transcriptome analysis by RNA-sequencing (RNA-Seq) was conducted for lowland and upland ecotypes to document their gene expression variations. Mapping of transcriptome to the reference genome (Panicum virgatum v1. 1) revealed that the lowland and upland ecotypes differ substantially in sets of genes transcribed as well as levels of expression. Differential gene expression analysis exhibited that transcripts related to photosynthesis efficiency and development and photosystem reaction center subunits were upregulated in lowlands compared to upland genotype. On the other hand, catalase isozymes, helix-loop-helix, late embryogenesis abundant group I, photosulfokinases, and S-adenosyl methionine synthase gene transcripts were upregulated in the upland compared to the lowlands. At >= 100x coverage and >= 5% minor allele frequency, a total of 25,894 and 16,979 single nucleotide polymorphism (SNP) markers were discovered for VS16 (upland ecotype) and K5 (lowland ecotype) against the reference genome. The allele combination of the SNPs revealed that the transition mutations are more prevalent than the transversion mutations. Conclusions: The gene ontology (GO) analysis of the transcriptome indicated lowland ecotype had significantly higher representation for cellular components associated with photosynthesis machinery controlling carbon fixation. In addition, using the transcriptome data, SNP markers were detected, which were distributed throughout the genome. The differentially expressed genes and SNP markers detected in this study would be useful resources for traits mapping and gene transfer across ecotypes in switchgrass breeding for increased biomass yield for biofuel conversion