Biology subjects

Jones, D. L.

Publications and source records attributed to Jones, D. L..

3 recordsLinked to original sources

bioRxiv2018

Two-step concentration of complex water samples for the detection of viruses

The accurate detection and quantification of pathogenic viruses in water is essential to understand and reduce the risk of human infection. In this paper, we validated a two-step method for the concentration of enteric viruses in water and wastewater samples. The method involves a tangential flow ultrafiltration step that reduces the sample volume of 1 - 10 L to approx. 50 mL, followed by secondary precipitation using polyethylene glycol 6000 that reduces the volume to 1 - 4 mL. For method validation, surface water samples were spiked with different concentrations of enteric viruses and viral recoveries in the concentrates exceeded 10% in all experiments. The method is suitable for water samples with high and low salinity and turbidity, allowing the accurate comparison of viral titers in a diverse range of water types. Furthermore, the method has the potential to concentrate other pathogens, e.g. bacteria or protozoa. Hence, the use of this method can improve the holistic assessment of risks associated with wastewater contaminated environments.\n\nO_LIModified tangential flow ultrafiltration method that reduces membrane clogging.\nC_LIO_LISecondary concentration with a beef extract-elution step to remove solid matter.\nC_LIO_LIThe two-step concentration method enables at least 10% recovery for different enteric viruses in difficult matrices.\nC_LIO_LIUsing the two-step concentration method 10,000x concentration can be achieved.\nC_LI\n\nSpecifications Table:\n\n\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@12d4fceorg.highwire.dtl.DTLVardef@1d2880borg.highwire.dtl.DTLVardef@e1acf6org.highwire.dtl.DTLVardef@226492org.highwire.dtl.DTLVardef@1f8edf0_HPS_FORMAT_FIGEXP M_TBL C_TBL

microbiology↗

bioRxiv2017

A systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria

Gene regulation is one of the most ubiquitous processes in biology. But while the catalog of bacterial genomes continues to expand rapidly, we remain ignorant about how almost all of the genes in these genomes are regulated. At present, characterizing the molecular mechanisms by which individual regulatory sequences operate requires focused efforts using low-throughput methods. Here we show how a combination of massively parallel reporter assays, mass spectrometry, and information-theoretic modeling can be used to dissect bacterial promoters in a systematic and scalable way. We demonstrate this method on both well-studied and previously uncharacterized promoters in the enteric bacterium Escherichia coli. In all cases we recover nucleotide-resolution models of promoter mechanism. For some promoters, including previously unannotated ones, the approach allowed us to further extract quantitative biophysical models describing input-output relationships. This method opens up the possibility of exhaustively dissecting the mechanisms of promoter function in E. coli and a wide range of other bacteria.

biophysics↗

bioRxiv2017

Structural and functional diversity of a dense sample of retinal ganglion cells

To aid understanding of retinal structure and function, we present as an online resource the dendritic arbors and visual responses of ganglion cells in a single patch of mouse retina. We divide the inner plexiform layer, which contains the dendritic arbors of ganglion cells, into four sublaminae defined by a purely anatomical principle of arbor segregation. The sublaminae serve as the starting point for a hierarchical clustering of our ganglion cells. We propose and apply a quantitative criterion for validating a cluster as a ganglion cell type: the aggregate neurite density of a type should be approximately uniform (\"density conservation\"). Finally, we find that ganglion cells arborizing in the inner marginal sublamina of the inner plexi-form layer exhibit significantly more sustained visual responses on average.

neuroscience↗