Randomly primed,strand-switching,MinION-based sequencing for the detection and characterization of cultured RNA viruses

RNA viruses rapidly mutate, which can result in increased virulence, increased escape from vaccine protection, and false-negative detection results. Targeted detection methods have a limited ability to detect unknown viruses and often provide insufficient data to detect coinfections or identify antigenic variants. Random, deep sequencing is a method that can more fully detect and characterize RNA viruses and is often coupled with molecular techniques or culture methods for viral enrichment. We tested viral culture coupled with third-generation sequencing for the ability to detect and characterize RNA viruses. Cultures of bovine viral diarrhea virus, canine distemper virus (CDV), epizootic hemorrhagic disease virus, infectious bronchitis virus, 2 influenza A viruses, and porcine respiratory and reproductive syndrome virus were sequenced on the MinION platform using a random, reverse primer in a strand-switching reaction, coupled with PCR-based barcoding. Reads were taxonomically classified and used for reference-based sequence building using a stock personal computer. This method accurately detected and identified complete coding sequence genomes with a minimum of 20× coverage depth for all 7 viruses, including a sample containing 2 viruses. Each lineage-typing region had at least 26× coverage depth for all viruses. Furthermore, analyzing the CDV sample through a pipeline devoid of CDV reference sequences modeled the ability of this protocol to detect unknown viruses. Our results show the ability of this technique to detect and characterize dsRNA, negative- and positive-sense ssRNA, and nonsegmented and segmented RNA viruses.     

Analysis of cerebrospinal fluid from dogs and cats after 24 and 48 hours of storage

OBJECTIVE: To compare differential cell counts and cell characteristics of CSF samples analyzed immediately or after storage for 24 and 48 hours at 4 C with and without the addition of autologous serum. DESIGN: Prospective study. ANIMALS: 36 dogs and 6 cats. PROCEDURE: CSF samples were collected from the cerebellomedullary cistern and divided into 250-microliter aliquots. Slides of CSF samples were prepared by use of cytocentrifugation immediately and after 24 and 48 hours of storage with addition of autologous serum (final concentrations, 11 and 29%). Differential cell counts and number of unrecognizable cells were compared among preparations. RESULTS: Significant differences in the differential cell counts were not detected among samples analyzed before or after storage. Although the number of unrecognizable cells increased with storage time, this did not result in a significant effect on cell distribution or diagnosis. Cells in CSF samples stored with 11% serum more closely resembled cells in fresh samples than did cells in samples stored with 29% serum. CONCLUSIONS AND CLINICAL RELEVANCE: CSF samples collected at veterinary clinics remote from a diagnostic laboratory or during nonoperational hours may be preserved through the addition of autologous serum. Evaluation of such samples is likely to result in an accurate diagnosis for at least 48 hours after collection.     

Influence of a probiotic adjunct culture of Enterococcus faecium on the quality of cheddar cheese

Cheddar cheese has previously been shown to be an effective vehicle for delivery of viable cells of a probiotic Enterococcus faecium strain to the gastrointestinal tract. The particular strain, E. faecium PR88, has proven efficacy in the treatment of irritable bowel syndrome, and in this study it was evaluated for suitability as a starter adjunct for Cheddar cheese manufacture. When added to cheesemilk at an inoculum of 2 x 10(7) cfu/mL, the enterococcal adjunct maintained viability in Cheddar cheese at levels of up to 3 x 10(8) cfu/g during 9 months of ripening. Increased proteolysis and higher levels of some odor-active volatile compounds were observed in Cheddar cheeses containing the PR88 adjunct compared with the control throughout the ripening period. In addition, the enterococcal adjunct strain did not affect cheese composition. Although sensory evaluation showed no significant difference in flavor/aroma and body/texture scores between control and experimental cheeses, repeated comments by the commercial grader consistently described the cheeses containing PR88 as 'more advanced than the control' and as having 'better flavor'. These findings indicate that the presence of the PR88 adjunct strain in Cheddar cheese at levels of >/=10(8) cfu/g may positively influence Cheddar flavor.     

Two-dimensional nanosheets produced by liquid exfoliation of layered materials

If they could be easily exfoliated, layered materials would become a diverse source of two-dimensional crystals whose properties would be useful in applications ranging from electronics to energy storage. We show that layered compounds such as MoS(2), WS(2), MoSe(2), MoTe(2), TaSe(2), NbSe(2), NiTe(2), BN, and Bi(2)Te(3) can be efficiently dispersed in common solvents and can be deposited as individual flakes or formed into films. Electron microscopy strongly suggests that the material is exfoliated into individual layers. By blending this material with suspensions of other nanomaterials or polymer solutions, we can prepare hybrid dispersions or composites, which can be cast into films. We show that WS(2) and MoS(2) effectively reinforce polymers, whereas WS(2)/carbon nanotube hybrid films have high conductivity, leading to promising thermoelectric properties.     

Atrial natriuretic peptide inhibits a cation channel in renal inner medullary collecting duct cells

The patch-clamp technique was used to examine the effects of atrial natriuretic peptide (ANP) and its second messenger guanosine 3',5'-monophosphate (cGMP) on an amiloride-sensitive cation channel in the apical membrane of renal inner medullary collecting duct cells. Both ANP (10(-11) M) and dibutyryl guanosine 3',5'-monophosphate (10(-4) M) inhibited the channel in cell-attached patches, and cGMP (10(-5) M) inhibited the channel in inside-out patches. The inner medullary collecting duct is the first tissue in which ANP, via its second messenger cGMP, has been shown to regulate single ion channels. The results suggest that the natriuretic action of ANP is related in part to cGMP-mediated inhibition of electrogenic Na+ absorption by the inner medullary collecting duct.     

Analytical method for the determination of atrazine and its dealkylated chlorotriazine metabolites in water using SPE sample preparation and GC-MSD analysis

A method is reported for the determination of atrazine and its dealkylated chlorotriazine metabolites in ground, surface, and deionized water. Water samples are adjusted to pH 3-4 prior to loading onto two SPE cartridges in series: C-18 and C-18/cation exchange mixed-mode polymeric phases. The analytes are eluted from each of the two cartridges separately, and the pooled and concentrated fraction is analyzed using gas chromatography-mass selective detection in the selected ion monitoring mode. The lower limit of method validation is 0.10 micrograms/L (ppb) for 2-chloro-4-(ethylamino)-6-(isopropylamino)-s-triazine (atrazine), 2-amino-4-chloro-6-(isopropylamino)-s-triazine (G-30033, deethylatrazine), 2-amino-4-chloro-6-(ethylamino)-s-triazine (G-28279, deisopropylatrazine), and 2,4-diamino-6-chloro-s-triazine (G-28273, didealkyatrazine). The overall mean procedural recoveries (and standard deviations) are 96 (6.9), 96 (5.5), 95 (6.8), and 100% (10%) for atrazine, G-30033, G-28279, and G-28273, respectively (n = 49). The method validation study was conducted under U.S. EPA FIFRA Good Laboratory Practice Guidelines 40 CFR 160. The reported procedure accounts for residues of G-28273 in water.