Christy Rand - Academia.edu (original) (raw)

Papers by Christy Rand

Journal of Bacteriology, Nov 1, 2010

We report here the complete 2.92-Mb genome sequence of a clinical isolate of methicillin-resistan... more We report here the complete 2.92-Mb genome sequence of a clinical isolate of methicillin-resistant Staphylococcus aureus subsp. aureus that demonstrates intermediate-level vancomycin resistance. The strain, named JKD6008, belongs to multilocus sequence type 239 and was isolated from the bloodstream of a patient in New Zealand in 2003.

Journal of Bacteriology, 2011

We report here the complete genome sequence of Staphylococcus aureus T0131, which is a multiresis... more We report here the complete genome sequence of Staphylococcus aureus T0131, which is a multiresistant clinical isolate recovered in China and the first sequenced epidemic ST239-MRSA-SCC mec type III strain obtained in Asia. Comparison with two published genomes of ST239 reveals the polymorphism among strains of this type from different continents.

Schematic above the graph indicates the position of each gene within the EV genome.</p

All 16S rRNA, ITS and rpoB reads identical between bite mark and teet... more All 16S rRNA, ITS and rpoB reads identical between bite mark and teeth samples were compiled into locus-specific files and uploaded into GenBank for standard nucleotide-nucleotide BLAST comparison to determine SLOTUs. The number of shared identical reads in each locus-specific file was 482, 639 and 178, respectively. (Pseudo-Streptococcus pseudopneumoniae; Pneu-Streptococcus pneumoniae; Ther-Streptococcus thermophilus; Vest-Streptococcus vestibularis).</p

Trees were rooted with PV1. Bootstrap values below 50 were removed. Bars indicate nucleo... more Trees were rooted with PV1. Bootstrap values below 50 were removed. Bars indicate nucleotide substitution distance.</p

Comparison of the average number of unique reads generated from samples with varying amo... more Comparison of the average number of unique reads generated from samples with varying amounts of DNA, containing either amplicons from one locus or amplicons from four loci.</p

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Bold numbers indicate the highest proportion of identical reads in each column. Sample 2... more Bold numbers indicate the highest proportion of identical reads in each column. Sample 2 contained less than 10 unique reads therefore was omitted from comparative analyses. Bite mark samples (B) and teeth samples (T) from the same participant have corresponding identifying numbers. The number of rpoB reads in bite mark sample 11 was less than 10 therefore was omitted from comparative analyses of all loci. For bite mark sample 1, teeth samples 10, 13 and 16 share the same proportion however, teeth sample 10 was selected because this data set contained the least number of reads (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0051757#pone-0051757-g001" target="_blank">Figure 1</a>).</p

Comparison of the number of unique 16S rRNA reads generated from samples in which amplic... more Comparison of the number of unique 16S rRNA reads generated from samples in which amplicons from four loci were pooled (gray) and those submitted for sequencing singly (black). Bite mark sample 2 contains less than 10 unique reads and was therefore excluded from comparative analyses for all loci.</p

Comparison of the number of unique rpoB reads generated from samples ... more Comparison of the number of unique rpoB reads generated from samples in which amplicons from four loci were pooled (gray) and those submitted for sequencing singly (black). Bite mark sample 11 contains less than 10 unique reads and was therefore excluded from comparative analyses for all loci.</p

Forward (F) and Reverse (R) primers for the amplification of 16S rRNA (16S), ITS, <i&... more Forward (F) and Reverse (R) primers for the amplification of 16S rRNA (16S), ITS, rnpB and rpoB fragments for GS-FLX DNA sequencing.</p

Probabilities (p) determined that the assignment of a binary outcome variable was influe... more Probabilities (p) determined that the assignment of a binary outcome variable was influenced by the proportion of shared identical reads between bite and teeth samples; OP- optimum proportion of shared identical reads yielding the greatest estimates of sensitivity, specificity, PPV and NPV; Sens- Sensitivity; Spec- Specificity; PPV- positive predictive values; NPV- negative predictive value. Values in the brackets indicate the lower and upper values of a 95% confidence interval.</p

Bold numbers indicate the highest proportion of identical reads in each column. Bite mar... more Bold numbers indicate the highest proportion of identical reads in each column. Bite mark samples (B) and teeth samples (T) from the same participant have corresponding identifying numbers. Bite mark sample 11 contained less than 10 unique reads therefore was omitted from comparative analyses of all loci. The number of 16S rRNA reads in bite mark sample 2 was less than 10 therefore was omitted from comparative analyses of all loci.</p

Scientific Reports, 2022

RNA sequencing offers unprecedented access to the transcriptome. Key to this is the identificatio... more RNA sequencing offers unprecedented access to the transcriptome. Key to this is the identification and quantification of many different species of RNA from the same sample at the same time. In this study we describe a novel protocol for simultaneous detection of coding and non-coding transcripts using modifications to the Ion Total RNA-Seq kit v2 protocol, with integration of QIASeq FastSelect rRNA removal kit. We report highly consistent sequencing libraries can be produced from both frozen high integrity mouse hippocampal tissue and the more challenging post-mortem human tissue. Removal of rRNA using FastSelect was extremely efficient, resulting in less than 1.5% rRNA content in the final library. We identified > 30,000 unique transcripts from all samples, including protein-coding genes and many species of non-coding RNA, in biologically-relevant proportions. Furthermore, the normalized sequencing read count for select genes significantly negatively correlated with Ct values fr...

RNA sequencing offers unprecedented access to the transcriptome. Key to this is the identificatio... more RNA sequencing offers unprecedented access to the transcriptome. Key to this is the identification and quantification of many different species of RNA from the same sample at the same time. In this study we describe a novel protocol for simultaneous detection of coding and non-coding transcripts using modifications to the Ion Total RNA-Seq kit v2 protocol, with integration of QIASeq FastSelect rRNA removal kit. We report highly consistent sequencing libraries can be produced from both frozen high integrity mouse hippocampal tissue and the more challenging post-mortem human tissue. Removal of rRNA using FastSelect was highly efficient, resulting in less than 1.5% rRNA content in the final library, significantly better than other reported rRNA removal techniques. We identified >30,000 unique transcripts from all samples, including protein-coding genes and many unique species of non-coding RNA, in biologically-relevant proportions. Furthermore, normalized sequencing read count for s...

BioTechniques, 2019

Background: PDQeX is a novel, single-step DNA extraction method that purifies nucleic acid from s... more Background: PDQeX is a novel, single-step DNA extraction method that purifies nucleic acid from sample in under 30 min. Materials & Methods: Six bacterial suspensions from species with different cell morphologies and growth optima were made. DNA from half the suspension was purified using PDQeX and the other half using a conventional column purification method. Sequencing and analyses using Ion PGM were performed, blinded to extraction method and species. Results: Genomes extracted with either method sequenced successfully. No significant sequence distribution biases were evident between PDQeX and column purification. Surveyed community preference suggested comparable performance between the two extraction methods. Conclusion: DNA prepared using the PDQeX performs as well for whole-genome sequencing as DNA purified using a conventional method, albeit much more rapidly.

The FASEB Journal, 2019

There is clear evidence for carrier-mediated transport of prolactin into the brain, and it has be... more There is clear evidence for carrier-mediated transport of prolactin into the brain, and it has been widely assumed that prolactin receptors (PRLRs) in the choroid plexus (ChP) might mediate this transport. Using PRLR knockout mice, we recently showed that PRLRs in ChP are not required for prolactin transport into the brain. Hence, the function of PRLR in the ChP remains unknown. PRLR expression is increased in the ChP during lactation, suggesting a possible role in adaptive function of prolactin at this time. To gain insight into prolactin function in the ChP, we have utilized RNA sequencing and NanoString techniques to characterize transcriptional changes in response to differing levels of prolactin at diestrus, during pregnancy, and in lactation. We have observed opposing transcriptional effects of prolactin on the ChP in different physiologic states, being primarily inhibitory during diestrus but stimulatory in lactation. Insulin-like growth factor 2 (Igf2), a highly expressing transcript found in the ChP, showed a 6-fold increase at lactation that returned to baseline on suppression of prolactin levels. These results indicate that Igf2 may be an important downstream mediator of prolactin-induced signaling in the ChP.-Phillipps,

Journal of Bacteriology, Nov 1, 2010

Journal of Bacteriology, 2011

Schematic above the graph indicates the position of each gene within the EV genome.</p

Scientific Reports, 2022

RNA sequencing offers unprecedented access to the transcriptome. Key to this is the identificatio... more RNA sequencing offers unprecedented access to the transcriptome. Key to this is the identification and quantification of many different species of RNA from the same sample at the same time. In this study we describe a novel protocol for simultaneous detection of coding and non-coding transcripts using modifications to the Ion Total RNA-Seq kit v2 protocol, with integration of QIASeq FastSelect rRNA removal kit. We report highly consistent sequencing libraries can be produced from both frozen high integrity mouse hippocampal tissue and the more challenging post-mortem human tissue. Removal of rRNA using FastSelect was highly efficient, resulting in less than 1.5% rRNA content in the final library, significantly better than other reported rRNA removal techniques. We identified >30,000 unique transcripts from all samples, including protein-coding genes and many unique species of non-coding RNA, in biologically-relevant proportions. Furthermore, normalized sequencing read count for s...

BioTechniques, 2019

The FASEB Journal, 2019