
Charles J. ArayataPhiladelphia District Attorney's Office · District Attorney's Transparency Analytics (DATA) Lab
Charles J. Arayata
Master of Arts, Experimental Psychology
About
35
Publications
1,999
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
205
Citations
Additional affiliations
July 2014 - July 2017
Publications
Publications (35)
Significance
What makes a molecule have a smell? This simple question represents a significant gap in our understanding of olfaction. To answer it, we trained models to predict whether molecules were odorous based on molecular characteristics and noted which characteristics were needed to make correct predictions. We found that molecules with suffi...
Odor perception in non-humans is poorly understood. Here, we generated the most comprehensive mouse olfactory ethological atlas to date, consisting of behavioral responses to a diverse panel of 73 odorants, including 12 at multiple concentrations. These data revealed that mouse behavior is incredibly diverse and changes in response to odorant ident...
In studies of vision and audition, stimuli can be chosen to span the visible or audible spectrum; in olfaction, the axes and boundaries defining the analogous odorous space are unknown. Features governing the physical transport of molecules to olfactory receptors are sufficient to reliably classify novel molecules as odorous or odorless (AUROC = 0....
Odor perception in non-humans is poorly understood. Here, we generated the most comprehensive murine olfactory ethological atlas to date, consisting of behavioral responses to a diverse panel of 73 odorants, including 12 at multiple concentrations. These data revealed that the mouse behavior is incredibly diverse, and changes in response to odor id...
The mammalian olfactory system displays species-specific adaptations to different ecological niches. To investigate the evolutionary dynamics of olfactory sensory neuron (OSN) subtypes across mammalian evolution, we applied RNA sequencing of whole olfactory mucosa samples from mouse, rat, dog, marmoset, macaque, and human. We find that OSN subtypes...
Many factors play a role in choosing what to eat or drink. Here we explored the role of sensation to explain these differences, drawing on consumer reviews for commercially available food products sold through an online retailer. We analyzed 393,568 unique food product reviews from Amazon customers with a total of 256,043 reviewers rating 67,553 pr...
Many factors play a role in choosing what to eat or drink. We explored the role of sensation to explain these differences, drawing on consumer reviews for commercially available food products sold through an online retailer. We analyzed 393,568 unique food product reviews from Amazon customers with a total of 256,043 reviewers rating 67,553 product...
The mammalian olfactory system displays species-specific adaptations to different ecological niches. To investigate the evolutionary dynamics of olfactory sensory neuron (OSN) sub-types across 95 million years of mammalian evolution, we applied RNA-sequencing of whole olfactory mucosa samples from mouse, rat, dog, marmoset macaque and human. We fin...
TAS2R38 is a human bitter receptor gene with a common but inactive allele; people homozygous for the inactive form cannot perceive low concentrations of certain bitter compounds. The frequency of the inactive and active form of this receptor is nearly equal in many human populations, and heterozygotes with one copy of the active form and one copy o...
The emerging importance of taste in medicine and biomedical research, and new knowledge about its genetic underpinnings, has motivated us to supplement classic taste-testing methods in two ways. First, we explain how to do a brief assessment of the mouth, including the tongue, to ensure that taste papillae are present and to note evidence of releva...
To fine map a mouse QTL for lean body mass (Burly1), we used information from intercross, backcross, consomic, and congenic mice derived from the C57BL/6ByJ (host) and 129P3/J (donor) strains. The results from these mapping populations were concordant and showed that Burly1 is located between 151.9 and 152.7 Mb (rs33197365 to rs3700604) on mouse ch...
TAS2R38 is a human bitter receptor gene with a common but inactive allele and people homozygous for the inactive form cannot perceive certain bitter compounds. The frequency of the inactive and active form of this receptor is nearly equal in many human populations and heterozygotes (with one copy of the active form and another copy of the inactive...
Our goal was to fine map a mouse QTL for lean body mass ( Burly1 ) using information from several populations including newly created congenic mice derived from the B6 (host) and 129 (donor) strains. The results from each mapping population were concordant and showed that Burly1 is likely a single QTL in a 0.8-Mb region at 151.9-152.7 Mb ( rs331973...
An average mouse in midlife weighs between 25 and 30 g, with about a gram of tissue in the largest adipose depot (gonadal), and the weight of this depot differs between inbred strains. Specifically, C57BL/6ByJ mice have heavier gonadal depots on average than do 129P3/J mice. To understand the genetic contributions to this trait, we mapped several q...
Distribution normality.
Statistics for descriptive and normality tests of gonadal adipose depot weight in congenic populations.
(XLSX)
Congenic mapping results.
Genotypes and phenotypes of the 12 congenic strains (strains with numbers of mice ≥12 mice/strain, and all mice having full-length donor regions). Column headings show IDs of congenic strains. We show here only markers informative for breakpoints of the donor regions. A = B6/B6 genotype; H = 129/B6 genotype; X = data are n...
Markers.
Markers used for genotyping and their physical positions on chromosome 9.
(XLSX)
Broad strain inclusion criterion.
Genotypes and phenotypes of the congenic strains of any sample size, except as noted below, including mice with partial or full-length donor regions. However, we still excluded three strains from this analysis (shaded in light grey) because they had very few mice (1.1.1, 3.1.3, 4.5). For other details, see S5 Table...
Regulatory variant function.
Regulatory variants within the four QTL regions predicted with an on-line tool Variant Effect Prediction.
(XLSX)
Microarray results.
Genome-wide overview of the microarray data from Experiment 1 with differentially expressed genes (blue dots) in adipose tissue between genotypes (129/B6 vs B6/B6) in congenic male mice. We observed potential heterozygosity (green dots) of this congenic strain in at least one of the samples at 25 of the 2,715 polymorphic markers...
Post-hoc results.
Narrow analysis of gonadal depot weight in the 12 congenic strains (with numbers of mice ≥12 mice/strain, and all mice having full-length donor regions): general linear model (GLM), least square means, and post hoc Fisher’s least significance difference (LSD) tests. N = Numbers of mice in each group with and without a donor region...
Congenic mapping results.
Broad analysis of gonadal depot weight using the criterion from S7 Table.
(XLSX)
Variant function in coding region.
Sorting Intolerant From Tolerant (SIFT) prediction of missense and stop codon gain/loss sequence variants of genes residing within the 4 adiposity QTL regions on chromosome 9.
(XLSX)
Filtering of microarray data to identify reproducible candidate genes.
aThere are 277 genes within the donor region of strain 4 (42.6 to 58.3 Mb). Genes that passed the filters for differential expression in both Experiment 1 and 2 we display with blue font. Two genes in red font miss this criterion but their human orthologues are associated with a...
Logic of the sequential method.
Explanation for each of the three branches of the minimum spanning tree (MST; central, left, and right) in Fig 3. Arrows after QTLs indicate the direction of effect of the 129-derived allele.
(DOC)
Distribution normality.
Cullen and Frey graphs and empirical and theoretical data for untransformed and log-transformed congenics data. We tested the distribution of the gonadal adipose depot weight data for normality; S3 Table contains the parameters of the model-fitting untransformed and log-transformed data. CDF = cumulative distribution functio...
Predicted effect for variants within four QTLs.
In total, we uploaded 44,009 variants for the variant function analyses to the online tool Variant Effect Predictor; we found data from nearly all variants (99.8%) using this tool; of these variants, 2% were regulatory variants, and 31% of variants in coding regions were missense variants.
(DOCX)
Excluded mice.
List of mice with tumors or otherwise excluded from analysis. Weight = Body weight in grams; Length, = body length in centimeters; Gonadal = gonadal adipose depot weight at the time of dissection in grams; Tumor location includes, weights if available.
(DOCX)
Mean weights for each congenic strain.
Weight of gonadal depot and body weight (BW) of congenic mice with donor regions of different genotypes of donor regions. aDonor region genotype: Host = B6/B6; Donor = 129/B6. bDonor region size: NA = mice without donor region; Partial = mice that inherited a partial-length (due to a recombination event) donor...
Summary of the mouse adiposity QTLs on chromosome 9.
Type = mapping population; Con = congenic; Overlap refers to QTL1- QTL4 as identified by the sequential method. Approach = method of estimating confidence interval (LDR = logarithmic transformed probability; LOD = logarithm of the odds); Ref = reference.
(DOCX)
Pearson correlations.
(A) gonadal adipose depot and body weight, (B) gonadal adipose depot and age as well as (C) body weight and age of all congenic mice. Gonadal = Gonadal adipose depot in grams; BW = body weight in grams; Age in days.
(DOCX)
An average mouse in midlife weighs between 25 and 30 g, with about a gram of tissue in the largest adipose depot (gonadal), and the weight of this depot differs between inbred strains. Specifically, C57BL/6ByJ mice have heavier gonadal depots on average than do 129P3/J mice. To understand the genetic contributions to this trait, we mapped several q...
Genetic variation contributes to individual differences in obesity, but defining the exact relationships between naturally occurring genotypes and their effects on fatness remains elusive. As a step toward positional cloning of previously identified body composition quantitative trait loci (QTLs) from F2 crosses of mice from the C57BL/6ByJ and 129P...