Publications by authors named "Blythe P Durbin-Johnson"

30 Publications

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Hepatic transcriptional profile reveals the role of diet and genetic backgrounds on metabolic traits in female progenitor strains of the Collaborative Cross.

Physiol Genomics 2021 Apr 5. Epub 2021 Apr 5.

Obesity and Metabolism Unit, United States Department of Agriculture, United States.

Mice have provided critical mechanistic understandings of clinical traits underlying Metabolic Syndrome (MetSyn) and susceptibility to MetSyn in mice is known to vary among inbred strains. We investigated the diet- and strain-dependent effects on metabolic traits in the eight Collaborative Cross (CC) founder strains (A/J, C57BL/6J, 129S1/SvImJ, NOD/ShiLtJ, NZO/HILtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ). Liver transcriptomics analysis showed that both atherogenic diet and host genetics have profound effects on the liver transcriptome, which may be related to differences in metabolic traits observed between strains. We found strain differences in circulating trimethylamine N-Oxide (TMAO) concentration and liver triglyceride content, both of which are traits associated with metabolic diseases. Using a network approach, we identified a module of transcripts associated with TMAO and liver triglyceride content which was enriched in functional pathways. Interrogation of the module related to metabolic traits identified NADPH oxidase 4 (Nox4), a gene for a key enzyme in the production of reactive oxygen species, which showed a strong association with plasma TMAO and liver triglyceride. Interestingly, Nox4 was identified as the highest expressed in the C57BL/6J and NZO/HILtJ strains and the lowest expressed in the CAST/EiJ strain. Based on these results, we suggest that there may be genetic variation in the contribution of Nox4 to the regulation of plasma TMAO and liver triglyceride content. In summary, we show that liver transcriptomic analysis identified diet- or strain-specific pathways for metabolic traits in the Collaborative Cross (CC) founder strains.
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http://dx.doi.org/10.1152/physiolgenomics.00140.2020DOI Listing
April 2021

Author Reply.

Urology 2021 Mar 13;149:267. Epub 2021 Jan 13.

Shriners Hospitals for Children - Northern California, Sacramento, CA; Department of Urology, University of California Davis Medical Center, Sacramento, CA.

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http://dx.doi.org/10.1016/j.urology.2021.01.001DOI Listing
March 2021

Association of the Lactase Persistence Haplotype Block With Disease Risk in Populations of European Descent.

Front Genet 2020 29;11:558762. Epub 2020 Oct 29.

UC Davis Genome Center, Davis, CA, United States.

Among people of European descent, the ability to digest lactose into adulthood arose via strong positive selection of a highly advantageous allele encompassing the lactase gene. Lactose-tolerant and intolerant individuals may have different disease risks due to the shared genetics of their haplotype block. Therefore, the overall objective of the study was to assess the genetic association of the lactase persistence haplotype to disease risk. Using data from the 1000Genomes project, we estimated the size of the lactase persistence haplotype block to be 1.9 Mbp containing up to 9 protein-coding genes and a microRNA. Based on the function of the genes and microRNA, we studied health phenotypes likely to be impacted by the lactase persistence allele: prostate cancer status, cardiovascular disease status, and bone mineral density. We used summary statistics from large genome-wide metanalyses-32,965 bone mineral density, 140,306 prostate cancer and 184,305 coronary artery disease subjects-to evaluate whether the lactase persistence allele was associated with these disease phenotypes. Despite the fact that previous work demonstrated that the lactase persistence haplotype block harbors increased deleterious mutations, these results suggest little effect on the studied disease phenotypes.
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http://dx.doi.org/10.3389/fgene.2020.558762DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7658388PMC
October 2020

Expression Changes in Epigenetic Gene Pathways Associated With One-Carbon Nutritional Metabolites in Maternal Blood From Pregnancies Resulting in Autism and Non-Typical Neurodevelopment.

Autism Res 2021 01 7;14(1):11-28. Epub 2020 Nov 7.

Department of Medical Microbiology and Immunology, Genome Center, and Perinatal Origins of Disparities Center, University of California, Davis, California, USA.

The prenatal period is a critical window for the development of autism spectrum disorder (ASD). The relationship between prenatal nutrients and gestational gene expression in mothers of children later diagnosed with ASD or non-typical development (Non-TD) is poorly understood. Maternal blood collected prospectively during pregnancy provides insights into the effects of nutrition, particularly one-carbon metabolites, on gene pathways and neurodevelopment. Genome-wide transcriptomes were measured with microarrays in 300 maternal blood samples in Markers of Autism Risk in Babies-Learning Early Signs. Sixteen different one-carbon metabolites, including folic acid, betaine, 5'-methyltretrahydrofolate (5-MeTHF), and dimethylglycine (DMG) were measured. Differential expression analysis and weighted gene correlation network analysis (WGCNA) were used to compare gene expression between children later diagnosed as typical development (TD), Non-TD and ASD, and to one-carbon metabolites. Using differential gene expression analysis, six transcripts (TGR-AS1, SQSTM1, HLA-C, and RFESD) were associated with child outcomes (ASD, Non-TD, and TD) with genome-wide significance. Genes nominally differentially expressed between ASD and TD significantly overlapped with seven high confidence ASD genes. WGCNA identified co-expressed gene modules significantly correlated with 5-MeTHF, folic acid, DMG, and betaine. A module enriched in DNA methylation functions showed a suggestive protective association with folic acid/5-MeTHF concentrations and ASD risk. Maternal plasma betaine and DMG concentrations were associated with a block of co-expressed genes enriched for adaptive immune, histone modification, and RNA processing functions. These results suggest that the prenatal maternal blood transcriptome is a sensitive indicator of gestational one-carbon metabolite status and changes relevant to children's later neurodevelopmental outcomes. LAY SUMMARY: Pregnancy is a time when maternal nutrition could interact with genetic risk for autism spectrum disorder. Blood samples collected during pregnancy from mothers who had a prior child with autism were examined for gene expression and nutrient metabolites, then compared to the diagnosis of the child at age three. Expression differences in gene pathways related to the immune system and gene regulation were observed for pregnancies of children with autism and non-typical neurodevelopment and were associated with maternal nutrients.
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http://dx.doi.org/10.1002/aur.2428DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7894157PMC
January 2021

Age-Related Changes in Hair Shaft Protein Profiling and Genetically Variant Peptides.

Forensic Sci Int Genet 2020 07 22;47:102309. Epub 2020 May 22.

Forensic Science Graduate Program, University of California, Davis, CA, USA; Department of Environmental Toxicology, University of California, Davis, CA, USA. Electronic address:

Recent reports highlight possible improvements in individual identification using proteomic information from human hair evidence. These reports have stimulated investigation of parameters that affect the utility of proteomic information. In addition to variables already studied relating to processing technique and anatomic origin of hair shafts, an important variable is hair ageing. Present work focuses on the effect of age on protein profiling and analysis of genetically variant peptides (GVPs). Hair protein profiles may be affected by developmental and physiological changes with age of the donor, exposure to different environmental conditions and intrinsic processes, including during storage. First, to explore whether general trends were evident in the population at different ages, hair samples were analyzed from groups of different subjects in their 20's, 40's and 60's. No significant differences were seen as a function of age, but consistent differences were evident between European American and African American hair profiles. Second, samples collected from single individuals at different ages were analyzed. Mostly, these showed few protein expression level differences over periods of 10 years or less, but samples from subjects at 44 and 65 year intervals were distinctly different in profile. The results indicate that use of protein profiling for personal identification, if practical, would be limited to decadal time intervals. Moreover, batch effects were clearly evident in samples processed by different staff. To investigate the contribution of storage (at room temperature) in affecting the outcomes, the same proteomic digests were analyzed for GVPs. In samples stored over 10 years, GVPs were reduced in number in parallel with the yield of identified proteins and unique peptides. However, a very different picture emerged with respect to personal identification. Numbers of GVPs sufficed to distinguish individuals despite the age differences of the samples. As a practical matter, three hair samples per person provided nearly the maximal number obtained from 5 or 6 samples. The random match probability (where the log increased in proportion to the number of GVPs) reached as high as 1 in 10. The data indicate that GVP results are dependent on the single nucleotide polymorphism profile of the donor genome, where environmental/processing factors affect only the yield, and thus are consistent despite the ages of the donors and samples and batchwise effects in processing. This conclusion is critical for application to casework where the samples may be in storage for long periods and used to match samples recently collected.
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http://dx.doi.org/10.1016/j.fsigen.2020.102309DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7388652PMC
July 2020

The p14ARF tumor suppressor restrains androgen receptor activity and prevents apoptosis in prostate cancer cells.

Cancer Lett 2020 07 21;483:12-21. Epub 2020 Apr 21.

Veterans Affairs-Northern California Health Care System, Mather, CA, USA; Department of Medical Microbiology and Immunology, USA. Electronic address:

Prostate cancer (PCa) is characterized by a unique dependence on optimal androgen receptor (AR) activity where physiological androgen concentrations induce proliferation but castrate and supraphysiological levels suppress growth. This feature has been exploited in bipolar androgen therapy (BAT) for castrate resistant malignancies. Here, we investigated the role of the tumor suppressor protein p14ARF in maintaining optimal AR activity and the function of the AR itself in regulating p14ARF levels. We used a tumor tissue array of differing stages and grades to define the relationships between these components and identified a strong positive correlation between p14ARF and AR expression. Mechanistic studies utilizing CWR22 xenograft and cell culture models revealed that a decrease in AR reduced p14ARF expression and deregulated E2F factors, which are linked to p14ARF and AR regulation. Chromatin immunoprecipitation studies identified AR binding sites upstream of p14ARF. p14ARF depletion enhanced AR-dependent PSA and TMPRSS2 transcription, hence p14ARF constrains AR activity. However, p14ARF depletion ultimately results in apoptosis. In PCa cells, AR co-ops p14ARF as part of a feedback mechanism to ensure optimal AR activity for maximal prostate cancer cell survival and proliferation.
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http://dx.doi.org/10.1016/j.canlet.2020.03.030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8034238PMC
July 2020

Proteomic genotyping: Using mass spectrometry to infer SNP genotypes in pigmented and non-pigmented hair.

Forensic Sci Int 2020 May 25;310:110200. Epub 2020 Feb 25.

Department of Environmental Toxicology, University of California, Davis, United States. Electronic address:

Proteomic genotyping uses genetically variant peptides that contain single amino acid polymorphisms to infer the genotype of corresponding non-synonymous SNP alleles. We have focused on hair proteins as a source of protein-based genetic information in a forensic context. An optimized sample processing protocol for hair shafts has been developed for use on a single hair that allows us to conduct validation protocols on real world samples. This includes whether the inferred SNP genotypes are robust and not systematically affected by biological or chemical variation in hair proteomes that might be obtained from a crime scene. To this end we analyzed the hair of 4 mature individuals with a mixture of pigmented and non-pigmented hair. We demonstrate significant changes in the proteomes of grey versus pigmented hair. Vesicle specific proteins and lipid catabolism proteins were enriched in pigmented hair, and housekeeping proteins and lipid anabolic enzymes were enriched in grey, non-pigmented hair. The resulting profiles of genetically variant peptides, however, were more correlated with profiles from the same individuals regardless of pigmentation status. Together with other published evidence, this finding indicates that profiles of genetically variant peptides are robust and more correlated with other genetically variant peptide profiles from the same individual irrespective of changes occurring in the hair protein profile. Based on this small sample, investigators using profiles of genetically variant peptides to infer random match probabilities should not expect to observe differences based on the pigmentation of the hair shaft.
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http://dx.doi.org/10.1016/j.forsciint.2020.110200DOI Listing
May 2020

Rectal Microbiome Composition Correlates with Humoral Immunity to HIV-1 in Vaccinated Rhesus Macaques.

mSphere 2019 12 11;4(6). Epub 2019 Dec 11.

The Center for Immunology and Infectious Diseases, University of California, Davis, California, USA

The microbiome is an integral and dynamic component of the host and is emerging as a critical determinant of immune responses; however, its influence on vaccine immunogenicity is largely not well understood. Here, we examined the pivotal relationship between the mucosal microbiome and vaccine-induced immune responses by assessing longitudinal changes in vaginal and rectal microbiome profiles after intradermal immunization with a human immunodeficiency virus type 1 (HIV-1) DNA vaccine in adult rhesus macaques that received two prior DNA primes. We report that both vaginal and rectal microbiomes were dominated by but were composed of distinct genera, denoting microbiome specialization across mucosal tissues. Following immunization, the vaginal microbiome was resilient, except for a transient decrease in In contrast, the rectal microbiome was far more responsive to vaccination, exhibiting an increase in the ratio of to Within , multiple genera were significantly decreased, including , and Decreased abundance of correlated with induction of gut-homing αβ effector CD4 T cells. abundance also negatively correlated with rectal HIV-1 specific IgG levels. While rectal was unaltered following DNA vaccination, baseline abundance showed strong associations with higher rectal HIV-1 gp140 IgA induced following a protein boost. Similarly, the abundance of in cluster IV was associated with higher rectal HIV-1 gp140 IgG responses. Collectively, these data reveal that the temporal stability of bacterial communities following DNA immunization is site dependent and highlight the importance of host-microbiome interactions in shaping HIV-1 vaccine responses. Our findings have significant implications for microbial manipulation as a strategy to enhance HIV vaccine-induced mucosal immunity. There is considerable effort directed toward evaluating HIV-1 vaccine platforms to select the most promising candidates for enhancing mucosal HIV-1 antibody. The most successful thus far, the RV144 trial provided partial protection due to waning HIV-1 antibody titers. In order to develop an effective HIV vaccine, it may therefore be important to understand how biological factors, such as the microbiome, modulate host immune responses. Furthermore, as intestinal microbiota antigens may generate antibodies cross-reactive to the HIV-1 envelope glycoprotein, understanding the relationship between gut microbiota composition and HIV-1 envelope antibody responses after vaccination is important. Here, we demonstrate for the first time in rhesus macaques that the rectal microbiome composition can influence HIV-1 vaccine immunogenicity, and we report temporal changes in the mucosal microbiome profile following HIV-1 vaccination. Our results could inform findings from the HIV Vaccine Trials Network (HVTN) vaccine studies and contribute to an understanding of how the microbiome influences HIV-1 antibody responses.
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http://dx.doi.org/10.1128/mSphere.00824-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6908426PMC
December 2019

Real-world management and long-term outcomes of diabetic macular oedema with good visual acuity.

Eye (Lond) 2020 06 28;34(6):1108-1115. Epub 2019 Oct 28.

Department of Ophthalmology & Vision Sciences, University of California, Davis, Sacramento, CA, USA.

Purpose: To evaluate the management and long-term outcomes of patients with diabetic macular oedema (DMO) and good initial visual acuity in real-world settings.

Methods: We reviewed 122 eyes of 100 patients with treatment-naive DMO and initial best-corrected visual acuity (BCVA) of 20/25 or better. We assessed clinical characteristics, logMAR BCVA, central subfield thickness (CST), cumulative intravitreal injections and laser treatments at yearly intervals, and characteristics at time of initial treatment. Linear mixed effects models were used to identify predictors of visual outcomes.

Results: At presentation, mean BCVA was 0.057 ± 0.048 logMAR (Snellen 20/23) and mean CST was 288 ± 57 μm. After a median follow-up of 3 years, 51% of eyes underwent treatment. More eyes underwent intravitreal injection as initial treatment (54%), but lasers were initiated at an earlier time and at better BCVA. Final BCVA was associated with better BCVA (P < 0.001) and earlier timing (P = 0.017) at initial treatment, but not CST at first treatment (P = 0.634) or cumulative number of injections or lasers (P = 0.441-0.606).

Conclusion: DMO with good initial visual acuity should be monitored closely, as delay in treatment initiation is associated with worse visual outcomes. BCVA at time of initial treatment is the strongest determinant of final visual acuity.
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http://dx.doi.org/10.1038/s41433-019-0647-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7253473PMC
June 2020

Divergent transcriptomic signatures in response to salinity exposure in two populations of an estuarine fish.

Evol Appl 2019 Jun 26;12(6):1212-1226. Epub 2019 Apr 26.

Wildlife, Fish & Conservation Biology University of California Davis California.

In estuary and coastal systems, human demand for freshwater, climate change-driven precipitation variability, and extreme weather impact salinity levels, reducing connectivity between mesohaline coastal fish populations and potentially contributing to genomic divergence. We examined gill transcriptome responses to salinity in wild-caught juveniles from two populations of Sacramento splittail (), a species of conservation concern that is endemic to the San Francisco Estuary, USA, and the lower reaches of its tributaries. Recent extreme droughts have led to salinities above the tolerance limits for this species, creating a migration barrier between these populations, which potentially contributed to population divergence. We identified transcripts involved in a conserved response to salinity; however, the more salinity-tolerant San Pablo population had greater transcriptome plasticity (3.6-fold more transcripts responded than the Central Valley population) and a response consistent with gill remodeling after 168 hr of exposure to elevated salinity. The reorganization of the gill in response to changing osmotic gradients is a process critical for acclimation and would facilitate enhanced salinity tolerance. We detected an upregulation of receptors that control the Wnt (wingless-type) cell signaling pathway that may be required for an adaptive response to increases in salinity, patterns not observed in the relatively salinity-sensitive Central Valley population. We detected 62 single nucleotide polymorphisms (SNPs) in coding regions of 26 transcripts that differed between the populations. Eight transcripts that contained SNPs were associated with immune responses, highlighting the importance of diversity in immune gene sequences as a defining characteristic of genomic divergence between these populations. Our data demonstrate that these populations have divergent transcriptomic responses to salinity, which is consistent with observed physiological differences in salinity tolerance.
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http://dx.doi.org/10.1111/eva.12799DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6597873PMC
June 2019

Long-term natural history of idiopathic epiretinal membranes with good visual acuity.

Eye (Lond) 2019 05 19;33(5):714-723. Epub 2019 Apr 19.

Department of Ophthalmology & Vision Sciences, University of California, Davis, Sacramento, CA, USA.

Background/objectives: To evaluate the long-term progression of idiopathic epiretinal membranes (iERMs) with good baseline visual acuity, and to identify predictors of visual decline.

Design: Retrospective case series SUBJECTS METHODS: We reviewed records of 145 eyes with iERM and best-corrected visual acuity (BCVA) of 20/40 or greater at presentation, including BCVA, lens status, and central macular thickness (CMT) at yearly visits; as well as anatomic biomarkers including vitreomacular adhesion, pseudohole, lamellar hole, intraretinal cysts, disorganization of the inner retinal layers (DRIL), and disruption of outer retinal layers. Linear mixed effects and mixed-effects Cox proportional hazards models were used to identify clinical and anatomic predictors of vision change and time to surgery.

Results: At presentation, mean BCVA was 0.17 ± 0.10 logMAR units (Snellen 20/30) and mean CMT was 353.3 ± 75.4 μm. After a median follow-up of 3.7 years (range 1-7 years), BCVA declined slowly at 0.012 ± 0.003 logMAR units/year, with phakic eyes declining more rapidly than pseudophakic eyes (0.019 ± 0.003 vs. 0.010 ± 0.004 logMAR units/year). Metamorphopsia, phakic lens status, lamellar hole, and inner nuclear layer cysts were associated with faster visual decline. Cumulative rates of progression to surgery were 2.9, 5.6, 12.2, and 21.1% at years 1-4. Visual symptoms, metamorphopsia, greater CMT, and disruption of outer retinal layers were associated with greater hazard for surgery.

Conclusion: Eyes with iERM and visual acuity ≥ 20/40 experience slow visual decline, with 21% of eyes requiring surgery after 4 years. Clinical and anatomic predictors of vision loss may be distinct from factors associated with earlier surgical intervention.
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http://dx.doi.org/10.1038/s41433-019-0397-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6707144PMC
May 2019

Comparison of protein expression levels and proteomically-inferred genotypes using human hair from different body sites.

Forensic Sci Int Genet 2019 07 11;41:19-23. Epub 2019 Mar 11.

Forensic Science Graduate Program and Department of Environmental Toxicology, University of California, Davis, CA, USA. Electronic address:

The microanatomy of human hair differs as a function of the site of origin on the body. This was a major consideration when anatomical features of hair were used as a means of comparison and human identification. Recent advances have demonstrated that proteomics of the hair shaft can be used to develop profiles of protein abundance and genetically variant peptides, the latter in turn being used to infer genotypes of SNP alleles. Because the profile of proteins would be expected to change as hair anatomy changes, it is an open question if the profile of genetically variant peptides will also change. While some sample to sample variation is expected, a potential drawback of using genetically variant peptides to infer an individual genotype is that the proteomic profile might change as a function of body site origin as well as an individual's genotype. The hypothesis in this study is that the profile of hair shaft genetically variant peptides depends more on an individual's genotype than on the site of hair shaft origin. To test this an analysis of both protein expression levels and genetically variant peptides was conducted on 4 body sites (scalp, axillary, beard and pubic hair) from 5 individuals with 4 biological replicates. Levels of protein expression were estimated using label-free quantification on resulting proteomic mass spectrometry datasets. The same datasets were then also analyzed for the presence of genetically variant peptides. This study demonstrates that the protein profiles of hair shafts varied as a function of somatic origin. By contrast the profile of genetically variant peptides, and resulting inferred genotype of SNP alleles, were more dependent on the individual. In this study random match probabilities ranged up to 1 in 196. Individual identification based on genetically variant peptides therefore can be obtained from human hair without regard to the site of origin. If the site of hair shaft origin was legally relevant then microscopic analysis is still necessary. This study demonstrates the utility of proteomic analysis for extracting forensic information from hair shaft evidence.
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http://dx.doi.org/10.1016/j.fsigen.2019.03.009DOI Listing
July 2019

Pictorial Urgency Scale: A New Tool for Evaluating Bladder Urgency in Children.

J Urol 2019 03;201(3):620-625

Department of Physical Medicine and Rehabilitation, University of California Davis, Sacramento, California.

Purpose: Bladder fullness and urgency are difficult for some patients to express. We hypothesized that images on a pictorial urgency scale would correlate with International Continence Society standard verbal descriptors and bladder volume.

Materials And Methods: The study population consisted of 267 toilet trained children with a mean age of 7.2 years and their parents (91 adults). Patients were excluded if they had a history of urinary infection, voiding dysfunction, genitourinary surgery or reflux. Participants were read each of the 4 descriptors and asked to point to an image. Correlation between descriptors and figures was analyzed using a mixed effects proportional odds logistic regression model (aim 1 of study). In addition, 73 children undergoing voiding cystourethrography were asked to point to the images during bladder filling. Correlation between percent of expected capacity and image was analyzed using a linear mixed effects model (aim 2 of study).

Results: Correlation between descriptors and images (aim 1) was 0.87 (95% CI 0.84 to 0.89) for all participants, 0.84 (95% CI 0.81 to 0.88) for patients younger than age 6 years and 0.88 (95% CI 0.85 to 0.90) for patients 6 to 17 years old. Sequencing of the images was appropriate for increasing degree of urgency. In 73 children undergoing voiding cystourethrography correlation between image and percent of expected capacity (aim 2) was 0.75 (95% CI 0.67 to 0.81, p <0.001).

Conclusions: Figures on the pictorial urgency scale correlate with standard verbal descriptors and bladder volume. The pictorial scale could be a supplemental tool to improve communication of urgency sensation in younger children.
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http://dx.doi.org/10.1016/j.juro.2018.09.047DOI Listing
March 2019

Corneocyte proteomics: Applications to skin biology and dermatology.

Exp Dermatol 2018 08;27(8):931-938

The Jackson Laboratory, Bar Harbor, Maine.

Advances in mass spectrometry-based proteomics now permit analysis of complex cellular structures. Application to epidermis and its appendages (nail plate, hair shaft) has revealed a wealth of information about their protein profiles. The results confirm known site-specific differences in levels of certain keratins and add great depth to our knowledge of site specificity of scores of other proteins, thereby connecting anatomy and pathology. An example is the evident overlap in protein profiles of hair shaft and nail plate, helping rationalize their sharing of certain dystrophic syndromes distinct from epidermis. In addition, interindividual differences in protein level are manifest as would be expected. This approach permits characterization of altered profiles as a result of disease, where the magnitude of perturbation can be quantified and monitored during treatment. Proteomic analysis has also clarified the nature of the isopeptide cross-linked residual insoluble material after vigorous extraction with protein denaturants, nearly intractable to analysis without fragmentation. These structures, including the cross-linked envelope of epidermal corneocytes, are comprised of hundreds of protein constituents, evidence for strengthening the terminal structure complementary to disulphide bonding. Along with other developing technologies, proteomic analysis is anticipated to find use in disease risk stratification, detection, diagnosis and prognosis after the discovery phase and clinical validation.
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http://dx.doi.org/10.1111/exd.13756DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6415749PMC
August 2018

MicroRNA profiling of dogs with transitional cell carcinoma of the bladder using blood and urine samples.

BMC Vet Res 2017 Nov 15;13(1):339. Epub 2017 Nov 15.

Department of Urology, University of California, Davis, School of Medicine, Sacramento, CA, USA.

Background: Early signs of canine transitional cell carcinoma (TCC) are frequently assumed to be caused by other lower urinary tract diseases (LUTD) such as urinary tract infections, resulting in late diagnosis of TCC which could be fatal. The development of a non-invasive clinical test for TCC could dramatically reduce mortality. To determine whether microRNAs (miRNAs) can be used as non-invasive diagnostic biomarkers, we assessed miRNA expression in blood and/or urine from dogs with clinically normal bladders (n = 28), LUTD (n = 25), and TCC (n = 17). Expression levels of 5 miRNA associated with TCC pathophysiology (miR-34a, let-7c, miR-16, miR-103b, and miR-106b) were assessed by quantitative real-time PCR.

Results: Statistical analyses using ranked ANOVA identified significant differences in miR-103b and miR-16 levels between urine samples from LUTD and TCC patients (miR-103b, p = 0.002; and miR-16, p = 0.016). No statistically significant differences in miRNA levels were observed between blood samples from LUTD versus TCC patients. Expression levels of miR-34a trended with miR-16, let-7c, and miR-103b levels in individual normal urine samples, however, this coordination was completely lost in TCC urine samples. In contrast, co-ordination of miR-34a, miR-16, let-7c, and miR-103b expression levels was maintained in blood samples from TCC patients.

Conclusions: Our combined data indicate a potential role for miR-103b and miR-16 as diagnostic urine biomarkers for TCC, and that further investigation of miR-103b and miR-16 in the dysregulation of coordinated miRNA expression in bladder carcinogenesis is warranted.
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http://dx.doi.org/10.1186/s12917-017-1259-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5688639PMC
November 2017

Absolute Quantification of Human Milk Caseins and the Whey/Casein Ratio during the First Year of Lactation.

J Proteome Res 2017 11 9;16(11):4113-4121. Epub 2017 Oct 9.

Department of Nutrition, University of California , Davis, 95616, United States.

Whey proteins and caseins in breast milk provide bioactivities and also have different amino acid composition. Accurate determination of these two major protein classes provides a better understanding of human milk composition and function, and further aids in developing improved infant formulas based on bovine whey proteins and caseins. In this study, we implemented a LC-MS/MS quantitative analysis based on iBAQ label-free quantitation, to estimate absolute concentrations of α-casein, β-casein, and κ-casein in human milk samples (n = 88) collected between day 1 and day 360 postpartum. Total protein concentration ranged from 2.03 to 17.52 with a mean of 9.37 ± 3.65 g/L. Casein subunits ranged from 0.04 to 1.68 g/L (α-), 0.04 to 4.42 g/L (β-), and 0.10 to 1.72 g/L (α-), with β-casein having the highest average concentration among the three subunits. Calculated whey/casein ratio ranged from 45:55 to 97:3. Linear regression analyses show significant decreases in total protein, β-casein, κ-casein, total casein, and a significant increase of whey/casein ratio during the course of lactation. Our study presents a novel and accurate quantitative analysis of human milk casein content, demonstrating a lower casein content than earlier believed, which has implications for improved infants formulas.
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http://dx.doi.org/10.1021/acs.jproteome.7b00486DOI Listing
November 2017

Proteomic profiling of Pachyonychia congenita plantar callus.

J Proteomics 2017 08 23;165:132-137. Epub 2017 Jun 23.

Proteomics Core Facility, University of California, Davis, CA.

Callus samples from the ball and the arch of the foot, collected on tape circles, were compared by shotgun proteomic profiling. Pachyonychia congenita subjects were sampled who exhibited a mutation in KRT6A, KRT6B, KRT6C, KRT16 or KRT17, and the proteins were digested and analyzed by tandem mass spectrometry. In comparison with samples from unaffected control subjects, those from subjects with KRT6A or KRT16 mutations displayed the most differences in profile from normal, while those from subjects with KRT6C or KRT17 mutations showed few differences from normal. The profiles from subjects with KRT6B mutations were intermediate in protein profile differences. Degree of departure from the normal profile could be estimated by expression of numerous proteins in callus from the ball of the foot that were consistently different. By contrast, the protein profile from the arch of the foot was hardly affected. The results provide a foundation for noninvasive monitoring of the efficacy of treatments with quantitative assessment of departure from the normal phenotype.

Significance: Pachyonychia congenita is an orphan disease in which the connection between the basic defect (keratin mutation) and debilitating symptoms (severe plantar pain) is poorly understood. Present work addresses the degree to which the protein profile is altered in the epidermis where the severe pain originates. The results indicate that the mutated keratins differ greatly in the degree to which they elicit perturbations in protein profile. In those cases with markedly altered protein levels, monitoring the callus profile may provide an objective measure of treatment efficacy.
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http://dx.doi.org/10.1016/j.jprot.2017.06.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5567846PMC
August 2017

Joint-specific risk of impaired function in fibrodysplasia ossificans progressiva (FOP).

Bone 2018 04 13;109:124-133. Epub 2017 Jun 13.

Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; The Center for Research in FOP and Related Disorders, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States. Electronic address:

Background: Fibrodysplasia ossificans progressiva (FOP) causes progressive disability due to heterotopic ossification from episodic flare-ups. Using data from 500 FOP patients (representing 63% of all known patients world-wide), age- and joint-specific risks of new joint involvement were estimated using parametric and nonparametric statistical methods.

Results: Compared to data from a 1994 survey of 44 individuals with FOP, our current estimates of age- and joint-specific risks of new joint involvement are more accurate (narrower confidence limits), based on a wider range of ages, and have less bias due to its greater comprehensiveness (captures over three-fifths of the known FOP patients worldwide). For the neck, chest, abdomen, and upper back, the estimated hazard decreases over time. For the jaw, lower back, shoulder, elbow, wrist, fingers, hip, knee, ankle, and foot, the estimated hazard increases initially then either plateaus or decreases. At any given time and for any anatomic site, the data indicate which joints are at risk.

Conclusions: This study of approximately 63% of the world's known population of FOP patients provides a refined estimate of risk for new involvement at any joint at any age, as well as the proportion of patients with uninvolved joints at any age. Importantly, these joint-specific survival curves can be used to facilitate clinical trial design and to determine if potential treatments can modify the predicted trajectory of progressive joint dysfunction.
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http://dx.doi.org/10.1016/j.bone.2017.06.009DOI Listing
April 2018

Proteomic analysis of hair shafts from monozygotic twins: Expression profiles and genetically variant peptides.

Proteomics 2017 Jul 23;17(13-14). Epub 2017 Jun 23.

Forensic Science Graduate Program and Department of Environmental Toxicology, University of California, Davis, CA, USA.

Forensic association of hair shaft evidence with individuals is currently assessed by comparing mitochondrial DNA haplotypes of reference and casework samples, primarily for exclusionary purposes. Present work tests and validates more recent proteomic approaches to extract quantitative transcriptional and genetic information from hair samples of monozygotic twin pairs, which would be predicted to partition away from unrelated individuals if the datasets contain identifying information. Protein expression profiles and polymorphic, genetically variant hair peptides were generated from ten pairs of monozygotic twins. Profiling using the protein tryptic digests revealed that samples from identical twins had typically an order of magnitude fewer protein expression differences than unrelated individuals. The data did not indicate that the degree of difference within twin pairs increased with age. In parallel, data from the digests were used to detect genetically variant peptides that result from common nonsynonymous single nucleotide polymorphisms in genes expressed in the hair follicle. Compilation of the variants permitted sorting of the samples by hierarchical clustering, permitting accurate matching of twin pairs. The results demonstrate that genetic differences are detectable by proteomic methods and provide a framework for developing quantitative statistical estimates of personal identification that increase the value of hair shaft evidence.
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http://dx.doi.org/10.1002/pmic.201600462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5540574PMC
July 2017

Demonstration of Protein-Based Human Identification Using the Hair Shaft Proteome.

PLoS One 2016 7;11(9):e0160653. Epub 2016 Sep 7.

Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America.

Human identification from biological material is largely dependent on the ability to characterize genetic polymorphisms in DNA. Unfortunately, DNA can degrade in the environment, sometimes below the level at which it can be amplified by PCR. Protein however is chemically more robust than DNA and can persist for longer periods. Protein also contains genetic variation in the form of single amino acid polymorphisms. These can be used to infer the status of non-synonymous single nucleotide polymorphism alleles. To demonstrate this, we used mass spectrometry-based shotgun proteomics to characterize hair shaft proteins in 66 European-American subjects. A total of 596 single nucleotide polymorphism alleles were correctly imputed in 32 loci from 22 genes of subjects' DNA and directly validated using Sanger sequencing. Estimates of the probability of resulting individual non-synonymous single nucleotide polymorphism allelic profiles in the European population, using the product rule, resulted in a maximum power of discrimination of 1 in 12,500. Imputed non-synonymous single nucleotide polymorphism profiles from European-American subjects were considerably less frequent in the African population (maximum likelihood ratio = 11,000). The converse was true for hair shafts collected from an additional 10 subjects with African ancestry, where some profiles were more frequent in the African population. Genetically variant peptides were also identified in hair shaft datasets from six archaeological skeletal remains (up to 260 years old). This study demonstrates that quantifiable measures of identity discrimination and biogeographic background can be obtained from detecting genetically variant peptides in hair shaft protein, including hair from bioarchaeological contexts.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0160653PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5014411PMC
August 2017

The Secreted Protease PrtA Controls Cell Growth, Biofilm Formation and Pathogenicity in Xylella fastidiosa.

Sci Rep 2016 08 5;6:31098. Epub 2016 Aug 5.

Plant Sciences Department, University of California, Davis, CA, USA.

Pierce's disease (PD) is a deadly disease of grapevines caused by the Gram-negative bacterium Xylella fastidiosa. Though disease symptoms were formerly attributed to bacteria blocking the plant xylem, this hypothesis is at best overly simplistic. Recently, we used a proteomic approach to characterize the secretome of X. fastidiosa, both in vitro and in planta, and identified LesA as one of the pathogenicity factors of X. fastidiosa in grapevines that leads to leaf scorching and chlorosis. Herein, we characterize another such factor encoded by PD0956, designated as an antivirulence secreted protease "PrtA" that displays a central role in controlling in vitro cell proliferation, length, motility, biofilm formation, and in planta virulence. The mutant in X. fastidiosa exhibited reduced cell length, hypermotility (and subsequent lack of biofilm formation) and hypervirulence in grapevines. These findings are supported by transcriptomic and proteomic analyses with corresponding plant infection data. Of particular interest, is the hypervirulent response in grapevines observed when X. fastidiosa is disrupted for production of PrtA, and that PD-model tobacco plants transformed to express PrtA exhibited decreased symptoms after infection by X. fastidiosa.
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http://dx.doi.org/10.1038/srep31098DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4974619PMC
August 2016

Proteomic Analysis of Loricrin Knockout Mouse Epidermis.

J Proteome Res 2016 08 26;15(8):2560-6. Epub 2016 Jul 26.

Department of Dermatology, Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus , Aurora, Colorado 80045, United States.

The crosslinked envelope of the mammalian epidermal corneocyte serves as a scaffold for assembly of the lipid barrier of the epidermis. Thus, deficient envelope crosslinking by keratinocyte transglutaminase (TGM1) is a major cause of the human autosomal recessive congenital ichthyoses characterized by barrier defects. Expectations that loss of some envelope protein components would also confer an ichthyosis phenotype have been difficult to demonstrate. To help rationalize this observation, the protein profile of epidermis from loricrin knockout mice has been compared to that of wild type. Despite the mild phenotype of the knockout, some 40 proteins were incorporated into envelope material to significantly different extents compared to those of wild type. Nearly half were also incorporated to similarly altered extents into the disulfide bonded keratin network of the corneocyte. The results suggest that loss of loricrin alters their incorporation into envelopes as a consequence of protein-protein interactions during cell maturation. Mass spectrometric protein profiling revealed that keratin 1, keratin 10, and loricrin are prominent envelope components and that dozens of other proteins are also components. This finding helps rationalize the potential formation of functional envelopes, despite loss of a single component, due to the availability of many alternative transglutaminase substrates.
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http://dx.doi.org/10.1021/acs.jproteome.6b00108DOI Listing
August 2016

Decreased expression of let-7c is associated with non-response of muscle-invasive bladder cancer patients to neoadjuvant chemotherapy.

Genes Cancer 2016 Mar;7(3-4):86-97

Department of Urology, University of California, Davis, School of Medicine and Comprehensive Cancer Center, Sacramento, California, USA.

The identification and development of biomarkers which predict response of muscle invasive bladder cancer (MIBC) patients to neoadjuvant chemotherapy would likely increase usage of this treatment option and thereby improve patient survival rates. MiRNA array and qRT-PCR validation was used to identify miRNA which are associated with response to neoadjuvant chemotherapy. RNA was extracted from a total of 41 archival, fully annotated, MIBC patient diagnostic biopsies (20 chemo-responders and 21 non-responders (response is defined as > 5 year survival rate and being pT0 post-chemotherapy)). Microarray and qPCR identified let-7c as being differentially expressed in chemo-responder versus non-responder patients. Patients with higher let-7c expression levels had significantly higher odds of responding to chemotherapy (p = 0.023, OR 2.493, 95% CI 1.121, 5.546), and assessment of let-7c levels allowed for prediction of patient response (AUC 0.72, positive predictive value 59%). Decreased let-7c was associated with MIBC incidence (p < 0.001), and significantly correlated with other related miRNA including those that were not differentially expressed between responders and non-responders. The combined data indicate let-7c plays a role in mediating chemoresistance to neoadjuvant chemotherapy in MIBC patients, and is a modest, yet clinically meaningful, predictor of patient response.
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http://dx.doi.org/10.18632/genesandcancer.103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4918947PMC
March 2016

The Natural History of Flare-Ups in Fibrodysplasia Ossificans Progressiva (FOP): A Comprehensive Global Assessment.

J Bone Miner Res 2016 Mar 14;31(3):650-6. Epub 2015 Nov 14.

Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

Fibrodysplasia ossificans progressiva (FOP) leads to disabling heterotopic ossification (HO) from episodic flare-ups. However, the natural history of FOP flare-ups is poorly understood. A 78-question survey on FOP flare-ups, translated into 15 languages, was sent to 685 classically-affected patients in 45 countries (six continents). Five hundred patients or knowledgeable informants responded (73%; 44% males, 56% females; ages: 1 to 71 years; median: 23 years). The most common presenting symptoms of flare-ups were swelling (93%), pain (86%), or decreased mobility (79%). Seventy-one percent experienced a flare-up within the preceding 12 months (52% spontaneous; 48% trauma-related). Twenty-five percent of those who had received an intramuscular injection reported an immediate flare-up at the injection site, 84% of whom developed HO. Axial flare-ups most frequently involved the back (41.6%), neck (26.4%), or jaw (19.4%). Flare-ups occurred more frequently in the upper limbs before 8 years of age, but more frequently in the lower limbs thereafter. Appendicular flare-ups occurred more frequently at proximal than at distal sites without preferential sidedness. Seventy percent of patients reported functional loss from a flare-up. Thirty-two percent reported complete resolution of at least one flare-up and 12% without any functional loss (mostly in the head or back). The most disabling flare-ups occurred at the shoulders or hips. Surprisingly, 47% reported progression of FOP without obvious flare-ups. Worldwide, 198 treatments were reported; anti-inflammatory agents were most common. Seventy-five percent used short-term glucocorticoids as a treatment for flare-ups at appendicular sites. Fifty-five percent reported that glucocorticoids improved symptoms occasionally whereas 31% reported that they always did. Only 12% reported complete resolution of a flare-up with glucocorticoids. Forty-three percent reported rebound symptoms within 1 to 7 days after completing a course of glucocorticoids. This study is the first comprehensive global assessment of FOP flare-ups and establishes a critical foundation for the design and evaluation of future clinical trials.
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http://dx.doi.org/10.1002/jbmr.2728DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4829946PMC
March 2016

Prevalence and Course of Atrial Fibrillation in Critically Ill Trauma Patients.

J Intensive Care Med 2017 Feb 9;32(2):140-145. Epub 2016 Jul 9.

4 Department of Surgery, University of California, Davis Health System, Sacramento, CA, USA.

Atrial fibrillation (AF) is the most common cardiac dysrhythmia. Its prevalence, risk factors, course, and complications are not well described in critically ill trauma patients. This was a retrospective, single-center, cohort study at an academic, level 1 trauma center. Trauma patients >18 years, identified from the trauma registry and admitted to the intensive care unit (ICU), were sequentially screened for AF. A matched cohort was created by selecting patients consecutively admitted before and after the patients who experienced AF. Of 2591 patients screened, 191 experienced AF, resulting in a prevalence of 7.4%. There was no difference in injury severity score (ISS) between those with and without AF, but patients with AF had higher observed mortality (15.5% vs 6.7%, P < .001). Patients with a history of AF (n = 75) differed from new-onset AF (n = 106) in their mean age, 78.9 ± 8.4 versus 69.2 ± 17.9 years; mean time to AF onset, 1.1 ± 2.3 versus 5.2 ± 10.2 days; median duration of AF, 29.8 (1-745.2) versus 5.9 (0-757) hours; and rate of AF resolution, 28% versus 82.1%, respectively. Despite a higher ISS, Sequential Organ Failure Assessment and length of stay, the new-onset AF group experienced a similar rate of mortality compared to the history of AF group (14.7% vs 16.0%). Patients with AF had a higher mortality when compared to those in sinus rhythm. The course of AF in the new-onset AF group occurred later was shorter and was more likely to convert; however, these patients had a longer ICU stay when compared to those who had a history of AF.
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http://dx.doi.org/10.1177/0885066615599150DOI Listing
February 2017

Blood glucose response to rescue dextrose in hypoglycemic, critically ill patients receiving an insulin infusion.

Ann Pharmacother 2015 Aug 18;49(8):892-6. Epub 2015 May 18.

University of California Davis, Sacramento, CA, USA

Background: There is inadequate guidance for clinicians on selection of the optimal dextrose 50% (D50W) dose for hypoglycemia correction in critically ill patients.

Objective: The purpose of this study was to determine the blood glucose (BG) response to D50W in critically ill patients.

Methods: A retrospective analysis was conducted of critically ill patients who received D50W for hypoglycemia (BG < 70 mg/dL) while on an insulin infusion. The primary objective of this study was to determine the BG response to D50W. The relationship between participant characteristics and the dose-adjusted change in BG following D50W was analyzed using simple and multiple linear mixed-effects models.

Results: There were 470 hypoglycemic events (BG < 70 mg/dL) corrected with D50W. The overall median BG response was 4.0 (2.53, 6.08) mg/dL per gram of D50W administered. Administration of D50W per protocol resulted in 32 episodes of hyperglycemia (BG > 150 mg/dL), resulting in a 6.8% rate of overcorrection; 49% of hypoglycemic episodes (230/470) corrected to a BG >100 mg/dL. A multivariable GEE analysis showed a significantly higher BG response in participants with diabetes (0.002) but a lower response in those with recurrent hypoglycemia (P = 0.049). The response to D50W increased with increasinginsulin infusion rate (P = 0.022). Burn patients experienced a significantly larger BG response compared with cardiac, medical, neurosurgical, or surgical patients.

Conclusions: The observed median effect of D50W on BG was approximately 4 mg/dL per gram of D50W administered. Application of these data may aid in rescue protocol development that may reduce glucose variability associated with hypoglycemic episodes and the correction.
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http://dx.doi.org/10.1177/1060028015585574DOI Listing
August 2015

Human hair shaft proteomic profiling: individual differences, site specificity and cuticle analysis.

PeerJ 2014 5;2:e506. Epub 2014 Aug 5.

Forensic Science Graduate Program and Department of Environmental Toxicology, University of California , Davis, CA , USA.

Hair from different individuals can be distinguished by physical properties. Although some data exist on other species, examination of the individual molecular differences within the human hair shaft has not been thoroughly investigated. Shotgun proteomic analysis revealed considerable variation in profile among samples from Caucasian, African-American, Kenyan and Korean subjects. Within these ethnic groups, prominent keratin proteins served to distinguish individual profiles. Differences between ethnic groups, less marked, relied to a large extent on levels of keratin associated proteins. In samples from Caucasian subjects, hair shafts from axillary, beard, pubic and scalp regions exhibited distinguishable profiles, with the last being most different from the others. Finally, the profile of isolated hair cuticle cells was distinguished from that of total hair shaft by levels of more than 20 proteins, the majority of which were prominent keratins. The cuticle also exhibited relatively high levels of epidermal transglutaminase (TGM3), accounting for its observed low degree of protein extraction by denaturants. In addition to providing insight into hair structure, present findings may lead to improvements in differentiating hair from various ethnic origins and offer an approach to extending use of hair in crime scene evidence for distinguishing among individuals.
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http://dx.doi.org/10.7717/peerj.506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4137660PMC
August 2014

Distinguishing ichthyoses by protein profiling.

PLoS One 2013 9;8(10):e75355. Epub 2013 Oct 9.

Department of Environmental Toxicology and Forensic Science Graduate Program, University of California Davis, Davis, California, United States of America.

To explore the usefulness of protein profiling for characterization of ichthyoses, we here determined the profile of human epidermal stratum corneum by shotgun proteomics. Samples were analyzed after collection on tape circles from six anatomic sites (forearm, palm, lower leg, forehead, abdomen, upper back), demonstrating site-specific differences in profiles. Additional samples were collected from the forearms of subjects with ichthyosis vulgaris (filaggrin (FLG) deficiency), recessive X-linked ichthyosis (steroid sulfatase (STS) deficiency) and autosomal recessive congenital ichthyosis type lamellar ichthyosis (transglutaminase 1 (TGM1) deficiency). The ichthyosis protein expression patterns were readily distinguishable from each other and from phenotypically normal epidermis. In general, the degree of departure from normal was lower from ichthyosis vulgaris than from lamellar ichthyosis, parallel to the severity of the phenotype. Analysis of samples from families with ichthyosis vulgaris and concomitant modifying gene mutations (STS deficiency, GJB2 deficiency) permitted correlation of alterations in protein profile with more complex genetic constellations.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0075355PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3793978PMC
June 2014

Chicken corneocyte cross-linked proteome.

J Proteome Res 2013 Feb 4;12(2):771-6. Epub 2013 Jan 4.

Department of Environmental Toxicology, University of California Davis, Davis, California 95616, USA.

Shotgun proteomic analysis was performed of epidermal scale, feather, beak and claw from the domestic chicken. To this end, the samples were separated first into solubilized and particulate fractions, the latter enriched in isopeptide cross-linking, by exhaustive extraction in sodium dodecyl sulfate under reducing conditions. Among the 205 proteins identified were 17 keratins (types α and β), 51 involved in protein synthesis, 8 junctional, 8 histone, 5 heat shock, and 5 14-3-3 proteins. Considerable overlap among the beak, claw, feather, and scale samples was observed in protein profiles, but those from beak and claw were the most similar. Scale and feather profiles were the most distinctive, each exhibiting specific proteins. Less than 20% of the proteins were found only in the detergent-solubilized fraction, while 34-57% were found only in the particulate fraction, depending on the source, and the rest in both fractions. The results provide the first comprehensive analysis of the content of these cornified structures, reveal the efficient use of available proteins in conferring mechanical and chemical stability to them, and emphasize the importance of isopeptide cross-linking in avian epithelial cornification.
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http://dx.doi.org/10.1021/pr301036kDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3569041PMC
February 2013

Differentiating inbred mouse strains from each other and those with single gene mutations using hair proteomics.

PLoS One 2012 14;7(12):e51956. Epub 2012 Dec 14.

Department of Environmental Toxicology and Forensic Science Graduate Program, University of California Davis, Davis, California, USA.

Mutant laboratory mice with distinctive hair phenotypes are useful for identifying genes responsible for hair diseases. The work presented here demonstrates that shotgun proteomic profiling can distinguish hair shafts from different inbred mouse strains. For this purpose, analyzing the total hair shaft provided better discrimination than analyzing the isolated solubilized and particulate (cross-linked) fractions. Over 100 proteins exhibited significant differences among the 11 strains and 5 mutant stocks across the wide spectrum of strains surveyed. Effects on the profile of single gene mutations causing hair shaft defects were profound. Since the hair shaft provides a discrete sampling of the species proteome, with constituents serving important functions in epidermal appendages and throughout the body, this work provides a foundation for non-invasive diagnosis of genetic diseases of hair and perhaps other tissues.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0051956PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522583PMC
September 2013