101
|
Miller MR, Müller U, Giesbrecht GF, Carpendale JI, Kerns KA. The contribution of executive function and social understanding to preschoolers’ letter and math skills. COGNITIVE DEVELOPMENT 2013. [DOI: 10.1016/j.cogdev.2012.10.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
102
|
Narum SR, Buerkle CA, Davey JW, Miller MR, Hohenlohe PA. Genotyping-by-sequencing in ecological and conservation genomics. Mol Ecol 2013; 22:2841-7. [PMID: 23711105 DOI: 10.1111/mec.12350] [Citation(s) in RCA: 343] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 04/09/2013] [Accepted: 04/10/2013] [Indexed: 12/12/2022]
|
103
|
Narum SR, Campbell NR, Meyer KA, Miller MR, Hardy RW. Thermal adaptation and acclimation of ectotherms from differing aquatic climates. Mol Ecol 2013; 22:3090-7. [DOI: 10.1111/mec.12240] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 11/02/2012] [Accepted: 11/16/2012] [Indexed: 11/24/2022]
|
104
|
Hohenlohe PA, Day MD, Amish SJ, Miller MR, Kamps-Hughes N, Boyer MC, Muhlfeld CC, Allendorf FW, Johnson EA, Luikart G. Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing. Mol Ecol 2013; 22:3002-13. [PMID: 23432212 DOI: 10.1111/mec.12239] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 12/05/2012] [Accepted: 12/11/2012] [Indexed: 12/14/2022]
Abstract
Rapid and inexpensive methods for genomewide single nucleotide polymorphism (SNP) discovery and genotyping are urgently needed for population management and conservation. In hybridized populations, genomic techniques that can identify and genotype thousands of species-diagnostic markers would allow precise estimates of population- and individual-level admixture as well as identification of 'super invasive' alleles, which show elevated rates of introgression above the genomewide background (likely due to natural selection). Techniques like restriction-site-associated DNA (RAD) sequencing can discover and genotype large numbers of SNPs, but they have been limited by the length of continuous sequence data they produce with Illumina short-read sequencing. We present a novel approach, overlapping paired-end RAD sequencing, to generate RAD contigs of >300-400 bp. These contigs provide sufficient flanking sequence for design of high-throughput SNP genotyping arrays and strict filtering to identify duplicate paralogous loci. We applied this approach in five populations of native westslope cutthroat trout that previously showed varying (low) levels of admixture from introduced rainbow trout (RBT). We produced 77 141 RAD contigs and used these data to filter and genotype 3180 previously identified species-diagnostic SNP loci. Our population-level and individual-level estimates of admixture were generally consistent with previous microsatellite-based estimates from the same individuals. However, we observed slightly lower admixture estimates from genomewide markers, which might result from natural selection against certain genome regions, different genomic locations for microsatellites vs. RAD-derived SNPs and/or sampling error from the small number of microsatellite loci (n = 7). We also identified candidate adaptive super invasive alleles from RBT that had excessively high admixture proportions in hybridized cutthroat trout populations.
Collapse
|
105
|
Lai SL, Miller MR, Robinson KJ, Doe CQ. The Snail family member Worniu is continuously required in neuroblasts to prevent Elav-induced premature differentiation. Dev Cell 2013; 23:849-57. [PMID: 23079601 DOI: 10.1016/j.devcel.2012.09.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 07/17/2012] [Accepted: 09/12/2012] [Indexed: 11/17/2022]
Abstract
Snail family transcription factors are best known for regulating epithelial-mesenchymal transition (EMT). The Drosophila Snail family member Worniu is specifically transcribed in neural progenitors (neuroblasts) throughout their lifespan, and worniu mutants show defects in neuroblast delamination (a form of EMT). However, the role of Worniu in neuroblasts beyond their formation is unknown. We performed RNA-seq on worniu mutant larval neuroblasts and observed reduced cell-cycle transcripts and increased neural differentiation transcripts. Consistent with these genomic data, worniu mutant neuroblasts showed a striking delay in prophase/metaphase transition by live imaging and increased levels of the conserved neuronal differentiation splicing factor Elav. Reducing Elav levels significantly suppressed the worniu mutant phenotype. We conclude that Worniu is continuously required in neuroblasts to maintain self-renewal by promoting cell-cycle progression and inhibiting premature differentiation.
Collapse
|
106
|
Esser AK, Miller MR, Huang Q, Meier MM, Beltran-Valero de Bernabé D, Stipp CS, Campbell KP, Lynch CF, Smith BJ, Cohen MB, Henry MD. Loss of LARGE2 disrupts functional glycosylation of α-dystroglycan in prostate cancer. J Biol Chem 2013; 288:2132-42. [PMID: 23223448 PMCID: PMC3554886 DOI: 10.1074/jbc.m112.432807] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Indexed: 11/06/2022] Open
Abstract
Dystroglycan (DG) is a cell surface receptor for extracellular matrix proteins and is involved in cell polarity, matrix organization, and mechanical stability of tissues. Previous studies documented loss of DG protein expression and glycosylation in a variety of cancer types, but the underlying mechanisms and the functional consequences with respect to cancer progression remain unclear. Here, we show that the level of expression of the βDG subunit as well as the glycosylation status of the αDG subunit inversely correlate with the Gleason scores of prostate cancers; furthermore, we show that the functional glycosylation of αDG is substantially reduced in prostate cancer metastases. Additionally, we demonstrate that LARGE2 (GYLTL1B), a gene not previously implicated in cancer, regulates functional αDG glycosylation in prostate cancer cell lines; knockdown of LARGE2 resulted in hypoglycosylation of αDG and loss of its ability to bind laminin-111 while overexpression restored ligand binding and diminished growth and migration of an aggressive prostate cancer cell line. Finally, our analysis of LARGE2 expression in human cancer specimens reveals that LARGE2 is significantly down-regulated in the context of prostate cancer, and that its reduction correlates with disease progression. Our results describe a novel molecular mechanism to account for the commonly observed hypoglycosylation of αDG in prostate cancer.
Collapse
|
107
|
Gay L, Miller MR, Ventura PB, Devasthali V, Vue Z, Thompson HL, Temple S, Zong H, Cleary MD, Stankunas K, Doe CQ. Mouse TU tagging: a chemical/genetic intersectional method for purifying cell type-specific nascent RNA. Genes Dev 2013; 27:98-115. [PMID: 23307870 PMCID: PMC3553287 DOI: 10.1101/gad.205278.112] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 11/19/2012] [Indexed: 12/16/2022]
Abstract
Transcriptional profiling is a powerful approach for understanding development and disease. Current cell type-specific RNA purification methods have limitations, including cell dissociation trauma or inability to identify all RNA species. Here, we describe "mouse thiouracil (TU) tagging," a genetic and chemical intersectional method for covalent labeling and purification of cell type-specific RNA in vivo. Cre-induced expression of uracil phosphoribosyltransferase (UPRT) provides spatial specificity; injection of 4-thiouracil (4TU) provides temporal specificity. Only UPRT(+) cells exposed to 4TU produce thio-RNA, which is then purified for RNA sequencing (RNA-seq). This method can purify transcripts from spatially complex and rare (<5%) cells, such as Tie2:Cre(+) brain endothelia/microglia (76% validated by expression pattern), or temporally dynamic transcripts, such as those acutely induced by lipopolysaccharide (LPS) injection. Moreover, generating chimeric mice via UPRT(+) bone marrow transplants identifies immune versus niche spleen RNA. TU tagging provides a novel method for identifying actively transcribed genes in specific cells at specific times within intact mice.
Collapse
|
108
|
Ward HM, Cooper BG, Miller MR. P37 Which Bronchodilator Reversibility Definition Best Avoids Bias. Thorax 2012. [DOI: 10.1136/thoraxjnl-2012-202678.178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
109
|
Everett MV, Miller MR, Seeb JE. Meiotic maps of sockeye salmon derived from massively parallel DNA sequencing. BMC Genomics 2012; 13:521. [PMID: 23031582 PMCID: PMC3563581 DOI: 10.1186/1471-2164-13-521] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 09/23/2012] [Indexed: 12/21/2022] Open
Abstract
Background Meiotic maps are a key tool for comparative genomics and association mapping studies. Next-generation sequencing and genotyping by sequencing are speeding the processes of SNP discovery and the development of new genetic tools, including meiotic maps for numerous species. Currently there are limited genetic resources for sockeye salmon, Oncorhynchus nerka. We develop the first dense meiotic map for sockeye salmon using a combination of novel SNPs found in restriction site associated DNA (RAD tags) and SNPs available from existing expressed sequence tag (EST) based assays. Results We discovered and genotyped putative SNPs in 3,430 RAD tags. We removed paralogous sequence variants leaving 1,672 SNPs; these were combined with 53 EST-based SNP genotypes for linkage mapping. The map contained 29 male and female linkage groups, consistent with the haploid chromosome number expected for sockeye salmon. The female map contains 1,057 loci spanning 4,896 cM, and the male map contains 1,118 loci spanning 4,220 cM. Regions of conservation with rainbow trout and synteny between the RAD based rainbow trout map and the sockeye salmon map were established. Conclusions Using RAD sequencing and EST-based SNP assays we successfully generated the first high density linkage map for sockeye salmon.
Collapse
|
110
|
Hecht BC, Thrower FP, Hale MC, Miller MR, Nichols KM. Genetic architecture of migration-related traits in rainbow and steelhead trout, Oncorhynchus mykiss. G3 (BETHESDA, MD.) 2012; 2:1113-27. [PMID: 22973549 PMCID: PMC3429926 DOI: 10.1534/g3.112.003137] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 07/14/2012] [Indexed: 12/26/2022]
Abstract
Although migration plays a critical role in the evolution and diversification of species, relatively little is known of the genetic architecture underlying this life history in any species. Rainbow and steelhead trout (Oncorhynchus mykiss) naturally segregate for both resident and migratory life-history types, respectively, as do other members of the salmonid family of fishes. Using an experimental cross derived from wild resident rainbow and wild migratory steelhead trout from Southeast Alaska and high throughput restriction-site associated DNA (RAD) tag sequencing, we perform a quantitative trait locus (QTL) analysis to identify the number, position, and relative contribution of genetic effects on a suite of 27 physiological and morphological traits associated with the migratory life history in this species. In total, 37 QTL are localized to 19 unique QTL positions, explaining 4-13.63% of the variation for 19 of the 27 migration-related traits measured. Two chromosomal positions, one on chromosome Omy12 and the other on Omy14 each harbor 7 QTL for migration-related traits, suggesting that these regions could harbor master genetic controls for the migratory life-history tactic in this species. Another QTL region on Omy5 has been implicated in several studies of adaptive life histories within this species and could represent another important locus underlying the migratory life history. We also evaluate whether loci identified in this out-crossed QTL study colocalize to genomic positions previously identified for associations with migration-related traits in a doubled haploid mapping family.
Collapse
|
111
|
Miller MR, Giesbrecht GF, Müller U, McInerney RJ, Kerns KA. A Latent Variable Approach to Determining the Structure of Executive Function in Preschool Children. JOURNAL OF COGNITION AND DEVELOPMENT 2012. [DOI: 10.1080/15248372.2011.585478] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
112
|
Miller MR, Esser AK, Weydert CJ, Meier MM, Smith BJ, Vessella RL, Lynch C, Cohen MB, Henry MD. Abstract 439: Glycosylation of α-dystroglycan in prostate cancer: Prognostic implications and regulation by LARGE2. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cancer cells exhibit altered interactions with their extracellular matrix microenvironment that are thought to underlie tumor progression and metastasis. Dystroglycan (DG) is a receptor for extracellular matrix proteins including laminins and perlecan that consists of a ligand-binding α subunit and a transmembrane β subunit. DG protein expression is reduced in numerous types of cancer, including prostate cancer. Typically DG mRNA expression is not remarkably altered and mutations in the DG gene have not been reported in any cancer to date. We have investigated the basis for reduced DG expression in prostate cancer. Using tissue microarray (n=50; Gleason score 6-8) we show that loss of either α or β DG independently predicts Gleason score. We show that loss of αDG immunostaining in human prostatectomy samples (n=138) trended towards predicting overall mortality independent of grade and stage with an estimated hazard ratio of 1.32 (CI=0.92, 1.89; p=0.1381). Furthermore, analysis of prostate cancer metastases in bone, lung and lymph node shows a near universal loss of αDG immunostaining. Importantly, we observed cases in which αDG is reduced while βDG persisted in serial sections, suggesting that these subunits may be differentially affected. In these studies, we detected αDG using a glycosylation-sensitive antibody IIH6. Therefore, we investigated the basis of altered αDG glycosylation using a series of prostate cancer cell lines. We found that αDG glycosylation is heterogeneous across several prostate cancer cell lines. Importantly, we found that an aggressive derivative of PC-3 cells lacks IIH6 immunoreactivity, but not core αDG protein expression; whereas the bulk PC-3 population is IIH6 positive. We evaluated the relative expression of a panel of glycosyltransferases known to modify αDG in these cell lines and found that loss of IIH6 immunoreactivity is correlated with loss of LARGE2 expression. This result contrasts with previous findings implicating LARGE or iGNT with abnormal glycosylation of αDG in breast and prostate cancer respectively. Reduced expression of LARGE2 is also observed in pancreatic cancer cell lines and is correlated with loss of IIH6 immunoreactivity. We show that LARGE2 is involved in the functional glycosylation of αDG in prostate cancer cells. shRNA-mediated knockdown of LARGE2 in prostate cancer cells does not affect growth rate, but does increase transwell migration across laminin-1 substrate. Our results are the first to implicate loss of LARGE2 expression as a means to explain the loss of appropriate glycosylation of αDG in prostate or other cancers, and indicates that LARGE2 function may modulate prostate cancer progression and metastasis.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 439. doi:1538-7445.AM2012-439
Collapse
|
113
|
Bernardi G, Wiley EO, Mansour H, Miller MR, Orti G, Haussler D, O'Brien SJ, Ryder OA, Venkatesh B. The fishes of Genome 10K. Mar Genomics 2012; 7:3-6. [PMID: 22897955 DOI: 10.1016/j.margen.2012.02.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 02/27/2012] [Accepted: 02/27/2012] [Indexed: 11/16/2022]
Abstract
The Genome 10K project aims to sequence the genomes of 10,000 vertebrates, representing approximately one genome for each vertebrate genus. Since fishes (cartilaginous fishes, ray-finned fishes and lobe-finned fishes) represent more than 50% of extant vertebrates, it is planned to target 4,000 fish genomes. At present, nearly 60 fish genomes are being sequenced at various public funded labs, and under a Genome 10K and BGI pilot project. An additional 100 fishes have been identified for sequencing in the next phase of Genome 10K project.
Collapse
|
114
|
Casazza ML, Coates PS, Miller MR, Overton CT, Yparraguirre DR. Hunting influences the diel patterns in habitat selection by northern pintailsAnas acuta. WILDLIFE BIOLOGY 2012. [DOI: 10.2981/09-099] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
|
115
|
Charon NW, Cockburn A, Li C, Liu J, Miller KA, Miller MR, Motaleb M, Wolgemuth CW. The unique paradigm of spirochete motility and chemotaxis. Annu Rev Microbiol 2012; 66:349-70. [PMID: 22994496 PMCID: PMC3771095 DOI: 10.1146/annurev-micro-092611-150145] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Spirochete motility is enigmatic: It differs from the motility of most other bacteria in that the entire bacterium is involved in translocation in the absence of external appendages. Using the Lyme disease spirochete Borrelia burgdorferi (Bb) as a model system, we explore the current research on spirochete motility and chemotaxis. Bb has periplasmic flagella (PFs) subterminally attached to each end of the protoplasmic cell cylinder, and surrounding the cell is an outer membrane. These internal helix-shaped PFs allow the spirochete to swim by generating backward-moving waves by rotation. Exciting advances using cryoelectron tomography are presented with respect to in situ analysis of cell, PF, and motor structure. In addition, advances in the dynamics of motility, chemotaxis, gene regulation, and the role of motility and chemotaxis in the life cycle of Bb are summarized. The results indicate that the motility paradigms of flagellated bacteria do not apply to these unique bacteria.
Collapse
|
116
|
Carney TD, Miller MR, Robinson KJ, Bayraktar OA, Osterhout JA, Doe CQ. Functional genomics identifies neural stem cell sub-type expression profiles and genes regulating neuroblast homeostasis. Dev Biol 2011; 361:137-46. [PMID: 22061480 DOI: 10.1016/j.ydbio.2011.10.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 10/17/2011] [Accepted: 10/18/2011] [Indexed: 11/18/2022]
Abstract
The Drosophila larval central brain contains about 10,000 differentiated neurons and 200 scattered neural progenitors (neuroblasts), which can be further subdivided into ~95 type I neuroblasts and eight type II neuroblasts per brain lobe. Only type II neuroblasts generate self-renewing intermediate neural progenitors (INPs), and consequently each contributes more neurons to the brain, including much of the central complex. We characterized six different mutant genotypes that lead to expansion of neuroblast numbers; some preferentially expand type II or type I neuroblasts. Transcriptional profiling of larval brains from these mutant genotypes versus wild-type allowed us to identify small clusters of transcripts enriched in type II or type I neuroblasts, and we validated these clusters by gene expression analysis. Unexpectedly, only a few genes were found to be differentially expressed between type I/II neuroblasts, suggesting that these genes play a large role in establishing the different cell types. We also identified a large group of genes predicted to be expressed in all neuroblasts but not in neurons. We performed a neuroblast-specific, RNAi-based functional screen and identified 84 genes that are required to maintain proper neuroblast numbers; all have conserved mammalian orthologs. These genes are excellent candidates for regulating neural progenitor self-renewal in Drosophila and mammals.
Collapse
|
117
|
Halstead BJ, Miller MR, Casazza ML, Coates PS, Farinha MA, Gustafson KB, Yee JL, Fleskes JP. Rapid assessment of rice seed availability for wildlife in harvested fields. WILDLIFE SOC B 2011. [DOI: 10.1002/wsb.72] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
118
|
Miller MR, Brunelli JP, Wheeler PA, Liu S, Rexroad CE, Palti Y, Doe CQ, Thorgaard GH. A conserved haplotype controls parallel adaptation in geographically distant salmonid populations. Mol Ecol 2011; 21:237-49. [PMID: 21988725 PMCID: PMC3664428 DOI: 10.1111/j.1365-294x.2011.05305.x] [Citation(s) in RCA: 185] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Salmonid fishes exhibit extensive local adaptations owing to abundant environmental variation and precise natal homing. This extensive local adaptation makes conservation and restoration of salmonids a challenge. For example, defining unambiguous units of conservation is difficult, and restoration attempts often fail owing to inadequate adaptive matching of translocated populations. A better understanding of the genetic architecture of local adaptation in salmonids could provide valuable information to assist in conserving and restoring natural populations of these important species. Here, we use a combination of laboratory crosses and next-generation sequencing to investigate the genetic architecture of the parallel adaptation of rapid development rate in two geographically and genetically distant populations of rainbow trout (Oncorhynchus mykiss). Strikingly, we find that not only is a parallel genetic mechanism used but that a conserved haplotype is responsible for this intriguing adaptation. The repeated use of adaptive genetic variation across distant geographical areas could be a general theme in salmonids and have important implications for conservation and restoration.
Collapse
|
119
|
Liu C, Sage JC, Miller MR, Verhaak RG, Hippenmeyer S, Vogel H, Foreman O, Bronson RT, Nishiyama A, Luo L, Zong H. Mosaic analysis with double markers reveals tumor cell of origin in glioma. Cell 2011; 146:209-21. [PMID: 21737130 PMCID: PMC3143261 DOI: 10.1016/j.cell.2011.06.014] [Citation(s) in RCA: 487] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 05/03/2011] [Accepted: 06/03/2011] [Indexed: 12/26/2022]
Abstract
Cancer cell of origin is difficult to identify by analyzing cells within terminal stage tumors, whose identity could be concealed by the acquired plasticity. Thus, an ideal approach to identify the cell of origin is to analyze proliferative abnormalities in distinct lineages prior to malignancy. Here, we use mosaic analysis with double markers (MADM) in mice to model gliomagenesis by initiating concurrent p53/Nf1 mutations sporadically in neural stem cells (NSCs). Surprisingly, MADM-based lineage tracing revealed significant aberrant growth prior to malignancy only in oligodendrocyte precursor cells (OPCs), but not in any other NSC-derived lineages or NSCs themselves. Upon tumor formation, phenotypic and transcriptome analyses of tumor cells revealed salient OPC features. Finally, introducing the same p53/Nf1 mutations directly into OPCs consistently led to gliomagenesis. Our findings suggest OPCs as the cell of origin in this model, even when initial mutations occur in NSCs, and highlight the importance of analyzing premalignant stages to identify the cancer cell of origin.
Collapse
|
120
|
Allen-Petersen BL, Miller MR, Neville MC, Anderson SM, Nakayama KI, Reyland ME. Loss of protein kinase C delta alters mammary gland development and apoptosis. Cell Death Dis 2011; 1:e17. [PMID: 21364618 PMCID: PMC3032509 DOI: 10.1038/cddis.2009.20] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
As apoptotic pathways are commonly deregulated in breast cancer, exploring how mammary gland cell death is regulated is critical for understanding human disease. We show that primary mammary epithelial cells from protein kinase C delta (PKCδ) −/− mice have a suppressed response to apoptotic agents in vitro. In the mammary gland in vivo, apoptosis is critical for ductal morphogenesis during puberty and involution following lactation. We have explored mammary gland development in the PKCδ −/− mouse during these two critical windows. Branching morphogenesis was altered in 4- to 6-week-old PKCδ −/− mice as indicated by reduced ductal branching; however, apoptosis and proliferation in the terminal end buds was unaltered. Conversely, activation of caspase-3 during involution was delayed in PKCδ −/− mice, but involution proceeded normally. The thymus also undergoes apoptosis in response to physiological signals. A dramatic suppression of caspase-3 activation was observed in the thymus of PKCδ −/− mice treated with irradiation, but not mice treated with dexamethasone, suggesting that there are both target- and tissue-dependent differences in the execution of apoptotic pathways in vivo. These findings highlight a role for PKCδ in both apoptotic and nonapoptotic processes in the mammary gland and underscore the redundancy of apoptotic pathways in vivo.
Collapse
|
121
|
Quanjer PH, Enright PL, Miller MR, Stocks J, Ruppel G, Swanney MP, Crapo RO, Pedersen OF, Falaschetti E, Schouten JP, Jensen RL. The need to change the method for defining mild airway obstruction. Eur Respir J 2011; 37:720-2. [PMID: 21357929 DOI: 10.1183/09031936.00135110] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
122
|
McNulty AL, Miller MR, O’Connor SK, Guilak F. The effects of adipokines on cartilage and meniscus catabolism. Connect Tissue Res 2011; 52:523-33. [PMID: 21787135 PMCID: PMC3616891 DOI: 10.3109/03008207.2011.597902] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Obesity is one of the primary risk factors for osteoarthritis. Increased adiposity is associated not only with alterations in joint loading, but also with increased systemic and joint concentrations of adipose tissue-derived cytokines, or "adipokines", that promote a state of chronic, low-grade inflammation that may act in concert with other cytokines in the joint to increase joint degeneration. However, the direct effect of adipokines, such as leptin, visfatin, and interleukin-6 (IL-6), on joint tissues, such as articular cartilage and meniscus, are not fully understood. In this study, we examined the hypothesis that these adipokines act synergistically with interleukin-1 (IL-1) to increase catabolism and the production of proinflammatory mediators in cartilage and meniscus. Explants of porcine cartilage and meniscus were treated with physiologically relevant concentrations of leptin, IL-6, or visfatin, alone or in combination with IL-1. Visfatin and IL-1 promoted the catabolic degradation of both cartilage and meniscus, as evidenced by increased metalloproteinase activity, nitric oxide production, and proteoglycan release. However, leptin or IL-6 at physiologic concentrations had no effect on the breakdown of these tissues. These findings suggest that the effects of obesity-induced osteoarthritis may not be through a direct effect of leptin or IL-6 on cartilaginous tissues, but support a potential role for increased visfatin levels in this regard. These data provide an important first step in understanding the role of adipokines in regulating cartilage and meniscus metabolism; however, these adipokines may have different effects in the context of the whole joint and must be evaluated further.
Collapse
|
123
|
Müller U, Miller MR, Michalczyk K, Karapinka A. False belief understanding: The influence of person, grammatical mood, counterfactual reasoning and working memory. BRITISH JOURNAL OF DEVELOPMENTAL PSYCHOLOGY 2010. [DOI: 10.1348/026151007x182962] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
124
|
Miller MR, Takekawa JY, Battaglia DS, Golightly RT, Perry WM. Spring Migration and Summer Destinations of Northern Pintails from the Coast of Southern California. SOUTHWEST NAT 2010. [DOI: 10.1894/kf-11.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
125
|
Washburn BK, Levin AE, Hennessy K, Miller MR. Identification of bacteria in scuba divers' rinse tanks. Undersea Hyperb Med 2010; 37:233-240. [PMID: 20737930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Scuba divers typically rinse equipment in communal tanks. Studies show these tanks are contaminated with bacteria, but the types of bacteria have not been studied. We sought to identify bacteria in rinse tanks at a dive facility at San Pedro, Belize, to determine the origin of the bacteria and determine whether the bacteria represented potential threats to human health. The identity of bacteria was investigated using reverse line blot (RLB) assays based on 28 different rDNA probes designed to detect known pathogens of sepsis, as well as by sequencing 23S rDNA from isolates and performing VITEK identification of several isolates. Based on the identities of bacteria in divers' rinse tanks, many likely originate from the ocean, and others likely originate from the divers themselves. None of the bacteria identified would be considered overt human pathogens. However, some of the bacteria found in the tanks are known to be associated with unsanitary conditions and can cause opportunistic infections, which may pose health problems to some individuals. Rinsing scuba equipment in communal tanks has the potential to transmit disease among some divers. Equipment, especially regulators and masks, should be rinsed/cleaned individually and not be placed in communal tanks.
Collapse
|