Peter Croucher - Profile on Academia.edu (original) (raw)

Papers by Peter Croucher

The biochemist, Feb 1, 2009

Although it has been convincingly shown that forest populations of the pathogen Phytophthora ramo... more Although it has been convincingly shown that forest populations of the pathogen Phytophthora ramorum have undergone a significant bottleneck and reproduce exclusively asexually , objective results showing that nurseries were the original source of the introduction remain elusive . A previous attempt to define routes of pathogen movement resulted in a largely unresolved network ), showing at best that populations from Santa Cruz and Marin Counties were important sources within California. Previous attempts at reconstructing the entire history of the sudden oak death (SOD) epidemic in California were limited by: 1) incomplete sampling; 2) the inability to include singleton samples; and 3) over-collapsing of non-spatially contiguous, yet genetically similar, samples into large meta-samples that confounded the coalescent analyses. Here, we employ a complete sampling coverage of 832 isolates of P. ramorum (the causative agent of SOD) from 60 California forests, genotyped at nine microsatellite loci. The following microsatellite loci were genotyped: PrMS39a, PrMS39b, PrMS43a, PrMS43b, PrMS45 ), locus 18, locus 64 (Ivors et al. 2006), and loci ILVO145PrMS145 (a and c) . Rather than using data simply based on number of microsatellite repeats, we employed Bruvo's distances as in previous studies ). This metric is appropriate for analyses of populations that comprise closely related genotypes originated from the same founder genotypes because larger shifts in the number of repeats are weighed, not proportionally, but in terms of likelihood. Analysis of molecular variance (AMOVA) , as implemented by ARLEQUIN v.3.5 (Excoffier et al. 2005), was employed to generate pair-wise estimates of Φ ST among all 62 P. ramorum forest and nursery populations. The Bruvo distance among each pair of unique multilocus genotypes (MGs) was estimated and fed to ARLEQUIN as an external file as the basis for the evolutionary distance in the AMOVA calculations.

Journal of Fungi, Mar 9, 2021

Phosphites have been used to control Sudden Oak Death; however, their precise mode of action is n... more Phosphites have been used to control Sudden Oak Death; however, their precise mode of action is not fully understood. To study the mechanism of action of phosphites, we conducted an inoculation experiment on two open-pollinated tanoak families, previously found to be partially resistant. Stems of treatment group individuals were sprayed with phosphite, and seven days later, distal leaves were inoculated with the Sudden Oak Death pathogen Phytophthora ramorum. Leaves from treated and untreated control plants were harvested before and seven days after inoculation, and transcriptomes of both host and pathogen were analyzed. We found that tanoak families differed in the presence of innate resistance (resistance displayed by untreated tanoak) and in the response to phosphite treatment. A set of expressed genes associated with innate resistance was found to overlap with an expressed gene set for phosphite-induced resistance. This observation may indicate that phosphite treatment increases the resistance of susceptible host plants. In addition, genes of the pathogen involved in detoxification were upregulated in phosphite-treated plants compared to phosphite-untreated plants. In summary, our RNA-Seq analysis supports a two-fold mode of action of phosphites, including a direct toxic effect on P. ramorum and an indirect enhancement of resistance in the tanoak host.

BMC Genomics, 2013

Background: A number of spider species within the family Theridiidae exhibit a dramatic abdominal... more Background: A number of spider species within the family Theridiidae exhibit a dramatic abdominal (opisthosomal) color polymorphism. The polymorphism is inherited in a broadly Mendelian fashion and in some species consists of dozens of discrete morphs that are convergent across taxa and populations. Few genomic resources exist for spiders. Here, as a first necessary step towards identifying the genetic basis for this trait we present the near complete transcriptomes of two species: the Hawaiian happy-face spider Theridion grallator and Theridion californicum. We mined the gene complement for pigment-pathway genes and examined differential expression (DE) between morphs that are unpatterned (plain yellow) and patterned (yellow with superimposed patches of red, white or very dark brown). Results: By deep sequencing both RNA-seq and normalized cDNA libraries from pooled specimens of each species we were able to assemble a comprehensive gene set for both species that we estimate to be 98-99% complete. It is likely that these species express more than 20,000 protein-coding genes, perhaps 4.5% (ca. 870) of which might be unique to spiders. Mining for pigment-associated Drosophila melanogaster genes indicated the presence of all ommochrome pathway genes and most pteridine pathway genes and DE analyses further indicate a possible role for the pteridine pathway in theridiid color patterning. Conclusions: Based upon our estimates, T. grallator and T. californicum express a large inventory of protein-coding genes. Our comprehensive assembly illustrates the continuing value of sequencing normalized cDNA libraries in addition to RNA-seq in order to generate a reference transcriptome for non-model species. The identification of pteridine-related genes and their possible involvement in color patterning is a novel finding in spiders and one that suggests a biochemical link between guanine deposits and the pigments exhibited by these species.

Journal of Arachnology, Apr 1, 2014

Molecular genetic tools have been a boon to arachnologists for decades and used to study many uni... more Molecular genetic tools have been a boon to arachnologists for decades and used to study many unique aspects of arachnid biology including genomics, phylogenetics, population genetics, and biogeography. These tools have evolved over time and now provide myriad methods for exploring evolutionary questions. Early tools, while still useful under the proper circumstances, are giving way to a new generation of DNA sequencing technologies. These new platforms yield impressive amounts of data at a fraction of the cost of traditional techniques. Herein, we discuss the history and future of molecular evolutionary arachnology in terms of available genetic/genomic tools and their potential applications, strengths, weaknesses, and relative costs. Next-generation sequencing (NGS) platforms are varied in their methods and potential uses, making high-throughput sequencing studies focusing on a wide array of questions tractable. To date, relatively few studies have employed NGS technologies using arachnids, but many could benefit from using them. Because no model species exist within the class Arachnida, we have a limited understanding of arachnid genomics. With the ever-advancing nature of sequencing technologies and bioinformatics, arachnologists can relatively easily implement NGS studies to bridge the gaps in our understanding and open avenues for deeper and more powerful experiments. To this end, we discuss examples of applications of NGS technologies focusing on arachnid taxa. Despite the allure of acquiring massive quantities of sequence data, we should recognize the limitations of existing NGS technologies and not forsake pre-NGS methods when these technologies could adequately address our questions.

European Journal of Human Genetics, 2003

Current debate focuses on the relevance of linkage disequilibrium (LD), ethnicity and underlying ... more Current debate focuses on the relevance of linkage disequilibrium (LD), ethnicity and underlying haplotype structure to the search for genes involved in complex disorders. The recently described association between single nucleotide polymorphisms (SNPs) of the CARD15 (NOD2) gene and Crohn's disease (CD) in populations of north-European descent provides a test case that we have subjected to detailed SNP haplotype based analyses. We examined 23 SNPs spanning 290 kb, including CARD15, in large North-European and Korean samples of patients with Crohn's disease and normal controls. In Europeans we confirmed that the three disease-associated SNPs occur independently but share a common background haplotype. This suggests a common origin and the possibility of an undiscovered more strongly predisposing mutation. Korean CD patients present a phenotype identical to the European patients and have not previously been screened for CARD15. The three disease-associated SNPs were absent and there was no evidence of association between CARD15 and CD. Consequently, the diseaseassociated mutations in the Europeans, which are rare, have arisen recently (after the Asian -European split). Our results highlight important issues relevant to mapping the genes that predispose to complex disorders. First, although ethnically divergent populations may present identical phenotypes they do not necessarily share the same set of predisposing genes. Second, although single-locus tests of association showed consistent association with markers throughout the gene, pair-wise LD between markers (r 2 and D') yielded very little information about actual disease-association. Third, a population comparative approach allowed refining of the marker set through the examination of shared polymorphisms and common LD-groups. This approach, in conjunction with the examination of the mutational steps in a haplotype network, allows unambiguous identification of the potentially causative mutations.

Evolution, May 9, 2012

Past geological and climatological processes shape extant biodiversity. In the Hawaiian Islands, ... more Past geological and climatological processes shape extant biodiversity. In the Hawaiian Islands, these processes have provided the physical environment for a number of extensive adaptive radiations. Yet, single species that occur throughout the islands provide some of the best cases for understanding how species respond to the shifting dynamics of the islands in the context of colonization history and associated demographic and adaptive shifts. Here, we focus on the Hawaiian happy-face spider, a single color-polymorphic species, and use mitochondrial and nuclear allozyme markers to examine (1) how the mosaic formation of the landscape has dictated population structure, and (2) how cycles of expansion and contraction of the habitat matrix have been associated with demographic shifts, including a "quantum shift" in the genetic basis of the color polymorphism. The results show a marked structure among populations consistent with the age progression of the islands. The finding of low genetic diversity at the youngest site coupled with the very high diversity of haplotypes on the slightly older substrates that are highly dissected by recent volcanism suggests that the mosaic structure of the landscape may play an important role in allowing differentiation of the adaptive color polymorphism.

Phytopathology®, 2019

The genetic structure of a sample of isolates of the oomycete plant pathogen Phytophthora cinnamo... more The genetic structure of a sample of isolates of the oomycete plant pathogen Phytophthora cinnamomi from natural and agricultural outbreaks and the long-distance movement of individual genotypes were studied using four microsatellite markers to genotype 159 isolates of Californian, Mexican, and worldwide origins. Allelic profiles identified 75 multilocus genotypes. A STRUCTURE analysis placed them in three groups characterized by different geographic and host ranges, different genic and genotypic diversity, and different reproductive modes. When relationships among genotypes were visualized on a minimum spanning network (MSN), genotypes belonging to the same STRUCTURE group were contiguous, with rare exceptions. A putatively ancestral group 1 had high genic diversity, included all A1 mating type isolates and all Papuan isolates in the sample, was rarely isolated from natural settings in California and Mexico, and was positioned at the center of the MSN. Putatively younger groups 2 a...

Molecular Ecology, 2013

A population genetics approach is used to identify the most likely introduction site and introduc... more A population genetics approach is used to identify the most likely introduction site and introduction pathway for the North American forest pathogen Heterobasidion irregulare using 101 isolates from six sites in Italy and 34 isolates from five sites in North America. Diversity indices based on sequences from ten loci indicate the highest diversity in Italy is found in Castelfusano/Castelporziano and that diversity progressively decreases with increasing distance from that site. AMOVA, Bayesian clustering and principal coordinates analyses based on 12 SSR loci indicate high levels of gene flow among sites, high frequency of admixing, and fail to identify groups of genotypes exclusive to single locations. Cumulatively, these analyses suggest the current infestation is the result of multiple genotypes expanding their range from a single site. Based on two sequenced loci, a single source site in North America could provide enough variability to explain the variability observed in Italy. These results support the notion that H. irregulare was introduced originally in Castelporziano: because Castelporziano has been sealed off from the rest of the world for centuries except for a camp set up by the US military in 1944, we conclude the fungus may have been transported in infected wood used by the military. Finally, spatial autocorrelation analyses using SSR data indicate a significant under-dispersion of alleles up to 0.5-10 km, while a significant overdispersion of alleles was detected at distances over 80 km: these ranges can be used to make predictions on the likely dispersal potential of the invasive pathogen.

Shifting habitats, morphology, and selective pressures: Developmental polyphenism in an adaptive radiation of Hawaiian spiders

Evolution, Dec 23, 2014

Particularly intriguing examples of adaptive radiation are those in which lineages show parallel ... more Particularly intriguing examples of adaptive radiation are those in which lineages show parallel or convergent evolution, suggesting utilization of similar genetic or developmental pathways. The current study focuses on an adaptive radiation of Hawaiian "spiny-leg" spiders in which diversification is associated with repeated convergent evolution leading to similar sets of ecomorphs on each island. However, two species on the oldest islands in the archipelago exhibit variability, occurring as two different ecomorphs. More derived species on the younger islands show much less variability, any one species displaying a single ecomorph. We measured ecomorphological features within individuals over time to determine the nature of the variability. Then, using transcriptomes, we conducted lineage-based tests for selection under varying models and analyses of gene tree versus species tree incongruencies. Our results provide strong evidence that variability in color in Tetragnatha kauaiensis and T. polychromata is associated with development within individuals (polyphenism). Moreover, a total of 28 loci showed a signature of selection associated with loss of the color-changing phenotype, and 37 loci showed a signature of selection associated with the colonization of a new environment. The results illustrate how developmental polyphenism might provide an avenue for the repeated evolution of ecomorphs during adaptive radiation.

A phase 2 study of onvansertib in combination with abiraterone and prednisone in patients with metastatic castration-resistant prostate cancer (mCRPC)

Journal of Clinical Oncology, 2022

TPS219 Background: Metastatic CRPC is a leading cause of cancer death worldwide. Although abirate... more TPS219 Background: Metastatic CRPC is a leading cause of cancer death worldwide. Although abiraterone (abi) + prednisone in either castration-sensitive or castration-resistant disease increases survival, resistance is universal and generally occurs within 9-16 months of initiating treatment. Polo-like kinase 1 (PLK1) is a serine/threonine protein kinase that regulates mitotic function and is upregulated in prostate cancer following androgen-deprivation therapy (ADT). Onvansertib is an oral and highly-selective PLK1 inhibitor that demonstrated safety and tolerability as a single agent in a Ph1 trial. Preclinical studies showed that PLK1 inhibition enhanced abi anti-tumor effect in cell line models and in patient-derived tumor xenografts via an AR-independent mechanism. Transcriptomic analyses revealed that abi induced mitosis-related gene sets in cells synergistic for abi + onvansertib, and identified an abi-onvansertib synergy gene signature. Methods: The goal of this phase 2 study ...

Abstract 1885: Selective Polo-like Kinase 1 (PLK1) inhibitor PCM-075 is highly active alone and shows synergy when combined with FLT3 inhibitors in models of acute myeloid leukemia (AML)

Experimental and Molecular Therapeutics, 2018

First generation FLT3 inhibitors have been useful in treating AML (sorafenib, midostaurin). Secon... more First generation FLT3 inhibitors have been useful in treating AML (sorafenib, midostaurin). Second generation inhibitors with more selectivity are currently in P3 trials in AML (quizartinib, gilteritinib). Despite the advances, resistance to FLT3 inhibitors and disease progression while on FLT3 inhibitors remains an important problem for patient care. We analyzed the activity of a highly-selective PLK1 inhibitor, PCM-075 (formerly NMS-1286937), in models of acute myeloid leukemia (AML) alone and in combination with various chemotherapies and targeted therapeutics including FLT3 inhibitors. PCM-075 is a potent, highly-selective adenosine triphosphate competitive inhibitor of PLK1, a serine/threonine kinase, which is over-expressed in hematologic malignancies and solid tumors such as AML, breast, prostate, ovarian, lung, gastric and colon. PCM-075 is highly active in blocking proliferation and inducing G2/M arrest in multiple AML cell lines. In a therapeutic model, PCM-075 was capable of inducing significant tumor growth inhibition (TGI)1, and increasing survival in an in vivo disseminated leukemia model (AML-NS8 Cells)2. Orally administered PCM-075 is currently in development for multiple tumor types and is in clinical trials for the treatment of AML (NCT03303339). Synergistic interactions between Quizartinib, other FLT3 inhibitors and PCM-075 were examined in cell culture models. In vivo, combination studies in an AML FLT3 mutant 21 day treatment xenograft model (MV4-11) revealed synergistic interactions between Quizartinib and PCM-075. PCM-075 (dosed orally 30 mg/kg, QD for days 1-10 and 12 -21) in combination with Quizartinib (1 mg/kg, QD for 21 days) resulted in 97.3% (96.2-98.4) TGI, compared to 77.9% (70.0-85.8) with Quizartinib and 80.2% (70.4-90.0) with PCM-075 as monotherapy. Body weight in treated mice remained within 20% of controls. To better understand the mechanism of the synergistic activity of PCM-075, we have conducted in vitro RNA-based profiling studies examining the combination of PCM-075 with FLT3 inhibitors for impact on specific gene pathways in AML cell lines and this will be presented. Combination therapy is the mainstay of current oncology treatment regimens and these results suggest that combining PCM-075 with FLT3 inhibitors could be useful in the treatment of AML and a potential next step for patients developing resistance to FLT3 inhibitors. 1 Mol Cancer Ther. 2012 Apr;11(4):1006-162 PLoS One. 2013;8(3):e58424 Citation Format: Karena Kosco, Maya Ridinger, Penn Whitley, Peter Croucher, Jeffrey N. Miner, Mark Erlander. Selective Polo-like Kinase 1 (PLK1) inhibitor PCM-075 is highly active alone and shows synergy when combined with FLT3 inhibitors in models of acute myeloid leukemia (AML) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1885.

Many a slip: dissecting the causes of reproductive isolation in two species of Tegenaria spiders (Agelenidae)

Biological Journal of the Linnean Society, 2014

Key to our understanding of the mechanisms underlying the process of speciation is the determinat... more Key to our understanding of the mechanisms underlying the process of speciation is the determination of the nature of the barriers to gene flow between related taxa. Species that show zero gene flow in sympatry or parapatry are of little use in this respect. In the present study, we used two closely-related species of large house spider, Tegenaria saeva and Tegenaria gigantea, which hybridize to a limited extent along a natural contact zone in southern Britain. The species are apparently indistinguishable with respect to habitat utilization and phenology. Laboratory crosses using individuals from both allopatric and parapatric populations suggest that, although male and female courtship, as well as web and cuticular-borne pheromones, are conserved between the species, mechanical difficulties are experienced during interspecific copulation. Copulation bouts are, on average, significantly shorter during interspecific matings because of these difficulties, and are probably not sufficiently long for effective sperm transfer to take place. In the two cases of successful interspecific crossing, and in subsequent F1 and backcross generations, there are few indications of differential fertility, fecundity or viability, suggesting little post-zygotic incompatibility. The high success rate of crosses between F1 hybrids and both parental species underlines the principally mechanical barrier to gene flow between these taxa. Once this is breached, there appears to be little impediment to continuing introgression, which could, in some geographical areas at least, ultimately lead to the fusion of the two species. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113, 355–367.

Journal of Thoracic Oncology, 2016

In approximately 60% of patients with NSCLC who are receiving EGFR tyrosine kinase inhibitors, re... more In approximately 60% of patients with NSCLC who are receiving EGFR tyrosine kinase inhibitors, resistance develops through the acquisition of EGFR T790M mutation. We aimed to demonstrate that a highly sensitive and quantitative next-generation sequencing analysis of EGFR mutations from urine and plasma specimens is feasible. Methods: Short footprint mutation enrichment nextgeneration sequencing assays were used to interrogate EGFR activating mutations and the T790M resistance mutation in urine or plasma specimens from patients enrolled in TIGER-X (NCT01526928), a phase 1/2 clinical study of rociletinib in previously treated patients with EGFR mutant-positive advanced NSCLC. Results: Of 63 patients, 60 had evaluable tissue specimens. When the tissue result was used as a reference, the sensitivity of EGFR mutation detection in urine was 72% (34 of 47 specimens) for T790M, 75% (12 of 16) for L858R, and 67% (28 of 42) for exon 19 deletions. With specimens that *Corresponding author. Drs. Reckamp, Melnikova, and Karlovich equally contributed to this work.

Association of genotype with clinical course of Crohn's disease: a cohort study

Lancet, 2002

Association between insertion mutation in gene and Crohn's disease in German and British populations

Lancet, 2001

Genetic predisposition to inflammatory bowel disease (IBD) has been shown by epidemiological and ... more Genetic predisposition to inflammatory bowel disease (IBD) has been shown by epidemiological and linkage studies. Genetic linkage of IBD to chromosome 16 has been previously observed and replicated in independent populations. The recently identified NOD2 gene is a good positional and functional candidate gene since it is located in the region of linkage on chromosome 16q12, and activates nuclear factor (NF) κB in response to bacterial lipopolysaccharides.We sequenced the coding region of the NOD2 gene and genotyped an insertion polymorphism affecting the leucine-rich region of the protein product in 512 individuals with IBD from 309 German or British families, 369 German trios (ie, German patients with sporadic IBD and their unaffected parents), and 272 normal controls. We then tested for association with Crohn's disease and ulcerative colitis.Family-based association analyses were consistently positive in 95 British and 99 German affected sibling pairs with Crohn's disease (combined p<0·0001); the association was confirmed in the 304 German trios with Crohn's disease. No association was seen in the 115 sibling pairs and 65 trios with ulcerative colitis. The genotype-specific disease risks conferred by heterozygous and homozygous mutant genotypes were 2·6 (95% CI 1·5–4·5) and 42·1 (4·3−∞), respectively.The insertion mutation in the NOD2 gene confers a substantially increased susceptibility to Crohn's disease but not to ulcerative colitis.

Lack of association between the C3435T gene polymorphism and inflammatory bowel disease in two independent Northern European populations

Gastroenterology, 2003

Genetic influence on reproductive behavior in female rhesus macaques

Twin research and human genetics : the official journal of the International Society for Twin Studies, 2005

Commentary on Cherkas et al. (2004). Genetic Influences on Female Infidelity and Number of Sexual... more Commentary on Cherkas et al. (2004). Genetic Influences on Female Infidelity and Number of Sexual Partners in Humans: A Linkage and Association Study on the Role of the Vasopressin Receptor Gene (AVPR1A).Twin Research, 7, 649–658.

The biochemist, Feb 1, 2009

Although it has been convincingly shown that forest populations of the pathogen Phytophthora ramo... more Although it has been convincingly shown that forest populations of the pathogen Phytophthora ramorum have undergone a significant bottleneck and reproduce exclusively asexually , objective results showing that nurseries were the original source of the introduction remain elusive . A previous attempt to define routes of pathogen movement resulted in a largely unresolved network ), showing at best that populations from Santa Cruz and Marin Counties were important sources within California. Previous attempts at reconstructing the entire history of the sudden oak death (SOD) epidemic in California were limited by: 1) incomplete sampling; 2) the inability to include singleton samples; and 3) over-collapsing of non-spatially contiguous, yet genetically similar, samples into large meta-samples that confounded the coalescent analyses. Here, we employ a complete sampling coverage of 832 isolates of P. ramorum (the causative agent of SOD) from 60 California forests, genotyped at nine microsatellite loci. The following microsatellite loci were genotyped: PrMS39a, PrMS39b, PrMS43a, PrMS43b, PrMS45 ), locus 18, locus 64 (Ivors et al. 2006), and loci ILVO145PrMS145 (a and c) . Rather than using data simply based on number of microsatellite repeats, we employed Bruvo's distances as in previous studies ). This metric is appropriate for analyses of populations that comprise closely related genotypes originated from the same founder genotypes because larger shifts in the number of repeats are weighed, not proportionally, but in terms of likelihood. Analysis of molecular variance (AMOVA) , as implemented by ARLEQUIN v.3.5 (Excoffier et al. 2005), was employed to generate pair-wise estimates of Φ ST among all 62 P. ramorum forest and nursery populations. The Bruvo distance among each pair of unique multilocus genotypes (MGs) was estimated and fed to ARLEQUIN as an external file as the basis for the evolutionary distance in the AMOVA calculations.

Journal of Fungi, Mar 9, 2021

Phosphites have been used to control Sudden Oak Death; however, their precise mode of action is n... more Phosphites have been used to control Sudden Oak Death; however, their precise mode of action is not fully understood. To study the mechanism of action of phosphites, we conducted an inoculation experiment on two open-pollinated tanoak families, previously found to be partially resistant. Stems of treatment group individuals were sprayed with phosphite, and seven days later, distal leaves were inoculated with the Sudden Oak Death pathogen Phytophthora ramorum. Leaves from treated and untreated control plants were harvested before and seven days after inoculation, and transcriptomes of both host and pathogen were analyzed. We found that tanoak families differed in the presence of innate resistance (resistance displayed by untreated tanoak) and in the response to phosphite treatment. A set of expressed genes associated with innate resistance was found to overlap with an expressed gene set for phosphite-induced resistance. This observation may indicate that phosphite treatment increases the resistance of susceptible host plants. In addition, genes of the pathogen involved in detoxification were upregulated in phosphite-treated plants compared to phosphite-untreated plants. In summary, our RNA-Seq analysis supports a two-fold mode of action of phosphites, including a direct toxic effect on P. ramorum and an indirect enhancement of resistance in the tanoak host.

BMC Genomics, 2013

Background: A number of spider species within the family Theridiidae exhibit a dramatic abdominal... more Background: A number of spider species within the family Theridiidae exhibit a dramatic abdominal (opisthosomal) color polymorphism. The polymorphism is inherited in a broadly Mendelian fashion and in some species consists of dozens of discrete morphs that are convergent across taxa and populations. Few genomic resources exist for spiders. Here, as a first necessary step towards identifying the genetic basis for this trait we present the near complete transcriptomes of two species: the Hawaiian happy-face spider Theridion grallator and Theridion californicum. We mined the gene complement for pigment-pathway genes and examined differential expression (DE) between morphs that are unpatterned (plain yellow) and patterned (yellow with superimposed patches of red, white or very dark brown). Results: By deep sequencing both RNA-seq and normalized cDNA libraries from pooled specimens of each species we were able to assemble a comprehensive gene set for both species that we estimate to be 98-99% complete. It is likely that these species express more than 20,000 protein-coding genes, perhaps 4.5% (ca. 870) of which might be unique to spiders. Mining for pigment-associated Drosophila melanogaster genes indicated the presence of all ommochrome pathway genes and most pteridine pathway genes and DE analyses further indicate a possible role for the pteridine pathway in theridiid color patterning. Conclusions: Based upon our estimates, T. grallator and T. californicum express a large inventory of protein-coding genes. Our comprehensive assembly illustrates the continuing value of sequencing normalized cDNA libraries in addition to RNA-seq in order to generate a reference transcriptome for non-model species. The identification of pteridine-related genes and their possible involvement in color patterning is a novel finding in spiders and one that suggests a biochemical link between guanine deposits and the pigments exhibited by these species.

Journal of Arachnology, Apr 1, 2014

Molecular genetic tools have been a boon to arachnologists for decades and used to study many uni... more Molecular genetic tools have been a boon to arachnologists for decades and used to study many unique aspects of arachnid biology including genomics, phylogenetics, population genetics, and biogeography. These tools have evolved over time and now provide myriad methods for exploring evolutionary questions. Early tools, while still useful under the proper circumstances, are giving way to a new generation of DNA sequencing technologies. These new platforms yield impressive amounts of data at a fraction of the cost of traditional techniques. Herein, we discuss the history and future of molecular evolutionary arachnology in terms of available genetic/genomic tools and their potential applications, strengths, weaknesses, and relative costs. Next-generation sequencing (NGS) platforms are varied in their methods and potential uses, making high-throughput sequencing studies focusing on a wide array of questions tractable. To date, relatively few studies have employed NGS technologies using arachnids, but many could benefit from using them. Because no model species exist within the class Arachnida, we have a limited understanding of arachnid genomics. With the ever-advancing nature of sequencing technologies and bioinformatics, arachnologists can relatively easily implement NGS studies to bridge the gaps in our understanding and open avenues for deeper and more powerful experiments. To this end, we discuss examples of applications of NGS technologies focusing on arachnid taxa. Despite the allure of acquiring massive quantities of sequence data, we should recognize the limitations of existing NGS technologies and not forsake pre-NGS methods when these technologies could adequately address our questions.

European Journal of Human Genetics, 2003

Current debate focuses on the relevance of linkage disequilibrium (LD), ethnicity and underlying ... more Current debate focuses on the relevance of linkage disequilibrium (LD), ethnicity and underlying haplotype structure to the search for genes involved in complex disorders. The recently described association between single nucleotide polymorphisms (SNPs) of the CARD15 (NOD2) gene and Crohn's disease (CD) in populations of north-European descent provides a test case that we have subjected to detailed SNP haplotype based analyses. We examined 23 SNPs spanning 290 kb, including CARD15, in large North-European and Korean samples of patients with Crohn's disease and normal controls. In Europeans we confirmed that the three disease-associated SNPs occur independently but share a common background haplotype. This suggests a common origin and the possibility of an undiscovered more strongly predisposing mutation. Korean CD patients present a phenotype identical to the European patients and have not previously been screened for CARD15. The three disease-associated SNPs were absent and there was no evidence of association between CARD15 and CD. Consequently, the diseaseassociated mutations in the Europeans, which are rare, have arisen recently (after the Asian -European split). Our results highlight important issues relevant to mapping the genes that predispose to complex disorders. First, although ethnically divergent populations may present identical phenotypes they do not necessarily share the same set of predisposing genes. Second, although single-locus tests of association showed consistent association with markers throughout the gene, pair-wise LD between markers (r 2 and D') yielded very little information about actual disease-association. Third, a population comparative approach allowed refining of the marker set through the examination of shared polymorphisms and common LD-groups. This approach, in conjunction with the examination of the mutational steps in a haplotype network, allows unambiguous identification of the potentially causative mutations.

Evolution, May 9, 2012

Past geological and climatological processes shape extant biodiversity. In the Hawaiian Islands, ... more Past geological and climatological processes shape extant biodiversity. In the Hawaiian Islands, these processes have provided the physical environment for a number of extensive adaptive radiations. Yet, single species that occur throughout the islands provide some of the best cases for understanding how species respond to the shifting dynamics of the islands in the context of colonization history and associated demographic and adaptive shifts. Here, we focus on the Hawaiian happy-face spider, a single color-polymorphic species, and use mitochondrial and nuclear allozyme markers to examine (1) how the mosaic formation of the landscape has dictated population structure, and (2) how cycles of expansion and contraction of the habitat matrix have been associated with demographic shifts, including a "quantum shift" in the genetic basis of the color polymorphism. The results show a marked structure among populations consistent with the age progression of the islands. The finding of low genetic diversity at the youngest site coupled with the very high diversity of haplotypes on the slightly older substrates that are highly dissected by recent volcanism suggests that the mosaic structure of the landscape may play an important role in allowing differentiation of the adaptive color polymorphism.

Phytopathology®, 2019

The genetic structure of a sample of isolates of the oomycete plant pathogen Phytophthora cinnamo... more The genetic structure of a sample of isolates of the oomycete plant pathogen Phytophthora cinnamomi from natural and agricultural outbreaks and the long-distance movement of individual genotypes were studied using four microsatellite markers to genotype 159 isolates of Californian, Mexican, and worldwide origins. Allelic profiles identified 75 multilocus genotypes. A STRUCTURE analysis placed them in three groups characterized by different geographic and host ranges, different genic and genotypic diversity, and different reproductive modes. When relationships among genotypes were visualized on a minimum spanning network (MSN), genotypes belonging to the same STRUCTURE group were contiguous, with rare exceptions. A putatively ancestral group 1 had high genic diversity, included all A1 mating type isolates and all Papuan isolates in the sample, was rarely isolated from natural settings in California and Mexico, and was positioned at the center of the MSN. Putatively younger groups 2 a...

Molecular Ecology, 2013

A population genetics approach is used to identify the most likely introduction site and introduc... more A population genetics approach is used to identify the most likely introduction site and introduction pathway for the North American forest pathogen Heterobasidion irregulare using 101 isolates from six sites in Italy and 34 isolates from five sites in North America. Diversity indices based on sequences from ten loci indicate the highest diversity in Italy is found in Castelfusano/Castelporziano and that diversity progressively decreases with increasing distance from that site. AMOVA, Bayesian clustering and principal coordinates analyses based on 12 SSR loci indicate high levels of gene flow among sites, high frequency of admixing, and fail to identify groups of genotypes exclusive to single locations. Cumulatively, these analyses suggest the current infestation is the result of multiple genotypes expanding their range from a single site. Based on two sequenced loci, a single source site in North America could provide enough variability to explain the variability observed in Italy. These results support the notion that H. irregulare was introduced originally in Castelporziano: because Castelporziano has been sealed off from the rest of the world for centuries except for a camp set up by the US military in 1944, we conclude the fungus may have been transported in infected wood used by the military. Finally, spatial autocorrelation analyses using SSR data indicate a significant under-dispersion of alleles up to 0.5-10 km, while a significant overdispersion of alleles was detected at distances over 80 km: these ranges can be used to make predictions on the likely dispersal potential of the invasive pathogen.

Shifting habitats, morphology, and selective pressures: Developmental polyphenism in an adaptive radiation of Hawaiian spiders

Evolution, Dec 23, 2014

Particularly intriguing examples of adaptive radiation are those in which lineages show parallel ... more Particularly intriguing examples of adaptive radiation are those in which lineages show parallel or convergent evolution, suggesting utilization of similar genetic or developmental pathways. The current study focuses on an adaptive radiation of Hawaiian "spiny-leg" spiders in which diversification is associated with repeated convergent evolution leading to similar sets of ecomorphs on each island. However, two species on the oldest islands in the archipelago exhibit variability, occurring as two different ecomorphs. More derived species on the younger islands show much less variability, any one species displaying a single ecomorph. We measured ecomorphological features within individuals over time to determine the nature of the variability. Then, using transcriptomes, we conducted lineage-based tests for selection under varying models and analyses of gene tree versus species tree incongruencies. Our results provide strong evidence that variability in color in Tetragnatha kauaiensis and T. polychromata is associated with development within individuals (polyphenism). Moreover, a total of 28 loci showed a signature of selection associated with loss of the color-changing phenotype, and 37 loci showed a signature of selection associated with the colonization of a new environment. The results illustrate how developmental polyphenism might provide an avenue for the repeated evolution of ecomorphs during adaptive radiation.

A phase 2 study of onvansertib in combination with abiraterone and prednisone in patients with metastatic castration-resistant prostate cancer (mCRPC)

Journal of Clinical Oncology, 2022

TPS219 Background: Metastatic CRPC is a leading cause of cancer death worldwide. Although abirate... more TPS219 Background: Metastatic CRPC is a leading cause of cancer death worldwide. Although abiraterone (abi) + prednisone in either castration-sensitive or castration-resistant disease increases survival, resistance is universal and generally occurs within 9-16 months of initiating treatment. Polo-like kinase 1 (PLK1) is a serine/threonine protein kinase that regulates mitotic function and is upregulated in prostate cancer following androgen-deprivation therapy (ADT). Onvansertib is an oral and highly-selective PLK1 inhibitor that demonstrated safety and tolerability as a single agent in a Ph1 trial. Preclinical studies showed that PLK1 inhibition enhanced abi anti-tumor effect in cell line models and in patient-derived tumor xenografts via an AR-independent mechanism. Transcriptomic analyses revealed that abi induced mitosis-related gene sets in cells synergistic for abi + onvansertib, and identified an abi-onvansertib synergy gene signature. Methods: The goal of this phase 2 study ...

Abstract 1885: Selective Polo-like Kinase 1 (PLK1) inhibitor PCM-075 is highly active alone and shows synergy when combined with FLT3 inhibitors in models of acute myeloid leukemia (AML)

Experimental and Molecular Therapeutics, 2018

First generation FLT3 inhibitors have been useful in treating AML (sorafenib, midostaurin). Secon... more First generation FLT3 inhibitors have been useful in treating AML (sorafenib, midostaurin). Second generation inhibitors with more selectivity are currently in P3 trials in AML (quizartinib, gilteritinib). Despite the advances, resistance to FLT3 inhibitors and disease progression while on FLT3 inhibitors remains an important problem for patient care. We analyzed the activity of a highly-selective PLK1 inhibitor, PCM-075 (formerly NMS-1286937), in models of acute myeloid leukemia (AML) alone and in combination with various chemotherapies and targeted therapeutics including FLT3 inhibitors. PCM-075 is a potent, highly-selective adenosine triphosphate competitive inhibitor of PLK1, a serine/threonine kinase, which is over-expressed in hematologic malignancies and solid tumors such as AML, breast, prostate, ovarian, lung, gastric and colon. PCM-075 is highly active in blocking proliferation and inducing G2/M arrest in multiple AML cell lines. In a therapeutic model, PCM-075 was capable of inducing significant tumor growth inhibition (TGI)1, and increasing survival in an in vivo disseminated leukemia model (AML-NS8 Cells)2. Orally administered PCM-075 is currently in development for multiple tumor types and is in clinical trials for the treatment of AML (NCT03303339). Synergistic interactions between Quizartinib, other FLT3 inhibitors and PCM-075 were examined in cell culture models. In vivo, combination studies in an AML FLT3 mutant 21 day treatment xenograft model (MV4-11) revealed synergistic interactions between Quizartinib and PCM-075. PCM-075 (dosed orally 30 mg/kg, QD for days 1-10 and 12 -21) in combination with Quizartinib (1 mg/kg, QD for 21 days) resulted in 97.3% (96.2-98.4) TGI, compared to 77.9% (70.0-85.8) with Quizartinib and 80.2% (70.4-90.0) with PCM-075 as monotherapy. Body weight in treated mice remained within 20% of controls. To better understand the mechanism of the synergistic activity of PCM-075, we have conducted in vitro RNA-based profiling studies examining the combination of PCM-075 with FLT3 inhibitors for impact on specific gene pathways in AML cell lines and this will be presented. Combination therapy is the mainstay of current oncology treatment regimens and these results suggest that combining PCM-075 with FLT3 inhibitors could be useful in the treatment of AML and a potential next step for patients developing resistance to FLT3 inhibitors. 1 Mol Cancer Ther. 2012 Apr;11(4):1006-162 PLoS One. 2013;8(3):e58424 Citation Format: Karena Kosco, Maya Ridinger, Penn Whitley, Peter Croucher, Jeffrey N. Miner, Mark Erlander. Selective Polo-like Kinase 1 (PLK1) inhibitor PCM-075 is highly active alone and shows synergy when combined with FLT3 inhibitors in models of acute myeloid leukemia (AML) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1885.

Many a slip: dissecting the causes of reproductive isolation in two species of Tegenaria spiders (Agelenidae)

Biological Journal of the Linnean Society, 2014

Key to our understanding of the mechanisms underlying the process of speciation is the determinat... more Key to our understanding of the mechanisms underlying the process of speciation is the determination of the nature of the barriers to gene flow between related taxa. Species that show zero gene flow in sympatry or parapatry are of little use in this respect. In the present study, we used two closely-related species of large house spider, Tegenaria saeva and Tegenaria gigantea, which hybridize to a limited extent along a natural contact zone in southern Britain. The species are apparently indistinguishable with respect to habitat utilization and phenology. Laboratory crosses using individuals from both allopatric and parapatric populations suggest that, although male and female courtship, as well as web and cuticular-borne pheromones, are conserved between the species, mechanical difficulties are experienced during interspecific copulation. Copulation bouts are, on average, significantly shorter during interspecific matings because of these difficulties, and are probably not sufficiently long for effective sperm transfer to take place. In the two cases of successful interspecific crossing, and in subsequent F1 and backcross generations, there are few indications of differential fertility, fecundity or viability, suggesting little post-zygotic incompatibility. The high success rate of crosses between F1 hybrids and both parental species underlines the principally mechanical barrier to gene flow between these taxa. Once this is breached, there appears to be little impediment to continuing introgression, which could, in some geographical areas at least, ultimately lead to the fusion of the two species. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113, 355–367.

Journal of Thoracic Oncology, 2016

In approximately 60% of patients with NSCLC who are receiving EGFR tyrosine kinase inhibitors, re... more In approximately 60% of patients with NSCLC who are receiving EGFR tyrosine kinase inhibitors, resistance develops through the acquisition of EGFR T790M mutation. We aimed to demonstrate that a highly sensitive and quantitative next-generation sequencing analysis of EGFR mutations from urine and plasma specimens is feasible. Methods: Short footprint mutation enrichment nextgeneration sequencing assays were used to interrogate EGFR activating mutations and the T790M resistance mutation in urine or plasma specimens from patients enrolled in TIGER-X (NCT01526928), a phase 1/2 clinical study of rociletinib in previously treated patients with EGFR mutant-positive advanced NSCLC. Results: Of 63 patients, 60 had evaluable tissue specimens. When the tissue result was used as a reference, the sensitivity of EGFR mutation detection in urine was 72% (34 of 47 specimens) for T790M, 75% (12 of 16) for L858R, and 67% (28 of 42) for exon 19 deletions. With specimens that *Corresponding author. Drs. Reckamp, Melnikova, and Karlovich equally contributed to this work.

Association of genotype with clinical course of Crohn's disease: a cohort study

Lancet, 2002

Association between insertion mutation in gene and Crohn's disease in German and British populations

Lancet, 2001

Genetic predisposition to inflammatory bowel disease (IBD) has been shown by epidemiological and ... more Genetic predisposition to inflammatory bowel disease (IBD) has been shown by epidemiological and linkage studies. Genetic linkage of IBD to chromosome 16 has been previously observed and replicated in independent populations. The recently identified NOD2 gene is a good positional and functional candidate gene since it is located in the region of linkage on chromosome 16q12, and activates nuclear factor (NF) κB in response to bacterial lipopolysaccharides.We sequenced the coding region of the NOD2 gene and genotyped an insertion polymorphism affecting the leucine-rich region of the protein product in 512 individuals with IBD from 309 German or British families, 369 German trios (ie, German patients with sporadic IBD and their unaffected parents), and 272 normal controls. We then tested for association with Crohn's disease and ulcerative colitis.Family-based association analyses were consistently positive in 95 British and 99 German affected sibling pairs with Crohn's disease (combined p<0·0001); the association was confirmed in the 304 German trios with Crohn's disease. No association was seen in the 115 sibling pairs and 65 trios with ulcerative colitis. The genotype-specific disease risks conferred by heterozygous and homozygous mutant genotypes were 2·6 (95% CI 1·5–4·5) and 42·1 (4·3−∞), respectively.The insertion mutation in the NOD2 gene confers a substantially increased susceptibility to Crohn's disease but not to ulcerative colitis.

Lack of association between the C3435T gene polymorphism and inflammatory bowel disease in two independent Northern European populations

Gastroenterology, 2003

Genetic influence on reproductive behavior in female rhesus macaques

Twin research and human genetics : the official journal of the International Society for Twin Studies, 2005

Commentary on Cherkas et al. (2004). Genetic Influences on Female Infidelity and Number of Sexual... more Commentary on Cherkas et al. (2004). Genetic Influences on Female Infidelity and Number of Sexual Partners in Humans: A Linkage and Association Study on the Role of the Vasopressin Receptor Gene (AVPR1A).Twin Research, 7, 649–658.