Determining Distribution and Size of Larval Pacific Geoduck Clams (Panopea Generosa Gould 1850) in Quartermaster Harbor (Washington, USA) Using a Novel Sampling Approach

Realistic species-specific information about larval life history is necessary for effective management of shellfish and parameterization of larval connectivity models. The patchiness of dispersing larvae, and the resources needed for sorting and identifying them, has limited many studies of larval distribution in the field, especially for species that are less common. In particular, little is known about in situ larval distribution of Pacific geoduck clams (Panopea generosa Gould 1850), a commercially important species found in Puget Sound, WA. A novel approach-time-integrating larval tube traps paired with molecular identification and sorting (FISH-CS)-was used to determine the distribution of geoduck larvae over 4 moat 3 stations in Quartermaster Harbor. Larvae were found consistently at the surface and thermocline rather than at the bottom. More and larger larvae were captured in the inside and middle of the harbor than the outer harbor, indicating at least some larval retention. Two pulses of larvae were captured, in March and late May to early June. Size frequency distributions of larvae indicate that these were 2 separate cohorts of larvae, with the possibility of a pulse of larvae from elsewhere toward the end of the season. The only physical parameter associated with relative larval abundance was degree of stratification, although the association was weak. These data represent the first reported study of geoduck larval distribution in the field and the first use of the FISH-CS technique for field collections. In the future, this approach can be used to answer many relevant management questions locally and more broadly, including quantifying larval export from shellfish farms, placement of restoration sites and marine protected areas, and spread of invasive species

Patterns of mtDNA diversity in North Atlantic populations of the mussel Mytilus edulis

Patterns of (female) mitochondrial DNA diversity were investigated in the blue mussel Mytilus edulis. Mytilus edulis is a ubiquitous member of contemporary North Atlantic hard-substrate communities and well represented in studies of this region. Mytilus edulis was surveyed in North America and Europe, as well as mid-Atlantic sites in Greenland, Iceland, and the Faroe Islands. Mitochondrial DNA sequences revealed considerable population structure but no monophyly of haplotypes between any major regions. Coalescent analyses suggest that migration across the Atlantic Ocean has prominently been from North American source populations and that Greenland was colonized recently and exclusively from North America. In North America, there was support for two regional groups along the North American coastline. Surprisingly, we also found evidence of recombination between some Mytilus edulis and Mytilus galloprovincialis female mtDNA sequences, particularly in northern Europe

Differential patterns of Male and Female mtDNA exchange across the Atlantic Ocean in the blue mussel, Mytilus edulis

Comparisons among loci with differing modes of inheritance can reveal unexpected aspects of population history. We employ a multilocus approach to ask whether two types of independently assorting mitochondrial DNAs (maternally and paternally inherited: F- and M-mtDNA) and a nuclear locus (ITS) yield concordant estimates of gene flow and population divergence. The blue mussel, Mytilus edulis, is distributed on both North American and European coastlines and these populations are separated by the waters of the Atlantic Ocean. Gene flow across the Atlantic Ocean differs among loci, with F-mtDNA and ITS showing an imprint of some genetic interchange and M-mtDNA showing no evidence for gene flow. Gene flow of F-mtDNA and ITS causes trans-Atlantic population divergence times to be greatly underestimated for these loci, although a single trans-Atlantic population divergence time (1.2 MYA) can be accommodated by considering all three loci in combination in a coalescent framework. The apparent lack of gene flow for M-mtDNA is not readily explained by different dispersal capacities of male and female mussels. A genetic barrier to M-mtDNA exchange between North American and European mussel populations is likely to explain the observed pattern, perhaps associated with the double uniparental system of mitochondrial DNA inheritance

Staged miRNA re-regulation patterns during reprogramming.

BackgroundMiRNAs often operate in feedback loops with transcription factors and represent a key mechanism for fine-tuning gene expression. In transcription factor-induced reprogramming, miRNAs play a critical role; however, detailed analyses of miRNA expression changes during reprogramming at the level of deep sequencing have not been previously reported.ResultsWe use four factor reprogramming to induce pluripotent stem cells from mouse fibroblasts and isolate FACS-sorted Thy1- and SSEA1+ intermediates and Oct4-GFP+ induced pluripotent stem cells (iPSCs). Small RNAs from these cells, and two partial-iPSC lines, another iPSC line, and mouse embryonic stem cells (mES cells) were deep sequenced. A comprehensive resetting of the miRNA profile occurs during reprogramming; however, analysis of miRNA co-expression patterns yields only a few patterns of change. Dlk1-Dio3 region miRNAs dominate the large pool of miRNAs experiencing small but significant fold changes early in reprogramming. Overexpression of Dlk1-Dio3 miRNAs early in reprogramming reduces reprogramming efficiency, suggesting the observed downregulation of these miRNAs may contribute to reprogramming. As reprogramming progresses, fewer miRNAs show changes in expression, but those changes are generally of greater magnitude.ConclusionsThe broad resetting of the miRNA profile during reprogramming that we observe is due to small changes in gene expression in many miRNAs early in the process, and large changes in only a few miRNAs late in reprogramming. This corresponds with a previously observed transition from a stochastic to a more deterministic signal

Diverse AR Gene Rearrangements Mediate Resistance to Androgen Receptor Inhibitors in Metastatic Prostate Cancer

PurposeProstate cancer is the second leading cause of male cancer deaths. Castration-resistant prostate cancer (CRPC) is a lethal stage of the disease that emerges when endocrine therapies are no longer effective at suppressing activity of the androgen receptor (AR) transcription factor. The purpose of this study was to identify genomic mechanisms that contribute to the development and progression of CRPC.Experimental designWe used whole-genome and targeted DNA-sequencing approaches to identify mechanisms underlying CRPC in an aggregate cohort of 272 prostate cancer patients. We analyzed structural rearrangements at the genome-wide level and carried out a detailed structural rearrangement analysis of the AR locus. We used genome engineering to perform experimental modeling of AR gene rearrangements and long-read RNA sequencing to analyze effects on expression of AR and truncated AR variants (AR-V).ResultsAR was among the most frequently rearranged genes in CRPC tumors. AR gene rearrangements promoted expression of diverse AR-V species. AR gene rearrangements occurring in the context of AR amplification correlated with AR overexpression. Cell lines with experimentally derived AR gene rearrangements displayed high expression of tumor-specific AR-Vs and were resistant to endocrine therapies, including the AR antagonist enzalutamide.ConclusionsAR gene rearrangements are an important mechanism of resistance to endocrine therapies in CRPC

Co-evolution of AR gene copy number and structural complexity in endocrine therapy resistant prostate cancer

Androgen receptor (AR) inhibition is standard of care for advanced prostate cancer (PC). However, efficacy is limited by progression to castration-resistant PC (CRPC), usually due to AR re-activation via mechanisms that include AR amplification and structural rearrangement. These two classes of AR alterations often co-occur in CRPC tumors, but it is unclear whether this reflects intercellular or intracellular heterogeneity of AR. Resolving this is important for developing new therapies and predictive biomarkers. Here, we analyzed 41 CRPC tumors and 6 patient-derived xenografts (PDXs) using linked-read DNA-sequencing, and identified 7 tumors that developed complex, multiply-rearranged AR gene structures in conjunction with very high AR copy number. Analysis of PDX models by optical genome mapping and fluorescence in situ hybridization showed that AR residing on extrachromosomal DNA (ecDNA) was an underlying mechanism, and was associated with elevated levels and diversity of AR expression. This study identifies co-evolution of AR gene copy number and structural complexity via ecDNA as a mechanism associated with endocrine therapy resistance