Inhibition of CD226 Co-Stimulation Suppresses Diabetes Development in the NOD Mouse by Augmenting Tregs and Diminishing Effector T Cell Function.

Aims/hypothesis: Immunotherapeutics targeting T cells are crucial for inhibiting autoimmune disease progression proximal to disease onset in type 1 diabetes. A growing number of T cell-directed therapeutics have demonstrated partial therapeutic efficacy, with anti-CD3 (α-CD3) representing the only regulatory agency-approved drug capable of slowing disease progression through a mechanism involving the induction of partial T cell exhaustion. There is an outstanding need to augment the durability and effectiveness of T cell targeting by directly restraining proinflammatory T helper type 1 (Th1) and type 1 cytotoxic CD8 + T cell (Tc1) subsets, while simultaneously augmenting regulatory T cell (Treg) activity. Here, we present a novel strategy for reducing diabetes incidence in the NOD mouse model using a blocking monoclonal antibody targeting the type 1 diabetes-risk associated T cell co-stimulatory receptor, CD226. Methods: Female NOD mice were treated with anti-CD226 between 7-8 weeks of age and then monitored for diabetes incidence and therapeutic mechanism of action. Results: Compared to isotype-treated controls, anti-CD226 treated NOD mice showed reduced insulitis severity at 12 weeks and decreased disease incidence at 30 weeks. Flow cytometric analysis performed five weeks post-treatment demonstrated reduced proliferation of CD4 + and CD8 + effector memory T cells in spleens of anti-CD226 treated mice. Phenotyping of pancreatic Tregs revealed increased CD25 expression and STAT5 phosphorylation following anti-CD226, with splenic Tregs displaying augmented suppression of CD4 + T cell responders in vitro. Anti-CD226 treated mice exhibited reduced frequencies of islet-specific glucose-6-phosphatase catalytic subunit related protein (IGRP)-reactive CD8 + T cells in the pancreas, using both ex vivo tetramer staining and single-cell T cell receptor sequencing (scTCR-seq) approaches. 51 Cr-release assays demonstrated reduced cell-mediated lysis of beta-cells by anti-CD226-treated autoreactive cytotoxic T lymphocytes. Conclusions/interpretation: CD226 blockade reduces T cell cytotoxicity and improves Treg function, representing a targeted and rational approach for restoring immune regulation in type 1 diabetes. Research in Context: What is already known about this subject?: The co-stimulatory receptor CD226 is upregulated upon activation and is highly expressed on NK cell subsets, myeloid cells, and effector T cells. A single nucleotide polymorphism in CD226 ( rs763361 ; C>T) results in a Gly307Ser missense mutation linked to genetic susceptibility for type 1 diabetes. Global knockout of Cd226 and conditional Cd226 knockout in FoxP3 + Tregs reduced insulitis severity and diabetes incidence in NOD mice, indicating a crucial role for CD226 in disease pathogenesis. What is the key question?: Can CD226 blockade reduce T cell cytotoxicity and improve Treg function to diminish diabetes incidence in NOD mice?What are the new findings?: Anti-CD226 treatment reduced insulitis, decreased disease incidence, and inhibited splenic CD4 + and CD8 + effector memory T cell proliferation. Pancreatic Tregs from anti-CD226 treated mice exhibited increased CD25 expression; splenic Tregs displayed augmented STAT5 phosphorylation and suppressive capacity in vitro . Anti-CD226 treatment reduced IGRP-specific pancreatic CD8 + T cell frequencies, and reduced autoreactive CD8 + T cell-mediated lysis of beta-cells in vitro . How might this impact on clinical practice in the foreseeable future?: CD226 blockade could reduce autoreactive T cell cytotoxicity, enhance Treg function, and slow disease progression in high-risk or recent-onset type 1 diabetes cases.

Total Joint Arthroplasty Outcomes in Eligible Patients Versus Patients Who Failed to Meet at Least 1 Eligibility Criterion: A Single-Center Retrospective Analysis.

BACKGROUND: This study looks to investigate how not meeting eligibility criteria affects postoperative outcomes following total joint arthroplasty surgery. METHODS: A retrospective review was conducted of total joint arthroplasty patients at a single academic institution. Demographics, laboratory values, and complications were recorded. Continuous and categorical variables were compared using the Student's T-test and the Chi-Square test, respectively. Multivariable analysis was used to control for confounding variables. RESULTS: Our study included 915 total hip and 1,579 total knee arthroplasty patients. For total hip and total knee arthroplasty, there were no significant differences in complications (P = .11 and .87), readmissions (P = .83 and .2), or revision surgeries (P = .3 and 1) when comparing those who met all criteria to those who did not. Total hip arthroplasty patients who did not meet two criteria had 16.1 higher odds (P = .02) of suffering a complication. There were no differences in complications (P = .34 and .41), readmissions (P = 1 and .55), or revision surgeries (P = 1 and .36) between ineligible patients treated by total joint arthroplasty surgeons and those who were not. Multivariable analysis demonstrated no eligibility factors were associated with outcomes for both total hip and knee arthroplasty. CONCLUSIONS: There was no significant difference in outcomes between those who met all eligibility criteria and those who did not. Not meeting two criteria conferred significantly higher odds of suffering a complication for total hip arthroplasty patients. Total joint arthroplasty surgeons had similar outcomes to non-total joint surgeons, although their patient population was more complex. LEVEL OF EVIDENCE: III.

Improvement in Stage of Lung Cancer Diagnosis With Incidental Pulmonary Nodules Followed With a Patient Tracking System and Computerized Registry.

Introduction: Given that an incidental pulmonary nodule (IPN) on chest computed tomography (CT) may represent nascent lung cancer, timely follow-up imaging is critical to assess nodule growth and the need for tissue sampling. We previously reported our institution's systematic process to identify and track patients with an IPN associated with improved CT on follow-up. We hypothesized that this improvement may have led to a higher frequency of early-stage lung cancer. To evaluate this, we performed a study to determine whether cases of early-stage lung cancer were more likely to have had our tracking system applied to suspicious findings. Methods: An observational study was performed by identifying cases of lung cancer that were detected as IPNs on chest CT scans performed at our institution, from 2006 to 2016. A total of 314 cases were dichotomized into early-stage (stage 1) or late-stage (stages II to IV) disease. A multivariant regression analysis with modeling was used to determine factors associated with a diagnosis of early-stage disease. Factors included the use of the tracking system and nodule registry. Results: The following factors were independently associated with early-stage lung cancer: index nodule diameter, (OR = 0.971, confidence interval [CI]: 0.948-0.995], p = 0.016), adenocarcinoma histology (OR = 2.930 [CI: 1.695-5.064], p = 0.0001) and use of tracker phrases on CT reports (OR = 1.939 [CI: 1.126-3.339], p = 0.016). Conclusions: The application of a patient tracking system and computerized lung nodule registry lead to an increased frequency in the diagnosis of stage 1 NSCLC from IPNs. This is a meaningful outcome for patients and should be adapted for IPN management.

Experimental data supporting adaptive locomotor responses to salt stress in the mud-tidal gastropod populations (Batillaria).

This article describes the experimental locomotor data used to study the general and adaptive responses to salt stress of the northern Pacific intertidal gastropod Batillaria attramentaria. The data were obtained from a series of 30-day experiments on snails acclimated to different salinity regimes. Snails were collected from coastal areas on the eastern and western sides of the North Pacific Ocean. The data consist of three parts: 1) raw videos recording the locomotion of the snails when exposed to novel artificial salinity regimes in laboratory settings, 2) Spectral Time-Lapse results of movement distance of the snails extracted from the recorded videos, and 3) CO1-gene sequences isolated from individuals collected from four sampling sites. A Linear Mixed-effect Model inference procedure was applied in an attempt to assess the impacts of geographic distribution and genetic composition on the locomotor response to salt stress in the snail B. attramentaria. The locomotor dataset we present are the first reports of locomotor response to salt stress of the snail B. attramentaria, that is valuable for further exploration and understanding of the impacts of environmental changes on the physiology and adaptive capacity of living marine molluscs.

Improvement in Follow-up Imaging With a Patient Tracking System and Computerized Registry for Lung Nodule Management.

PURPOSE: Despite established guidelines, radiologists' recommendations and timely follow-up of incidental lung nodules remain variable. To improve follow-up of nodules, a system using standardized language (tracker phrases) recommending time-based follow-up in chest CT reports, coupled with a computerized registry, was created. MATERIALS AND METHODS: Data were obtained from the electronic health record and a facility-built electronic lung nodule registry. We evaluated two randomly selected patient cohorts with incidental nodules on chest CT reports: before intervention (September 2008 to March 2011) and after intervention (August 2011 to December 2016). Multivariable logistic regression was used to compare the cohorts for the main outcome of timely follow-up, defined as a subsequent report within 13 months of the initial report. RESULTS: In all, 410 patients were included in the pretracker cohort versus 626 in the tracker cohort. Before system inception, 30% of CT reports lacked an explicit time-based recommendation for nodule follow-up. The proportion of patients with timely follow-up increased from 46% to 55%, and the proportion of those with no documented follow-up or follow-up beyond 24 months decreased from 48% to 31%. The likelihood of timely follow-up increased 41%, adjusted for high risk for lung cancer and age 65 years or older. After system inception, reports missing a tracker phrase for nodule recommendation averaged 6%, without significant interyear variation. CONCLUSIONS: Standardized language added to CT reports combined with a computerized registry designed to identify and track patients with incidental lung nodules was associated with improved likelihood of follow-up imaging.

Locomotor responses to salt stress in native and invasive mud-tidal gastropod populations (Batillaria).

Plasticity in salt tolerance can be crucial for successful biological invasions of novel habitats by marine gastropods. The intertidal snail Batillaria attramentaria, which is native to East Asia but invaded the western shores of North America from Japan 80 years ago, provides an opportunity to examine how environmental salinity may shape behavioral and morphological traits. In this study, we compared the movement distance of four B. attramentaria populations from native (Korea and Japan) and introduced (United States) habitats under various salinity levels (13, 23, 33, and 43 PSU) during 30 days of exposure in the lab. We sequenced a partial mitochondrial CO1 gene to infer phylogenetic relationships among populations and confirmed two divergent mitochondrial lineages constituting our sample sets. Using a statistical model-selection approach, we investigated the effects of geographic distribution and genetic composition on locomotor performance in response to salt stress. Snails exposed to acute low salinity (13 PSU) reduced their locomotion and were unable to perform at their normal level (the moving pace of snails exposed to 33 PSU). We did not detect any meaningful differences in locomotor response to salt stress between the two genetic lineages or between the native snails (Japan vs. Korea populations), but we found significant locomotor differences between the native and introduced groups (Japan or Korea vs. the United States). We suggest that the greater magnitude of tidal salinity fluctuation at the US location may have influenced locomotor responses to salt stress in introduced snails.

Phylogeography of Mytilisepta virgata (Mytilidae: Bivalvia) in the northwestern Pacific: Cryptic mitochondrial lineages and mito-nuclear discordance.

The purplish bifurcate mussel Mytilisepta virgata is widely distributed and represents one of the major components of the intertidal community in the northwestern Pacific (NWP). Here, we characterized population genetic structure of NWP populations throughout nearly their whole distribution range using both mitochondrial (mtDNA cox1) and nuclear (ITS1) markers. Population genetic analyses for mtDNA cox 1 sequences revealed two monophyletic lineages (i.e., southern and northern lineages) geographically distributed according to the two different surface water temperature zones in the NWP. The timing of the lineage split is estimated at the Pliocene- mid-Pleistocene (5.49-1.61 Mya), which is consistent with the timing of the historical isolation of the East Sea/Sea of Japan from the South and East China Seas due to sea level decline during glacial cycles. Historical sea level fluctuation during the Pliocene-Pleistocene and subsequent adaptation of mussels to different surface water temperature zones may have contributed to shaping the contemporary genetic diversity and deep divergence of the two mitochondrial lineages. In contrast to mtDNA sequences, a clear lineage split between the two mitochondrial lineages was not found in ITS1 sequences, which showed a star-like structure composed of a mixture of southern and northern mitochondrial lineages. Possible reasons for this type of mito-nuclear discordance include stochastic divergence in the coalescent processes of the two molecular markers, or balancing selection under different marine environments. Cryptic speciation cannot be ruled out from these results, and future work using genomic analyses is required to address whether the thermal physiology of these mussels corresponds to the deep divergence of their mitochondrial genes and to test for the existence of morphologically indistinguishable but genetically separate cryptic species.

Identifying Smoking-Related Disease on Lung Cancer Screening CT Scans: Increasing the Value.

BACKGROUND: Lung cancer screening (LCS) via chest computed tomography (CT) scans can save lives by identifying early-stage tumors. However, most smokers die of comorbid smoking-related diseases. LCS scans contain information about smoking-related conditions that is not currently systematically assessed. Identifying these common comorbid diseases on CT could increase the value of screening with minimal impact on LCS programs. We determined the prevalence of 3 comorbid diseases from LCS eligible scans and quantified related adverse outcomes. METHODS: We studied COPD Genetic Epidemiology study (COPDGene®) participants (n=4078) who met criteria for LCS screening at enrollment (age > 55 years, and < 80 years, > 30 pack years smoking, current smoker or former smoker within 15 years of smoking cessation). CT scans were assessed for coronary artery calcification (CAC), emphysema, and vertebral bone density. We tracked the following clinically significant events: myocardial infarctions (MIs), strokes, pneumonia, respiratory exacerbations, and hip and vertebral fractures. RESULTS: Overall, 77% of eligible CT scans had one or more of these diagnoses identified. CAC (> 100 mg) was identified in 51% of scans, emphysema in 44%, and osteoporosis in 54%. Adverse events related to the underlying smoking-related diseases were common, with 50% of participants reporting at least one. New diagnoses of cardiovascular disease, emphysema and osteoporosis were made in 25%, 7% and 46%, of participants respectively. New diagnosis of disease was associated with significantly more adverse events than in participants who did not have CT diagnoses for both osteoporosis and cardiovascular risk. CONCLUSIONS: Expanded analysis of LCS CT scans identified individuals with evidence of previously undiagnosed cardiovascular disease, emphysema or osteoporosis that corresponded with adverse events. LCS CT scans can potentially facilitate diagnoses of these smoking-related diseases and provide an opportunity for treatment or prevention.

Phylogeography of the highly invasive sugar beet nematode, Heterodera schachtii (Schmidt, 1871), based on microsatellites.

Plant-parasitic nematodes (PPNs) threaten crop production worldwide. Yet few studies have examined their intraspecific genetic diversity or patterns of invasion, critical data for managing the spread of these cryptic pests. The sugar beet nematode Heterodera schachtii, a global invader that parasitizes over 200 plant species, represents a model for addressing important questions about the invasion genetics of PPNs. Here, a phylogeographic study using 15 microsatellite markers was conducted on 231 H. schachtii individuals sampled from four continents, and invasion history was reconstructed through an approximate Bayesian computation approach, with emphasis on the origin of newly discovered populations in Korea. Multiple analyses confirmed the existence of cryptic lineages within this species, with the Korean populations comprising one group (group 1) and the populations from Europe, Australia, North America, and western Asia comprising another (group 2). No multilocus genotypes were shared between the two groups, and large genetic distance was inferred between them. Population subdivision was also revealed among the populations of group 2 in both population comparison and STRUCTURE analyses, mostly due to different divergent times between invasive and source populations. The Korean populations showed substantial genetic homogeneity and likely originated from a single invasion event. However, none of the other studied populations were implicated as the source. Further studies with additional populations are needed to better describe the distribution of the potential source population for the East Asian lineage.

A revision of the genus Littorina (Mollusca: Gastropoda) in Korea.

Littorina Férussac, 1822 is an abundant genus of small gastropods found in the upper littoral zone of rocky seashores worldwide. Although ecologically important, shell-based species identification in this genus is challenging due to phenotypic variation in shell morphology and lack of diagnostic characters among morphologically similar species. In this study, we revised the taxonomy of Korean Littorina species using morphological characters (shell and radula) and cox1 mitochondrial DNA sequences for three Korean species: L. brevicula, L. sitkana, and L. horikawai. Results suggest that L. sitkana was erroneously reported as L. kasatka in a previous study. A new record for Littorina horikawai (Matsubayashi & Habe in Habe, 1979), previously unknown from Korea, is described, which can be distinguished from L. sitkana by the presence of alternating white and brown spiral ribs on each whorl. Comparison of the mtDNA cox1 gene sequences shows very low intraspecific variation even between geographically distant populations. A phylogenetic tree supports a close relationship between L. horikawai and L. sitkana, consistent with earlier phylogenetic studies.

Population Genomic Analysis Reveals Contrasting Demographic Changes of Two Closely Related Dolphin Species in the Last Glacial.

Population genomic data can be used to infer historical effective population sizes (Ne), which help study the impact of past climate changes on biodiversity. Previous genome sequencing of one individual of the common bottlenose dolphin Tursiops truncatus revealed an unusual, sharp rise in Ne during the last glacial, raising questions about the reliability, generality, underlying cause, and biological implication of this finding. Here we first verify this result by additional sampling of T. truncatus. We then sequence and analyze the genomes of its close relative, the Indo-Pacific bottlenose dolphin T. aduncus. The two species exhibit contrasting demographic changes in the last glacial, likely through actual changes in population size and/or alterations in the level of gene flow among populations. Our findings suggest that even closely related species can have drastically different responses to climatic changes, making predicting the fate of individual species in the ongoing global warming a serious challenge.

The bipartite mitochondrial genome of Ruizia karukerae (Rhigonematomorpha, Nematoda).

Mitochondrial genes and whole mitochondrial genome sequences are widely used as molecular markers in studying population genetics and resolving both deep and shallow nodes in phylogenetics. In animals the mitochondrial genome is generally composed of a single chromosome, but mystifying exceptions sometimes occur. We determined the complete mitochondrial genome of the millipede-parasitic nematode Ruizia karukerae and found its mitochondrial genome consists of two circular chromosomes, which is highly unusual in bilateral animals. Chromosome I is 7,659 bp and includes six protein-coding genes, two rRNA genes and nine tRNA genes. Chromosome II comprises 7,647 bp, with seven protein-coding genes and 16 tRNA genes. Interestingly, both chromosomes share a 1,010 bp sequence containing duplicate copies of cox2 and three tRNA genes (trnD, trnG and trnH), and the nucleotide sequences between the duplicated homologous gene copies are nearly identical, suggesting a possible recent genesis for this bipartite mitochondrial genome. Given that little is known about the formation, maintenance or evolution of abnormal mitochondrial genome structures, R. karukerae mtDNA may provide an important early glimpse into this process.

The developmental transcriptome atlas of the spoon worm Urechis unicinctus (Echiurida: Annelida).

Background: Echiurida is one of the most intriguing major subgroups of annelida because, unlike most other annelids, echiurids lack metameric body segmentation as adults. For this reason, transcriptome analyses from various developmental stages of echiurid species can be of substantial value for understanding precise expression levels and the complex regulatory networks during early and larval development. Results: A total of 914 million raw RNA-Seq reads were produced from 14 developmental stages of Urechis unicinctus and were de novo assembled into contigs spanning 63,928,225 bp with an N50 length of 2700 bp. The resulting comprehensive transcriptome database of the early developmental stages of U. unicinctus consists of 20,305 representative functional protein-coding transcripts. Approximately 66% of unigenes were assigned to superphylum-level taxa, including Lophotrochozoa (40%). The completeness of the transcriptome assembly was assessed using benchmarking universal single-copy orthologs; 75.7% of the single-copy orthologs were presented in our transcriptome database. We observed 3 distinct patterns of global transcriptome profiles from 14 developmental stages and identified 12,705 genes that showed dynamic regulation patterns during the differentiation and maturation of U. unicinctus cells. Conclusions: We present the first large-scale developmental transcriptome dataset of U. unicinctus and provide a general overview of the dynamics of global gene expression changes during its early developmental stages. The analysis of time-course gene expression data is a first step toward understanding the complex developmental gene regulatory networks in U. unicinctus and will furnish a valuable resource for analyzing the functions of gene repertoires in various developmental phases.

Urbanization drives contemporary evolution in stream fish.

Human activities reduce biodiversity but may also drive diversification by modifying selection. Urbanization alters stream hydrology by increasing peak water velocities, which should in turn alter selection on the body morphology of aquatic species. Here, we show how urbanization can generate evolutionary divergence in the body morphology of two species of stream fish, western blacknose dace (Rhinichthys obtusus) and creek chub (Semotilus atromaculatus). We predicted that fish should evolve more streamlined body shapes within urbanized streams. We found that in urban streams, dace consistently exhibited more streamlined bodies while chub consistently showed deeper bodies. Comparing modern creek chub populations with historical museum collections spanning 50 years, we found that creek chub (1) rapidly became deeper bodied in streams that experienced increasing urbanization over time, (2) had already achieved deepened bodies 50 years ago in streams that were then already urban (and showed no additional deepening over time), and (3) remained relatively shallow bodied in streams that stayed rural over time. By raising creek chub from five populations under common conditions in the laboratory, we found that morphological differences largely reflected genetically based differences, not velocity-induced phenotypic plasticity. We suggest that urbanization can drive rapid, adaptive evolutionary responses to disturbance, and that these responses may vary unpredictably in different species.

Clinical Characteristics in Patients with Triple Negative Breast Cancer.

PURPOSE: The purpose of this study was to compare and contrast the clinical characteristics of the triple negative breast cancer (TNBC) and non-TNBC patients, with a particular focus on genetic susceptibility and risk factors prior to diagnosis. METHODS: Our institutional database was queried for all patients diagnosed with invasive breast cancer between January 2010 and May 2016. RESULTS: Out of a total of 1964 patients, 190 (10%) patients had TNBC. The median age for both TNBC and non-TNBC was 59 years. There was a significantly higher proportion of African American and Asian patients with TNBC (p = 0.0003) compared to patients with non-TNBC. BRCA1 and BRCA2 were significantly associated with TNBC (p < 0.0001, p = 0.0007). A prior history of breast cancer was significantly associated with TNBC (p = 0.0003). There was no relationship observed between TNBC and a history of chemoprevention or patients who had a history of AH or LCIS. CONCLUSIONS: We found that having Asian ancestry, a prior history of breast cancer, and a BRCA1 or BRCA2 mutation all appear to be positively associated with TNBC. In order to develop more effective treatments, better surveillance, and improved prevention strategies, it is necessary to improve our understanding of the population at risk for TNBC.

More than meets the eye: The barrier effect of the Yangtze River outflow.

The Yangtze (Changjiang) River enters the East China Sea with huge annual freshwater and sediment deposits. This outflow, known as the Changjiang diluted water (CDW), causes striking ecological gradients that potentially shape coastal species' distribution and differentiation. The CDW has long been rendered as a marine biogeographic boundary separating cold-temperature and warm-water faunas, but it remains unclear whether and to what extent it acts as an intraspecific barrier. Here, we synthesize published phylogeographic studies related to the CDW to address these issues. We find that the influence of the CDW on population differentiation is taxonomically variable, and even congeneric species may respond differently. In studies that claim the CDW is a phylogeographic barrier, the underlying assumptions explaining observed genetic breaks are sometimes incorrect, and some may have misinterpreted results due to conceptual confusion or insufficient geographic sampling. After excluding these studies, the remaining ones generally show shallow genetic divergence but significant population structure for coastal species across the CDW, suggesting that the CDW has not been a historically persistent barrier, but rather has acted as a filter within some species recently, probably after the last glacial maximum.

Measuring to Improve Medication Reconciliation in a Large Subspecialty Outpatient Practice.

BACKGROUND: To assess performance in medication reconciliation (med rec)-the process of comparing and reconciling patients' medication lists at clinical transition points-and demonstrate improvement in an outpatient setting, sustainable and valid measures are needed. METHODS: An interdisciplinary team at National Jewish Health (Denver) attempted to improve med rec in an ambulatory practice serving patients with respiratory and related diseases. Interventions, which were aimed at physicians, nurses (RNs), and medical assistants, involved changes in practice and changes in documentation in the electronic health record (EHR). New measures designed to assess med rec performance, and to validate the measures, were derived from EHR data. RESULTS: Across 18 months, electronic attestation that med rec was completed at clinic visits increased from 9.8% to 91.3% (p <0.0001). Consistent with this improvement, patients with medication lists missing dose/frequency for at least one prescription-type medication decreased from 18.1% to 15.8% (p <0.0001). Patients with duplicate albuterol inhalers on their list decreased from 4.0% to 2.6% (p <0.0001). Percentages of patients increased for printing of the medication list at the visit (18.7% to 94.0%; p <0.0001) and receipt of the printed medication list at the visit (52.3% to 67.0%; p = 0.0074). Documentation that patient education handouts were offered increased initially then declined to an overall poor performance of 32.4% of clinic visits. Investigation of this result revealed poor buy-in and a highly redundant process. CONCLUSION: Deriving measures reflecting performance and quality of med rec from EHR data is feasible and sustainable over the time periods necessary to demonstrate change. Concurrent, complementary measures may be used to support the validity of summary measures.

Draft genome of the sea cucumber Apostichopus japonicus and genetic polymorphism among color variants.

The Japanese sea cucumber (Apostichopus japonicus Selenka 1867) is an economically important species as a source of seafood and ingredient in traditional medicine. It is mainly found off the coasts of northeast Asia. Recently, substantial exploitation and widespread biotic diseases in A. japonicus have generated increasing conservation concern. However, the genomic knowledge base and resources available for researchers to use in managing this natural resource and to establish genetically based breeding systems for sea cucumber aquaculture are still in a nascent stage. A total of 312 Gb of raw sequences were generated using the Illumina HiSeq 2000 platform and assembled to a final size of 0.66 Gb, which is about 80.5% of the estimated genome size (0.82 Gb). We observed nucleotide-level heterozygosity within the assembled genome to be 0.986%. The resulting draft genome assembly comprising 132 607 scaffolds with an N50 value of 10.5 kb contains a total of 21 771 predicted protein-coding genes. We identified 6.6-14.5 million heterozygous single nucleotide polymorphisms in the assembled genome of the three natural color variants (green, red, and black), resulting in an estimated nucleotide diversity of 0.00146. We report the first draft genome of A. japonicus and provide a general overview of the genetic variation in the three major color variants of A. japonicus. These data will help provide a comprehensive view of the genetic, physiological, and evolutionary relationships among color variants in A. japonicus, and will be invaluable resources for sea cucumber genomic research.