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Supplementary Table S6. ChIP-sequencing datasets used in the present study.

Supplementary Figure S1. mRNA levels of PRC2 components in CML and normal samples used in this study. Supplementary Figure S2. Effect of TKI treatment on mRNA levels of PRC2 components on CML cells in vitro. Supplementary Figure S3. Analysis of promoters reprogrammed for H3K27me3 levels at promoters. Supplementary Figure S4. Relationship between changes in levels of H3K27me3 and changes in mRNA expression at H3K27me3 targets. Supplementary Figure S5. EZH2i treatment of CML and normal CD34+ cells. Supplementary Figure S6. EZH2i treatment of CML CD34+CD38- cells (LSCs). Supplementary Figure S7. Validation of EZH2 shRNAs in a CML cell line. Supplementary Figure S8. The effect of treatment of CML or normal CD34+ cells with EZH2i (GSK343; 1000 nM) on the global mRNA levels of H3K27me3 and H3K27me1 targets. Supplementary Figure S9. Both imatinib and EZH2i selectively target upregulation of H3K27me3 target genes. Supplementary Figure S10. Nilotinib, dasatinib and EZH2i selectively target upregulation of H3K27me3 target genes. Supplementary Figure S11. mRNA expression levels for H3K27me3 target genes in HSC and LSCs and their behaviour after TKI treatment. Supplementary Figure S12. mRNA expression levels for H3K27me3 target genes in HPC and LPCs (â‰^ CML CD34+) and their behaviour after EZH2i treatment. Supplementary Figure S13. Primary CML cells engrafted in NSG mice treated in vivo with EZH2i and TKI, alone and in combination. Supplementary Figure S14. Validation of mRNA expression changes determined by Affymetrix GeneChip analysis (E-MTAB-2581, Affymetrix HuGe 1.0 ST). Supplementary Figure S15. PRC2 mis-regulation in the three CML patient samples used for Affymetrix GeneChIP and ChIP-sequencing in this study. Supplementary Figure S16. Determining thresholds for identifying H3K27me3 target genes. Supplementary Figure S17. Validation of seqMiner(3) promoter classifications.

Supplementary Table S2 from Inactivation of HOXA Genes by Hypermethylation in Myeloid and Lymphoid Malignancy is Frequent and Associated with Poor Prognosis

Purpose: The HOX genes comprise a large family of homeodomain-containing transcription factors, present in four separate clusters, which are key regulators of embryonic development, hematopoietic differentiation, and leukemogenesis. We aimed to study the role of DNA methylation as an inducer of HOX gene silencing in leukemia.Experimental Design: Three hundred and seventy-eight samples of myeloid and lymphoid leukemia were quantitatively analyzed (by COBRA analysis and pyrosequencing of bisulfite-modified DNA) for methylation of eight HOXA and HOXB cluster genes. The biological significance of the methylation identified was studied by expression analysis and through re-expression of HOXA5 in a chronic myeloid leukemia (CML) blast crisis cell line model.Results: Here, we identify frequent hypermethylation and gene inactivation of HOXA and HOXB cluster genes in leukemia. In particular, hypermethylation of HOXA4 and HOXA5 was frequently observed (26-79%) in all types of leukemias studied. HOXA6 hypermethylation was predominantly restricted to lymphoid malignancies, whereas hypermethylation of other HOXA and HOXB genes was only observed in childhood leukemia. HOX gene methylation exhibited clear correlations with important clinical variables, most notably in CML, in which hypermethylation of both HOXA5 (P = 0.00002) and HOXA4 (P = 0.006) was strongly correlated with progression to blast crisis. Furthermore, re-expression of HOXA5 in CML blast crisis cells resulted in the induction of markers of granulocytic differentiation.Conclusion: We propose that in addition to the oncogenic role of some HOX family members, other HOX genes are frequent targets for gene inactivation and normally play suppressor roles in leukemia development.

Subsurface imaging from surface seismic reflection data is often complex as a result of issues related to the surface and the near surface including noise (ambient or otherwise), differing coupling of the geophones/geophone arrays and different coupling between the sources and mixed sources and the ground. With the diversity in land seismic exploration and increasingly complex near-surface conditions advanced modelling capabilities are being used for velocity model generation in processing. In this article the use of a multi-physics approach that does not suffer from velocity-depth ambiguity and provides a robust shallow velocity model is presented. This case study is taken from a project in the Permian Basin, USA. It presents the integration of Airborne Full Tensor Gravity Gradiometry (FTG) with tomography and the unique approach applied by the authors for modelling the near surface velocity structure integrated with surface seismic data.

Although the importance of emotions to self-regulation has been noted in the extant literature, little empirical research has examined how fluctuations across a range of emotions are related to per...

Metalloendopeptidase ADAM-Like Decysin 1 (ADAMDEC1) is an anti-inflammatory peptidase that is almost exclusively expressed in the gastrointestinal (GI) tract. We have recently found abundant and selective expression of Adamdec1 in colonic mucosal PDGFRα

Accumulation of circular RNAs (circRNAs) during aging occurs on a genome-wide level for multiple organisms, but its significance is unknown. Generating circRNA loss-of-function mutants is difficult because the vast majority of these RNAs are comprised of exons shared with protein-coding mRNAs. In Caenorhabditis elegans, most circRNAs were previously found to accumulate during aging. Two of the most abundant, age-accumulating circRNAs are generated from exon 4 of the crh-1 gene (circ-crh-1). Here, we found that the biogenesis of circ-crh-1 was regulated by the double-stranded RNA-binding protein ADR-1. We identified Reverse Complementary Match (RCM) sequences in introns flanking circ-crh-1. Using CRISPR-Cas9, we deleted the downstream RCM and found that this completely eliminated expression of the circRNA without affecting linear mRNA expression from the crh-1 gene. Remarkably, worms lacking circ-crh-1 exhibited a significantly longer mean lifespan. Lifespan was partially restored to wild type by expression of circ-crh-1 in neural tissues. Widespread transcriptome alterations in circ-crh-1 mutants were identified using RNA-Seq. Moving forward, intronic RCM deletion using CRISPR should be a widely applicable method to identify lifespan-regulating circRNAs in C. elegans.

The gastrointestinal (GI) tract in mammals is comprised of dozens of cell types with varied functions, structures, and histological locations that respond in a myriad of ways to epigenetic and genetic factors, environmental cues, diet, and microbiota. The homeostatic functioning of these cells contained within this complex organ system has been shown to be highly regulated by the effect of microRNAs (miRNA). Multiple efforts have uncovered that these miRNAs are often tightly influential in either the suppression or overexpression of inflammatory, apoptotic, and differentiation-related genes and proteins in a variety of cell types in colorectal cancer (CRC). The early detection of CRC and other GI cancers can be difficult, attributable to the invasive nature of prophylactic colonoscopies. Additionally, the levels of miRNAs associated with CRC in biofluids can be contradictory and, therefore, must be considered in the context of other inhibiting competitive endogenous RNAs (ceRNA) such as lncRNAs and circRNAs. There is now a high demand for disease treatments and noninvasive screenings such as testing for bloodborne or fecal miRNAs and their inhibitors/targets. The breadth of this review encompasses current literature on well-established CRC-related miRNAs and the possibilities for their use as biomarkers in the diagnoses of this potentially fatal GI cancer.

Background: The E-wave propagation index (EPI) is a measure of apical blood flow and has been proposed as a risk marker of left ventricular thrombus (LVT) formation. We sought to investigate the association between EPI and LVT in patients with heart failure with reduced ejection fraction (HFrEF). Methods: This was a retrospective cohort study of patients with HFrEF. Follow-up echocardiograms were investigated for development of LVT. EPI was measured at baseline investigation as the velocity time integral of the transmitral E-wave divided by the left ventricular length. Logistic regression was used to investigate the association between EPI and LVT. Multivariable adjustments were made for age, significant mitral regurgitation, apical aneurysm, prior myocardial infarction, and left ventricular ejection fraction (LVEF). Results: Of 785 patients, 24 (3%) developed LVT. Mean age was 66 years, 73% were men, and LVEF was 28%. Those who developed LVT had significantly lower EPI (1.12 vs. 1.36, p=0.02). EPI was significantly associated with LVT in univariable logistic regression (OR=1.16 (1.03-1.31), per 0.1 decrease) (figure). These findings were unchanged after multivariable adjustments (OR=1.15 (1.00-1.31), per 0.1 decrease). The EPI provided an area under the curve of 0.68 with an optimal cutoff of 1.2. This cutoff had a sensitivity of 75%, specificity of 60%, positive predictive value of 6%, and negative predictive value of 99%. A low EPI was associated with a more than 4-fold increased risk of LVT (OR=4.56 (1.79-11.62), p=0.001). Conclusion: Decreasing EPI is associated with a higher risk of LVT. While a low EPI poses a markedly increased risk of LVT, a high EPI may be used to rule out LVT.

Background Videogames are emerging as increasingly popular tools for training complex skills, in part due to their potential for improving the transfer of learning to changing demands. One caveat is that training outcomes are primarily influenced by a learner’s capability and willingness to engage in adaptive learning processes. The present study examined the role of epistemic curiosity as a predisposition for seeking information and resolving gaps in knowledge. Method Using a game-based learning environment with strong cognitive and perceptual-motor demands, we tested the effects of interest- and deprivation-type epistemic curiosity on performance during skill acquisition and adaptation to unforeseen change. A task-change paradigm and piecewise latent trajectory model disentangled the effects on performance trajectories corresponding to skill acquisition and adaptation. Results Interest-type epistemic curiosity, but not deprivation-type, was positively related to baseline performance, even after controlling for cognitive ability and videogame experience. Moreover, the positive effect of interest-type epistemic curiosity on post-change performance (i.e., adaptation) was fully mediated by pre-change performance. Discussion These findings indicate that interest-type epistemic curiosity is particularly important in the earlier phases of learning, but explains little variability in adaptive performance beyond its direct influence on performance acquired prior to change. This research speaks to the roles of individual differences in cognition and motivation during game-based learning.

The mammalian intestine contains many different cell types but is comprised of 2 main cell types: epithelial cells and smooth muscle cells. Recent in vivo and in vitro evidence has revealed that various alterations to the DNA methylation apparatus within both of these cell types can result in a variety of cellular phenotypes including modified differentiation status, apoptosis, and uncontrolled growth. Methyl groups added to cytosines in regulatory genomic regions typically act to repress associated gene transcription. Aberrant DNA methylation patterns are often found in cells with abnormal growth/differentiation patterns, including those cells involved in burdensome intestinal pathologies including inflammatory bowel diseases and intestinal pseudo-obstructions. The altered methylation patterns being observed in various cell cultures and DNA methyltransferase knockout models indicate an influential connection between DNA methylation and gastrointestinal cells’ development and their response to environmental signaling. As these modified DNA methylation levels are found in a number of pathological gastrointestinal conditions, further investigations into uncovering the causative nature, and controlled regulation, of this epigenetic modification is of great interest.

Maturity-Onset Diabetes of the Young (MODY) is a rare form of diabetes which affects between 1% and 5% of diagnosed diabetes cases. Clinical characterizations of MODY include onset of diabetes at an early age (before the age of 30), autosomal dominant inheritance pattern, impaired glucose-induced secretion of insulin, and hyperglycemia. Presently, 14 MODY subtypes have been identified. Within these subtypes are several mutations which contribute to the different MODY phenotypes. Despite the identification of these 14 subtypes, MODY is often misdiagnosed as type 1 or type 2 diabetes mellitus due to an overlap in clinical features, high cost and limited availability of genetic testing, and unfamiliarity with MODY outside of the medical profession. The primary aim of this review is to investigate the genetic characterization of the MODY subtypes. Additionally, this review will elucidate the link between the genetics, function, and clinical manifestations of MODY in each of the 14 subtypes. In providing this knowledge, we hope to assist in the accurate diagnosis of MODY patients and, subsequently, in ensuring they receive appropriate treatment.

Sand and gravel mining creates novel ecosystems along the Platte, Loup, and Elkhorn rivers in Nebraska, USA. Piping plovers and least terns are state and/or federally threatened and endangered species, respectively, that nest and raise young at these sites and their derivatives. Despite hosting relatively large numbers of piping plovers and least terns for decades, an important question that has largely gone unaddressed is whether the industry that has produced these novel ecosystems is stable and will continue to produce habitat consistently in the future. We evaluated how the number, size, and spatial distribution of different site types hosting different numbers of nesting plovers and terns have changed over time and how current trends in the number of different site types will affect future habitat using a multi‐state modeling approach. Overall area and total number of sites declined during the period 1993–2020. More important, one site type, traditional mines, are being replaced by another site type, modern mines, which host lower numbers of nests of both species. The difference between these two site types is primarily how waste sand is stored. Traditional mines store waste sand in spoil piles or plumes along the edge of a lake created by the mining process, forming relatively large expanses of nesting habitat used by both species. Modern mines store waste sand in limited quantities along the edge of the lake but also in piles away from the lake. Traditional mines also differ from modern mines in that they are routinely converted to housing developments with intermediate transition sites that host the largest number of nests for brief periods. Based on the previous 28 yr of decline, traditional mines and their productive derivatives are projected to continue to decline, thereby further reducing overall nesting habitat. Piping plovers and least terns are expected to nest in our study sites for the foreseeable future, but overall numbers are expected to be smaller than what has been observed in previous decades. Local declines in our study area will have local and regional implications for the recovery and management of these two species of conservation concern.

Background: Child maltreatment is a major public issue in the United States, yet most children affected by abuse or neglect never engage in evidence-based practices (EBP) for child mental health. Children’s Advocacy Centers (CACs’) are uniquely situated to serve as Family Navigators who connect children impacted by maltreatment to appropriate EBPs. In fact, the CAC position of Victim Advocate mirrors the Mental Health Family Navigator national initiative.Methods: We developed, implemented, and will evaluate web-based and consultative training for Victim Advocates to enhance early engagement in services (E3 training). The interactive web-based training will embed key targets of knowledge and skills related to family engagement, trauma, and EBP services. Participating CACs will be randomized to E3 webinar-based training, E3 webinar plus consultation, or delayed training. The project will test the E3 training’s impact on key mechanisms of change (e.g., knowledge, skills) to improve rates of screening, referral, and access to EBP services. The feasibility of implementing the training program, and differential impact and costs by level of training will be examined.Discussion: The overarching goal of this project is to test a training that is readily implemented through CACs and examine the mechanisms for improving early engagement and, ultimately, child and adolescent mental health outcomes. Results and cost findings will be used to plan a large-scale comprehensive, mixed-methods Hybrid Type II effectiveness-implementation and cost-effectiveness trial of Family Navigator E3 training. If outcomes are positive, considerable infrastructure exists to support the scale-up and sustainability of E3 training nationwide, by embedding the training in national CAC training protocols.Trial registration: NCT04221633Date and version identifier: March 25 2021; Vers. 1.0 (original)

Subepithelial platelet-derived growth factor receptor alpha (PDGFRα)+ cells found in the colonic mucosal tissue come in close contact with epithelial cells, immune cells, neurons, capillaries, and lymphatic networks. Mucosal subepithelial PDGFRα+ cells (MuPαC) are important regulators in various intestinal diseases including fibrosis and inflammation. However, the transcriptome of MuPαC has not yet been elucidated. Using Pdgfra-eGFP mice and flow cytometry, we isolated colonic MuPαC and obtained their transcriptome data. In analyzing the transcriptome, we identified three novel, and selectively expressed, markers (Adamdec1, Fin1, and Col6a4) found in MuPαC. In addition, we identified a unique set of MuPαC-enriched genetic signatures including groups of growth factors, transcription factors, gap junction proteins, extracellular proteins, receptors, cytokines, protein kinases, phosphatases, and peptidases. These selective groups of genetic signatures are linked to the unique cellular identity and function of MuPαC. Furthermore, we have added this MuPαC transcriptome data to our Smooth Muscle Genome Browser that contains the transcriptome data of jejunal and colonic smooth muscle cells (SMC), interstitial cells of Cajal (ICC), and smooth muscle resident PDGFRα+ cells: (https://med.unr.edu/physio/transcriptome). This online resource provides a comprehensive reference of all currently known genetic transcripts expressed in primary MuPαC in the colon along with smooth muscle resident PDGFRα cells, SMC, and ICC in the murine colon and jejunum.

Background: Child maltreatment is a major public issue in the United States, yet most children affected by abuse or neglect never engage in evidence-based practices (EBP) for child mental health. Children’s Advocacy Centers (CACs’) are uniquely situated to serve as Family Navigators who connect children impacted by maltreatment to appropriate EBPs. In fact, the CAC position of Victim Advocate mirrors the Mental Health Family Navigator national initiative. Methods: We will develop, implement, and evaluate web-based and consultative training for Victim Advocates to enhance early engagement in services (E3 training). The interactive web-based training will embed key targets of knowledge and skills related to family engagement, trauma, and EBP services. Participating CACs will be randomized to E3 webinar-based training, E3 webinar plus consultation, or delayed training. The project will test the E3 training’s impact on key mechanisms of change (e.g., knowledge, skills) to improve rates of screening, referral, and access to EBP services. The feasibility of implementing the training program, and differential impact and costs by level of training will be examined.Discussion: The overarching goal of this project is to test a training that is readily implemented through CACs and examine the mechanisms for improving early engagement and, ultimately, child and adolescent mental health outcomes. Results and cost findings will be used to plan a large-scale comprehensive, mixed-methods Hybrid Type II effectiveness-implementation and cost-effectiveness trial of Family Navigator E3 training. If outcomes are positive, considerable infrastructure exists to support the scale-up and sustainability of E3 training nationwide, by embedding the training in national CAC training protocols.Trial registration: NCT04221633

Nest usurpation is a strategy in which an individual or pair of one species takes over the nest of another species. This is the first documented occurrence of a Piping Plover (Charadrius melodus) pair usurping an Interior Least Tern (Sternula antillarum athalassos) nest. The Piping Plovers incubated the three Interior Least Tern eggs in the nest, and all three eggs hatched. The adult Piping Plovers accompanied and brooded the Interior Least Tern chicks for 1 day post-hatching, but we did not see the adult Piping Plovers nor the Interior Least Tern chicks after that day. The Piping Plovers likely usurped the Interior Least Tern nest because they developed hormonemediated broodiness after they lost the eggs from their two previous nesting attempts. When the Piping Plovers encountered an unattended Interior Least Tern nest with eggs, they instinctively took the nest and its contents as their own.

In a recent study, Farnsworth et al. (2017) used distributions of nest initiation dates drawn mostly from human-created, off-channel habitats and a model of emergent sandbar habitat to evaluate the hypothesis that least terns (Sternula antillarum) and piping plovers (Charadrius melodus) are physiologically adapted to initiate nests concurrent with the cessation of spring river flow rises on two sections of the Platte River, Nebraska. The study by Farnsworth et al. (2017) has several shortcomings which bring into question the authors' principal assertion that interior least tern and piping plovers are not adapted to occupying and nesting on river sandbars on the Platte River system. We identify these shortcomings and provide information, which, we suggest, would change their conclusions if incorporated. Linked Article: https://doi.org/10.1002/ece3.4097.

Effective conservation for listed migratory species requires an understanding of how drivers of population decline vary spatially and temporally, as well as knowledge of range-wide connectivity between breeding and nonbreeding areas. Environmental conditions distant from breeding areas can have lasting effects on the demography of migratory species, yet these consequences are often the least understood. Our objectives were to 1) evaluate associations between survival and extreme environmental disturbances at nonbreeding areas, including hurricanes, harmful algal blooms, and oil spills, and 2) estimate migratory connectivity between breeding and nonbreeding areas of midcontinental piping plovers (Charadrius melodus). We used capture and resighting data from 5067 individuals collected between 2002 and 2019 from breeding areas across the midcontinent, and nonbreeding areas throughout the Gulf of Mexico and southern Atlantic coasts of North America. We developed a hidden Markov multistate model to estimate seasonal survival and account for unobservable geographic locations. Hurricanes and harmful algal blooms were negatively associated with nonbreeding season survival, but we did not detect a similarly negative relationship with oil spills. Our results indicated that individuals from separate breeding areas mixed across nonbreeding areas with low migratory connectivity. Mixing among individuals in the nonbreeding season may provide a buffering effect against impacts of extreme events on any one breeding region. Our results suggest that understanding migratory connectivity and linking seasonal threats to population dynamics can better inform conservation strategies for migratory shorebirds.

Birds are altering the phenology of critical life history events, including migration, in response to the effects of global climate change. Whooping Cranes (Grus americana) are one of the most critically endangered birds in the world. Their remnant population, referred to as the Aransas-Wood Buffalo Population, numbers between 300–400 individuals and migrates between the U.S. Gulf of Mexico coast and north-central Canada twice each year. Previous analyses suggested Whooping Crane migration was temporally constant in spring and fall. New analyses of observations spanning 1942–2016 show Whooping Crane migration is now occurring earlier in spring by approximately 22 days and later in fall by approximately 21 days. Spring temperatures have also increased in the migration corridor during the same period; however, there is no apparent temperature pattern during the fall. In spring, earlier migrating Whooping Cranes stopped over for longer periods of time compared to late-migrating cranes. This result may be partially explained by single Whooping Cranes migrating with earlier migrating Sandhill Cranes (Antigone canadensis). These results have important conservation implications as the timing of Whooping Crane migration and availability of the habitat and foraging resources, including those associated with agriculture, on which this species relies will be increasingly affected by climate change.

Background & Aims Gastrointestinal (GI) motility is regulated by serotonin (5-hydroxytryptamine [5-HT]), which is primarily produced by enterochromaffin (EC) cells in the GI tract. However, the precise roles of EC cell-derived 5-HT in regulating gastric motility remain a major point of conjecture. Using a novel transgenic mouse line, we investigated the distribution of EC cells and the pathophysiologic roles of 5-HT deficiency in gastric motility in mice and humans. Methods We developed an inducible, EC cell–specific Tph1CreERT2/+ mouse, which was used to generate a reporter mouse line, Tph1-tdTom, and an EC cell–depleted line, Tph1-DTA. We examined EC cell distribution, morphology, and subpopulations in reporter mice. GI motility was measured in vivo and ex vivo in EC cell–depleted mice. Additionally, we evaluated 5-HT content in biopsy and plasma specimens from patients with idiopathic gastroparesis (IG). Results Tph1-tdTom mice showed EC cells that were heterogeneously distributed throughout the GI tract with the greatest abundance in the antrum and proximal colon. Two subpopulations of EC cells were identified in the gut: self-renewal cells located at the base of the crypt and mature cells observed in the villi. Tph1-DTA mice displayed delayed gastric emptying, total GI transit, and colonic transit. These gut motility alterations were reversed by exogenous provision of 5-HT. Patients with IG had a significant reduction of antral EC cell numbers and 5-HT content, which negatively correlated with gastric emptying rate. Conclusions The Tph1CreERT2/+ mouse provides a powerful tool to study the functional roles of EC cells in the GI tract. Our findings suggest a new pathophysiologic mechanism of 5-HT deficiency in IG.

Visitors to public recreation areas where dogs are permitted often choose not to place their pets on leashes despite the presence of enforceable leash law regulations. Unleashed dogs can impact the safety of visitors, wildlife, and the environment and burden managers with additional duties. Often, improving leash law compliance is considered a law enforcement issue rather than a behavior that can be modified through education. We tested several persuasive messages addressing leash law compliance at a western Nebraska public recreation area where visitors are allowed to be accompanied by dogs. The area is an important nesting area for a legally protected shorebird, the piping plover ( Charadrius melodus ); unleashed dogs in plover nesting areas present a serious concern for managers. The majority of dog owners (81.3%) was aware of existing leash law regulations and expressed a high likelihood (4.13/5) of leashing their pet even though observations showed chronically low (16%) compliance rates. Urban and rural visitors perceived persuasive messages similarly. A persuasive message that emphasized avoiding dog bites and fights was the most likely to persuade dog owners to leash their pets. An education campaign focusing on this message may be helpful in improving leash law compliance in public recreation areas.

West Nile virus (WNV) is an introduced pathogen, transmitted by mosquitos, that spread across North America following its arrival there in 1999. Birds host the virus, but consequences of the disease to bird species have been variable. A small number of avian species are especially susceptible to WNV, experience high mortality rates when infected, and have shown regional declines apparently because of the disease. Other species have seemingly been unaffected. Transmission of WNV is associated with climate, with higher incidence of transmission in dry areas with warm winters. The north-central United States is an area that exhibits clines in temperature and precipitation, and in this area changes in species abundance due to WNV have not been closely examined. We used Christmas Bird Count (CBC) data to investigate changes in winter abundance of selected species before and after the arrival of WNV in the Great Plains. After arrival of WNV, average estimated abundances of Black-billed Magpie (Pica hudsonia) were significantly lower than projected abundances across much of the Great Plains. Black-capped Chickadee (Poecile atricapillus) abundances reached their lowest counts in portions of the Great Plains immediately after the arrival of WNV and experienced overall negative annual declines from 1988 to 2017. Two other species that were examined did not experience changes in abundance across the study area. Abundances of Black-billed Magpies and Black-capped Chickadees have declined over the past 30 years in the Great Plains, and WNV has likely played a major role in recent declines of magpies throughout the study area.

Transcriptome data on the quantitative numbers of transcriptional variants expressed in primary cells offer essential clues into specific cellular functions and biological processes. We have previously collected transcriptomes from primary smooth muscle cells (SMC), interstitial cells of Cajal (ICC), and PDGFRα+ cells (fibroblast-like cells) isolated from murine jejunal and colonic smooth muscle and/or mucosal tissues as well as transcriptomes from the associated tissues (jejunal smooth muscle, colonic smooth muscle, and colonic mucosa). In this study, we have built the Smooth Muscle Transcriptome Browser (SMTB), https://med.unr.edu/physio/transcriptome, a web-based, graphical user interface that offers genetic references and expression profiles of all transcripts expressed at both the cellular (SMC, ICC, and PDGFRα+ cells) and tissue level (smooth muscle and mucosal tissue). This browser brings new insights into the cellular and biological functions of the cell types in gastrointestinal smooth muscle biology.

DNA methylation is a key epigenetic modification that can regulate gene expression. Genomic DNA hypomethylation is commonly found in many gastrointestinal (GI) diseases. Dysregulated gene expression in GI smooth muscle cells (GI-SMCs) can lead to motility disorders. However, the consequences of genomic DNA hypomethylation within GI-SMCs are still elusive. Utilizing a Cre-lox murine model, we have generated SMC-restricted DNA methyltransferase 1 (Dnmt1) knockout (KO) mice and analyzed the effects of Dnmt1 deficiency. Dnmt1-KO pups are born smaller than their wild-type littermates, have shortened GI tracts, and lose peristaltic movement due to loss of the tunica muscularis in their intestine, causing massive intestinal dilation, and death around postnatal day 21. Within smooth muscle tissue, significant CpG hypomethylation occurs across the genome at promoters, introns, and exons. Additionally, there is a marked loss of differentiated SMC markers (Srf, Myh11, miR-133, miR-143/145), an increase in pro-apoptotic markers (Nr4a1, Gadd45g), loss of cellular connectivity, and an accumulation of coated vesicles within SMC. Interestingly, we observed consistent abnormal expression patterns of enzymes involved in DNA methylation between both Dnmt1-KO mice and diseased human GI tissue. These data demonstrate that DNA hypomethylation in embryonic SMC, via congenital Dnmt1 deficiency, contributes to massive dysregulation of gene expression and is lethal to GI-SMC. These results suggest that Dnmt1 has a necessary role in the embryonic, primary development process of SMC with consistent patterns being found in human GI diseased tissue.

Intestinal obstructions, that impede or block peristaltic movement, can be caused by abdominal adhesions and most gastrointestinal (GI) diseases including tumorous growths. However, the cellular remodeling mechanisms involved in, and caused by, intestinal obstructions are poorly understood. Several animal models of intestinal obstructions have been developed, but the mouse model is the most cost/time effective. The mouse model uses the surgical implantation of an intestinal partial obstruction (PO) that has a high mortality rate if it is not performed correctly. In addition, mice receiving PO surgery fail to develop hypertrophy if an appropriate blockade is not used or not properly placed. Here, we describe a detailed protocol for PO surgery which produces reliable and reproducible intestinal obstructions with a very low mortality rate. This protocol utilizes a surgically placed silicone ring that surrounds the ileum which partially blocks digestive movement in the small intestine. The partial blockage makes the intestine become dilated due to the halt of digestive movement. The dilation of the intestine induces smooth muscle hypertrophy on the oral side of the ring that progressively develops over 2 weeks until it causes death. The surgical PO mouse model offers an in vivo model of hypertrophic intestinal tissue useful for studying pathological changes of intestinal cells including smooth muscle cells (SMC), interstitial cells of Cajal (ICC), PDGFRα(+), and neuronal cells during the development of intestinal obstruction.

Piping Plovers (Charadrius melodus) are primarily monogamous birds that usually raise only one brood per season, but rare instances of double brooding have been documented. Piping Plovers breeding in the northern Great Plains, USA were studied in two locations: the Missouri River near the Gavins Point Dam (2005– 2013) and the lower Platte River (2008–2013). There were 25 confirmed instances of double brooding on the Missouri River across the 9-year duration of the study. There were no instances of double brooding observed locally on the lower Platte River. However, in 2013, two female Piping Plovers successfully hatched eggs and fledged chicks from nests on the lower Platte River and later were observed nesting for a second time on the Missouri River. Factors predicted to increase the frequency of double brooding are: early nest initiation, male biased sex ratio, age of breeding adults, and decreased nesting density. Our results indicate density is an important factor that accounts for some of t...

Piping plovers (Charadrius melodus) are shorebirds federally protected by the U.S. Endangered Species Act that often nest on beaches in proximity to human recreation. We evaluated whether awareness...

This study examined the microbial diversity and community assembly of oral microbiota in periodontal health and disease and after nonsurgical periodontal treatment. The V4 region of 16S rRNA gene from DNA of 238 saliva and subgingival samples of 21 healthy and 48 diseased subjects was amplified and sequenced. Among 1979 OTUs identified, 28 were overabundant in diseased plaque. Six of these taxa were also overabundant in diseased saliva. Twelve OTUs were overabundant in healthy plaque. There was a trend for disease-associated taxa to decrease and health-associated taxa to increase after treatment with notable variations among individual sites. Network analysis revealed modularity of the microbial communities and identified several health- and disease-specific modules. Ecological drift was a major factor that governed community turnovers in both plaque and saliva. Dispersal limitation and homogeneous selection affected the community assembly in plaque, with the additional contribution of homogenizing dispersal for plaque within individuals. Homogeneous selection and dispersal limitation played important roles, respectively, in healthy saliva and diseased pre-treatment saliva between individuals. Our results revealed distinctions in both taxa and assembly processes of oral microbiota between periodontal health and disease. Furthermore, the community assembly analysis has identified potentially effective approaches for managing periodontitis.

Transcriptome-scale data can reveal essential clues into understanding the underlying molecular mechanisms behind specific cellular functions and biological processes. Transcriptomics is a continually growing field of research utilized in biomarker discovery. The transcriptomic profile of interstitial cells of Cajal (ICC), which serve as slow-wave electrical pacemakers for gastrointestinal (GI) smooth muscle, has yet to be uncovered. Using copGFP-labeled ICC mice and flow cytometry, we isolated ICC populations from the murine small intestine and colon and obtained their transcriptomes. In analyzing the transcriptome, we identified a unique set of ICC-restricted markers including transcription factors, epigenetic enzymes/regulators, growth factors, receptors, protein kinases/phosphatases, and ion channels/transporters. This analysis provides new and unique insights into the cellular and biological functions of ICC in GI physiology. Additionally, we constructed an interactive ICC genome browser (http://med.unr.edu/physio/transcriptome) based on the UCSC genome database. To our knowledge, this is the first online resource that provides a comprehensive library of all known genetic transcripts expressed in primary ICC. Our genome browser offers a new perspective into the alternative expression of genes in ICC and provides a valuable reference for future functional studies.

Background Many species are distributed as metapopulations in dynamic landscapes, where habitats change through space and time. Individuals locate habitat through dispersal, and the relationship between a species and landscape characteristics can have profound effects on population persistence. Despite the importance of connectivity in dynamic environments, few empirical studies have examined temporal variability in dispersal or its effect on metapopulation dynamics. In response to this knowledge gap, we studied the dispersal, demography, and viability of a metapopulation of an endangered, disturbance-dependent shorebird. We examined three subpopulations of piping plovers (Charadrius melodus) on the lower Platte and Missouri rivers from 2008–2013. High flow events from an upstream dam on the Missouri River in 2010 and 2011 allowed us to assess the effect of total habitat loss and the subsequent creation of new habitat associated with a large disturbance at one ‘natural’ study location. The other two sites within the metapopulation, which were maintained by anthropogenic activities (e.g., mining, development, habitat restoration), were largely unaffected by this disturbance, resulting in a controlled natural experiment. Results High flow events were associated with increased emigration, decreased immigration, and decreased survival in the subpopulation that experienced high flows. Following the high flow event, immigration into that subpopulation increased. Dispersal rates among subpopulations were negatively correlated with distance. The metapopulation had a low probability of extinction over 100 years (0 %) under the current disturbance interval and associated dispersal and survival rates. However, persistence depended on relatively stable, human-created habitats, not the dynamic, natural habitat (47.7 % extinction probability for this subpopulation). Conclusions We found that functional connectivity, as measured by the rate of dispersal among subpopulations, increased as a result of the high flow event in our study metapopulation. Plovers also increased reproductive output following this event. Although the study metapopulation had a low overall probability of extinction, metapopulation persistence depended on anthropogenically created habitats that provided a small but stable source of nesting habitat and dispersers through time. However, all subpopulations remained small, even if persistent, making them individually vulnerable to extinction through stochastic events. Given the highly dynamic nature of habitat availability in this system, maintaining several subpopulations within the metapopulation and stable sources of habitat will be critical, and this species will likely remain conservation-reliant. Electronic supplementary material The online version of this article (doi:10.1186/s40462-016-0072-y) contains supplementary material, which is available to authorized users.

Long-billed Curlews (Numenius americanus) are shorebirds of high conservation concern in North America. Populations have de- clined in the last 150 yr primarily due to habitat loss and conversion. We conducted a 2-yr study to estimate the density and state- wide abundance of breeding Long-billed Curlews in Nebraska during 2008 and 2009. Surveys were conducted during the prenest- ing period in April when Long-billed Curlews were likely to be detected. We used a simple random sample of roadside survey routes (N = 39), each consisting of 40 5-min point-counts at 800-m intervals. We modeled detection probability and found that wind speed negatively affected detectability, but found no evidence of either year effects or observer bias. We estimated there were 0.0038 Long-billed Curlews per hectare (0.38 Long-billed Curlews per km 2 ) along survey routes and, by extrapolation, esti- mated there were 23,909 (SE = 1685; 95% CI: 20,810—27,471) Long-billed Curlews in Nebraska. Our population estimate suggests that ~15 to 22% of the United States population of Long-billed Curlews is found in Nebraska. Curlews were not evenly distrib- uted within our survey area, with the highest densities in the central Sandhills, an area dominated by grass-stabilized sand dunes and shallow wetlands, and the lowest densities in predominantly agricultural areas. Because Long-billed Curlews in Nebraska face many potential threats resulting from land-use changes, monitoring of the breeding population should be continued. Our survey method was efficient and yielded interpretable results; other states or regions should consider adopting this approach for estimating curlew abundance.

The least tern and piping plover are threatened and endangered species that are indigenous to at least part of the natural Missouri River. However, would the river’s natural hydrograph near Sioux City, Iowa, including the spring rise, have historically been harmful to the birds? Three methods of hydrograph analysis, which were based on 1938–1939 stream-flow measurements at the Sioux City gauge site and based on new information of the time needed for mating, nesting, and rearing of the birds, were made. The results of the analyses are consistent with historical biologic observations of June rise flooding and suggest that the natural hydrograph of the Missouri River near Sioux City was not “friendly” to the two bird species as the hydrograph likely did not result in long-term recruitment.

The Buff-breasted Sandpiper (Tryngites subruficollis) is a shorebird of conservation concern whose migration patterns and population size are poorly known. We conducted surveys in the Eastern Rainwater Basin, Nebraska, in 2004 and 2005 using distance sampling. This survey produced density estimates of 0.09 birds per ha in 2004 and 0.04 birds per ha in 2005. Because the study area was explicitly defined by soil characteristics, we were able to extrapolate from density estimates to produce predictions of overall numbers in the study area. We produced minimum estimates of the numbers of Buff-breasted Sandpipers stopping over in the region—43 300 in 2004 and 22 924 in 2005. When we restricted our predictions to only the area adjacent to roads, numbers of birds ranged from 13 488 to 41 513, depending on the area used. These predictions indicate two important findings—that 1) the current estimate of the world population of Buff-breasted Sandpipers of 15 000 to 20 000 individuals is too low, and 2) the ...