Influence of invasive quagga mussels, phosphorus loads, and climate on spatial and temporal patterns of productivity in Lake Michigan: A biophysical modeling study

We applied a three‐dimensional biophysical model to Lake Michigan for the years 2000, 2005, and 2010 to consider the mechanisms controlling spatial and temporal patterns of phytoplankton abundance (chlorophyll a) and lake‐wide productivity. Model skill was assessed by comparison to satellite‐derived Chl a and field‐measured water quality variables. We evaluated model sensitivity to scenarios of varying mussel filter feeding intensity, tributary phosphorus loads, and warm vs. cool winter‐spring climate scenarios. During the winter‐spring phytoplankton bloom, spatial patterns of Chl a were controlled by variables that influenced surface mixed layer depth: deep mixing reduced net phytoplankton growth through light limitation and by exposing the full water column to mussel filter feeding. Onset of summer and winter stratification promoted higher surface Chl a initially by increasing mean light exposure and by separating the euphotic zone from mussels. During the summer stratified period, areas of relatively high Chl a were associated with coastal plumes influenced by tributary‐derived nutrients and coastal upwelling‐downwelling. While mussels influenced spatial and temporal distribution of Chl a, lake‐wide, annual mean primary production was more sensitive to phosphorus and warm/cool meteorology scenarios than to mussel filter feeding scenarios. Although Chl a and primary production declined over the quagga mussel invasion, our results suggest that increased nutrient loads would increase lake‐wide productivity even in the presence of mussels; however, altered spatial and temporal patterns of productivity caused by mussel filter feeding would likely persist.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/139984/1/lno10595-sup-0001-suppinfo.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/139984/2/lno10595.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/139984/3/lno10595_am.pd

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.

Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes. Here we present a genome-wide chromatin landscape for Drosophila melanogaster based on eighteen histone modifications, summarized by nine prevalent combinatorial patterns. Integrative analysis with other data (non-histone chromatin proteins, DNase I hypersensitivity, GRO-Seq reads produced by engaged polymerase, short/long RNA products) reveals discrete characteristics of chromosomes, genes, regulatory elements and other functional domains. We find that active genes display distinct chromatin signatures that are correlated with disparate gene lengths, exon patterns, regulatory functions and genomic contexts. We also demonstrate a diversity of signatures among Polycomb targets that include a subset with paused polymerase. This systematic profiling and integrative analysis of chromatin signatures provides insights into how genomic elements are regulated, and will serve as a resource for future experimental investigations of genome structure and function

A central support system can facilitate implementation and sustainability of a Classroom-based Undergraduate Research Experience (CURE) in Genomics

In their 2012 report, the President\u27s Council of Advisors on Science and Technology advocated replacing standard science laboratory courses with discovery-based research courses -a challenging proposition that presents practical and pedagogical difficulties. In this paper, we describe our collective experiences working with the Genomics Education Partnership, a nationwide faculty consortium that aims to provide undergraduates with a research experience in genomics through a scheduled course (a classroom-based undergraduate research experience, or CURE). We examine the common barriers encountered in implementing a CURE, program elements of most value to faculty, ways in which a shared core support system can help, and the incentives for and rewards of establishing a CURE on our diverse campuses. While some of the barriers and rewards are specific to a research project utilizing a genomics approach, other lessons learned should be broadly applicable. We find that a central system that supports a shared investigation can mitigate some shortfalls in campus infrastructure (such as time for new curriculum development, availability of IT services) and provides collegial support for change. Our findings should be useful for designing similar supportive programs to facilitate change in the way we teach science for undergraduates

A course-based research experience: how benefits change with increased investment in instructional time

There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge. We have developed a bioinformatics project that provides a course-based research experience for students at a diverse group of schools and offers the opportunity to tailor this experience to local curriculum and institution-specific student needs. We assessed both attitude and knowledge gains, looking for insights into how students respond given this wide range of curricular and institutional variables. While different approaches all appear to result in learning gains, we find that a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. An alumni survey revealed that time spent on a research project is also a significant factor in the value former students assign to the experience one or more years later. We conclude: 1) implementation of a bioinformatics project within the biology curriculum provides a mechanism for successfully engaging large numbers of students in undergraduate research; 2) benefits to students are achievable at a wide variety of academic institutions; and 3) successful implementation of course-based research experiences requires significant investment of instructional time for students to gain full benefit

Identification of functional elements and regulatory circuits by Drosophila modENCODE

To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation

ST-Elevation Myocardial Infarction Associated With Infective Endocarditis.

ST-elevation myocardial infarction (STEMI) as a complication of infective endocarditis (IE) is a rarely reported entity. No clear guidelines exist with regards to the management of this medical emergency. We sought to systematically review the clinical presentation and management of this condition. We searched relevant articles on STEMI associated with IE and extracted data on demographic variables, key clinical characteristics upon presentation, treatment strategies, and clinical outcomes. We identified 100 patients from 95 articles. The mean age at presentation was 53 ± 17 years with male preponderance (n = 63, 63%, p = 0.01). Most patients (63 of 100, 63%) presented with STEMI as their first manifestation of IE, with others occurring at 15 ± 17 days after diagnosis of IE. Findings that suggested possible septic emboli were not consistently present, including history of prosthetic valve placement (15%), presence of other embolic disease (27%), fever (42%) increased leukocyte count (80%), and presence of murmur (88%). Atherosclerotic disease was absent in 95% on cardiac catheterization. Eleven patients receiving tissue plasminogen activator fared poorly, with 9 major bleeds; balloon angioplasty was successful in 56% (9 of 16 cases), aspiration thombectomy in 68% (21 of 31 cases), and coronary stenting in 81% (14 of 16 cases). The 30-day mortality was 43%. In conclusion, patients with STEMI in the face of recent IE, new precordial murmur, fever, increased leukocyte count or other embolic events, septic emboli should be considered as a cause for STEMI. Best practices for management are not known, but thrombolytics appear to carry significant bleeding and embolic risks