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"Burns, Robert"
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Visitors’ support of ocean protection in a low-use marine protected area: Gray’s reef national marine sanctuary
Marine protected areas (MPAs) are important tools for conserving biodiversity and supporting healthy ocean ecosystems and economies. However, the effectiveness of MPAs is dependent upon the support of those who use and are affected by them. Understanding how recreational users relate to protected areas can provide key insights into long-term support for conservation initiatives. This study focused on a low-use MPA in the Atlantic Ocean, 20 miles offshore from Savannah, Georgia, USA. The study used an online survey of recreational users, primarily anglers, to understand human nature interactions and perceptions of support for environmental protection in the MPA and surrounding coastal settings. Understanding these perceptions is important to the success of environmental protection and helps to parse out willingness to act to ensure a sustainable use of ocean resources. The results of a series of regression models highlight the complexity of human behavior, showing that support for protection and willingness to act were influenced by broader attitudes, such as environmental concern, in combination with coastal or non-coastal residency. These findings indicate the need for managers to consider and address both the broader public and the local communities affected by potential restrictions associated with a given area’s protection status.
Journal Article
The coffee lover's diet : change your coffee, change your life
Draws on counterintuitive new research to reveal the health potential of coffee, explaining how to consume coffee strategically to enable specific benefits, including weight loss and resilience against disease.
Book
Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing
Background
Sample index cross-talk can result in false positive calls when massively parallel sequencing (MPS) is used for sensitive applications such as low-frequency somatic variant discovery, ancient DNA investigations, microbial detection in human samples, or circulating cell-free tumor DNA (ctDNA) variant detection. Therefore, the limit-of-detection of an MPS assay is directly related to the degree of index cross-talk.
Results
Cross-talk rates up to 0.29% were observed when using standard, combinatorial adapters, resulting in 110,180 (0.1% cross-talk rate) or 1,121,074 (0.29% cross-talk rate) misassigned reads per lane in non-patterned and patterned Illumina flow cells, respectively. Here, we demonstrate that using unique, dual-matched indexed adapters dramatically reduces index cross-talk to ≤1 misassigned reads per flow cell lane. While the current study was performed using dual-matched indices, using unique, dual-unrelated indices would also be an effective alternative.
Conclusions
For sensitive downstream analyses, the use of combinatorial indices for multiplexed hybrid capture and sequencing is inappropriate, as it results in an unacceptable number of misassigned reads. Cross-talk can be virtually eliminated using dual-matched indexed adapters. These results suggest that use of such adapters is critical to reduce false positive rates in assays that aim to identify low allele frequency events, and strongly indicate that dual-matched adapters be implemented for all sensitive MPS applications.
Journal Article
Genetic and transcriptional evolution alters cancer cell line drug response
Human cancer cell lines are the workhorse of cancer research. Although cell lines are known to evolve in culture, the extent of the resultant genetic and transcriptional heterogeneity and its functional consequences remain understudied. Here we use genomic analyses of 106 human cell lines grown in two laboratories to show extensive clonal diversity. Further comprehensive genomic characterization of 27 strains of the common breast cancer cell line MCF7 uncovered rapid genetic diversification. Similar results were obtained with multiple strains of 13 additional cell lines. Notably, genetic changes were associated with differential activation of gene expression programs and marked differences in cell morphology and proliferation. Barcoding experiments showed that cell line evolution occurs as a result of positive clonal selection that is highly sensitive to culture conditions. Analyses of single-cell-derived clones demonstrated that continuous instability quickly translates into heterogeneity of the cell line. When the 27 MCF7 strains were tested against 321 anti-cancer compounds, we uncovered considerably different drug responses: at least 75% of compounds that strongly inhibited some strains were completely inactive in others. This study documents the extent, origins and consequences of genetic variation within cell lines, and provides a framework for researchers to measure such variation in efforts to support maximally reproducible cancer research.
The extent, origins and consequences of genetic variation within human cell lines are studied, providing a framework for researchers to measure such variation in efforts to support maximally reproducible cancer research.
Journal Article
Heterogeneity of human bone marrow and blood natural killer cells defined by single-cell transcriptome
Natural killer (NK) cells are critical to both innate and adaptive immunity. However, the development and heterogeneity of human NK cells are yet to be fully defined. Using single-cell RNA-sequencing technology, here we identify distinct NK populations in human bone marrow and blood, including one population expressing higher levels of immediate early genes indicative of a homeostatic activation. Functionally matured NK cells with high expression of
CX3CR1
,
HAVCR2
(TIM-3), and
ZEB2
represents terminally differentiated status with the unique transcriptional profile. Transcriptomic and pseudotime analyses identify a transitional population between CD56
bright
and CD56
dim
NK cells. Finally, a donor with GATA2
T354M
mutation exhibits reduced percentage of CD56
bright
NK cells with altered transcriptome and elevated cell death. These data expand our understanding of the heterogeneity and development of human NK cells.
Natural killer (NK) cells are important innate immune cells with diverse functions. Here the authors use single-cell RNA-sequencing of purified human bone marrow and peripheral blood NK cells to define five populations of NK cells with distinct transcriptomic profile to further our understanding of NK development and heterogeneity.
Journal Article
Experiencing progressive rock : a listener's companion
Robert G. H. Burns brings together the several strands that define the \"prog rock\" movement of the late 1960s and early 1970 and follows the evolution of this remarkable rock tradition into the modern era.
Book
Is National Park Affinity Related to Visitors’ Satisfaction with Park Service and Recreation Quality? A Case Study from a Thai Forest National Park
The provision of high-quality national park tourism services depends on an understanding of the role of the national park brand in visitors’ decision-making on visiting parks. The consideration of forest recreation and park brand awareness not only helps to increase the quality of visitors’ experiences but also assists in the management of natural park resources. This study explored whether national park affinity can explain differences in visitor satisfaction with the national park trip, tourism services and facilities, visitor loyalty, and perceptions of recreation quality as well as visitor expenditures. This study classified 400 on-site visitors to the Khao Yai National Park into three national park affinity segments. The results indicated that about two-fifths of respondents had a low national park affinity with less satisfaction with the national park tourism facilities and services and visitor management. This segment reported lower visitor loyalty and that visitors felt more crowded, while no differences in expenditures for the trip were found between the affinity segments.
Journal Article