13 research outputs found
Photogrammetry of blue whales with an unmanned hexacopter
No full textAuthor Posting. © Society for Marine Mammalogy, 2016. This article is posted here by permission of Society for Marine Mammalogy for personal use, not for redistribution. The definitive version was published in Marine Mammal Science 32 (2016):1510–1515, doi:10.1111/mms.12328.Baleen whales are the largest animals ever to live on earth, and many populations
were hunted close to extinction in the 20th century (Clapham et al. 1999). Their
recovery is now a key international conservation goal, and they are important in marine
ecosystems as massive consumers that can promote primary production through
nutrient cycling (Roman et al. 2014). However, although abundance has been
assessed to monitor the recovery of some large whale populations (e.g., Barlow et al.
2011, Laake et al. 2012) many populations are wide-ranging and pelagic, and this
inaccessibility has generally impeded quantitative assessments of recovery (Peel et al.
2015). To augment traditional abundance monitoring, we suggest that photogrammetric
measures of individual growth and body condition can also inform about population
status, enabling assessment of individual health as well as population numbers. Photogrammetry
from manned aircraft has used photographs taken from directly above
whales to estimate individual lengths (Gilpatrick and Perryman 2008) and monitor growth trends (Fearnbach et al. 2011), and shape profiles can be measured to assess
body condition to infer reproductive and nutritional status (e.g., Perryman and Lynn
2002, Miller et al. 2012). Recently, Durban et al. (2015) demonstrated the utility of
an unmanned hexacopter for collecting aerial photogrammetry images of killer
whales (Orcinus orca); this provided a noninvasive, cost-effective, and safe platform
that could be deployed from a boat to obtain vertical images of whales. Here we
describe the use of this small, unmanned aerial system (UAS) to measure length and
condition of blue whales (Balaenoptera musculus), the largest of all whales.María Francisca Cortés Solari;
Rafaela Landea Briones;
MERI Foundation;
Woods Hole Oceanographic Institution Acces
Reprogramming of Polycomb-Mediated Gene Silencing in Embryonic Stem Cells by the miR-290 Family and the Methyltransferase Ash1l
No full textSummaryMembers of the miR-290 family are the most abundantly expressed microRNAs (miRNAs) in mouse embryonic stem cells (ESCs). They regulate aspects of differentiation, pluripotency, and proliferation of ESCs, but the molecular program that they control has not been fully delineated. In the absence of Dicer, ESCs fail to express mature miR-290 miRNAs and have selective aberrant overexpression of Hoxa, Hoxb, Hoxc, and Hoxd genes essential for body plan patterning during embryogenesis, but they do not undergo a full differentiation program. Introduction of mature miR-291 into DCR−/− ESCs restores Hox gene silencing. This was attributed to the unexpected regulation of Polycomb-mediated gene targeting by miR-291. We identified the methyltransferase Ash1l as a pivotal target of miR-291 mediating this effect. Collectively, our data shed light on the role of Dicer in ESC homeostasis by revealing a facet of molecular regulation by the miR-290 family
Characterization of human telomerase reverse transcriptase promoter methylation and transcription factor binding in differentiated thyroid cancer cell lines
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Long read mitochondrial genome sequencing using Cas9-guided adaptor ligation
No full textThe mitochondrial genome (mtDNA) is an important source of disease-causing genetic variability, but existing sequencing methods limit understanding, precluding phased measurement of mutations and clear detection of large sporadic deletions. We adapted a method for amplification-free sequence enrichment using Cas9 cleavage to obtain full length nanopore reads of mtDNA. We then utilized the long reads to phase mutations in a patient with an mtDNA-linked syndrome and demonstrated that this method can map age-induced mtDNA deletions. We believe this method will offer deeper insight into our understanding of mtDNA variation
Author Correction: Nanopore native RNA sequencing of a human poly(A) transcriptome
No full textAn amendment to this paper has been published and can be accessed via a link at the top of the paper
Methylation and accessibility profiling of GM12878, MCF-10A, MCF-7, and MDA-MB-231 using nanopore sequencing
No full textProbing epigenetic features on long molecules of DNA has tremendous potential to advance our understanding of the phased epigenome. In this study, we evaluate CpG methylation and chromatin accessibility simultaneously on long strands of DNA using GpC methyltransferase to exogenously label open chromatin, coupled with nanopore sequencing technology. We performed nanopore sequencing of Nucleosome Occupancy and Methylome (nanoNOMe) on four human cell lines (GM12878, MCF-10A, MCF-7, MDA-MB-231), and demonstrate the ability to directly measure methylation and chromatin accessibility in genomic features such as structural variations and repetitive elements. The long single-molecule resolution allows footprinting of protein and nucleosome binding and determining the combinatorial promoter epigenetic state on individual molecules. Long-read sequencing makes it possible to robustly assign reads to haplotypes, enabling allele-specific epigenetic analysis across the genome. We use existing SNV data on GM12878 to present the first fully phased human Probing epigenetic features on long molecules of DNA has tremendous potential to advance our understanding of the phased epigenome. We evaluate CpG methylation and chromatin accessibility simultaneously on long strands of DNA using GpC methyltransferase to exogenously label open chromatin, coupled with nanopore sequencing technology. We performed nanopore sequencing of Nucleosome Occupancy and Methylome (nanoNOMe) on four human cell lines (GM12878, MCF-10A, MCF-7, MDA-MB-231), and demonstrate the ability to directly measure methylation and chromatin accessibility in genomic features such as structural variations and repetitive elements. The long single-molecule resolution allows footprinting of protein and nucleosome binding and determining the combinatorial promoter epigenetic state on individual molecules. Long-read sequencing makes it possible to robustly assign reads to haplotypes, enabling allele-specific epigenetic analysis across the genome. We use existing SNV data on GM12878 to present the first fully phased human epigenome, consisting of chromosome-level allele-specific profiles of CpG methylation and chromatin accessibility.mosome-level allele-specific profiles of CpG methylation and chromatin accessibility
Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing
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Initial Operation of the LEDA Beam-Induced Fluorescence Diagnostic
No full textA diagnostic based on beam-induced fluorescence has been developed and used to examine the expanded beam in the High-Energy Beam Transport (HEBT) section of the Low Energy Demonstration Accelerator (LEDA). The system consists of a camera, a gas injector, a spectrometer, and a control system. Gas is injected to provide a medium for the beam to excite, the camera captures the resulting image of the fluorescing gas, and the spectrometer measures the spectrum of the emitted light. EPICS was used to control the camera and acquire and store images. Data analysis is presently being performed offline. A Kodak DCS420m professional CCD camera is the primary component of the optical system. InterScience, Inc. modified the camera with the addition of a gain of 4000 image intensifier, thereby producing an intensified camera with a sensitivity of {approximately}0.5 milli-lux. Light is gathered with a 1 inch format, 16-160 mm, Computar zoom lens. This lens is attached to the camera via a Century Precision Optics relay lens. Images obtained using only hydrogen from the beam stop exhibited features not yet understood. Images with good signal-to-noise ratio were obtained with the injection of sufficient nitrogen to raise the HEBT pressure to 2-8x10{sup {minus}6} torr. Two strong nitrogen lines, believed to be of the first negative group of N{sub 2}{sup +}, were identified at 391 and 428 nm
