AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis

BACKGROUND: The invariant lineage of the nematode Caenorhabditis elegans has potential as a powerful tool for the description of mutant phenotypes and gene expression patterns. We previously described procedures for the imaging and automatic extraction of the cell lineage from C. elegans embryos. That method uses time-lapse confocal imaging of a strain expressing histone-GFP fusions and a software package, StarryNite, processes the thousands of images and produces output files that describe the location and lineage relationship of each nucleus at each time point. RESULTS: We have developed a companion software package, AceTree, which links the images and the annotations using tree representations of the lineage. This facilitates curation and editing of the lineage. AceTree also contains powerful visualization and interpretive tools, such as space filling models and tree-based expression patterning, that can be used to extract biological significance from the data. CONCLUSION: By pairing a fast lineaging program written in C with a user interface program written in Java we have produced a powerful software suite for exploring embryonic development

A Linkage-Based Genome Assembly for the Mosquito Aedes albopictus and Identification of Chromosomal Regions Affecting Diapause

The Asian tiger mosquito, Aedes albopictus, is an invasive vector mosquito of substantial public health concern. The large genome size (similar to 1.19-1.28 Gb by cytofluorometric estimates), comprised of similar to 68% repetitive DNA sequences, has made it difficult to produce a high-quality genome assembly for this species. We constructed a high-density linkage map for Ae. albopictus based on 111,328 informative SNPs obtained by RNAseq. We then performed a linkage-map anchored reassembly of AalbF2, the genome assembly produced by Palatini et al. (2020). Our reassembled genome sequence, AalbF3, represents several improvements relative to AalbF2. First, the size of the AalbF3 assembly is 1.45 Gb, almost half the size of AalbF2. Furthermore, relative to AalbF2, AalbF3 contains a higher proportion of complete and single-copy BUSCO genes (84.3%) and a higher proportion of aligned RNAseq reads that map concordantly to a single location of the genome (46%). We demonstrate the utility of AalbF3 by using it as a reference for a bulk-segregant-based comparative genomics analysis that identifies chromosomal regions with clusters of candidate SNPs putatively associated with photoperiodic diapause, a crucial ecological adaptation underpinning the rapid range expansion and climatic adaptation of A. albopictus.Peer reviewe

A Linkage-Based Genome Assembly for the Mosquito Aedes albopictus and Identification of Chromosomal Regions Affecting Diapause

The Asian tiger mosquito, Aedes albopictus, is an invasive vector mosquito of substantial public health concern. The large genome size (~1.19–1.28 Gb by cytofluorometric estimates), comprised of ~68% repetitive DNA sequences, has made it difficult to produce a high-quality genome assembly for this species. We constructed a high-density linkage map for Ae. albopictus based on 111,328 informative SNPs obtained by RNAseq. We then performed a linkage-map anchored reassembly of AalbF2, the genome assembly produced by Palatini et al. (2020). Our reassembled genome sequence, AalbF3, represents several improvements relative to AalbF2. First, the size of the AalbF3 assembly is 1.45 Gb, almost half the size of AalbF2. Furthermore, relative to AalbF2, AalbF3 contains a higher proportion of complete and single-copy BUSCO genes (84.3%) and a higher proportion of aligned RNAseq reads that map concordantly to a single location of the genome (46%). We demonstrate the utility of AalbF3 by using it as a reference for a bulk-segregant-based comparative genomics analysis that identifies chromosomal regions with clusters of candidate SNPs putatively associated with photoperiodic diapause, a crucial ecological adaptation underpinning the rapid range expansion and climatic adaptation of A. albopictus

A Composite HST Spectrum of Quasars

We construct a composite quasar spectrum from 284 HST FOS spectra of 101 quasars with redshifts z > 0.33. The spectrum covers the wavelengths between 350 and 3000 A in the rest frame. There is a significant steepening of the continuum slope around 1050 A. The continuum between 1050 and 2200 A can be modeled as a power law with alpha = -0.99. For the full sample the power-law index in the extreme ultraviolet (EUV) between 350 and 1050 A is alpha = -1.96. The continuum flux in the wavelengths near the Lyman limit shows a depression of about 10 percent. The break in the power-law index and the slight depression of the continuum near the Lyman limit are features expected in Comptonized accretion-disk spectra.Comment: 10 figures To appear in the February 1, 1997, issue of the Ap.

Increased accumulation of sulfur in lake sediments of the high Arctic

Author Posting. © The Author(s), 2010. This is the author's version of the work. It is posted here by permission of American Chemical Society for personal use, not for redistribution. The definitive version was published in Environmental Science & Technology 44 (2010): 8415-8421, doi:10.1021/es101991p.We report a synchronous increase in accumulation of reduced inorganic sulfur since c. 1980 in sediment cores from eight of nine lakes studied in the Canadian Arctic and Svalbard (Norway). Sediment incubations and detailed analyses of sediment profiles from two of the lakes indicate that increases in sulfur accumulation may be due ultimately to a changing climate. Warming-induced lengthening of the ice-free season is resulting in well-documented increases in algal production and sedimentation of the resulting detrital matter. Algal detritus is a rich source of labile carbon, which in these sediments stimulates dissimilatory sulfate reduction. The sulfide produced is stored in sediment (as acid volatile sulfide), converted to other forms of sulfur, or reoxidized to sulfate and lost to the water column. An acceleration of the sulfur cycle in Arctic lakes could have profound effects on important biogeochemical processes, such as carbon burial and mercury methylation.Funding was provided by the WHOI Ocean and Climate Change Institute, the USGS WHOI Postdoctoral Scholar Program, Environment Canada, the Danmarks Grundforskningsfond, and the Norges forskningsråd (grant number 107745/730)

The British economy [August 1986]

External events have had a considerable impact on the UK economy. In line with developments elsewhere, UK growth has slowed, interest rates have been reduced and the inflation rate has fallen. However, underlying inflationary pressures in the UK continue to operate with relatively rapid growth of average earnings and substantial growth of private sector liquidity

The world economy [November 1986]

Recent developments in the UK economy suggest that the slowdown of growth in 1985 may only have been a temporary phenomenon. External events are continuing to play a significant role. Yet it is the trends within the domestic economy that are a major source of unease. Underlying inflationary pressures continue to operate via the relatively fast growth in average earnings, low productivity growth, the growth of private sector liquidity and the recent significant decrease in the value of sterling. An increase in the growth of non-oil imports adds to fears for the current account of the balance of payments. Perceptions of uncertainty in Government policy particularly towards the exchange rate are a continuing cause for concern