5 research outputs found
The Draft Assembly of the Radically Organized Stylonychia lemnae Macronuclear Genome.
Stylonychia lemnae is a classical model single-celled eukaryote, and a quintessential ciliate typified by dimorphic nuclei: A small, germline micronucleus and a massive, vegetative macronucleus. The genome within Stylonychia's macronucleus has a very unusual architecture, comprised variably and highly amplified "nanochromosomes," each usually encoding a single gene with a minimal amount of surrounding noncoding DNA. As only a tiny fraction of the Stylonychia genes has been sequenced, and to promote research using this organism, we sequenced its macronuclear genome. We report the analysis of the 50.2-Mb draft S. lemnae macronuclear genome assembly, containing in excess of 16,000 complete nanochromosomes, assembled as less than 20,000 contigs. We found considerable conservation of fundamental genomic properties between S. lemnae and its close relative, Oxytricha trifallax, including nanochromosomal gene synteny, alternative fragmentation, and copy number. Protein domain searches in Stylonychia revealed two new telomere-binding protein homologs and the presence of linker histones. Among the diverse histone variants of S. lemnae and O. trifallax, we found divergent, coexpressed variants corresponding to four of the five core nucleosomal proteins (H1.2, H2A.6, H2B.4, and H3.7) suggesting that these ciliates may possess specialized nucleosomes involved in genome processing during nuclear differentiation. The assembly of the S. lemnae macronuclear genome demonstrates that largely complete, well-assembled highly fragmented genomes of similar size and complexity may be produced from one library and lane of Illumina HiSeq 2000 shotgun sequencing. The provision of the S. lemnae macronuclear genome sets the stage for future detailed experimental studies of chromatin-mediated, RNA-guided developmental genome rearrangements
Ultrafast nano-focusing with full optical waveform control
The spatial confinement and temporal control of an optical excitation on
nanometer length scales and femtosecond time scales has been a long-standing
challenge in optics. It would provide spectroscopic access to the elementary
optical excitations in matter on their natural length and time scales and
enable applications from ultrafast nano-opto-electronics to single molecule
quantum coherent control. Previous approaches have largely focused on using
surface plasmon polariton (SPP) resonant nanostructures or SPP waveguides to
generate nanometer localized excitations. However, these implementations
generally suffer from mode mismatch between the far-field propagating light and
the near-field confinement. In addition, the spatial localization in itself may
depend on the spectral phase and amplitude of the driving laser pulse thus
limiting the degrees of freedom available to independently control the
nano-optical waveform. Here we utilize femtosecond broadband SPP coupling, by
laterally chirped fan gratings, onto the shaft of a monolithic noble metal tip,
leading to adiabatic SPP compression and localization at the tip apex. In
combination with spectral pulse shaping with feedback on the intrinsic
nonlinear response of the tip apex, we demonstrate the continuous micro- to
nano-scale self-similar mode matched transformation of the propagating
femtosecond SPP field into a 20 nm spatially and 16 fs temporally confined
light pulse at the tip apex. Furthermore, with the essentially wavelength and
phase independent 3D focusing mechanism we show the generation of arbitrary
optical waveforms nanofocused at the tip. This unique femtosecond nano-torch
with high nano-scale power delivery in free space and full spectral and
temporal control opens the door for the extension of the powerful nonlinear and
ultrafast vibrational and electronic spectroscopies to the nanoscale.Comment: Contains manuscript with 4 figures as well as supplementary material
with 2 figure
The Draft Assembly of the Radically Organized Stylonychia lemnae Macronuclear Genome
Stylonychia lemnae is a classical model single-celled eukaryote, and a quintessential ciliate typified by dimorphic nuclei: A small, germline micronucleus and a massive, vegetative macronucleus. The genome within Stylonychia's macronucleus has a very unusual architecture, comprised variably and highly amplified "nanochromosomes," each usually encoding a single gene with a minimal amount of surrounding noncoding DNA. As only a tiny fraction of the Stylonychia genes has been sequenced, and to promote research using this organism, we sequenced its macronuclear genome. We report the analysis of the 50.2-Mb draft S. lemnae macronuclear genome assembly, containing in excess of 16,000 complete nanochromosomes, assembled as less than 20,000 contigs. We found considerable conservation of fundamental genomic properties between S. lemnae and its close relative, Oxytricha trifallax, including nanochromosomal gene synteny, alternative fragmentation, and copy number. Protein domain searches in Stylonychia revealed two new telomere-binding protein homologs and the presence of linker histones. Among the diverse histone variants of S. lemnae and O. trifallax, we found divergent, coexpressed variants corresponding to four of the five core nucleosomal proteins (H1.2, H2A.6, H2B.4, and H3.7) suggesting that these ciliates may possess specialized nucleosomes involved in genome processing during nuclear differentiation. The assembly of the S. lemnae macronuclear genome demonstrates that largely complete, well-assembled highly fragmented genomes of similar size and complexity may be produced from one library and lane of Illumina HiSeq 2000 shotgun sequencing. The provision of the S. lemnae macronuclear genome sets the stage for future detailed experimental studies of chromatin-mediated, RNA-guided developmental genome rearrangements