BleTIES: Annotation of natural genome editing in ciliates using long read sequencing

Ciliates are single-celled eukaryotes that eliminate specific, interspersed DNA sequences (internally eliminated sequences, IESs) from their genomes during development. These are challenging to annotate and assemble because IES-containing sequences are much less abundant in the cell than those without, and IES sequences themselves often contain repetitive and low-complexity sequences. Long read sequencing technologies from Pacific Biosciences and Oxford Nanopore have the potential to reconstruct longer IESs than has been possible with short reads, and also the ability to detect correlations of neighboring element elimination. Here we present BleTIES, a software toolkit for detecting, assembling, and analyzing IESs using mapped long reads. Availability and implementation: BleTIES is implemented in Python 3. Source code is available at https://github.com/Swart-lab/bleties (MIT license), and also distributed via Bioconda. Contact: [email protected] Supplementary information: Benchmarking of BleTIES with published sequence data.

An Investigation of Silica Aerogel to Reduce Acoustic Crosstalk in CMUT Arrays

This paper presents a novel technique to reduce acoustic crosstalk in capacitive micromachined ultrasonic transducer (CMUT) arrays. The technique involves fabricating a thin layer of diisocyanate enhanced silica aerogel on the top surface of a CMUT array. The silica aerogel layer introduces a highly nanoporous permeable layer to reduce the intensity of the Scholte wave at the CMUT-fluid interface. 3D finite element analysis (FEA) simulation in COMSOL shows that the developed technique can provide a 31.5% improvement in crosstalk reduction for the first neighboring element in a 7.5 MHz CMUT array. The average improvement of crosstalk level over the −6 dB fractional bandwidth was 22.1%, which is approximately 5 dB lower than that without an aerogel layer. The results are in excellent agreement with published experimental results to validate the efficacy of the new technique.

Strategies for solving neighboring-element problems: a case study using resonant X-ray diffraction and pulsed neutron diffraction to examine Sr8Ga16Ge30

The distribution of gallium and germanium over the available framework sites in the type-I clathrate Sr8Ga16Ge30(Pm\bar{3}n) has been determined by powder diffraction using several different combinations of resonant scattering data sets, collected at energies close to both the Ga and GeK-edges, and time-of-flight (TOF) neutron diffraction data. Based on a combined refinement using three X-ray data sets and a composition restraint, the fractional occupancies of the 6c, 16iand 24ksites by gallium are estimated to be 0.705 (5), 0.181 (3) and 0.376 (2), respectively. The required resonant scattering factors were determined by Kramers–Kronig transformation from X-ray absorption spectra. The results from refinements using single data sets and various combinations of data sets are compared. The high degree of scattering contrast that resonant diffraction can provide leads to very precise site occupancies. However, systematic errors in the resonant diffraction intensity data can considerably degrade the accuracy of the results. The use of a carefully chosen multiple-data-set strategy can minimize bias in the refinement results by reducing the correlations between site occupancies, atomic displacement parameters and histogram scale factors. The effect of errors in the resonant scattering factors on the refinement results was also examined.

Physiological and genetic analysis of the carbon regulation of the NAD-dependent glutamate dehydrogenase of Saccharomyces cerevisiae

We found that cells of Saccharomyces cerevisiae have an elevated level of the NAD-dependent glutamate dehydrogenase (NAD-GDH; encoded by the GDH2 gene) when grown with a nonfermentable carbon source or with limiting amounts of glucose, even in the presence of the repressing nitrogen source glutamine. This regulation was found to be transcriptional, and an upstream activation site (GDH2 UASc) sufficient for activation of transcription during respiratory growth conditions was identified. This UAS was found to be separable from a neighboring element which is necessary for the nitrogen source regulation of the gene, and strains deficient for the GLN3 gene product, required for expression of NAD-GDH during growth with the activating nitrogen source glutamate, were unaffected for the expression of NAD-GDH during growth with activating carbon sources. Two classes of mutations which prevented the normal activation of NAD-GDH in response to growth with nonfermentable carbon sources, but which did not affect the nitrogen-regulated expression of NAD-GDH, were found and characterized. Carbon regulation of GDH2 was found to be normal in hxk2, hap3, and hap4 strains and to be only slightly altered in a ssn6 strain; thus, in comparison with the regulation of previously identified glucose-repressed genes, a new pathway appears to be involved in the regulation of GDH2.

Physiological and genetic analysis of the carbon regulation of the NAD-dependent glutamate dehydrogenase of Saccharomyces cerevisiae.

We found that cells of Saccharomyces cerevisiae have an elevated level of the NAD-dependent glutamate dehydrogenase (NAD-GDH; encoded by the GDH2 gene) when grown with a nonfermentable carbon source or with limiting amounts of glucose, even in the presence of the repressing nitrogen source glutamine. This regulation was found to be transcriptional, and an upstream activation site (GDH2 UASc) sufficient for activation of transcription during respiratory growth conditions was identified. This UAS was found to be separable from a neighboring element which is necessary for the nitrogen source regulation of the gene, and strains deficient for the GLN3 gene product, required for expression of NAD-GDH during growth with the activating nitrogen source glutamate, were unaffected for the expression of NAD-GDH during growth with activating carbon sources. Two classes of mutations which prevented the normal activation of NAD-GDH in response to growth with nonfermentable carbon sources, but which did not affect the nitrogen-regulated expression of NAD-GDH, were found and characterized. Carbon regulation of GDH2 was found to be normal in hxk2, hap3, and hap4 strains and to be only slightly altered in a ssn6 strain; thus, in comparison with the regulation of previously identified glucose-repressed genes, a new pathway appears to be involved in the regulation of GDH2.

Use of 155Eu in the Measurement of Gd L Subshell Yields

The subshell fluorescence yields ω2 and ω3 and the Coster–Kronig yield f23 have been measured for Gd by the method of coincidence study of the X rays emitted by 155Eu.The result is ω2 = 0.182 ± 0.008, ω3 = 0.187 ± 0.006, and f23 = 0.223 ± 0.011. The values for ω2 and ω3 are close to theoretical predictions and to the experimental results of other workers on the neighboring element Tb. However, there is serious disagreement in the f23 values.