Sequencing-based functional assays for classification of BRCA2 variants in mouse ESCs.

Sequencing of genes, such as BRCA1 and BRCA2, is recommended for individuals with a personal or family history of early onset and/or bilateral breast and/or ovarian cancer or a history of male breast cancer. Such sequencing efforts have resulted in the identification of more than 17,000 BRCA2 variants. The functional significance of most variants remains unknown; consequently, they are called variants of uncertain clinical significance (VUSs). We have previously developed mouse embryonic stem cell (mESC)-based assays for functional classification of BRCA2 variants. We now developed a next-generation sequencing (NGS)-based approach for functional evaluation of BRCA2 variants using pools of mESCs expressing 10-25 BRCA2 variants from a given exon. We use this approach for functional evaluation of 223 variants listed in ClinVar. Our functional classification of BRCA2 variants is concordant with the classification reported in ClinVar or those reported by other orthogonal assays.

Rare germline variants in PALB2 and BRCA2 in familial and sporadic chordoma.

Chordoma is a rare bone tumor with genetic risk factors largely unknown. We conducted a whole-exome sequencing (WES) analysis of germline DNA from 19 familial chordoma cases in five pedigrees and 137 sporadic chordoma patients and identified 17 rare germline variants in PALB2 and BRCA2, whose products play essential roles in homologous recombination (HR) and tumor suppression. One PALB2 variant showed disease cosegregation in a family with four affected people or obligate gene carrier. Chordoma cases had a significantly increased burden of rare variants in both genes when compared to population-based controls. Four of the six PALB2 variants identified from chordoma patients modestly affected HR function and three of the 11 BRCA2 variants caused loss of function in experimental assays. These results, together with previous reports of abnormal morphology and Brachyury expression of the notochord in Palb2 knockout mouse embryos and genomic signatures associated with HR defect and HR gene mutations in advanced chordomas, suggest that germline mutations in PALB2 and BRCA2 may increase chordoma susceptibility. Our data shed light on the etiology of chordoma and support the previous finding that PARP-1 inhibitors may be a potential therapy for some chordoma patients.

Photodynamics of [FeFe]-Hydrogenase Model Compounds with Bidentate Heterocyclic Ligands.

Two asymmetrically structured model compounds for the hydrogen-generating [Fe-Fe]-hydrogenase active site were investigated to determine the ultrafast photodynamics, structural intermediates, and photoproducts compared to more common symmetric di-iron species. The bidentate-ligand-containing compounds studied were Fe2(µ-S2C3H6)(CO)4(bipy), 1, and Fe2(µ-S2C3H6)(CO)4(phen), 2, in dilute room temperature acetonitrile solution and low-temperature 2Me-THF matrix isolation using static FTIR difference and time-resolved infrared spectroscopic methods (TRIR). Ultraviolet-visible spectra were also compared to time-dependent density functional theory (TD-DFT) to ascertain the orbital origins of long wavelength electronic absorption features. The spectroscopic evidence supports the conclusions that only a propyl-bridge flip occurs in low-temperature matrix, while early time CO ejection leads to the formation of solvated isomeric species on the 25 ps time scale in room temperature solution.

Femtosecond Laser Eyewear Protection: Measurements and Precautions for Amplified High Power Applications.

Ultrafast lasers have become increasingly important as research tools in laboratories and commercial enterprises suggesting laser safety, personal protection and awareness become ever more important. Laser safety eyewear are typically rated by their optical densities (OD) over various spectral ranges, but these measurements are usually made using low power, large beam size, and continuous beam conditions. These measurement scenarios are vastly different than the high power, small beam size, and pulsed laser beam conditions where ultrafast lasers have extremely high peak powers and broad spectra due to the short pulse durations. Many solid-state lasers are also tunable over a broad wavelength range, further complicating the selection of adequate laser safety eyewear. Eighteen laser eyewear filter samples were tested under real-world conditions using a Ti:Sapphire regenerative amplifier with output pulses centered at 800 nm running from 2 Hz to 1 KHz repetition rate. The typical maximum peak laser irrandiance employed was ca. 3 TW/cm2 (800 nm wavelength, 450 uJ/pulse with 80 fs FWHM pulse duration) or less when damage occurred, depending on the sample. While many samples maintained their integrity under these test conditions, many plastic samples showed signs of failure which reduced their OD, in some cases transmitting 4 to 5 orders of magnitude higher than expected. In general, glass filters performed significantly better than plastic filters, exhibiting less physical damage to the substrate and less absorber degradation.