The photodissociation dynamics of alkyl iodides along the C-I bond are captured by attosecond extreme-ultraviolet (XUV) transient absorption spectroscopy employing resonant ∼20 fs UV pump pulses. The methodology of previous experiments on CH₃I [Chang et al., J. Chem. Phys. 154, 234301 (2021)] is extended to the investigation of a C-I bond-breaking reaction in the dissociative A-band of C₂H₅I, i-C₃H₇I, and t-C₄H₉I. Probing iodine 4d core-to-valence transitions in the XUV enables one to map wave packet bifurcation at a conical intersection in the A-band as well as coherent vibrations in the ground state of the parent molecules. Analysis of spectroscopic bifurcation signatures yields conical intersection crossing times of 15 ± 4 fs for CH₃I, 14 ± 5 fs for C₂H₅I, and 24 ± 4 fs for i-C₃H₇I and t-C₄H₉I, respectively. Observations of coherent vibrations, resulting from a projection of A-band structural dynamics onto the ground state by resonant impulsive stimulated Raman scattering, indirectly reveal multimode C-I stretch and CCI bend vibrations in the A-bands of C₂H₅I, i-C₃H₇I, and t-C₄H₉I.

High-throughput sequencing of full-length transcripts using long reads has paved the way for the discovery of thousands of novel transcripts, even in well-annotated mammalian species. The advances in sequencing technology have created a need for studies and tools that can characterize these novel variants. Here, we present SQANTI, an automated pipeline for the classification of long-read transcripts that can assess the quality of data and the preprocessing pipeline using 47 unique descriptors. We apply SQANTI to a neuronal mouse transcriptome using Pacific Biosciences (PacBio) long reads and illustrate how the tool is effective in characterizing and describing the composition of the full-length transcriptome. We perform extensive evaluation of ToFU PacBio transcripts by PCR to reveal that an important number of the novel transcripts are technical artifacts of the sequencing approach and that SQANTI quality descriptors can be used to engineer a filtering strategy to remove them. Most novel transcripts in this curated transcriptome are novel combinations of existing splice sites, resulting more frequently in novel ORFs than novel UTRs, and are enriched in both general metabolic and neural-specific functions. We show that these new transcripts have a major impact in the correct quantification of transcript levels by state-of-the-art short-read-based quantification algorithms. By comparing our iso-transcriptome with public proteomics databases, we find that alternative isoforms are elusive to proteogenomics detection. SQANTI allows the user to maximize the analytical outcome of long-read technologies by providing the tools to deliver quality-evaluated and curated full-length transcriptomes.

Background

In most eukaryotic cells, the mitochondrial DNA (mtDNA) is transmitted uniparentally and present in multiple copies derived from the clonal expansion of maternally inherited mtDNA. All copies are therefore near-identical, or homoplasmic. The presence of >1 mtDNA variant in the same cytoplasm can arise naturally or result from new medical technologies aimed at preventing mitochondrial genetic diseases and improving fertility. The latter is called divergent nonpathologic mtDNA heteroplasmy (DNPH). We hypothesized that DNPH is maladaptive and usually prevented by the cell.

Methods

We engineered and characterized DNPH mice throughout their lifespan using transcriptomic, metabolomic, biochemical, physiologic, and phenotyping techniques. We focused on in vivo imaging techniques for noninvasive assessment of cardiac and pulmonary energy metabolism.

Results

We show that DNPH impairs mitochondrial function, with profound consequences in critical tissues that cannot resolve heteroplasmy, particularly cardiac and skeletal muscle. Progressive metabolic stress in these tissues leads to severe pathology in adulthood, including pulmonary hypertension and heart failure, skeletal muscle wasting, frailty, and premature death. Symptom severity is strongly modulated by the nuclear context.

Conclusions

Medical interventions that may generate DNPH should address potential incompatibilities between donor and recipient mtDNA.