Strongly aligned gas-phase molecules at Free-Electron Lasers

We demonstrate a novel experimental implementation to strongly align molecules at full repetition rates of free-electron lasers. We utilized the available in-house laser system at the coherent x-ray imaging beamline at the Linac Coherent Light Source. Chirped laser pulses, i. e., the direct output from the regenerative amplifier of the Ti:Sa chirped pulse amplification laser system, were used to strongly align 2,5-diiodothiophene molecules in a molecular beam. The alignment laser pulses had pulse energies of a few mJ and a pulse duration of 94 ps. A degree of alignment of \left = 0.85 was measured, limited by the intrinsic temperature of the molecular beam rather than by the available laser system. With the general availability of synchronized chirped-pulse-amplified near-infrared laser systems at short-wavelength laser facilities, our approach allows for the universal preparation of molecules tightly fixed in space for experiments with x-ray pulses.Comment: 10 pages, 5 figure

X-ray diffractive imaging of controlled gas-phase molecules: Toward imaging of dynamics in the molecular frame

We report experimental results on the diffractive imaging of three-dimensionally aligned 2,5-diiodothiophene molecules. The molecules were aligned by chirped near-infrared laser pulses, and their structure was probed at a photon energy of 9.5 keV ($\lambda\approx130 \text{pm}$) provided by the Linac Coherent Light Source. Diffracted photons were recorded on the CSPAD detector and a two-dimensional diffraction pattern of the equilibrium structure of 2,5-diiodothiophene was recorded. The retrieved distance between the two iodine atoms agrees with the quantum-chemically calculated molecular structure to within 5 %. The experimental approach allows for the imaging of intrinsic molecular dynamics in the molecular frame, albeit this requires more experimental data which should be readily available at upcoming high-repetition-rate facilities

Mutational processes molding the genomes of 21 breast cancers

All cancers carry somatic mutations. The patterns of mutation in cancer genomes reflect the DNA damage and repair processes to which cancer cells and their precursors have been exposed. To explore these mechanisms further, we generated catalogs of somatic mutation from 21 breast cancers and applied mathematical methods to extract mutational signatures of the underlying processes. Multiple distinct single- and double-nucleotide substitution signatures were discernible. Cancers with BRCA1 or BRCA2 mutations exhibited a characteristic combination of substitution mutation signatures and a distinctive profile of deletions. Complex relationships between somatic mutation prevalence and transcription were detected. A remarkable phenomenon of localized hypermutation, termed “kataegis,” was observed. Regions of kataegis differed between cancers but usually colocalized with somatic rearrangements. Base substitutions in these regions were almost exclusively of cytosine at TpC dinucleotides. The mechanisms underlying most of these mutational signatures are unknown. However, a role for the APOBEC family of cytidine deaminases is proposed

Mutational processes molding the genomes of 21 breast cancers

All cancers carry somatic mutations. The patterns of mutation in cancer genomes reflect the DNA damage and repair processes to which cancer cells and their precursors have been exposed. To explore these mechanisms further, we generated catalogs of somatic mutation from 21 breast cancers and applied mathematical methods to extract mutational signatures of the underlying processes. Multiple distinct single- and double-nucleotide substitution signatures were discernible. Cancers with BRCA1 or BRCA2 mutations exhibited a characteristic combination of substitution mutation signatures and a distinctive profile of deletions. Complex relationships between somatic mutation prevalence and transcription were detected. A remarkable phenomenon of localized hypermutation, termed "kataegis," was observed. Regions of kataegis differed between cancers but usually colocalized with somatic rearrangements. Base substitutions in these regions were almost exclusively of cytosine at TpC dinucleotides. The mechanisms underlying most of these mutational signatures are unknown. However, a role for the APOBEC family of cytidine deaminases is proposed

Processed pseudogenes acquired somatically during cancer development

Cancer evolves by mutation, with somatic reactivation of retrotransposons being one such mutational process. Germline retrotransposition can cause processed pseudogenes, but whether this occurs somatically has not been evaluated. Here we screen sequencing data from 660 cancer samples for somatically acquired pseudogenes. We find 42 events in 17 samples, especially non-small cell lung cancer (5/27) and colorectal cancer (2/11). Genomic features mirror those of germline LINE element retrotranspositions, with frequent target-site duplications (67%), consensus TTTTAA sites at insertion points, inverted rearrangements (21%), 5′ truncation (74%) and polyA tails (88%). Transcriptional consequences include expression of pseudogenes from UTRs or introns of target genes. In addition, a somatic pseudogene that integrated into the promoter and first exon of the tumour suppressor gene, MGA, abrogated expression from that allele. Thus, formation of processed pseudogenes represents a new class of mutation occurring during cancer development, with potentially diverse functional consequences depending on genomic context

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Matter in Mind

Elaborating a theory of consciousness that Kant made only partially explicit in the Transcendental Deduction of the Critique of Pure Reason, Richard E. Aquila offers a novel reading of Kant's theories of synthesis and conceptual rules, productive and reproductive imagination, the distinction between judgments of perception and experience, and the relations between self and objects. Aquila builds on the Transcendental Aesthetic's view of the formation of intuitional consciousness out of sensory matter and proposes a theory of concept formation, in the Transcendental Deduction, out of analogously conceived bodies of imaginative matter. Kant is seen here as offering a formidable synthesis of the purely animal and the distinctively human in human consciousness

Representational Mind

While many works on Kant's theory of knowledge place primary emphasis on assessing the validity of Kant's arguments, Richard E. Aquila aims first at clarifying the meaning of basic claims and concepts as Kant himself understood them. Representational Mind offers an interpretation of some of the most fundamental epistemological distinctions that Kant drew: between matter and form, intuition and concept, and things in themselves and appearances. Aquila's analysis centers on a theory of consciousness as the conceptual determination of intentional objects, the structure of which is grounded in forms of intuition. This approach, which distinguishes between concepts as mere predicates of judgments and as representations that phenomenologically inform intuitions, leads to a fuller grasp of the role of conceptualization in thinking. Shedding new light on the meaning of Kant's Transcendental Aesthetic, Aquila also gives extended treatment to imag- ination and schematism. The concluding chapter is devoted to the problem of self- awareness and the flow of time . An important contribution to the dialogue between phenomenological and analytical perspectives, Representational Mind will be of interest to scholars and students concerned with the history of modern philosophy and with philosophical problems involving the nature of mind and the intentionality of consciousness

Mitochondrial fission induces glycolytic reprogramming in cancer-associated myofibroblasts, driving stromal lactate production, and early tumor growth

Recent studies have suggested that cancer cells behave as metabolic parasites, by inducing oxidative stress in adjacent normal fibroblasts. More specifically, oncogenic mutations in cancer cells lead to ROS production and the secretion of hydrogen peroxide species. Oxidative stress in stromal fibroblasts then induces their metabolic conversion into cancer-associated fibroblasts. Such oxidative stress drives the onset of autophagy, mitophagy, and aerobic glycolysis in fibroblasts, resulting in the local production of high-energy mitochondrial fuels (such as L-lactate, ketone bodies, and glutamine). These recycled nutrients are then transferred to cancer cells, where they are efficiently burned via oxidative mitochondrial metabolism (OXPHOS). We have termed this new energy-transfer mechanism Two-Compartment Tumor Metabolism , to reflect that the production and consumption of nutrients (L-lactate and other catabolites) is highly compartmentalized. Thus, high-energy onco-catabolites are produced by the tumor stroma. Here, we used a genetic approach to stringently test this energy-transfer hypothesis. First, we generated hTERT-immortalized fibroblasts which were genetically re-programmed towards catabolic metabolism. Metabolic re-programming towards glycolytic metabolism was achieved by the recombinant over-expression of MFF (mitochondrial fission factor). MFF over-expression results in extensive mitochondrial fragmentation, driving mitochondrial dysfunction. Our results directly show that MFFfibroblasts undergo oxidative stress, with increased ROS production, and the onset of autophagy and mitophagy, both catabolic processes. Mechanistically, oxidative stress induces autophagy via NF-kB activation, also providing a link with inflammation. As a consequence MFF-fibroblasts showed intracellular ATP depletion and the extracellular secretion of L-lactate, a critical onco-catabolite. MFF-fibroblasts also showed signs of myofibroblast differentiation, with the expression of SMA and calponin. Importantly, MFF-fibroblasts signficantly promoted early tumor growth (up to 6.5-fold), despite a 20% overall reduction in angiogenesis. Thus, catabolic metabolism in cancer-associated fibroblasts may be a critical event during tumor intiation, allowing accelerated tumor growth, especially prior to the onset of neoangiogenesis