Abstract: The magnitude of aerosol radiative forcing caused by anthropogenic emissions depends on the baseline state of the atmosphere under pristine preindustrial conditions. Measurements show that particle formation in atmospheric conditions can occur solely from biogenic vapors. Here, we evaluate the potential effect of this source of particles on preindustrial cloud condensation nuclei (CCN) concentrations and aerosol–cloud radiative forcing over the industrial period. Model simulations show that the pure biogenic particle formation mechanism has a much larger relative effect on CCN concentrations in the preindustrial atmosphere than in the present atmosphere because of the lower aerosol concentrations. Consequently, preindustrial cloud albedo is increased more than under present day conditions, and therefore the cooling forcing of anthropogenic aerosols is reduced. The mechanism increases CCN concentrations by 20–100% over a large fraction of the preindustrial lower atmosphere, and the magnitude of annual global mean radiative forcing caused by changes of cloud albedo since 1750 is reduced by 0.22   W   m − 2 (27%) to − 0.60   W   m − 2 . Model uncertainties, relatively slow formation rates, and limited available ambient measurements make it difficult to establish the significance of a mechanism that has its dominant effect under preindustrial conditions. Our simulations predict more particle formation in the Amazon than is observed. However, the first observation of pure organic nucleation has now been reported for the free troposphere. Given the potentially significant effect on anthropogenic forcing, effort should be made to better understand such naturally driven aerosol processes.

Abstract: De novo mutations (DNMs), or mutations that appear in an individual despite not being seen in their parents, are an important source of genetic variation whose impact is relevant to studies of human evolution, genetics, and disease. Utilizing high-coverage whole-genome sequencing data as part of the Trans-Omics for Precision Medicine (TOPMed) Program, we called 93,325 single-nucleotide DNMs across 1,465 trios from an array of diverse human populations, and used them to directly estimate and analyze DNM counts, rates, and spectra. We find a significant positive correlation between local recombination rate and local DNM rate, and that DNM rate explains a substantial portion (8.98 to 34.92%, depending on the model) of the genome-wide variation in population-level genetic variation from 41K unrelated TOPMed samples. Genome-wide heterozygosity does correlate with DNM rate, but only explains 〈 1% of variation. While we are underpowered to see small differences, we do not find significant differences in DNM rate between individuals of European, African, and Latino ancestry, nor across ancestrally distinct segments within admixed individuals. However, we did find significantly fewer DNMs in Amish individuals, even when compared with other Europeans, and even after accounting for parental age and sequencing center. Specifically, we found significant reductions in the number of C→A and T→C mutations in the Amish, which seem to underpin their overall reduction in DNMs. Finally, we calculated near-zero estimates of narrow sense heritability ( h 2 ), which suggest that variation in DNM rate is significantly shaped by nonadditive genetic effects and the environment.

Abstract: Under the instruction of cell-fate–determining, DNA-binding transcription factors, chromatin-modifying enzymes mediate and maintain cell states throughout development in multicellular organisms. Currently, small molecules modulating the activity of several classes of chromatin-modifying enzymes are available, including clinically approved histone deacetylase (HDAC) and DNA methyltransferase (DNMT) inhibitors. We describe the genome-wide expression changes induced by 29 compounds targeting HDACs, DNMTs, histone lysine methyltransferases (HKMTs), and protein arginine methyltransferases (PRMTs) in pancreatic α- and β-cell lines. HDAC inhibitors regulate several hundred transcripts irrespective of the cell type, with distinct clusters of dissimilar activity for hydroxamic acids and orthoamino anilides. In contrast, compounds targeting histone methyltransferases modulate the expression of restricted gene sets in distinct cell types. For example, we find that G9a/GLP methyltransferase inhibitors selectively up-regulate the cholesterol biosynthetic pathway in pancreatic but not liver cells. These data suggest that, despite their conservation across the entire genome and in different cell types, chromatin pathways can be targeted to modulate the expression of selected transcripts.

Abstract: Nucleation and growth of aerosol particles from atmospheric vapors constitutes a major source of global cloud condensation nuclei (CCN). The fraction of newly formed particles that reaches CCN sizes is highly sensitive to particle growth rates, especially for particle sizes 〈 10 nm, where coagulation losses to larger aerosol particles are greatest. Recent results show that some oxidation products from biogenic volatile organic compounds are major contributors to particle formation and initial growth. However, whether oxidized organics contribute to particle growth over the broad span of tropospheric temperatures remains an open question, and quantitative mass balance for organic growth has yet to be demonstrated at any temperature. Here, in experiments performed under atmospheric conditions in the Cosmics Leaving Outdoor Droplets (CLOUD) chamber at the European Organization for Nuclear Research (CERN), we show that rapid growth of organic particles occurs over the range from − 25   ° C to 25   ° C. The lower extent of autoxidation at reduced temperatures is compensated by the decreased volatility of all oxidized molecules. This is confirmed by particle-phase composition measurements, showing enhanced uptake of relatively less oxygenated products at cold temperatures. We can reproduce the measured growth rates using an aerosol growth model based entirely on the experimentally measured gas-phase spectra of oxidized organic molecules obtained from two complementary mass spectrometers. We show that the growth rates are sensitive to particle curvature, explaining widespread atmospheric observations that particle growth rates increase in the single-digit-nanometer size range. Our results demonstrate that organic vapors can contribute to particle growth over a wide range of tropospheric temperatures from molecular cluster sizes onward.

Abstract: Across multiancestry groups, we analyzed Human Leukocyte Antigen (HLA) associations in over 176,000 individuals with Parkinson’s disease (PD) and Alzheimer’s disease (AD) versus controls. We demonstrate that the two diseases share the same protective association at the HLA locus. HLA-specific fine-mapping showed that hierarchical protective effects of HLA-DRB1 *04 subtypes best accounted for the association, strongest with HLA-DRB1 *04:04 and HLA-DRB1 *04:07, and intermediary with HLA-DRB1 *04:01 and HLA-DRB1 *04:03. The same signal was associated with decreased neurofibrillary tangles in postmortem brains and was associated with reduced tau levels in cerebrospinal fluid and to a lower extent with increased Aβ42. Protective HLA-DRB1 *04 subtypes strongly bound the aggregation-prone tau PHF6 sequence, however only when acetylated at a lysine (K311), a common posttranslational modification central to tau aggregation. An HLA-DRB1 *04-mediated adaptive immune response decreases PD and AD risks, potentially by acting against tau, offering the possibility of therapeutic avenues.

Abstract: The pathological end-state of Parkinson disease is well described from postmortem tissue, but there remains a pressing need to define early functional changes to susceptible neurons and circuits. In particular, mechanisms underlying the vulnerability of the dopamine neurons of the substantia nigra pars compacta (SNc) and the importance of protein aggregation in driving the disease process remain to be determined. To better understand the sequence of events occurring in familial and sporadic Parkinson disease, we generated bacterial artificial chromosome transgenic mice ( SNCA -OVX) that express wild-type α-synuclein from the complete human SNCA locus at disease-relevant levels and display a transgene expression profile that recapitulates that of endogenous α-synuclein. SNCA -OVX mice display age-dependent loss of nigrostriatal dopamine neurons and motor impairments characteristic of Parkinson disease. This phenotype is preceded by early deficits in dopamine release from terminals in the dorsal, but not ventral, striatum. Such neurotransmission deficits are not seen at either noradrenergic or serotoninergic terminals. Dopamine release deficits are associated with an altered distribution of vesicles in dopaminergic axons in the dorsal striatum. Aged SNCA -OVX mice exhibit reduced firing of SNc dopamine neurons in vivo measured by juxtacellular recording of neurochemically identified neurons. These progressive changes in vulnerable SNc neurons were observed independently of overt protein aggregation, suggesting neurophysiological changes precede, and are not driven by, aggregate formation. This longitudinal phenotyping strategy in SNCA -OVX mice thus provides insights into the region-specific neuronal disturbances preceding and accompanying Parkinson disease.

Abstract: Nm23 genes, which encode nucleoside diphosphate kinases, have been implicated in suppressing tumor metastasis. The motility of human breast carcinoma cells can be suppressed by transfection with wild-type nm23-H1 , but not by transfections with two nm23-H1 mutants, nm23-H1 S12OG and nm23-H1 P96S . Here we report that nm23-H1 can transfer a phosphate from its catalytic histidine to aspartate or glutamate residues on 43-kDa membrane proteins. One of the 43-kDa membrane proteins was not phosphorylated by either nm23-H1 P96S or nm23-H1 S120G , and another was phosphorylated much more slowly by nm23-H1 P96S and by nm23-H1 S120G than by wild-type nm23-H1. Nm23-H1 also can transfer phosphate from its catalytic histidine to histidines on ATP-citrate lyase and succinic thiokinase. The rates of phosphorylation of ATP-citrate lyase by nm23-H1 S120G and nm23-H1 P96S were similar to that by wild-type nm23-H1. The rate of phosphorylation of succinic thiokinase by nm23-H1 S120 was similar to that by wild-type nm23-H1, and the rate of phosphorylation of succinic thiokinase by nm23-H1 P96S was about half that by wild-type nm23-H1. Thus, the transfer of phosphate from nm23-H1 to aspartates or glutamates on other proteins appears to correlate better with the suppression of motility than does the transfer to histidines.

Abstract: Active Src localization at focal adhesions (FAs) is essential for cell migration. How this pool is linked mechanistically to the large pool of Src at late endosomes (LEs)/lysosomes (LY) is not well understood. Here, we used inducible Tsg101 gene deletion, TSG101 knockdown, and dominant-negative VPS4 expression to demonstrate that the localization of activated cellular Src and viral Src at FAs requires the endosomal-sorting complexes required for transport (ESCRT) pathway. Tsg101 deletion also led to impaired Src-dependent activation of STAT3 and focal adhesion kinase and reduced cell migration. Impairment of the ESCRT pathway or Rab7 function led to the accumulation of active Src at aberrant LE/LY compartments followed by its loss. Analyses using fluorescence recovery after photo-bleaching show that dynamic mobility of Src in endosomes is ESCRT pathway-dependent. These results reveal a critical role for an ESCRT pathway-dependent LE/LY trafficking step in Src function by promoting localization of active Src to FAs.

Abstract: We showed here that the radiochemical and radiobiological mechanisms and outcomes of fs IR laser-induced filamentation are equivalent to conventional ionizing radiation. Moreover, we have shown here that this (to our knowledge) conceptually unique approach to cancer therapy ( 5 ) may bring us one step closer to achieving the ultimate goal of radiation therapy: maximizing the energy dose inside the tumor volume while not exposing healthy tissue. Our IR laser pulses produce high-density avalanches of low-energy electrons via laser filamentation ( 3 , 4 ), a phenomenon that results in a spatial energy density and temporal dose rate that both exceed by several orders of magnitude any values previously reported even for the most intense clinical radiotherapy systems. We compared the effect of the laser filamentation with those of gamma radiation on thymidine decomposition, DNA damage, and a tumor in vivo. Our results show that ( a ) the type of final damage and its mechanisms in aqueous media are comparable to those of conventional ionizing radiation, and ( b ) laser irradiation method was more effective in treating tumors with respect to reducing their size and even eliminating them. Femtosecond laser filamentation paves the way for new applications of photonic processes in radiotherapy. By using intense ultra-short infrared (IR) laser pulses, a very large energy dose can now be deposited at unprecedented microscopic dose rates (up to 10 11  Gy/s) deep inside an adjustable, well-controlled macroscopic volume, without any dose deposit in front or behind the target volume. The macroscopic dose rate of the laser-induced filamentation process was determined here using two different chemical dosimeters. The spatial dose distribution, and hence the microscopic energy density and dose rate, of the laser-induced filamentation process was captured by a polymer gel dosimeter and visualized by magnetic resonance imaging (MRI). Our results clearly show that changing the duration of the laser pulse enables precise control of the distance in the medium over which the entrance dose is zero. The two counterbalanced processes keep the filament core intensity almost constant below the optical breakdown threshold, yielding a self-regulated generation of spatially homogenous low-density plasma spots along the propagation axis of the laser beam. This plasma makes it possible to produce a high rate of ionizations in the heart of such filaments while minimizing thermo-mechanical effects related to “hot” high-density plasmas. We propose that these ionizing properties of laser-induced filamentation give rise to changes in the medium that are equivalent to conventional therapeutic ionizing radiation. More importantly, the filamentation process deposits a large dose of energy localized deep inside a well-controlled macroscopic volume, because the depth at which filamentation begins and ends is regulated by operator-controlled laser pulse parameters. This process is related to the self-focusing of an intense laser pulse induced by the Kerr effect that is counterbalanced by the induction of self-defocusing induced by subsequent laser-plasma interactions. The Kerr effect is characterized by a nonlinear change in the refractive index of a medium such as water, which varies proportionately with the square of the electric field strength. Applied to intense laser pulses with Gaussian intensity profiles, this local, nonlinear change of refractive index acts as a convex lens and results in intense self-focusing of the laser beam along its propagation axis. Thus, after some propagation distance, the laser intensity becomes so high that it overcomes the thresholds for nonlinear ionization, generating local plasma. The interaction of the laser light with the highly defocusing environment created by this plasma will now diverge the laser beam, such that the resulting decrease in light intensity will arrest the process of plasma generation, thus allowing the laser pulse to undergo self-focusing again at a slightly deeper position along the laser pulse propagation axis. This dynamic equilibrium continues as long as the magnitude of the laser pulse intensity, which slowly decreases due to such energy transfers to the medium, allows nonlinear processes, such as the Kerr effect. Numerous biophotonics applications of ultra-fast lasers are available; however, they are not used for radiotherapy of tumors that reside within macroscopic distances inside human tissue. This is of interest, because many of the modern, long-wavelength, high-power lasers can deliver high-energy-density pulses (doses and dose rates), which, in principle, surpass those of any clinical radiation source. This raises fundamental questions: ( i ) Can lasers, non-linear optics, and near-visible photons (IR, visible) generate a true radiotherapeutic effect, not upon entry in the tissue, but at a macroscopic distance within a tissue? and (ii) Can IR lasers, in particular, which emit non-ionizing radiation, replace ionizing radiation (viz radioactive materials) in certain cancer treatments? Nonlinear energy deposition can occur during the propagation of a powerful femtosecond (fs) laser pulse in a medium such as water, when the intensity of the light is sufficiently high so that its electromagnetic field will strongly perturb and change the optical properties of the medium. Here, we propose that a nonlinear photonic process called filamentation ( Fig. P1 ) ( 3 , 4 ) can solve the main problem of radiotherapy, which is the undesirable dose distribution upon tissue entry. Fig. P1. Photographic illustration of the femtosecond laser pulses filamentation in water. Here, a scattering product (milk) was diluted at a weak concentration in water to visualize multiple filamentation, which results in an elongated sparkly glowing region in the figure. Scientifically speaking, due to the presence of the scattering product, multiple filamentation can be observed through the scattering of the supercontinuum white light generated by self-phase modulation and self-steepening of the laser pulses. The direction of laser beam propagation is from top to bottom. The camera was positioned at an angle of elevation of approximately 45° from the on-axis direction in order to capture both the filaments and the transmission of the supercontinuum strong spectral broadening at the rear side of a screen oriented perpendicularly across the laser propagation axis (circular spectral pattern at the bottom of the picture). Since the invention of cancer radiotherapy, its primary goal has been to maximize lethal radiation doses to the tumor volume while keeping the dose to surrounding healthy tissues at zero. Sadly, conventional radiation sources (γ- or X-rays, electrons) and methods used over the decades, including multiple or modulated beams, inevitably deposit the majority of their dose in front of or behind the tumor, thus damaging healthy tissue and causing secondary cancers years after treatment ( 1 ). Even the most recent pioneering advances in costly proton or carbon ion therapies can not completely avoid dose buildup in front of the tumor volume ( 2 ).

Abstract: Using a diverse collection of small molecules we recently found that compound sets from different sources (commercial; academic; natural) have different protein-binding behaviors, and these behaviors correlate with trends in stereochemical complexity for these compound sets. These results lend insight into structural features that synthetic chemists might target when synthesizing screening collections for biological discovery. We report extensive characterization of structural properties and diversity of biological performance for these compounds and expand comparative analyses to include physicochemical properties and three-dimensional shapes of predicted conformers. The results highlight additional similarities and differences between the sets, but also the dependence of such comparisons on the choice of molecular descriptors. Using a protein-binding dataset, we introduce an information-theoretic measure to assess diversity of performance with a constraint on specificity. Rather than relying on finding individual active compounds, this measure allows rational judgment of compound subsets as groups. We also apply this measure to publicly available data from ChemBank for the same compound sets across a diverse group of functional assays. We find that performance diversity of compound sets is relatively stable across a range of property values as judged by this measure, both in protein-binding studies and functional assays. Because building screening collections with improved performance depends on efficient use of synthetic organic chemistry resources, these studies illustrate an important quantitative framework to help prioritize choices made in building such collections.