The Development of New Tools for the Investigation of Protein Function Using Photo-Reactive Unnatural Amino Acids

Reported here is the direct synthesis and application of unnatural amino acids for the development of exploratory tools for protein studies. This work takes advantage of an expanded genetic code to extract a more precise chemical understanding of protein function with novel additions to the unnatural amino acid catalogue, as well as the expansion of techniques with previously developed compounds. The photochemical crosslinker, [D11]-p-benzoylphenylalanine (pBpa), is synthesized for isotopic labeling in proteins. When [D11]-pBpa is co-incorporated into protein with [D0]-¬pBpa it is a mass spectral tool for rapid and conclusive identification of crosslinked fragments. Following enzymatic digestion the fingerprint of M, M+ 11 is readily identified allowing for rapid peak identification and the determined site of crosslink formation with single amino acid accuracy. In a means to extract a level of spatiotemporal control over fluorescent labeling of protein, the photo-protected unnatural amino acid, o-nitrobenzyl cysteine (ONBC), is introduced to a small amino acid tag sequence CCPGCC. This tag is required and specifically binds the pro-fluorescent compound 5-bis(1,3,2-dithiasolan-2-yl)fluorescein (FlAsH). This work takes advantage of the inability of FlAsH to bind the cysteine-tag motif in the presence of an ONBC mutation. The photo-protected amino acid is deprotected with light, affording natural cysteine and the successful binding of FlasH to the tetracysteine tag only following ultraviolet irradiation. Finally, fluorinated tyrosine derivatives are synthetically modified to contain photo-protecting groups, which act as a disguise during unnatural amino acid mutagenesis techniques. Fluorinated tyrosines are recognized by endogenous tyrosyl-tRNA synthetases and incorporated globally throughout a protein at tyrosine positions. To circumvent this problem the o-nitrobenzyl photo-protecting group is installed on the tyrosine derivatives 2-fluorotyrosine, 3-fluorotyrosine, and 2,6-difluorotyrosine. The directed evolution of an orthogonal amber-tRNA synthetase, specific for these unnatural amino acids, is performed, providing the translational machinery for site-specific incorporation of these compounds. Following expression of protein with the protected tyrosine derivatives, protein exposed to ultraviolet irradiation subsequently loses the protecting group affording the site-specific incorporation of fluorinated tyrosine. Fluorinated tyrosines are introduced to the critical trysoine residue in the chromophore of super-folder green fluorescent protein to determine how the altered pKa affects its fluorescent properties

A multi-analysis approach for estimating regional health impacts from the 2017 Northern California wildfires

Smoke impacts from large wildfires are mounting, and the projection is for more such events in the future as the one experienced October 2017 in Northern California, and subsequently in 2018 and 2020. Further, the evidence is growing about the health impacts from these events which are also difficult to simulate. Therefore, we simulated air quality conditions using a suite of remotely-sensed data, surface observational data, chemical transport modeling with WRF-CMAQ, one data fusion, and three machine learning methods to arrive at datasets useful to air quality and health impact analyses. To demonstrate these analyses, we estimated the health impacts from smoke impacts during wildfires in October 8–20, 2017, in Northern California, when over 7 million people were exposed to Unhealthy to Very Unhealthy air quality conditions. We investigated using the 5-min available GOES-16 fire detection data to simulate timing of fire activity to allocate emissions hourly for the WRF-CMAQ system. Interestingly, this approach did not necessarily improve overall results, however it was key to simulating the initial 12-hr explosive fire activity and smoke impacts. To improve these results, we applied one data fusion and three machine learning algorithms. We also had a unique opportunity to evaluate results with temporary monitors deployed specifically for wildfires, and performance was markedly different. For example, at the permanent monitoring locations, the WRF-CMAQ simulations had a Pearson correlation of 0.65, and the data fusion approach improved this (Pearson correlation = 0.95), while at the temporary monitor locations across all cases, the best Pearson correlation was 0.5. Overall, WRF-CMAQ simulations were biased high and the geostatistical methods were biased low. Finally, we applied the optimized PM2.5 exposure estimate in an exposure-response function. Estimated mortality attributable to PM2.5 exposure during the smoke episode was 83 (95% CI: 0, 196) with 47% attributable to wildland fire smoke. Implications: Large wildfires in the United States and in particular California are becoming increasingly common. Associated with these large wildfires are air quality and health impact to millions of people from the smoke. We simulated air quality conditions using a suite of remotely-sensed data, surface observational data, chemical transport modeling, one data fusion, and three machine learning methods to arrive at datasets useful to air quality and health impact analyses from the October 2017 Northern California wildfires. Temporary monitors deployed for the wildfires provided an important model evaluation dataset. Total estimated regional mortality attributable to PM2.5 exposure during the smoke episode was 83 (95% confidence interval: 0, 196) with 47% of these deaths attributable to the wildland fire smoke. This illustrates the profound effect that even a 12-day exposure to wildland fire smoke can have on human health

Steep Faint-end Slopes of Galaxy Mass and Luminosity Functions at z>=6 and the Implications for Reionisation

We present the results of a numerical study comparing photometric and physical properties of simulated z=6-9 galaxies to the observations taken by the WFC3 instrument aboard the Hubble Space Telescope. Using cosmological hydrodynamical simulations we find good agreement with observations in color-color space at all studied redshifts. We also find good agreement between observations and our Schechter luminosity function fit in the observable range, Muv<= -18, provided that a moderate dust extinction effect exists for massive galaxies. However beyond what currently can be observed, simulations predict a very large number of low-mass galaxies and evolving steep faint-end slopes from alpha_L = -2.15 at z=6 to alpha_L = -2.64 at z=9, with a dependence of |alpha_L| \propto (1+z)^0.59. During the same epoch, the normalization phi* increases and the characteristic magnitude Muv* becomes moderately brighter with decreasing redshift. We find similar trends for galaxy stellar mass function with evolving low-mass end slope from alpha_M = - 2.26 at z=6 to alpha_M = -2.87 at z=9, with a dependence of |alpha_M| \propto (1+z)^0.65. Together with our recent result on the high escape fraction of ionizing photons for low-mass galaxies, our results suggest that the low-mass galaxies are important contributor of ionizing photons for the reionisation of the Universe at z>=6.Comment: Revised metadata, 16 pages, 5 tables, 17 figures. MNRAS, in pres

Coherent correlation imaging for resolving fluctuating states of matter

Fluctuations and stochastic transitions are ubiquitous in nanometre-scale systems, especially in the presence of disorder. However, their direct observation has so far been impeded by a seemingly fundamental, signal-limited compromise between spatial and temporal resolution. Here we develop coherent correlation imaging (CCI) to overcome this dilemma. Our method begins by classifying recorded camera frames in Fourier space. Contrast and spatial resolution emerge by averaging selectively over same-state frames. Temporal resolution down to the acquisition time of a single frame arises independently from an exceptionally low misclassification rate, which we achieve by combining a correlation-based similarity metric1,2 with a modified, iterative hierarchical clustering algorithm3,4. We apply CCI to study previously inaccessible magnetic fluctuations in a highly degenerate magnetic stripe domain state with nanometre-scale resolution. We uncover an intricate network of transitions between more than 30 discrete states. Our spatiotemporal data enable us to reconstruct the pinning energy landscape and to thereby explain the dynamics observed on a microscopic level. CCI massively expands the potential of emerging high-coherence X-ray sources and paves the way for addressing large fundamental questions such as the contribution of pinning5–8 and topology9–12 in phase transitions and the role of spin and charge order fluctuations in high-temperature superconductivity13,14

A Maternal–Offspring Coadaptation Theory for the Evolution of Genomic Imprinting

Imprinted genes are expressed either from the maternally or paternally inherited copy only, and they play a key role in regulating complex biological processes, including offspring development and mother–offspring interactions. There are several competing theories attempting to explain the evolutionary origin of this monoallelic pattern of gene expression, but a prevailing view has emerged that holds that genomic imprinting is a consequence of conflict between maternal and paternal gene copies over maternal investment. However, many imprinting patterns and the apparent overabundance of maternally expressed genes remain unexplained and may be incompatible with current theory. Here we demonstrate that sole expression of maternal gene copies is favored by natural selection because it increases the adaptive integration of offspring and maternal genomes, leading to higher offspring fitness. This novel coadaptation theory for the evolution of genomic imprinting is consistent with results of recent studies on epigenetic effects, and it provides a testable hypothesis for the origin of previously unexplained major imprinting patterns across different taxa. In conjunction with existing hypotheses, our results suggest that imprinting may have evolved due to different selective pressures at different loci

Duty Cycle and the Increasing Star Formation History of z>=6 Galaxies

We examine the duty cycle and the history of star formation (SFH) for high-redshift galaxies at z>=6 using cosmological hydrodynamic simulations. We find that, even though individual galaxies have bursty SFH, the averaged SFH between z~15 to z=6 can be characterized well by either an exponentially increasing functional form with characteristic time-scales of 70 Myr to 200 Myr for galaxies with stellar masses Ms~10^6 Msun to >10^10 Msun respectively, or by a simple power-law form which exhibits a similar mass dependent time-scales. Using the SFH of individual galaxies, we measure the duty cycle of star formation (DC_SFH); i.e., the fraction of time a galaxy of a particular mass spends above a star formation rate (SFR) threshold which would make it observable to the Hubble Space Telescope (HST) during a given epoch. We also examine the fraction of galaxies at a given redshift that are brighter than a rest-frame UV magnitude (Muv ~ -18), which is sufficient enough to make them observable (DC_Muv). We find that both DC_SFH and DC_Muv make a sharp transition from zero (for galaxies with Ms 10^9 Msun). The measured duty cycle is also manifested in the intrinsic scatter in the Ms-SFR relationship (~ 1 dex) and Ms-Muv relationship (\Delta Muv ~ +-1 mag). We provide analytic fits to the DC as a function of Ms using a sigmoid function, which can be used to correct for catalogue incompleteness. We consider the effects of duty cycle to the observational estimate of galaxy stellar mass functions (GSMF) and the star formation rate density (SFRD), and find that it results in a much shallower low-mass end slopes of the GSMF and a reduction of >~ 70% of our intrinsic SFRD, making our simulation results more compatible with observational estimates.Comment: 13 pages, 11 figures, 5 tables. Accepted for publication MNRA

Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions

BACKGROUND: Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previously been provided in a broad array of diverse formats, making access to this very difficult. The publication and wide implementation of the Human Proteome Organisation Proteomics Standards Initiative Molecular Interactions (HUPO PSI-MI) format in 2004 was a major step towards the establishment of a single, unified format by which molecular interactions should be presented, but focused purely on protein-protein interactions. RESULTS: The HUPO-PSI has further developed the PSI-MI XML schema to enable the description of interactions between a wider range of molecular types, for example nucleic acids, chemical entities, and molecular complexes. Extensive details about each supported molecular interaction can now be captured, including the biological role of each molecule within that interaction, detailed description of interacting domains, and the kinetic parameters of the interaction. The format is supported by data management and analysis tools and has been adopted by major interaction data providers. Additionally, a simpler, tab-delimited format MITAB2.5 has been developed for the benefit of users who require only minimal information in an easy to access configuration. CONCLUSION: The PSI-MI XML2.5 and MITAB2.5 formats have been jointly developed by interaction data producers and providers from both the academic and commercial sector, and are already widely implemented and well supported by an active development community. PSI-MI XML2.5 enables the description of highly detailed molecular interaction data and facilitates data exchange between databases and users without loss of information. MITAB2.5 is a simpler format appropriate for fast Perl parsing or loading into Microsoft Excel

COSMOS-Web: Intrinsically Luminous z≳\gtrsim10 Galaxy Candidates Test Early Stellar Mass Assembly

We report the discovery of 15 exceptionally luminous $10\lesssim z\lesssim14$ candidate galaxies discovered in the first 0.28 deg$^2$ of JWST/NIRCam imaging from the COSMOS-Web Survey. These sources span rest-frame UV magnitudes of $-20.5>M_{\rm UV}>-22$, and thus constitute the most intrinsically luminous $z\gtrsim10$ candidates identified by JWST to-date. Selected via NIRCam imaging with Hubble ACS/F814W, deep ground-based observations corroborate their detection and help significantly constrain their photometric redshifts. We analyze their spectral energy distributions using multiple open-source codes and evaluate the probability of low-redshift solutions; we conclude that 12/15 (80%) are likely genuine $z\gtrsim10$ sources and 3/15 (20%) likely low-redshift contaminants. Three of our $z\sim12$ candidates push the limits of early stellar mass assembly: they have estimated stellar masses $\sim5\times10^{9}\,M_\odot$, implying an effective stellar baryon fraction of $\epsilon_{\star}\sim0.2-0.5$, where $\epsilon_{\star}\equiv M_{\star}/(f_{b}M_{halo})$. The assembly of such stellar reservoirs is made possible due to rapid, burst-driven star formation on timescales $<$100\,Myr where the star-formation rate may far outpace the growth of the underlying dark matter halos. This is supported by the similar volume densities inferred for $M_\star\sim10^{10}\,M_\odot$ galaxies relative to $M_\star\sim10^{9}\,M_\odot$ -- both about $10^{-6}$ Mpc$^{-3}$ -- implying they live in halos of comparable mass. At such high redshifts, the duty cycle for starbursts would be of order unity, which could cause the observed change in the shape of the UVLF from a double powerlaw to Schechter at $z\approx8$. Spectroscopic redshift confirmation and ensuing constraints of their masses will be critical to understanding how, and if, such early massive galaxies push the limits of galaxy formation in $\Lambda$CDM.Comment: 30 pages, 9 figures; ApJ submitte

Unveiling the distant Universe: Characterizing z≥9z\ge9 Galaxies in the first epoch of COSMOS-Web

We report the identification of 15 galaxy candidates at $z\ge9$ using the initial COSMOS-Web JWST observations over 77 arcmin$^2$ through four NIRCam filters (F115W, F150W, F277W, F444W) with an overlap with MIRI (F770W) of 8.7 arcmin$^2$. We fit the sample using several publicly-available SED fitting and photometric redshift codes and determine their redshifts between $z=9.3$ and $z=10.9$ ($\langle z\rangle=10.0$), UV-magnitudes between M$_{\rm UV}$ = $-$21.2 and $-$19.5 (with $\langle$M$_{\rm UV}\rangle=-20.2$) and rest-frame UV slopes ($\langle \beta\rangle=-2.4$). These galaxies are, on average, more luminous than most $z\ge9$ candidates discovered by JWST so far in the literature, while exhibiting similar blue colors in their rest-frame UV. The rest-frame UV slopes derived from SED-fitting are blue ($\beta\sim$[$-$2.0, $-$2.7]) without reaching extremely blue values as reported in other recent studies at these redshifts. The blue color is consistent with models that suggest the underlying stellar population is not yet fully enriched in metals like similarly luminous galaxies in the lower redshift Universe. The derived stellar masses with $\langle \log_{\rm 10} ($M$_\star/$M$_\odot)\rangle\approx8-9$ are not in tension with the standard $\Lambda$CDM model and our measurement of the volume density of such UV luminous galaxies aligns well with previously measured values presented in the literature at $z\sim9-10$. Our sample of galaxies, although compact, are significantly resolved.Comment: Submitted to Ap