Genome-scale transcriptional dynamics and environmental biosensing.

Genome-scale technologies have enabled mapping of the complex molecular networks that govern cellular behavior. An emerging theme in the analyses of these networks is that cells use many layers of regulatory feedback to constantly assess and precisely react to their environment. The importance of complex feedback in controlling the real-time response to external stimuli has led to a need for the next generation of cell-based technologies that enable both the collection and analysis of high-throughput temporal data. Toward this end, we have developed a microfluidic platform capable of monitoring temporal gene expression from over 2,000 promoters. By coupling the "Dynomics" platform with deep neural network (DNN) and associated explainable artificial intelligence (XAI) algorithms, we show how machine learning can be harnessed to assess patterns in transcriptional data on a genome scale and identify which genes contribute to these patterns. Furthermore, we demonstrate the utility of the Dynomics platform as a field-deployable real-time biosensor through prediction of the presence of heavy metals in urban water and mine spill samples, based on the the dynamic transcription profiles of 1,807 unique Escherichia coli promoters.

Fluence-induced reversal of saturable absorption in a ruthenium-based porphyrin.

Experimental nonlinear absorption data obtained using the open-aperture Z-scan technique are presented for 2, 3, 7, 8, 12, 17, 18-octaethyl-21H, 23H-porphine ruthenium (II) carbonyl in tetrahydrofuran. These data show saturation of nonlinear absorption dominating at low fluence but being overcome by induced absorption (reverse saturable absorption) at high fluence. Large-angle scattering measurements demonstrate that the induced absorption is real and not merely the result of scattering of light outside of the collection aperture of the detector by scattering centers induced at high fluence. A possible mechanism based on a four-band effective rate equation model is proposed. The model is used to accurately predict the results of Z scans taken at different pulse energies and to extract values for excited-state lifetimes and absorption cross sections from the experimental data.

Nonlinear optical characterization of multinuclear iridium compounds containing tricycloquinazoline.

Nonlinear optical properties were characterized for a series of multinuclear iridium compounds of the form TCQ[IrIII(ppz)2]n, where n=1, 2, or 3, TCQ is tricycloquinazoline, and ppz is 1-phenylpyrazole. Transient absorption (TA) spectroscopy indicated that the triplet metal-to-ligand charge transfer excited state was formed on a subpicosecond time scale and decayed back to the ground state on a microsecond time scale, consistent with precedents in the literature. TA bands were observed for all three compounds from 475 to 900 nm, implying the potential for reverse-saturable absorption (RSA) at those wavelengths. Z-scan measurements using picosecond and nanosecond pulses were obtained at 532 nm and confirmed the presence of RSA behavior for all three compounds. The triplet excited state cross sections and the RSA figure of merit were found to decrease with increasing n:1>2∼3.

A high-specific-strength and corrosion-resistant magnesium alloy.

Ultra-lightweight alloys with high strength, ductility and corrosion resistance are desirable for applications in the automotive, aerospace, defence, biomedical, sporting and electronic goods sectors. Ductility and corrosion resistance are generally inversely correlated with strength, making it difficult to optimize all three simultaneously. Here we design an ultralow density (1.4 g cm(-3)) Mg-Li-based alloy that is strong, ductile, and more corrosion resistant than Mg-based alloys reported so far. The alloy is Li-rich and a solute nanostructure within a body-centred cubic matrix is achieved by a series of extrusion, heat-treatment and rolling processes. Corrosion resistance from the environment is believed to occur by a uniform lithium carbonate film in which surface coverage is much greater than in traditional hexagonal close-packed Mg-based alloys, explaining the superior corrosion resistance of the alloy.

Strong triplet excited-state absorption in a phenanthrolinyl iridium(III) complex with benzothiazolylfluorenyl-substituted ligands.

Femtosecond transient difference absorption (fs TA) measurements, together with a series of open-aperture Z scans at picosecond and nanosecond pulse widths and a variety of pulse energies, were performed on a 1,10-phenanthrolinyl iridium(III) complex bearing ligands containing a benzothiazolylfluorenyl motif. An analysis of decay data from the fs TA experiment yields a value of 1.24±0.26 ns for the singlet excited-state lifetime τ(S) of the complex. By fitting the Z scans to a five-level dynamic model incorporating the independently measured value of τ(S) and previously reported values of the complex's triplet quantum yield (0.13) and triplet excited-state lifetime (230 ns), we obtain values of 3.5×10(-17) cm(2) (singlet) and 5.0×10(-16) cm(2) (triplet) for the excited-state absorption cross-sections of the complex in toluene solution at 532 nm; the latter value represents one of the largest triplet excited-state absorption cross-sections ever reported at this wavelength. The ratio of the triplet excited-state cross-section to the ground-state absorption cross-section exceeds 3800.

Antagonistic gene transcripts regulate adaptation to new growth environments.

Cells have evolved complex regulatory networks that reorganize gene expression patterns in response to changing environmental conditions. These changes often involve redundant mechanisms that affect various levels of gene expression. Here, we examine the consequences of enhanced mRNA degradation in the galactose utilization network of Saccharomyces cerevisiae. We observe that glucose-induced degradation of GAL1 transcripts provides a transient growth advantage to cells upon addition of glucose. We show that the advantage arises from relief of translational competition between GAL1 transcripts and those of cyclin CLN3, a translationally regulated initiator of cell division. This competition creates a translational bottleneck that balances the production of Gal1p and Cln3p and represents a posttranscriptional control mechanism that enhances the cell's ability to adapt to changes in carbon source. We present evidence that the spatial regulation of GAL1 and CLN3 transcripts is what allows growth to be maintained during fluctuations of glucose availability. Our results provide unique insights into how cells optimize energy use during growth in a dynamic environment.

Ultrahigh specific strength in a magnesium alloy strengthened by spinodal decomposition.

Strengthening of magnesium (Mg) is known to occur through dislocation accumulation, grain refinement, deformation twinning, and texture control or dislocation pinning by solute atoms or nano-sized precipitates. These modes generate yield strengths comparable to other engineering alloys such as certain grades of aluminum but below that of high-strength aluminum and titanium alloys and steels. Here, we report a spinodal strengthened ultralightweight Mg alloy with specific yield strengths surpassing almost every other engineering alloy. We provide compelling morphological, chemical, structural, and thermodynamic evidence for the spinodal decomposition and show that the lattice mismatch at the diffuse transition region between the spinodal zones and matrix is the dominating factor for enhancing yield strength in this class of alloy.

Circadian rhythms in Neurospora crassa: dynamics of the clock component frequency visualized using a fluorescent reporter.

The frequency (frq) gene of Neurospora crassa has long been considered essential to the function of this organism's circadian rhythm. Increasingly, deciphering the coupling of core oscillator genes such as frq to the output pathways of the circadian rhythm has become a major focus of circadian research. To address this coupling it is critical to have a reporter of circadian activity that can deliver high resolution spatial and temporal information about the dynamics of core oscillatory proteins such as FRQ. However, due to the difficulty of studying the expression of circadian rhythm genes in aerobic N. crassa cultures, little is known about the dynamics of this gene under physiologically realistic conditions. To address these issues we report a fluorescent fusion to the frq gene using a codon optimized version of the mCherry gene. To trace the expression and accumulation of FRQ-mCherryNC (FRQ-mCh) during the circadian rhythm, growing vegetative hyphae were scanned every hour under confocal microscopy (100x). Fluorescence of FRQ-mCh was detected only at the growing edge of the colony, and located in the cytoplasm and nuclei of vegetative hyphae for a distance of approximately 150-200microm from the apices of leading hyphae. When driven by the frq promoter, apparently there was also a second FRQ entrance into the nucleus during the circadian cycle; however the second entrance had a lower accumulation level than the first entrance. Thus this fluorescent fusion protein has proven useful in tracking the spatial dynamics of the frq protein and has indicated that the dynamics of the FRQ protein's nuclear trafficking may be more complex than previously realized.

Excited-state absorption of a bipyridyl platinum(II) complex with alkynyl-benzothiazolylfluorene units.

The singlet excited-state lifetime of a bipyridyl platinum(II) complex containing two alkynyl-benzothiazolylfluorene units was determined to be 145+/-105 ps by fitting femtosecond transient difference absorption data, and the triplet quantum yield was measured to be 0.14. A ground-state absorption cross section of 6.1 x 10(-19) cm(2) at 532 nm was deduced from UV-visible absorption data. Excited-state absorption cross sections of (6.7+/-0.1) x 10(-17) cm(2) (singlet) and (4.6+/-0.1) x 10(-16) cm(2) (triplet) were obtained by using a five-level dynamic model to fit open-aperture Z scans at picosecond and nanosecond pulse widths and a variety of pulse energies. For this complex, the ratio of the triplet excited-state absorption cross section to the ground-state absorption cross section--long used as a figure of merit for reverse saturable absorbers--thus stands at 754, to our knowledge the largest ever reported at 532 nm wavelength.

Precipitation strengthening in an ultralight magnesium alloy.

Body-centred cubic magnesium-lithium-aluminium-base alloys are the lightest of all the structural alloys, with recently developed alloy compositions showing a unique multi-dimensional property profile. By hitherto unrecognised mechanisms, such alloys also exhibit exceptional immediate strengthening after solution treatment and water quenching, but strength eventually decreases during prolonged low temperature ageing. We show that such phenomena are due to the precipitation of semi-coherent D03-Mg3Al nanoparticles during rapid cooling followed by gradual coarsening and subsequent loss of coherency. Physical explanation of these phenomena allowed the creation of an exceptionally low-density alloy that is also structurally stable by controlling the lattice mismatch and volume fraction of the Mg3Al nanoparticles. The outcome is one of highest specific-strength engineering alloys ever developed.

A molecular noise generator.

Recent studies have demonstrated that intracellular variations in the rate of gene expression are of fundamental importance to cellular function and development. While such 'noise' is often considered detrimental in the context of perturbing genetic systems, it can be beneficial in processes such as species diversification and facilitation of evolution. A major difficulty in exploring such effects is that the magnitude and spectral properties of the induced variations arise from some intrinsic cellular process that is difficult to manipulate. Here, we present two designs of a molecular noise generator that allow for the flexible modulation of the noise profile of a target gene. The first design uses a dual-signal mechanism that enables independent tuning of the mean and variability of an output protein. This is achieved through the combinatorial control of two signals that regulate transcription and translation separately. We then extend the design to allow for DNA copy-number regulation, which leads to a wider tuning spectrum for the output molecule. To gain a deeper understanding of the circuit's functionality in a realistic environment, we introduce variability in the input signals in order to ascertain the degree of noise induced by the control process itself. We conclude by illustrating potential applications of the noise generator, demonstrating how it could be used to ascertain the robust or fragile properties of a genetic circuit.

Segmentation of 3D EBSD data for subgrain boundary identification and feature characterization.

Subgrain structures formed during plastic deformation of metals can be observed by electron backscatter diffraction (EBSD) but are challenging to identify automatically. We have adapted a 2D image segmentation technique, fast multiscale clustering (FMC), to 3D EBSD data using a novel variance function to accommodate quaternion data. This adaptation, which has been incorporated into the free open source texture analysis software package MTEX, is capable of segmenting based on subtle and gradual variation as well as on sharp boundaries within the data. FMC has been further modified to group the resulting closed 3D segment boundaries into distinct coherent surfaces based on local normals of a triangulated surface. We demonstrate the excellent capabilities of this technique with application to 3D EBSD data sets generated from cold rolled aluminum containing well-defined microbands, cold rolled and partly recrystallized extra low carbon steel microstructure containing three magnitudes of boundary misorientations, and channel-die plane strain compressed Goss-oriented nickel crystal containing microbands with very subtle changes in orientation.

Quantitative in vitro assessment of Mg65 Zn30 Ca5 degradation and its effect on cell viability.

A bulk metallic glass (BMG) of composition Mg(65) Zn(30) Ca(5) was cast directly from the melt and explored as a potential bioresorbable metallic material. The in vitro degradation behavior of the amorphous alloy and its associated effects on cellular activities were assessed against pure crystalline magnesium. Biocorrosion tests using potentiodynamic polarization showed that the amorphous alloy corroded at a much slower rate than the crystalline Mg. Analysis of the exchanged media using inductively coupled plasma optical emission spectrometry revealed that the dissolution rate of Mg ions in the BMG was 446 µg/cm(2)/day, approximately half the rate of crystalline Mg (859 µg/cm(2)/day). A cytotoxicity study, using L929 murine fibroblasts, revealed that both the BMG and pure Mg are capable of supporting cellular activities. However, direct contact with the samples created regions of minimal cell growth around both amorphous and crystalline samples, and no cell attachment was observed.

Boundary identification in EBSD data with a generalization of fast multiscale clustering.

Electron backscatter diffraction (EBSD) studies of cellular or subgrain microstructures present problems beyond those in the study of coarse-grained polycrystalline aggregates. In particular, identification of boundaries delineating some subgrain structures, such as microbands, cannot be accomplished simply with pixel-to-pixel misorientation thresholding because many of the boundaries are gradual transitions in crystallographic orientation. Fast multiscale clustering (FMC) is an established data segmentation technique that is combined here with quaternion representation of orientation to segment EBSD data with gradual transitions. This implementation of FMC addresses a common problem with segmentation algorithms, handling data sets with both high and low magnitude boundaries, by using a novel distance function that is a modification of Mahalanobis distance. It accommodates data representations, such as quaternions, whose features are not necessarily linearly correlated but have known distance functions. To maintain the linear run time of FMC with such data, the method requires a novel variance update rule. Although FMC was originally an algorithm for two-dimensional data segmentation, it can be generalized to analyze three-dimensional data sets. As examples, several segmentations of quaternion EBSD data sets are presented.

Excited-state absorption in a terpyridyl platinum(II) pentynyl complex.

The singlet excited-state lifetime of a terpyridyl platinum(II) pentynyl complex was determined to be 268+/-87 ps by fitting femtosecond transient absorption data, the triplet excited-state lifetime was found to be 62 ns by fitting nanosecond transient absorption decay data, and the triplet quantum yield was measured to be 0.16. A ground-state absorption cross section of 2.5 x 10(-19) cm(2) at 532 nm was deduced from UV-vis absorption data. Excited-state absorption cross sections of 3.5 x 10(-17) cm(2) (singlet) and 4.5 x 10(-17) cm(2) (triplet) were obtained by using a five-level dynamic model to fit open-aperture Z scans at picosecond and nanosecond pulse widths and a variety of pulse energies.