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Experimental restrictions imposed on the collection and detection of shortwave-infrared photons (SWIR) have impeded single molecule work on a large class of materials whose optical activity lies in the SWIR. Here we report the successful observation of room-temperature single nanocrystal photoluminescence at SWIR wavelengths using a highly efficient multielement superconducting nanowire single photon detector. We confirm that the photoluminescence from single lead sulfide nanocrystals is strongly antibunched, demonstrating the feasibility of performing sophisticated photon correlation experiments on individual weak SWIR emitters, and, more broadly, paving the way for sensitive measurements of spectral observables on infrared quantum systems that are incompatible with current detection techniques.

We report the formation and photonic properties of CdSe/ZnS quantum dot (QD)/J-aggregate donor−acceptor Forster resonant energy transfer (FRET) pairs that are electrostatically bound and dispersed in water. Assembly occurs when the positively charged dye, 1,1′,3,3′-tetraethyl-5,5′,6,6′-tetrachlorobenzimidazolocarbocyanine (TTBC), binds electrostatically to QDs that are coated with a negatively charged amphiphilic polymer. QD/J-aggregate FRET pairs display the broadband absorption in the visible and the ultraviolet (UV) part of the spectrum typical of quantum dots, along with the narrow emission linewidths characteristic of J-band emitters (∼12 nm full width at half-maximum). We use dynamic light scattering, transmission electron microscopy, photoluminescence spectroscopy, and photoluminescence lifetimes to conclude that the size of the aggregates formed in the presence of QDs is between 1−6 nm. We find the FRET radius of the QD/J-aggregate to be 5.1 nm. We further demonstrate electrostatic binding as a ge...

Populations of cultured mouse embryonic stem cells (ESCs) exhibit a subfraction of cells expressing uncharacteristically low levels of pluripotency markers such as Nanog. Yet, the extent to which individual Nanog-negative cells are differentiated, both from ESCs and from each other, remains unclear. Here, we show the transcriptome of Nanog-negative cells exhibits expression of classes of genes associated with differentiation that are not yet active in cells exposed to differentiation conditions for one day. Long non-coding RNAs, however, exhibit more changes in expression in the one-day-differentiated cells than in Nanog-negative cells. These results are consistent with the concept that Nanog-negative cells may contain subpopulations of both lineage-primed and differentiated cells. Single cell analysis showed that Nanog-negative cells display substantial and coherent heterogeneity in lineage marker expression in progressively nested subsets of cells exhibiting low levels of Nanog, then low levels of Oct4 and then a set of lineage markers, which express intensely in a small subset of these more differentiated cells. Our results suggest that the observed enrichment of lineage-specific marker gene expression in Nanog-negative cells is associated with spontaneous differentiation of a subset of these cells rather than the more random expression that may be associated with reversible lineage priming.

Individual mammalian cells exhibit large variability in cellular volume even with the same absolute DNA content and so must compensate for differences in DNA concentration in order to maintain constant concentration of gene expression products. Using single molecule counting and computational image analysis, we show that transcript abundance correlates with cellular volume at the single cell level due to increased global transcription in larger cells. Cell fusion experiments establish that increased cellular content itself can directly increase transcription. Quantitative analysis shows that this mechanism measures the ratio of cellular volume to DNA content, mostly likely through sequestration of a transcriptional factor to DNA. Analysis of transcriptional bursts reveals a separate mechanism for gene dosage compensation after DNA replication that enables proper transcriptional output during early and late S-phase. Our results provide a framework for quantitatively understanding the relationships between DNA content, cell size and gene expression variability in single cells.

While many transcriptional regulators of pluripotent and terminally differentiated states have been identified, regulation of intermediate progenitor states is less well understood. Previous high throughput cellular resolution expression studies identified dozens of transcription factors with lineage-specific expression patterns in C. elegans embryos that could regulate progenitor identity. In this study we identified a broad embryonic role for the C. elegans OTX transcription factor ceh-36, which was previously shown to be required for the terminal specification of four neurons. ceh-36 is expressed in progenitors of over 30% of embryonic cells, yet is not required for embryonic viability. Quantitative phenotyping by computational analysis of time-lapse movies of ceh-36 mutant embryos identified cell cycle or cell migration defects in over 100 of these cells, but most defects were low-penetrance, suggesting redundancy. Expression of ceh-36 partially overlaps with that of the PITX transcription factor unc-30. unc-30 single mutants are viable but loss of both ceh-36 and unc-30 causes 100% lethality, and double mutants have significantly higher frequencies of cellular developmental defects in the cells where their expression normally overlaps. These factors are also required for robust expression of the downstream developmental regulator mls-2/HMX. This work provides the first example of genetic redundancy between the related yet evolutionarily distant OTX and PITX families of bicoid class homeodomain factors and demonstrates the power of quantitative developmental phenotyping in C. elegans to identify developmental regulators acting in progenitor cells., Author Summary Animals develop as one initial cell, the fertilized egg, repeatedly divides and its progeny differentiate, ultimately producing diverse cell types. This occurs in large part by the expression of unique combinations of regulatory genes, such as transcription factors, in precursors of each cell type. These early factors are typically reused in precursors of different cell types. The nematode worm Caenorhabditis elegans is a powerful system in which to identify developmental regulators because it has a rapid and reproducible development, yet it shares most of its developmental regulators with more complex organisms such as humans. We used state-of-the-art microscopy and computer-aided cell tracking methods to identify the developmental role of worm homologs of the OTX and PITX genes, whose human homologs play a role in the development of the brain, eye, and pituitary among other tissues. We identified broad roles for OTX in regulating development for many distinct cell types including muscles, neurons and skin, and found a redundant role for both OTX and PITX in a subset of cells. Future studies of these genes should address whether these genes also act redundantly in mammals.

The termolecular association reaction OH + NO2 + M was studied in a low-pressure discharge flow reactor, and both HONO2 and HOONO products were detected by infrared cavity ringdown spectroscopy (IR-CRDS). The absorption spectrum of the fundamental ν1 band of the cis-cis isomer of HOONO (pernitrous or peroxynitrous acid) was observed at 3306 cm-1, in good agreement with matrix isolation studies and ab initio predictions. The rotational contour of this band was partially resolved at 1 cm-1 resolution and matched the profile predicted by ab initio calculations. The integrated absorbances of the ν1 bands of the cis-cis HOONO and HONO2 products were measured as a function of temperature and pressure. These were converted to product branching ratios by scaling the experimentally observed absorbances with ab initio integrated cross sections for HOONO and HONO2 computed at the CCSD(T)/cc-pVTZ level. The product branching ratio for cis-cis HOONO to HONO2 was 0.075 ± 0.020(2σ) at room temperature in a 20 Torr mixtu...

Cell differentiation and proliferation are coordinated during animal development, but the link between them remains uncharacterized. To examine this relationship, we combined single-molecule RNA imaging with time-lapse microscopy to generate high-resolution measurements of transcriptional dynamics in Caenorhabditis elegans embryogenesis. We found that globally slowing the overall development rate of the embryo by altering temperature or by mutation resulted in cell proliferation and transcription slowing, but maintaining, their relative timings, suggesting that cell division may directly control transcription. However, using mutants with specific defects in cell cycle pathways that lead to abnormal lineages, we found that the order between cell divisions and expression onset can switch, showing that expression of developmental regulators is not strictly dependent on cell division. Delaying cell divisions resulted in only slight changes in absolute expression time, suggesting that expression and proliferation are independently entrained to a separate clock-like process. These changes in relative timing can change the number of cells expressing a gene at a given time, suggesting that timing may help determine which cells adopt particular transcriptional patterns. Our results place limits on the types of mechanisms that are used during normal development to ensure that division timing and fate specification occur at appropriate times.

Tumor endothelial marker 1 (TEM1; also known as endosialin or CD248) is a protein found on tumor vasculature and in tumor stroma. Here, we tested whether TEM1 has potential as a therapeutic target for cancer immunotherapy by immunizing immunocompetent mice with Tem1 cDNA fused to the minimal domain of the C fragment of tetanus toxoid (referred to herein as Tem1-TT vaccine). Tem1-TT vaccination elicited CD8+ and/or CD4+ T cell responses against immunodominant TEM1 protein sequences. Prophylactic immunization of animals with Tem1-TT prevented or delayed tumor formation in several murine tumor models. Therapeutic vaccination of tumor-bearing mice reduced tumor vascularity, increased infiltration of CD3+ T cells into the tumor, and controlled progression of established tumors. Tem1-TT vaccination also elicited CD8+ cytotoxic T cell responses against murine tumor-specific antigens. Effective Tem1-TT vaccination did not affect angiogenesis-dependent physiological processes, including wound healing and reproduction. Based on these data and the widespread expression of TEM1 on the vasculature of different tumor types, we conclude that targeting TEM1 has therapeutic potential in cancer immunotherapy.

Cellular messenger RNA levels are achieved by the combinatorial complexity of factors controlling transcription, yet the small number of molecules involved in these pathways fluctuates stochastically. It has not yet been experimentally possible to observe the activity of single polymerases on an endogenous gene to elucidate how these events occur in vivo. Here, we describe a method of fluctuation analysis of fluorescently labeled RNA to measure dynamics of nascent RNA—including initiation, elongation, and termination—at an active yeast locus. We find no transcriptional memory between initiation events, and elongation speed can vary by threefold throughout the cell cycle. By measuring the abundance and intranuclear mobility of an upstream transcription factor, we observe that the gene firing rate is directly determined by trans-activating factor search times.

This article presents a perspective on the experimental and theoretical work to date on the efficiency of carrier multiplication (CM) in colloidal semiconductor nanocrystals (NCs). Early reports on CM in NCs suggested large CM efficiency enhancements. However, recent experiments have shown that CM in nanocrystalline samples is not significantly stronger, and often is weaker, than in the parent bulk when compared on an absolute photon energy basis. This finding is supported by theoretical consideration of the CM process and the competing intraband relaxation. We discuss the experimental artifacts that may have led to the apparently strong CM estimated in early reports. The finding of bulklike CM in NCs suggests that the main promise of quantum confinement is to boost the photovoltage at which carriers can be extracted. With this in mind, we discuss research directions that may result in effective use of CM in a solar cell.

Biexciton properties strongly affect the usability of a light emitter in quantum photon sources and lasers but are difficult to measure for single fluorophores at room temperature due to luminescence intermittency and bleaching at the high excitation fluences usually required. Here, we observe the biexciton (BX) to exciton (X) to ground photoluminescence cascade of single colloidal semiconductor nanocrystals (NCs) under weak excitation in a g((2)) photon correlation measurement and show that the normalized amplitude of the cascade feature is equal to the ratio of the BX to X fluorescence quantum yields. This imposes a limit on the attainable depth of photon antibunching and provides a robust means to study single emitter biexciton physics. In NC samples, we show that the BX quantum yield is considerably inhomogeneous, consistent with the defect sensitivity expected of the Auger nonradiative recombination mechanism. The method can be extended to study X,BX spectral and polarization correlations.

Cell differentiation and cell proliferation are coordinated during animal development by mechanisms that remain largely unknown. We use the fact that the timespan of development in C. elegans can be varied significantly by changes in temperature and mutations to discern the nature of the coordination mechanism at play in this organism. We have measured time profiles of gene expression in key organogenesis pathways of C. elegans embryos that have grown under conditions and genetic backgrounds that significantly change the overall rate of development. We used the single molecule RNA fluorescence in situ hybridization technique recently developed by our group to obtain absolute RNA transcript numbers with single molecule sensitivity. The data allow us to determine the extent to which RNA dynamics remain locked to the cell cycle as lifespan is varied and infer the existence of coordinator processes from changes of apparent induction thresholds in transcriptional cascades.

We report narrow-band absorption enhancement of semiconductor nanocrystals via Forster resonance energy transfer from cyanine J-aggregates. These J-aggregated dyes associate electrostatically with short quantum-dot (QD) surface ligands in solution. Energy transfer efficiencies approach unity for this light sensitization and result in a 5-fold enhancement in the QD excitation near the J-aggregate absorption maximum. Because a thin layer of J-aggregates attenuates the same amount of light (at peak absorbance) as a far thicker film of monomer dye, these absorption-enhanced materials may have applications in light-sensitizing applications such as photodetection and optical down-conversion.

We report here an assessment of carrier multiplication (CM) yields in PbSe and PbS nanocrystals (NCs) by a quantitative analysis of biexciton and exciton dynamics in transient photoluminescence decays. Interest in CM, the generation of more than one electron and hole in a semiconductor after absorption of one photon, has renewed in recent years because of reports suggesting greatly increased efficiencies in nanocrystalline materials compared to the bulk form, in which CM was otherwise too weak to be of consequence in photovoltaic energy conversion devices. In our PbSe and PbS NC samples, however, we estimate using transient photoluminescence that at most 0.25 additional e-h pairs are generated per photon even at energies hv > 5Eg, instead of the much higher values reported in the literature. We argue by comparing NC CM estimates and reported bulk values on an absolute energy basis, which we justify as appropriate on physical grounds, that the data reported thus far are inconclusive with respect to the importance of nanoscale-specific phenomena in the CM process., 10 pages, 7 figures

Engineering semiconductors to enhance carrier multiplication (CM) could lead to increased photovoltaic cell performance and a significant widening of the materials range suitable for future solar technologies. Semiconductor nanocrystals (NCs) have been proposed as a favorable structure for CM enhancement, and recent measurements by transient absorption have shown evidence for highly efficient CM in lead chalcogenide and $\mathrm{CdSe}$ NCs. We report here an assessment of CM yields in $\mathrm{CdSe}$ and $\mathrm{CdTe}$ NCs by a quantitative analysis of biexciton and exciton signatures in transient photoluminescence decays. Although the technique is particularly sensitive due to enhanced biexciton radiative rates relative to the exciton, ${k}_{BX}^{\mathrm{rad}}g2{k}_{X}^{\mathrm{rad}}$, we find no evidence for CM in $\mathrm{CdSe}$ and $\mathrm{CdTe}$ NCs up to photon energies $\ensuremath{\hbar}\ensuremath{\omega}g3{E}_{g}$, well above previously reported relative energy thresholds.

We have developed a photostable nanocrystal-silica (NC-silica) laser that is robust under different chemical environments, making it suitable for integration with a microfluidic network. We demonstrate that the optical properties of this microscale laser can be a dynamic function of its local environment, thus providing a platform for potential applications such as nonlinear optical chemosensing on a miniaturized scale.

[reaction: see text] The conformational equilibria of 2-carboxy-1,4-butanedioic acid and its mono-, di-, and trianions were estimated by NMR couplings in dimethyl sulfoxide (DMSO). Intramolecular hydrogen bonding was inferred for the mono- and dianions, but not for the triacid. For the di- and trianions, the (3)J(HH) couplings were consistent with the negative carboxylate groups being much closer together than might be expected from electrostatic repulsion considerations. The successive triacid pK(a) values were estimated as 7.0, 13.4, and approximately 20(?) on the Bordwell scale.

Measurements that involve averaging values from large numbers of cells can obscure the fact that processes such as gene expression are fundamentally dynamic and can vary greatly from cell to cell ( 1 ). Similarly, static snapshots of individual cells can reveal instantaneous differences between cells but cannot reveal often important changes over time; for example, it is impossible to tell whether a yellow light follows a green light using only static pictures of traffic lights. On pages 472 and 475 of this issue, Suter et al. ( 2 ) and Larson et al. ( 3 ) report on using a time-lapse approach to document the dynamics of a key cellular process, RNA transcription. Using carefully constructed experimental systems and sophisticated analyses, they tracked changes in RNA transcription in single live cells. Their results provide new details about the dynamics of key steps in transcription.

The development of a reversible chemical sensor based on a CdSe/ZnS nanocrystal (NC) is described. Signal transduction is accomplished by fluorescence resonance energy transfer (FRET) between the NC and a fluorescent pH-sensitive squaraine dye attached to the surface of the NC. The efficiency of FRET, and consequently the relative intensity of NC and dye emissions, is modulated with the pH-dependent absorption cross section of the squaraine dye. The design of a NC sensor based on FRET results in a ratiometric sensor since the emission intensities of dye and NC may be referenced to the isosbestic point between NC and dye emissions. The ratiometric approach allows sensing to be performed, regardless of issues surrounding collection efficiency (scattering environment, light fluctuations, etc.) and dye:NC loadings.

We are deeply disturbed by the recent escalation of political assaults on scientists in general and on climate scientists in particular. All citizens should understand some basic scientific facts. There is always some uncertainty associated with scientific conclusions; science never absolutely proves anything. When someone says that society should wait until scientists are absolutely certain before taking any action, it is the same as saying society should never take action. For a problem as potentially catastrophic as climate change, taking no action poses a dangerous risk for our planet.