An optical coherence photoacoustic microscopy system using a fiber optic sensor

In this work, a novel fiber optic sensor based on Fabry-Pérot interferometry is adopted in an optical coherence photoacoustic microscopy (OC-PAM) system to enable high-resolution in vivo imaging. The complete OC-PAM system is characterized using the fiber optic sensor for photoacoustic measurement. After characterization, the performance of the system is evaluated by imaging zebrafish larvae in vivo. With a lateral resolution of 3.4 μm and an axial resolution of 3.7 μm in air, the optical coherence microscopy subsystem visualizes the anatomy of the zebrafish larvae. The photoacoustic microscopy subsystem reveals the vasculature of the zebrafish larvae with a lateral resolution of 1.9 μm and an axial resolution of 37.3 μm. As the two modalities share the same sample arm, we obtain inherently co-registered morphological and vascular images. This OC-PAM system provides comprehensive information on the anatomy and vasculature of the zebrafish larvae. Featuring compactness, broad detection bandwidth, and wide detection angle, the fiber optic sensor enables a large field of view with a static sensor position. We verified the feasibility of the fiber optic sensor for dual-modality in vivo imaging. The OC-PAM system, as a non-invasive imaging method, demonstrates its superiority in the investigation of zebrafish larvae, an animal model with increasing significance in developmental biology and disease research. This technique can also be applied for functional as well as longitudinal studies in the future

Photocaged Hoechst enables subnuclear visualization and cell selective staining of DNA in vivo

Selective targeting of DNA by means of fluorescent labelling has become a mainstay in the life sciences. While genetic engineering serves as a powerful technique and allows for the visualization of nucleic acid by using DNA-targeting fluorescent fusion proteins in a cell-type and subcellular specific manner, it relies on the introduction of foreign genes. On the other hand, DNA-binding small fluorescent molecules can be used without genetic engineering but they are not spatially restricted. Here, we report a photocaged version of the DNA dye Hoechst33342 (pcHoechst), which can be uncaged using UV to blue light for the selective staining of chromosomal DNA in subnuclear regions of live cells. Expanding its application to a vertebrate model organism, we demonstrate uncaging in epithelial cells and short-term cell tracking  in vivo  in zebrafish. We envision pcHoechst as a valuable tool for targeting and interrogating DNA with precise spatiotemporal resolution in living cells and wild-type organisms

COMAP Early Science: VIII. A Joint Stacking Analysis with eBOSS Quasars

We present a new upper limit on the cosmic molecular gas density at $z=2.4-3.4$ obtained using the first year of observations from the CO Mapping Array Project (COMAP). COMAP data cubes are stacked on the 3D positions of 282 quasars selected from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS) catalog, yielding a 95% upper limit for flux from CO(1-0) line emission of 0.210 Jy km/s. Depending on the assumptions made, this value can be interpreted as either an average CO line luminosity $L'_\mathrm{CO}$ of eBOSS quasars of $\leq 7.30\times10^{10}$ K km pc$^2$ s$^{-1}$, or an average molecular gas density $\rho_\mathrm{H_2}$ in regions of the universe containing a quasar of $\leq 2.02\times10^8$ M$_\odot$ cMpc$^{-3}$. The $L'_\mathrm{CO}$ upper limit falls among CO line luminosities obtained from individually-targeted quasars in the COMAP redshift range, and the $\rho_\mathrm{H_2}$ value is comparable to upper limits obtained from other Line Intensity Mapping (LIM) surveys and their joint analyses. Further, we forecast the values obtainable with the COMAP/eBOSS stack after the full 5-year COMAP Pathfinder survey. We predict that a detection is probable with this method, depending on the CO properties of the quasar sample. Based on these achieved sensitivities, we believe that this technique of stacking LIM data on the positions of traditional galaxy or quasar catalogs is extremely promising, both as a technique for investigating large galaxy catalogs efficiently at high redshift and as a technique for bolstering the sensitivity of LIM experiments, even with a fraction of their total expected survey data.Comment: 15 pages, 8 figures. To be submitted to Ap

COMAP Early Science: VIII. A Joint Stacking Analysis with eBOSS Quasars

We present a new upper limit on the cosmic molecular gas density at z = 2.4 − 3.4 obtained using the first year of observations from the CO Mapping Array Project (COMAP). COMAP data cubes are stacked on the 3D positions of 243 quasars selected from the Extended Baryon Oscillation SpectroscopicSurvey (eBOSS) catalog, yielding a 95% upper limit for flux from CO(1-0) line emission of 0.129 Jykm/s. Depending on the balance of the emission between the quasar host and its environment, this value can be interpreted as an average CO line luminosity L′CO of eBOSS quasars of ≤ 1.26 × 1011 K km pc2s−1, or an average molecular gas density ρH2 in regions of the universe containing a quasar of ≤ 1.52 × 108 M⊙ cMpc−3. The L′ CO upper limit falls among CO line luminosities obtained fromindividually-targeted quasars in the COMAP redshift range, and the ρH2 value is comparable to upper limits obtained from other Line Intensity Mapping (LIM) surveys and their joint analyses. Further, we forecast the values obtainable with the COMAP/eBOSS stack after the full 5-year COMAP Pathfinder survey. We predict that a detection is probable with this method, depending on the CO properties of the quasar sample. Based on the achieved sensitivity, we believe that this technique of stacking LIM data on the positions of traditional galaxy or quasar catalogs is extremely promising, both asa technique for investigating large galaxy catalogs efficiently at high redshift and as a technique for bolstering the sensitivity of LIM experiments, even with a fraction of their total expected survey data

Refined high-content imaging-based phenotypic drug screening in zebrafish xenografts

Zebrafish xenotransplantation models are increasingly applied for phenotypic drug screening to identify small compounds for precision oncology. Larval zebrafish xenografts offer the opportunity to perform drug screens at high-throughput in a complex in vivo environment. However, the full potential of the larval zebrafish xenograft model has not yet been realized and several steps of the drug screening workflow still await automation to increase throughput. Here, we present a robust workflow for drug screening in zebrafish xenografts using high-content imaging. We established embedding methods for high-content imaging of xenografts in 96-well format over consecutive days. In addition, we provide strategies for automated imaging and analysis of zebrafish xenografts including automated tumor cell detection and tumor size analysis over time. We also compared commonly used injection sites and cell labeling dyes and show specific site requirements for tumor cells from different entities. We demonstrate that our setup allows us to investigate proliferation and response to small compounds in several zebrafish xenografts ranging from pediatric sarcomas and neuroblastoma to glioblastoma and leukemia. This fast and cost-efficient assay enables the quantification of anti-tumor efficacy of small compounds in large cohorts of a vertebrate model system in vivo. Our assay may aid in prioritizing compounds or compound combinations for further preclinical and clinical investigations

COMAP Early Science: V. Constraints and Forecasts at z∼3z \sim 3

We present the current state of models for the $z\sim3$ carbon monoxide (CO) line-intensity signal targeted by the CO Mapping Array Project (COMAP) Pathfinder in the context of its early science results. Our fiducial model, relating dark matter halo properties to CO luminosities, informs parameter priors with empirical models of the galaxy-halo connection and previous CO(1-0) observations. The Pathfinder early science data spanning wavenumbers $k=0.051$-$0.62\,$Mpc$^{-1}$ represent the first direct 3D constraint on the clustering component of the CO(1-0) power spectrum. Our 95% upper limit on the redshift-space clustering amplitude $A_{\rm clust}\lesssim70\,\mu$K$^2$ greatly improves on the indirect upper limit of $420\,\mu$K$^2$ reported from the CO Power Spectrum Survey (COPSS) measurement at $k\sim1\,$Mpc$^{-1}$. The COMAP limit excludes a subset of models from previous literature, and constrains interpretation of the COPSS results, demonstrating the complementary nature of COMAP and interferometric CO surveys. Using line bias expectations from our priors, we also constrain the squared mean line intensity-bias product, $\langle{Tb}\rangle^2\lesssim50\,\mu$K$^2$, and the cosmic molecular gas density, $\rho_\text{H2}<2.5\times10^8\,M_\odot\,$Mpc$^{-3}$ (95% upper limits). Based on early instrument performance and our current CO signal estimates, we forecast that the five-year Pathfinder campaign will detect the CO power spectrum with overall signal-to-noise of 9-17. Between then and now, we also expect to detect the CO-galaxy cross-spectrum using overlapping galaxy survey data, enabling enhanced inferences of cosmic star-formation and galaxy-evolution history.Comment: Paper 5 of 7 in series. 17 pages + appendix and bibliography (30 pages total); 15 figures, 6 tables; accepted for publication in ApJ; v3 reflects the accepted version with minor changes and additions to tex

A human neural crest model reveals the developmental impact of neuroblastoma-associated chromosomal aberrations

Early childhood tumours arise from transformed embryonic cells, which often carry large copy number alterations (CNA). However, it remains unclear how CNAs contribute to embryonic tumourigenesis due to a lack of suitable models. Here we employ female human embryonic stem cell (hESC) differentiation and single-cell transcriptome and epigenome analysis to assess the effects of chromosome 17q/1q gains, which are prevalent in the embryonal tumour neuroblastoma (NB). We show that CNAs impair the specification of trunk neural crest (NC) cells and their sympathoadrenal derivatives, the putative cells-of-origin of NB. This effect is exacerbated upon overexpression of MYCN, whose amplification co-occurs with CNAs in NB. Moreover, CNAs potentiate the pro-tumourigenic effects of MYCN and mutant NC cells resemble NB cells in tumours. These changes correlate with a stepwise aberration of developmental transcription factor networks. Together, our results sketch a mechanistic framework for the CNA-driven initiation of embryonal tumours

Practical guidelines for rigor and reproducibility in preclinical and clinical studies on cardioprotection

The potential for ischemic preconditioning to reduce infarct size was first recognized more than 30 years ago. Despite extension of the concept to ischemic postconditioning and remote ischemic conditioning and literally thousands of experimental studies in various species and models which identified a multitude of signaling steps, so far there is only a single and very recent study, which has unequivocally translated cardioprotection to improved clinical outcome as the primary endpoint in patients. Many potential reasons for this disappointing lack of clinical translation of cardioprotection have been proposed, including lack of rigor and reproducibility in preclinical studies, and poor design and conduct of clinical trials. There is, however, universal agreement that robust preclinical data are a mandatory prerequisite to initiate a meaningful clinical trial. In this context, it is disconcerting that the CAESAR consortium (Consortium for preclinicAl assESsment of cARdioprotective therapies) in a highly standardized multi-center approach of preclinical studies identified only ischemic preconditioning, but not nitrite or sildenafil, when given as adjunct to reperfusion, to reduce infarct size. However, ischemic preconditioning—due to its very nature—can only be used in elective interventions, and not in acute myocardial infarction. Therefore, better strategies to identify robust and reproducible strategies of cardioprotection, which can subsequently be tested in clinical trials must be developed. We refer to the recent guidelines for experimental models of myocardial ischemia and infarction, and aim to provide now practical guidelines to ensure rigor and reproducibility in preclinical and clinical studies on cardioprotection. In line with the above guideline, we define rigor as standardized state-of-the-art design, conduct and reporting of a study, which is then a prerequisite for reproducibility, i.e. replication of results by another laboratory when performing exactly the same experiment