Vitamin A-Retinoic Acid Signaling Regulates Hematopoietic Stem Cell Dormancy.

Dormant hematopoietic stem cells (dHSCs) are atop the hematopoietic hierarchy. The molecular identity of dHSCs and the mechanisms regulating their maintenance or exit from dormancy remain uncertain. Here, we use single-cell RNA sequencing (RNA-seq) analysis to show that the transition from dormancy toward cell-cycle entry is a continuous developmental path associated with upregulation of biosynthetic processes rather than a stepwise progression. In addition, low Myc levels and high expression of a retinoic acid program are characteristic for dHSCs. To follow the behavior of dHSCs in situ, a Gprc5c-controlled reporter mouse was established. Treatment with all-trans retinoic acid antagonizes stress-induced activation of dHSCs by restricting protein translation and levels of reactive oxygen species (ROS) and Myc. Mice maintained on a vitamin A-free diet lose HSCs and show a disrupted re-entry into dormancy after exposure to inflammatory stress stimuli. Our results highlight the impact of dietary vitamin A on the regulation of cell-cycle-mediated stem cell plasticity. VIDEO ABSTRACT.

Pronounced early differentiation underlies zebra finch gonadal germ cell development.

The diversity of germ cell developmental strategies has been well documented across many vertebrate clades. However, much of our understanding of avian primordial germ cell (PGC) specification and differentiation has derived from only one species, the chicken (Gallus gallus). Of the three major classes of birds, chickens belong to Galloanserae, representing less than 4% of species, while nearly 95% of extant bird species belong to Neoaves. This represents a significant gap in our knowledge of germ cell development across avian species, hampering efforts to adapt genome editing and reproductive technologies developed in chicken to other birds. We therefore applied single-cell RNA sequencing to investigate inter-species differences in germ cell development between chicken and zebra finch (Taeniopygia castanotis), a Neoaves songbird species and a common model of vocal learning. Analysis of early embryonic male and female gonads revealed the presence of two distinct early germ cell types in zebra finch and only one in chicken. Both germ cell types expressed zebra finch Germline Restricted Chromosome (GRC) genes, present only in songbirds among birds. One of the zebra finch germ cell types expressed the canonical PGC markers, as did chicken, but with expression differences in several signaling pathways and biological processes. The second zebra finch germ cell cluster was marked by proliferation and fate determination markers, indicating beginning of differentiation. Notably, these two zebra finch germ cell populations were present in both male and female zebra finch gonads as early as HH25. Using additional chicken developmental stages, similar germ cell heterogeneity was identified in the more developed gonads of females, but not males. Overall, our study demonstrates a substantial heterochrony in zebra finch germ cell development compared to chicken, indicating a richer diversity of avian germ cell developmental strategies than previously known.

Accessing Mg-Ion Storage in V2PS10 via Combined Cationic-Anionic Redox with Selective Bond Cleavage.

Magnesium batteries attract interest as alternative energy-storage devices because of elemental abundance and potential for high energy density. Development is limited by the absence of suitable cathodes, associated with poor diffusion kinetics resulting from strong interactions between Mg2+ and the host structure. V2PS10 is reported as a positive electrode material for rechargeable magnesium batteries. Cyclable capacity of 100 mAh g-1 is achieved with fast Mg2+ diffusion of 7.2 × ${\times }$ 10-11-4 × ${\times }$ 10-14 cm2 s-1. The fast insertion mechanism results from combined cationic redox on the V site and anionic redox on the (S2)2- site; enabled by reversible cleavage of S-S bonds, identified by X-ray photoelectron and X-ray absorption spectroscopy. Detailed structural characterisation with maximum entropy method analysis, supported by density functional theory and projected density of states analysis, reveals that the sulphur species involved in anion redox are not connected to the transition metal centres, spatially separating the two redox processes. This facilitates fast and reversible Mg insertion in which the nature of the redox process depends on the cation insertion site, creating a synergy between the occupancy of specific Mg sites and the location of the electrons transferred.

Schizophrenia is defined by cell-specific neuropathology and multiple neurodevelopmental mechanisms in patient-derived cerebral organoids.

Due to an inability to ethically access developing human brain tissue as well as identify prospective cases, early-arising neurodevelopmental and cell-specific signatures of Schizophrenia (Scz) have remained unknown and thus undefined. To overcome these challenges, we utilized patient-derived induced pluripotent stem cells (iPSCs) to generate 3D cerebral organoids to model neuropathology of Scz during this critical period. We discovered that Scz organoids exhibited ventricular neuropathology resulting in altered progenitor survival and disrupted neurogenesis. This ultimately yielded fewer neurons within developing cortical fields of Scz organoids. Single-cell sequencing revealed that Scz progenitors were specifically depleted of neuronal programming factors leading to a remodeling of cell-lineages, altered differentiation trajectories, and distorted cortical cell-type diversity. While Scz organoids were similar in their macromolecular diversity to organoids generated from healthy controls (Ctrls), four GWAS factors (PTN, COMT, PLCL1, and PODXL) and peptide fragments belonging to the POU-domain transcription factor family (e.g., POU3F2/BRN2) were altered. This revealed that Scz organoids principally differed not in their proteomic diversity, but specifically in their total quantity of disease and neurodevelopmental factors at the molecular level. Single-cell sequencing subsequently identified cell-type specific alterations in neuronal programming factors as well as a developmental switch in neurotrophic growth factor expression, indicating that Scz neuropathology can be encoded on a cell-type-by-cell-type basis. Furthermore, single-cell sequencing also specifically replicated the depletion of BRN2 (POU3F2) and PTN in both Scz progenitors and neurons. Subsequently, in two mechanistic rescue experiments we identified that the transcription factor BRN2 and growth factor PTN operate as mechanistic substrates of neurogenesis and cellular survival, respectively, in Scz organoids. Collectively, our work suggests that multiple mechanisms of Scz exist in patient-derived organoids, and that these disparate mechanisms converge upon primordial brain developmental pathways such as neuronal differentiation, survival, and growth factor support, which may amalgamate to elevate intrinsic risk of Scz.

mRNA 3' uridylation and poly(A) tail length sculpt the mammalian maternal transcriptome.

A fundamental principle in biology is that the program for early development is established during oogenesis in the form of the maternal transcriptome. How the maternal transcriptome acquires the appropriate content and dosage of transcripts is not fully understood. Here we show that 3' terminal uridylation of mRNA mediated by TUT4 and TUT7 sculpts the mouse maternal transcriptome by eliminating transcripts during oocyte growth. Uridylation mediated by TUT4 and TUT7 is essential for both oocyte maturation and fertility. In comparison to somatic cells, the oocyte transcriptome has a shorter poly(A) tail and a higher relative proportion of terminal oligo-uridylation. Deletion of TUT4 and TUT7 leads to the accumulation of a cohort of transcripts with a high frequency of very short poly(A) tails, and a loss of 3' oligo-uridylation. By contrast, deficiency of TUT4 and TUT7 does not alter gene expression in a variety of somatic cells. In summary, we show that poly(A) tail length and 3' terminal uridylation have essential and specific functions in shaping a functional maternal transcriptome.

Combining quasielastic neutron scattering and molecular dynamics to study methane motions in ZSM-5.

Quasi-elastic neutron scattering (QENS) and molecular dynamics (MD) simulations are applied in combination to investigate the dynamics of methane in H-ZSM-5 zeolite catalysts used for methanol-to-hydrocarbons reactions. Methane is employed as an inert model for the methanol reaction feedstock, and studies are made of the fresh catalyst and used catalysts with varying levels of coke buildup to investigate the effect of coking on reactant mobility. Measurements are made in the temperature range from 5 to 373 K. Methane mobility under these conditions is found to be extremely high in fresh ZSM-5, with the majority of movements occurring too fast to be resolved by the QENS instrument used. A small fraction of molecules undergoing jump diffusion on QENS time scales is identified and found to correspond with short-range jump diffusion within single zeolite pores as identified in MD simulations. Agreement between QENS and MD mobility measurements is found to be within 50%, validating the simulation approach employed. Methane diffusion is found to be minimally affected by moderate levels of coke buildup, while highly coked samples result in the confinement of methane to single pores within the zeolite with minimal long-range diffusion.

Enhanced Photoacoustic Visualisation of Clinical Needles by Combining Interstitial and Extracorporeal Illumination of Elastomeric Nanocomposite Coatings.

Ultrasound (US) image guidance is widely used for minimally invasive procedures, but the invasive medical devices (such as metallic needles), especially their tips, can be poorly visualised in US images, leading to significant complications. Photoacoustic (PA) imaging is promising for visualising invasive devices and peripheral tissue targets. Light-emitting diodes (LEDs) acting as PA excitation sources facilitate the clinical translation of PA imaging, but the image quality is degraded due to the low pulse energy leading to insufficient contrast with needles at deep locations. In this paper, photoacoustic visualisation of clinical needles was enhanced by elastomeric nanocomposite coatings with superficial and interstitial illumination. Candle soot nanoparticle-polydimethylsiloxane (CSNP-PDMS) composites with high optical absorption and large thermal expansion coefficients were applied onto the needle exterior and the end-face of an optical fibre placed in the needle lumen. The excitation light was delivered at the surface by LED arrays and through the embedded optical fibre by a pulsed diode laser to improve the visibility of the needle tip. The performance was validated using an ex-vivo tissue model. An LED-based PA/US imaging system was used for imaging the needle out-of-plane and in-plane insertions over approach angles of 20 deg to 55 deg. The CSNP-PDMS composite conferred substantial visual enhancements on both the needle shaft and the tip, with an average of 1.7- and 1.6-fold improvements in signal-to-noise ratios (SNRs), respectively. With the extended light field involving extracorporeal and interstitial illumination and the highly absorbing coatings, enhanced visualisation of the needle shaft and needle tip was achieved with PA imaging, which could be helpful in current US-guided minimally invasive surgeries.

Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome.

Understanding transcriptome complexity is crucial for understanding human biology and disease. Technologies such as Synthetic long-read RNA sequencing (SLR-RNA-seq) delivered 5 million isoforms and allowed assessing splicing coordination. Pacific Biosciences and Oxford Nanopore increase throughput also but require high input amounts or amplification. Our new droplet-based method, sparse isoform sequencing (spISO-seq), sequences 100k-200k partitions of 10-200 molecules at a time, enabling analysis of 10-100 million RNA molecules. SpISO-seq requires less than 1 ng of input cDNA, limiting or removing the need for prior amplification with its associated biases. Adjusting the number of reads devoted to each molecule reduces sequencing lanes and cost, with little loss in detection power. The increased number of molecules expands our understanding of isoform complexity. In addition to confirming our previously published cases of splicing coordination (e.g., BIN1), the greater depth reveals many new cases, such as MAPT Coordination of internal exons is found to be extensive among protein coding genes: 23.5%-59.3% (95% confidence interval) of highly expressed genes with distant alternative exons exhibit coordination, showcasing the need for long-read transcriptomics. However, coordination is less frequent for noncoding sequences, suggesting a larger role of splicing coordination in shaping proteins. Groups of genes with coordination are involved in protein-protein interactions with each other, raising the possibility that coordination facilitates complex formation and/or function. We also find new splicing coordination types, involving initial and terminal exons. Our results provide a more comprehensive understanding of the human transcriptome and a general, cost-effective method to analyze it.

Unbiased classification of mosquito blood cells by single-cell genomics and high-content imaging.

Mosquito blood cells are immune cells that help control infection by vector-borne pathogens. Despite their importance, little is known about mosquito blood cell biology beyond morphological and functional criteria used for their classification. Here, we combined the power of single-cell RNA sequencing, high-content imaging flow cytometry, and single-molecule RNA hybridization to analyze a subset of blood cells of the malaria mosquito Anopheles gambiae By demonstrating that blood cells express nearly half of the mosquito transcriptome, our dataset represents an unprecedented view into their transcriptional program. Analyses of differentially expressed genes identified transcriptional signatures of two cell types and provide insights into the current classification of these cells. We further demonstrate the active transfer of a cellular marker between blood cells that may confound their identification. We propose that cell-to-cell exchange may contribute to cellular diversity and functional plasticity seen across biological systems.

Multimodal Imaging of Autofluorescent Sites Reveals Varied Chemical Speciation in SSZ-13 Crystals.

A multimodal imaging study of chabazite is used to show the distribution of and discriminate between different emissive deposits arising as a result of the detemplation process. Confocal imaging, 3D fluorescence lifetime imaging, 3D multispectral fluorescence imaging, and Raman mapping are used to show three different types of emissive behaviours each characterised by different spatial distributions, trends in lifetime, spectral signals, and Raman signatures. A notable difference is seen in the morphology of agglomerated surface deposits and larger subsurface deposits, which experience lifetime augmentation due to spatial confinement. The distribution of organic residue throughout the crystal volume is comparable to XRF mapping that shows Si enrichment on the outer edges and higher Al content through the centre, demonstrating that a fluorescence-based technique can also be used to indirectly comment on the compositional chemistry of the inorganic framework.