Molecular logic of cellular diversification in the mouse cerebral cortex.

The mammalian cerebral cortex has an unparalleled diversity of cell types, which are generated during development through a series of temporally orchestrated events that are under tight evolutionary constraint and are critical for proper cortical assembly and function1,2. However, the molecular logic that governs the establishment and organization of cortical cell types remains unknown, largely due to the large number of cell classes that undergo dynamic cell-state transitions over extended developmental timelines. Here we generate a comprehensive atlas of the developing mouse neocortex, using single-cell RNA sequencing and single-cell assay for transposase-accessible chromatin using sequencing. We sampled the neocortex every day throughout embryonic corticogenesis and at early postnatal ages, and complemented the sequencing data with a spatial transcriptomics time course. We computationally reconstruct developmental trajectories across the diversity of cortical cell classes, and infer their spatial organization and the gene regulatory programs that accompany their lineage bifurcation decisions and differentiation trajectories. Finally, we demonstrate how this developmental map pinpoints the origin of lineage-specific developmental abnormalities that are linked to aberrant corticogenesis in mutant mice. The data provide a global picture of the regulatory mechanisms that govern cellular diversification in the neocortex.

The role of prior sleep for divergent thinking in infants.

Higher-order cognitive functions seem particularly vulnerable to disruptions in prior sleep in school-aged children and adult populations. This study tested whether divergent thinking in infants varied as a function of prior sleep. Forty-three infants aged 13-16 months participated in a behavioural assessment of divergent thinking. Length of wakefulness since last sleep was experimentally manipulated. In addition, potential relations between divergent thinking and sleep quantity and quality during the night immediately before the assessment, as well as during three consecutive nights preceding the assessment, were examined using actigraphy recordings in combination with parent diaries. Divergent thinking was not impaired by lack of sleep within the previous 4 h. Divergent thinking was consistently related to night-time sleep quality and quantity prior to the assessment. These results suggest that timing of prior naturally occurring daytime sleep is less relevant for emergent divergent thinking capacity than quality and quantity of preceding night-time sleep.

Evaluation of a Pilot Anaerobic Secondary Effluent for Potable Reuse: Impact of Different Disinfection Schemes on Organic Fouling of RO Membranes and DBP Formation.

Anaerobic biological secondary treatment has the potential to substantially reduce the energy cost and footprint of wastewater treatment. However, for utilities seeking to meet future water demand through potable reuse, the compatibility of anaerobically treated secondary effluent with potable reuse trains has not been evaluated. This study characterized the effects of different combinations of chloramines, ozone, and biological activated carbon (BAC), applied as pretreatments to mitigate organic chemical fouling of reverse osmosis (RO) membranes, and the production of 43 disinfection byproducts (DBPs). The study employed effluent from a pilot-scale anaerobic reactor and soluble microbial products (SMPs) generated from a synthetic wastewater. Ozonation alone minimized RO flux decline by rendering the dissolved organic carbon (DOC) more hydrophilic. When combined with chloramination, ozone addition after chloramines maintained a higher RO flux. BAC treatment was ineffective for reducing the pressure and energy requirements for a set permeate flux. Regardless of pretreatment method prior to RO, the total DBP concentrations were <14 µg/L upstream of RO. After treatment by RO, the UV/hydrogen peroxide advanced oxidation process, and chloramination, the total DBP concentrations were ≤5 µg/L. When DBP concentrations were weighted by metrics of toxic potency, the total DBP calculated toxicity was 4-fold lower than observed previously in full-scale potable reuse facilities receiving aerobically treated secondary effluent. The RO fouling and DBP formation behavior of anaerobic SMPs were similar to that of the pilot-scale anaerobic effluent. The results of this study are promising, but more research is needed to evaluate whether anaerobic effluent is suitable as an influent to potable reuse trains.

RUSH and CRUSH: a rapid and conditional RNA interference method in mice.

RNA interference (RNAi) is a powerful approach to phenocopy mutations in many organisms. Gold standard conventional knock-out mouse technology is labor- and time-intensive; however, off-target effects may confound transgenic RNAi approaches. Here, we describe a rapid method for conditional and reversible gene silencing in RNAi transgenic mouse models and embryonic stem (ES) cells. RUSH and CRUSH RNAi vectors were designed for reversible or conditional knockdown, respectively, demonstrated using targeted replacement in an engineered ROSA26(lacZ) ES cell line and wildtype V6.5 ES cells. RUSH was validated by reversible knockdown of Dnmt1 in vitro. Conditional mouse model production using CRUSH was expedited by deriving ES cell lines from Cre transgenic mouse strains (nestin, cTnnT, and Isl1) and generating all-ES G0 transgenic founders by tetraploid complementation. A control CRUSH(GFP) RNAi mouse strain showed quantitative knockdown of GFP fluorescence as observed in compound CRUSH(GFP) , Ds-Red Cre-reporter transgenic mice, and confirmed by Western blotting. The capability to turn RUSH and CRUSH alleles off or on using Cre recombinase enables this method to rapidly address questions of tissue-specificity and cell autonomy of gene function in development.

In vivo reprogramming of adult pancreatic exocrine cells to beta-cells.

One goal of regenerative medicine is to instructively convert adult cells into other cell types for tissue repair and regeneration. Although isolated examples of adult cell reprogramming are known, there is no general understanding of how to turn one cell type into another in a controlled manner. Here, using a strategy of re-expressing key developmental regulators in vivo, we identify a specific combination of three transcription factors (Ngn3 (also known as Neurog3) Pdx1 and Mafa) that reprograms differentiated pancreatic exocrine cells in adult mice into cells that closely resemble beta-cells. The induced beta-cells are indistinguishable from endogenous islet beta-cells in size, shape and ultrastructure. They express genes essential for beta-cell function and can ameliorate hyperglycaemia by remodelling local vasculature and secreting insulin. This study provides an example of cellular reprogramming using defined factors in an adult organ and suggests a general paradigm for directing cell reprogramming without reversion to a pluripotent stem cell state.

Making Ramón y Cajal proud: Development of cell identity and diversity in the cerebral cortex.

Since the beautiful images of Santiago Ramón y Cajal provided a first glimpse into the immense diversity and complexity of cell types found in the cerebral cortex, neuroscience has been challenged and inspired to understand how these diverse cells are generated and how they interact with each other to orchestrate the development of this remarkable tissue. Some fundamental questions drive the field's quest to understand cortical development: what are the mechanistic principles that govern the emergence of neuronal diversity? How do extrinsic and intrinsic signals integrate with physical forces and activity to shape cell identity? How do the diverse populations of neurons and glia influence each other during development to guarantee proper integration and function? The advent of powerful new technologies to profile and perturb cortical development at unprecedented resolution and across a variety of modalities has offered a new opportunity to integrate past knowledge with brand new data. Here, we review some of this progress using cortical excitatory projection neurons as a system to draw out general principles of cell diversification and the role of cell-cell interactions during cortical development.

Transcriptional dynamics orchestrating the development and integration of neurons born in the adult hippocampus.

The adult hippocampus generates new granule cells (aGCs) that exhibit distinct functional capabilities along development, conveying a unique form of plasticity to the preexisting circuits. While early differentiation of adult radial glia-like neural stem cells (RGL) has been studied extensively, the molecular mechanisms guiding the maturation of postmitotic neurons remain unknown. Here, we used a precise birthdating strategy to follow newborn aGCs along differentiation using single-nuclei RNA sequencing (snRNA-seq). Transcriptional profiling revealed a continuous trajectory from RGLs to mature aGCs, with multiple sequential immature stages bearing increasing levels of effector genes supporting growth, excitability and synaptogenesis. Remarkably, four discrete cellular states were defined by the expression of distinct sets of transcription factors (TFs): quiescent neural stem cells, proliferative progenitors, postmitotic immature aGCs, and mature aGCs. The transition from immature to mature aCGs involved a transcriptional switch that shutdown molecular cascades promoting cell growth, such as the SoxC family of TFs, to activate programs controlling neuronal homeostasis. Indeed, aGCs overexpressing Sox4 or Sox11 remained stalled at the immature state. Our results unveil precise molecular mechanisms driving adult neural stem cells through the pathway of neuronal differentiation.

Transcriptional dynamics orchestrating the development and integration of neurons born in the adult hippocampus.

The adult hippocampus generates new granule cells (aGCs) with functional capabilities that convey unique forms of plasticity to the preexisting circuits. While early differentiation of adult radial glia-like cells (RGLs) has been studied extensively, the molecular mechanisms guiding the maturation of postmitotic neurons remain unknown. Here, we used a precise birthdating strategy to study aGC differentiation using single-nuclei RNA sequencing. Transcriptional profiling revealed a continuous trajectory from RGLs to mature aGCs, with multiple immature stages bearing increasing levels of effector genes supporting growth, excitability, and synaptogenesis. Analysis of differential gene expression, pseudo-time trajectory, and transcription factors (TFs) revealed critical transitions defining four cellular states: quiescent RGLs, proliferative progenitors, immature aGCs, and mature aGCs. Becoming mature aGCs involved a transcriptional switch that shuts down pathways promoting cell growth, such SoxC TFs, to activate programs that likely control neuronal homeostasis. aGCs overexpressing Sox4 or Sox11 remained immature. Our results unveil precise molecular mechanisms driving adult RGLs through the pathway of neuronal differentiation.

A mixed-methods evaluation of the one-way door and CitySafe patrol policies in Whangarei, New Zealand.

In this paper, we evaluate the impacts of one-way door and CitySafe patrol policies in Whangarei, New Zealand, using a mixed-methods approach. In the quantitative analyses, we apply interrupted time series analysis and difference-in-differences analysis to data on antisocial behaviour derived from CCTV footage, and to police calls-for-service data. In the qualitative analysis, we apply thematic analysis to data from semi-structured interviews with 33 local stakeholders. We find a statistically significant increase in observed antisocial behaviour, but statistically significant decreases in violence and drug and alcohol offences, except when other small cities are used as a control group. In the qualitative analysis, a large majority of interviewees thought that the policy had reduced alcohol-related harm and increased safety, although a number of possible unintended consequences were also noted, including a reallocation of police resources, a redistribution of night-time drinking towards the suburbs, and a change in the demand for taxi companies. Overall, there is evidence only that the policies have reduced perceived alcohol-related harm, rather than reducing measures of harm.

Temporally divergent regulatory mechanisms govern neuronal diversification and maturation in the mouse and marmoset neocortex.

Mammalian neocortical neurons span one of the most diverse cell type spectra of any tissue. Cortical neurons are born during embryonic development, and their maturation extends into postnatal life. The regulatory strategies underlying progressive neuronal development and maturation remain unclear. Here we present an integrated single-cell epigenomic and transcriptional analysis of individual mouse and marmoset cortical neuron classes, spanning both early postmitotic stages of identity acquisition and later stages of neuronal plasticity and circuit integration. We found that, in both species, the regulatory strategies controlling early and late stages of pan-neuronal development diverge. Early postmitotic neurons use more widely shared and evolutionarily conserved molecular regulatory programs. In contrast, programs active during later neuronal maturation are more brain- and neuron-specific and more evolutionarily divergent. Our work uncovers a temporal shift in regulatory choices during neuronal diversification and maturation in both mice and marmosets, which likely reflects unique evolutionary constraints on distinct events of neuronal development in the neocortex.

Application of a depositional facies model to an acid mine drainage site.

Lower Red Eyes is an acid mine drainage site in Pennsylvania where low-pH Fe(II) oxidation has created a large, terraced iron mound downstream of an anoxic, acidic, metal-rich spring. Aqueous chemistry, mineral precipitates, microbial communities, and laboratory-based Fe(II) oxidation rates for this site were analyzed in the context of a depositional facies model. Depositional facies were defined as pools, terraces, or microterracettes based on cm-scale sediment morphology, irrespective of the distance downstream from the spring. The sediments were composed entirely of Fe precipitates and cemented organic matter. The Fe precipitates were identified as schwertmannite at all locations, regardless of facies. Microbial composition was studied with fluorescence in situ hybridization (FISH) and transitioned from a microaerophilic, Euglena-dominated community at the spring, to a Betaproteobacteria (primarily Ferrovum spp.)-dominated community at the upstream end of the iron mound, to a Gammaproteobacteria (primarily Acidithiobacillus)-dominated community at the downstream end of the iron mound. Microbial community structure was more strongly correlated with pH and geochemical conditions than depositional facies. Intact pieces of terrace and pool sediments from upstream and downstream locations were used in flowthrough laboratory reactors to measure the rate and extent of low-pH Fe(II) oxidation. No change in Fe(II) concentration was observed with (60)Co-irradiated sediments or with no-sediment controls, indicating that abiotic Fe(II) oxidation was negligible. Upstream sediments attained lower effluent Fe(II) concentrations compared to downstream sediments, regardless of depositional facies.

Control of sulfides and coliphage MS2 using hydrogen peroxide and UV disinfection for non-potable reuse of pilot-scale anaerobic membrane bioreactor effluent.

Anaerobic membrane bioreactors reduce the energy cost of wastewater treatment and meet filtration requirements for non-potable reuse. However, sulfides (H2S/HS-) formed during anaerobic treatment exert a high chlorine demand and inhibit UV disinfection by photon shielding at 254 nm. This study evaluated the feasibility of hydrogen peroxide (H2O2) for sulfide oxidation, UV disinfection for inactivation of MS2 bacteriophage, and chlorine to provide a residual for distribution. H2O2 treatment at pH ≥ 8 favored sulfide oxidation to sulfate in 30 min at a 4:1 H2O2:sulfide stoichiometry. Compared to a 6:1 H2O2:sulfide molar ratio, treatment of anaerobic effluent with 0.5 mM sulfides with a 4:1 H2O2:sulfide molar ratio would increase the applied UV fluence needed for 5-log MS2 inactivation from 180 mJ cm-2 to 225 mJ cm-2. However, the lower H2O2 dose reduced the dose of chlorine needed to quench residual H2O2 and provide a residual for distribution. Treatment at the 4:1 H2O2:sulfide molar ratio was favored, because the cost savings in H2O2 and chlorine reagents outweighed the energy savings associated with UV treatment. However, H2O2/UV/chlorine treatment of anaerobic effluent was cost-competitive with conventional treatment of aerobic effluent for non-potable reuse only for < 285 µM sulfides.

Adult pancreatic beta-cells are formed by self-duplication rather than stem-cell differentiation.

How tissues generate and maintain the correct number of cells is a fundamental problem in biology. In principle, tissue turnover can occur by the differentiation of stem cells, as is well documented for blood, skin and intestine, or by the duplication of existing differentiated cells. Recent work on adult stem cells has highlighted their potential contribution to organ maintenance and repair. However, the extent to which stem cells actually participate in these processes in vivo is not clear. Here we introduce a method for genetic lineage tracing to determine the contribution of stem cells to a tissue of interest. We focus on pancreatic beta-cells, whose postnatal origins remain controversial. Our analysis shows that pre-existing beta-cells, rather than pluripotent stem cells, are the major source of new beta-cells during adult life and after pancreatectomy in mice. These results suggest that terminally differentiated beta-cells retain a significant proliferative capacity in vivo and cast doubt on the idea that adult stem cells have a significant role in beta-cell replenishment.

Studying the Brain in a Dish: 3D Cell Culture Models of Human Brain Development and Disease.

The study of the cellular and molecular processes of the developing human brain has been hindered by access to suitable models of living human brain tissue. Recently developed 3D cell culture models offer the promise of studying fundamental brain processes in the context of human genetic background and species-specific developmental mechanisms. Here, we review the current state of 3D human brain organoid models and consider their potential to enable investigation of complex aspects of human brain development and the underpinning of human neurological disease.

The promises and challenges of human brain organoids as models of neuropsychiatric disease.

Neuropsychiatric disorders such as autism spectrum disorder (ASD), schizophrenia (SCZ) and bipolar disorder (BPD) are of great societal and medical importance, but the complexity of these diseases and the challenges of modeling the development and function of the human brain have made these disorders difficult to study experimentally. The recent development of 3D brain organoids derived from human pluripotent stem cells offers a promising approach for investigating the phenotypic underpinnings of these highly polygenic disorders and for understanding the contribution of individual risk variants and complex genetic background to human pathology. Here we discuss the advantages, limitations and future applications of human brain organoids as in vitro models of neuropsychiatric disease.

Functional genomics of the endocrine pancreas: the pancreas clone set and PancChip, new resources for diabetes research.

Over the past 5 years, microarrays have greatly facilitated large-scale analysis of gene expression levels. Although these arrays were not specifically geared to represent tissues and pathways known to be affected by diabetes, they have been used in both type 1 and type 2 diabetes research. To prepare a tool that is particularly useful in the study of type 1 diabetes, we have assembled a nonredundant set of 3,400 clones representing genes expressed in the mouse pancreas or pathways known to be affected by diabetes. We have demonstrated the usefulness of this clone set by preparing a cDNA glass microarray, the PancChip, and using it to analyze pancreatic gene expression from embryonic day 14.5 through adulthood in mice. The clone set and corresponding array are useful resources for diabetes research.

Transcriptional program of the endocrine pancreas in mice and humans.

The Endocrine Pancreas Consortium was formed in late 1999 to derive and sequence cDNA libraries enriched for rare transcripts expressed in the mammalian endocrine pancreas. Over the past 3 years, the Consortium has generated 20 cDNA libraries from mouse and human pancreatic tissues and deposited >150,000 sequences into the public expressed sequence tag databases. A special effort was made to enrich for cDNAs from the endocrine pancreas by constructing libraries from isolated islets. In addition, we constructed a library in which fetal pancreas from Neurogenin 3 null mice, which consists of only exocrine and duct cells, was subtracted from fetal wild-type pancreas to enrich for the transcripts from the endocrine compartment. Sequence analysis showed that these clones cluster into 9,464 assembly groups (approximating unique transcripts) for the mouse and 13,910 for the human sequences. Of these, >4,300 were unique to Consortium libraries. We have assembled a core clone set containing one cDNA for each assembly group for the mouse and have constructed the corresponding microarray, termed "PancChip 4.0," which contains >9,000 nonredundant elements. We show that this PancChip is highly enriched for genes expressed in the endocrine pancreas. The mouse and human clone sets and corresponding arrays will be important resources for diabetes research.

Direct lineage tracing reveals the ontogeny of pancreatic cell fates during mouse embryogenesis.

Lineage tracing follows the progeny of labeled cells through development. This technique identifies precursors of mature cell types in vivo and describes the cell fate restriction steps they undergo in temporal order. In the mouse pancreas, direct cell lineage tracing reveals that Pdx1- expressing progenitors in the early embryo give rise to all pancreatic cells. The progenitors for the mature pancreatic ducts separate from the endocrine/exocrine tissues before E12.5. Expression of Ngn3 and pancreatic polypeptide marks endocrine cell lineages during early embryogenesis, and these cells behave as transient progenitors rather than stem cells. In adults, Ngn3 is expressed within the endocrine islets, and the NGN3+ cells seem to contribute to pancreatic islet renewal. These results indicate the stage at which each progenitor population is restricted to a particular fate and provide markers for isolating progenitors to study their growth, differentiation, and the genes necessary for their development.

Instructing Perisomatic Inhibition by Direct Lineage Reprogramming of Neocortical Projection Neurons.

During development of the cerebral cortex, local GABAergic interneurons recognize and pair with excitatory projection neurons to ensure the fine excitatory-inhibitory balance essential for proper circuit function. Whether the class-specific identity of projection neurons has a role in the establishment of afferent inhibitory synapses is debated. Here, we report that direct in vivo lineage reprogramming of layer 2/3 (L2/3) callosal projection neurons (CPNs) into induced corticofugal projection neurons (iCFuPNs) increases inhibitory input onto the converted neurons to levels similar to that of endogenous CFuPNs normally found in layer 5 (L5). iCFuPNs recruit increased numbers of inhibitory perisomatic synapses from parvalbumin (PV)-positive interneurons, with single-cell precision and despite their ectopic location in L2/3. The data show that individual reprogrammed excitatory projection neurons extrinsically modulate afferent input by local PV(+) interneurons, suggesting that projection neuron class-specific identity can actively control the wiring of the cortical microcircuit.