Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.

Cells, the basic units of biological structure and function, vary broadly in type and state. Single-cell genomics can characterize cell identity and function, but limitations of ease and scale have prevented its broad application. Here we describe Drop-seq, a strategy for quickly profiling thousands of individual cells by separating them into nanoliter-sized aqueous droplets, associating a different barcode with each cell's RNAs, and sequencing them all together. Drop-seq analyzes mRNA transcripts from thousands of individual cells simultaneously while remembering transcripts' cell of origin. We analyzed transcriptomes from 44,808 mouse retinal cells and identified 39 transcriptionally distinct cell populations, creating a molecular atlas of gene expression for known retinal cell classes and novel candidate cell subtypes. Drop-seq will accelerate biological discovery by enabling routine transcriptional profiling at single-cell resolution. VIDEO ABSTRACT.

Taking time to compose thoughts with prefrontal schemata.

Under what conditions can prefrontal cortex direct the composition of brain states, to generate coherent streams of thoughts? Using a simplified Potts model of cortical dynamics, crudely differentiated into two halves, we show that once activity levels are regulated, so as to disambiguate a single temporal sequence, whether the contents of the sequence are mainly determined by the frontal or by the posterior half, or by neither, depends on statistical parameters that describe its microcircuits. The frontal cortex tends to lead if it has more local attractors, longer lasting and stronger ones, in order of increasing importance. Its guidance is particularly effective to the extent that posterior cortices do not tend to transition from state to state on their own. The result may be related to prefrontal cortex enforcing its temporally-oriented schemata driving coherent sequences of brain states, unlike the atemporal "context" contributed by the hippocampus. Modelling a mild prefrontal (vs. posterior) lesion offers an account of mind-wandering and event construction deficits observed in prefrontal patients.

Hedgehog-FGF signaling axis patterns anterior mesoderm during gastrulation.

The mechanisms used by embryos to pattern tissues across their axes has fascinated developmental biologists since the founding of embryology. Here, using single-cell technology, we interrogate complex patterning defects and define a Hedgehog (Hh)-fibroblast growth factor (FGF) signaling axis required for anterior mesoderm lineage development during gastrulation. Single-cell transcriptome analysis of Hh-deficient mesoderm revealed selective deficits in anterior mesoderm populations, culminating in defects to anterior embryonic structures, including the pharyngeal arches, heart, and anterior somites. Transcriptional profiling of Hh-deficient mesoderm during gastrulation revealed disruptions to both transcriptional patterning of the mesoderm and FGF signaling for mesoderm migration. Mesoderm-specific Fgf4/Fgf8 double-mutants recapitulated anterior mesoderm defects and Hh-dependent GLI transcription factors modulated enhancers at FGF gene loci. Cellular migration defects during gastrulation induced by Hh pathway antagonism were mitigated by the addition of FGF4 protein. These findings implicate a multicomponent signaling hierarchy activated by Hh ligands from the embryonic node and executed by FGF signals in nascent mesoderm to control anterior mesoderm patterning.

Déjà vu: A botched memory operation, illegitimate to start with.

Rather than a natural product, a computational analysis leads us to characterize déjà vu as a failure of memory retrieval, linked to the activation in neocortex of familiar items from a compositional memory in the absence of hippocampal input, and to a misappropriation by the self of what is of others.

Massively parallel single-nucleus RNA-seq with DroNc-seq.

Single-nucleus RNA sequencing (sNuc-seq) profiles RNA from tissues that are preserved or cannot be dissociated, but it does not provide high throughput. Here, we develop DroNc-seq: massively parallel sNuc-seq with droplet technology. We profile 39,111 nuclei from mouse and human archived brain samples to demonstrate sensitive, efficient, and unbiased classification of cell types, paving the way for systematic charting of cell atlases.

Hemodynamic effects of hemodialyzer pump speed on arteriovenous fistulas
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AIM: Arteriovenous fistulas (AVF) are the optimal vascular access for hemodialysis although many fistulas fail. The impetus to increase hemodialyzer blood flow (QB) in order to maximize solute clearances may be counterbalanced if AVF suffer adverse hemodynamic effects from accelerated pump flows. The optimal QB to maintain adequate hemodialysis without potentially contributing to AVF dysfunction is unknown. The aim of this study was to measure the hemodynamic effects of increased QB on AVF. MATERIALS AND METHODS: A prospective cohort of 14 patients with primary brachiocephalic AVF underwent venous Doppler measurements prior to cannulation (QB0) and during hemodialysis with QB of 350 mL/min at a standardized anatomical location over 3 - 16 consecutive months. Measurements included vein diameter, blood flow velocity, and volumetric flow. RESULTS: 163 paired Doppler measurements (QB0 and QB350) were made in 14 subjects. There were no significant differences in venous diameter, but significant increases in blood flow velocity and volumetric flow (p < 0.001). Mean blood flow velocity increased from 86.6 ± 35.0 cm/s at QB0 to 105.7 ± 35.0 cm/s at QB350. Mean volumetric flow increased from 849 mL/min at QB0 to 1,059 mL/min at QB350. Vein diameters increased linearly over time, with no significant changes in blood velocity or volumetric flow, suggesting AVF maturation may improve tolerance of pumped blood flow. CONCLUSION: Blood flow velocity and volumetric flow increased when hemodialyzer blood pump was applied to an AVF, creating a situation in which increased turbulence and shear stress might be plausible. Further study is needed to determine if increased QB affects clinical outcomes of AVF.
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Rheology of soft colloids across the onset of rigidity: scaling behavior, thermal, and non-thermal responses.

We study the rheological behavior of colloidal suspensions composed of soft sub-micron-size hydrogel particles across the liquid-solid transition. The measured stress and strain-rate data, when normalized by thermal stress and time scales, suggest our systems reside in a regime wherein thermal effects are important. In a different vein, critical point scaling predictions for the jamming transition, typical in athermal systems, are tested. Near dynamic arrest, the suspensions exhibit scaling exponents similar to those reported in Nordstrom et al., Phys. Rev. Lett., 2010, 105, 175701. The observation suggests that our system exhibits a glass transition near the onset of rigidity, but it also exhibits a jamming-like scaling further from the transition point. These observations are thought-provoking in light of recent theoretical and simulation findings, which show that suspension rheology across the full range of microgel particle experiments can exhibit both thermal and athermal mechanisms.

Role of rare earth oxide nanoparticles (CeO2 and La2O3) in suppressing the photobleaching of fluorescent organic dyes.

Aqueous solutions with Rhodamine dye, and fluorescently labeled polymer samples of fibrin and collagen were mixed with aqueous dispersions of cerium oxide, lanthanum oxide, iron (II) oxide nanoparticles, and OxyFluor, a commonly used reagent for suppressing photobleaching. From time dependent studies of the fluorescence from these samples, we observed that the dyes in samples containing rare earth oxide nanoparticles exhibited significantly slower rates of fluorescence decay compared to control samples without additives, or containing OxyFluor or iron oxide nanoparticles. We posit that this may be related to the oxygen free radical scavenging properties of rare earth oxides.

Bile acid fitness determinants of a Bacteroides fragilis isolate from a human pouchitis patient.

IMPORTANCE: The Gram-negative bacterium Bacteroides fragilis is a common member of the human gut microbiota that colonizes multiple host niches and can influence human physiology through a variety of mechanisms. Identification of genes that enable B. fragilis to grow across a range of host environments has been impeded in part by the relatively limited genetic tractability of this species. We have developed a high-throughput genetic resource for a B. fragilis strain isolated from a UC pouchitis patient. Bile acids limit microbial growth and are altered in abundance in UC pouches, where B. fragilis often blooms. Using this resource, we uncovered pathways and processes that impact B. fragilis fitness in bile and that may contribute to population expansions during bouts of gut inflammation.

Exploring the tumor micro-environment in primary and metastatic tumors of different ovarian cancer histotypes.

Ovarian cancer is a highly heterogeneous disease consisting of at least five different histological subtypes with varying clinical features, cells of origin, molecular composition, risk factors, and treatments. While most single-cell studies have focused on High grade serous ovarian cancer, a comprehensive landscape of the constituent cell types and their interactions within the tumor microenvironment are yet to be established in the different ovarian cancer histotypes. Further characterization of tumor progression, metastasis, and various histotypes are also needed to connect molecular signatures to pathological grading for personalized diagnosis and tailored treatment. In this study, we leveraged high-resolution single-cell RNA sequencing technology to elucidate the cellular compositions on 21 solid tumor samples collected from 12 patients with six ovarian cancer histotypes and both primary (ovaries) and metastatic (omentum, rectum) sites. The diverse collection allowed us to deconstruct the histotypes and tumor site-specific expression patterns of cells in the tumor, and identify key marker genes and ligand-receptor pairs that are active in the ovarian tumor microenvironment. Our findings can be used in improving precision disease stratification and optimizing treatment options.

Single-cell genomics improves the discovery of risk variants and genes of atrial fibrillation.

Genome-wide association studies (GWAS) have linked hundreds of loci to cardiac diseases. However, in most loci the causal variants and their target genes remain unknown. We developed a combined experimental and analytical approach that integrates single cell epigenomics with GWAS to prioritize risk variants and genes. We profiled accessible chromatin in single cells obtained from human hearts and leveraged the data to study genetics of Atrial Fibrillation (AF), the most common cardiac arrhythmia. Enrichment analysis of AF risk variants using cell-type-resolved open chromatin regions (OCRs) implicated cardiomyocytes as the main mediator of AF risk. We then performed statistical fine-mapping, leveraging the information in OCRs, and identified putative causal variants in 122 AF-associated loci. Taking advantage of the fine-mapping results, our novel statistical procedure for gene discovery prioritized 46 high-confidence risk genes, highlighting transcription factors and signal transduction pathways important for heart development. In summary, our analysis provides a comprehensive map of AF risk variants and genes, and a general framework to integrate single-cell genomics with genetic studies of complex traits.

Integration of silicon chip microstructures for in-line microbial cell lysis in soft microfluidics.

The paper presents fabrication methodologies that integrate silicon components into soft microfluidic devices to perform microbial cell lysis for biological applications. The integration methodology consists of a silicon chip that is fabricated with microstructure arrays and embedded in a microfluidic device, which is driven by piezoelectric actuation to perform cell lysis by physically breaking microbial cell walls via micromechanical impaction. We present different silicon microarray geometries, their fabrication techniques, integration of said micropatterned silicon impactor chips into microfluidic devices, and device operation and testing on synthetic microbeads and two yeast species (S. cerevisiae and C. albicans) to evaluate their efficacy. The generalized strategy developed for integration of the micropatterned silicon impactor chip into soft microfluidic devices can serve as an important process step for a new class of hybrid silicon-polymeric devices for future cellular processing applications. The proposed integration methodology can be scalable and integrated as an in-line cell lysis tool with existing microfluidics assays.

Bile acid fitness determinants of a Bacteroides fragilis isolate from a human pouchitis patient.

Bacteroides fragilis comprises 1-5% of the gut microbiota in healthy humans but can expand to >50% of the population in ulcerative colitis (UC) patients experiencing inflammation. The mechanisms underlying such microbial blooms are poorly understood, but the gut of UC patients has physicochemical features that differ from healthy patients and likely impact microbial physiology. For example, levels of the secondary bile acid deoxycholate (DC) are highly reduced in the ileoanal J-pouch of UC colectomy patients. We isolated a B. fragilis strain from a UC patient with pouch inflammation (i.e. pouchitis) and developed it as a genetic model system to identify genes and pathways that are regulated by DC and that impact B. fragilis fitness in DC and crude bile. Treatment of B. fragilis with a physiologically relevant concentration of DC reduced cell growth and remodeled transcription of one-quarter of the genome. DC strongly induced expression of chaperones and select transcriptional regulators and efflux systems and downregulated protein synthesis genes. Using a barcoded collection of ≈50,000 unique insertional mutants, we further defined B. fragilis genes that contribute to fitness in media containing DC or crude bile. Genes impacting cell envelope functions including cardiolipin synthesis, cell surface glycosylation, and systems implicated in sodium-dependent bioenergetics were major bile acid fitness factors. As expected, there was limited overlap between transcriptionally regulated genes and genes that impacted fitness in bile when disrupted. Our study provides a genome-scale view of a B. fragilis bile response and genetic determinants of its fitness in DC and crude bile.

Multiomic analysis reveals cellular and epigenetic plasticity in intestinal pouches of ulcerative colitis patients.

Background & Aims: Total proctocolectomy with ileal pouch anal anastomosis (IPAA) is the standard of care for patients with severe treatment resistant ulcerative colitis (UC). Despite improvements in patient outcomes, about 50% of patients will develop inflammation of the pouch within 1-2 years following surgery. Establishment of UC pouches is associated with profound histological changes of the mucosa. A detailed characterization of these changes on a cellular and molecular level is crucial for an improved understanding of pouch physiology and diseases management. Methods: We generated cell-type-resolved transcriptional and epigenetic atlases of UC pouches using scRNA-seq and scATAC-seq data from paired biopsy samples from the ileal pouch and ileal segment above the pouch (pre-pouch) of UC-IPAA patients (n=6, female=2) without symptoms. We also collected data from paired biopsies of the terminal ileum (TI) and ascending colon (AC) from healthy controls (n=6, female=3). Results: We identified novel populations of colon-like absorptive and secretory epithelial cells, constituting a significant proportion of the epithelial cell fraction in the pouch but not in matched pre-pouch samples. Pouch-specific enterocytes expressed colon-specific genes, including CEACAM5, CA2. However, in contrast to normal colonic epithelium, these cells also expressed a range of inflammatory and secretory genes, similar to previously detected gene expression signatures in IBD patients. Comparison to longitudinal bulk RNA-seq data from UC pouches demonstrated that colon-like epithelial cells are present early after pouch functionalization and independently of subsequent pouchitis. Finally, single cell chromatin accessibility revealed activation colonic transcriptional regulators, including CDX1, NFIA, and EHF. Conclusion: UC pouches are characterized by partial colonic metaplasia of the epithelium. These data constitute a resource of transcriptomic and epigenetic signatures of cell populations in the pouch and provide an anchor for understanding the underlying molecular mechanisms of pouchitis.

Ribonucleotide reductase regulatory subunit M2 drives glioblastoma TMZ resistance through modulation of dNTP production.

During therapy, adaptations driven by cellular plasticity are partly responsible for driving the inevitable recurrence of glioblastoma (GBM). To investigate plasticity-induced adaptation during standard-of-care chemotherapy temozolomide (TMZ), we performed in vivo single-cell RNA sequencing in patient-derived xenograft (PDX) tumors of GBM before, during, and after therapy. Comparing single-cell transcriptomic patterns identified distinct cellular populations present during TMZ therapy. Of interest was the increased expression of ribonucleotide reductase regulatory subunit M2 (RRM2), which we found to regulate dGTP and dCTP production vital for DNA damage response during TMZ therapy. Furthermore, multidimensional modeling of spatially resolved transcriptomic and metabolomic analysis in patients' tissues revealed strong correlations between RRM2 and dGTP. This supports our data that RRM2 regulates the demand for specific dNTPs during therapy. In addition, treatment with the RRM2 inhibitor 3-AP (Triapine) enhances the efficacy of TMZ therapy in PDX models. We present a previously unidentified understanding of chemoresistance through critical RRM2-mediated nucleotide production.

Non-affine deformations in polymer hydrogels.

Most theories of soft matter elasticity assume that the local strain in a sample after deformation is identical everywhere and equal to the macroscopic strain, or equivalently that the deformation is affine. We discuss the elasticity of hydrogels of crosslinked polymers with special attention to affine and non-affine theories of elasticity. Experimental procedures to measure non-affine deformations are also described. Entropic theories, which account for gel elasticity based on stretching out individual polymer chains, predict affine deformations. In contrast, simulations of network deformation that result in bending of the stiff constituent filaments generally predict non-affine behavior. Results from experiments show significant non-affine deformation in hydrogels even when they are formed by flexible polymers for which bending would appear to be negligible compared to stretching. However, this finding is not necessarily an experimental proof of the non-affine model for elasticity. We emphasize the insights gained from experiments using confocal rheoscope and show that, in addition to filament bending, sample micro-inhomogeneity can be a significant alternative source of non-affine deformation.

Effect of plastic pollution on freshwater flora: A meta-analysis approach to elucidate the factors influencing plant growth and biochemical markers.

The deterioration in the water quality of urban water bodies through plastic contamination is emerging as a matter of serious concern. Microplastics (MPs) and nanoplastics (NPs) both affect the growth and productivity of aquatic flora. However, there have been a lot of variations in the reported studies which calls for revisiting the results with an analytical approach. Therefore, this study was designed to systematically evaluate the publications based on PRISMA (2020) guidelines. In this connection, 43 eligible articles were selected for meta-analysis followed by subgroup analysis to determine the impact of size, concentration, plastic polymers, and effect of plant classes on several physiological and biochemical parameters (growth, chlorophyll-a, carotenoids, protein, and antioxidant enzymes). The results indicated that the higher concentrations of plastics negatively affected the growth, and also enhanced the protein content and antioxidative enzyme activity. While, NPs were found to impart an inhibitory effect on pigment contents, along with a significant increase in protein content and antioxidative enzyme activity. Among the plastic polymers, dibutyl phthalate (DBP) showed a comparatively higher effect on growth, whereas the photosynthetic pigments were disrupted to a greater extent in the presence of polyvinyl chloride (PVC) plastics. Moreover, the growth parameters under plastic exposure were affected in the algal members to a greater extent in comparison to the other plant groups. Lastly, several plants like Komvophoron, Elodea, Myriophyllum, Nostoc, Raphidocelis, Scenedesmus, Utricularia, Dunaliella, and Lemna appeared to be more tolerant than others (Tolerance Index ≥ 0.8), showing a significantly minimal effect on growth inhibition.

Creating patient-specific vein models to characterize wall shear stress in hemodialysis population.

End-Stage Renal Disease (ESRD) patients require arteriovenous fistulas (AVF) that allow a mature vein to withstand hemodialysis. Unfortunately, venous thrombosis and stenosis in the cephalic vein arch after AVF placement is common and heavily influenced by hemodynamics. To better assess forces and flow behavior in the cephalic arch, we have built patient-specific millifluidic models that allow us to explore the complex interplay between patient-specific vein geometry and fluctuating hemodynamics. These 3D models were created from patient-specific intravascular ultrasound and venogram images obtained three- and twelve-months post AVF creation and fabricated into soft elastomer-based millifluidic devices. Geometric validation of fabricated phantom millifluidic device shows successful replication of original computational 3D model. Millifluidic devices were perfused with a blood-mimicking fluid containing fluorescent tracer beads under steady-state physiologic cephalic vein flow conditions (20 mL/min). Particle image velocimetry was employed to calculate wall shear stress (WSS) across the cephalic arches. Experimental WSS profile evaluation reveals that the physiologic cephalic arch model yields WSS values within physiologic range [76-760 mPa]. Moreover, upon comparing WSS profiles across all models, it is noticeable that WSS values increase as vein diameter decreases, which further supports employed experimental and analysis strategy. The presented millifluidic devices show promise for experimental WSS characterization under pathologic flow conditions to contrast from calculated physiologic hemodynamics and better understand WSS influence on thrombosis and stenosis in hemodialysis patients.

A molecular atlas of the human postmenopausal fallopian tube and ovary from single-cell RNA and ATAC sequencing.

As part of the Human Cell Atlas Initiative, our goal is to generate single-cell transcriptomics (single-cell RNA sequencing [scRNA-seq], 86,708 cells) and regulatory (single-cell assay on transposase accessible chromatin sequencing [scATAC-seq], 59,830 cells) profiles of the normal postmenopausal ovary and fallopian tube (FT). The FT contains 11 major cell types, and the ovary contains 6. The dominating cell type in the FT and ovary is the stromal cell, which expresses aging-associated genes. FT epithelial cells express multiple ovarian cancer risk-associated genes (CCDC170, RND3, TACC2, STK33, and ADGB) and show active communication between fimbrial epithelial cells and ovarian stromal cells. Integrated single-cell transcriptomics and chromatin accessibility data show that the regulatory landscape of the fimbriae is different from other anatomic regions. Cell types with similar gene expression in the FT display transcriptional profiles. These findings allow us to disentangle the cellular makeup of the postmenopausal FT and ovary, advancing our knowledge of gynecologic diseases in menopause.

Engineered exosomes targeting MYC reverse the proneural-mesenchymal transition and extend survival of glioblastoma.

Dysregulated Myc signaling is a key oncogenic pathway in glioblastoma multiforme (GBM). Yet, effective therapeutic targeting of Myc continues to be challenging. Here, we demonstrate that exosomes generated from human bone marrow mesenchymal stem cells (MSCs) engineered to encapsulate siRNAs targeting Myc (iExo-Myc) localize to orthotopic GBM tumors in mice. Treatment of late stage GBM tumors with iExo-Myc inhibits proliferation and angiogenesis, suppresses tumor growth, and extends survival. Transcriptional profiling of tumors reveals that the mesenchymal transition and estrogen receptor signaling pathways are impacted by Myc inhibition. Single nuclei RNA sequencing (snRNA-seq) shows that iExo-Myc treatment induces transcriptional repression of multiple growth factor and interleukin signaling pathways, triggering a mesenchymal to proneural transition and shifting the cellular landscape of the tumor. These data confirm that Myc is an effective anti-glioma target and that iExo-Myc offers a feasible, readily translational strategy to inhibit challenging oncogene targets for the treatment of brain tumors.