Hyperoxia prevents the dynamic neonatal increases in lung mesenchymal cell diversity

Rapid expansion of the pulmonary microvasculature through angiogenesis drives alveolarization, the final stage of lung development that occurs postnatally and dramatically increases lung gas-exchange surface area. Disruption of pulmonary angiogenesis induces long-term structural and physiologic lung abnormalities, including bronchopulmonary dysplasia, a disease characterized by compromised alveolarization. Although endothelial cells are primary determinants of pulmonary angiogenesis, mesenchymal cells (MC) play a critical and dual role in angiogenesis and alveolarization. Therefore, we performed single cell transcriptomics and in-situ imaging of the developing lung to profile mesenchymal cells during alveolarization and in the context of lung injury. Specific mesenchymal cell subtypes were present at birth with increasing diversity during alveolarization even while expressing a distinct transcriptomic profile from more mature correlates. Hyperoxia arrested the transcriptomic progression of the MC, revealed differential cell subtype vulnerability with pericytes and myofibroblasts most affected, altered cell to cell communication, and led to the emergence of Acta1 expressing cells. These insights hold the promise of targeted treatment for neonatal lung disease, which remains a major cause of infant morbidity and mortality across the world.

Fetal circular shunt in Ebstein's anomaly and non-steroidal anti-inflammatory treatment

A circular shunt is a poor prognostic factor associated with Ebstein's anomaly. Targeting the constriction of the ductus arteriosus (DA) in order to limit or resolve the circular shunt, has been shown to improve fetal outcomes. Prenatal non-steroidal anti-inflammatory drugs (NSAIDs) have been known to constrict the DA. Recently, prenatal NSAIDs have been used for that purpose in the treatment of circular shunt. Limited research shows that it may be an effective treatment leading to improved fetal outcomes. In this article, we did an extensive review of literature to describe this therapy's effectiveness and outcomes. 82% of fetuses were able to achieve ductal constriction with prenatal NSAID therapy. For fetuses who achieved ductal constriction, fetal demise was less likely (6%) when compared to those who were unable to achieve the same (50%). Of all the fetuses with hydrops, 50% had resoluation of hydrops with prenatal NSAID treatment.

Aging Fly Cell Atlas identifies exhaustive aging features at cellular resolution

Aging is characterized by a decline in tissue function, but the underlying changes at cellular resolution across the organism remain unclear. Here, we present the Aging Fly Cell Atlas, a single-nucleus transcriptomic map of the whole aging Drosophila. We characterized 163 distinct cell types and performed an in-depth analysis of changes in tissue cell composition, gene expression, and cell identities. We further developed aging clock models to predict fly age and show that ribosomal gene expression is a conserved predictive factor for age. Combining all aging features, we find distinctive cell type-specific aging patterns. This atlas provides a valuable resource for studying fundamental principles of aging in complex organisms.

Developmental diversity and unique sensitivity to injury of lung endothelial subtypes during postnatal growth

At birth, the lung is still immature, heightening susceptibility to injury but enhancing regenerative capacity. Angiogenesis drives postnatal lung development. Therefore, we profiled the transcriptional ontogeny and sensitivity to injury of pulmonary endothelial cells (EC) during early postnatal life. Although subtype speciation was evident at birth, immature lung EC exhibited transcriptomes distinct from mature counterparts, which progressed dynamically over time. Gradual, temporal changes in aerocyte capillary EC (CAP2) contrasted with more marked alterations in general capillary EC (CAP1) phenotype, including distinct CAP1 present only in the early alveolar lung expressing Peg3, a paternally imprinted transcription factor. Hyperoxia, an injury that impairs angiogenesis induced both common and unique endothelial gene signatures, dysregulated capillary EC crosstalk, and suppressed CAP1 proliferation while stimulating venous EC proliferation. These data highlight the diversity, transcriptomic evolution, and pleiotropic responses to injury of immature lung EC, possessing broad implications for lung development and injury across the lifespan.

A global and regional view of the opportunity for climate-smart mariculture

Food systems and the communities they support are increasingly challenged by climate change and the need to arrest escalating threats through mitigation and adaptation. To ensure climate change mitigation strategies can be implemented effectively and to support substantial gains in greenhouse gas emissions reduction, it is, therefore, valuable to understand where climate-smart strategies might be used for best effect. We assessed mariculture in 171 coastal countries for vulnerabilities to climate change (12 indicators) and opportunities to deliver climate mitigation outcomes (nine indicators). We identified Northern America and Europe as having comparatively lower regional vulnerability and higher opportunity for impact on climate mitigation. Australia, Canada, France, Italy, Japan, Republic of Korea, New Zealand, Norway and the United States of America were identified as well-positioned to advance strategies linked to mariculture. However, the nature of vulnerabilities and opportunities within and between all regions and countries varied, due to the formation of existing mariculture, human development factors and governance capacity. Our analysis demonstrates that global discussion will be valuable to motivating climate-smart approaches associated with mariculture, but to ensure these solutions contribute to a resilient future, for industry, ecosystems and communities, local adaptation will be needed to address constraints and to leverage local prospects.

This article is part of the theme issue ‘Nurturing resilient marine ecosystems’.

The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

Molecular characterization of cell types using single-cell transcriptome sequencing is revolutionizing cell biology and enabling new insights into the physiology of human organs. We created a human reference atlas comprising nearly 500,000 cells from 24 different tissues and organs, many from the same donor. This atlas enabled molecular characterization of more than 400 cell types, their distribution across tissues, and tissue-specific variation in gene expression. Using multiple tissues from a single donor enabled identification of the clonal distribution of T cells between tissues, identification of the tissue-specific mutation rate in B cells, and analysis of the cell cycle state and proliferative potential of shared cell types across tissues. Cell type-specific RNA splicing was discovered and analyzed across tissues within an individual.

Inhibiting USP16 rescues stem cell aging and memory in an Alzheimer's model

Alzheimer’s disease (AD) is a progressive neurodegenerative disease observed with aging that represents the most common form of dementia. To date, therapies targeting end-stage disease plaques, tangles, or inflammation have limited efficacy. Therefore, we set out to identify a potential earlier targetable phenotype. Utilizing a mouse model of AD and human fetal cells harboring mutant amyloid precursor protein, we show cell intrinsic neural precursor cell (NPC) dysfunction precedes widespread inflammation and amyloid plaque pathology, making it the earliest defect in the evolution of the disease. We demonstrate that reversing impaired NPC self-renewal via genetic reduction of USP16, a histone modifier and critical physiological antagonist of the Polycomb Repressor Complex 1, can prevent downstream cognitive defects and decrease astrogliosis in vivo. Reduction of USP16 led to decreased expression of senescence gene Cdkn2a and mitigated aberrant regulation of the Bone Morphogenetic Signaling (BMP) pathway, a previously unknown function of USP16. Thus, we reveal USP16 as a novel target in an AD model that can both ameliorate the NPC defect and rescue memory and learning through its regulation of both Cdkn2a and BMP signaling.

Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly

For more than 100 years, the fruit fly Drosophila melanogaster has been one of the most studied model organisms. Here, we present a single-cell atlas of the adult fly, Tabula Drosophilae, that includes 580,000 nuclei from 15 individually dissected sexed tissues as well as the entire head and body, annotated to >250 distinct cell types. We provide an in-depth analysis of cell type-related gene signatures and transcription factor markers, as well as sexual dimorphism, across the whole animal. Analysis of common cell types between tissues, such as blood and muscle cells, reveals rare cell types and tissue-specific subtypes. This atlas provides a valuable resource for the Drosophila community and serves as a reference to study genetic perturbations and disease models at single-cell resolution.

Heterogenous impairment of α cell function in type 2 diabetes is linked to cell maturation state

In diabetes, glucagon secretion from pancreatic α cells is dysregulated. The underlying mechanisms, and whether dysfunction occurs uniformly among cells, remain unclear. We examined α cells from human donors and mice using electrophysiological, transcriptomic, and computational approaches. Rising glucose suppresses α cell exocytosis by reducing P/Q-type Ca2+ channel activity, and this is disrupted in type 2 diabetes (T2D). Upon high-fat feeding of mice, α cells shift toward a "β cell-like" electrophysiological profile in concert with indications of impaired identity. In human α cells we identified links between cell membrane properties and cell surface signaling receptors, mitochondrial respiratory chain complex assembly, and cell maturation. Cell-type classification using machine learning of electrophysiology data demonstrated a heterogenous loss of "electrophysiologic identity" in α cells from donors with type 2 diabetes. Indeed, a subset of α cells with impaired exocytosis is defined by an enrichment in progenitor and lineage markers and upregulation of an immature transcriptomic phenotype, suggesting important links between α cell maturation state and dysfunction.

Climate-Friendly Seafood: The Potential for Emissions Reduction and Carbon Capture in Marine Aquaculture

Aquaculture is a critical food source for the world's growing population, producing 52% of the aquatic animal products consumed. Marine aquaculture (mariculture) generates 37.5% of this production and 97% of the world's seaweed harvest. Mariculture products may offer a climate-friendly, high-protein food source, because they often have lower greenhouse gas (GHG) emission footprints than do the equivalent products farmed on land. However, sustainable intensification of low-emissions mariculture is key to maintaining a low GHG footprint as production scales up to meet future demand. We examine the major GHG sources and carbon sinks associated with fed finfish, macroalgae and bivalve mariculture, and the factors influencing variability across sectors. We highlight knowledge gaps and provide recommendations for GHG emissions reductions and carbon storage, including accounting for interactions between mariculture operations and surrounding marine ecosystems. By linking the provision of maricultured products to GHG abatement opportunities, we can advance climate-friendly practices that generate sustainable environmental, social, and economic outcomes.

Expansion of the rare Eucalyptus risdonii under climate change through hybridization with a closely related species despite hybrid inferiority

BACKGROUND AND AIMS

Hybridization is increasingly recognized as an integral part of the dynamics of species range expansion and contraction. Thus, it is important to understand the reproductive barriers between co-occurring species. Extending previous studies that argued that the rare Eucalyptus risdonii was expanding into the range of the surrounding E. amygdalina by both seed and pollen dispersal, we here investigate the long-term fitness of both species and their hybrids and whether expansion is continuing.

METHODS

We assessed the survival of phenotypes representing a continuum between the two pure species in a natural hybrid swarm after 29 years, along with seedling recruitment. The performance of pure species as well as of artificial and natural hybrids was also assessed over 28 years in a common garden trial.

KEY RESULTS

In the hybrid zone, E. amygdalina adults showed greater mortality than E. risdonii, and the current seedling cohort is still dominated by E. risdonii phenotypes. Morphologically intermediate individuals appeared to be the least fit. Similar results were observed after growing artificial first-generation and natural hybrids alongside pure species families in a common garden trial. Here, the survival, reproduction, health and growth of the intermediate hybrids were significantly less than those of either pure species, consistent with hybrid inferiority, although this did not manifest until later reproductive ages. Among the variable progeny of natural intermediate hybrids, the most E. risdonii-like phenotypes were the most fit.

CONCLUSIONS

This study contributes to the increasing number of reports of hybrid inferiority in Eucalyptus, suggesting that post-zygotic barriers contribute to the maintenance of species integrity even between closely related species. However, with fitness rapidly recovered following backcrossing, it is argued that hybridization can still be an important evolutionary process, in the present case appearing to contribute to the range expansion of the rare E. risdonii in response to climate change.

Coronary blood vessels from distinct origins converge to equivalent states during mouse and human development

Most cell fate trajectories during development follow a diverging, tree-like branching pattern, but the opposite can occur when distinct progenitors contribute to the same cell type. During this convergent differentiation, it is unknown if cells ‘remember’ their origins transcriptionally or whether this influences cell behavior. Most coronary blood vessels of the heart develop from two different progenitor sources—the endocardium (Endo) and sinus venosus (SV)—but whether transcriptional or functional differences related to origin are retained is unknown. We addressed this by combining lineage tracing with single-cell RNA sequencing (scRNAseq) in embryonic and adult mouse hearts. Shortly after coronary development begins, capillary endothelial cells (ECs) transcriptionally segregated into two states that retained progenitor-specific gene expression. Later in development, when the coronary vasculature is well established but still remodeling, capillary ECs again segregated into two populations, but transcriptional differences were primarily related to tissue localization rather than lineage. Specifically, ECs in the heart septum expressed genes indicative of increased local hypoxia and decreased blood flow. Adult capillary ECs were more homogeneous with respect to both lineage and location. In agreement, SV- and Endo-derived ECs in adult hearts displayed similar responses to injury. Finally, scRNAseq of developing human coronary vessels indicated that the human heart followed similar principles. Thus, over the course of development, transcriptional heterogeneity in coronary ECs is first influenced by lineage, then by location, until heterogeneity declines in the homeostatic adult heart. These results highlight the plasticity of ECs during development, and the validity of the mouse as a model for human coronary development.

A plug and play microfluidic platform for standardized sensitive low-input chromatin immunoprecipitation

Epigenetic profiling by chromatin immunoprecipitation followed by sequencing (ChIP-seq) has become a powerful tool for genome-wide identification of regulatory elements, for defining transcriptional regulatory networks, and for screening for biomarkers. However, the ChIP-seq protocol for low-input samples is laborious and time-consuming and suffers from experimental variation, resulting in poor reproducibility and low throughput. Although prototypic microfluidic ChIP-seq platforms have been developed, these are poorly transferable as they require sophisticated custom-made equipment and in-depth microfluidic and ChIP expertise, while lacking parallelization. To enable standardized, automated ChIP-seq profiling of low-input samples, we constructed microfluidic PDMS-based plates capable of performing 24 sensitive ChIP reactions within 30 min of hands-on time and 4.5 h of machine-running time. These disposable plates can be conveniently loaded into a widely available controller for pneumatics and thermocycling. In light of the plug and play (PnP) ChIP plates and workflow, we named our procedure PnP-ChIP-seq. We show high-quality ChIP-seq on hundreds to a few thousand of cells for all six post-translational histone modifications that are included in the International Human Epigenome Consortium set of reference epigenomes. PnP-ChIP-seq robustly detects epigenetic differences on promoters and enhancers between naive and more primed mouse embryonic stem cells (mESCs). Furthermore, we used our platform to generate epigenetic profiles of rare subpopulations of mESCs that resemble the two-cell stage of embryonic development. PnP-ChIP-seq allows nonexpert laboratories worldwide to conveniently run robust, standardized ChIP-seq, whereas its high throughput, consistency, and sensitivity pave the way toward large-scale profiling of precious sample types such as rare subpopulations of cells or biopsies.

Single-cell transcriptomes of developing and adult olfactory receptor neurons in Drosophila

Recognition of environmental cues is essential for the survival of all organisms. Transcriptional changes occur to enable the generation and function of the neural circuits underlying sensory perception. To gain insight into these changes, we generated single-cell transcriptomes of Drosophila olfactory- (ORNs), thermo-, and hygro-sensory neurons at an early developmental and adult stage using single-cell and single-nucleus RNA sequencing. We discovered that ORNs maintain expression of the same olfactory receptors across development. Using receptor expression and computational approaches, we matched transcriptomic clusters corresponding to anatomically and physiologically defined neuron types across multiple developmental stages. We found that cell-type-specific transcriptomes partly reflected axon trajectory choices in development and sensory modality in adults. We uncovered stage-specific genes that could regulate the wiring and sensory responses of distinct ORN types. Collectively, our data reveal transcriptomic features of sensory neuron biology and provide a resource for future studies of their development and physiology.

Temporal evolution of single-cell transcriptomes of Drosophila olfactory projection neurons

Neurons undergo substantial morphological and functional changes during development to form precise synaptic connections and acquire specific physiological properties. What are the underlying transcriptomic bases? Here, we obtained the single-cell transcriptomes of Drosophila olfactory projection neurons (PNs) at four developmental stages. We decoded the identity of 21 transcriptomic clusters corresponding to 20 PN types and developed methods to match transcriptomic clusters representing the same PN type across development. We discovered that PN transcriptomes reflect unique biological processes unfolding at each stage-neurite growth and pruning during metamorphosis at an early pupal stage; peaked transcriptomic diversity during olfactory circuit assembly at mid-pupal stages; and neuronal signaling in adults. At early developmental stages, PN types with adjacent birth order share similar transcriptomes. Together, our work reveals principles of cellular diversity during brain development and provides a resource for future studies of neural development in PNs and other neuronal types.

Cerebellar nuclei evolved by repeatedly duplicating a conserved cell-type set

How have complex brains evolved from simple circuits? Here we investigated brain region evolution at cell-type resolution in the cerebellar nuclei, the output structures of the cerebellum. Using single-nucleus RNA sequencing in mice, chickens, and humans, as well as STARmap spatial transcriptomic analysis and whole-central nervous system projection tracing, we identified a conserved cell-type set containing two region-specific excitatory neuron classes and three region-invariant inhibitory neuron classes. This set constitutes an archetypal cerebellar nucleus that was repeatedly duplicated to form new regions. The excitatory cell class that preferentially funnels information to lateral frontal cortices in mice becomes predominant in the massively expanded human lateral nucleus. Our data suggest a model of brain region evolution by duplication and divergence of entire cell-type sets.

Northstar enables automatic classification of known and novel cell types from tumor samples

Single cell transcriptomics is revolutionising our understanding of tissue and disease heterogeneity, yet cell type identification remains a partially manual task. Published algorithms for automatic cell annotation are limited to known cell types and fail to capture novel populations, especially cancer cells. We developed northstar, a computational approach to classify thousands of cells based on published data within seconds while simultaneously identifying and highlighting new cell states such as malignancies. We tested northstar on data from glioblastoma, melanoma, and seven different healthy tissues and obtained high accuracy and robustness. We collected eleven pancreatic tumors and identified three shared and five private neoplastic cell populations, offering insight into the origins of neuroendocrine and exocrine tumors. Northstar is a useful tool to assign known and novel cell type and states in the age of cell atlases.

Diverse homeostatic and immunomodulatory roles of immune cells in the developing mouse lung at single cell resolution

At birth, the lungs rapidly transition from a pathogen-free, hypoxic environment to a pathogen-rich, rhythmically distended air-liquid interface. Although many studies have focused on the adult lung, the perinatal lung remains unexplored. Here, we present an atlas of the murine lung immune compartment during early postnatal development. We show that the late embryonic lung is dominated by specialized proliferative macrophages with a surprising physical interaction with the developing vasculature. These macrophages disappear after birth and are replaced by a dynamic mixture of macrophage subtypes, dendritic cells, granulocytes, and lymphocytes. Detailed characterization of macrophage diversity revealed an orchestration of distinct subpopulations across postnatal development to fill context-specific functions in tissue remodeling, angiogenesis, and immunity. These data both broaden the putative roles for immune cells in the developing lung and provide a framework for understanding how external insults alter immune cell phenotype during a period of rapid lung growth and heightened vulnerability.

Single-Cell Transcriptomes Reveal Diverse Regulatory Strategies for Olfactory Receptor Expression and Axon Targeting

The regulatory mechanisms by which neurons coordinate their physiology and connectivity are not well understood. The Drosophila olfactory receptor neurons (ORNs) provide an excellent system to investigate this question. Each ORN type expresses a unique olfactory receptor, or a combination thereof, and sends their axons to a stereotyped glomerulus. Using single-cell RNA sequencing, we identified 33 transcriptomic clusters for ORNs and mapped 20 to their glomerular types, demonstrating that transcriptomic clusters correspond well with anatomically and physiologically defined ORN types. Each ORN type expresses hundreds of transcription factors. Transcriptome-instructed genetic analyses revealed that (1) one broadly expressed transcription factor (Acj6) only regulates olfactory receptor expression in one ORN type and only wiring specificity in another type, (2) one type-restricted transcription factor (Forkhead) only regulates receptor expression, and (3) another type-restricted transcription factor (Unplugged) regulates both events. Thus, ORNs utilize diverse strategies and complex regulatory networks to coordinate their physiology and connectivity.

A global spatial analysis reveals where marine aquaculture can benefit nature and people

Aquaculture of bivalve shellfish and seaweed represents a global opportunity to simultaneously advance coastal ecosystem recovery and provide substantive benefits to humanity. To identify marine ecoregions with the greatest potential for development of shellfish and seaweed aquaculture to meet this opportunity, we conducted a global spatial analysis using key environmental (e.g., nutrient pollution status), socioeconomic (e.g., governance quality), and human health factors (e.g., wastewater treatment prevalence). We identify a substantial opportunity for strategic sector development, with the highest opportunity marine ecoregions for shellfish aquaculture centered on Oceania, North America, and portions of Asia, and the highest opportunity for seaweed aquaculture distributed throughout Europe, Asia, Oceania, and North and South America. This study provides insights into specific areas where governments, international development organizations, and investors should prioritize new efforts to drive changes in public policy, capacity-building, and business planning to realize the ecosystem and societal benefits of shellfish and seaweed aquaculture.

Miniaturised interaction proteomics on a microfluidic platform with ultra-low input requirements

Essentially all cellular processes are orchestrated by protein-protein interactions (PPIs). In recent years, affinity purification coupled to mass spectrometry (AP-MS) has been the preferred method to identify cellular PPIs. Here we present a microfluidic-based AP-MS workflow, called on-chip AP-MS, to identify PPIs using minute amounts of input material. By using this automated platform we purify the human Cohesin, CCC and Mediator complexes from as little as 4 micrograms of input lysate, representing a 50─100-fold downscaling compared to regular microcentrifuge tube-based protocols. We show that our platform can be used to affinity purify tagged baits as well as native cellular proteins and their interaction partners. As such, our method holds great promise for future biological and clinical AP-MS applications in which sample amounts are limited.

Chondroprotection by urocortin involves blockade of the mechanosensitive ion channel Piezo1

Osteoarthritis (OA) is characterised by progressive destruction of articular cartilage and chondrocyte cell death. Here, we show the expression of the endogenous peptide urocortin1 (Ucn1) and two receptor subtypes, CRF-R1 and CRF-R2, in primary human articular chondrocytes (AC) and demonstrate its role as an autocrine/paracrine pro-survival factor. This effect could only be removed using the CRF-R1 selective antagonist CP-154526, suggesting Ucn1 acts through CRF-R1 when promoting chondrocyte survival. This cell death was characterised by an increase in p53 expression, and cleavage of caspase 9 and 3. Antagonism of CRF-R1 with CP-154526 caused an accumulation of intracellular calcium (Ca²⁺) over time and cell death. These effects could be prevented with the non-selective cation channel blocker Gadolinium (Gd³⁺). Therefore, opening of a non-selective cation channel causes cell death and Ucn1 maintains this channel in a closed conformation. This channel was identified to be the mechanosensitive channel Piezo1. We go on to determine that this channel inhibition by Ucn1 is mediated initially by an increase in cyclic adenosine monophosphate (cAMP) and a subsequent inactivation of phospholipase A₂ (PLA₂), whose metabolites are known to modulate ion channels. Knowledge of these novel pathways may present opportunities for interventions that could abrogate the progression of OA.

Genetic differentiation in spite of high gene flow in the dominant rainforest tree of southeastern Australia, Nothofagus cunninghamii

Nothofagus cunninghamii is a long-lived, wind-pollinated tree species that dominates the cool temperate rainforests of southeastern Australia. The species' distribution is more or less continuous in western Tasmania but is fragmented elsewhere. However, it is unknown whether this fragmentation has affected the species' genetic architecture. Thus, we examined N. cunninghamii using 12 nuclear microsatellites and 633 individuals from 18 populations spanning the species' natural range. Typical of wind-pollinated trees, there was low range-wide genetic structure (FST=0.04) consistent with significant gene flow across most of the species' range. However, gene flow was not high enough to overcome the effects of drift across some disjunctions. Victorian populations (separated from Tasmania by the 240 km wide Bass Strait) formed a genetic group distinct from Tasmanian populations, had lower diversity (mean allelic richness (Ar)=5.4 in Victoria versus 6.9 in Tasmania) and were significantly more differentiated from one another than those in Tasmania (FST=0.045 in Victoria versus 0.012 in Tasmania). Evidence for bottlenecking was found in small populations that were at least 20 km from other populations. Interestingly, we found little divergence in microsatellite markers between the extremes of genetically based morphological and physiological altitudinal clines suggesting adaptive differentiation is strongly driven by selection because it is likely to be occurring in the presence of gene flow. Even though the cool temperate rainforests of Australia are highly relictual, the species is relatively robust to population fragmentation due to high levels of genetic diversity and gene flow, especially in Tasmania.

Pathogenicity and molecular characteristics of infectious bronchitis virus (IBV) strains isolated from broilers showing diarrhoea and respiratory disease

Abstract 1. The possibility that infectious bronchitis virus (IBV) variants isolated from broilers with enteric and respiratory problems have a different tropism and pathological outcome from those IBV strains causing classical respiratory disease was investigated. 2. IBV variants were isolated from broiler flocks with enteric and respiratory problems in two regions of Brazil. The USP-10 isolate, of enteric origin, was inoculated via the oral oroculonasal routes into IBV-antibody-free broilers and specific pathogen-free (SPF) chickens to determine tissue tropism and pathogenicity and compared with an IBV variant (USP-50) isolated from chickens showing signs of respiratory disease only. 3. Both USP-10 and USP-50 strains caused similar pathological patterns by either route of inoculation. Both variants were detected in respiratory and non-respiratory tissues, including the kidney, intestine and testis. 4. Broilers were more susceptible to infection than SPF chickens, and seroconversion was detected in all of the chicks.

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex

Large-scale surveys of single-cell gene expression have the potential to reveal rare cell populations and lineage relationships, but require efficient methods for cell capture and mRNA sequencing^1–4. Although cellular barcoding strategies allow parallel sequencing of single cells at ultra-low depths⁵, the limitations of shallow sequencing have not been directly investigated. By capturing 301 single cells from 11 populations using microfluidics and analyzing single-cell transcriptomes across downsampled sequencing depths, we demonstrate that shallow single-cell mRNA sequencing (~50,000 reads per cell) is sufficient for unbiased cell-type classification and biomarker identification. In developing cortex we identify diverse cell types including multiple progenitor and neuronal subtypes, and we identify EGR1 and FOS as previously unreported candidate targets of Notch signaling in human but not mouse radial glia. Our strategy establishes an efficient method for unbiased analysis and comparison of cell populations from heterogeneous tissue by microfluidic single-cell capture and low-coverage sequencing of many cells.

A review of the Institute of Medicine's analysis of using chimpanzees in biomedical research

We argue that the recommendations made by the Institute of Medicine's 2011 report, Chimpanzees in Biomedical and Behavioral Research: Assessing the Necessity, are methodologically and ethically confused. We argue that a proper understanding of evolution and complexity theory in terms of the science and ethics of using chimpanzees in biomedical research would have had led the committee to recommend not merely limiting but eliminating the use of chimpanzees in biomedical research. Specifically, we argue that a proper understanding of the difference between the gross level of examination of species and examinations on finer levels can shed light on important methodological and ethical inconsistencies leading to ignorance of potentially unethical practices and policies regarding the use of animals in scientific research.

Chiropractors as Primary Spine Care Providers: precedents and essential measures

Chiropractors have the potential to address a substantial portion of spinal disorders; however the utilization rate of chiropractic services has remained low and largely unchanged for decades. Other health care professions such as podiatry/chiropody, physiotherapy and naturopathy have successfully gained public and professional trust, increases in scope of practice and distinct niche positions within mainstream health care. Due to the overwhelming burden of spine care upon the health care system, the establishment of a 'primary spine care provider' may be a worthwhile niche position to create for society's needs. Chiropractors could fulfill this role, but not without first reviewing and improving its approach to the management of spinal disorders. Such changes have already been achieved by the chiropractic profession in Switzerland, Denmark, and New Mexico, whose examples may serve as important templates for renewal here in Canada.

A microfluidic device for preparing next generation DNA sequencing libraries and for automating other laboratory protocols that require one or more column chromatography steps

Library preparation for next-generation DNA sequencing (NGS) remains a key bottleneck in the sequencing process which can be relieved through improved automation and miniaturization. We describe a microfluidic device for automating laboratory protocols that require one or more column chromatography steps and demonstrate its utility for preparing Next Generation sequencing libraries for the Illumina and Ion Torrent platforms. Sixteen different libraries can be generated simultaneously with significantly reduced reagent cost and hands-on time compared to manual library preparation. Using an appropriate column matrix and buffers, size selection can be performed on-chip following end-repair, dA tailing, and linker ligation, so that the libraries eluted from the chip are ready for sequencing. The core architecture of the device ensures uniform, reproducible column packing without user supervision and accommodates multiple routine protocol steps in any sequence, such as reagent mixing and incubation; column packing, loading, washing, elution, and regeneration; capture of eluted material for use as a substrate in a later step of the protocol; and removal of one column matrix so that two or more column matrices with different functional properties can be used in the same protocol. The microfluidic device is mounted on a plastic carrier so that reagents and products can be aliquoted and recovered using standard pipettors and liquid handling robots. The carrier-mounted device is operated using a benchtop controller that seals and operates the device with programmable temperature control, eliminating any requirement for the user to manually attach tubing or connectors. In addition to NGS library preparation, the device and controller are suitable for automating other time-consuming and error-prone laboratory protocols requiring column chromatography steps, such as chromatin immunoprecipitation.

Enteric viruses in Brazilian turkey flocks: single and multiple virus infection frequency according to age and clinical signs of intestinal disease

Poult enteritis complex has been associated with enteritis and reduction in growth rates in commercial turkeys worldwide. Intestinal samples from 76 turkey flocks from different Brazilian states affected or not with intestinal disorders were evaluated for the presence of adenovirus groups 1 and 2 (TAV), astrovirus types 1 and 2 (TAstV-1 and TAstV-2), turkey coronavirus (TCoV), reovirus, rotavirus, and avian nephritis virus (ANV) using PCR. The percentage of positive samples was categorized according to the geographic origin, age of the flocks, and presence of clinical signs of intestinal disease. The percentage of samples that were positive for at least one virus was 93.4%, whereas the percentage of samples that were positive for more than one virus was 69.7%. An average of 3.20 viruses per sample was detected in turkeys in the growing phase of the production cycle (1 to 4 wk of age). The TAstV-1 and TCoV were the most frequently observed viruses in growing phase turkeys and occurred simultaneously in 85% of these samples. In turkeys in the finishing phase of development (5 to 18 wk), a lower average number of viruses was observed (2.41), and the most frequent viruses isolated in these turkeys were TAstV-1 (57.1%) and rotavirus (51.8%). Overall, every virus was detected more frequently in growing phase turkeys than in finishing phase turkeys with the exception of TAV. Samples from flocks exhibiting clinical signs of intestinal disease showed a higher rate of positivity, and TAstV-1, TAstV-2, and TCoV were the most frequently occurring viruses in this cohort. Birds without clinical signs most frequently harbored TAstV-1 and rotavirus. Future studies should focus on the description and elucidation of the role of each virus, as well as the pathogenic and immunological implications of the different combinations of viruses in turkeys.

Effect of T-cell suppression by cyclosporin on primary and persistent infections of infectious bronchitis virus in chickens

Two-week-old white leghorn (WL) chickens were inoculated intra-nasally with 4.51ogio median ciliostatic doses (CD50) of IBV strain M41. Cyclosporin (CSP) (100 mg/kg body weight) was injected intra-muscularly 3 days before virus infection and every 3 days till day 15 post-infection (p.i.). Significant reduction in proliferation responses of whole blood lymphocytes to a T-cell mitogen, concanavalin A were induced, but not to a B and T-cell mitogen, pokeweed mitogen. Mortality in the IBV + CSP group was 18%, but in the IBV group it was 2%. No significant differences in the total number of virus isolations were seen between the two groups. Virus titres in trachea, lung and kidneys of the T-cell suppressed chickens were slightly higher and histopathological lesions more severe. Thus it appeared that T-cells may play a major role in limiting severity and lethality of IBV infections rather than clearing virus. To confirm this, another experiment was performed in which 2-week-old brown leghorn (BrL) chickens, relatively resistant to IBV were infected with a pool of IBV strains. Mortality was 43% in the IBV + CSP group and zero with IBV alone. Earlier reports using the same pool of IBV strains have shown a mortality of 47% in line 151 chicks, a line sensitive to IBV infection. Thus, a resistant line was induced to behave like a susceptible line by T-cell suppression. Virus titres were always 1 to 3 logs higher in the kidneys of T-cell suppressed BrL chicks. Attempts to induce re-excretion of virus by CSP treatment of WL chickens infected with the IBV strain M41 when 2 weeks old were unsuccessful, but when chicks were infected with the same strain at day-old and given CSP injections from 5 weeks p.i., virus re-excretion was primarily seen from the kidneys and not the caecal tonsil. Thus the kidney appears to be the primary site of IBV persistence. The pathogenesis of the disease in T-cell suppressed chickens is discussed.

Effect of heterophil depletion by 5-fluorouracil on infectious bronchitis virus infection in chickens

An anti-tumour drug, 5-fluorouracil (5 FU) was used to deplete heterophils in 11-day-old white leghorn chickens. The reduction in heterophil numbers was monitored by total and differential white cell counts in the peripheral blood. Three days after injection of 5 FU, when the heterophil numbers were significantly reduced, chickens were infected with the Massachusetts strain of infectious bronchitis virus (IBV). Following infection, although the numbers of birds exhibiting clinical signs (nasal exudate) were significantly higher in the 5 FU treated group, the consistency of the nasal exudate was characteristically thin and watery. No significant differences were seen in the virus titres in trachea, lung and kidney between normal and heteropaenic chickens infected with IBV. However, the epithelial cell damage in the tracheal sections was less in the heterophil-depleted chickens.

An in vitro comparison of the virulence of seven strains of infectious bronchitis virus using tracheal and oviduct organ cultures

The virulence of seven infectious bronchitis virus (IBV) strains for tracheal and oviduct ciliated epithelium was assessed using an in vitro tracheal organ culture (TOC) and oviduct organ culture (OOC) system. The OOC were prepared using oviducts obtained from oestrogen-treated chicks. All strains tested stopped ciliary beating in the oviduct by day 5 post-inoculation (p.i.) and in the trachea by day 3 p.i. This corresponded with the absence of immunofluorescent-stained cells in the epithelium at that time. The time taken for a 50% reduction of relative ciliary activity (RCA) of oviduct cilia was shortest for strain 6 (serotype D207) and longest for strain G (enterotropic variant). Strains 7 (serotype D3896) and M41 were the most pathogenic for tracheal cilia, while strains 6 and G were less pathogenic. A calmod-ulin (CAM) assay was standardized to quantify the epithelial cell damage to oviducts caused by IBV. It was found that strains 6 and M41 were the most pathogenic. The use of time taken to achieve a 50% reduction in RCA and the CAM assay for in vitro pathotyping of IBV isolates is discussed. The susceptibility of OOC or TOC for five IBV strains was compared. It was found that strains 25 and 793B had equal predilection for both, while for 25, G and M41, TOC was more susceptible.

Cross-reactive cellular immune responses in chickens vaccinated with live infectious bronchitis virus vaccine

Two-week-old chickens were vaccinated intra-nasally with a live infectious bronchitis virus (IBV) vaccine (H120). On days 4, 7, 11 and 14 post-vaccination (p.v.) spleen mononuclear cells (MNC) prepared from control and vaccinated chickens were stimulated in vitro with homologous (strain M41) and heterologous (strains 7 and 793/B) virus antigens. Antigen-specific lymphoproliferation and interleukin-2 (IL-2) and interferon-y (IFN) production were used to measure cross-reactive cell mediated immune responses. In antigen-specific lymphoproliferation assays, it was found that while 4/16 vaccinated birds responded to the homologous antigen, only one responded to an heterologous antigen (strain 7). However, IL-2 production was seen in the supernatants of spleen MNC from vaccinated chickens stimulated with all three antigens. Production of IFN was also demonstrated in samples stimulated with the homologous and one heterologous (strain 7) antigen. Thus it appears that, following vaccination of chickens with live IBV vaccine, cross-reactive cellular immune responses occur that vary in magnitude with the strain of IBV used for in vitro stimulation.

Susceptibility of organ cultures from chicken tissues for strains of infectious bronchitis virus isolated from the intestine

Organ cultures were prepared from various levels of intestine and kidney of 2 to 4-week old specific-pathogen-free chickens, and their susceptibility to ten strains of infectious bronchitis virus isolated from the chicken intestine and the Massachusetts strain M41 was investigated. The ability of a virus to grow depended on the strain of virus and size of the inoculum. While proventriculus, bursa and kidney were found to be universally susceptible to all viruses tested, some strains did not grow in caecal tonsils or rectum. Strain M41 showed little difference in pattern of tissue replication compared with several other strains isolated from the gut and actually grew in a wider range than some. Duodenum, jejunum and ileum were found to be non-permissive to all strains tested, even after a high input inoculum.

Microwave or autoclave treatments destroy the infectivity of infectious bronchitis virus and avian pneumovirus but allow detection by reverse transcriptase-polymerase chain reaction

A method is described for enabling safe transit of denatured virus samples for polymerase chain reaction (PCR) identification without the risk of unwanted viable viruses. Cotton swabs dipped in avian infectious bronchitis virus (IBV) or avian pneumovirus (APV) were allowed to dry. Newcastle disease virus and avian influenza viruses were used as controls. Autoclaving and microwave treatment for as little as 20 sec destroyed the infectivity of all four viruses. However, both IBV and APV could be detected by reverse transcriptase (RT)-PCR after autoclaving and as long as 5 min microwave treatment (Newcastle disease virus and avian influenza viruses were not tested). Double microwave treatment of IBV and APV with an interval of 2 to 7 days between was tested. After the second treatment, RT-PCR products were readily detected in all samples. Swabs from the tracheas and cloacas of chicks infected with IBV shown to contain infectious virus were microwaved. Swabs from both sources were positive by RT-PCR. Microwave treatment appears to be a satisfactory method of inactivating virus while preserving nucleic acid for PCR identification.

Abstract 1164: Parallel preparation of targeted resequencing libraries from 480 genomic regions using multiplex PCR on the Access Array system

Next generation sequencing platforms have dramatically reduced sequencing costs. However, it currently remains too expensive to routinely resequence entire human genomes in order to discover genetic variants or somatic mutations underlying tumorigenesis. Therefore, a need exists for multiplexed, targeted amplification methods that allow for the analysis of multiple genomic regions in large cohorts. Available targeted enrichment technologies are either aimed at the capture of regions of interest from a single sample, exhibit uneven representation or require significant amounts of input material. The novel microfluidic platform, the Access Array system, combines 48 samples with 48 primer sets resulting in 2,304 simultaneously occurring PCR amplifications requiring as little as 50ng DNA per sample. PCR products generated on the Access Array system can be used for sequencing on all next-generation sequencing platforms, including 454 GS FLX and Illumina GAII. To increase coverage and throughput, PCR reactions can be multiplexed within Access Array chips generating up to 480 amplicons per sample.

As proof-of-principal experiments, we have carried out multiplexed amplifications of a set of commonly mutated cancer gene exons across 48 genomic DNA samples. In initial experiments, 580 primer pairs were validated in individual PCR reactions in 96-well plates. Each primer pair was designed to include 5’ sequences that allow for the incorporation of 454 and Illumina adapters necessary for subsequent emPCR and cluster generation, respectively. 480 primer pairs that produced a single band of the correct size, as determined on a Caliper LabChip system, were selected for multiplex PCR experiments. Primer pairs yielding amplicons with a similar size were combined in groups of 10 sets, resulting in 48 primer pools of 10 primer pairs each. Multiplex PCR was carried out on Access Array chips, followed by harvesting of the 48 amplicon pools. Each pool was diluted and then subjected to a second round of PCR in standard 96-well plates with barcoded universal primers corresponding to the 454 and Illumina sequences. The resulting products are 48 uniquely barcoded amplicon pools, each comprising 480 amplicons derived from one sample, that are ready for sequencing. We will present sequencing data generated on both 454 and Illumina systems.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1164.

Abstract 1147: High-throughput nanofluidic PCR-based preparation of 454 sequencing libraries for identifying mutations in EGFR and MET

The epidermal growth factor receptor (EGFR) and mesenchymal-epithelial transition factor (MET) play important roles in cancer development and are promising targets for anticancer therapies. Mutations in the EGFR and MET genes are associated with multiple types of cancer and the ability to detect variants in these genes is crucial for a better understanding of disease progression and response to targeted therapeutics. Next-generation sequencers (e.g. 454, Illumina) hold great potential for detecting disease-specific alterations within patient populations for a given cancer type. However, current approaches for targeted resequencing of specific genetic regions are not well suited to studying the hundreds or thousands of patient samples required to assign significance to mutations.

We have developed a novel nanofluidic platform, the Access Array™ system, which enables the robust, simultaneous amplification of 48 PCR products (amplicon) from 48 samples in parallel using only 50ng input DNA per sample. In addition, we have developed a primer design strategy that incorporates sample-specific barcodes and 454 sequencing adaptors into each amplicon, removing the need for library preparation before sequencing. We will present sequencing data collected from amplicon libraries prepared using the Access Array system to amplify 48 exon regions of the EGFR and MET genes from the NCI-60 cell lines. Sequencing data from these libraries demonstrates excellent uniformity in representation between amplicons and across samples. We will present data mapping mutations within these genes across the NCI-60, and discuss the use of Access Array enrichment panels in monitoring mutations across large patient populations.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1147.

Quantifying EGFR Alterations in the Lung Cancer Genome with Nanofluidic Digital PCR Arrays

Background: The EGFR [epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)] gene is known to harbor genomic alterations in advanced lung cancer involving gene amplification and kinase mutations that predict the clinical response to EGFR-targeted inhibitors. Methods for detecting such molecular changes in lung cancer tumors are desirable.

Methods: We used a nanofluidic digital PCR array platform and 16 cell lines and 20 samples of genomic DNA from resected tumors (stages I–III) to quantify the relative numbers of copies of the EGFR gene and to detect mutated EGFR alleles in lung cancer. We assessed the relative number of EGFR gene copies by calculating the ratio of the number of EGFR molecules (measured with a 6-carboxyfluorescein–labeled Scorpion™ assay) to the number of molecules of the single-copy gene RPP30 (ribonuclease P/MRP 30kDa subunit) (measured with a 6-carboxy-X-rhodamine–labeled TaqMan™ assay) in each panel. To assay for the EGFR L858R (exon 21) mutation and exon 19 in-frame deletions, we used the ARMS™ and Scorpion technologies in a DxS/Qiagen EGFR29 Mutation Test Kit for the digital PCR array.

Results: The digital array detected and quantified rare gefitinib/erlotinib-sensitizing EGFR mutations (0.02%–9.26% abundance) that were present in formalin-fixed, paraffin-embedded samples of early-stage resectable lung tumors without an associated increase in gene copy number. Our results also demonstrated the presence of intratumor molecular heterogeneity for the clinically relevant EGFR mutated alleles in these early-stage lung tumors.

Conclusions: The digital PCR array platform allows characterization and quantification of oncogenes, such as EGFR, at the single-molecule level. Use of this nanofluidics platform may provide deeper insight into the specific roles of clinically relevant kinase mutations during different stages of lung tumor progression and may be useful in predicting the clinical response to EGFR-targeted inhibitors.