Single cell transcriptome profiling of the human alcohol-dependent brain.

Alcoholism remains a prevalent health concern throughout the world. Previous studies have identified transcriptomic patterns in the brain associated with alcohol dependence in both humans and animal models. But none of these studies have systematically investigated expression within the unique cell types present in the brain. We utilized single nucleus RNA sequencing (snRNA-seq) to examine the transcriptomes of over 16 000 nuclei isolated from the prefrontal cortex of alcoholic and control individuals. Each nucleus was assigned to one of seven major cell types by unsupervised clustering. Cell type enrichment patterns varied greatly among neuroinflammatory-related genes, which are known to play roles in alcohol dependence and neurodegeneration. Differential expression analysis identified cell type-specific genes with altered expression in alcoholics. The largest number of differentially expressed genes (DEGs), including both protein-coding and non-coding, were detected in astrocytes, oligodendrocytes and microglia. To our knowledge, this is the first single cell transcriptome analysis of alcohol-associated gene expression in any species and the first such analysis in humans for any addictive substance. These findings greatly advance the understanding of transcriptomic changes in the brain of alcohol-dependent individuals.

Integrating transcriptomics and bulk time course data into a mathematical framework to describe and predict therapeutic resistance in cancer.

A significant challenge in the field of biomedicine is the development of methods to integrate the multitude of dispersed data sets into comprehensive frameworks to be used to generate optimal clinical decisions. Recent technological advances in single cell analysis allow for high-dimensional molecular characterization of cells and populations, but to date, few mathematical models have attempted to integrate measurements from the single cell scale with other types of longitudinal data. Here, we present a framework that actionizes static outputs from a machine learning model and leverages these as measurements of state variables in a dynamic model of treatment response. We apply this framework to breast cancer cells to integrate single cell transcriptomic data with longitudinal bulk cell population (bulk time course) data. We demonstrate that the explicit inclusion of the phenotypic composition estimate, derived from single cell RNA-sequencing data (scRNA-seq), improves accuracy in the prediction of new treatments with a concordance correlation coefficient (CCC) of 0.92 compared to a prediction accuracy of CCC = 0.64 when fitting on longitudinal bulk cell population data alone. To our knowledge, this is the first work that explicitly integrates single cell clonally-resolved transcriptome datasets with bulk time-course data to jointly calibrate a mathematical model of drug resistance dynamics. We anticipate this approach to be a first step that demonstrates the feasibility of incorporating multiple data types into mathematical models to develop optimized treatment regimens from data.

Metal Confinement through N-(9-Alkyl)fluorenyl-Substituted N-Heterocyclic Carbenes and Its Consequences in Gold-Catalysed Reactions Involving Enynes.

A series of gold(I) and gold(III) complexes containing bulky bis-N,N'-(9-alkylfluorenyl) heterocyclic carbene (R F-NHC) ligands have been prepared in high yields from appropriate imidazolinium, imidazolium and benzimidazolium salts. In all complexes, the carbene ligand provides high steric protection of the Au-X bond trans to the carbenic C atom. Irrespective of the metal oxidation state, the complexes showed high efficiency in a tandem 3,3-rearrangement/Nazarov reaction of an enynyl acetate. One of the AuIII complexes, [AuCl3 (R F-NHC)], was further found to be suitable for the efficient cyclisation of a propargylcarboxamide. Furthermore, unlike related NHC-gold(I) complexes based on conventional bulky N-heterocyclic carbenes (notably, 1,3-bis-(2,6-diisopropylphenyl)imidazol-2-ylidene (IPr), 1,3-bis-(2,4,6-trimethylphenyl)imidazol-2-ylidene (IMes) and 1,3-(bis-tert-butyl)imidazol-2-ylidene (ItBu)), the studied [AuI Cl(R F-NHC)] complexes catalysed the conversion of a 1,6-enyne in the presence of indole into a single product; this arises from the embracing character of the ligand, which prevents indole addition on one of the catalytic intermediates. A structure/selectivity relationship was established for all carbenes tested that took into account percent buried volumes and topographic steric maps. The results illustrate the high potential of confining NHCs in organic synthesis.

"Hummingbird" behaviour of N-heterocyclic carbenes stabilises out-of-plane bonding of AuCl and CuCl units.

An N-heterocyclic carbene substituted by two expanded 9-ethyl-9-fluorenyl groups was shown to bind an AuCl unit in an unusual manner, namely with the AuX rod sitting out of the plane defined by the heterocyclic carbene unit. As shown by X-ray studies and DFT calculations, the observed large pitch angle (21°) arises from an easy displacement of the gold(I) atom away from the carbene lone-pair axis, combined with the stabilisation provided by weak CH⋅⋅⋅Au interactions involving aliphatic and aromatic H atoms of the NHC wingtips. Weak, intermolecular Cl⋅⋅⋅H bonds are likely to cooperate with the H⋅⋅⋅Au interactions to stabilise the out-of-plane conformation. A general belief until now was that tilt angles in NHC complexes arise mainly from steric effects within the first coordination sphere.

Origin of a novel regulatory module by duplication and degeneration of an ancient plant transcription factor.

It is commonly believed that gene duplications provide the raw material for morphological evolution. Both the number of genes and size of gene families have increased during the diversification of land plants. Several small proteins that regulate transcription factors have recently been identified in plants, including the LITTLE ZIPPER (ZPR) proteins. ZPRs are post-translational negative regulators, via heterodimerization, of class III Homeodomain Leucine Zipper (C3HDZ) proteins that play a key role in directing plant form and growth. We show that ZPR genes originated as a duplication of a C3HDZ transcription factor paralog in the common ancestor of euphyllophytes (ferns and seed plants). The ZPRs evolved by degenerative mutations resulting in loss all of the C3HDZ functional domains, except the leucine zipper that modulates dimerization. ZPRs represent a novel regulatory module of the C3HDZ network unique to the euphyllophyte lineage, and their origin correlates to a period of rapid morphological changes and increased complexity in land plants. The origin of the ZPRs illustrates the significance of gene duplications in creating developmental complexity during land plant evolution that likely led to morphological evolution.

Genetic analysis of resistance to six virus diseases in a multiple virus-resistant maize inbred line.

KEY MESSAGE: Novel and previously known resistance loci for six phylogenetically diverse viruses were tightly clustered on chromosomes 2, 3, 6 and 10 in the multiply virus-resistant maize inbred line, Oh1VI. Virus diseases in maize can cause severe yield reductions that threaten crop production and food supplies in some regions of the world. Genetic resistance to different viruses has been characterized in maize populations in diverse environments using different screening techniques, and resistance loci have been mapped to all maize chromosomes. The maize inbred line, Oh1VI, is resistant to at least ten viruses, including viruses in five different families. To determine the genes and inheritance mechanisms responsible for the multiple virus resistance in this line, F1 hybrids, F2 progeny and a recombinant inbred line (RIL) population derived from a cross of Oh1VI and the virus-susceptible inbred line Oh28 were evaluated. Progeny were screened for their responses to Maize dwarf mosaic virus, Sugarcane mosaic virus, Wheat streak mosaic virus, Maize chlorotic dwarf virus, Maize fine streak virus, and Maize mosaic virus. Depending on the virus, dominant, recessive, or additive gene effects were responsible for the resistance observed in F1 plants. One to three gene models explained the observed segregation of resistance in the F2 generation for all six viruses. Composite interval mapping in the RIL population identified 17 resistance QTLs associated with the six viruses. Of these, 15 were clustered in specific regions of chr. 2, 3, 6, and 10. It is unknown whether these QTL clusters contain single or multiple virus resistance genes, but the coupling phase linkage of genes conferring resistance to multiple virus diseases in this population could facilitate breeding efforts to develop multi-virus resistant crops.

Integrative genomics approach identifies glial transcriptomic dysregulation and risk in the cortex of individuals with Alcohol Use Disorder.

Alcohol use disorder (AUD) is a prevalent neuropsychiatric disorder that is a major global health concern, affecting millions of people worldwide. Past molecular studies of AUD used underpowered single cell analysis or bulk homogenates of postmortem brain tissue, which obscures gene expression changes in specific cell types. Here we performed single nuclei RNA-sequencing analysis of 73 post-mortem samples from individuals with AUD (N=36, N nuclei = 248,873) and neurotypical controls (N=37, N nuclei = 210,573) in both sexes across two institutional sites. We identified 32 clusters and found widespread cell type-specific transcriptomic changes across the cortex in AUD, particularly affecting glia. We found the greatest dysregulation in novel microglial and astrocytic subtypes that accounted for the majority of differential gene expression and co-expression modules linked to AUD. Analysis for cell type-specific enrichment of aggregate genetic risk for AUD identified subtypes of microglia and astrocytes as potential key players not only affected by but causally linked to the progression of AUD. These results highlight the importance of cell-type specific molecular changes in AUD and offer opportunities to identify novel targets for treatment.

Kinetic modeling and occupancy measures of the norepinephrine transporters in baboons using single photon emission computed tomography with (123)I-INER.

This study aims to investigate the pharmacokinetics of a recently developed radiotracer for imaging of the norepinephrine transporter (NET) in baboon brain, (123)I-INER, using single photon emission computed tomography (SPECT). In addition, it also aims to determine NET occupancy by atomoxetine and reboxetine, two selective norepinephrine reuptake inhibitors, using (123)I-INER in baboons. Baseline and preblocking studies with a high dose of atomoxetine (0.85 mg/kg) were conducted in three baboons using SPECT with (123)I-INER administered as a bolus. Kinetic modeling analysis was investigated for different models, namely invasive and reference tissue models. Bolus plus constant infusion experiments with displacement at equilibrium using six different doses of atomoxetine (0.03-0.85 mg/kg) and four different doses of reboxetine (0.5-3.0 mg/kg) were carried out in several baboons to obtain occupancy measurements as a function of dose for the two NET selective drugs. Results showed that reference tissue models can be used to estimate binding potential values and occupancy measures of (123)I-INER in different brain regions. In addition, the apparent volume of distribution was estimated by dividing concentration in tissue by the concentration in blood at 3 hours postinjection. After administration of atomoxetine or reboxetine, a dose-dependent occupancy was observed in brain regions known to contain high densities of NET. In conclusion, pharmacokinetic properties of (123) I-INER were successfully described, and obtained results may be used to simplify future data acquisition and image processing. Dose-dependent NET occupancy for two selective norepinephrine reuptake inhibitors was successfully measured in vivo in baboon brain using SPECT and (123) I-INER.

A deep learning approach to track Arabidopsis seedlings' circumnutation from time-lapse videos.

BACKGROUND: Circumnutation (Darwin et al., Sci Rep 10(1):1-13, 2000) is the side-to-side movement common among growing plant appendages but the purpose of circumnutation is not always clear. Accurately tracking and quantifying circumnutation can help researchers to better study its underlying purpose. RESULTS: In this paper, a deep learning-based model is proposed to track the circumnutating flowering apices in the plant Arabidopsis thaliana from time-lapse videos. By utilizing U-Net to segment the apex, and combining it with the model update mechanism, pre- and post- processing steps, the proposed model significantly improves the tracking time and accuracy over other baseline tracking methods. Additionally, we evaluate the computational complexity of the proposed model and further develop a method to accelerate the inference speed of the model. The fast algorithm can track the apices in real-time on a computer without a dedicated GPU. CONCLUSION: We demonstrate that the accuracy of tracking the flowering apices in the plant Arabidopsis thaliana can be improved with our proposed deep learning-based model in terms of both the racking success rate and the tracking error. We also show that the improvement in the tracking accuracy is statistically significant. The time-lapse video dataset of Arabidopsis is also provided which can be used for future studies on Arabidopsis in various takes.

Structural and conformational analysis of a biaryl phosphine integrating a calix[4]arene cavity. Can the phosphorus atom behave as an introverted donor?

The conformational preference of a cavity-based biaryl phosphine, namely 5-(2-diphenylphosphinyl-phenyl)-25,26,27,28-tetrapropyloxycalix[4]arene (L) has been investigated by density functional theory calculations. The analysis showed that the barrier to rotation about the C-C axle of the biaryl unit is only 10.7 kcal mol-1, this rendering possible access to conformers of two types, those in which the P lone pair sits at the cavity entrance and points to the calixarene interior, others with a more open structure where the P atom is located outside the cavity. As revealed by a single crystal X-ray diffraction study, the biaryl phosphine appears virtually as an atropisomer in the solid state in which the phosphorus atom lies totally out of the cavity defined by the four phenoxy rings.

Nodding behavior observed in Japanese stiltgrass, Microstegium vimineum , seedlings from time-lapse observations.

Invasive species are the second main cause of biodiversity loss because of their exceptional ability to supplant native species by creating major upheavals in ecosystems. Inexpensive and prevalent time-lapse photography provides an exciting opportunity to better understand the aggressive behavior of invasive species including how they invade and conquer new territory. One of the most pervasive invasive species in the Eastern United States is Japanese stiltgrass, Microstegium vimineum (Trin.) A. Campus, which originated from Southeast Asia. Previous research has examined the conditions that enable Japanese stiltgrass to become invasive, but nothing is known regarding root and shoot behavior. Here time-lapse was used to examine Japanese stiltgrass seedlings, early in their development, as a first step to observe its behavior. Our results demonstrate that Japanese stiltgrass shoots appear to drop or collapse and then resurrect back to an upright stature - sometimes the same plant exhibits this behavior multiple times. We have shown, in addition, that emergent stilt root growth rate increases with increased root length. This and similar kinds of analyses may provide insight into how Japanese stiltgrass thrives aggressively in a non-native environment with the goal of developing better methods of controlling this noxious weed.

iTIME.219: An Immortalized KSHV Infected Endothelial Cell Line Inducible by a KSHV-Specific Stimulus to Transition From Latency to Lytic Replication and Infectious Virus Release.

Kaposi's sarcoma-associated herpesvirus (KSHV/HHV-8) is the causative agent of Kaposi's sarcoma and two B cell lymphoproliferative disorders: primary effusion lymphoma and KSHV-associated multicentric Castleman's disease. These distinct pathologies involve different infected cell types. In Kaposi's sarcoma, the virus is harbored in spindle-like tumor cells of endothelial origin, in contrast with the two pathologies of B cells. These distinctions highlight the importance of elucidating potential differences in the mechanisms of infection for these alternate target cell types and in the properties of virus generated from each. To date there is no available chronically KSHV-infected cell line of endothelial phenotype that can be activated by the viral lytic switch protein to transition from latency to lytic replication and production of infectious virus. To advance these efforts, we engineered a novel KSHV chronically infected derivative of TIME (telomerase immortalized endothelial) cells harboring a previously reported recombinant virus (rKSHV.219) and the viral replication and transcription activator (RTA) gene under the control of a doxycycline-inducible system. The resulting cells (designated iTIME.219) maintained latent virus as indicated by expression of constitutively expressed (eGFP) but not a lytic phase (RFP) reporter gene and can be sustained under long term selection. When exposed to either sodium butyrate or doxycycline, the cells were activated to lytic replication as evidenced by the expression of RFP and KSHV lytic genes and release of large quantities of infectious virus. The identity of the iTIME.219 cells was confirmed both phenotypically (specific antigen expression) and genetically (short tandem repeat analysis), and cell stability was maintained following repeated serial passage. These results suggest the potential utility of the iTime.219 cells in future studies of the KSHV replication in endothelial cells, properties of virus generated from this biologically relevant cell type and mechanisms underlying KSHV tropism and pathogenesis.

Using the Integrated Genome Viewer to reveal amplicon-derived polymorphism enriched at the phenylthiocarbamide locus in the teaching lab.

Due to its distinct phenotype and relatively simple inheritance pattern, the phenylthiocarbamide (PTC) loci is frequently utilized in teaching laboratories to demonstrate genetic concepts such as Mendelian inheritance and population genetics. We have developed a next-generation sequencing and bioinformatics approach to analyze the PTC gene locus to reveal single nucleotide polymorphism (SNP) variation at nucleotide position 785 that predicts tasting ability in humans. Here students purify DNA from their own cheek cells, perform polymerase chain reaction (PCR) amplification of the PTC gene followed by cleaved amplified polymorphic sequence (CAPS) testing. Students perform a second PCR on the PTC loci using high-fidelity Taq to create bar-coded amplicons for next-generation sequencing on the Ion Torrent Personal Genome Machine. Bioinformatic verification reveals polymorphic variation by aligning the entire class PTC PCR fragment sequence to the human gene using Bowtie2 and visualizing the results in the Integrated Genome Viewer. This exercise presents a learning opportunity for students to use next-generation sequencing to predict their own PTC taste sensitivity phenotype coupled with the standard CAPS method. This approach brings the PTC teaching method into the genomics era.

Multifunctional barcoding with ClonMapper enables high-resolution study of clonal dynamics during tumor evolution and treatment.

Lineage-tracing methods have enabled characterization of clonal dynamics in complex populations, but generally lack the ability to integrate genomic, epigenomic and transcriptomic measurements with live-cell manipulation of specific clones of interest. We developed a functionalized lineage-tracing system, ClonMapper, which integrates DNA barcoding with single-cell RNA sequencing and clonal isolation to comprehensively characterize thousands of clones within heterogeneous populations. Using ClonMapper, we identified subpopulations of a chronic lymphocytic leukemia cell line with distinct clonal compositions, transcriptional signatures and chemotherapy survivorship trajectories; patterns that were also observed in primary human chronic lymphocytic leukemia. The ability to retrieve specific clones before, during and after treatment enabled direct measurements of clonal diversification and durable subpopulation transcriptional signatures. ClonMapper is a powerful multifunctional approach to dissect the complex clonal dynamics of tumor progression and therapeutic response.

A mutation in the Proteosomal Regulatory Particle AAA-ATPase-3 in Arabidopsis impairs the light-specific hypocotyl elongation response elicited by a glutamate receptor agonist, BMAA.

BMAA is a cycad-derived glutamate receptor agonist that causes a two- to three-fold increase in hypocotyl elongation on Arabidopsis seedlings grown in the light. To probe the role of plant glutamate receptors and their downstream mediators, we utilized a previously described genetic screen to identify a novel, BMAA insensitive morphology (bim) mutant, bim409. The normal BMAA-induced hypocotyl elongation response observed on wild-type seedlings grown in the light is impaired in the bim409 mutant. This BMAA-induced phenotype is light-specific, as the bim409 mutant exhibits normal hypocotyl elongation in etiolated (dark grown) plants (+ or - BMAA). The mutation in bim409 was identified to be in a gene encoding the Proteosomal Regulatory Particle AAA-ATPase-3 (RPT3). Possible roles of the proteosome in Glu-mediated signaling in plants is discussed.

Palladium complexes of N-heterocyclic carbenes displaying an unsymmetrical N-alkylfluorenyl/N'-aryl substitution pattern and their behaviour in Suzuki-Miyaura cross coupling.

A series of new Pd-PEPPSI complexes containing imidazolylidene ligands with a mixed 9-alkyl-9-fluorenyl/aryl N,N'-substitution pattern have been synthesised. Single crystal X-ray diffraction studies were carried out for four complexes, which revealed that the N-heterocyclic carbene ligands display a semi-open, unsymmetrical space occupancy about the metal. Despite their particular unsymmetrical shape, the new complexes were found to perform as well in Suzuki-Miyaura cross coupling (dioxane, 80 °C) as previously reported, highly active analogues bearing two sterically protecting 9-alkylfluorenyl substituents. They were further found to be considerably more active than the standard Pd-PEPPSI complexes [PdCl2IMes(pyridine)] and [PdCl2IPr(pyridine)]. Surprisingly, unlike the latter, the unsymmetrical complexes of this study were practically inactive in isopropanol at 80 °C. Under these conditions the complexes appear to decompose with formation of non-stabilised nanoparticles.

Plant neurobiology: an integrated view of plant signaling.

Plant neurobiology is a newly focused field of plant biology research that aims to understand how plants process the information they obtain from their environment to develop, prosper and reproduce optimally. The behavior plants exhibit is coordinated across the whole organism by some form of integrated signaling, communication and response system. This system includes long-distance electrical signals, vesicle-mediated transport of auxin in specialized vascular tissues, and production of chemicals known to be neuronal in animals. Here we review how plant neurobiology is being directed toward discovering the mechanisms of signaling in whole plants, as well as among plants and their neighbors.

Human tobacco smokers in early abstinence have higher levels of beta2* nicotinic acetylcholine receptors than nonsmokers.

Nicotine, the addictive chemical in tobacco smoke, initiates its actions in brain through nicotinic acetylcholine receptors (nAChRs). In particular, nAChRs containing beta2-subunits (beta2*-nAChRs) the most prevalent subtype, mediate the reinforcing properties of nicotine. We hypothesized that abnormal numbers of beta2*-nAChRs during early abstinence contribute to the perpetuation of addiction to tobacco smoking. Using molecular imaging, specifically single-photon emission computed tomography with the nAChR agonist radiotracer [123I]5-IA-85380 ([123I]5-IA), we imaged beta2*-nAChR availability in human smokers. First, using nonhuman primates treated chronically with nicotine, we estimated the time interval necessary for smokers to abstain from smoking so that residual nicotine would not interfere with [123I]5-IA binding to the beta2*-nAChR as approximately 7 d. Thus, we imaged human smokers at 6.8 +/- 1.9 d (mean +/- SD) of abstinence. Abstinence was confirmed by daily assessments of urinary cotinine and expired carbon monoxide levels. In smokers, [123I]5-IA uptake was significantly higher throughout the cerebral cortex (26-36%) and in the striatum (27%) than in nonsmokers, suggesting higher beta2*-nAChR in recently abstinent smokers. Beta2*-nAChR availability in recently abstinent smokers correlated with the days since last cigarette and the urge to smoke to relieve withdrawal symptoms but not the severity of nicotine dependence, severity of nicotine withdrawal, or the desire to smoke. Higher brain beta2*-nAChR during early abstinence indicates that, when smokers quit smoking, they do so in the face of a significant increase in the receptors normally activated by nicotine. Greater beta2*-nAChR availability during early abstinence may impact the ability of smokers to maintain abstinence.

ESTimating plant phylogeny: lessons from partitioning.

BACKGROUND: While Expressed Sequence Tags (ESTs) have proven a viable and efficient way to sample genomes, particularly those for which whole-genome sequencing is impractical, phylogenetic analysis using ESTs remains difficult. Sequencing errors and orthology determination are the major problems when using ESTs as a source of characters for systematics. Here we develop methods to incorporate EST sequence information in a simultaneous analysis framework to address controversial phylogenetic questions regarding the relationships among the major groups of seed plants. We use an automated, phylogenetically derived approach to orthology determination called OrthologID generate a phylogeny based on 43 process partitions, many of which are derived from ESTs, and examine several measures of support to assess the utility of EST data for phylogenies. RESULTS: A maximum parsimony (MP) analysis resulted in a single tree with relatively high support at all nodes in the tree despite rampant conflict among trees generated from the separate analysis of individual partitions. In a comparison of broader-scale groupings based on cellular compartment (ie: chloroplast, mitochondrial or nuclear) or function, only the nuclear partition tree (based largely on EST data) was found to be topologically identical to the tree based on the simultaneous analysis of all data. Despite topological conflict among the broader-scale groupings examined, only the tree based on morphological data showed statistically significant differences. CONCLUSION: Based on the amount of character support contributed by EST data which make up a majority of the nuclear data set, and the lack of conflict of the nuclear data set with the simultaneous analysis tree, we conclude that the inclusion of EST data does provide a viable and efficient approach to address phylogenetic questions within a parsimony framework on a genomic scale, if problems of orthology determination and potential sequencing errors can be overcome. In addition, approaches that examine conflict and support in a simultaneous analysis framework allow for a more precise understanding of the evolutionary history of individual process partitions and may be a novel way to understand functional aspects of different kinds of cellular classes of gene products.

Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA).

In the eight years since phylogenomics was introduced as the intersection of genomics and phylogenetics, the field has provided fundamental insights into gene function, genome history and organismal relationships. The utility of phylogenomics is growing with the increase in the number and diversity of taxa for which whole genome and large transcriptome sequence sets are being generated. We assert that the synergy between genomic and phylogenetic perspectives in comparative biology would be enhanced by the development and refinement of minimal reporting standards for phylogenetic analyses. Encouraged by the development of the Minimum Information About a Microarray Experiment (MIAME) standard, we propose a similar roadmap for the development of a Minimal Information About a Phylogenetic Analysis (MIAPA) standard. Key in the successful development and implementation of such a standard will be broad participation by developers of phylogenetic analysis software, phylogenetic database developers, practitioners of phylogenomics, and journal editors.