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.

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.

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.

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.

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.

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.

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.

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.

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.

Alkylfluorenyl substituted N-heterocyclic carbenes in copper(I) catalysed hydrosilylation of aldehydes and ketones.

Copper(i) complexes featuring N-heterocyclic carbenes (NHCs) in which the nitrogen atoms are substituted by a 9-ethyl-9-fluorenyl group (EF) have been synthesised and tested in the hydrosylilation of functionalized and/or sterically demanding ketones and aldehydes. These reactions, carried out with triethylsilane as hydride source, were best achieved with the imidazolylidene copper complex in which the EF substituents can freely rotate about the corresponding N-CEF bonds. The remarkable stability of the active species, which surpasses that of previously reported Cu-NHC catalysts is likely to rely on the ability of the NHC side arms to protect the copper centre during the catalytic cycle by forming sandwich-like intermediates, but also on its steric flexibility facilitating approach of encumbered substrates. TONs up to 1000 were reached.

N-Alkylfluorenyl-substituted N-heterocyclic carbenes as bimodal pincers.

Two N-heterocyclic carbene precursors having their nitrogen atoms substituted by the expanded 9-ethyl-9-fluorenyl group, namely imidazolinium chloride 6 and imidazolium chloride 7, have been synthesized in high yields from fluorenone (1). The key intermediate of their syntheses is the new primary amine 9-ethyl-9-fluorenylamine (3), which was prepared in 75% yield. Both salts were readily converted into the corresponding PEPPSI-type palladium complexes, 8 and 9 (PEPPSI: pyridine-enhanced precatalyst preparation stabilisation and initiation). Despite rotational freedom of the ethylfluorenyl moieties about the N­C(fluorenyl) bond in their cationic precursors, the carbene ligands of the Pd(II)-complexes 8 and 9 both behave as bimodal pincers in solution and in the solid state, the resulting confinement being essentially due to (weak) attractive anagostic interactions between the CH2(fluorenyl) groups and the metal centre. Unlike in 8 and 9, there was no indication for similar anagostic interactions in the imidazolylidene chlorosilver complex 11, which could be obtained from 7. In the solid state, however, 11 adopts a remarkable "open sandwich" structure, with the two alkylfluorenilidene planes η2-bonded to the silver, this constituting a further bimodal pincer-type bonding mode of this ligand class. Complexes 8 and 9 were assessed in Suzuki­Miyaura cross-coupling reactions. The imidazolylidene complex 9 displayed high activity towards unencumbered aryl chlorides. Its activity is comparable to that of the previously reported, highly efficient benzimidazolylidene analogue 10.

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.

Directional properties of fluorenylidene moieties in unsymmetrically substituted N-heterocyclic carbenes. Unexpected CH activation of a methylfluorenyl group with palladium. Use in palladium catalysed Suzuki-Miyaura cross coupling of aryl chlorides.

Benzimidazolium salts having their two nitrogen atoms substituted by different 9-alkylfluorenyl groups ( and , alkyl(1)/alkyl(2) = Me/Et, Me/Pr, Me/n-Bu, Me/i-Pr, Me/Bn, Me/CH2SMe have been synthesised in high yields in two or three steps from N,N'-bis(9H-fluoren-9-ylidene)benzene-1,2-diamine (). The imidazolium salts were converted readily into the corresponding PEPPSI-type palladium complexes (PEPPSI = pyridine-enhanced precatalyst preparation stabilisation and initiation), while reaction of the methylthioether-substituted salt with PdCl2/K2CO3/pyridine afforded the palladacycle resulting from metallation of the methyl group attached to the fluorenylidene moiety. NMR and X-ray diffraction studies revealed that the carbene ligands in behave as clamp-like ligands, the resulting metal confinement arising from a combination of the orientational properties of the fluorenylidene moieties that push the alkyl groups towards the metal centre and attractive anagostic interactions involving CH2(fluorenyl) groups. Complexes were assessed in Suzuki-Miyaura cross-coupling reactions. Like their symmetrical analogues they displayed high activity in the coupling of phenyl boronic acid with p-tolylchloride but their performance remained slightly inferior to that of the related, symmetrical Et/Et complex .

An undergraduate study of two transcription factors that promote lateral root formation.

We present a lab that enables students to test the role of genes involved in the regulation of lateral roots growth in the model plant Arabidopsis thaliana. Here, students design an experiment that follows the effects of the hormone auxin on the stimulation of genes involved in the formation of lateral root initials. These genes, known as lateral organ boundary domain containing protein (LBD) genes, are upregulated in the presence of auxin as part of a multistep molecular and biochemically controlled pathway. Depending on which LBD gene is tested, and the stage of root development, expression patterns are localized in a discrete and punctate fashion at the site of lateral root initials (LBD33), or reveal a broader localization pattern (LBD16). Students view expression using the reporter gene GUS (beta-glucuronidase). Before GUS staining, students view root growth in a "pseudo-aseptic" agar-based environment that allows complete visualization of whole root development to determine the proper stage to test molecular expression.

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.

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.

The legal and ethical framework governing Body Donation in Europe - 1st update on current practice

Previously, we have reported on the legal and ethical aspects and current practice of body donation in several European countries, reflecting cultural and religious variations as well as different legal and constitutional frameworks. We have also established good practice in body donation. Here we shall further extend the legal and ethical frameworks in place and also focus on novelties in the law and different directives. Of particular interest are points that address the commercialization of human bodies and body parts and weaknesses in the legal directives. Therefore, it is important to define what is ethical and what needs to be considered unethical in body donation and the subsequent utilisation of human bodies for teaching and research (AU)

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