Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies

Next-generation sequencing (NGS) technologies – Illumina RNA-seq, Pacific Biosciences isoform sequencing (PacBio Iso-seq), and Oxford Nanopore direct RNA sequencing (DRS) - have revealed the complexity of plant transcriptomes and their regulation at the co-/posttranscriptional level. Global analysis of mature mRNAs, transcripts from nuclear run-on assays, and nascent chromatin-bound mRNAs using short as well as full-length and single-molecule DRS reads have uncovered potential roles of different forms of RNA polymerase II during the transcription process, and the extent of co-transcriptional pre-mRNA splicing and polyadenylation. These tools have also allowed mapping of transcriptome-wide start sites in cap-containing RNAs, poly(A) site choice, poly(A) tail length, and RNA base modifications. Analysis of a large number of plant transcriptomes using high-throughput short and long reads under different conditions has established that diverse abiotic and biotic stresses and environmental cues such as light, which regulates many aspects of plant growth and development, have a profound impact on gene expression at the co-/post-transcriptional level. The emerging theme from these studies is that reprogramming of gene expression in response to developmental cues and stresses at the co-/post transcriptional level likely plays a crucial role in eliciting appropriate responses for optimal growth and plant survival under adverse conditions. Although the mechanisms by which developmental cues and different stresses regulate co-/posttranscriptional splicing are largely unknown, a few recent studies are beginning to provide some insights into these mechanisms. These studies indicate that the external cues target spliceosomal and splicing regulatory proteins to modulate alternative splicing. In this review, we provide an overview of recent discoveries on the dynamics and complexities of plant transcriptomes, mechanistic insights into splicing regulation, and discuss critical gaps in co-/post-transcriptional research that need to be addressed using diverse genomic and biochemical approaches

Deep three-dimensional solid-state qubit arrays with long-lived spin coherence

Nitrogen-vacancy centers (NVCs) in diamond show promise for quantum computing, communication, and sensing. However, the best current method for entangling two NVCs requires that each one is in a separate cryostat, which is not scalable. We show that single NVCs can be laser written 6–15-µm deep inside of a diamond with spin coherence times that are an order of magnitude longer than previous laser-written NVCs and at least as long as naturally occurring NVCs. This depth is suitable for integration with solid immersion lenses or optical cavities and we present depth-dependent T2 measurements. 200 000 of these NVCs would fit into one diamond

A reduced complexity numerical method for optimal gate synthesis

Although quantum computers have the potential to efficiently solve certain problems considered difficult by known classical approaches, the design of a quantum circuit remains computationally difficult. It is known that the optimal gate design problem is equivalent to the solution of an associated optimal control problem, the solution to which is also computationally intensive. Hence, in this article, we introduce the application of a class of numerical methods (termed the max-plus curse of dimensionality free techniques) that determine the optimal control thereby synthesizing the desired unitary gate. The application of this technique to quantum systems has a growth in complexity that depends on the cardinality of the control set approximation rather than the much larger growth with respect to spatial dimensions in approaches based on gridding of the space, used in previous literature. This technique is demonstrated by obtaining an approximate solution for the gate synthesis on $SU(4)$- a problem that is computationally intractable by grid based approaches.Comment: 8 pages, 4 figure

A new paradigm of quantifying ecosystem stress through chemical signatures

Stress-induced emissions of biogenic volatile organic compounds (VOCs) from terrestrial eco- systems may be one of the dominant sources of VOC emissions worldwide. Understanding the ecosystem stress response could reveal how ecosystems will respond and adapt to climate change and, in turn, quan- tify changes in the atmospheric burden of VOC oxidants and secondary organic aerosols. Here, we argue, based on preliminary evidence from several opportunistic measurement sources, that chemical signatures of stress can be identified and quantified at the ecosystem scale. We also outline future endeavors that we see as next steps toward uncovering quantitative signatures of stress, including new advances in both VOC data collection and analysis of "big data.

Conservation and diversification of the transcriptomes of adult Paragonimus westermani and P. skrjabini

Gene Ontology term enrichment among transcript sets of interest from P. westermani and P. skrjabini. (XLSX 42 kb

P2X7 is an archaic scavenger receptor recognizing apoptotic neuroblasts in early human neurogenesis

The expression and function of P2X7 receptors in adult CNS have been widely studied, however, the roles of these purinergic receptors in human neural development has largely focused on the effects of receptor activation. Previous studies of embryonic and adult rodent neural precursors suggest adenosine triphosphate (ATP), the physiological agonist for P2X receptors, can act as a potent modifier of proliferation, migration and differentiation, mediated via intracellular calcium ([Ca2+]i) signaling. The P2X7 receptor has a ubiquitous distribution in the body but is most abundant on macrophages and microglia where its activation by ATP leads to secretion of proinflammatory cytokines. However, extracellular ATP concentrations in the CNS are usually at sub-micromolar levels suggesting that ATP-induced activation of the P2X7 receptor will not occur under physiological circumstances in the CNS. Another possible role for P2X7 receptors has been suggested by recent work on macrophages and neural precursor cells. In these studies the P2X7 receptor was shown to act as a scavenger receptor i.e. a receptor present on a phagocytotic cell which detects molecules present on the surface of apoptotic cells and facilitates phagocytosis of the apoptotic cell. In a recent study of human neural precursor cells (hNPCs) and neuroblasts isolated from human fetal telencephalons at 16-19 WG, our group showed that both P2X7Rhigh/DCXlow hNPCs and P2X7Rhigh/DCXhigh neuroblasts were capable of phagocytic engulfment of a range of targets including latex beads, apoptotic ReN cells and apoptotic neuroblasts. We found that these neuroblasts and their precursor cells expressed functional P2X7 receptors on their cell surface. Although expression of P2X7 is widespread in the cells of the neuroblast, it is those DCX+ neuroblasts with the highest expression of P2X7 which are actively phagocytic towards an autologous apoptotic neighbour or other phagocytic targets, including latex beads and apoptotic ReNcells. Pre-incubation of P2X7high neuroblasts with ATP or oxidized ATP inhibited phagocytosis of targets by these cells. Moreover siRNA knockdown of P2X7R also inhibited phagocytosis of the apoptotic targets. This review considers this major new role for the P2X7 receptor in early human neurogenesis

Dose distribution prediction for head-and-neck cancer radiotherapy using a generative adversarial network: influence of input data

PurposeA three-dimensional deep generative adversarial network (GAN) was used to predict dose distributions for locally advanced head and neck cancer radiotherapy. Given the labor- and time-intensive nature of manual planning target volume (PTV) and organ-at-risk (OAR) segmentation, we investigated whether dose distributions could be predicted without the need for fully segmented datasets.Materials and methodsGANs were trained/validated/tested using 320/30/35 previously segmented CT datasets and treatment plans. The following input combinations were used to train and test the models: CT-scan only (C); CT+PTVboost/elective (CP); CT+PTVs+OARs+body structure (CPOB); PTVs+OARs+body structure (POB); PTVs+body structure (PB). Mean absolute errors (MAEs) for the predicted dose distribution and mean doses to individual OARs (individual salivary glands, individual swallowing structures) were analyzed.ResultsFor the five models listed, MAEs were 7.3 Gy, 3.5 Gy, 3.4 Gy, 3.4 Gy, and 3.5 Gy, respectively, without significant differences among CP-CPOB, CP-POB, CP-PB, among CPOB-POB. Dose volume histograms showed that all four models that included PTV contours predicted dose distributions that had a high level of agreement with clinical treatment plans. The best model CPOB and the worst model PB (except model C) predicted mean dose to within ±3 Gy of the clinical dose, for 82.6%/88.6%/82.9% and 71.4%/67.1%/72.2% of all OARs, parotid glands (PG), and submandibular glands (SMG), respectively. The R2 values (0.17/0.96/0.97/0.95/0.95) of OAR mean doses for each model also indicated that except for model C, the predictions correlated highly with the clinical dose distributions. Interestingly model C could reasonably predict the dose in eight patients, but on average, it performed inadequately.ConclusionWe demonstrated the influence of the CT scan, and PTV and OAR contours on dose prediction. Model CP was not statistically different from model CPOB and represents the minimum data statistically required to adequately predict the clinical dose distribution in a group of patients

Transmutations and spectral parameter power series in eigenvalue problems

We give an overview of recent developments in Sturm-Liouville theory concerning operators of transmutation (transformation) and spectral parameter power series (SPPS). The possibility to write down the dispersion (characteristic) equations corresponding to a variety of spectral problems related to Sturm-Liouville equations in an analytic form is an attractive feature of the SPPS method. It is based on a computation of certain systems of recursive integrals. Considered as families of functions these systems are complete in the $L_{2}$-space and result to be the images of the nonnegative integer powers of the independent variable under the action of a corresponding transmutation operator. This recently revealed property of the Delsarte transmutations opens the way to apply the transmutation operator even when its integral kernel is unknown and gives the possibility to obtain further interesting properties concerning the Darboux transformed Schr\"{o}dinger operators. We introduce the systems of recursive integrals and the SPPS approach, explain some of its applications to spectral problems with numerical illustrations, give the definition and basic properties of transmutation operators, introduce a parametrized family of transmutation operators, study their mapping properties and construct the transmutation operators for Darboux transformed Schr\"{o}dinger operators.Comment: 30 pages, 4 figures. arXiv admin note: text overlap with arXiv:1111.444

Possible Disintegrating Short-Period Super-Mercury Orbiting KIC 12557548

We report here on the discovery of stellar occultations, observed with Kepler, that recur periodically at 15.685 hour intervals, but which vary in depth from a maximum of 1.3% to a minimum that can be less than 0.2%. The star that is apparently being occulted is KIC 12557548, a K dwarf with T_eff = 4400 K and V = 16. Because the eclipse depths are highly variable, they cannot be due solely to transits of a single planet with a fixed size. We discuss but dismiss a scenario involving a binary giant planet whose mutual orbit plane precesses, bringing one of the planets into and out of a grazing transit. We also briefly consider an eclipsing binary, that either orbits KIC 12557548 in a hierarchical triple configuration or is nearby on the sky, but we find such a scenario inadequate to reproduce the observations. We come down in favor of an explanation that involves macroscopic particles escaping the atmosphere of a slowly disintegrating planet not much larger than Mercury. The particles could take the form of micron-sized pyroxene or aluminum oxide dust grains. The planetary surface is hot enough to sublimate and create a high-Z atmosphere; this atmosphere may be loaded with dust via cloud condensation or explosive volcanism. Atmospheric gas escapes the planet via a Parker-type thermal wind, dragging dust grains with it. We infer a mass loss rate from the observations of order 1 M_E/Gyr, with a dust-to-gas ratio possibly of order unity. For our fiducial 0.1 M_E planet, the evaporation timescale may be ~0.2 Gyr. Smaller mass planets are disfavored because they evaporate still more quickly, as are larger mass planets because they have surface gravities too strong to sustain outflows with the requisite mass-loss rates. The occultation profile evinces an ingress-egress asymmetry that could reflect a comet-like dust tail trailing the planet; we present simulations of such a tail.Comment: 14 pages, 7 figures; submitted to ApJ, January 10, 2012; accepted March 21, 201