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Summary Plant secondary cell walls constitute the majority of plant biomass. They are predominantly found in xylem cells, which are derived from vascular initials during vascularization. Little is known about these processes in grass species despite their emerging importance as biomass feedstocks. The targeted biofuel crop Sorghum bicolor has a sequenced and well‐annotated genome, making it an ideal monocot model for addressing vascularization and biomass deposition.Here we generated tissue‐specific transcriptome and DNA methylome data from sorghum shoots, roots and developing root vascular and nonvascular tissues.Many genes associated with vascular development in other species show enriched expression in developing vasculature. However, several transcription factor families varied in vascular expression in sorghum compared with Arabidopsis and maize. Furthermore, differential expression of genes associated with DNA methylation were identified between vascular and nonvascular tissues, implying that changes in DNA methylation are a feature of sorghum root vascularization, which we confirmed using tissue‐specific DNA methylome data. Roots treated with a DNA methylation inhibitor also showed a significant decrease in root length.Tissues and organs can be discriminated based on their genomic methylation patterns and methylation context. Consequently, tissue‐specific changes in DNA methylation are part of the normal developmental process.

SummaryOncocytomas are predominantly benign neoplasms possessing pathogenic mitochondrial mutations and accumulation of respiration-defective mitochondria, characteristics of unknown significance. Using exome and transcriptome sequencing, we identified two main subtypes of renal oncocytoma. Type 1 is diploid with CCND1 rearrangements, whereas type 2 is aneuploid with recurrent loss of chromosome 1, X or Y, and/or 14 and 21, which may proceed to more aggressive eosinophilic chromophobe renal cell carcinoma (ChRCC). Oncocytomas activate 5′ adenosine monophosphate-activated protein kinase (AMPK) and Tp53 (p53) and display disruption of Golgi and autophagy/lysosome trafficking, events attributed to defective mitochondrial function. This suggests that the genetic defects in mitochondria activate a metabolic checkpoint, producing autophagy impairment and mitochondrial accumulation that limit tumor progression, revealing a novel tumor-suppressive mechanism for mitochondrial inhibition with metformin. Alleviation of this metabolic checkpoint in type 2 by p53 mutations may allow progression to eosinophilic ChRCC, indicating that they represent higher risk.

The Li-Fraumeni syndrome (LFS) and its variant form (LFL) is a familial predisposition to multiple forms of childhood, adolescent, and adult cancers associated with germ-line mutation in the TP53 tumor suppressor gene. Individual disparities in tumor patterns are compounded by acceleration of cancer onset with successive generations. It has been suggested that this apparent anticipation pattern may result from germ-line genomic instability in TP53 mutation carriers, causing increased DNA copy-number variations (CNVs) with successive generations. To address the genetic basis of phenotypic disparities of LFS/LFL, we performed whole-genome sequencing (WGS) of 13 subjects from two generations of an LFS kindred. Neither de novo CNV nor significant difference in total CNV was detected in relation with successive generations or with age at cancer onset. These observations were consistent with an experimental mouse model system showing that trp53 deficiency in the germ line of father or mother did not increase CNV occurrence in the offspring. On the other hand, individual records on 1,771 TP53 mutation carriers from 294 pedigrees were compiled to assess genetic anticipation patterns (International Agency for Research on Cancer TP53 database). No strictly defined anticipation pattern was observed. Rather, in multigeneration families, cancer onset was delayed in older compared with recent generations. These observations support an alternative model for apparent anticipation in which rare variants from noncarrier parents may attenuate constitutive resistance to tumorigenesis in the offspring of TP53 mutation carriers with late cancer onset.

To study the frequency with which targeted tumor sequencing results will lead to implemented change in care, this study assessed tumors from 100 patients for utility, feasibility, and limitations of genomic sequencing for genomically guided therapy or other clinical purpose in the setting of a multidisciplinary molecular tumor board. Comprehensive profiling led to implementable clinical action in 35% of tumors with genomic alterations., Background. The frequency with which targeted tumor sequencing results will lead to implemented change in care is unclear. Prospective assessment of the feasibility and limitations of using genomic sequencing is critically important. Methods. A prospective clinical study was conducted on 100 patients with diverse-histology, rare, or poor-prognosis cancers to evaluate the clinical actionability of a Clinical Laboratory Improvement Amendments (CLIA)-certified, comprehensive genomic profiling assay (FoundationOne), using formalin-fixed, paraffin-embedded tumors. The primary objectives were to assess utility, feasibility, and limitations of genomic sequencing for genomically guided therapy or other clinical purpose in the setting of a multidisciplinary molecular tumor board. Results. Of the tumors from the 92 patients with sufficient tissue, 88 (96%) had at least one genomic alteration (average 3.6, range 0–10). Commonly altered pathways included p53 (46%), RAS/RAF/MAPK (rat sarcoma; rapidly accelerated fibrosarcoma; mitogen-activated protein kinase) (45%), receptor tyrosine kinases/ligand (44%), PI3K/AKT/mTOR (phosphatidylinositol-4,5-bisphosphate 3-kinase; protein kinase B; mammalian target of rapamycin) (35%), transcription factors/regulators (31%), and cell cycle regulators (30%). Many low frequency but potentially actionable alterations were identified in diverse histologies. Use of comprehensive profiling led to implementable clinical action in 35% of tumors with genomic alterations, including genomically guided therapy, diagnostic modification, and trigger for germline genetic testing. Conclusion. Use of targeted next-generation sequencing in the setting of an institutional molecular tumor board led to implementable clinical action in more than one third of patients with rare and poor-prognosis cancers. Major barriers to implementation of genomically guided therapy were clinical status of the patient and drug access. Early and serial sequencing in the clinical course and expanded access to genomically guided early-phase clinical trials and targeted agents may increase actionability. Implications for Practice: Identification of key factors that facilitate use of genomic tumor testing results and implementation of genomically guided therapy may lead to enhanced benefit for patients with rare or difficult to treat cancers. Clinical use of a targeted next-generation sequencing assay in the setting of an institutional molecular tumor board led to implementable clinical action in over one third of patients with rare and poor prognosis cancers. The major barriers to implementation of genomically guided therapy were clinical status of the patient and drug access both on trial and off label. Approaches to increase actionability include early and serial sequencing in the clinical course and expanded access to genomically guided early phase clinical trials and targeted agents.

Chromatin remodelers help equilibrate nucleosome arrays, yet do not strongly affect transcriptional reprogramming caused by a change in carbon source., Most promoters in yeast contain a nucleosome-depleted region (NDR), but the mechanisms by which NDRs are established and maintained in vivo are currently unclear. We have examined how genome-wide nucleosome placement is altered in the absence of two distinct types of nucleosome remodeling activity. In mutants of both SNF2, which encodes the ATPase component of the Swi/Snf remodeling complex, and ASF1, which encodes a histone chaperone, distinct sets of gene promoters carry excess nucleosomes in their NDRs relative to wild-type. In snf2 mutants, excess promoter nucleosomes correlate with reduced gene expression. In both mutants, the excess nucleosomes occupy DNA sequences that are energetically less favorable for nucleosome formation, indicating that intrinsic histone–DNA interactions are not sufficient for nucleosome positioning in vivo, and that Snf2 and Asf1 promote thermodynamic equilibration of nucleosomal arrays. Cells lacking SNF2 or ASF1 still accomplish the changes in promoter nucleosome structure associated with large-scale transcriptional reprogramming. However, chromatin reorganization in the mutants is reduced in extent compared to wild-type cells, even though transcriptional changes proceed normally. In summary, active remodeling is required for distributing nucleosomes to energetically favorable positions in vivo and for reorganizing chromatin in response to changes in transcriptional activity.

We propose a new strategy for Monte Carlo (MC) optimization on rugged multidimensional landscapes. The strategy is based on querying the statistical properties of the landscape in order to find the temperature at which the mean first passage time across the current region of the landscape is minimized. Thus, in contrast to other algorithms such as simulated annealing (SA), we explicitly match the temperature schedule to the statistics of landscape irregularities. In cases where this statistics is approximately the same over the entire landscape, or where non-local moves couple distant parts of the landscape, single-temperature MC will outperform any other MC algorithm with the same move set. We also find that in strongly anisotropic Coulomb spin glass and traveling salesman problems, the only relevant statistics (which we use to assign a single MC temperature) is that of irregularities in low-energy funnels. Our results may explain why protein folding in nature is efficient at room temperatures., 5 pages, 3 figures

One-dimensional arrays of nucleosomes (DNA-bound histone octamers separated by stretches of linker DNA) fold into higher-order chromatin structures which ultimately make up eukaryotic chromosomes. Chromatin structure formation leads to 10-11 base pair (bp) discretization of linker lengths caused by the smaller free energy cost of packaging nucleosomes into a regular chromatin fiber if their rotational setting (defined by DNA helical twist) is conserved. We describe nucleosome positions along the fiber using a thermodynamic model of finite-size particles with effective two-body interactions, subject to an arbitrary external potential. We infer both one-body and two-body energies from readily available large-scale maps of nucleosome positions. We show that two-body forces play a leading role in establishing well-known 10-11 bp genome-wide periodicity of nucleosome occupancies. They also explain nucleosome ordering over transcribed regions observed in both in vitro and in vivo high-throughput experiments., 4 pages, 3 figures

Chromatin is a complex of DNA, RNA, and proteins whose primary function is to package genomic DNA into the tight confines of a cell nucleus. A fundamental repeating unit of chromatin is the nucleosome, an octamer of histone proteins around which 147 base pairs of DNA are wound in almost two turns of a left-handed superhelix. Chromatin is a dynamic structure that exerts profound influence on regulation of gene expression and other cellular functions. These chromatin-directed processes are facilitated by optimizing nucleosome positions throughout the genome and by remodeling nucleosomes in response to various external and internal signals such as environmental perturbations. Here we discuss the large-scale maps of nucleosome positions made available through recent advances in parallel high-throughput sequencing and microarray technologies. We show that these maps reveal common features of nucleosome organization in eukaryotic genomes. We also survey the computational models designed to predict nucleosome formation scores or energies and demonstrate how these predictions can be used to position multiple nucleosomes on the genome without steric overlap.

We use nucleosome maps obtained by high-throughput sequencing to study sequence specificity of intrinsic histone-DNA interactions. In contrast with previous approaches, we employ an analogy between a classical one-dimensional fluid of finite-size particles in an arbitrary external potential and arrays of DNA-bound histone octamers. We derive an analytical solution to infer free energies of nucleosome formation directly from nucleosome occupancies measured in high-throughput experiments. The sequence-specific part of free energies is then captured by fitting them to a sum of energies assigned to individual nucleotide motifs. We have developed hierarchical models of increasing complexity and spatial resolution, establishing that nucleosome occupancies can be explained by systematic differences in mono- and dinucleotide content between nucleosomal and linker DNA sequences, with periodic dinucleotide distributions and longer sequence motifs playing a secondary role. Furthermore, similar sequence signatures are exhibited by control experiments in which genomic DNA is either sonicated or digested with micrococcal nuclease in the absence of nucleosomes, making it possible that current predictions based on high-throughput nucleosome positioning maps are biased by experimental artifacts., Comment: 36 pages, 13 figures

Chromatin is a complex of DNA, RNA, and proteins whose primary function is to package genomic DNA into the tight confines of a cell nucleus. A fundamental repeating unit of chromatin is the nucleosome, an octamer of histone proteins around which 147 base pairs of DNA are wound in almost two turns of a left-handed superhelix. Chromatin is a dynamic structure that exerts profound influence on regulation of gene expression and other cellular functions. These chromatin-directed processes are facilitated by optimizing nucleosome positions throughout the genome and by remodeling nucleosomes in response to various external and internal signals such as environmental perturbations. Here we discuss the large-scale maps of nucleosome positions made available through recent advances in parallel high-throughput sequencing and microarray technologies. We show that these maps reveal common features of nucleosome organization in eukaryotic genomes. We also survey the computational models designed to predict nucleosome formation scores or energies and demonstrate how these predictions can be used to position multiple nucleosomes on the genome without steric overlap.

Alarm substances are airborne chemical signals, released by an individual into the environment, which communicate emotional stress between conspecifics. Here we tested whether humans, like other mammals, are able to detect emotional stress in others by chemosensory cues. Sweat samples collected from individuals undergoing an acute emotional stressor, with exercise as a control, were pooled and presented to a separate group of participants (blind to condition) during four experiments. In an fMRI experiment and its replication, we showed that scanned participants showed amygdala activation in response to samples obtained from donors undergoing an emotional, but not physical, stressor. An odor-discrimination experiment suggested the effect was primarily due to emotional, and not odor, differences between the two stimuli. A fourth experiment investigated behavioral effects, demonstrating that stress samples sharpened emotion-perception of ambiguous facial stimuli. Together, our findings suggest human chemosensory signaling of emotional stress, with neurobiological and behavioral effects.

Alarm pheromones are airborne chemical signals, released by an individual into the environment, which transmit warning of danger to conspecifics via olfaction. Using fMRI, we provide the first neurobiological evidence for a human alarm pheromone. Individuals showed activation of the amygdala in response to sweat produced by others during emotional stress, with exercise sweat as a control; behavioral data suggest facilitated evaluation of ambiguous threat.

We analyze the indirect exchange interaction between two two-state systems, e.g., spins $1∕2$, subject to a common finite-temperature environment modeled by bosonic modes. The environmental modes, e.g., phonons or cavity photons, are also a source of quantum noise. We analyze the coherent vs noise-induced features of the two-spin dynamics and predict that for low enough temperatures the induced interaction is coherent over time scales sufficient to create entanglement. A nonperturbative approach is utilized to obtain an exact solution for the onset of the induced interaction, whereas for large times, a Markovian scheme is used. We identify the time scales for which the spins develop entanglement for various spatial separations. For large enough times, the initially created entanglement is erased by quantum noise. Estimates for the interaction and the level of quantum noise for localized impurity electron spins in Si-Ge type semiconductors are given.

We study the localization of bosonic atoms in an optical lattice, which interact in a spatially confined region. The classical theory predicts that there is no localization below a threshold value for the strength of interaction that is inversely proportional to the number of participating atoms. In a full quantum treatment, however, we find that localized states exist for arbitrarily weak attractive or repulsive interactions for any number ($>1$) of atoms. We further show, using an explicit solution of the two-particle bound state and an appropriate measure of entanglement, that the entanglement tends to a finite value in the limit of weak interactions. Coupled with the non-existence of localization in an optimized quantum product state, we conclude that the localization exists by virtue of entanglement., 6 pages, 4 figures; final published version with small changes in response to reviewer comments

Clinically effective next generation androgen deprivation therapy (ADT) and androgen receptor (AR)-directed therapies have been developed to treat castration-resistant prostate cancer (CRPC). However, disease progression inevitably occurs, and majority of relapsed tumors continue to overexpress AR. AR mutations and constitutively active AR splice variants (AR-Vs) are detected during ADT and may lead to drug resistance. Therefore, there is dire need to develop models that provide a better understanding of AR signaling and determine markers of ADT resistance in prostate cancer patient cells. Mouse models and existing human prostate cancer cell lines have inherent limitations for deciphering mechanisms of therapy resistance. Unlike the recently reported prostate tissue organoids that were derived at a low efficiency from 7/49 metastatic prostate cancer samples, we have developed a novel and exciting technology to generate normal, benign prostatic hyperplasia (BPH) and cancer “mini-prostates” from both early-stage and advanced prostate cancer patient samples. We have successfully rederived mini-prostates from 17 out of 19 primary prostatectomy tissues. We incorporated developmental epithelial and mesenchymal signals, stem-like cells and growth requirements in 3D cultures for maintaining primary normal, BPH and prostate cancer patient-derived cells as stem-like cell-derived organoids. Our preliminary data show the establishment of patient- single cell-derived normal, BPH and cancer mini-prostates comprised of organoids with glandular tissues that have a thick basement membrane, an outer mesenchymal and inner epithelial cells conveying AR signaling, expressing cytokeratins and secreting PSA. RNA sequencing, expression profiling and ADT revealed that mini-prostate cells maintain the genetic, chemoresistance, and growth rate features of the primary prostate. To model tumor heterogeneity, prostate cells from surgical tissues were isolated upon digital imaging and tissue mapping in mirror sections for AMACR, AR, AR-Vs, p63, Ki67, ERG expression and FISH analysis for TMPRSS2-ERG fusion. Living cells from mapped BPH and cancer clones are being utilized to derive single cells into mini-prostates. Our studies generated novel therapy sensitivity and drug discovery models that would allow for precision medicine and coclinical approaches to be enlisted to reveal chemo- or hormonal-resistance profiles in genetically defined mini-prostates, apply combinatory-targeted therapies and study therapy-induced clonal selection processes to ultimately guide future clinical trials. Citation Format: Monica Bartucci, Michele Patrizii, Eric Huselid, Shamila Yussuf, Nitu Bansal, Kathleen Flaherty, Denis Tolkunov, Hua Zhong, Mark N. Stein, Joseph Bertino, Robert DiPaola, Isaac Kim, Hatem E. Sabaawy. Generation of single cell-derived normal, benign and cancer mini-prostates from primary patient-derived tissues. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 223. doi:10.1158/1538-7445.AM2015-223

An investigation of the quantum phase transition in both discrete and continuum field Dicke models is presented. A series of anticrossing features following the criticality is revealed in the band of the field modes. Critical exponents are calculated. We investigate the properties of a pairwise entanglement measured by a concurrence and obtain analytical results in the thermodynamic limit., 7 pages, 3 figures

Quantum states of a discrete breather are studied in two ways. One method involves numerical diagonalization of the Hamiltonian, the other uses the path integral to examine correlations in the eigenstates. In both cases only the central nonlinearity is retained. To reduce truncation effects in the numerical diagonalization, a basis is used that involves a quadratic local mode. A similar device is used in the path integral method for deducing localization. Both approaches lead to the conclusion that aside from quantum tunneling the quantized discrete breather is stable., 33 pages, 20 figures, to appear in J. Chem. Phys

We demonstrate by an explicit model calculation that the decay of entanglement of two two-state systems (two qubits) is governed by the product of the factors that measure the degree of decoherence of each of the qubits, subject to independent sources of quantum noise. This demonstrates an important physical property that separated open quantum systems can evolve quantum mechanically on time scales larger than the times for which they remain entangled., Comment: 4 pages, 1 figure

We review our recent work establishing by an explicit many-body calculation for an open quantum-mechanical system of two qubits subject to independent noise modelled by bosonic baths, a newly identified connection between two important quantities in the studies of entanglement and decoherence. We demonstrate that the decay of entanglement is governed by the product of the suppression factors describing decoherence of the subsystems (qubits). This result is a detailed model calculation proving an important and intuitively natural physical property that separated open quantum systems can evolve coherently, quantum mechanically on time scales larger than the times for which they remain entangled. Our result also suggests avenues for future work. Specifically, for multiqubit systems, it is expected that similar arguments should apply "by induction." This will stimulate research to develop appropriate quantitative measures of entanglement, and attempts to quantify entanglement and decoherence in a unified way. We considered one "physically meaningful" measure of two-qubit entanglement, the concurrence. In future research, it would be of interest to obtain similar results for other measures of entanglement as well.© (2005) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.

We obtain and analyze the indirect exchange interaction between two two-state systems, e.g., spins, in a formulation that also incorporates the quantum noise that they experience, due to a bosonic environment, for instance, phonons. We utilize a perturbative approach to obtain a quantum evolution equation for the two-spin dynamics. A non-perturbative approach is used to study the onset of the induced interaction, which is calculated exactly. We predict that for low enough temperatures the interaction is coherent over time scales sufficient to create entanglement, dominated by the zero-point quantum fluctuations of the environment. We identify the time scales for which the spins develop entanglement for various spatial separations., Comment: 10 pages, 3 figures; typos corrected

Short time approximation is developed for system-environmental bath mode interactions involving a general non-Hermitian system operator $\Lambda$, and its conjugate, $\Lambda^\dagger$, in order to evaluate onset of decoherence at low temperatures in quantum systems interacting with environment. The developed approach is complementary to Markovian approximations and appropriate for evaluation of quantum computing schemes. Example of a spin system coupled to a bosonic heat bath via $\Lambda \propto \sigma_-$ is worked out in detail., Comment: 8 pages, 2 figures