Prethermal Fragmentation in a Periodically Driven Fermionic Chain

We study a fermionic chain with nearest-neighbor hopping and density-density interactions, where the nearest-neighbor interaction term is driven periodically. We show that such a driven chain exhibits prethermal strong Hilbert space fragmentation (HSF) in the high drive amplitude regime at specific drive frequencies ω_{m}^{*}. This constitutes the first realization of HSF for out-of-equilibrium systems. We obtain analytic expressions of ω_{m}^{*} using a Floquet perturbation theory and provide exact numerical computation of entanglement entropy, equal-time correlation functions, and the density autocorrelation of fermions for finite chains. All of these quantities indicate clear signatures of strong HSF. We study the fate of the HSF as one tunes away from ω_{m}^{*} and discuss the extent of the prethermal regime as a function of the drive amplitude.

Nuclear envelope protein lamin B receptor protects the genome from chromosomal instability and tumorigenesis

Lamin B Receptor (LBR) is an inner nuclear membrane protein that assembles the nuclear envelope post mitosis. Here we show that LBR depletion induces mitotic defects accompanied by recurrent chromosomal losses. In addition, LBR knockdown results in nuclear aberrations such as nuclear blebs and micronuclei, with chromosomes showing higher frequency of losses, being enriched within the micronucleus. Furthermore, doxycycline-induced conditional depletion of LBR significantly increased tumor volumes that form within the subcutaneous xenografts of mice. Of note, the tumor-derived primary cells recapitulated chromosomal losses and gains, revealing a novel role for LBR as a tumor suppressor. Co-immunoprecipitation of LBR uncovered an association of LBR with telomere-associated factors. Interestingly, qPCR array-based gene expression profiling showed a significant upregulation of telomere repeat-binding factor 1 (TRF1) upon LBR depletion. Remarkably, TRF1 knockdown in the background of LBR depletion maintains chromosomal stability, unraveling a novel mechanism involving LBR and TRF in the maintenance of chromosomal stability in colorectal cancer cells.

Nuclear envelope, chromatin organizers, histones, and DNA: The many achilles heels exploited across cancers

In eukaryotic cells, the genome is organized in the form of chromatin composed of DNA and histones that organize and regulate gene expression. The dysregulation of chromatin remodeling, including the aberrant incorporation of histone variants and their consequent post-translational modifications, is prevalent across cancers. Additionally, nuclear envelope proteins are often deregulated in cancers, which impacts the 3D organization of the genome. Altered nuclear morphology, genome organization, and gene expression are defining features of cancers. With advances in single-cell sequencing, imaging technologies, and high-end data mining approaches, we are now at the forefront of designing appropriate small molecules to selectively inhibit the growth and proliferation of cancer cells in a genome- and epigenome-specific manner. Here, we review recent advances and the emerging significance of aberrations in nuclear envelope proteins, histone variants, and oncohistones in deregulating chromatin organization and gene expression in oncogenesis.

Direct Demonstration of Seed Size-Dependent α-Synuclein Amyloid Amplification

The size of amyloid seeds is known to modulate their autocatalytic amplification and cellular toxicity. However, the seed size-dependent secondary nucleation mechanism, toxicity, and disease-associated biological processes mediated by α-synuclein (α-Syn) fibrils are largely unknown. Using the cellular model and in vitro reconstitution, we showed that the size of α-Syn fibril seeds dictates not only their cellular internalization and associated cell death but also the distinct mechanisms of fibril amplification pathways involved in the pathological conformational change of α-Syn. Specifically, small fibril seeds showed elongation possibly through monomer addition at the fibril termini, whereas longer fibrils template the fibril amplification by surface-mediated nucleation as demonstrated by super-resolution microscopy. The distinct mechanism of fibril amplification and cellular uptake along with toxicity suggest that breakage of fibrils into seeds of different sizes determines the underlying pathological outcome of synucleinopathies.

Nup93 and CTCF modulate spatiotemporal dynamics and function of the HOXA gene locus during differentiation

Nucleoporins regulate nuclear transport and are also involved in DNA damage, repair, cell cycle, chromatin organization, and gene expression. Here, we studied the role of nucleoporin Nup93 and the chromatin organizer CTCF in regulating HOXA expression during differentiation. ChIP sequencing revealed a significant overlap between Nup93 and CTCF peaks. Interestingly, Nup93 and CTCF are associated with the 3' and 5'HOXA genes respectively. Depletions of Nup93 and CTCF antagonistically modulate expression levels of 3'and 5'HOXA genes in undifferentiated NT2/D1 cells. Nup93 also regulates the localization of the HOXA gene locus, which disengages from the nuclear periphery upon Nup93 but not CTCF depletion, consistent with its upregulation. The dynamic association of Nup93 and CTCF with the HOXA locus during differentiation correlates with its spatial positioning and expression. While Nup93 tethers the HOXA locus to the nuclear periphery, CTCF potentially regulates looping of the HOXA gene cluster in a temporal manner. In summary, Nup93 and CTCF complement one another in modulating the spatiotemporal dynamics and function of the HOXA gene locus during differentiation.

Studying the Role of Chromosomal Instability (CIN) in GI Cancers Using Patient-derived Organoids

Chromosomal instability (CIN) is associated with the initiation and progression of gastrointestinal (GI) tract cancers. Cancers of the GI tract are typically characterized by altered chromosome numbers. While the dynamics of CIN have been extensively characterized in 2D monolayer cell cultures derived from GI tumors, the tumor microenvironment and 3D tumor architecture also contribute to the progression of CIN, which is not captured in 2D cell culture systems. To overcome these limitations, self-organizing cellular structures that retain organ-specific 3D architecture, namely organoids, have been derived from various tissues of the GI tract. Organoids derived from normal tissue and patient tumors serve as a useful paradigm to study the crosstalk between tumor cells in the context of a tissue microenvironment and its impact on chromosomal stability. Such a paradigm, therefore, has a considerable advantage over 2D cell culture systems in drug screening and personalized medicine. Here, we review the importance of patient-derived tumor organoids (PDTOs) as a model to study CIN in cancers of the GI tract.

Analytic approaches to periodically driven closed quantum systems: methods and applications

We present a brief overview of some of the analytic perturbative techniques for the computation of the Floquet Hamiltonian for a periodically driven, or Floquet, quantum many-body system. The key technical points about each of the methods discussed are presented in a pedagogical manner. They are followed by a brief account of some chosen phenomena where these methods have provided useful insights. We provide an extensive discussion of the Floquet-Magnus (FM) expansion, the adiabatic-impulse approximation, and the Floquet perturbation theory. This is followed by a relatively short discourse on the rotating wave approximation, a FM resummation technique and the Hamiltonian flow method. We also provide a discussion of some open problems which may possibly be addressed using these methods.

Active microrheology using pulsed optical tweezers to probe viscoelasticity of lamin A

Lamins are nucleoskeletal proteins of mammalian cells that stabilize the structure and maintain the rigidity of the nucleus. These type V intermediate filament proteins which are predominantly of A and B types provide necessary tensile strength to the nucleus. Single amino acid missense mutations occurring all over the lamin A protein form a cluster of human diseases termed as laminopathies, most of which principally affect the muscle and cardiac tissues responsible for load bearing functionalities of the body. One such mutation is A350P which causes dilated cardiomyopathy in patients. It is postulated that a change from alanine to proline in the α-helical coiled-coil forming 2B rod domain of the protein might severely disrupt the propensity of the filaments to polymerise into functional higher order structures required to form a fully functional lamina with its characteristic elasticity. In this study, we have elucidated for the very first time, the application of active microrheology employing oscillating optical tweezers to investigate any alterations in the viscoelastic parameters of the mutant protein meshwork in vitro, which might translate into possible changes in nuclear plasticity. We confirmed our findings from this robust yet fast method by imaging both the wild type and mutant lamin A networks using a super resolution microscope, and observed changes in the mesh size which corroborate our measured changes in the viscoelastic parameters of the lamins. This method could thus be extended to conduct microrheological measurements on any intermediate filament protein thus bearing significant implications in laminopathies and other diseases associated with intermediate filaments.

Role of A- and B-type lamins in nuclear structure-function relationships

Nuclear lamins are type V intermediate filament proteins that form a filamentous meshwork beneath the inner nuclear membrane. Additionally, a sub-population of A- and B-type lamins localizes in the nuclear interior. The nuclear lamina protects the nucleus from mechanical stress and mediates nucleo-cytoskeletal coupling. Lamins form a scaffold that partially tethers chromatin at the nuclear envelope. The nuclear lamina also stabilises protein-protein interactions involved in gene regulation and DNA repair. The lamin-based protein sub-complexes are implicated in both nuclear and cytoskeletal organisation, the mechanical stability of the nucleus, genome organisation, transcriptional regulation, genome stability and cellular differentiation. Here, we review recent research on nuclear lamins and unique roles of A- and B-type lamins in modulating various nuclear processes and their impact on cell function.

One-dimensional spin-orbit coupled Dirac system with extendeds-wave superconductivity: Majorana modes and Josephson effects

Motivated by the spin-momentum locking of electrons at the boundaries of certain topological insulators, we study a one-dimensional system of spin-orbit coupled massless Dirac electrons withs-wave superconducting pairing. As a result of the spin-orbit coupling, our model has only two kinds of linearly dispersing modes, and we take these to be right-moving spin-up and left-moving spin-down. Both lattice and continuum models are studied. In the lattice model, we find that a single Majorana zero energy mode appears at each end of a finite system provided that thes-wave pairing has an extended form, with the nearest-neighbor pairing being larger than the on-site pairing. We confirm this both numerically and analytically by calculating the winding number. We find that the continuum model also has zero energy end modes. Next we study a lattice version of a model with both Schrödinger and Dirac-like terms and find that the model hosts a topological transition between topologically trivial and non-trivial phases depending on the relative strength of the Schrödinger and Dirac terms. We then study a continuum system consisting of twos-wave superconductors with different phases of the pairing, with aδ-function potential barrier lying at the junction of the two superconductors. Remarkably, we find that the system has asingleAndreev bound state (ABS) which is localized at the junction. When the pairing phase difference crosses a multiple of 2π, an ABS touches the top of the superconducting gap and disappears, and a different state appears from the bottom of the gap. We also study the AC Josephson effect in such a junction with a voltage bias that has both a constantV₀and a term which oscillates with a frequencyω. We find that, in contrast to standard Josephson junctions, Shapiro plateaus appear when the Josephson frequencyω_J= 2eV₀/ℏis a rational fraction ofω. We discuss experiments which can realize such junctions.

Inequality, Familial Aggregation, and Risk Prediction of Caries in Siblings

INTRODUCTION

Social and family conditions are likely of great importance to dental health; however, limited evidence of familial aggregation of caries among adolescent siblings exists. Moreover, social and family-level factors have never been evaluated as isolated caries predictors at the individual level.

OBJECTIVES

The objectives were to evaluate socioeconomic patterning of caries among siblings, assess sibling-specific aggregation of caries within families, and examine if such aggregation differed by parental socioeconomic position (SEP). We also evaluated the discriminant ability of sibling caries, SEP, and other social and familial factors in predicting caries in cosiblings.

METHODS

This nationwide register-based study included all 15-y-olds in Denmark in 2003 (index siblings) and their biological siblings born within ±3 y (cosiblings). Clinical and sociodemographic data for each subject were compiled from Danish national dental, social, and population registers. Caries was measured by the decayed, missing, and filled tooth surfaces (DMFS) index. Predictors included SEP (parental education, income, and occupational social class), gender, birth order, immigration status, and household type. Adjusted SEP-caries associations were estimated using negative binomial regression. Familial aggregation was evaluated using adjusted pairwise odds ratios from alternating logistic regressions. Caries prediction was based on classification and regression tree (CART) analyses.

RESULTS

The study included 23,847 sibling pairs (n = 47,694). Socioeconomic patterning of caries was similar among the index and cosiblings with significant graded SEP-caries associations. Significant sibling-specific aggregation of caries was observed; cosiblings of caries-affected index siblings had odds of having caries 3.9 times (95% confidence interval: 3.65-4.18) as high as that of cosiblings with caries-free index siblings. This sibling similarity was stronger in socioeconomically disadvantaged families (adjusted pairwise odds ratios: 3.08-5.47). CART revealed index sibling caries as the single most important caries predictor, with caries predicted in ≥84% of cosiblings of adolescents with ≥3 carious tooth surfaces.

CONCLUSIONS

Caries in a sibling should prompt preventive family-based approaches targeting cosiblings.

KNOWLEDGE TRANSFER STATEMENT

This study revealed significant socioeconomic patterning of caries in adolescent siblings. Prediction modeling indicated that the single most important caries predictor among cosiblings was index sibling caries. Information on sibling caries level should be routinely combined with clinical evaluation to identify children at risk. Moreover, information on social and family conditions should be used to target prevention and health promotion at the school or municipal level. These approaches could possibly contribute to reducing the existing caries inequalities.

Twist1 induces chromosomal instability (CIN) in colorectal cancer cells

Twist1 is a basic helix-loop-helix transcription factor, essential during early development in mammals. While Twist1 induces epithelial-to-mesenchymal transition (EMT), here we show that Twist1 overexpression enhances nuclear and mitotic aberrations. This is accompanied by an increase in whole chromosomal copy number gains and losses, underscoring the role of Twist1 in inducing chromosomal instability (CIN) in colorectal cancer cells. Array comparative genomic hybridization (array CGH) analysis further shows sub-chromosomal deletions, consistent with an increased frequency of DNA double strand breaks (DSBs). Remarkably, Twist1 overexpression downmodulates key cell cycle checkpoint factors-Bub1, BubR1, Mad1 and Mad2-that regulate CIN. Mathematical simulations using the RACIPE tool show a negative correlation of Twist1 with E-cadherin and BubR1. Data analyses of gene expression profiles of patient samples from The Cancer Genome Atlas (TCGA) reveal a positive correlation between Twist1 and mesenchymal genes across cancers, whereas the correlation of TWIST1 with CIN and DSB genes is cancer subtype-specific. Taken together, these studies highlight the mechanistic involvement of Twist1 in the deregulation of factors that maintain genome stability during EMT in colorectal cancer cells. Twist1 overexpression enhances genome instability in the context of EMT that further contributes to cellular heterogeneity. In addition, these studies imply that Twist1 downmodulates nuclear lamins that further alter spatiotemporal organization of the cancer genome and epigenome. Notwithstanding their genetic background, colorectal cancer cells nevertheless maintain their overall ploidy, while the downstream effects of Twist1 enhance CIN and DNA damage enriching for sub-populations of aggressive cancer cells.

Size-dependent influence of NOx on the growth rates of organic aerosol particles

Atmospheric new-particle formation (NPF) affects climate by contributing to a large fraction of the cloud condensation nuclei (CCN). Highly oxygenated organic molecules (HOMs) drive the early particle growth and therefore substantially influence the survival of newly formed particles to CCN. Nitrogen oxide (NOx) is known to suppress the NPF driven by HOMs, but the underlying mechanism remains largely unclear. Here, we examine the response of particle growth to the changes of HOM formation caused by NOx. We show that NOx suppresses particle growth in general, but the suppression is rather nonuniform and size dependent, which can be quantitatively explained by the shifted HOM volatility after adding NOx. By illustrating how NOx affects the early growth of new particles, a critical step of CCN formation, our results help provide a refined assessment of the potential climatic effects caused by the diverse changes of NOx level in forest regions around the globe.

Lamin A/C modulates spatial organization and function of the Hsp70 gene locus via nuclear myosin I

The structure-function relationship of the nucleus is tightly regulated, especially during heat shock. Typically, heat shock activates molecular chaperones that prevent protein misfolding and preserve genome integrity. However, the molecular mechanisms that regulate nuclear structure-function relationships during heat shock remain unclear. Here, we show that lamin A and C (hereafter lamin A/C; both lamin A and C are encoded by LMNA) are required for heat-shock-mediated transcriptional induction of the Hsp70 gene locus (HSPA genes). Interestingly, lamin A/C regulates redistribution of nuclear myosin I (NM1) into the nucleus upon heat shock, and depletion of either lamin A/C or NM1 abrogates heat-shock-induced repositioning of Hsp70 gene locus away from the nuclear envelope. Lamins and NM1 also regulate spatial positioning of the SC35 (also known as SRSF2) speckles - important nuclear landmarks that modulates Hsp70 gene locus expression upon heat shock. This suggests an intricate crosstalk between nuclear lamins, NM1 and SC35 organization in modulating transcriptional responses of the Hsp70 gene locus during heat shock. Taken together, this study unravels a novel role for lamin A/C in the regulation of the spatial dynamics and function of the Hsp70 gene locus upon heat shock, via the nuclear motor protein NM1.This article has an associated First Person interview with the first author of the paper.

Lamin A/C and Emerin depletion impacts chromatin organization and dynamics in the interphase nucleus

Background

Nuclear lamins are type V intermediate filament proteins that maintain nuclear structure and function. Furthermore, Emerin - an interactor of Lamin A/C, facilitates crosstalk between the cytoskeleton and the nucleus as it also interacts with actin and Nuclear Myosin 1 (NM1).

Results

Here we show that the depletion of Lamin A/C or Emerin, alters the localization of the nuclear motor protein - Nuclear Myosin 1 (NM1) that manifests as an increase in NM1 foci in the nucleus and are rescued to basal levels upon the combined knockdown of Lamin A/C and Emerin. Furthermore, Lamin A/C-Emerin co-depletion destabilizes cytoskeletal organization as it increases actin stress fibers. This further impinges on nuclear organization, as it enhances chromatin mobility more toward the nuclear interior in Lamin A/C-Emerin co-depleted cells. This enhanced chromatin mobility was restored to basal levels either upon inhibition of Nuclear Myosin 1 (NM1) activity or actin depolymerization. In addition, the combined loss of Lamin A/C and Emerin alters the otherwise highly conserved spatial positions of chromosome territories. Furthermore, knockdown of Lamin A/C or Lamin A/C-Emerin combined, deregulates expression levels of a candidate subset of genes. Amongst these genes, both KLK10 (Chr.19, Lamina Associated Domain (LAD+)) and MADH2 (Chr.18, LAD-) were significantly repressed, while BCL2L12 (Chr.19, LAD-) is de-repressed. These genes differentially reposition with respect to the nuclear envelope.

Conclusions

Taken together, these studies underscore a remarkable interplay between Lamin A/C and Emerin in modulating cytoskeletal organization of actin and NM1 that impinges on chromatin dynamics and function in the interphase nucleus.

Electronic supplementary material

The online version of this article (10.1186/s12860-019-0192-5) contains supplementary material, which is available to authorized users.

Nucleolin modulates compartmentalization and dynamics of histone 2B-ECFP in the nucleolus

Eukaryotic cells have 2 to ​3 discrete nucleoli required for ribosome synthesis. Nucleoli are phase separated nuclear sub-organelles. Here we examined the role of nuclear Lamins and nucleolar factors in modulating the compartmentalization and dynamics of histone 2B (H2B-ECFP) in the nucleolus. Live imaging and Fluorescence Recovery After Photobleaching (FRAP) of labelled H2B, showed that the depletion of Lamin B1, Fibrillarin (FBL) or Nucleostemin (GNL3), enhances H2B-ECFP mobility in the nucleolus. Furthermore, Nucleolin knockdown significantly decreases H2B-ECFP compartmentalization in the nucleolus, while H2B-ECFP residence and mobility in the nucleolus was prolonged upon Nucleolin overexpression. Co-expression of N-terminal and RNA binding domain (RBD) deletion mutants of Nucleolin or inhibiting 45S rRNA synthesis reduces the sequestration of H2B-ECFP in the nucleolus. Taken together, these studies reveal a crucial role of Nucleolin-rRNA complex in modulating the compartmentalization, stability and dynamics of H2B within the nucleolus.

Emerin modulates spatial organization of chromosome territories in cells on softer matrices

Cells perceive and relay external mechanical forces into the nucleus through the nuclear envelope. Here we examined the effect of lowering substrate stiffness as a paradigm to address the impact of altered mechanical forces on nuclear structure-function relationships. RNA sequencing of cells on softer matrices revealed significant transcriptional imbalances, predominantly in chromatin associated processes and transcriptional deregulation of human Chromosome 1. Furthermore, 3-Dimensional fluorescence in situ hybridization (3D-FISH) analyses showed a significant mislocalization of Chromosome 1 and 19 Territories (CT) into the nuclear interior, consistent with their transcriptional deregulation. However, CT18 with relatively lower transcriptional dysregulation, also mislocalized into the nuclear interior. Furthermore, nuclear Lamins that regulate chromosome positioning, were mislocalized into the nuclear interior in response to lowered matrix stiffness. Notably, Lamin B2 overexpression retained CT18 near the nuclear periphery in cells on softer matrices. While, cells on softer matrices also activated emerin phosphorylation at a novel Tyr99 residue, the inhibition of which in a phospho-deficient mutant (emerinY99F), selectively retained chromosome 18 and 19 but not chromosome 1 territories at their conserved nuclear locations. Taken together, emerin functions as a key mechanosensor, that modulates the spatial organization of chromosome territories in the interphase nucleus.

Genome 3D-architecture: Its plasticity in relation to function

The genome of higher eukaryotes is non-randomly organized in the interphase nucleus. However, notwithstanding the absence of membrane bound sub-compartments, the nucleus coordinates a number of functions largely by organizing chromatin in a non-random but dynamic manner. The plasticity of chromatin structure and function relies on epigenetic modifications as well as its association with nuclear landmarks such as the nuclear envelope, nuclear lamina, nuclear pore complex and nuclear bodies such as the nucleolus among others. In the absence of membrane-bound compartments, cells and the nucleus, in particular, employ phase-separation, which unmixes phases that constrain biochemical reactions in complex non-membranous sub-compartments such as the nucleolus or even the heterochromatin. This review attempts to provide a glimpse into the microcosm of phase-separated nuclear sub-compartments, that regulate nuclear structure- function relationships.

Lamin B2 Modulates Nucleolar Morphology, Dynamics, and Function

The nucleolus is required for ribosome biogenesis. Human cells have 2 or 3 nucleoli associated with nucleolar organizer region (NOR)-bearing chromosomes. An increase in number and altered nucleolar morphology define cancer cells. However, the mechanisms that modulate nucleolar morphology and function are unclear. Here we show that in addition to localizing at the nuclear envelope, lamin B2 localizes proximal to nucleolin at the granular component (GC) of the nucleolus and associates with the nucleolar proteins nucleolin and nucleophosmin. Lamin B2 knockdown severely disrupted the nucleolar morphology, which was rescued to intact and discrete nucleoli upon lamin B2 overexpression. Furthermore, two mutually exclusive lamin B2 deletion mutants, ΔHead and ΔSLS, rescued nuclear and nucleolar morphology defects, respectively, induced upon lamin B2 depletion, suggesting independent roles for lamin B2 at the nucleolus and nuclear envelope. Lamin B2 depletion increased nucleolin aggregation in the nucleoplasm, implicating lamin B2 in stabilizing nucleolin within the nucleolus. Lamin B2 knockdown upregulated nucleolus-specific 45S rRNA and upstream intergenic sequence (IGS) transcripts. The IGS transcripts colocalized with aggregates of nucleolin speckles, which were sustained in the nucleoplasm upon lamin B2 depletion. Taken together, these studies uncover a novel role for lamin B2 in modulating the morphology, dynamics, and function of the nucleolus.

Anisotropic transport of normal metal-barrier-normal metal junctions in monolayer phosphorene

We study transport properties of a phosphorene monolayer in the presence of single and multiple potential barriers of height U ₀ and width d, using both continuum and microscopic lattice models, and show that the nature of electron transport along its armchair edge (x direction) is qualitatively different from its counterpart in both conventional two-dimensional electron gas with Schrödinger-like quasiparticles and graphene or surfaces of topological insulators hosting massless Dirac quasiparticles. We show that the transport, mediated by massive Dirac electrons, allows one to achieve collimated quasiparticle motion along x and thus makes monolayer phosphorene an ideal experimental platform for studying Klein paradox in the context of gapped Dirac materials. We study the dependence of the tunneling conductance [Formula: see text] as a function of d and U ₀, and demonstrate that for a given applied voltage V its behavior changes from oscillatory to decaying function of d for a range of U ₀ with finite non-zero upper and lower bounds, and provide analytical expression for these bounds within which G decays with d. We contrast such behavior of G with that of massless Dirac electrons in graphene and also with that along the zigzag edge (y direction) in phosphorene where the quasiparticles obey an effective Schrödinger equation at low energy. We also study transport through multiple barriers along x and demonstrate that these properties hold for transport through multiple barriers as well. Finally, we suggest concrete experiments which may verify our theoretical predictions.

Chromosomal aneuploidies induced upon Lamin B2 depletion are mislocalized in the interphase nucleus

Chromosome territories assume non-random positions in the interphase nucleus with gene-rich chromosomes localized toward the nuclear interior and gene-poor chromosome territories toward the nuclear periphery. Lamins are intermediate filament proteins of the inner nuclear membrane required for the maintenance of nuclear structure and function. Here, we show using whole-genome expression profiling that Lamin A/C or Lamin B2 depletion in an otherwise diploid colorectal cancer cell line (DLD1) deregulates transcript levels from specific chromosomes. Further, three-dimensional fluorescence in situ hybridization (3D-FISH) analyses of a subset of these transcriptionally deregulated chromosome territories revealed that the diploid chromosome territories in Lamin-depleted cells largely maintain conserved positions in the interphase nucleus in a gene-density-dependent manner. In addition, chromosomal aneuploidies were induced in ~25 % of Lamin A/C or Lamin B2-depleted cells. Sub-populations of these aneuploid cells consistently showed a mislocalization of the gene-rich aneuploid chromosome 19 territory toward the nuclear periphery, while gene-poor aneuploid chromosome 18 territory was mislocalized toward the nuclear interior predominantly upon Lamin B2 than Lamin A/C depletion. In addition, a candidate gene locus ZNF570 (Chr.19q13.12) significantly overexpressed upon Lamin B2 depletion was remarkably repositioned away from the nuclear lamina. Taken together, our studies strongly implicate an overarching role for Lamin B2 in the maintenance of nuclear architecture since loss of Lamin B2 relieves the spatial positional constraints required for maintaining conserved localization of aneuploid chromosome territories in the interphase nucleus.

HOXA repression is mediated by nucleoporin Nup93 assisted by its interactors Nup188 and Nup205

Background

The nuclear pore complex (NPC) mediates nuclear transport of RNA and proteins into and out of the nucleus. Certain nucleoporins have additional functions in chromatin organization and transcription regulation. Nup93 is a scaffold nucleoporin at the nuclear pore complex which is associated with human chromosomes 5, 7 and 16 and with the promoters of the HOXA gene as revealed by ChIP-on-chip studies using tiling microarrays for these chromosomes. However, the functional consequences of the association of Nup93 with HOXA is unknown.

Results

Here, we examined the association of Nup93 with the HOXA gene cluster and its consequences on HOXA gene expression in diploid colorectal cancer cells (DLD1). Nup93 showed a specific enrichment ~1 Kb upstream of the transcription start site of each of the HOXA1, HOXA3 and HOXA5 promoters, respectively. Furthermore, the association of Nup93 with HOXA was assisted by its interacting partners Nup188 and Nup205. The depletion of the Nup93 sub-complex significantly upregulated HOXA gene expression levels. However, expression levels of a control gene locus (GLCCI1) on human chromosome 7 were unaffected. Three-dimensional fluorescence in situ hybridization (3D-FISH) analyses revealed that the depletion of the Nup93 sub-complex (but not Nup98) disengages the HOXA gene locus from the nuclear periphery, suggesting a potential role for Nup93 in tethering and repressing the HOXA gene cluster. Consistently, Nup93 knockdown increased active histone marks (H3K9ac), decreased repressive histone marks (H3K27me3) on the HOXA1 promoter and increased transcription elongation marks (H3K36me3) within the HOXA1 gene. Moreover, the combined depletion of Nup93 and CTCF (a known organizer of HOXA gene cluster) but not Nup93 alone, significantly increased GLCCI1 gene expression levels. Taken together, this suggests a novel role for Nup93 and its interactors in repressing the HOXA gene cluster.

Conclusions

This study reveals that the nucleoporin Nup93 assisted by its interactors Nup188 and Nup205 mediates the repression of HOXA gene expression.

Electronic supplementary material

The online version of this article (doi:10.1186/s13072-016-0106-0) contains supplementary material, which is available to authorized users.

Role of trap-induced scales in non-equilibrium dynamics of strongly interacting trapped bosons

We use a time-dependent hopping expansion technique to study the non-equilibrium dynamics of strongly interacting bosons in an optical lattice in the presence of a harmonic trap characterized by a force constant K. We show that after a sudden quench of the hopping amplitude J across the superfluid (SF)-Mott insulator (MI) transition, the SF order parameter [Formula: see text] and the local density fluctuation [Formula: see text] exhibit sudden decoherence beyond a trap-induced time scale [Formula: see text]. We also show that after a slow linear ramp down of J, [Formula: see text] and the boson defect density [Formula: see text] display a novel non-monotonic spatial profile. Both these phenomena can be explained as consequences of trap-induced time and length scales affecting the dynamics and can be tested by concrete experiments.

Dynamical Detection of Topological Phase Transitions in Short-Lived Atomic Systems

We demonstrate that dynamical probes provide direct means of detecting the topological phase transition (TPT) between conventional and topological phases, which would otherwise be difficult to access because of loss or heating processes. We propose to avoid such heating by rapidly quenching in and out of the short-lived topological phase across the transition that supports gapless excitations. Following the quench, the distribution of excitations in the final conventional phase carries signatures of the TPT. We apply this strategy to study the TPT into a Majorana-carrying topological phase predicted in one-dimensional spin-orbit-coupled Fermi gases with attractive interactions. The resulting spin-resolved momentum distribution, computed by self-consistently solving the time-dependent Bogoliubov-de Gennes equations, exhibits Kibble-Zurek scaling and Stückelberg oscillations characteristic of the TPT. We discuss parameter regimes where the TPT is experimentally accessible.

Statistics of work distribution in periodically driven closed quantum systems

We study the statistics of the work distribution P(w) in a d-dimensional closed quantum system with linear dimension L subjected to a periodic drive with frequency ω(0). We show that the corresponding rate function I(w)=-ln[P(w)/Λ(0)]/L^{d} after a drive period satisfies a universal lower bound I(0)≥n(d) and has a zero at w=QL(d)/N, where n(d) and Q are the excitation and the residual energy densities generated during the drive, Λ(0) is a constant fixed by the normalization of P(w), and N is the total number of constituent particles or spins in the system. We supplement our results by calculating I(w) for a class of d-dimensional integrable models and show that I(w) has an oscillatory dependence on ω(0) originating from Stuckelberg interference generated due to double passage through the critical point or region during the drive. We suggest experiments to test our theory.

A highly selective sulfinate ester probe for thiol bioimaging

We describe here hitherto unexplored chemistry of the sulfinate ester functional group as being highly selective towards nucleophilic substitution by thiols at physiological pH. Using this cleavable trigger, an optical thiol probe that is suitable for thiol bioimaging has been developed.

A perturbative renormalization group approach to driven quantum systems

We use a perturbative momentum shell renormalization group (RG) approach to study the properties of a driven quantum system at zero temperature. To illustrate the technique, we consider a bosonic ϕ(4) theory with an arbitrary time dependent interaction parameter λ(t) = λ f(ω0t), where ω0 is the drive frequency and we derive the RG equations for the system using a Keldysh diagrammatic technique. We show that the scaling of ω0 is analogous to that of temperature for a system in thermal equilibrium and its presence provides a cutoff scale for the RG flow. We analyze the resultant RG equations, derive an analytical condition for such a drive to take the system out of the gaussian regime, and show that the onset of the non-gaussian regime occurs concomitantly with the appearance of non-perturbative mode coupling terms in the effective action of the system. We supplement the above-mentioned results by obtaining them from equations of motion of the bosons and discuss their significance for systems near critical points described by time-dependent Landau-Ginzburg theories.

Ramp dynamics of phonons in an ion trap: entanglement generation and cooling

We show that the ramp dynamics of phonons in a one-dimensional ion trap can be used for both generating multiparticle entangled states and motional state cooling of a string of trapped ions. We study such ramp dynamics using an effective Bose-Hubbard model which describes these phonons at low energies and show that specific protocols, involving site-specific dynamical tuning of the on-site potential of the model, can be used to generate entangled states and to achieve motional state cooling without involving electronic states of the ions. We compare and contrast our schemes for these to the earlier suggested ones and discuss specific experiments to realize the suggested protocols.

Tunable superlattice in graphene to control the number of Dirac points

Superlattice in graphene generates extra Dirac points in the band structure and their number depends on the superlattice potential strength. Here, we have created a lateral superlattice in a graphene device with a tunable barrier height using a combination of two gates. In this Letter, we demonstrate the use of lateral superlattice to modify the band structure of graphene leading to the emergence of new Dirac cones. This controlled modification of the band structure persists up to 100 K.

Periodic dynamics of fermionic superfluids in the BCS regime

We study the zero temperature non-equilibrium dynamics of a fermionic superfluid in the BCS limit and in the presence of a drive leading to a time-dependent chemical potential μ(t). We choose a periodic driving protocol characterized by a frequency ω and compute the fermion density, the wavefunction overlap, and the residual energy of the system at the end of N periods of the drive. We demonstrate that the BCS self-consistency condition is crucial in shaping the long time behaviour of the fermions subjected to the drive and provide an analytical understanding of the behaviour of the fermion density nkF (where kF is the Fermi momentum vector) after a drive period and for large ω. We also show that the momentum distribution of the excitations generated due to such a drive bears the signature of the pairing symmetry and can be used, for example, to distinguish between s- and d-wave superfluids. We propose experiments to test our theory.

Depth matters: cells grown on nano-porous anodic alumina respond to pore depth

Recent experiments have shown unambiguously that living cells respond to the nano-topography of surfaces they grow on-specifically, the fate of stem cells grown on nano-porous titania or alumina have been shown to be decided by the pore size. However, most experiments have focused on pore size or pitch. Here we show that in addition to pore size and pitch, the depth of the pores has a profound effect on cell morphology and the arrangement of the actin cytoskeleton.

Large variations in the magnetic ordering behavior of EuCu(2)As(2) with the application of external pressure and magnetic field

The influence of external pressure on the electrical transport and magnetic properties of EuCu(2)As(2), crystallizing in a ThCr(2)Si(2)-type structure, is reported. The system is known to be an antiferromagnet below T(N) ≈ 15 K in the absence of external magnetic fields. We find that there is a gradual reduction of T(N) with the application of a magnetic field with an extrapolated value of the critical field of around 18 kOe which can drive T(N) to zero. Electrical resistivity under pressure (<11 GPa) reveals that the magnetic ordering temperature is pushed up dramatically to higher temperatures which is quite interesting if compared with the behavior in isostructural FeAs-based systems containing Eu. Above 7 GPa, the pressure-induced state appears to be ferromagnetic. The results thus reveal interesting changes in the magnetic ordering behavior of this compound with increasing pressure and magnetic fields.

Nonequilibrium dynamics of the Bose-Hubbard model: a projection-operator approach

We study the phase diagram and nonequilibrium dynamics involving ramp of the hopping amplitude J(t)=Jt/τ with ramp time τ of the Bose-Hubbard model at zero temperature using a projection-operator formalism which allows us to incorporate the effects of quantum fluctuations beyond mean-field approximations in the strong-coupling regime. Our formalism yields a phase diagram which provides a near exact match with quantum Monte Carlo results in three dimensions. We also compute the residual energy Q, the superfluid order parameter Δ(t), the equal-time order parameter correlation function C(t), and the wave function overlap F which yields the defect formation probability P during nonequilibrium dynamics of the model. We find that Q, F, and P do not exhibit the expected universal scaling. We explain this absence of universality and show that our results compare well with recent experiments.

Superconductivity in SnO: a nonmagnetic analog to Fe-based superconductors?

We discovered that under pressure SnO with α-PbO structure, the same structure as in many Fe-based superconductors, e.g., β-FeSe, undergoes a transition to a superconducting state for p≳6 GPa with a maximum Tc of 1.4 K at p=9.3 GPa. The pressure dependence of Tc reveals a domelike shape and superconductivity disappears for p≳16 GPa. It is further shown from band structure calculations that SnO under pressure exhibits a Fermi surface topology similar to that reported for some Fe-based superconductors and that the nesting between the hole and electron pockets correlates with the change of Tc as a function of pressure.

Abstract 1964: Genetic instability and mammary tumor formation in mice carrying mammary-specific disruption of Chk1

Chk1 is a key element in the DNA damage response pathway that is required for maintaining genomic stability. To study the potential role of Chk1 in mammary tumorigenesis, we disrupted it using a Cre/loxP system. We showed that although Chk1 haploinsufficiency caused abnormal development of the mammary gland, it was not sufficient to induce tumorigenesis. Simultaneous deletion of one copy of p53 failed to rescue the developmental defects; however, it synergistically induced mammary tumor formation in Chk1+/-;MMTV-Cre animals with a median time to tumor latency of about 10 months. Chk1 deficiency caused a preponderance of abnormalities, including prolongation, multipolarity, misalignment, mitotic catastrophe and loss of spindle checkpoint that is accompanied by reduced expression of several cell cycle regulators, including Mad2. On the other hand, we also showed that Chk1 deficiency inhibited mammary tumor formation in mice carrying a homozygous deletion of p53, uncovering a complex relationship between Chk1 and p53. Furthermore, inhibition of Chk1 with a specific inhibitor, SB-218078, or acute deletion of Chk1 using shRNA killed mammary tumor cells effectively. These data demonstrate that Chk1 is critical for maintaining genome integrity and serves as a double-edged sword for cancer: while its inhibition kills cancer cells, it also triggers tumorigenesis when avorable mutations are accumulated for cell growth.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1964.

Multiprobe experiments under high pressure: resistivity, magnetic susceptibility, heat capacity, and thermopower measurements around 5 GPa

We have performed multiprobe experiments using a Bridgman-anvil pressure cell, adapted to trap Daphne oil as pressure medium. Resistivity, ac-magnetic susceptibility, thermopower, and ac-heat capacity of a type-I superconductor, lead, have been studied at low temperature up to 5+/-0.1 GPa. This is the first report where ac-magnetic susceptibility has been measured in this type of pressure cell and at such a high pressure range. The signature of the superconducting transition temperature, obtained from all these different measurements, agrees well within the experimental errors.

Tuning the conductance of dirac fermions on the surface of a topological insulator

We study the transport properties of the Dirac fermions with a Fermi velocity v{F} on the surface of a topological insulator across a ferromagnetic strip providing an exchange field J over a region of width d. We show that the conductance of such a junction, in the clean limit and at low temperature, changes from oscillatory to a monotonically decreasing function of d beyond a critical J. This leads to the possible realization of a magnetic switch using these junctions. We also study the conductance of these Dirac fermions across a potential barrier of width d and potential V0 in the presence of such a ferromagnetic strip and show that beyond a critical J, the criteria of conductance maxima changes from chi=eV{0}d/variant Planck's over v{F}=npi to chi=(n+1/2)pi for integer n. We point out that these novel phenomena have no analogs in graphene and suggest experiments which can probe them.

Evaluating annotations of an Agilent expression chip suggests that many features cannot be interpreted

Background

While attempting to reanalyze published data from Agilent 4 × 44 human expression chips, we found that some of the 60-mer olignucleotide features could not be interpreted as representing single human genes. For example, some of the oligonucleotides align with the transcripts of more than one gene. We decided to check the annotations for all autosomes and the X chromosome systematically using bioinformatics methods.

Results

Out of 42683 reporters, we found that 25505 (60%) passed all our tests and are considered "fully valid". 9964 (23%) reporters did not have a meaningful identifier, mapped to the wrong chromosome, or did not pass basic alignment tests preventing us from correlating the expression values of these reporters with a unique annotated human gene. The remaining 7214 (17%) reporters could be associated with either a unique gene or a unique intergenic location, but could not be mapped to a transcript in RefSeq. The 7214 reporters are further partitioned into three different levels of validity.

Conclusion

Expression array studies should evaluate the annotations of reporters and remove those reporters that have suspect annotations. This evaluation can be done systematically and semi-automatically, but one must recognize that data sources are frequently updated leading to slightly changing validation results over time.