Fundamental Structural Unit Research Articles

DNA physical properties outperform sequence compositional information in classifying nucleosome-enriched and -depleted regions

The nucleosome is the fundamental structural unit of eukaryotic chromatin and plays an essential role in the epigenetic regulation of cellular processes, such as DNA replication, recombination, and transcription. Hence, it is important to identify nucleosome positions in the genome. Our previous model based on DNA deformation energy, in which a set of DNA physical descriptors was used, performed well in predicting nucleosome dyad positions and occupancy. In this study, we established a machine-learning model for predicting nucleosome occupancy in order to further verify the physical descriptors. Results showed that (1) our model outperformed several other sequence compositional information-based models, indicating a stronger dependence of nucleosome positioning on DNA physical properties; (2) nucleosome-enriched and -depleted regions have distinct features in terms of DNA physical descriptors like sequence-dependent flexibility and equilibrium structure parameters; (3) gene transcription start sites and termination sites can be well characterized with the distribution patterns of the physical descriptors, indicating the regulatory role of DNA physical properties in gene transcription. In addition, we developed a web server for the model, which is freely accessible at http://lin-group.cn/server/iNuc-force/.

An FPGA-Based Massively Parallel Neuromorphic Cortex Simulator.

This paper presents a massively parallel and scalable neuromorphic cortex simulator designed for simulating large and structurally connected spiking neural networks, such as complex models of various areas of the cortex. The main novelty of this work is the abstraction of a neuromorphic architecture into clusters represented by minicolumns and hypercolumns, analogously to the fundamental structural units observed in neurobiology. Without this approach, simulating large-scale fully connected networks needs prohibitively large memory to store look-up tables for point-to-point connections. Instead, we use a novel architecture, based on the structural connectivity in the neocortex, such that all the required parameters and connections can be stored in on-chip memory. The cortex simulator can be easily reconfigured for simulating different neural networks without any change in hardware structure by programming the memory. A hierarchical communication scheme allows one neuron to have a fan-out of up to 200 k neurons. As a proof-of-concept, an implementation on one Altera Stratix V FPGA was able to simulate 20 million to 2.6 billion leaky-integrate-and-fire (LIF) neurons in real time. We verified the system by emulating a simplified auditory cortex (with 100 million neurons). This cortex simulator achieved a low power dissipation of 1.62 μW per neuron. With the advent of commercially available FPGA boards, our system offers an accessible and scalable tool for the design, real-time simulation, and analysis of large-scale spiking neural networks.

Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA.

The eukaryotic genome is packaged into a nucleus in the form of chromatin. The fundamental structural unit of chromatin is a protein-DNA complex, the nucleosome, where 146 or 147 base pairs of DNA wrap 1.75 times around a histone core. To function in cellular processes, however, nucleosomal DNA must be unwrapped. Although this unwrapping has been experimentally investigated, details of the process at an atomic level are not yet well understood. Here, we used molecular dynamics simulation with an enhanced sampling method to calculate the free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA. A free energy change of about 11.5 kcal/mol for the unwrapping agrees well with values obtained in single molecule experiments. This simulation revealed a variety of conformational states, indicating there are many potential paths to outer superhelicdal turn unwrapping, but the dominant path is likely asymmetric. At one end of the DNA, the first five bps unwrap, after which a second five bps unwrap at the same end with no increase in free energy. The unwrapping then starts at the other end of the DNA, where 10 bps are unwrapped. During further unwrapping of 15 bps, the unwrapping advances at one of the ends, after which the other end of the DNA unwraps to complete the unwrapping of the outer superhelical turn. These results provide insight into the construction, disruption, and repositioning of nucleosomes, which are continuously ongoing during cellular processes.

Detection of SUN1 Splicing Variants at the mRNA and Protein Levels in Cancer.

The linker of nucleoskeleton and cytoskeleton (LINC) complex, containing the proteins SUN and nesprin, is the fundamental structural unit of the nuclear envelope. The neoplastic-based regulation of the LINC complex in cancer tissues has become increasingly recognized in recent years, including the altered expression, somatic mutation, and methylation of genes. However, precisely how mutations and deregulated expression of the LINC complex contribute to the pathogenic mechanisms of tumorigenesis remain to be elucidated, mainly because of several technical difficulties. First, both the SUN and SYNE (encoding nesprin) genes give rise to a vast number of splicing variants. Second, immunoprecipitation experiments of endogenous SUN and nesprin proteins are difficult owing to the lack of suitable reagents as well as the limited solubility of these proteins in mild extraction conditions. Here, we describe three protocols to investigate these aspects: (1) immunohistochemistry to determine the expression levels and localization of the LINC complex in cancer tissue, (2) detection of SUN1 splicing variants at the mRNA level, and (3) detection of SUN1 splicing variants and binding partners at the protein level.

Structural Evolution in BaSn2F5X (X = Cl, Br, I): A Family of Alkaline Earth Metal Tin Mixed Halides.

As the first family of Sn-based alkaline earth metal mixed halides, three new compounds, BaSn2F5X (X = Cl, Br, and I), are synthesized by hydrothermal method. These compounds are crystallized in the centrosymmetric space groups of P21/c, P4/nmm, and Pmma for BaSn2F5Cl, BaSn2F5Br, and BaSn2F5I, respectively, and their microscopic frameworks are all composed of the fundamental structural unit [SnF4]2- and its derivatives ([SnF4Cl]3- and [SnF5]3- groups). Interestingly, the structures in BaSn2F5X are significantly changed from one-dimensional (1D) to two-dimensional (2D) and then to 1D motifs as X varies from Cl, Br, to I. Structural analysis combined with theoretical calculations reveals that the structural diversities are caused by the difference of ionic radius and electronegativity of X- anions as well as the orientation of the lone-pair electrons on Sn2+ cations. Moreover, the optical, electronic, and thermal properties for these three compounds are determined. This work provides a representative example to show how microscopic ions influence the structures, thus in favor of the design for new mixed halides, a type of important functional materials with many optoelectronic applications.

A room-temperature heptazine core discotic liquid crystal

ABSTRACTHeptazine is the fundamental structural and functional unit of graphitic carbon nitrides and has a π-conjugated planar symmetry with semiconducting properties. Molecular self-assembly is one of the key factors to drive the electronic behaviour of π-conjugated organic molecules. To enhance the semiconductivity, heptazine is decorated at its active sites with 2,3,5-tris(dodecyloxy)aniline to get well-organised columnar packing. A novel heptazine-core room-temperature discotic liquid crystal (HDLC) with hexagonal columnar geometry is discovered. The molecular structure and mesomorphic properties of HDLC are investigated by 1H-NMR, 13C-NMR, IR, polarised optical microscopy, differential scanning calorimetry and X-ray diffraction. Photophysical and electrochemical properties of HDLC are studied by UV–vis/fluorescence spectroscopy and cyclic voltammetry (CV), respectively. The energy band gap of HDLC estimated from CV at room temperature is 1.63 eV, which is much narrower than the previously reported band gap for heptazine derivatives. This decrease in the energy band can be attributed to the particular designing of HDLC for columnar packing. As a columnar liquid crystal providing a smooth path to the charge transport, HDLC with such a narrow energy band gap may find applications in organic electronics.

Dynamic Reorganization of Nucleosome Positioning in Somatic Cells after Transfer into Porcine Enucleated Oocytes.

SummaryThe nucleosome, the fundamental structural unit of chromatin, is a critical regulator of gene expression. The mechanisms governing changes to nucleosome occupancy and positioning during somatic cell reprogramming remain poorly understood. We established a method for generating genome-wide nucleosome maps of porcine embryonic fibroblasts (PEF), reconstructed 1-cell embryos generated by somatic cell nuclear transfer (SCNT), and fertilized zygotes (FZ) using MNase sequencing with only 1,000 cells. We found that donor PEF chromatin, especially X chromosome, became more open after transfer into porcine oocytes and nucleosome occupancy decreased in promoters but increased in the genic regions. Nucleosome arrangements around transcriptional start sites of genes with different expression levels in somatic cells tended to become transcriptionally silent in SCNT; however, some pluripotency genes adopted transcriptionally active nucleosome arrangements. FZ and SCNT had similar characteristics, unlike PEF. This study reveals the dynamics and importance of nucleosome positioning and chromatin organization early after reprogramming.

Mitotic chromosome assembly despite nucleosome depletion in Xenopus egg extracts.

The nucleosome is the fundamental structural unit of eukaryotic chromatin. During mitosis, duplicated nucleosome fibers are organized into a pair of rod-shaped structures (chromatids) within a mitotic chromosome. However, it remains unclear whether nucleosome assembly is indeed an essential prerequisite for mitotic chromosome assembly. We combined mouse sperm nuclei and Xenopus cell-free egg extracts depleted of the histone chaperone Asf1 and found that chromatid-like structures could be assembled even in the near absence of nucleosomes. The resultant "nucleosome-depleted" chromatids contained discrete central axes positive for condensins, although they were more fragile than normal nucleosome-containing chromatids. Combinatorial depletion experiments underscored the central importance of condensins in mitotic chromosome assembly, which sheds light on their functional cross-talk with nucleosomes in this process.

Interactive Chromatin Modeling with Genome Browser

Nucleosomes are the fundamental structural unit of chromatin, therefore all genomic functions are influenced by nucleosome structure and dynamics. The standard nucleosome is an octasome and consists of 147 base pairs of double stranded DNA wrapped 1.7 times around eight histones. Sub-octasome (tetrasome, hexasome, hemisome) and super-octasome (chromatosome) states also exist. We have integrated our Interactive Chromatin Modeling(ICM) tools with the Dalliance genome browser (DGB) as a means of integrating physical modeling with bioinformatics. ICM is an interactive web based tool that allows users to rapidly fold any sequence of DNA into atomic or coarse grained models of chromatin. ICM-DGB is designed to unite ICM's physical modeling with informatics data obtained from public databases, e.g. experimentally or theoretically determined nucleosome positions. ICM-DGB currently allows users to manipulate nucleosome positions (add, delete and move), assign different conformational states to each nucleosome (e.g. tetrasome, octasome, chromatosome), display structural data from a model as track data in DGB (e.g. Roll, Slide or Twist) and map informatics data onto a molecular structure (e.g. nucleosome positions, DNA damage sites). Our web based implementation of ICM-DGB utilizes a coarse grained model of chromatin implemented in LAMMPS for structure relaxation and displays the model with JMol. Here we utilize experimentally determined reference maps of nucleosome positions for the Saccharomyces cerevisiae genome to assess chromatin folding for the CHA1, HIS3 and PHO5 promoters. The models demonstrate that experimentally determined nucleosome positions are insufficient to achieve tight packing of chromatin. As a tool, ICM-DGB supports cross-validation of physical modeling and informatics approaches and the ability to investigate structure-function relationships for regions of the genome ranging from kilobases to megabases.

Modelling genome-wide topological associating domains in mouse embryonic stem cells

Chromosome conformation capture (3C)-based techniques such as chromosome conformation capture carbon copy (5C) and Hi-C revealed that the folding of mammalian chromosomes is highly hierarchical. A fundamental structural unit in the hierarchy is represented by topologically associating domains (TADs), sub-megabase regions of the genome within which the chromatin fibre preferentially interacts. 3C-based methods provide the mean contact probabilities between chromosomal loci, averaged over a large number of cells, and do not give immediate access to the single-cell conformations of the chromatin fibre. However, coarse-grained polymer models based on 5C data can be used to extract the single-cell conformations of single TADs. Here, we extend this approach to analyse around 2500 TADs in murine embryonic stem cells based on high-resolution Hi-C data. This allowed to predict the cell-to-cell variability in single contacts within genome-wide TADs and correlations between them. Based on these results, we predict that TADs are more similar to ideal chains than to globules in terms of their physical size and three-dimensional shape distribution. Furthermore, we show that their physical size and the degree of structural anisotropy of single TADs are correlated with the level of transcriptional activity of the genes that it harbours. Finally, we show that a large number of multiplets of genomic loci co-localize more often than expected by random, and these loci are particularly enriched in promoters, enhancers and CTCF-bound sites. These results provide the first genome-wide structural reconstruction of TADs using polymeric models obeying the laws of thermodynamics and reveal important universal trends in the correlation between chromosome structure and transcription.

Shaping Chromatin in the Nucleus: The Bricks and the Architects.

Chromatin organization in the nucleus provides a vast repertoire of information in addition to that encoded genetically. Understanding how this organization impacts genome stability and influences cell fate and tumorigenesis is an area of rapid progress. Considering the nucleosome, the fundamental unit of chromatin structure, the study of histone variants (the bricks) and their selective loading by histone chaperones (the architects) is particularly informative. Here, we report recent advances in understanding how relationships between histone variants and their chaperones contribute to tumorigenesis using cell lines and Xenopus development as model systems. In addition to their role in histone deposition, we also document interactions between histone chaperones and other chromatin factors that govern higher-order structure and control DNA metabolism. We highlight how a fine-tuned assembly line of bricks (H3.3 and CENP-A) and architects (HIRA, HJURP, and DAXX) is key in adaptation to developmental and pathological changes. An example of this conceptual advance is the exquisite sensitivity displayed by p53-null tumor cells to modulation of HJURP, the histone chaperone for CENP-A (CenH3 variant). We discuss how these findings open avenues for novel therapeutic paradigms in cancer care.

The WD40 Domain of HIRA Is Essential for RI-nucleosome Assembly in Xenopus Egg Extracts.

Histone chaperones are a group of histone-binding proteins that facilitate the assembly of nucleosomes, the fundamental structural units of chromatin in eukaryotes. In nucleosome assembly, deposition of a histone H3-H4 tetramer onto DNA is the first and critical step, which is mediated by the histone chaperones HIRA and CAF-1. HIRA and CAF-1 are reportedly involved in DNA replication independent (RI) and replication coupled nucleosome assembly, respectively. However, the mechanisms by which they mediate histone deposition remain unclear. In this study, we focused on the mechanism by which HIRA induces RI-nucleosome assembly. We looked for HIRA domains that are required for nucleosome assembly and its localization to chromatin. We used cell-free extracts from Xenopus eggs that carry out RI-nucleosome assembly of plasmid DNA. We confirmed that HIRA formed stable complexes with Asf1, another histone H3-H4 chaperone, and the HIRA-Asf1 complex was solely responsible for RI-nucleosome assembly in egg extracts. We further demonstrated that the HIRA N-terminus containing the WD40 domain, which comprises seven WD40 repeats, and the B domain, to which Asf1 binds, were essential for RI-nucleosome assembly; the three WD40 repeats from the N-terminus were especially critical. Using egg extracts that reproduce nuclear formation accompanying the duplication of chromatin, we also demonstrated that the Hir domain was indispensable for the binding of HIRA to chromatin. Thus, the WD40 and B domains are the core elements for inducing RI-nucleosome assembly. Hir domain regulates the binding to chromatin. Based on these findings, similarities and differences between HIRA and CAF-1 are discussed.

In vitro reconstitution and biochemical analyses of the Schizosaccharomyces pombe nucleosome

Schizosaccharomyces pombe, which has a small genome but shares many physiological functions with higher eukaryotes, is a useful single-cell, model eukaryotic organism. In particular, many features concerning chromatin structure and dynamics, including heterochromatin, centromeres, telomeres, and DNA replication origins, are well conserved between S. pombe and higher eukaryotes. However, the S. pombe nucleosome, the fundamental structural unit of chromatin, has not been reconstituted in vitro. In the present study, we established the method to purify S. pombe histones H2A, H2B, H3, and H4, and successfully reconstituted the S. pombe nucleosome in vitro. Our thermal stability assay and micrococcal nuclease treatment assay revealed that the S. pombe nucleosome is markedly unstable and its DNA ends are quite accessible, as compared to the canonical human nucleosome. These findings are important to understand the mechanisms of epigenetic genomic DNA regulation in fission yeast.

Progress Towards Mammalian Whole-Brain Cellular Connectomics.

Neurons are the fundamental structural units of the nervous system—i.e., the Neuron Doctrine—as the pioneering work of Santiago Ramón y Cajal in the 1880’s clearly demonstrated through careful observation of Golgi-stained neuronal morphologies. However, at that time sample preparation, imaging methods and computational tools were either nonexistent or insufficiently developed to permit the precise mapping of an entire brain with all of its neurons and their connections. Some measure of the “mesoscopic” connectional organization of the mammalian brain has been obtained over the past decade by alignment of sparse subsets of labeled neurons onto a reference atlas or via MRI-based diffusion tensor imaging. Neither method, however, provides data on the complete connectivity of all neurons comprising an individual brain. Fortunately, whole-brain cellular connectomics now appears within reach due to recent advances in whole-brain sample preparation and high-throughput electron microscopy (EM), though substantial obstacles remain with respect to large volume electron microscopic acquisitions and automated neurite reconstructions. This perspective examines the current status and problems associated with generating a mammalian whole-brain cellular connectome and argues that the time is right to launch a concerted connectomic attack on a small mammalian whole-brain.

Role of surface gauging in extended particle interactions: The case for spin

The matter, being extended in space, should be first characterized by a surface of separation from the empty space. This surface cannot be neatly, i.e. purely geometrically, defined. When it comes to extended particles, which thereby are to be considered the fundamental structural units of the matter, the physical evidence points out that they are not even stable: they are in a continuous transformation; and so is their limit of separation from space. The present work describes a concept of extended particle with special emphasis on this limit of separation. It turns out that the properties of inertia, as classically understood, are intrinsically related to the spin properties of quantum origin. Thus, an extended particle model cannot be but “holographic” when it comes to imbedding it in a physical structure. The spin properties turn out to be essential, inasmuch as they decide the forces of interaction issuing from particles.

AFM-based mechanical characterization of single nanofibres.

Nanofibres are found in a broad variety of hierarchical biological systems as fundamental structural units, and nanofibrillar components are playing an increasing role in the development of advanced functional materials. Accurate determination of the mechanical properties of single nanofibres is thus of great interest, yet measurement of these properties is challenging due to the intricate specimen handling and the exceptional force and deformation resolution that is required. The atomic force microscope (AFM) has emerged as an effective, reliable tool in the investigation of nanofibrillar mechanics, with the three most popular approaches-AFM-based tensile testing, three-point deformation testing, and nanoindentation-proving preferable to conventional tensile testing in many (but not all) cases. Here, we review the capabilities and limitations of each of these methods and give a comprehensive overview of the recent advances in this field.

Mineralized collagen biomaterial for reconstruction of cranial bone defects and its clinical applications

Event Abstract Back to Event Mineralized collagen biomaterial for reconstruction of cranial bone defects and its clinical applications Zhiye Qiu1, 2, Tianxi Song2*, Yuqi Zhang3 and Xiumei Wang1 1 Tsinghua University, School of Materials Science and Engineering, China 2 Beijing Allgens Medical Science and Technology Co., Ltd., China 3 Yuquan Hospital, Tsinghua University, Department of Neurosurgery, China Introduction: Cranial bone defects result from congenital malformation, trauma, tumor, as well as produced by trephination in craniotomy are common symptoms in neurosurgery. Such defects should be repaired appropriate methods, in order to provide biomechanical stability for the skull, protect the brain, and achieve cosmetic results. Metals, bioceramics and polymers were tried to be used for repairing cranial defects, however, many disadvantages induced by these materials limited their clinical outcomes[1]. Especially for those pediatric patients with growing cranial bone, titanium mesh or polyetheretherketone restrict the growth of the cranial bone and result in high risk of malformation of the skull. Therefore, a biodegradable and osteoconductive biomaterial is required for the reconstruction of cranial bone defects[2]. Materials and Methods: Mineralized collagen was prepared by an in vitro biomimetic mineralization process. Briefly, calcium and phosphorous salts were added into acidic collagen solution, respectively; then the pH value and temperature were adjusted to form mineralized collagen deposition; after washing and freeze-drying, mineralized collagen biomaterial with the same chemical composition and microstructure to the nature bone matrix was obtained. Such mineralized collagen could be fabricated into many bone grafts, such as burr-hole plug, trepanation gap filling strip, as well as patient specific irregular implant according to CT scanning data of the patient. Phase composition and chemical structure were characterized by XRD and FTIR. Clinical outcomes of cranial bone defect reconstructions were evaluated by plain radiographs and CT scanning at the 6th and 12th month post-operation. Results and Discussion: For each patient, there were no inflammatory responses, itching, or exudation at the surgical sites, and the wounds healed well. The defects implanted with mineralized collagen biomaterials healed well. As shown by Figure 1, bone mineral density gradually increased and approximated surrounding host bone. However, the defects as the blank control without any implants unchanged during the follow-up period. Mineralized collagen is the fundamental structural unit of many connective tissues, including bone, the biomimetic mineralized collagen material therefore has the same chemical composition and microstructure to the natural bone[3]. Animal experiments demonstrated that the mineralized collagen could be gradually substituted by newly regenerated bone tissues. For the reconstruction of cranial bone defect, mineralized collagen biomaterial serves as a scaffold for bone regeneration induced by dura matter. Conclusion: Mineralized collagen biomaterial has good biodegradability and osteoconductivity. Clinical outcomes demonstrated mineralized collagen implants promoted bone reconstruction of cranial defects, without any adverse responses. National Basic Research Program (973 Program) of China (2011CB606205); ‘Twelfth Five-Year’ National Science and Technology Support Program (2012BAI17B02) funded by the Ministry of Science and Technology of China; National Natural Science Foundation of China (21371106, 51402167)

Boundaries of the homologous phases in Sb–Te and Bi–Te binary alloy systems

Sb–Te and Bi–Te binary systems have long-period stacking structures called homologous phases. Within these structures, two types of fundamental structural units change their numbers according to their composition, and the stacking periods also change systematically. X-ray powder diffraction data on bulk specimens with different compositions reveal both the phase boundaries of the homologous phases and the structures of the boundary phases. The boundary phases are Sb20Te3 in the Sb–Te system and Bi8Te3 in the Bi–Te system.

ChemInform Abstract: Bioactive Benzofuran Derivatives: Moracins A—Z in Medicinal Chemistry

AbstractReview: 79 refs.

Wnt signaling orients the proximal-distal axis of chick kidney nephrons.

The nephron is the fundamental structural and functional unit of the kidney. Each mature nephron is patterned along a proximal-distal axis, with blood filtered at the proximal end and urine emerging from the distal end. In order to filter the blood and produce urine, specialized structures are formed at specific proximal-distal locations along the nephron, including the glomerulus at the proximal end, the tubule in the middle and the collecting duct at the distal end. The developmental processes that specify these different nephron segments are not fully understood. Wnt ligands, which are expressed in the nephric duct and later in the nascent nephron itself, are well-characterized inducers of nephrons, and are both required and sufficient for initiation of nephron formation from nephrogenic mesenchyme. Here, we present evidence that Wnt signaling also patterns the proximal-distal nephron axis. Using the chick mesonephros as a model system, a Wnt ligand was ectopically expressed in the coelomic lining, thereby introducing a source of Wnt signaling that is at right angles to the endogenous Wnt signal of the nephric duct. Under these conditions, the nephron axis was re-oriented, such that the glomerulus was always located at a position farthest from the Wnt sources. This re-orientation occurred within hours of exposure to ectopic Wnt signaling, and was accompanied initially by a repression of the early glomerular podocyte markers Wt1 and Pod1, followed by their re-emergence at a position distant from the Wnt signals. Activation of the Wnt signaling pathway in mesonephric explant cultures resulted in strong and specific repression of early and late glomerular markers. Finally, cytoplasmic β-catenin, indicative of active canonical Wnt signaling, was found to be enriched in the distal as compared with the proximal region of the forming nephron. Together, these data indicate that Wnt signaling patterns the proximal-distal axis of the nephron, with glomeruli differentiating in regions of lowest Wnt signaling.