Pathway tracing using biotinylated dextran amines

Biotinylated dextran amines (BDA) are highly sensitive tools for anterograde and retrograde pathway tracing studies of the nervous system. BDA can be reliably delivered into the nervous system by iontophoretic or pressure injection and visualized with an avidin-biotinylated HRP (ABC) procedure, followed by a standard or metal-enhanced diaminobenzidine (DAB) reaction. High molecular weight BDA (10 k) yields sensitive and exquisitely detailed labeling of axons and terminals, while low molecular weight BDA (3 k) yields sensitive and detailed retrograde labeling of neuronal cell bodies. The detail of neuronal cell body labeling can be Golgi-like. BDA tolerates EM fixation and processing well and can, therefore, be readily used in ultrastructural studies. Additionally, BDA can be combined with other anterograde or retrograde tracers (e.g. PHA-L or cholera toxin B fragment) and visualized either by multi-color DAB multiple-labeling - if permanent labels are desired, or by using multiple simultaneous immunofluorescence - if fluorescence viewing is desired. In the same manner, BDA pathway tracing and neurotransmitter immunolabeling can be combined. Note that BDA pathway tracing can also be combined with anterograde or retrograde labeling with fluorescent dextran amines, if one wishes to exclusively use tracers with the favorable transport properties and sensitivities of dextran amines. In this case, the BDA can be visualized together with the fluorescent dextran amines using fluorescence labeling for the BDA, or the fluorescent dextran amines can be visualized together with the BDA by multicolor DAB labeling via immunolabeling of the fluorescent dextran amines using anti-fluorophore antisera. BDA is, thus, a flexible and valuable pathway tracing tool that has gained widespread popularity in recent years.

Dense packings of the Platonic and Archimedean solids

Dense particle packings have served as useful models of the structures of liquid, glassy and crystalline states of matter, granular media, heterogeneous materials and biological systems. Probing the symmetries and other mathematical properties of the densest packings is a problem of interest in discrete geometry and number theory. Previous work has focused mainly on spherical particles-very little is known about dense polyhedral packings. Here we formulate the generation of dense packings of polyhedra as an optimization problem, using an adaptive fundamental cell subject to periodic boundary conditions (we term this the 'adaptive shrinking cell' scheme). Using a variety of multi-particle initial configurations, we find the densest known packings of the four non-tiling Platonic solids (the tetrahedron, octahedron, dodecahedron and icosahedron) in three-dimensional Euclidean space. The densities are 0.782..., 0.947..., 0.904... and 0.836..., respectively. Unlike the densest tetrahedral packing, which must not be a Bravais lattice packing, the densest packings of the other non-tiling Platonic solids that we obtain are their previously known optimal (Bravais) lattice packings. Combining our simulation results with derived rigorous upper bounds and theoretical arguments leads us to the conjecture that the densest packings of the Platonic and Archimedean solids with central symmetry are given by their corresponding densest lattice packings. This is the analogue of Kepler's sphere conjecture for these solids.

A simple and sensitive antigen retrieval method for free-floating and slide-mounted tissue sections

The masking of antigens by aldehyde-containing fixatives or by paraffin embedding procedures is a problem for immunohistochemical studies. Enzymatic digestion, formic acid treatment, microwave heating and autoclave heating have been used to deal with this problem, with microwave heating-based antigen retrieval having become widely used as the method of choice. Microwave heating, however, has the shortcoming that it is difficult to precisely control the heating temperature and it is difficult to apply this method of heating to free-floating sections without damaging the sections. We describe here a simple, reliable and sensitive antigen retrieval method that uses water-bath heating. By this method, the temperature can be precisely controlled to yield effective antigen retrieval with minimal tissue damage in free-floating or paraffin-embedded slide-mounted sections. We found that the best results were obtained with a 30 min incubation in a 10-50 mM sodium citrate solution (pH 8.5-9.0) preheated to and maintained at 80 degrees C in a water-bath, followed by 30 min incubation in 0.3-3% nonfat dry milk to reduce nonspecfic staining. This method is highly effective for both 40 microm free floating sections, slide-mounted cryostat sections and paraffin-embedded slide-mounted sections, and it works well for tissue from diverse species (human, rat, mouse, pigeon, and zebra finch) and for diverse antigens (e.g. enkephalin, substance P, huntingtin, GluR1, GFAP, and ubiquitin). This method was also found to enhance immunolabeling in glutaraldehyde-fixed tissue that had been prepared for ultrastructural examination, without having a deleterious effect on the ultrastructure.

Reduced miR-128 in breast tumor-initiating cells induces chemotherapeutic resistance via Bmi-1 and ABCC5

PURPOSE

Tumor-initiating cells are resistant to chemotherapy, but how microRNAs play a role in regulating drug resistance of breast tumor-initiating cells (BT-IC) needs to be clarified.

EXPERIMENTAL DESIGN

Lentivirus-mediated miR-128 transduction was done in BT-ICs, enriched by mammosphere cultures or CD44(+)CD24(-) fluorescence-activated cell sorting. Apoptosis and DNA damage were determined upon treatment with doxorubicin. Expression of miR-128 in breast cancer tissues was examined by in situ hybridization and correlated with breast tumor response to neoadjuvant chemotherapy and patient survival.

RESULTS

MiR-128 was significantly reduced in chemoresistant BT-ICs enriched from breast cancer cell lines and primary breast tumors (P < 0.01), accompanied by an overexpression of Bmi-1 and ABCC5, which were identified as targets of miR-128. Ectopic expression of miR-128 reduced the protein levels of Bmi-1 and ABCC5 in BT-ICs, along with decreased cell viability (P < 0.001) and increased apoptosis (P < 0.001) and DNA damage (P < 0.001) in the presence of doxorubicin. Reduced miR-128 expression in breast tumor tissues was associated with chemotherapeutic resistance (P < 0.001) and poor survival of breast cancer patients (P < 0.05; n = 57).

CONCLUSIONS

Reduction in miR-128 leading to Bmi-1 and ABCC5 overexpression is a stem cell-like feature of BT-ICs, which contributes to chemotherapeutic resistance in breast cancers. Ectopic expression of miR-128 sensitizes BT-ICs to the proapoptotic and DNA-damaging effects of doxorubicin, indicating therapeutic potential.

Production of gamma-aminobutyric acid by Streptococcus salivarius subsp. thermophilus Y2 under submerged fermentation

Gamma-aminobutyric acid (GABA), a major inhibitory neurotransmitter in the central nervous system, has several well-known physiological functions and has been applied to the production of many drugs and functional foods. The technology of GABA production via submerged fermentation by Streptococcus salivarius subsp. thermophilus Y2 was investigated in this paper. It indicated that the GABA production was related to the biochemical characteristics of glutamate decarboxylase (GAD) of S. salivarius subsp. thermophilus Y2. After 24 h of fermentation at 37 degrees C, which is the suitable culture conditions for GAD-production, then the culture condition were adjusted to the optimal temperature (40 degrees C) and pH (4.5) for the GAD reaction activity in biotransformation of cells and pyridoxal 5'-phosphate (0.02 mmol/l) were added to the broth at the 48 h, the GABA production was increased up to 1.76-fold, reaching 7984.75 +/- 293.33 mg/l. The strain shows great potential use as a starter for GABA-containing yoghurt, cheese and other functional fermented food productions.

Ultrastructural architecture and mechanical properties of attachment pads in Tettigonia viridissima (Orthoptera Tettigoniidae)

Natural releasable attachment systems of insect legs, where attachment-detachment performances are often very fast, seem to be optimized to get a maximum of real contact to the substratum. Tarsi of Tettigonia viridissima bear flexible attachment pads with unusual ultrastructural architecture of the cuticle. The indentation of the attachment pads was measured under different loads using a force-tester. Since the mechanical properties are influenced by material structure, the freeze-substitution experiments were undertaken to investigate the influence of loads on material structure. Both profile changes of the surface and the orientation of cuticle microfibrils were visualized by means of scanning electron microscopy followed by fracturing of the frozen material. The results show that the flexible pad material deforms replicating the substrate profile down to the micrometer roughness. The pad material showed both elastic and viscous behavior under loads. Elastic deformation of the pad occurred under normal force applied for 4-6 s (elastic modulus 27.2 +/- 11.6 kPa). Two viscous relaxation processes were found, of time constants tau1 = 1.88+/-0.616 s and tau2 =41.2 +/- 9.95 s. Low stiffness of material studied here aids in surface replication and increase of area of real contact between the pad and the underlying substrate.

MicroRNA 34c gene down-regulation via DNA methylation promotes self-renewal and epithelial-mesenchymal transition in breast tumor-initiating cells

Tumor-initiating cells (T-ICs), a subpopulation of cancer cells with stem cell-like properties, are related to tumor relapse and metastasis. Our previous studies identified a distinct profile of microRNA (miRNA) expression in breast T-ICs (BT-ICs), and the dysregulated miRNAs contribute to the self-renewal and tumorigenesis of these cells. However, the underlying mechanisms for miRNA dysregulation in BT-ICs remain obscure. In the present study, we demonstrated that the expression and function of miR-34c were reduced in the BT-ICs of MCF-7 and SK-3rd cells, a breast cancer cell line enriched for BT-ICs. Ectopic expression of miR-34c reduced the self-renewal of BT-ICs, inhibited epithelial-mesenchymal transition, and suppressed migration of the tumor cells via silencing target gene Notch4. Furthermore, we identified a single hypermethylated CpG site in the promoter region of miR-34c gene that contributed to transcriptional repression of miR-34c in BT-ICs by reducing DNA binding activities of Sp1. Therefore, miR-34c reduction in BT-ICs induced by a single hypermethylated CpG site in the promoter region promotes self-renewal and epithelial-mesenchymal transition of BT-ICs.

The pearl oyster Pinctada fucata martensii genome and multi-omic analyses provide insights into biomineralization

Nacre, the iridescent material found in pearls and shells of molluscs, is formed through an extraordinary process of matrix-assisted biomineralization. Despite recent advances, many aspects of the biomineralization process and its evolutionary origin remain unknown. The pearl oyster Pinctada fucata martensii is a well-known master of biomineralization, but the molecular mechanisms that underlie its production of shells and pearls are not fully understood. We sequenced the highly polymorphic genome of the pearl oyster and conducted multi-omic and biochemical studies to probe nacre formation. We identified a large set of novel proteins participating in matrix-framework formation, many in expanded families, including components similar to that found in vertebrate bones such as collagen-related VWA-containing proteins, chondroitin sulfotransferases, and regulatory elements. Considering that there are only collagen-based matrices in vertebrate bones and chitin-based matrices in most invertebrate skeletons, the presence of both chitin and elements of collagen-based matrices in nacre suggests that elements of chitin- and collagen-based matrices have deep roots and might be part of an ancient biomineralizing matrix. Our results expand the current shell matrix-framework model and provide new insights into the evolution of diverse biomineralization systems.

Adhesion measured on the attachment pads of Tettigonia viridissima (Orthoptera, insecta)

The tarsi of the cricket Tettigonia viridissima bear flexible attachment pads that are able to deform, replicating the profile of a surface to which they are apposed. This attachment system is supplemented by a secretion produced by epidermal cells and transported onto the surface of the pad through the pore canals of the pad cuticle. This study shows that the secretion alone is necessary, but not sufficient, for adhesion. To account for the full adhesive force, the deformation of the pad and the resulting changes in contact area were considered. In two series of experiments, the adhesive properties of the secretion and the adhesion of the whole pad were measured using a force tester, the sensitivity of which ranged from micronewtons to centinewtons. The adhesive forces of the secretion measured between a smooth sapphire ball with a diameter of 1.47 mm and a flat silicon surface ranged from 0.1 to 0.6 mN. In a control experiment on the silicon surface without secretion, no adhesive force was measured. There was no dependence of the adhesive force on the applied compressive force. When an intact pad was pulled off a flat silicon surface, the adhesive force increased with increasing applied compressive force, but it did not increase further once the applied force exceeded a certain value. The saturated adhesive force, ranging from 0.7 to 1.2 mN, was obtained at applied forces of 0.7-1.5 mN. The hemispherical surface of the pad had a larger contact area and demonstrated greater adhesion under a larger applied force. Adhesion became saturated when a pad was deformed such that contact area was maximal. The tenacity (the adhesive force per unit area) was 1.7-2.2 mN mm(−)(2).

Dense packings of polyhedra: Platonic and Archimedean solids

Understanding the nature of dense particle packings is a subject of intense research in the physical, mathematical, and biological sciences. The preponderance of previous work has focused on spherical particles and very little is known about dense polyhedral packings. We formulate the problem of generating dense packings of nonoverlapping, nontiling polyhedra within an adaptive fundamental cell subject to periodic boundary conditions as an optimization problem, which we call the adaptive shrinking cell (ASC) scheme. This optimization problem is solved here (using a variety of multiparticle initial configurations) to find the dense packings of each of the Platonic solids in three-dimensional Euclidean space R3 , except for the cube, which is the only Platonic solid that tiles space. We find the densest known packings of tetrahedra, icosahedra, dodecahedra, and octahedra with densities 0.823..., 0.836..., 0.904..., and 0.947..., respectively. It is noteworthy that the densest tetrahedral packing possesses no long-range order. Unlike the densest tetrahedral packing, which must not be a Bravais lattice packing, the densest packings of the other nontiling Platonic solids that we obtain are their previously known optimal (Bravais) lattice packings. We also derive a simple upper bound on the maximal density of packings of congruent nonspherical particles and apply it to Platonic solids, Archimedean solids, superballs, and ellipsoids. Provided that what we term the "asphericity" (ratio of the circumradius to inradius) is sufficiently small, the upper bounds are relatively tight and thus close to the corresponding densities of the optimal lattice packings of the centrally symmetric Platonic and Archimedean solids. Our simulation results, rigorous upper bounds, and other theoretical arguments lead us to the conjecture that the densest packings of Platonic and Archimedean solids with central symmetry are given by their corresponding densest lattice packings. This can be regarded to be the analog of Kepler's sphere conjecture for these solids.The truncated tetrahedron is the only nonchiral Archimedean solid that is not centrally symmetric [corrected], the densest known packing of which is a non-lattice packing with density at least as high as 23/24=0.958 333... . We discuss the validity of our conjecture to packings of superballs, prisms, and antiprisms as well as to high-dimensional analogs of the Platonic solids. In addition, we conjecture that the optimal packing of any convex, congruent polyhedron without central symmetry generally is not a lattice packing. Finally, we discuss the possible applications and generalizations of the ASC scheme in predicting the crystal structures of polyhedral nanoparticles and the study of random packings of hard polyhedra.

Modeling heterogeneous materials via two-point correlation functions: basic principles

Heterogeneous materials abound in nature and man-made situations. Examples include porous media, biological materials, and composite materials. Diverse and interesting properties exhibited by these materials result from their complex microstructures, which also make it difficult to model the materials. Yeong and Torquato [Phys. Rev. E 57, 495 (1998)] introduced a stochastic optimization technique that enables one to generate realizations of heterogeneous materials from a prescribed set of correlation functions. In this first part of a series of two papers, we collect the known necessary conditions on the standard two-point correlation function S2(r) and formulate a conjecture. In particular, we argue that given a complete two-point correlation function space, S2(r) of any statistically homogeneous material can be expressed through a map on a selected set of bases of the function space. We provide examples of realizable two-point correlation functions and suggest a set of analytical basis functions. We also discuss an exact mathematical formulation of the (re)construction problem and prove that S2(r) cannot completely specify a two-phase heterogeneous material alone. Moreover, we devise an efficient and isotropy-preserving construction algorithm, namely, the lattice-point algorithm to generate realizations of materials from their two-point correlation functions based on the Yeong-Torquato technique. Subsequent analysis can be performed on the generated images to obtain desired macroscopic properties. These developments are integrated here into a general scheme that enables one to model and categorize heterogeneous materials via two-point correlation functions. We will mainly focus on basic principles in this paper. The algorithmic details and applications of the general scheme are given in the second part of this series of two papers.

The overexpression of hypomethylated miR-663 induces chemotherapy resistance in human breast cancer cells by targeting heparin sulfate proteoglycan 2 (HSPG2)

MicroRNAs are involved in regulating the biology of cancer cells, but their involvement in chemoresistance is not fully understood. We found that miR-663 was up-regulated in our induced multidrug-resistant MDA-MB-231/ADM cell line and that this up-regulation was closely related to chemosensitivity. In the present study, we aimed to clarify the role of miR-663 in regulating the chemoresistance of breast cancer. MicroRNA microarray and quantitative RT-PCR assays were used to identify differentially expressed microRNAs. Cell apoptosis was evaluated by annexin V/propidium iodide staining, TUNEL, and reactive oxygen species generation analysis. The expression of miR-663 and HSPG2 in breast cancer tissues was detected by in situ hybridization and immunohistochemistry. The potential targets of miR-663 were defined by a luciferase reporter assay. Bisulfite sequencing PCR was used to analyze the methylation status. We found that miR-663 was significantly elevated in MDA-MB-231/ADM cells, and the down-regulation of miR-663 sensitized MDA-MB-231/ADM cells to both cyclophosphamide and docetaxel. The overexpression of miR-663 in breast tumor tissues was associated with chemoresistance; in MDA-MB-231 cells, this chemoresistance was accompanied by the down-regulation of HSPG2, which was identified as a target of miR-663. MDA-MB-231/ADM contained fewer methylated CpG sites than its parental cell line, and miR-663 expression in MDA-MB-231 cells was reactivated by 5-aza-29-deoxycytidine treatment, indicating that DNA methylation may play a functional role in the expression of miR-663. Our findings suggest that the overexpression of hypomethylated miR-663 induced chemoresistance in breast cancer cells by down-regulating HSPG2, thus providing a potential target for the development of an microRNA-based approach for breast cancer therapy.

Evidence from a novel human cell clone that adult vascular smooth muscle cells can convert reversibly between noncontractile and contractile phenotypes

Smooth muscle cells (SMCs) perform diverse functions that can be categorized as contractile and synthetic. A traditional model holds that these distinct functions are performed by the same cell, by virtue of its capacity for bidirectional modulation of phenotype. However, this model has been challenged, in part because there is no physiological evidence that an adult synthetic SMC can acquire the ability to contract. We sought evidence for this by cloning adult SMCs from human internal thoracic artery. One clone, HITB5, expressed smooth muscle alpha-actin, smooth myosin heavy chains, heavy caldesmon, and calponin and showed robust calcium transients in response to histamine and angiotensin II, which confirmed intact transmembrane signaling cascades. On serum withdrawal, these cells adopted an elongated and spindle-shaped morphology, random migration slowed, extracellular matrix protein production fell, and cell proliferation and [(3)H]thymidine incorporation fell to near 0. Cell viability was not compromised, however; in fact, apoptosis rate fell significantly. In this state, agonist-induced elevation of cytoplasmic calcium was even more pronounced and was accompanied by SMC contraction. Readdition of 10% serum completely returned HITB5 cells to a noncontractile, proliferative phenotype. Contractile protein expression increased after serum withdrawal, although modestly, which suggested that the switch to contractile function involved reorganization or sensitization of existing contractile structures. To our knowledge, the physiological properties of HITB5 SMCs provide the first direct demonstration that cultured human adult SMCs can convert between a synthetic, noncontracting state and a contracting state. HITB5 cells should be valuable for characterizing the basis of this critical transition.

Atomic Interlamellar Ion Path in High Sulfur Content Lithium-Montmorillonite Host Enables High-Rate and Stable Lithium-Sulfur Battery

Fast lithium ion transport with a high current density is critical for thick sulfur cathodes, stemming mainly from the difficulties in creating effective lithium ion pathways in high sulfur content electrodes. To develop a high-rate cathode for lithium-sulfur (Li-S) batteries, extenuation of the lithium ion diffusion barrier in thick electrodes is potentially straightforward. Here, a phyllosilicate material with a large interlamellar distance is demonstrated in high-rate cathodes as high sulfur loading. The interlayer space (≈1.396 nm) incorporated into a low lithium ion diffusion barrier (0.155 eV) significantly facilitates lithium ion diffusion within the entire sulfur cathode, and gives rise to remarkable nearly sulfur loading-independent cell performances. When combined with 80% sulfur contents, the electrodes achieve a high capacity of 865 mAh g-1 at 1 mA cm-2 and a retention of 345 mAh g-1 at a high discharging/charging rate of 15 mA cm-2 , with a sulfur loading up to 4 mg. This strategy represents a major advance in high-rate Li-S batteries via the construction of fast ions transfer paths toward real-life applications, and contributes to the research community for the fundamental mechanism study of loading-independent electrode systems.

miR-27a regulates endothelial differentiation of breast cancer stem like cells

Recent studies suggested that cancer stem cells (CSCs) are capable of differentiating into endothelial cells and tumor endothelium may be derived from CSCs. But the mechanism remains unclear. We showed that vascular endothelial growth factor (VEGF) induced the expression of endothelial markers in breast cancer stem like cells (BCSLCs). In addition, the VEGF-treated BCSLCs formed capillary structure in matrigel and released vWF upon histamine treatment. The miR-27a expression was significantly increased in VEGF-treated BCSLCs. Antagonizing miR-27a by miR-27a anti-sense oligos (ASOs) in VEGF-treated BCSLCs led to decreased endothelial markers and function, while increasing miR-27a in BCSLCs resulted in enhanced endothelial properties. VEGF enhanced the transcription of miR-27a by increasing RUNX1 binding to miR-27a promoter. Increased miR-27a paralleled the reduced expression of ZBTB10, a known miR-27a target. Both expression of miR-27a and knockdown of ZBTB10 in BCSLCs promoted in vivo angiogenesis and tumor metastasis. Further, we demonstrated that VEGF-treated BCSLCs secreted more endogenous VEGF compared with undifferentiated BCSLCs. Thus, miR-27a promotes angiogenesis by mediating endothelial differentiation of BCSLCs and it may be a new target for anti-angiogenesis cancer therapy.

The Role of Oral Pathobionts in Dysbiosis during Periodontitis Development

An emerging concept is the tight relationship between dysbiosis (microbiota imbalance) and disease. The increase in knowledge about alterations in microbial communities that reside within the host has made a strong impact not only on dental science, but also on immunology and microbiology as well as on our understanding of several diseases. Periodontitis is a well-characterized human disease associated with dysbiosis, characterized by the accumulation of multiple bacteria that play individual and critical roles in bone loss around the teeth. Dysbiosis is largely dependent on cooperative and competitive interactions among oral microbes during the formation of the pathogenic biofilm community at gingival sites. Oral pathobionts play different and synergistic roles in periodontitis development, depending on their host-damaging and immunostimulatory activities. Host immune responses to oral pathobionts act as a double-edged sword not only by protecting the host against pathobionts, but also by promoting alveolar bone loss. Recent studies have begun to elucidate the roles of individual oral bacteria, including a new type of pathobionts that possess strong immunostimulatory activity, which is critical for alveolar bone loss. Better understanding of the roles of oral pathobionts is expected to lead to a better understanding of periodontitis disease and to the development of novel preventive and therapeutic approaches for the disease.

Epigenetic Modifications of Histones in Periodontal Disease

Periodontitis is a chronic infectious disease driven by dysbiosis, an imbalance between commensal bacteria and the host organism. Periodontitis is a leading cause of tooth loss in adults and occurs in about 50% of the US population. In addition to the clinical challenges associated with treating periodontitis, the progression and chronic nature of this disease seriously affect human health. Emerging evidence suggests that periodontitis is associated with mechanisms beyond bacteria-induced protein and tissue degradation. Here, we hypothesize that bacteria are able to induce epigenetic modifications in oral epithelial cells mediated by histone modifications. In this study, we found that dysbiosis in vivo led to epigenetic modifications, including acetylation of histones and downregulation of DNA methyltransferase 1. In addition, in vitro exposure of oral epithelial cells to lipopolysaccharides resulted in histone modifications, activation of transcriptional coactivators, such as p300/CBP, and accumulation of nuclear factor-κB (NF-κB). Given that oral epithelial cells are the first line of defense for the periodontium against bacteria, we also evaluated whether activation of pathogen recognition receptors induced histone modifications. We found that activation of the Toll-like receptors 1, 2, and 4 and the nucleotide-binding oligomerization domain protein 1 induced histone acetylation in oral epithelial cells. Our findings corroborate the emerging concept that epigenetic modifications play a role in the development of periodontitis.

Modeling heterogeneous materials via two-point correlation functions. II. Algorithmic details and applications

In the first part of this series of two papers, we proposed a theoretical formalism that enables one to model and categorize heterogeneous materials (media) via two-point correlation functions S(2) and introduced an efficient heterogeneous-medium (re)construction algorithm called the "lattice-point" algorithm. Here we discuss the algorithmic details of the lattice-point procedure and an algorithm modification using surface optimization to further speed up the (re)construction process. The importance of the error tolerance, which indicates to what accuracy the media are (re)constructed, is also emphasized and discussed. We apply the algorithm to generate three-dimensional digitized realizations of a Fontainebleau sandstone and a boron-carbide/aluminum composite from the two-dimensional tomographic images of their slices through the materials. To ascertain whether the information contained in S(2) is sufficient to capture the salient structural features, we compute the two-point cluster functions of the media, which are superior signatures of the microstructure because they incorporate topological connectedness information. We also study the reconstruction of a binary laser-speckle pattern in two dimensions, in which the algorithm fails to reproduce the pattern accurately. We conclude that in general reconstructions using S(2) only work well for heterogeneous materials with single-scale structures. However, two-point information via S(2) is not sufficient to accurately model multiscale random media. Moreover, we construct realizations of hypothetical materials with desired structural characteristics obtained by manipulating their two-point correlation functions.

Dynamic interactions of p53 with DNA in solution by time-lapse atomic force microscopy

Dynamic interactions of the tumor suppressor protein p53 with a DNA fragment containing a p53-specific recognition sequence were directly observed by time-lapse tapping mode atomic force microscopy (AFM) in liquid. The divalent cation Mg(2+) was used to loosely attach both DNA and p53 to a mica surface so they could be imaged by the AFM while interacting with each other. Various interactions of p53 with DNA were observed, including dissociation/re-association, sliding and possibly direct binding to the specific sequence. Two modes of target recognition of p53 were detected: (a) direct binding, and (b) initial non-specific binding with subsequent translocation by one-dimensional diffusion of the protein along the DNA to the specific site.

miR-124 suppresses multiple steps of breast cancer metastasis by targeting a cohort of pro-metastatic genes in vitro

Metastasis is a multistep process involving modification of morphology to suit migration, reduction of tumor cell adhesion to the extracellular matrix, increase of cell mobility, tumor cell resistance to anoikis, and other steps. MicroRNAs are well-suited to regulate tumor metastasis due to their capacity to repress numerous target genes in a coordinated manner, thereby enabling their intervention at multiple steps of the invasion-metastasis cascade. In this study, we identified a microRNA exemplifying these attributes, miR-124, whose expression was reduced in aggressive MDA-MB-231 and SK-3rd breast cancer cells. Downregulation of miR-124 expression in highly aggressive breast cancer cells contributed in part to DNA hypermethylation around the promoters of the three genes encoding miR-124. Ectopic expression of miR-124 in MDA-MB-231 cells suppressed metastasis-related traits including formation of spindle-like morphology, migratory capacity, adhesion to fibronectin, and anoikis. These findings indicate that miR-124 suppresses multiple steps of metastasis by diverse mechanisms in breast cancer cells and suggest a potential application of miR-124 in breast cancer treatment.

Distinctive features arising in maximally random jammed packings of superballs

Dense random packings of hard particles are useful models of granular media and are closely related to the structure of nonequilibrium low-temperature amorphous phases of matter. Most work has been done for random jammed packings of spheres and it is only recently that corresponding packings of nonspherical particles (e.g., ellipsoids) have received attention. Here we report a study of the maximally random jammed (MRJ) packings of binary superdisks and monodispersed superballs whose shapes are defined by |x1|2p+...+|xd|2p<or=1 with d=2 and 3, respectively, where p is the deformation parameter with values in the interval (0,infinity). As p increases from zero, one can get a family of both concave (0<p<0.5) and convex (p>or=0.5) particles with square symmetry (d=2), or octahedral and cubic symmetry (d=3). In particular, for p=1 the particle is a perfect sphere (circular disk) and for p-->infinity the particle is a perfect cube (square). We find that the MRJ densities of such packings increase dramatically and nonanalytically as one moves away from the circular-disk and sphere point (p=1). Moreover, the disordered packings are hypostatic, i.e., the average number of contacting neighbors is less than twice the total number of degrees of freedom per particle, and yet the packings are mechanically stable. As a result, the local arrangements of particles are necessarily nontrivially correlated to achieve jamming. We term such correlated structures "nongeneric." The degree of "nongenericity" of the packings is quantitatively characterized by determining the fraction of local coordination structures in which the central particles have fewer contacting neighbors than average. We also show that such seemingly "special" packing configurations are counterintuitively not rare. As the anisotropy of the particles increases, the fraction of rattlers decreases while the minimal orientational order as measured by the tetratic and cubatic order parameters increases. These characteristics result from the unique manner in which superballs break their rotational symmetry, which also makes the superdisk and superball packings distinctly different from other known nonspherical hard-particle packings.

Optimal control policy for probabilistic Boolean networks with hard constraints

It is well known that the control/intervention of some genes in a genetic regulatory network is useful for avoiding undesirable states associated with some diseases like cancer. For this purpose, both optimal finite-horizon control and infinite-horizon control policies have been proposed. Boolean networks (BNs) and its extension probabilistic Boolean networks (PBNs) as useful and effective tools for modelling gene regulatory systems have received much attention in the biophysics community. The control problem for these models has been studied widely. The optimal control problem in a PBN can be formulated as a probabilistic dynamic programming problem. In the previous studies, the optimal control problems did not take into account the hard constraints, i.e. to include an upper bound for the number of controls that can be applied to the captured PBN. This is important as more treatments may bring more side effects and the patients may not bear too many treatments. A formulation for the optimal finite-horizon control problem with hard constraints introduced by the authors. This model is state independent and the objective function is only dependent on the distance between the desirable states and the terminal states. An approximation method is also given to reduce the computational cost in solving the problem. Experimental results are given to demonstrate the efficiency of our proposed formulations and methods.

Phosphorus and nitrogen physiology of two contrasting poplar genotypes when exposed to phosphorus and/or nitrogen starvation

Phosphorus (P) and nitrogen (N) are the two essential macronutrients for tree growth and development. To elucidate the P and N physiology of woody plants during acclimation to P and/or N starvation, we exposed saplings of the slow-growing Populus simonii Carr (Ps) and the fast-growing Populus × euramericana Dode (Pe) to complete nutrients or starvation of P, N or both elements (NP). P. × euramericana had lower P and N concentrations and greater P and N amounts due to higher biomass production, thereby resulting in greater phosphorus use efficiency/N use efficiency (PUE/NUE) compared with Ps. Compared with the roots of Ps, the roots of Pe exhibited higher enzymatic activities in terms of acid phosphatases (APs) and malate dehydrogenase (MDH), which are involved in P mobilization, and nitrate reductase (NR), glutamate synthase (GOGAT) and glutamate dehydrogenase (GDH), which participate in N assimilation. The responsiveness of the transcriptional regulation of key genes encoding transporters for phosphate, ammonium and nitrate was stronger in Pe than in Ps. These results suggest that Pe possesses a higher capacity for P/N uptake and assimilation, which promote faster growth compared with Ps. In both poplars, P or NP starvation caused significant decreases in the P concentrations and increases in PUE. Phosphorus deprivation induced the activity levels of APs, phosphoenolpyruvate carboxylase and MDH in both genotypes. Nitrogen or NP deficiency resulted in lower N concentrations, amino acid levels, NR and GOGAT activities, and higher NUE in both poplars. Thus, in Ps and Pe, the mRNA levels of PHT1;5, PHT1;9, PHT2;1, AMT2;1 and NR increased in the roots, while PHT1;9, PHO1;H1, PHO2, AMT1;1 and NRT2;1 increased in the leaves during acclimation to P, N or NP deprivation. These results suggest that both poplars suppress P/N uptake, mobilization and assimilation during acclimation to P, N or NP starvation.