Knockdown of JMJD1C, a target gene of hsa-miR-590-3p, inhibits mitochondrial dysfunction and oxidative stress in MPP+-treated MES23.5 and SH-SY5Y cells

MicroRNAs have been shown to be closely related to many neurodegenerative disorders. The present study focuses on the role of hsa-miR-590-3p and its function in Parkinson's disease (PD). Our study showed a remarkable down-regulation of miR-590-3p expression in the 1-methyl-4 phenylpyridinium (MPP+)-treated MES23.5 and SH-SY5Y cells. Furthermore, JMJD1C was identified as a target gene of miR-590-3p in humans via the luciferase reporter assay. Our study also demonstrated that up-regulation of miR-590-3p and knockdown of JMJD1C increased the expression of peroxisome proliferator-activated receptor γ coactivator-1α (PGC-1α) and the downstream targets of PGC-1α, including nuclear respiratory factor 1 (NRF-1) and mitochondrial transcription factor A (TFAM), which are the key genes regulating mitochondrial function. Also, the expression of heme oxygenase-1 (HO-1), NAD (P) H quinone oxidoreductase-1 (NQO-1) and γ-glutamylcysteine synthetase (γ-GCS) involved in anti-oxidation was increased. Moreover, there was a significant increase in the total cellular ATP with an associated decrease in levels of ROS in the absence of JMJD1C. Taken together, these results show that miR-590-3p plays an important role in the pathogenesis of PD, which may be further regarded as a therapeutic target.

Elevated gold ellipse nanoantenna dimers as sensitive and tunable surface enhanced Raman spectroscopy substrates

We demonstrate large area arrays of elevated gold ellipse dimers with precisely controlled gaps for use as sensitive and highly controllable surface enhanced Raman scattering (SERS) substrates. The enhanced Raman signal observed with SERS arises from both localized and long range plasmonic effects. By controlling the geometry of a SERS substrate, in this case the size and aspect ratio of individual ellipses, the plasmon resonance can be tuned in a broad wavelength range, providing a method for designing the response of SERS substrates at different excitation wavelengths. Plasmon effects exhibited by the elevated gold ellipse dimer substrates are also demonstrated and confirmed through finite difference time domain (FDTD) simulations. A plasmon resonance red shift with an increase of the ellipse aspect ratio is observed, allowing systematic control of the resulting SERS signal intensity. Optimized elevated ellipse dimer substrates with 10 ± 2 nm gaps exhibit uniform SERS enhancement factors on the order of 10(9) for adsorbed p-mercaptoaniline molecules.

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.

Single nucleotide polymorphism analysis of the endopolygalacturonase gene in peach and its potential use in crossbreeding programs

Single nucleotide polymorphisms (SNPs) are the most abundant sequence variations found in plant genomes and are widely used as molecular genetic markers in genetic diversity studies and crossbreeding programs. In this study, we examined 113 DNA sequences of the endopolygalacturonase (endo-PG) gene from 67 peach accessions and found a total of 56 SNPs and 6 insertion/deletions (indels), with a frequency of 3, 1, and 3% for the transitions, transversions, and indels, respectively. Meanwhile, the majority of the observed SNPs were found in the intron regions, while only 2 variable sites and a single indel were detected in the exon regions. A dendrogram was obtained using neighbor-joining cluster analysis and divided into 2 main groups, providing evidence that most of the accessions of the clingstone nonmelting flesh phenotypes generally clustered together and were comparatively nonrelated to the "stony hard" peach cultivars, which were in a different branch altogether. Furthermore, 4 major haplotypes were formed and 3 cleaved amplified polymorphic sequence primer sets were mined according to fruit texture and stone adhesion, displaying their potential as candidate molecular markers for discriminating genotypes. This research will assist peach genetic enhancement by introducing a novel crossbreeding strategy.

HIF1α is necessary for exercise-induced neuroprotection while HIF2α is needed for dopaminergic neuron survival in the substantia nigra pars compacta

Exercise reduces the risk of developing a number of neurological disorders and increases the efficiency of cellular energy production. However, overly strenuous exercise produces oxidative stress. Proper oxygenation is crucial for the health of all tissues, and tight regulation of cellular oxygen is critical to balance O2 levels and redox homeostasis in the brain. Hypoxia Inducible Factor (HIF)1α and HIF2α are transcription factors regulated by cellular oxygen concentration that initiate gene regulation of vascular development, redox homeostasis, and cell cycle control. HIF1α and HIF2α contribute to important adaptive mechanisms that occur when oxygen and ROS homeostasis become unbalanced. It has been shown that preconditioning by exposure to a stressor prior to a hypoxic event reduces damage that would otherwise occur. Previously we reported that 3 months of exercise protects SNpc dopaminergic (DA) neurons from toxicity caused by Complex I inhibition. Here, we identify the cells in the SNpc that express HIF1α and HIF2α and show that running exercise produces hypoxia in SNpc DA neurons, and alters the expression of HIF1α and HIF2α. In mice carrying a conditional knockout of Hif1α in postnatal neurons we observe that exercise alone produces SNpc TH+ DA neuron loss. Loss of HIF1α also abolishes exercise-induced neuroprotection. In mice lacking Hif2α in postnatal neurons, the number of TH+ DA neurons in the adult SNpc is diminished, but 3months of exercise rescues this loss. We conclude that HIF1α is necessary for exercise-induced neuroprotection and both HIF1α and HIF2α are necessary for the survival and function of adult SNpc DA neurons.

Polyploidy-associated genome modifications during land plant evolution

The occurrence of polyploidy in land plant evolution has led to an acceleration of genome modifications relative to other crown eukaryotes and is correlated with key innovations in plant evolution. Extensive genome resources provide for relating genomic changes to the origins of novel morphological and physiological features of plants. Ancestral gene contents for key nodes of the plant family tree are inferred. Pervasive polyploidy in angiosperms appears likely to be the major factor generating novel angiosperm genes and expanding some gene families. However, most gene families lose most duplicated copies in a quasi-neutral process, and a few families are actively selected for single-copy status. One of the great challenges of evolutionary genomics is to link genome modifications to speciation, diversification and the morphological and/or physiological innovations that collectively compose biodiversity. Rapid accumulation of genomic data and its ongoing investigation may greatly improve the resolution at which evolutionary approaches can contribute to the identification of specific genes responsible for particular innovations. The resulting, more 'particulate' understanding of plant evolution, may elevate to a new level fundamental knowledge of botanical diversity, including economically important traits in the crop plants that sustain humanity.

Molecular characterization and expression analysis of purple acid phosphatase gene from pearl oyster Pinctada martensii

Purple acid phosphatases (PAPs), also known as type 5 acid phosphatases, are widely present in animals, plants, and fungi. In mammal, PAP was reported to participate in immune defense and bone resorption. In this study, the characteristics and potential functions of a PAP gene from pearl oyster Pinctada martensii (pm-PAP) were examined. The Pm-PAP cDNA was found to be 2777 base pairs, containing a 1581-base pair open reading fragment encoding for 526 amino acids with an estimated molecular mass of 60.1 kDa and theoretical isoelectric point of 5.82. One signal peptide and five conserved motifs [GDXX/GDXXY/GNH(D/E)/XXXH/(A/G)HXH] were present in the entire sequence. Tissue expression profile analysis showed that pm-PAP mRNA was constitutively expressed in all tissues studied with abundant mRNA found in mollusk defense system, including hepatopancreas, gill, and hemocytes. After lipopolysaccharide stimulation, the expression of pm-PAP mRNA in hemocytes was dramatically upregulated at 2 h and achieved the highest level at 36 h. Additionally, pm-PAP mRNA expression was significantly increased and achieved the highest level at 2 days after the surgical implantation during pearl production. These results suggest that pm-PAP is a constitutive and inducible protein that may be involved in the immune defense of pearl oyster.

Effects of ROCK inhibitor Y27632 and EGFR inhibitor PD168393 on human neural precursors co-cultured with rat auditory brainstem explant

Hearing function lost by degeneration of inner ear spiral ganglion neurons (SGNs) in the auditory nervous system could potentially be compensated by cellular replacement using suitable donor cells. Donor cell-derived neuronal development with functional synaptic formation with auditory neurons of the cochlear nucleus (CN) in the brainstem is a prerequisite for a successful transplantation. Here a rat auditory brainstem explant culture system was used as a screening platform for donor cells. The explants were co-cultured with human neural precursor cells (HNPCs) to determine HNPCs developmental potential in the presence of environmental cues characteristic for the auditory brainstem region in vitro. We explored effects of pharmacological inhibition of GTPase Rho with its effector Rho-associated kinase (ROCK) and epidermal growth factor receptor (EGFR) signaling on the co-cultures. Pharmacological agents ROCK inhibitor Y27632 and EGFR blocker PD168393 were tested. Effect of the treatment on explant penetration by green fluorescent protein (GFP)-labeled HNPCs was evaluated based on the following criteria: number of GFP-HNPCs located within the explant; distance migrated by the GFP-HNPCs deep into the explant; length of the GFP+/neuronal class III β-tubulin (TUJ1)+ processes developed and phenotypes displayed. In a short 2-week co-culture both inhibitors had growth-promoting effects on HNPCs, prominent in neurite extension elongation. Significant enhancement of migration and in-growth of HNPCs into the brain slice tissue was only observed in Y27632-treated co-cultures. Difference between Y27632- and PD168393-treated HNPCs acquiring neuronal fate was significant, though not different from the fates acquired in control co-culture. Our data suggest the presence of inhibitory mechanisms in the graft-host environment of the auditory brainstem slice co-culture system with neurite growth arresting properties which can be modulated by administration of signaling pathways antagonists. Therefore the co-culture system can be utilized for screens of donor cells and compounds regulating neuronal fate determination.

Integrated syntenic and phylogenomic analyses reveal an ancient genome duplication in monocots

Unraveling widespread polyploidy events throughout plant evolution is a necessity for inferring the impacts of whole-genome duplication (WGD) on speciation, functional innovations, and to guide identification of true orthologs in divergent taxa. Here, we employed an integrated syntenic and phylogenomic analyses to reveal an ancient WGD that shaped the genomes of all commelinid monocots, including grasses, bromeliads, bananas (Musa acuminata), ginger, palms, and other plants of fundamental, agricultural, and/or horticultural interest. First, comprehensive phylogenomic analyses revealed 1421 putative gene families that retained ancient duplication shared by Musa (Zingiberales) and grass (Poales) genomes, indicating an ancient WGD in monocots. Intergenomic synteny blocks of Musa and Oryza were investigated, and 30 blocks were shown to be duplicated before Musa-Oryza divergence an estimated 120 to 150 million years ago. Synteny comparisons of four monocot (rice [Oryza sativa], sorghum [Sorghum bicolor], banana, and oil palm [Elaeis guineensis]) and two eudicot (grape [Vitis vinifera] and sacred lotus [Nelumbo nucifera]) genomes also support this additional WGD in monocots, herein called Tau (τ). Integrating synteny and phylogenomic comparisons achieves better resolution of ancient polyploidy events than either approach individually, a principle that is exemplified in the disambiguation of a WGD series of rho (ρ)-sigma (σ)-tau (τ) in the grass lineages that echoes the alpha (α)-beta (β)-gamma (γ) series previously revealed in the Arabidopsis thaliana lineage.

Cyclic additional optical true time delay for microwave beam steering with spectral filtering

Optical true time delay (OTTD) is an attractive way to realize microwave beam steering (MBS) due to its inherent features of broadband, low-loss, and compactness. In this Letter, we propose a novel OTTD approach named cyclic additional optical true time delay (CAO-TTD). It applies additional integer delays of the microwave carrier frequency to achieve spectral filtering but without disturbing the spatial filtering (beam steering). Based on such concept, a broadband MBS scheme for high-capacity wireless communication is proposed, which allows the tuning of both spectral filtering and spatial filtering. The experimental results match well with the theoretical analysis.

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.

Critical evaluation of transcription factor Atf2 as a candidate modulator of alcohol preference in mouse and human populations

In prior work, congenic strains carrying the DBA/2Igb (D2) region of chromosome 2 (Chr2) for alcohol preference were bred onto a C57BL/6Ibg (B6) background and as predicted were found to reduce voluntary consumption. Subsequently, interval-specific congenic recombinant strains (ISCRS) were generated and also tested. These ISCRS strains reduced the quantitative trait loci (QTL) interval to a comparatively small 3.4 Mb region. Here, we have exploited an integrative approach using both murine and human populations to critically evaluate candidate genes within this region. First, we used bioinformatics tools to search for genes relevant to alcohol preference within the QTL region. Second, we searched for single nucleotide polymorphisms (SNPs) within exons of every gene in this region. Third, we conducted follow-up microarray analyses to identify differentially expressed genes between the B6 and ISCRS strains in mice from each group. Fourth, we analyzed correlations between the expression level of candidate genes and phenotypes of alcohol preference in a large family of BXD recombinant inbred strains derived from B6 and D2. Finally, we evaluated SNP segregation in both BXD mouse strains and in humans who were heavy alcohol drinkers or non-drinkers. Among several potential candidate genes in this region, we identified activating transcription factor 2 (Atf2) as the most plausible gene that would influence alcohol preference. However, the candidacy of Atf2 was only weakly supported when we used a genetic network approach and by focused reanalysis of genome-wide association study data from European-American and African-American populations. Thus, we cannot conclude that Atf2 plays a role in the regulation of the QTL of mouse Chr2.

Potential role of Atp5g3 in epigenetic regulation of alcohol preference or obesity from a mouse genomic perspective

The mitochondrial ATP synthase, subunit c, isoform 3 gene (Atp5g3) encodes subunit 9, the subunit of the multisubunit enzyme that catalyzes ATP synthesis during oxidative phosphorylation in mitochondria. According to the Ensembl database, Atp5g3 in mice is located on chromosome 2 between 73746504 and 73749383 bp, within the genomic regions of two sets of quantitative trait loci - alcohol preference and body weight. Both of those traits are more influenced by epigenetic factors than many other traits are. Using currently available phenotype and gene expression profiles from the GeneNetwork database, we obtained correlations between Atp5g3 and alcoholism- and obesity-relevant phenotypes. The correlation in expression levels between Atp5g3 and each of its 12 partner genes in the molecular interaction are different in various tissues and genes. Transcriptome mapping indicated that Atp5g3 is differentially regulated in the hippocampus, cerebellum, and liver. Owing to a lack of known polymorphisms of Atp5g3 among three relevant mouse strains, C57BL/6J (B6), DBA/2J (D2), and BALB/ cJ, the molecular mechanism for the connection between Atp5g3 and alcoholism and body weight requires further investigation.

Investigating univariate temporal patterns for intrinsic connectivity networks based on complexity and low-frequency oscillation: a test-retest reliability study

Intrinsic connectivity networks (ICNs) are composed of spatial components and time courses. The spatial components of ICNs were discovered with moderate-to-high reliability. So far as we know, few studies focused on the reliability of the temporal patterns for ICNs based their individual time courses. The goals of this study were twofold: to investigate the test-retest reliability of temporal patterns for ICNs, and to analyze these informative univariate metrics. Additionally, a correlation analysis was performed to enhance interpretability. Our study included three datasets: (a) short- and long-term scans, (b) multi-band echo-planar imaging (mEPI), and (c) eyes open or closed. Using dual regression, we obtained the time courses of ICNs for each subject. To produce temporal patterns for ICNs, we applied two categories of univariate metrics: network-wise complexity and network-wise low-frequency oscillation. Furthermore, we validated the test-retest reliability for each metric. The network-wise temporal patterns for most ICNs (especially for default mode network, DMN) exhibited moderate-to-high reliability and reproducibility under different scan conditions. Network-wise complexity for DMN exhibited fair reliability (ICC<0.5) based on eyes-closed sessions. Specially, our results supported that mEPI could be a useful method with high reliability and reproducibility. In addition, these temporal patterns were with physiological meanings, and certain temporal patterns were correlated to the node strength of the corresponding ICN. Overall, network-wise temporal patterns of ICNs were reliable and informative and could be complementary to spatial patterns of ICNs for further study.

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.

Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.)

Background

Sacred lotus is a basal eudicot with agricultural, medicinal, cultural and religious importance. It was domesticated in Asia about 7,000 years ago, and cultivated for its rhizomes and seeds as a food crop. It is particularly noted for its 1,300-year seed longevity and exceptional water repellency, known as the lotus effect. The latter property is due to the nanoscopic closely packed protuberances of its self-cleaning leaf surface, which have been adapted for the manufacture of a self-cleaning industrial paint, Lotusan.

Results

The genome of the China Antique variety of the sacred lotus was sequenced with Illumina and 454 technologies, at respective depths of 101× and 5.2×. The final assembly has a contig N50 of 38.8 kbp and a scaffold N50 of 3.4 Mbp, and covers 86.5% of the estimated 929 Mbp total genome size. The genome notably lacks the paleo-triplication observed in other eudicots, but reveals a lineage-specific duplication. The genome has evidence of slow evolution, with a 30% slower nucleotide mutation rate than observed in grape. Comparisons of the available sequenced genomes suggest a minimum gene set for vascular plants of 4,223 genes. Strikingly, the sacred lotus has 16 COG2132 multi-copper oxidase family proteins with root-specific expression; these are involved in root meristem phosphate starvation, reflecting adaptation to limited nutrient availability in an aquatic environment.

Conclusions

The slow nucleotide substitution rate makes the sacred lotus a better resource than the current standard, grape, for reconstructing the pan-eudicot genome, and should therefore accelerate comparative analysis between eudicots and monocots.

Synthesis and Application of the Cationic Lignin Amine Flocculant

Cationic lignin amine flocculants were obtained by the Mannich reaction of Kraft lignin with formaldehyde and polyamines. The cationic reaction products were tested as a flocculating agent by flocculation of reactive brilliant blue KN-R and linear alkylbenzene sulphonates in an aqueous system. The effects of flocculant dosage and pH on the flocculation performance are discussed in detail. The results indicate that under optimum conditions, the rate of eliminating reactive brilliant blue KN-R and linear alkylbenzene sulphonates from the water exceed 99% and 96% respectively, which illustrated that the cationic reaction products are extremely effective as flocculants for reactive brilliant blue KN-R and linear alkylbenzene sulphonates.

Evolution of a horizontally acquired legume gene, albumin 1, in the parasitic plant Phelipanche aegyptiaca and related species

Background

Parasitic plants, represented by several thousand species of angiosperms, use modified structures known as haustoria to tap into photosynthetic host plants and extract nutrients and water. As a result of their direct plant-plant connections with their host plant, parasitic plants have special opportunities for horizontal gene transfer, the nonsexual transmission of genetic material across species boundaries. There is increasing evidence that parasitic plants have served as recipients and donors of horizontal gene transfer (HGT), but the long-term impacts of eukaryotic HGT in parasitic plants are largely unknown.

Results

Here we show that a gene encoding albumin 1 KNOTTIN-like protein, closely related to the albumin 1 genes only known from papilionoid legumes, where they serve dual roles as food storage and insect toxin, was found in Phelipanche aegyptiaca and related parasitic species of family Orobanchaceae, and was likely acquired by a Phelipanche ancestor via HGT from a legume host based on phylogenetic analyses. The KNOTTINs are well known for their unique “disulfide through disulfide knot” structure and have been extensively studied in various contexts, including drug design. Genomic sequences from nine related parasite species were obtained, and 3D protein structure simulation tests and evolutionary constraint analyses were performed. The parasite gene we identified here retains the intron structure, six highly conserved cysteine residues necessary to form a KNOTTIN protein, and displays levels of purifying selection like those seen in legumes. The albumin 1 xenogene has evolved through >150 speciation events over ca. 16 million years, forming a small family of differentially expressed genes that may confer novel functions in the parasites. Moreover, further data show that a distantly related parasitic plant, Cuscuta, obtained two copies of albumin 1 KNOTTIN-like genes from legumes through a separate HGT event, suggesting that legume KNOTTIN structures have been repeatedly co-opted by parasitic plants.

Conclusions

The HGT-derived albumins in Phelipanche represent a novel example of how plants can acquire genes from other plants via HGT that then go on to duplicate, evolve, and retain the specialized features required to perform a unique host-derived function.

Effect of dimensionality on the percolation threshold of overlapping nonspherical hyperparticles

We study the effect of dimensionality on the percolation threshold η(c) of identical overlapping nonspherical convex hyperparticles in d-dimensional Euclidean space R(d). This is done by formulating a scaling relation for η(c) that is based on a rigorous lower bound [Torquato, J. Chem. Phys. 136, 054106 (2012)] and a conjecture that hyperspheres provide the highest threshold, for any d, among all convex hyperparticle shapes (that are not a trivial affine transformation of a hypersphere). This scaling relation also exploits the recently discovered principle that low-dimensional continuum percolation behavior encodes high-dimensional information. We derive an explicit formula for the exclusion volume v(ex) of a hyperparticle of arbitrary shape in terms of its d-dimensional volume v, surface area s, and radius of mean curvature R[over ¯] (or, equivalently, mean width). These basic geometrical properties are computed for a wide variety of nonspherical hyperparticle shapes with random orientations across all dimensions, including, among other shapes, various polygons for d=2, Platonic solids, spherocylinders, parallepipeds, and zero-volume plates for d=3 and their appropriate generalizations for d≥4. Using this information, we compute the lower bound and scaling relation for η(c) for this comprehensive set of continuum percolation models across dimensions. We demonstrate that the scaling relation provides accurate upper-bound estimates of the threshold η(c) across dimensions and becomes increasingly accurate as the space dimension increases.

Characterization of the basal angiosperm Aristolochia fimbriata: a potential experimental system for genetic studies

BACKGROUND

Previous studies in basal angiosperms have provided insight into the diversity within the angiosperm lineage and helped to polarize analyses of flowering plant evolution. However, there is still not an experimental system for genetic studies among basal angiosperms to facilitate comparative studies and functional investigation. It would be desirable to identify a basal angiosperm experimental system that possesses many of the features found in existing plant model systems (e.g., Arabidopsis and Oryza).

RESULTS

We have considered all basal angiosperm families for general characteristics important for experimental systems, including availability to the scientific community, growth habit, and membership in a large basal angiosperm group that displays a wide spectrum of phenotypic diversity. Most basal angiosperms are woody or aquatic, thus are not well-suited for large scale cultivation, and were excluded. We further investigated members of Aristolochiaceae for ease of culture, life cycle, genome size, and chromosome number. We demonstrated self-compatibility for Aristolochia elegans and A. fimbriata, and transformation with a GFP reporter construct for Saruma henryi and A. fimbriata. Furthermore, A. fimbriata was easily cultivated with a life cycle of just three months, could be regenerated in a tissue culture system, and had one of the smallest genomes among basal angiosperms. An extensive multi-tissue EST dataset was produced for A. fimbriata that includes over 3.8 million 454 sequence reads.

CONCLUSIONS

Aristolochia fimbriata has numerous features that facilitate genetic studies and is suggested as a potential model system for use with a wide variety of technologies. Emerging genetic and genomic tools for A. fimbriata and closely related species can aid the investigation of floral biology, developmental genetics, biochemical pathways important in plant-insect interactions as well as human health, and various other features present in early angiosperms.

Divergence of the systemic immune response following oral infection with distinct strains of Porphyromonas gingivalis

Periodontitis is a polymicrobial oral infection characterized by the destruction of tooth-supporting structures that can be linked to systemic diseases such as cardiovascular disease, diabetes or rheumatoid arthritis. Porphyromonas gingivalis, a bacterium implicated in the etiology of periodontitis, has shown variation in inducing T-cell responses among different strains. Therefore, in this study we investigated the strain-specific immune response using a murine experimental model of periodontitis. Periodontitis was induced by P. gingivalis strains A7A1-28, W83 and W50, and later confirmed by the presence of P. gingivalis in the oral microflora and by alveolar bone resorption. Splenocytes were evaluated for gene expression, cellular proteins and cytokine expression. Dendritic cells were stimulated in vitro for T helper cell-cytokine profiling. Results showed that P. gingivalis had the ability to alter the systemic immune response after bacterial exposure. Strains W50 and W83 were shown to induce alveolar bone loss, whereas the A7A1-28 strain did not significantly promote bone resorption in mice. Splenocytes derived from mice infected with strains W50 and W83 induced expression of high levels of interleukin-4 (IL-4) but A7A1-28 stimulated increased IL-10. Stimulation of dendritic cells in vitro showed a similar pattern of cytokine expression of IL-12p40, IL-6 and transforming growth factor-β among strains. A distinct systemic response in vivo was observed among different strains of P. gingivalis, with IL-10 associated with the least amount of alveolar bone loss. Evaluation of pathogen-driven systemic immune responses associated with periodontal disease pathogenesis may assist in defining how periodontitis may impact other diseases.

Microstructural degeneracy associated with a two-point correlation function and its information content

A two-point correlation function provides a crucial yet an incomplete characterization of a microstructure because distinctly different microstructures may have the same correlation function. In an earlier Letter [Gommes, Jiao, and Torquato, Phys. Rev. Lett. 108, 080601 (2012)], we addressed the microstructural degeneracy question: What is the number of microstructures compatible with a specified correlation function? We computed this degeneracy, i.e., configurational entropy, in the framework of reconstruction methods, which enabled us to map the problem to the determination of ground-state degeneracies. Here, we provide a more comprehensive presentation of the methodology and analyses, as well as additional results. Since the configuration space of a reconstruction problem is a hypercube on which a Hamming distance is defined, we can calculate analytically the energy profile of any reconstruction problem, corresponding to the average energy of all microstructures at a given Hamming distance from a ground state. The steepness of the energy profile is a measure of the roughness of the energy landscape associated with the reconstruction problem, which can be used as a proxy for the ground-state degeneracy. The relationship between this roughness metric and the ground-state degeneracy is calibrated using a Monte Carlo algorithm for determining the ground-state degeneracy of a variety of microstructures, including realizations of hard disks and Poisson point processes at various densities as well as those with known degeneracies (e.g., single disks of various sizes and a particular crystalline microstructure). We show that our results can be expressed in terms of the information content of the two-point correlation functions. From this perspective, the a priori condition for a reconstruction to be accurate is that the information content, expressed in bits, should be comparable to the number of pixels in the unknown microstructure. We provide a formula to calculate the information content of any two-point correlation function, which makes our results broadly applicable to any field in which correlation functions are employed.

Long-lasting transcriptional refractoriness triggered by a single exposure to 1-methyl-4-phenyl-1,2,3,6-tetrahydropyrimidine

Parkinson's disease (PD) is a progressive neurodegenerative disorder whose etiology is thought to have environmental (toxin) and genetic contributions. The neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyrimidine (MPTP) induces pathological features of PD including loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc) and striatal dopamine (DA) depletion. We previously described the striatal transcriptional response following acute MPTP administration in MPTP-sensitive C57BL/6J mice. We identified three distinct phases: early (5h), intermediate (24h) and late (72h) and reported that the intermediate and late responses were absent in MPTP-resistant Swiss-Webster (SWR) mice. Here we show that C57BL/6J mice pre-treated with a single 40 mg/kg dose of MPTP and treated 9 days later with 4×20 mg/kg MPTP, display a striatal transcriptional response similar to that of MPTP-resistant SWR mice, i.e. a robust acute response but no intermediate or late response. Transcriptional refractoriness is dependent upon the dose of the priming challenge with as little as 10mg/kg MPTP being effective and can persist for more than 28 days. Priming of SWR mice has no effect on their response to subsequent challenge with MPTP. We also report that paraquat, another free radical producer, also elicits striatal transcriptional alterations but these are largely distinct from those triggered by MPTP. Paraquat-induced changes are also refractory to priming with paraquat. However neither paraquat nor MPTP elicits cross-attenuation. Thus exposure to specific toxins triggers distinct transcriptional responses in striatum that are influenced by prior exposure to the same toxin. The prolonged refractory period described here for MPTP could explain at the molecular level the reported discrepancies between different MPTP administration regimens and may have implications for our understanding of the relationship between environmental toxin exposure and PD.

Density of States for a specified correlation function and the energy landscape

The degeneracy of two-phase disordered microstructures consistent with a specified correlation function is analyzed by mapping it to a ground-state degeneracy. We determine for the first time the associated density of states via a Monte Carlo algorithm. Our results are explained in terms of the roughness of an energy landscape, defined on a hypercubic configuration space. The use of a Hamming distance in this space enables us to define a roughness metric, which is calculated from the correlation function alone and related quantitatively to the structural degeneracy. This relation is validated for a wide variety of disordered structures.

A genome triplication associated with early diversification of the core eudicots

Background

Although it is agreed that a major polyploidy event, gamma, occurred within the eudicots, the phylogenetic placement of the event remains unclear.

Results

To determine when this polyploidization occurred relative to speciation events in angiosperm history, we employed a phylogenomic approach to investigate the timing of gene set duplications located on syntenic gamma blocks. We populated 769 putative gene families with large sets of homologs obtained from public transcriptomes of basal angiosperms, magnoliids, asterids, and more than 91.8 gigabases of new next-generation transcriptome sequences of non-grass monocots and basal eudicots. The overwhelming majority (95%) of well-resolved gamma duplications was placed before the separation of rosids and asterids and after the split of monocots and eudicots, providing strong evidence that the gamma polyploidy event occurred early in eudicot evolution. Further, the majority of gene duplications was placed after the divergence of the Ranunculales and core eudicots, indicating that the gamma appears to be restricted to core eudicots. Molecular dating estimates indicate that the duplication events were intensely concentrated around 117 million years ago.

Conclusions

The rapid radiation of core eudicot lineages that gave rise to nearly 75% of angiosperm species appears to have occurred coincidentally or shortly following the gamma triplication event. Reconciliation of gene trees with a species phylogeny can elucidate the timing of major events in genome evolution, even when genome sequences are only available for a subset of species represented in the gene trees. Comprehensive transcriptome datasets are valuable complements to genome sequences for high-resolution phylogenomic analysis.

Molecular characterization, polymorphism of the ACOX1 gene and association with ultrasound traits in Bos taurus

Acyl-coenzyme A oxidase 1 (ACOX1) is the first enzyme in peroxisomal fatty acid β-oxidation; it is rate-limiting and plays a key role in fatty acid metabolism and fat deposition. ACOX1 is an important candidate gene for meat quality selection through marker-assisted selection. Genomic structural analysis showed that bovine ACOX1 shares 86% identity with human ACOX1. Using PCR-SSCP technology, we discovered a single nucleotide polymorphism (SNP) (A1865C) in exon 13 of the ACOX1 gene. Allele frequencies of this SNP were investigated and evaluated with the χ(2) test in 641 cattle populations; only the Jiaxian red population was not in Hardy-Weinberg equilibrium. Gene heterozygosity, effective allele numbers and polymorphism information content of the bovine ACOX1 locus in seven populations varied from 0.2778 to 0.4954, 1.3846 to 1.9817 and 0.2392 to 0.3727, respectively. We also looked for a potential association of this SNP with ultrasound traits in 327 individuals and found a significant effect on ultrasound backfat thickness and ultrasound marbling score (P < 0.05). Meat quality traits were analyzed in another 71 Qinchuan individuals to determine associations with genotype. Animals with genotype AA had higher mean values of backfat thickness than those with genotypes AC and CC. A represents the base before mutation and C represents the base after mutation. We conclude that this SNP of the ACOX1 gene has potential as a genetic marker for meat quality traits in cattle reproduction and breeding.

A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure

Background

Recent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant species. The Amborella genome is a unique reference for understanding the evolution of angiosperm genomes because it can serve as an outgroup to root comparative analyses. A physical map, BAC end sequences and sample shotgun sequences provide a first view of the 870 Mbp Amborella genome.

Results

Analysis of Amborella BAC ends sequenced from each contig suggests that the density of long terminal repeat retrotransposons is negatively correlated with that of protein coding genes. Syntenic, presumably ancestral, gene blocks were identified in comparisons of the Amborella BAC contigs and the sequenced Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa genomes. Parsimony mapping of the loss of synteny corroborates previous analyses suggesting that the rate of structural change has been more rapid on lineages leading to Arabidopsis and Oryza compared with lineages leading to Populus and Vitis. The gamma paleohexiploidy event identified in the Arabidopsis, Populus and Vitis genomes is shown to have occurred after the divergence of all other known angiosperms from the lineage leading to Amborella.

Conclusions

When placed in the context of a physical map, BAC end sequences representing just 5.4% of the Amborella genome have facilitated reconstruction of gene blocks that existed in the last common ancestor of all flowering plants. The Amborella genome is an invaluable reference for inferences concerning the ancestral angiosperm and subsequent genome evolution.

Ancestral polyploidy in seed plants and angiosperms

Whole-genome duplication (WGD), or polyploidy, followed by gene loss and diploidization has long been recognized as an important evolutionary force in animals, fungi and other organisms, especially plants. The success of angiosperms has been attributed, in part, to innovations associated with gene or whole-genome duplications, but evidence for proposed ancient genome duplications pre-dating the divergence of monocots and eudicots remains equivocal in analyses of conserved gene order. Here we use comprehensive phylogenomic analyses of sequenced plant genomes and more than 12.6 million new expressed-sequence-tag sequences from phylogenetically pivotal lineages to elucidate two groups of ancient gene duplications-one in the common ancestor of extant seed plants and the other in the common ancestor of extant angiosperms. Gene duplication events were intensely concentrated around 319 and 192 million years ago, implicating two WGDs in ancestral lineages shortly before the diversification of extant seed plants and extant angiosperms, respectively. Significantly, these ancestral WGDs resulted in the diversification of regulatory genes important to seed and flower development, suggesting that they were involved in major innovations that ultimately contributed to the rise and eventual dominance of seed plants and angiosperms.

Robust algorithm to generate a diverse class of dense disordered and ordered sphere packings via linear programming

We have formulated the problem of generating dense packings of nonoverlapping, nontiling nonspherical particles within an adaptive fundamental cell subject to periodic boundary conditions as an optimization problem called the adaptive-shrinking cell (ASC) formulation [S. Torquato and Y. Jiao, Phys. Rev. E 80, 041104 (2009)]. Because the objective function and impenetrability constraints can be exactly linearized for sphere packings with a size distribution in d-dimensional Euclidean space R(d), it is most suitable and natural to solve the corresponding ASC optimization problem using sequential-linear-programming (SLP) techniques. We implement an SLP solution to produce robustly a wide spectrum of jammed sphere packings in R(d) for d=2, 3, 4, 5, and 6 with a diversity of disorder and densities up to the respective maximal densities. A novel feature of this deterministic algorithm is that it can produce a broad range of inherent structures (locally maximally dense and mechanically stable packings), besides the usual disordered ones (such as the maximally random jammed state), with very small computational cost compared to that of the best known packing algorithms by tuning the radius of the influence sphere. For example, in three dimensions, we show that it can produce with high probability a variety of strictly jammed packings with a packing density anywhere in the wide range [0.6, 0.7408...], where π/√18 = 0.7408... corresponds to the density of the densest packing. We also apply the algorithm to generate various disordered packings as well as the maximally dense packings for d=2, 4, 5, and 6. Our jammed sphere packings are characterized and compared to the corresponding packings generated by the well-known Lubachevsky-Stillinger (LS) molecular-dynamics packing algorithm. Compared to the LS procedure, our SLP protocol is able to ensure that the final packings are truly jammed, produces disordered jammed packings with anomalously low densities, and is appreciably more robust and computationally faster at generating maximally dense packings, especially as the space dimension increases.

A novel polymorphism of the lactoferrin gene and its association with milk composition and body traits in dairy goats

Milk composition and body measurement traits, influenced by genes and environmental factors, play important roles in value assessments of efficiency and productivity in dairy goats. Lactoferrin (LF), involved in the efficient expression of protein in milk, is also an anabolic factor in skeletal tissue and a potent osteoblast survival factor. Therefore, it is an important candidate gene for milk composition and body measurement trait selection in marker-assisted selection. We employed PCR-SSCP and DNA sequencing to screen the genetic variations of the LF gene in 549 Chinese dairy goats. A novel single-nucleotide polymorphism (SNP) (G198A in exon II) of the LF gene was detected. The frequencies of the AA genotype were 0.0285 and 0.0261 in GZ and SN populations, respectively. Both populations were found to have low levels of polymorphism and were in Hardy-Weinberg disequilibrium (P < 0.05). We found significant (P < 0.05) associations of the SNP marker with milk protein and acidity in the total population; animals with the AA genotype had higher mean values for milk protein than those with the GA genotype. Animals with genotype AA had higher mean values for withers height than those with genotype GG (P < 0.05). We concluded that this SNP of the LF gene has potential as a genetic marker for milk composition and body traits in dairy goat breeding.

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.