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.

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.

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.

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.

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.

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.