Total Nuclear Reaction Cross Section Induced by Halo Nuclei and Stable Nuclei

We develop the method for the calculation of the total reaction cross sections induced by the halo nuclei and stable nuclei. This approach is based on the Glauber theory, which is valid for nuclear reactions at high energy. It is extended for nuclear reactions at low energy and intermediate energy by including both the quantum correction and Coulomb correction under the assumption of the effective nuclear density distribution. The calculated results of the total reaction cross section induced by stable nuclei agree well with the 30 experimental data within 10 percent accuracy.The comparison between the numerical results and the 20 experimental data for the total nuclear reaction cross section induced by the neutron halo nuclei and the proton halo nuclei indicates a satisfactory agreement after considering the halo structure of these nuclei, which implies the quite different mean fields for the nuclear reactions induced by halo nuclei and stable nuclei. The halo nucleon distributions and the root mean square radii of these nuclei can be extracted from above comparison based on the improved Glauber model, which indicate clearly the halo structures of these nuclei. Especially, it is clear to see that the medium correction of the nucleon-nucleon collision has little effect on the total reaction cross sections induced by the halo nuclei due to the very weak binding and the very extended density distribution.Comment: 15 pages,2 figures. Communucations in Theoretical Physics, (2003) in pres

Excitonic energy transfer in light-harvesting complexes in purple bacteria

Two distinct approaches, the Frenkel-Dirac time-dependent variation and the Haken-Strobl model, are adopted to study energy transfer dynamics in single-ring and double-ring light-harvesting systems in purple bacteria. It is found that inclusion of long-range dipolar interactions in the two methods results in significant increases in intra- or inter-ring exciton transfer efficiency. The dependence of exciton transfer efficiency on trapping positions on single rings of LH2 (B850) and LH1 is similar to that in toy models with nearest-neighbor coupling only. However, owing to the symmetry breaking caused by the dimerization of BChls and dipolar couplings, such dependence has been largely suppressed. In the studies of coupled-ring systems, both methods reveal interesting role of dipolar interaction in increasing energy transfer efficiency by introducing multiple intra/inter-ring transfer paths. Importantly, the time scale (~4ps) of inter-ring exciton transfer obtained from polaron dynamics is in good agreement with previous studies. In a double-ring LH2 system, dipole-induced symmetry breaking leads to global minima and local minima of the average trapping time when there is a finite value of non-zero dephasing rate, suggesting that environment plays a role in preserving quantum coherent energy transfer. In contrast, dephasing comes into play only when the perfect cylindrical symmetry in the hypothetic system is broken. This study has revealed that dipolar interaction between chromophores may play an important part in the high energy transfer efficiency in the LH2 system and many other natural photosynthetic systems.Comment: 14 pages 9 figure

Estimating Allele Frequency from Next-Generation Sequencing of Pooled Mitochondrial DNA Samples

Background: Both common and rare mitochondrial DNA (mtDNA) variants may contribute to genetic susceptibility to some complex human diseases. Understanding of the role of mtDNA variants will provide valuable insights into the etiology of these diseases. However, to date, there have not been any large-scale, genome-wide association studies of complete mtDNA variants and disease risk. One reason for this might be the substantial cost of sequencing the large number of samples required for genetic epidemiology studies. Next-generation sequencing of pooled mtDNA samples will dramatically reduce the cost of such studies and may represent an appealing approach for large-scale genetic epidemiology studies. However, the performance of the different designs of sequencing pooled mtDNA has not been evaluated. Methods: We examined the approach of sequencing pooled mtDNA of multiple individuals for estimating allele frequency using the Illumina genome analyzer (GA) II sequencing system. In this study the pool included mtDNA samples of 20 subjects that had been sequenced previously using Sanger sequencing. Each pool was replicated once to assess variation of the sequencing error between pools. To reduce such variation, barcoding was used for sequencing different pools in the same lane of the flow cell. To evaluate the effect of different pooling strategies pooling was done at both the pre- and post-PCR amplification step. Results: The sequencing error rate was close to that expected based on the Phred score. When only reads with Phred ≥ 20 were considered, the average error rate was about 0.3%. However, there was significant variation of the base-calling errors for different types of bases or at different loci. Using the results of the Sanger sequencing as the standard, the sensitivity of single nucleotide polymorphism detection with post-PCR pooling (about 99%) was higher than that of the pre-PCR pooling (about 82%), while the two approaches had similar specificity (about 99%). Among a total of 298 variants in the sample, the allele frequencies of 293 variants (98%) were correctly estimated with post-PCR pooling, the correlation between the estimated and the true allele frequencies being >0.99, while only 206 allele frequencies (69%) were correctly estimated in the pre-PCR pooling, the correlation being 0.89. Conclusion: Sequencing of mtDNA pooled after PCR amplification is a viable tool for screening mitochondrial variants potentially related to human diseases

Korean Red Ginseng protects dopaminergic neurons by suppressing the cleavage of p35 to p25 in a Parkinson's disease mouse model

AbstractBackgroundGinseng is known to have antiapoptotic, anti-inflammatory, and antioxidant effects. The present study investigated a possible role of Korean Red Ginseng (KRG) in suppressing dopaminergic neuronal cell death and the cleavage of p35 to p25 in the substantia nigra (SN) and striatum (ST) using a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced Parkinson's disease mouse model.MethodsTen-week-old male C57BL/6 mice were injected intraperitoneally with 30 mg/kg of MPTP at 24-h intervals for 5 d, and then administered KRG (1 mg/kg, 10 mg/kg, or 100 mg/kg) once a day for 12 consecutive days from the first injection. Pole tests were performed to assess the motor function of the mice, dopaminergic neuronal survival in the SN and ST was evaluated using tyrosine hydroxylase-immunohistochemistry, and the expressions of cyclin-dependent kinase 5 (Cdk5), p35, and p25 in the SN and ST were measured using Western blotting.ResultsMPTP administration caused behavioral impairment, dopaminergic neuronal death, increased Cdk5 and p25 expression, and decreased p35 expression in the nigrostriatal system of mice, whereas KRG dose-dependently alleviated these MPTP-induced changes.ConclusionThese results indicate that KRG can inhibit MPTP-induced dopaminergic neuronal death and suppress the cleavage of p35 to p25 in the SN and the ST, suggesting a possible role for KRG in the treatment of Parkinson's disease

Collision-induced C_60 rovibrational relaxation probed by state-resolved nonlinear spectroscopy

Quantum state-resolved spectroscopy was recently achieved for C60 molecules when cooled by buffer gas collisions and probed with a midinfrared frequency comb. This rovibrational quantum state resolution for the largest molecule on record is facilitated by the remarkable symmetry and rigidity of C60, which also present new opportunities and challenges to explore energy transfer between quantum states in this many-atom system. Here we combine state-specific optical pumping, buffer gas collisions, and ultrasensitive intracavity nonlinear spectroscopy to initiate and probe the rotation-vibration energy transfer and relaxation. This approach provides the first detailed characterization of C60 collisional energy transfer for a variety of collision partners, and determines the rotational and vibrational inelastic collision cross sections. These results compare well with our theoretical modeling of the collisions, and establish a route towards quantum state control of a new class of unprecedentedly large molecules

PKA-activated ApAF–ApC/EBP heterodimer is a key downstream effector of ApCREB and is necessary and sufficient for the consolidation of long-term facilitation

Long-term memory requires transcriptional regulation by a combination of positive and negative transcription factors. Aplysia activating factor (ApAF) is known to be a positive transcription factor that forms heterodimers with ApC/EBP and ApCREB2. How these heterodimers are regulated and how they participate in the consolidation of long-term facilitation (LTF) has not, however, been characterized. We found that the functional activation of ApAF required phosphorylation of ApAF by PKA on Ser-266. In addition, ApAF lowered the threshold of LTF by forming a heterodimer with ApCREB2. Moreover, once activated by PKA, the ApAF–ApC/EBP heterodimer transactivates enhancer response element–containing genes and can induce LTF in the absence of CRE- and CREB-mediated gene expression. Collectively, these results suggest that PKA-activated ApAF–ApC/EBP heterodimer is a core downstream effector of ApCREB in the consolidation of LTF

TonEBP suppresses IL-10-mediated immunomodulation

TonEBP is a key transcriptional activator of M1 phenotype in macrophage, and its high expression is associated with many inflammatory diseases. During the progression of the inflammatory responses, the M1 to M2 phenotypic switch enables the dual role of macrophages in controlling the initiation and resolution of inflammation. Here we report that in human and mouse M1 macrophages TonEBP suppresses IL-10 expression and M2 phenotype. TonEBP knockdown promoted the transcription of the IL-10 gene by enhancing chromatin accessibility and Sp1 recruitment to its promoter. The enhanced expression of M2 genes by TonEBP knockdown was abrogated by antagonism of IL-10 by either neutralizing antibodies or siRNA-mediated silencing. In addition, pharmacological suppression of TonEBP leads to similar upregulation of IL-10 and M2 genes. Thus, TonEBP suppresses M2 phenotype via downregulation of the IL-10 in M1 macrophagesope

Interface-tuned epoxy/clay nanocomposites

Though interface has been known for a critical role in determining the properties of conventional composites, its role in polymer nanocomposites is still fragmented and in its infancy. This study synthesized a series of epoxy/clay nanocomposites with different interface strength by using three types of modifiers: ethanolamine (denoted ETH), Jeffamine� M2070 (M27) and Jeffamine� XTJ502 (XTJ). XTJ created a strong interface between clay layers and matrix because it bridged the layers with matrix by a chemical reaction as proved by Fourier transform infrared spectroscopy; M27 produced an interme-diate interface strength due to the molecular entanglement between grafted M27 chains and matrix molecules; the interface made by ETH was weak because neither chemical bridging nor molecular entanglement was involved. The studies of mechanical and thermal properties and morphology at a wide range of magnification show that the strong interface promoted the highest level of exfoliation and dispersion of clay layers, and achieved the most increment in Young’s modulus, fracture toughness and glass transition temperature (Tg) of matrix. With w1.3 wt% clay, the critical strain energy release rate G1c of neat epoxy improved from 179.0 to 384.7 J/m, 115% improvement and Tg enhanced from 93.7 to 99.

Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells.

Chromatin architecture has been implicated in cell type-specific gene regulatory programs, yet how chromatin remodels during development remains to be fully elucidated. Here, by interrogating chromatin reorganization during human pluripotent stem cell (hPSC) differentiation, we discover a role for the primate-specific endogenous retrotransposon human endogenous retrovirus subfamily H (HERV-H) in creating topologically associating domains (TADs) in hPSCs. Deleting these HERV-H elements eliminates their corresponding TAD boundaries and reduces the transcription of upstream genes, while de novo insertion of HERV-H elements can introduce new TAD boundaries. The ability of HERV-H to create TAD boundaries depends on high transcription, as transcriptional repression of HERV-H elements prevents the formation of boundaries. This ability is not limited to hPSCs, as these actively transcribed HERV-H elements and their corresponding TAD boundaries also appear in pluripotent stem cells from other hominids but not in more distantly related species lacking HERV-H elements. Overall, our results provide direct evidence for retrotransposons in actively shaping cell type- and species-specific chromatin architecture