Davydov Soliton Dynamics in Proteins: II. The General Case

We performed long time simulations using the |D₁> approximation for the solution of the Davydov Hamiltonian. In addition we computed expectation values of the relevant operators with the state (_D/J)|D₁> and the deviation |> from the exact solution over long times, namely 10 ns. We found that in the very long time scale the |D₁> ansatz is very close to an exact solution, showing expectation values of the relevant physical observables in the state (_D/J)|D₁> being about 5-6 orders of magnitudes larger than in the deviation state |>. In the intermediate time scale of the ps range such errors, as known from our previous work, are somewhat larger, but still more or less negligibly. Thus we also report results from an investigation of the very short time (in the range 0-0.4 ps) behaviour of the |D₁> state compared with that of an expansion of the exact solution in powers of time t. This expansion is reliable for about 0.12 ps for special cases as shown in the previous paper. However, the accuracy of the exactly known value of the norm and the expectation value of the Hamiltonian finally indicates up to what time a given expansion is valid, as also shown in the preceding paper. The comparison of the expectation values of the operators representing the relevant physical observables, formed with the third order wave function and with the corresponding results of |D₁> simulations has shown, that our expansion is valid up to a time of roughly 0.10-0.15 ps. Within this time the second and third order corrections turned out to be not very important. This is due to the fact that our first order state contains already some terms of the expansion, summed up to inifinite order. Further we found good agreement of the results obtained with our expansion and those from the corresponding |D₁> simulations within the time of about 0.10 ps. At later times, the factors with explicit powers of t in second and third order become dominant, making the expansion meaningless. Possibilities for the use of such expansions for larger times are described. Alltogether we have shown (together with previous work on medium times), that the |D₁> state, although of approximative nature, is very close to an exact solution of the Davydov model on time scales from some femtoseconds up to nanoseconds. Especially the very small time region is of importance, because in this time a possible soliton formation from the initial excitation would start.     

利用IL－3／GM－CSF融合蛋白（PIXY－321）扩增脐血造血细胞方法的初步建立

利用单克隆抗体免疫磁珠吸附方法分离脐血ＣＤ３４＋细胞,并观察了ＩＬ３／ＧＭＣＳＦ融合蛋白（ＰＩＸＹ３２１）对脐血ＣＤ３４＋细胞的刺激作用。ＰＩＸＹ３２１对脐血ＣＤ３４＋细胞扩增作用大于ＩＬ３和ＧＭＣＳＦ单独及联合应用。在液体培养条件下,每毫升２０ｎｇＰＩＸＹ３２１可有效地扩增脐血造血祖细胞,适宜扩增时间为５－８天,扩增后造血祖细胞的数量可达扩增前的８－１０倍,从而初步建立了一种简单可行的脐血造血细胞扩增方法。     

Expansion of mesenchymal stem cells under atmospheric carbon dioxide

Stem cells are needed for an increasing number of scientific applications, including both fundamental research and clinical disease treatment. To meet this rising demand, improved expansion methods to generate high quantities of high quality stem cells must be developed. Unfortunately, the bicarbonate buffering system – which relies upon an elevated CO₂ environment – typically used to maintain pH in stem cell cultures introduces several unnecessary limitations in bioreactor systems. In addition to artificially high dissolved CO₂ levels negatively affecting cell growth, but more importantly, the need to sparge CO₂ into the system complicates the ability to control culture parameters. This control is especially important for stem cells, whose behavior and phenotype is highly sensitive to changes in culture conditions such as dissolved oxygen and pH. As a first step, this study developed a buffer to support expansion of mesenchymal stem cells (MSC) under an atmospheric CO₂ environment in static cultures. MSC expanded under atmospheric CO₂ with this buffer achieved equivalent growth rates without adaptation compared to those grown in standard conditions and also maintained a stem cell phenotype, self‐renewal properties, and the ability to differentiate into multiple lineages after expansion. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29:1298–1306, 2013     

Expansion of Aedes africanus (Diptera: Culicidae), a sylvatic vector of arboviruses,into an urban environment of Abidjan,Côte d'Ivoire

In 2008, an outbreak of yellow fever occurred in Abidjan. The entomological investigations confirm that Abidjan is at risk of yellow fever with a suspicion of the National Park of Banco (NPB) forest as a likely area of re‐emergence. This study aims to assess the dispersion of sylvatic vectors of arboviruses from the NPB forest to the surrounding areas (Andokoi and Sagbé). The sampling was done in the rainy season using the WHO layer‐traps technique. Among the six species of Aedes sampled, Aedes aegypti and Aedes africanus were the potential vectors of arboviruses. Both species were collected in Sagbé but only Ae. aegypti in Andokoi. Only Ae. aegypti were present 400 and 800 m from NPB forest, but at 200 m, it showed respective proportions of 75.5% and 87.5% in Sagbé and Andokoi. In the NPB forest, however, Ae. africanus has been the predominant species. The study showed the presence of Ae. aegypti in Andokoi and Sagbé. However, Ae. africanus was found in the NPB forest and in the 200 m radius in Sagbé. The establishment of an entomological surveillance program in all areas would therefore be essential for the prevention of arboviruses outbreaks in Abidjan.     

How to correct relative voxel scale factors for calculations of vector-difference Fourier maps in cryo-EM

The atomic coordinates derived from cryo-electron microscopy (cryo-EM) maps can be inaccurate when the voxel scaling factors are not properly calibrated. Here, we describe a method for correcting relative voxel scaling factors between pairs of cryo-EM maps for the same or similar structures that are expanded or contracted relative to each other. We find that the correction of scaling factors reduces the amplitude differences of Fourier-inverted structure factors from voxel-rescaled maps by up to 20–30%, as shown by two cryo-EM maps of the SARS-CoV-2 spike protein measured at pH 4.0 and pH 8.0. This allows for the calculation of the difference map after properly scaling, revealing differences between the two structures for individual amino acid residues. Unexpectedly, the analysis uncovers two previously overlooked differences of amino acid residues in structures and their local structural changes. Furthermore, we demonstrate the method as applied to two cryo-EM maps of monomeric apo-photosystem II from the cyanobacteria Synechocystis sp. PCC 6803 and Thermosynechococcus elongatus. The resulting difference maps reveal many changes in the peripheral transmembrane PsbX subunit between the two species.     

茉莉酸信号受体COI蛋白家族的分子进化与基因表达分析

茉莉酸(Jasmonic acid,JA)存在于所有高等植物中,是植物对病原微生物和虫害防御反应的关键激素。在茉莉酸信号转导中,COI1(COR-insensitive 1)作为茉莉酸信号受体蛋白在其中发挥关键作用。本研究采用生物信息学方法,从藻类、苔藓类、蕨类、裸子及单、双子叶植物多谱系对COI蛋白家族进行比较基因组学研究,并取得以下结果:(1)同源基因鉴定结果发现,在所选的7种陆生植物中一共鉴定了55个COIs同源基因,然而,在低等的水生植物包括绿藻类(Chlorophytes)、红藻类(Rhodophytes)、硅藻类(Bacillariophytes)、灰胞藻类(Glaucophytes)及褐藻类(Phaeophytes)等基因组中均未发现其同源基因;(2)系统进化树分析表明,植物COI蛋白家族可以分为4个保守的亚家族,且在陆生植物扩增的同时可能已发生功能分化;(3)基因结构分析显示,植物COI家族基因结构表现多样性,主要体现在内含子的数目和长度上;(4)基因表达数据提示,COI基因家族成员参与植物生长发育的多个时期,且在不同组织器官以及不同的胁迫应答反应中发挥不同的作用。以上结果将为植物COI基因家族的深入研究提供参考。     

The Repeat Expansion Diseases: The dark side of DNA repair

DNA repair normally protects the genome against mutations that threaten genome integrity and thus cell viability. However, growing evidence suggests that in the case of the Repeat Expansion Diseases, disorders that result from an increase in the size of a disease-specific microsatellite, the disease-causing mutation is actually the result of aberrant DNA repair. A variety of proteins from different DNA repair pathways have thus far been implicated in this process. This review will summarize recent findings from patients and from mouse models of these diseases that shed light on how these pathways may interact to cause repeat expansion.     

Comparison of rat mesenchymal stem cells derived from bone marrow,synovium, periosteum,adipose tissue,and muscle

Mesenchymal stem cells (MSCs) are increasingly being reported as occurring in a variety of tissues. Although MSCs from human bone marrow are relatively easy to harvest, the isolation of rodent MSCs is more difficult, thereby limiting the number of experiments in vivo. To determine a suitable cell source, we isolated rat MSCs from bone marrow, synovium, periosteum, adipose, and muscle and compared their properties for yield, expansion, and multipotentiality. After two passages, the cells in each population were CD11b (−), CD45 (−), and CD90 (+). The colony number per nucleated cells derived from synovium was 100-fold higher than that for cells derived from bone marrow. With regard to expansion potential, synovium-derived cells were the highest in colony-forming efficiency, fold increase, and growth kinetics. An in vitro chondrogenesis assay demonstrated that the pellets derived from synovium were heavier, because of their greater production of cartilage matrix, than those from other tissues, indicating their superiority in chondrogenesis. Synovium-derived cells retained their chondrogenic potential after a few passages. The Oil Red-O positive colony-rate assay demonstrated higher adipogenic potential in synovium- and adipose-derived cells. Alkaline phosphatase activity was greater in periosteum- and muscle-derived cells during calcification. The yield and proliferation potential of rat MSCs from solid tissues was much better than those from bone marrow. In particular, synovium-derived cells had the greatest potential for both proliferation and chondrogenesis, indicating their usefulness for cartilage study in a rat model. This study was supported in part by grants from the Japan Latest Osteoarthritis Society and from the Center of Excellence Program for Frontier Research on Molecular Destruction and Reconstruction of Tooth and Bone in Tokyo Medical and Dental University (to T.M.), and by the Japan Society for the Promotion of Science (grant no. 18591657 to I.S.). Recombinant human bone morphogenetic protein-2 was kindly provided by Astellas Pharma.     

The FBXL10/KDM2B Scaffolding Protein Associates with Novel Polycomb Repressive Complex-1 to Regulate Adipogenesis

Polycomb repressive complex 1 (PRC1) plays an essential role in the epigenetic repression of gene expression during development and cellular differentiation via multiple effector mechanisms, including ubiquitination of H2A and chromatin compaction. However, whether it regulates the stepwise progression of adipogenesis is unknown. Here, we show that FBXL10/KDM2B is an anti-adipogenic factor that is up-regulated during the early phase of 3T3-L1 preadipocyte differentiation and in adipose tissue in a diet-induced model of obesity. Interestingly, inhibition of adipogenesis does not require the JmjC demethylase domain of FBXL10, but it does require the F-box and leucine-rich repeat domains, which we show recruit a noncanonical polycomb repressive complex 1 (PRC1) containing RING1B, SKP1, PCGF1, and BCOR. Knockdown of either RING1B or SKP1 prevented FBXL10-mediated repression of 3T3-L1 preadipocyte differentiation indicating that PRC1 formation mediates the inhibitory effect of FBXL10 on adipogenesis. Using ChIP-seq, we show that FBXL10 recruits RING1B to key specific genomic loci surrounding the key cell cycle and the adipogenic genes Cdk1, Uhrf1, Pparg1, and Pparg2 to repress adipogenesis. These results suggest that FBXL10 represses adipogenesis by targeting a noncanonical PRC1 complex to repress key genes (e.g. Pparg) that control conversion of pluripotent cells into the adipogenic lineage.     

Dehydrodiconiferyl alcohol isolated from Cucurbita moschata shows anti-adipogenic and anti-lipogenic effects in 3T3-L1 cells and primary mouse embryonic fibroblasts

A water-soluble extract from the stems of Cucurbita moschata, code named PG105, was previously found to contain strong anti-obesity activities in a high fat diet-induced obesity mouse model. One of its biological characteristics is that it inhibits 3T3-L1 adipocyte differentiation. To isolate the biologically active compound(s), conventional solvent fractionation was performed, and the various fractions were tested for anti-adipogenic activity using Oil Red O staining method. A single spot on thin layer chromatography of the chloroform fraction showed a potent anti-adipogenic activity. When purified, the structure of its major component was resolved as dehydrodiconiferyl alcohol (DHCA), a lignan, by NMR and mass spectrometry analysis. In 3T3-L1 cells, synthesized DHCA significantly reduced the expression of several adipocyte marker genes, including peroxisome proliferator-activated receptor γ (Pparg), CCAAT/enhancer-binding protein α (Cebpa), fatty acid-binding protein 4 (Fabp4), sterol response element-binding protein-1c (Srebp1c), and stearoyl-coenzyme A desaturase-1 (Scd), and decreased lipid accumulation without affecting cell viability. DHCA also suppressed the mitotic clonal expansion of preadipocytes (an early event of adipogenesis), probably by suppressing the DNA binding activity of C/EBPβ, and lowered the production level of cyclinA and cyclin-dependent kinase 2 (Cdk2), coinciding with the decrease in DNA synthesis and cell division. In addition, DHCA directly inhibited the expression of SREBP-1c and SCD-1. Similar observations were made, using primary mouse embryonic fibroblasts. Taken together, our data indicate that DHCA may contain dual activities, affecting both adipogenesis and lipogenesis.