Different protein tyrosine phosphatase superfamilies resulting from different gene reading frames

Protein tyrosine phosphatases (PTPs) are comprised of two superfamilies, the phosphatase I superfamily containing a single low-molecular-weight PTP (lmwPTP) family and the phosphatase II superfamily including both the higher-molecular-weight PTP (hmwPTP) and the dual-specificity phosphatase (DSP) families. The phosphatase I and H superfamilies are often considered to be the result of convergent evolution. The PTP sequence and structure analyses indicate that lmwPTPs, hmwPTPs, and DSPs share similar structures, functions, and a common signature motif, although they have low sequence identities and a different order of active sites in sequence or a circular permutation. The results of this work suggest that lmwPTPs and hmwPTPs/DSPs are remotely related in evolution. The earliest ancestral gene of PTPs could be from a short fragment containing about 90similar to120 nucleotides or 30similar to40 residues; however, a probable full PTP ancestral gene contained one transcript unit with two lmwPTP genes. All three PTP families may have resulted from a common ancestral gene by a series of duplications, fusions, and circular permutations. The circular permutation in PTPs is caused by a reading frame difference, which is similar to that in DNA methyltransferases. Nevertheless, the evolutionary mechanism of circular permutation in PTP genes seems to be more complicated than that in DNA methyltransferase genes. Both mechanisms in PTPs and DNA methyltransferases can be used to explain how some protein families and superfamilies came to be formed by circular permutations during molecular evolution.

Characterization of DYRK2 (dual-specificity tyrosine-phosphorylation-regulated kinase 2) from Zebrafish (Dario rerio)

Proteins of the DYRK (dual-specificity tyrosine-phosphorylation-regulated kinase) family are characterized by the presence of a conserved kinase domain and N-terminal DH box. DYRK2 is involved in regulating key developmental and cellular processes, such as neurogenesis, cell proliferation, cytokinesis, and cellular differentiation. Herein, we report that the ortholog of DYRK2 found in zebrafish shares about 70% identity with that of human, mouse, and chick. RT-PCR showed that DYRK2 is expressed maternally and zygotically. In-situ hybridization results show that DYRK2 is expressed in somite cells that will develop into muscles. Our results provide preliminary evidence for investigating the in-vivo function of DYRK2 in zebrafish muscle development.

CO2升高对土壤微生物群落影响的模拟研究

大气CO2浓度升高可以通过植物间接影响土壤生态系统。土壤生态系统的结构和功能改变将影响有机质矿化和营养物质循环，进而可能对CO2浓度升高产生正反馈或负反馈。微生物是土壤生态系统的主体，在对CO2浓度升高的反馈中起着至关重要的作用。本研究以开顶箱系统为平台，采用微生物分子生态学技术和现代酶学技术，通过对长期接受500 ppm CO2的红松幼树、长白赤松幼树和蒙古栎幼树非根际土壤连续两个生长季的测定，系统研究了高浓度CO2对温带森林土壤微生物群落的生物量和微生物活性的影响，检测了土壤微生物群落的结构和功能以及土壤化学性质变化，主要结论如下： （1）高浓度CO2处理提高了土壤有机碳含量。与对照组相比较，红松幼树土壤有机碳含量提高9.4%；长白赤松幼树土壤提高0.6%；蒙古栎幼树土壤提高1.3%。 （2）高浓度CO2处理使土壤磷酸酶（phosphatase）、几丁质酶（1,4-β-acetylglucosaminidase, 1,4-β-NAG）和多酚氧化酶（phenol oxidase）活性发生了显著变化，高浓度CO2使红松土壤 1,4-β-NAG活性提高7-25%，长白松土壤1,4-β-NAG平均活性降低14%，蒙古栎土壤1,4-β-NAG平均活性提高31%。 同时研究还发现，过氧化物酶（peroxidase）和多酚氧化酶(phenol oxidase)活性与微生物量碳和微生物量氮呈显著的正相关。相关分析还显示，土壤湿度与1,4-α-葡萄糖苷酶（1,4-α-glucosidase）活性、 微生物生物量碳和微生物生物量氮呈显著的正相关。 高浓度CO2在不同程度上改变了土壤转化酶活性和脱氢酶活性。高浓度CO2显著提高了红松和长白赤松土壤硝化酶活性；而显著降低反硝化酶活性。 （3）研究发现三种树土壤的真菌和细菌群落存在着季节性演替，并且高浓度CO2熏蒸处理使真菌群落结构发生了显著的变化，表现为一些种群优势度下降，另一些升高。虽然，细菌群落没有如真菌群落变化的明显，但研究中也发现高浓度CO2的确使个别细菌种群的优势度发生了显著改变。 亲缘关系与Calocybe carnea，Magmatodrilus obscurus密切的真菌是红松土壤优势种群，与Humicola fuscoatra关系相近的是长白松土壤的优势种群，并且此三种真菌的季节性变化不显著。研究发现高浓度CO2使红松土壤中亲缘关系与Pachyella clypeata，Cochlonema euryblastum，Lepiota cristata，Eimeriidae sp.， Trichoderma sp.相近的种群的丰富度显著提高，使蒙古栎土壤中亲缘关系与Serendipita vermifera，Calocybe carnea种群丰富度显著下降，使蒙古栎土壤中与Candida sp.，Magmatodrilus obscurus和Pachyella clypeata亲缘关系密切种群的丰富度显著提高。 （4）三种幼树叶的原位分解培养429天结果显示，红松和长白松凋落物的β-葡萄糖苷酶（1,4-β-glucosidase）和木糖苷酶（1,4-β-xylosidase）活性随着分解而逐渐增加，而这两种酶在蒙古栎凋落物分解过程中保持相对恒定；高浓度CO2显著影响叶凋落物分解磷酸酶（phosphatase），纤维二糖酶（cellobiohydrolase）, 几丁质酶(1,4-β-NAG)，多酚氧化酶（phenol oxidase）和过氧化物酶（peroxidase）的活性。研究发现，凋落物的生物化学性质变化能引起分解的微生物群落发生变化，进而引起分泌的胞外酶活性变化，科学印证了大气CO2浓度升高“通过影响凋落物质量进而影响分解叶凋落物的微生物群落的结构和功能”的猜测。 不同凋落物之间酶活性差异显著，真菌和细菌群落结构也显著不同。序列与Hyphodiscus hymeniophilus亲缘关系密切的真菌和亲缘关系与Verrucomicrobia bacterium密切的细菌是长白松凋落分解的最优势种群，序列与Lophium mytilinum亲缘关系密切的真菌是红松凋落分解的最优势种群。 另外，研究还发现，高浓度CO2使参与分解红松凋落物Beta proteobacterium OS-15A亲缘关系相近的细菌种群和与Azospirillum amazonense亲缘关系相近的种群丰富度显著降低；使与Luteibactor rhizovicina亲缘关系相近的种群和与Luteibactor rhizovicina亲缘关系相近的种群显著提高。高浓度CO2使定殖于长白松凋落物上Hyphodiscus hymeniophilus亲缘关系相近的种群和与Bionectria pityrodes亲缘关系相近的种群显著提高，而使与Neofabraea malicorticis亲缘关系相近的种群和与Hyphodiscus hymeniophilus亲缘关系相近的种群显著下降。

Identification of a novel DNA methyltransferase 2 from the brine shrimp, Artemia franciscana

DNA methyltransferase 2 (Dnmt2) is a dual-specificity DNA methyltransferase, which contains a weak DNA methyltransferase and novel tRNA methyltransferase activity. However, its biological function is still enigmatic. To elucidate the expression profiles of Dnmt2 in Artemia franciscana, we isolated the gene encoding a Dnmt2 from A. franciscana and named it as AfDnmt2. The cDNA of AfDnmt2 contained a 1140-bp open reading frame that encoded a putative Dnmt2 protein of 379 amino acids exhibiting 32%similar to 39% identities with other known Dnmt2 homologs. This is the first report of a DNA methyltransferase gene in Crustacean. By using semi-quantitative RT-PCR, A)Dnmt2 was found to be expressed through all developmental stages and its expression increased during resumption of diapause cysts development. Southern blot analysis indicated the presence of multiple copies of AfDnmt2 genes in A. franciscana. (C) 2007 Published by Elsevier Inc.

知觉负荷与线索通道特征对注意捕获的影响

A dual task paradigm which consisted of RSVP task and orthogonal spatial cuing task was adopted to study the effects of perceptual load and cue modality on attention capture. This dual task paradigm was modified from Santangelo’s tasks in which only the high load condition used the dual task. Experiment 1 found that in the low perceptual load condition, the visual cues showed advantage in capturing attention compared with the audiovisual ones. While in the high perceptual load condition, the audiovisual cues were better to capture attention. SOA was introduced into Experiment 2, 3 and 4 in order to help clarify the relationship among perceptual load, cuing modality and attention capture. The low load visual cuing task testified the period time course characteristics in attention capture which was found by Liang et.al. Differing from Liang’s conclusion that attention capture occurred at 333ms, attention capture occurred at 50ms here which might be caused by the different paradigms used. Moreover, the similar period time course was found in high load audiovisual cuing task when SOA equaled 50ms. And no such period time course characteristics were found neither in the high load visual cuing task nor the low load audiovisual cuing task. These results found the period time course characteristics in attention capture. And it was suggested that these characteristics were influenced by perceptual load and cuing modality.

Gal(1-x)Mn(1-x)Sb Grown on GaSb with Mass-Analyzed Low-Energy Dual Ion Beam Deposition

The Ga1-xMnxSb samples were fabricated by the implantation of Mn ions into GaSb (1 0 0) substrate with mass-analyzed low-energy dual ion beam deposition system, and post-annealing. Auger electron spectroscopy depth profile of the Ga1-xMnxSb samples showed

Dual-wavelength competitive output in Nd:Y3Sc1.5Al3.5O12 ceramic disk laser

In this paper, we demonstrated a dual-wavelength competitive output in Nd:Y3SC1.5Al3.5O12 ceramic disk laser. Different dual-wavelength output behaviors for Nd:YSAG and Nd:YAG ceramic disk laser were investigated and discussed. By applying the energy transfer model, we suggested the reasonable explanation for this new phenomenon as the disordered replacing of Al3+ ions by Sc3+ ions. The main advantage of the dual-wavelength ceramic laser is the possibility to serve as the seed source to generate Terahertz radiation. (C) 2008 Elsevier B.V. All rights reserved.

1.55-mu m ridge DFB laser integrated with a buried-ridge-stripe dual-core spot-size converter by quantum-well intermixing

A ridge distributed feedback laser monolithically integrated with a buried-ridge-stripe spot-size converter operating at 1.55 mu m was successfully fabricated by means of low-energy ion implantation quantum-well intermixing and dual-core technologies. The passive waveguide was optically combined with a laterally exponentially tapered active core to control the mode size. The devices emit in a single transverse and single longitudinal mode with a sidemode suppression ratio of 38.0 dB. The threshold current was 25 mA. The beam divergence angles in the horizontal and vertical directions were as small as 8.0 degrees x 12.6 degrees, respectively, resulting in 3.0-dB coupling loss with a cleaved single-mode optical fiber.

Gal(1-x)Mn(1-x)Sb grown on GaSb with mass-analyzed low-energy dual ion beam deposition

The Ga1-xMnxSb samples were fabricated by the implantation of Mn ions into GaSb (1 0 0) substrate with mass-analyzed low-energy dual ion beam deposition system, and post-annealing. Auger electron spectroscopy depth profile of the Ga1-xMnxSb samples showed that the Mn ions were successfully implanted into GaSb substrate. Clear double-crystal X-ray diffraction patterns of the Ga1-xMnxSb samples indicate that the Ga1-xMnxSb epilayers have the zinc-blende structure without detectable second phase. Magnetic hysteresis-loop of the Ga1-xMnxSb epilayers were obtained at room temperature (293 K) with alternating gradient magnetometry. (c) 2005 Elsevier B.V. All rights reserved.

1.55-mu m Ridge DFB laser and electroabsorption modulator integrated with buried-ridge-stripe dual-waveguide spot-size converter output

A 1.55-mu m ridge distributed feedback laser and electroabsorption modulator monolithically integrated with a buried-ridge-stripe dual-waveguide spot-size converter (SSC) at the output port for low-loss coupling to a cleaved single-mode optical fiber was fabricated by means of selective area growth, quantum-well intermixing, and dual-core technologies. These devices exhibit threshold current of 28 mA, 3-dB modulation bandwidth of 12.0 GHz, modulator extinction ratios of 25.0-dB dc. The output beam divergence angles of the SSC in the horizontal and vertical directions are as small as 8.0 degrees x 12.6 degrees, respectively, resulting in 3.2-dB coupling loss with a cleaved single-mode optical fiber.

MnSi similar to 1.73 grown on silicon with mass-analyzed low energy dual ion beam epitaxy technique

Semiconducting manganese silicide, Mn27Si47 and Mn15Si26, were obtained using mass-analyzed low energy dual ion beam epitaxy technique, Auger electron spectroscopy depth profiles showed that some of the Mn ions were deposited on single-crystal silicon substrate and formed a 37.5 nm thick Mn film, and the other Mn ions were successfully implanted into the Si substrate with the implantation depth of 618 nm. Some samples were annealed in the atmosphere of flowing N-2 at 840 degreesC. X-ray diffraction measurements showed that the annealing was beneficial to the formation of Mn27Si47 and Mn15Si26 (C) 2001 Published by Elsevier Science B.V.

Weibull modulus for diverse strength due to sample-specificity

By sample specificity it is meant that specimens with the same nominal material parameters and tested under the same environmental conditions may exhibit different behavior with diversified strength. Such an effect has been widely observed in the testing of material failure and is usually attributed to the heterogeneity of material at the mesoscopic level. The degree with which mesoscopic heterogeneity affects macroscopic failure is still not clear. Recently, the problem has been examined by making use of statistical ensemble evolution of dynamical system and the mesoscopic stress re-distribution model (SRD). Sample specificity was observed for non-global mean stress field models, such as the duster mean field model, stress concentration at tip of microdamage, etc. Certain heterogeneity of microdamage could be sensitive to particular SRD leading to domino type of coalescence. Such an effect could start from the microdamage heterogeneity and then be magnified to other scale levels. This trans-scale sensitivity is the origin of sample specificity. The sample specificity leads to a failure probability Phi (N) with a transitional region 0 < (N) < 1, so that globally stable and catastrophic modes could co-exist. It is found that the scatter in strength can fit the Weibull distribution very well. Hence, the Weibull modulus is indicative of sample specificity. Numerical results obtained from the SRD for different non-global mean stress fields show that Weibull modulus increases with increasing sample span and influence region of microdamage.

Properties of high k gate dielectric gadolinium oxide deposited on Si(100) by dual ion beam deposition (DIBD)

Gadolinium oxide thin films have been prepared on silicon (100) substrates with a low-energy dual ion-beam epitaxial technique. Substrate temperature was an important factor to affect the crystal structures and textures in an ion energy range of 100-500 eV. The films had a monoclinic Gd2O3 structure with preferred orientation ((4) over bar 02) at low substrate temperatures. When the substrate temperature was increased, the orientation turned to (202), and finally, the cubic structure appeared at the substrate temperature of 700 degreesC, which disagreed with the previous report because of the ion energy. The AES studies found that Gadolinium oxide shared Gd2O3 structures, although there were a lot of oxygen deficiencies in the films, and the XPS results confirmed this. AFM was also used to investigate the surface images of the samples. Finally, the electrical properties were presented. (C) 2004 Elsevier B.V. All rights reserved.

FexSi grown with mass-analyzed low-energy dual ion beam deposition

Heavily iron-implanted silicon was prepared by mass-analyzed low-energy dual ion beam deposition technique. Auger electron spectroscopy depth profiles indicate that iron ions are shallowly implanted into the single-crystal silicon substrate and formed 35 nm thick FexSi films. X-ray diffraction measurements show that as-implanted sample is amorphous and the structure of crystal is partially restored after as-implanted sample was annealed at 400degreesC. There are no new phases formed. Carrier concentration depth profile of annealed sample was measured by Electrochemical C-V method and indicated that FexSi film shows n-type conductivity while silicon substrate is p-type. The p-n junction is formed between FexSi film and silicon substrate showing rectifying effect. (C) 2003 Elsevier B.V. All rights reserved.

Fatigue crack-growth rate in ferrite martensite dual-phase steel

An empirical study is made on the fatigue crack growth rate in ferrite-martensite dual-phase (FMDP) steel. Particular attention is given to the effect of ferrite content in the range of 24.2% to 41.5% where good fatigue resistance was found at 33.8%. Variations in ferrite content did not affect the crack growth rate when plotted against the effective stress intensity factor range  which was assumed to follow a linear relation with the crack tip stress intensity factor range ΔK. A high  corresponds to uniformly distributed small size ferrite and martensite. No other appreciable correlation could be ralated to the microstructure morphology of the FMDP steel. The closure stress intensity factor , however, is affected by the ferrite content with  reaching a maximum value of 0.7. In general, crack growth followed the interphase between the martensite and ferrite.

Dividing the fatigue crack growth process into Stage I and II where the former would be highly sensitive to changes in ΔK and the latter would increase with ΔK depending on the  ratio. The same data when correlated with the strain energy density factor range ΔS showed negligible dependence on mean stress or R ratio for Stage I crack growth. A parameter α involving the ratio of ultimate stress to yield stress, percent reduction of area and R is introduced for Stage II crack growth so that the  data for different R would collapse onto a single curve with a narrow scatter band when plotted against αΔS.