Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei : Cypriniformes)

The mitochondrial 16S ribosomal RNA (rRNA) gene sequences from 93 cyprinid fishes were examined to reconstruct the phylogenetic relationships within the diverse and economically important subfamily Cyprininae. Within the subfamily a biased nucleotide composition (A > T, C > G) was observed in the loop regions of the gene, and in stem regions apparent selective pressures of base pairing showed a bias in favor of G over C and T over A. The bias may be associated with transition-transversion bias. Rates of nucleotide substitution were lower in stems than in loops. Analysis of compensatory substitutions across these taxa demonstrates 68% covariation in the gene and a logical weighting factor to account for dependence in mutations for phylogenetic inference should be 0.66. Comparisons of varied stem-loop weighting schemes indicate that the down-weightings for stem regions could improve the phylogenetic analysis and the degree of non-independence of stem substitutions was not as important as expected. Bayesian inference under four models of nucleotide substitution indicated that likelihood-based phylogenetic analyses were more effective in improving the phylogenetic performance than was weighted parsimony analysis. In Bayesian analyses, the resolution of phylogenies under the 16-state models for paired regions, incorporating GTR + G + I models for unpaired regions was better than those under other models. The subfamily Cyprininae was resolved as a monophyletic group, as well as tribe Labein and several genera. However, the monophyly of the currently recognized tribes, such as Schizothoracin, Barbin, Cyprinion + Onychostoma lineages, and some genera was rejected. Furthermore, comparisons of the parsimony and Bayesian analyses and results of variable length bootstrap analysis indicates that the mitochondrial 16S rRNA gene should contain important character variation to recover well-supported phylogeny of cyprinid taxa whose divergences occurred within the recent 8 MY, but could not provide resolution power for deep phylogenies spanning 10-19 MYA. (c) 2008 Published by Elsevier Inc.

Carrier channels of multimodal-sized quantum dots: A surface-mediated adatom migration picture

This paper focuses on the study of carrier channels of multimodal-sized quantum dots formed on patterned substrate by a rate-equation-based model. Surface-mediated indium adatom migration is revealed by a direct comparison between quantum dot wetting layer, which acts as carrier channel, formed on a flat substrate and on a patterned substrate. For the assessment of suitability, the carrier channel of the dot-in-well structure has also been studied by the present model, and the transition energies of the carrier channel (e.g., InGaAs quantum well) obtained from theoretical simulation agree fairly well with those obtained from the reflectance measurements.

Circular photogalvanic effect of the two-dimensional electron gas in AlXGa1-XN/GaN heterostructures under uniaxial strain

The circular photogalvanic effect (CPGE) of the two-dimensional electron gas (2DEG) in Al0.25Ga0.75N/GaN heterostructures induced by infrared radiation has been investigated under uniaxial strain. The observed photocurrent consists of the superposition of the CPGE and the linear photogalvanic effect currents, both of which are up to 10(-2) nA. The amplitude of the CPGE current increases linearly with additional strain and is enhanced by 18.6% with a strain of 2.2x10(-3). Based on the experimental results, the contribution of bulk-inversion asymmetry (BIA) and structure-inversion asymmetry (SIA) spin splitting of the 2DEG to the CPGE current in the heterostructures is separated, and the ratio of SIA and BIA terms is estimated to be about 13.2, indicating that the SIA is the dominant mechanism to induce the k-linear spin splitting of the subbands in the triangular quantum well at AlxGa1-xN/GaN heterointerfaces. (C) 2007 American Institute of Physics.

Room-temperature spin-oriented photocurrent under near-infrared irradiation and comparison of optical means with Shubnikov de-Haas measurements in AlXGa1-XN/GaN heterostructures

The admixture of linear and circular photogalvanic effects and (CPGEs) in AlxGa1-xN/GaN heterostructures has been investigated quantitatively by near-infrared irradiation at room temperature. The spin-based photocurrent that the authors have observed solidly indicates the sizable spin-orbital interaction of the two-dimensional electron gas in the heterostructures. Further analysis shows consistency between studies by optical and magnetic (Shubnikov de-Haas) measurements on the spin-orbital coupling effects among different AlxGa1-xN/GaN heterostructures, indicating that the CPGE measurement is a good way to investigate the spin splitting and the spin polarization in semiconductors. (C) 2007 American Institute of Physics.

Photoluminescence from Er-doped Si-in-SiNx thin films

Photoluminescence from Er3+-implanted Si-in-SiN, films emitting efficiently visible light were investigated. A Stark structure in the Er3+ photoluminescence spectrum was observed at room temperature, which reveals more than one site symmetry for the Er3+-centers in the Si-in-SiN, matrix. The correlation between the visible photoluminescence from the silicon nanoparticles and the 1.54 mu m emission from the Er3+-centers was discussed. (c) 2006 Elsevier B.V. All rights reserved.

Effect of growth conditions on the GaN thin film by sputtering deposition

The phase transition between thermodynamically stable hexagonal wurtzite (h-WZ) gallium nitride (GaN) and metastable cubic zinc-blende (c-ZB) GaN during growth by radio-frequency planar magnetron sputtering is studied. GaN films grown on substrates with lower mismatches tend to have a h-WZ structure, but when grown on substrates with higher mismatches, a c-ZB structure is preferred. GaN films grown under high nitrogen pressure also tend to have a h-WZ structure, whereas a c-ZB structure is preferred when grown under low nitrogen pressure. In addition, low target-power growth not only helps to improve hexagonal GaN (h-GaN) crystalline quality at high nitrogen pressure on low-mismatch substrates, but also enhances cubic GaN (c-GaN) quality at low nitrogen pressure on high-mismatch substrates. (c) 2007 Elsevier B.V. All rights reserved.

Strain-induced in-plane optical anisotropy in (001) GaAs/AlGaAs superlattice studied by reflectance difference spectroscopy

In-plane optical anisotropy (IPOA) in (001) GaAs/AlGaAs superlattice induced by uniaxial strain has been investigated by reflectance difference spectroscopy (RDS). Uniaxial strain on the order of 10(-4) was introduced by bending a strip sample with a stress apparatus. The IPOA of all interband transitions shows a linear dependence on strain. The birefringence and dichroism spectra induced by strain are obtained by RDS on the basis of a three-phase model, which is in good agreement with the reported results. (c) 2006 American Institute of Physics.

Local environment of Er3+ in Er-doped Si nanoclusters embedded in SiO2 films

The local environment of Er3+ in heavily Er-doped (Er, 2.5 at. %) Si nanoclusters embedded in SiO2 films annealed at various temperatures was investigated by using the fluorescence-extended x-ray absorption fine structure spectroscopy. The results show that annealing caused a large effect on the local environment of Er3+ surrounded by O atoms and the 1.54 mu m photoluminescence intensity. The correlation between the local environment around Er3+ and the corresponding 1.54 mu m photoluminescence was discussed. (c) 2006 American Institute of Physics.

Effects of ZnO interlayers on thick GaN/Si film prepared by RF magnetron sputtering

We have successfully prepared a high-quality 2 mu m-thick GaN film with three inserted 30 nm-thick ZnO interlayers on Si (111) substrate without cracks by magnetron sputtering. The effects of the thickness and number of ZnO interlayers on the crystal quality of the GaN films were studied. It was found that the GaN crystal quality initially improved with the increase of the thickness of ZnO interlayers, but deteriorated quickly when the thickness exceeded 30 nm. Multiple ZnO interlayers were used as an effective means to further improve the crystal quality of the GaN film. By increasing the number of interlayers up to three, the cracks can be constrained to a certain extent, and the crystal quality of the GaN film greatly improved. (c) 2006 Elsevier B.V. All rights reserved.

Observation of photogalvanic current for interband absorption in InN films at room temperature

The linear and circular photogalvanic effects have been observed in undoped InN films for the interband transition by irradiation of 1060 nm laser at room temperature. The spin polarized photocurrent depends on the degree of polarization, and changes its sip when the radiation helicity changes from left-handed to right-handed. This result indicates the sizeable spin-orbit interaction in the InN epitaxial layer and provides an effective method to generate spin polarized photocurrent and to detect spin-splitting effect in semiconductors with promising applications on spintronics.

DNA装配中的纠错

DNA装配问题是指把各个读出序列（reads）拼接成一条完整的DNA链，即确定原DNA链的核苷酸“A，T，C���G���的排列顺序。实验中，由于各种原因测出的读出片段序列与DNA链的实际结果会有误差，这些误差会影响到用于装配的算法的性能，因此需要对测出的读出序列进行纠错。现有的算法如： ECINDEL和SRCorr都能够对实验数据进行纠错。但是它们都是根据某个读出序列出现的次数来判断它的正确性。这类算法首先选择参数k和M，若读出序列所有长度为k的子串出现的次数均大于M次，则它为正确的读出序列，即确实为原DNA链的子串。同时，还可以利用这些长度为k的子串来对原来的读出序列片段进行纠错。 然而，在这些算法中，M的选择要么是一个固定值，要么是随机的，使得这些算法在纠错问题上的表现并不稳定。 本文我们计算长度为k的子串出现M次时，它的真阳性（确实为原DNA链的一部分）的概率以及假阳性和假阴性的概率。根据计算结果，我们可以选择一个最优的M值使得最后选取的子串的错误最少，即假阳性的子串与假阴性的子串的数量之和最少。我们在模拟数据和实际数据上进行了验证，与之前的纠错算法ECINDEL，SRCorr相比，我们的算法总的错误率降低了77.6％和65.1％。

可溶性甲壳素制取及其稀溶液性质的研究

从螃蟹壳中提取出甲壳素，并进一步进行脱乙酰基反应，制得了脱乙酰度（D.D）在49－100％范围的阳离子聚电解质可溶性甲壳素－壳聚糖。首次通过壳聚糖乙酸溶液的超声波降解快速制得了各个脱乙酰度系列，不同分子量的壳聚糖样品。将不同系列的各个样品在0.2M CH_3COOH + 0.1M CH_3COONa溶液中进行粘度和光散射（L.S）的研究，订定出了不同D.D壳聚糖的Mark-Houwink方程（30±0.05℃）如下：69％：[η]=0.1036*10~(-3) M_w~(1.12) (ml/g) 84%: [η]=1.424*10~(-3) M_w~(0.96) (ml/g) 91%: [η]=11.27*10~(-3)M_w~(0.84) (ml/g) 100%: [η]=16.80*10~(-3)M_w~(0.81) (ml/g)同时，对壳聚糖的其它某些稀溶液性质，如分子尺寸，第二维利系数，扩散因子等进行了求算，并对结果进行了讨论。将胶体滴定法应用到聚电解质壳聚糖的脱乙酰度（D.D）分析上，取得了满意的结果，建立了完整的测试方法，推导出了计算公式：D.D=(N_(PVSK)*ΔV*M_壳)/(5*C)*100%式中：N_(PVSK)-PVSK的当量浓度M_壳－完全脱乙酰基的壳聚糖链节分子量：161.15ΔV－消耗掉PVSK的体积差ΔV=V_1-V_2（升）C���壳聚糖溶液的浓度(g/ml)实验表明，不同D.D值的壳聚糖有着不同的折光指数增量dn/dc���由此创立了一个根据测dn/dc���求壳聚糖脱乙酰度的新方法。在0.2M CH_3COOH/0.1M CH_3COONa中，436nm，25±0.05℃时的计算公式如下：y=9.397*0.943式中：x-dn/dc (ml/g) y-D.D (%)。

哀牢山金山丫口夜间网捕鸟类多样性及其影响因素

2007 年9 月5 日至11 月5 日和2008 年9 月3 日至11 月7 日期间，主要利用灯光诱捕，对云南省新平县哀牢山金山丫口（23°57′N, 101°30′E）夜间迁徙鸟类多样性进行调查。同时记录网捕鸟类的时序和几种主要鸟类的迁徙时序。分析各种因子（地理、温度、湿度、雾天、风向、风力以及月相周期）对夜间网捕鸟类数量和种类的影响。 2 年期间共网捕鸟类7943 只，129 种，分别属于14 目23 科。雀形目鸟类占总网捕数量的58.9%。网捕数量超过1%的科共10 个科。网捕数量占总网捕数量1%以上的共14 种。其中红尾伯劳Lanius cristatus、小杜鹃Cuculus poliocephalus、红喉歌鸲Luscinia calliope 三者的数量超过网捕鸟类总数的5%。所有网捕鸟类中，东洋型鸟类占最多共54 种，占41.85%。 2 年期间网捕鸟类多样性指数H′为2.60989，均匀度指数J 为0.29063，优势度指数C 为 0.22503，G-F 指数为0.71366。2007 年的优势指数C 和G-F 指数较2008 年高，但2008 年的 Shannon-Wiener 指数和Pielou 指数较2007 年高。红尾伯劳是造成两年多样性测度指数差异的主要原因。云南省不同“打雀山”夜间捕获鸟类的种类和数量存在差异。地理和气候可能是造成这些差异的主要因素。 2 年工作期间将观察时间平均分为早期（9 月3 日至9 月24 日）、中期（9 月25 日至10 月16 日）、晚期（10 月17 日至11 月8 日）三个时期。早期网捕鸟类数量最多5263 只，多样性指数最低，优势度指数最高；中期记录的种类最多86 种，多样性指数和均匀度指数中期最高。造成这种差异的主要原因是早期红尾伯劳的数量尤其突出。单独分析2007 年和2008 年各时期，除了2007 年晚期种类最多67 种以外，其余变化都与2 年总体一致。每个时期都有部分鸟类数量达到高峰，而也有部分鸟类数量处在低谷期。飞经哀牢山金山丫口的秋季夜间迁徙鸟类开始迁徙的时间大致在8 月中旬，结束在11 月下旬。每种鸟类的迁徙持续时间不一致，其中迁徙持续时间超过30 天的鸟有36 种。同种鸟类不同年份迁徙时间不一致。夜间每个时段捕获数量和种类有差异，在夜间20:00-22:00 和凌晨04:00-06:00 捕获数量和种类较多。24:00-02:00 网捕鸟类数量和种类最少。调查结果显示不是所有鸟类都是整夜迁徙，夜间开始迁徙较早的鸟类清晨也停止迁徙较早，夜间开始迁徙较晚的鸟类清晨停止迁徙较晚。除红喉歌鸲以外的4 种鸟，它们的迁徙时间是从9 月前至11 月后。红尾伯劳、小杜鹃以及大杜鹃的迁徙高峰期是9 月上旬至9 月中旬。厚嘴苇莺Acrocephalus aedon 的迁徙高峰期为 9 月中旬至10 月下旬。红喉歌鸲的迁徙时间是9 月下旬至11 月上旬后，迁徙高峰期为整个 10 月。5 个优势种都是整夜迁徙，不过每种鸟的迁徙高峰时段和低谷时段不一致。红尾伯劳、小杜鹃、大杜鹃在20:00-22:00 捕获数量最多；红喉歌鸲、厚嘴苇莺在凌晨04:00-06:00 捕获数量最多。红尾伯劳、红喉歌鸲、大杜鹃在24:00-02:00 捕获数量最少；厚嘴苇莺在22:00-24:00 捕获数量最少；小杜鹃在凌晨02:00-04:00 捕获数量最少。对5 个优势种在各迁徙时期的体重进行分析，采用双样本T 检验（Independent-Samples T Test）表明：红喉歌鸲和小杜鹃早中晚期的体重差异极为显著（P<0.01）。运用单因素方差分析（One-Way ANONA）表明：小杜鹃早中晚期的体重变化极其显著（P<0.01）。进一步采用双样本T 检验（Independent-Samples T Test）：小杜鹃晚期体重与早期和中期体重差异都极其著（P<0.01），早期与中期的体量没有显著差异（P>0.01）。其余3 个优势种各时期体量差异不显著（P>0.01）。影响夜间网捕鸟类种类和数量的因素较多。地理特点是影响夜间网捕鸟类种类的主要因素。气候条件是影响夜间网捕鸟类种类和数量的重要因素。风向和风力对夜间网捕数量和种类都有极其显著的影响（P<0.01），其中风向对其影响比风力大，西南风时夜间网捕鸟类数量和种类较多。雾天对夜间网捕数量和种类影响极其显著（P<0.01），大雾天气夜间网捕鸟类数量和种类较多。月相周期对夜间网捕数量及其种类的影响极其显著 (P<0.01)，新月和残月期间夜间网捕鸟类数量和种类较多。温湿度对夜间网捕鸟类数量和种类影响不显著(P>0.05)。除此之外，光也是捕获夜间鸟类的必要条件。

The two- to three-dimensional growth transition of InAs/GaAs epitaxy layer studied by reflectance difference spectroscopy

In this work, we have adopted reflectance difference spectroscopy to study the evolution of InAs layer grown at different temperatures in GaAs matrix. Associated with the two- to three-dimensional growth transition of InAs layer, the transition energies and the in-plane optical anisotropy of InAs wetting layer exhibit abrupt changes. This provides a new way to decide the critical thickness h(c) for the growth transition. The obtained h(c)s are compared with those determined by atomic force microscope measurement, and discrepancy is found at high temperatures. The origin of the difference is clarified and the variations in hc with temperature are further discussed. (C) 2010 American Institute of Physics. [doi:10.1063/1.3494043]

阔叶红松林碳循环及细根与凋落物生产、分解研究

森林凋落物、细根及红松阔叶林碳循环 摘要: 由于全球变化进程的加快使生态系统碳循环在科学研究中的重要性日益突出。森林生态系统作为陆地生态系统的一个重要组成部分，其碳循环过程和源、汇功能一直是人们研究的热点。本文以森林生态系统物质循环的两个关键过程－凋落物和细根的生产和分解过程为主要研究目标，探讨了两者的时空动态格局和主驱动因子；同时采用传统的森林调查与通量观测相结合的方法，系统的刻画了红松阔叶林生态系统的碳循环过程。 主要结论如下：（1）区域平均温度是决定东北地区不同气候区域森林凋落量发生变化的主要因素，优势树种生物学特性不同导致同一气候区域内森林类型之间凋落量呈现显著差异。（2）红松阔叶林不同凋落组分凋落量对气候因子的年际波动和林分生长的反应不同，红松生长使其落叶量和在凋落总量中所占的比重显著增加，这将导致林地的凋落物组成和物理化学性质发生根本改变。（3）6个不同气候区域内地带性树种凋落物分解率和养分元素释放率随纬度增加而降低，并且与区域年平均温度和降水量呈显著正相关关系，随着分解的进行凋落物分解率与温度和降水的相关性降低。凋落物初始化学指标与其分解率呈显著相关关系。回归模型的预测结果显示温度和降水的增加均可促进凋落物分解，并且其对分解的影响强度大于CO2浓度升高对凋落物分解间接影响。（4）3种原始群落——红松阔叶林，云冷杉林和岳桦林的细根生产量、周转率和养分元素归还量随着海拔的升高而降低，对于同一海拔带上的3种林型而言，红松阔叶林生长量最高而周转率和养分元素释放率最低，白桦纯林细根周转率和养分元素释放率最高，山杨林细根生长量最小，细根周转率和养分元素释放率介于前两者之间。（5）红松阔叶林生态系统碳储量为25962.17±2002.1 C g m-2，其中植物（乔、灌木和草本）、土壤和林地（凋落物和倒木）内的碳储量占总体的79%, 15% 和6%。生态系统碳的净交换(NEE)为366.8±110.6 C g m-2year-1, 林地和土壤的碳输入量为504.9±28.9 C g m-2year-1，输出量为405.9±28.7 C g m-2year-1。植物净固碳量为287±34.5 C g m-2year-1，乔木和灌木净固碳量分别占植物净固碳总量的98.6％和1.4％。 关键词：森林凋落物，凋落物分解，细根，碳储量，碳循环