Power Minimization for CDMA under Colored Noise

Rate-constrained power minimization (PMIN) over a code division multiple-access (CDMA) channel with correlated noise is studied. PMIN is. shown to be an instance of a separable convex optimization problem subject to linear ascending constraints. PMIN is further reduced to a dual problem of sum-rate maximization (RMAX). The results highlight the underlying unity between PMIN, RMAX, and a problem closely related to PMIN but with linear receiver constraints. Subsequently, conceptually simple sequence design algorithms are proposed to explicitly identify an assignment of sequences and powers that solve PMIN. The algorithms yield an upper bound of 2N - 1 on the number of distinct sequences where N is the processing gain. The sequences generated using the proposed algorithms are in general real-valued. If a rate-splitting and multi-dimensional CDMA approach is allowed, the upper bound reduces to N distinct sequences, in which case the sequences can form an orthogonal set and be binary +/- 1-valued.

NUVIEW:software for display and interactive manipulation of nucleic acid models

The NUVIEW software package allows skeletal models of any double helical nucleic acid molecule to be displayed out a graphics monitor and to apply various rotations, translations and scaling transformations interactively, through the keyboard. The skeletal model is generated by connecting any pair of representative points, one from each of the bases in the basepair. In addition to the above mentioned manipulations, the base residues can be identified by using a locator and the distance between any pair of residues can be obtained. A sequence based color coded display allows easy identification of sequence repeats, such as runs of Adenines. The real time interactive manipulation of such skeletal models for large DNA/RNA double helices, can be used to trace the path of the nucleic acid chain in three dimensions and hence get a better idea of its topology, location of linear or curved regions, distances between far off regions in the sequence etc. A physical picture of these features will assist in understanding the relationship between base sequence, structure and biological function in nucleic acids.

On the duality between rate and power optimizations

Sequence design problems are considered in this paper. The problem of sum power minimization in a spread spectrum system can be reduced to the problem of sum capacity maximization, and vice versa. A solution to one of the problems yields a solution to the other. Subsequently, conceptually simple sequence design algorithms known to hold for the white-noise case are extended to the colored noise case. The algorithms yield an upper bound of 2N - L on the number of sequences where N is the processing gain and L the number of non-interfering subsets of users. If some users (at most N - 1) are allowed to signal along a limited number of multiple dimensions, then N orthogonal sequences suffice.

A total synthesis of the epoxyquinone based antifungal natural product (±)-ambuic acid

A total synthesis of the recently isolated polyketide natural product (+/-)-ambuic acid has been accomplished from the readily available Diels-Alder adduct of cyclopentadiene and 2-allyl-p-benzoquinone through a simple sequence with sound stereocontrol. (c) 2005 Elsevier Ltd. All rights reserved.

Conformational Polymorphism in Telomeric Structures: Loop Orientation and Interloop Pairing in d(G4TnG4),

Sequence repeats constituting the telomeric regions of chromosomes are known to adopt a variety of unusual structures, consisting of a G tetraplex stem and short stretches of thymines or thymines and adenines forming loops over the stem. Detailed model building and molecular mechanics studies have been carried out for these telomeric sequences to elucidate different types of loop orientations and possible conformations of thymines in the loop. The model building studies indicate that a minimum of two thymines have to be interspersed between guanine stretches to form folded-back structures with loops across adjacent strands in a G tetraplex (both over the small as well as large groove), while the minimum number of thymines required to build a loop across the diagonal strands in a G tetraplex is three. For two repeat sequences, these hairpins, resulting from different types of folding, can dimerize in three distinct ways-i.e., with loops across adjacent strands and on same side, with loops across adjacent strands and on opposite sides, and with loops across diagonal strands and on opposite sides-to form hairpin dimer structures. Energy minimization studies indicate that all possible hairpin dimers have very similar total energy values, though different structures are stabilized by different types of interactions. When the two loops are on the same side, in the hairpin dimer structures of d(G(4)T(n)G(4)), the thymines form favorably stacked tetrads in the loop region and there is interloop hydrogen bonding involving two hydrogen bonds for each thymine-thymine pair. Our molecular mechanics calculations on various folded-back as well as parallel tetraplex structures of these telomeric sequences provide a theoretical rationale for the experimentally observed feature that the presence of intervening thymine stretches stabilizes folded-back structures, while isolated stretches of guanines adopt a parallel tetraplex structure

Population genetic structure of Carchesium polypinum (Ciliophora : Peritrichia) in four chinese lakes inferred from ISSR fingerprinting: High diversity but low differentiation

Although the peritrichous ciliate Carchesium polypinum is common in freshwater, its population genetic structure is largely unknown. We used inter-simple sequence repeat (ISSR) fingerprinting to analyze the genetic structure of 48 different isolates of the species from four lakes in Wuhan, central China. Using eight polymorphic primers, 81 discernible DNA fragments were detected, among which 76 (93.83%) were polymorphic, indicating high genetic diversity at the isolate level. Further, Nei's gene diversity (h) and Shannon's Information index (I) between the different isolates both revealed a remarkable genetic diversity, higher than previously indicated by their morphology. At the same time, substantial gene flow was found. So the main factors responsible for the high level of diversity within populations are probably due to conjugation (sexual reproduction) and wide distribution of swarmers. Analysis of molecular variance (AMOVA) showed that there was low genetic differentiation among the four populations probably due to common ancestry and flooding events. The cluster analysis and principal component analysis (PCA) suggested that genotypes isolated from the same lake displayed a higher genetic similarity than those from different lakes. Both analyses separated C. polypinum isolates into subgroups according to the geographical locations. However, there is only a weak positive correlation between the genetic distance and geographical distance, suggesting a minor effect of geographical distance on the distribution of genetic diversity between populations of C. polypinum at the local level. In conclusion, our studies clearly demonstrated that a single morphospecies may harbor high levels of genetic diversity, and that the degree of resolution offered by morphology as a marker for measuring distribution patterns of genetically distinct entities is too low.

Genetic linkage map of bay scallop, Argopecten irradians irradians (Lamarck 1819)

The bay scallop (Argopecten irradians irradians Lamarck 1819) has become one of the most important aquaculture species in China. Genetic improvement of cultured bay scallop can benefit greatly from a better understanding of its genome. In this study, we developed amplified fragment length polymorphisms (AFLPs) and simple sequence repeat markers from expressed sequence tags (EST-SSRs) for linkage analysis in bay scallop. Segregation of 390 AFLP and eight SSR markers was analysed in a mapping population of 97 progeny. Of the AFLP markers analysed, 326 segregated in the expected 1:1 Mendelian ratio, while the remaining 74 (or 19.0%) showed significant deviation, with 33 (44.6%) being deficient in heterozygotes (A/a). Among the eight polymorphic EST-SSR loci, one marker (12.5%) was found skewing from its expected Mendelian ratios. Eighteen per cent of the markers segregating from female parent were distorted compared with 21% of the markers segregating from male parent. The female map included 147 markers in 17 linkage groups (LGs) and covered 1892.4 cM of the genome. In the male map, totally 146 AFLP and SSR markers were grouped in 18 LGs spanning 1937.1 cM. The average inter-marker spacing in female and male map was 12.9 and 13.3 cM respectively. The AFLP and SSR markers were distributed evenly throughout the genome except for a few large gaps over 20 cM. Although preliminary, the genetic maps presented here provide a starting point for the mapping of the bay scallop genome.

Loss of allele diversity in introduced populations of the hermaphroditic bay scallop Argopecten irradians

The bay scallop Argopecten irradians is a hermaphroditic bivalve native to the Atlantic coast of the United States that was introduced to China for aquaculture production in 1982. It now supports a major aquaculture industry in China. Introduced species often start with limited genetic variability, which is problematic for the further selective breeding. Bay scallop aquaculture is exclusively hatchery based and as the initial introduction consisted of only 26 scallops, there have been concerns about inbreeding and inbreeding depression in cultured populations in China. In this study, eleven simple sequence repeat (SSR) markers were used to compare genetic variation in cultured populations from China with that in a natural population from the east coast of America. Although the difference in heterozygosity was small, the Chinese populations lost 9 of the 45 alleles (20%) found in the wild population. The reduced allele diversity suggests that the Chinese bay scallop populations experienced a bottleneck in genetic diversity that remains significant despite several recent introductions of new stocks aimed at expanding the gene pool. The loss of allele diversity may affect future efforts in selective breeding and domestication, and results of this study highlight the need for additional introductions, advanced breeding programs that minimize inbreeding and continued genetic monitoring. (c) 2007 Elsevier B.V. All rights reserved.

Genetic structure analysis of natural Sargassum muticum (Fucales, Phaeophyta) populations using RAPD and ISSR markers

Sargassum muticum is important in maintaining the structure and function of littoral ecosystems, and is used in aquaculture and alginate production, however, little is known about its population genetic attributes. In this study, random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers were used to investigate the genetic structure of four populations of S. muticum and one outgroup of S. fusiforme (Harv.) Setchell from Shandong peninsula of China. The selected 24 RAPD primers and 19 ISSR primers amplified 164 loci and 122 loci, respectively. Estimates of genetic diversity with different indicators (P%, percentage of polymorphic loci; H, the expected heterozygosity; I, Shannon's information index) revealed low or moderate level of genetic variations within each S. muticum population, and a high level of genetic differentiations were determined with pairwise unbiased genetic distance (D) and fixation index (F-ST ) among the populations. The Mantel test showed that two types of matrices of D and F-ST were highly correlated whether from RAPD (r = 0.9706, P = 0.009) or ISSR data (r = 0.9161, P = 0.009). Analysis of molecular variance (AMOVA) was conducted to apportion the variations among and within the S. muticum populations. It indicated that variations among populations were higher than those within populations, being 55.82% verse 44.18% by RAPD and 55.21% verse 44.79% by ISSR, respectively. Furthermore, the Mantel test suggested that genetic differentiations among populations were related to the geographical distances (r > 0.6), namely, conformed to the IBD (isolation by distance) model, as expected from UPGMA (unweighted pair group method with arithmetic averages) cluster analysis. On the whole, the high genetic structuring among the four S. muticum populations along the distant locations was clearly indicated in RAPD and ISSR analyses (r > 0.9, P < 0.05) in our study.

Population genetic structure of Sargassum thunbergii (Fucales, Phaeophyta) detected by RAPD and ISSR markers

Genetic variation of four populations of Sargassum thunbergii (Mert.) O. Kuntze and one outgroup of S. fusiforme (Harv.) Setchell from Shandong peninsula of China was studied with random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. A total of 28 RAPD primers and 19 ISSR primers were amplified, showing 174 loci and 125 loci, respectively. Calculation of genetic diversity with different indicators (P%, percentage of polymorphic loci; H, the expected heterozygosity; I, Shannon's information index) revealed low or moderate levels of genetic variations within each S. thunbergii population. High genetic differentiations were determined with pairwise Nei's unbiased genetic distance (D) and fixation index (F-ST) between the populations. The Mantel test showed that two types of matrices of D and FST were highly correlated, whether from RAPD or ISSR data, r=0.9310 (P = 0.008) and 0.9313 (P=0.009) respectively. Analysis of molecular variance (AMOVA) was used to apportion the variations between and within the S. thunbergii populations. It indicated that the variations among populations were higher than those within populations, being 57.57% versus 42.43% by RAPD and 59.52% versus 40.08% by ISSR, respectively. Furthermore, the Mantel test suggested that the genetic differentiations between the four populations were related to the geographical distances (r > 0.5), i.e., they conformed to the IBD (isolation by distance) model, as expected from UPGMA (unweighted pair group method with arithmetic averages) cluster analysis. As a whole, the high genetic structuring between the four S. thunbergii populations along distant locations was clearly indicated in the RAPD and ISSR analyses (r > 0.8) in our study.

QTL Mapping for Frond Length and Width in Laminaria japonica Aresch (Laminarales, Phaeophyta) Using AFLP and SSR Markers

In Laminaria japonica Aresch breeding practice, two quantitative traits, frond length (FL) and frond width (FW), are the most important phenotypic selection index. In order to increase the breeding efficiency by integrating phenotypic selection and marker-assisted selection, the first set of QTL controlling the two traits were determined in F-2 family using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers. Two prominent L. japonicas inbred lines, one with "broad and thin blade" characteristics and another with "long and narrow blade" characteristics, were applied in the hybridization to yield the F-2 mapping population with 92 individuals. A total of 287 AFLP markers and 11 SSR markers were used to construct a L. japonica genetic map. The yielded map was consisted of 28 linkage groups (LG) named LG1 to LG28, spanning 1,811.1 cM with an average interval of 6.7 cM and covering the 82.8% of the estimated genome 2,186.7 cM. While three genome-wide significant QTL were detected on LG1 (two QTL) and LG4 for "FL," explaining in total 42.36% of the phenotypic variance, two QTL were identified on LG3 and LG5 for the trait "FW," accounting for the total of 36.39% of the phenotypic variance. The gene action of these QTL was additive and partially dominant. The yielded linkage map and the detected QTL can provide a tool for further genetic analysis of two traits and be potential for maker-assisted selection in L. japonica breeding.

Genetic analysis of the gametophytes of Undaria pinnatifida (Phaeophyceae) with ISSR method

Inter-simple sequence repeat (ISSR) analysis was used to assess eleven pairs of Undaria pinnatifida (Harv.) Suringar male and female gametophytes. After screening fifty primers, 18 ISSR primers were selected for final analysis. A total of 104 loci were obtained, of which 77 were polymorphic, among the gametophytes studied. Genetic relationships were analyzed with simple matching (S), Jaccard's (J) and Dice's (D) distance coefficients. Little genetic variations were found among the selected Undaria gametophytes, for instance, the genetic distances ranging from 0.010 to 0.125 with Dice coefficients. UPGMA dendrograms showed that 11 pairs of Undaria gametophytes were distributed into five groups. Most Undaria strains cultivated in China exhibited closely genetic relationships with the strains from Japan. However, gametophytes from Qingdao appeared as distinct clades from other Undaria strains with all three distance coefficients used. Mantel test showed that the three distance measurements generated congruent clustering patterns on the same data. Our results demonstrated the feasibility of applying ISSR markers for genetic analysis of Undaria gametophytes. (c) 2006 Elsevier B.V. All rights reserved.

羊栖菜养殖品系DNA指纹分析及遗传变异的研究

羊栖菜是重要的大型经济海藻之一，在食品、医药、化工领域都有广泛应用。本研究对羊栖菜养殖生产中常见的品系“鹿丰1号”及另外2种品系进行了DNA指纹分析及遗传变异的研究，构建了遗传指纹图谱，分析了不同种群的遗传关系，为羊栖菜的种质鉴定及遗传选育提供了理论依据。 运用RAPD分子标记技术，对5个羊栖菜的种群中共125个个体进行了分析，从300个引物中筛选出12条随机扩增引物共扩增135个位点，多态位点比率为84.4%。从中选择了4个多态性位点，构建了5种羊栖菜DNA指纹图谱，并获得了“鹿丰1号”SCAR标记。另外，进行了5种羊栖菜种群的遗传背景的分析，结果表明“鹿丰1号”与品系2可以明显的与野生种群分开。根据Dice常数计算所得的5个种群的遗传距离在0.1116-0.2563之间。 运用ISSR分子标记技术，对5个种群的125个羊栖菜个体进行分析，通过90条引物的筛选，获得10条ISSR引物，扩增出92个位点，多态位点比率为67.4%。5个种群的遗传距离在0.0863-0.1454之间。 本研究以铜藻作为外群，通过2种遗传标记分析，证明铜藻与5种羊栖菜种群的遗传距离均远远大于其种群之间的遗传距离；另外，“鹿丰1号”不同年份的种群之间的遗传距离均为其中的最小值，相关结果对羊栖菜遗传选育和种质鉴定等有参考价值。

马尾藻种群遗传及早期发育的研究

本研究运用RAPD和ISSR两种分子标记技术，对采自山东半岛4个不同地理位置的鼠尾藻（Sargassum thunbergii）和海黍子（S. muticum）种群进行了遗传多样性和遗传结构的研究，从而对其种群间的地理隔离、基因流动水平及其影响因素做出估计和判断，为马尾藻自然资源的保护和开发提供依据。在室内对鼠尾藻有性生殖幼苗的早期发育和生长进行了研究，了解其繁殖生物学特性，为鼠尾藻人工种苗的培育提供依据。主要研究结果如下： 对4个鼠尾藻（S. thunbergii）地理种群的遗传多样性研究中，筛选出了28条RAPD 引物和19条ISSR引物，分别扩增产生了174和125个位点。选用的三种不同指标，即多态位点比率（P％，percentage of polymorphic loci），平均预期杂合度（H，the expected heterozygosity）和 Shannon's 信息多样性指数（I，Shannon's information index），均可反映出鼠尾藻种群内部的遗传多样性呈较低水平。而群体间遗传距离（D，Nei’s unbiased genetic distance）矩阵和固定化指数（FST,the fixation index）矩阵均反映出群体间高度的遗传分化。通过分子变异分析（AMOVA，Analysis of molecular variance）来区分来自种群内部和种群之间的遗传变异，揭示出多数的遗传变异（57.57% 或59.52%）来自于鼠尾藻种群之间。另外，Mantel分析表明，4个鼠尾藻种群间的遗传分化与地理距离呈正相关（r>0.5），遵循传统的IBD（isolation by distance）模式，UPGMA（unweighted pair group method with arithmetic averages）聚类分析也反映出相似的结果。 对4个海黍子（S. muticum）地理种群遗传结构的研究中，筛选出的24条RAPD 引物和19条ISSR引物分别扩增出164和122个位点。遗传多样性评估结果表明，海黍子种群内部存在较低或者中等水平的遗传多样性，而D矩阵和FST 矩阵均显示种群间存在高水平的遗传分化。并且，发现D和FST 矩阵在RAPD和ISSR分析中均具有高且显著的相关性。AMOVA分析显示，种群之间的遗传变异高于种群内部。Mantel分析和UPGMA聚类分析均发现海黍子种群间的遗传分化遵循IBD模式，即与地理隔离呈正相关（r>0.6）。 并且，RAPD和ISSR分析的结果高度一致（r>0.9，P<0.05），均揭示4个海黍子种群之间存在高度的遗传分化。 对鼠尾藻有性生殖幼苗早期生长发育的研究结果表明，其早期发育过程属于马尾藻科（Sargassaceae）中典型的“8核1卵”型。在一定条件下培养两个月后，产生了1～2个小叶，幼苗的长度达2～3毫米。生长实验发现，温度（10, 15, 20, 25℃）和光照强度（9, 18, 44, 88 µEm-2s-1）对培养第一周幼苗的生长均有显著的影响（ANOVA, P<0.01）。在两个月的培养中，幼苗对温度和光强的耐受范围较宽，在10℃～25℃，9～88 µEm-2s-1条件下均可生长，最适温度和光强为25℃，44 µEm-2s-1；低温（10℃）对幼苗的生长有显著抑制。不同光质对幼苗生长的影响显著（P<0.01），相同光强条件下，蓝光和白光相比较，蓝光显然不能满足鼠尾藻幼苗早期生长的需要。

ISSR analysis of genetic diversity of the Qinghai-Tibet Plateau endemic, Rhodiola chrysanthemifolia (Crassulaceae)

Inter-simple sequence repeat markers (ISSR) were used to estimate genetic diversity within and among 10 populations of Rhodiola chrysanthemifolia along Nianqingtangula Mountains and Brahmaputra, a species endemic to the Qinghai-Tibet Plateau and an endangered medicinal plant. Of the 100 primers screened, 13 produced highly polymorphic DNA fragments. Using these primers, 116 discernible DNA fragments were generated of which 104 (89.7%) were polymorphic, indicating substantial genetic diversity at the species level. Genetic diversity measured by the percentage of polymorphic bands (PPB) at the population level ranged from 21.97% to 48.8%. Analysis of molecular variance (AMOVA) showed that the genetic variation was found mainly among populations (77.3%), but no regional differentiation was discernible. Variance within populations was only 22.7%. The main factor responsible for this high level of differentiation among populations is probably the historical geographical and genetic isolation of populations in a harsh mountainous environment. Concerning the management of R. chrysanthemifolia, the high genetic differentiation of populations indicates the necessity of conserving the maximum possible number of populations. (c) 2006 Elsevier Ltd. All rights reserved.