The impact of chromosome sorting and painting on the comparative analysis of primate genomes

Chromosome sorting by flow cytometry is the main source of chromosome-specific DNA for the production of painting probes. These probes have been used for cross-species in situ hybridization in the construction of comparative maps, in the study of karyotype evolution and phylogenetics, in delineating territories in interphase nuclei, and in the analysis of chromosome breakpoints. We review here the contributions that this technology has made to the analysis of primate genomes. Copyright (C) 2005 S. Karger AG, Basel.

Independent Transport and Sorting of Functionally Distinct Protein Families in Tetrahymena thermophila Dense Core Secretory Granules

Dense core granules (DCGs) in Tetrahymena thermophila contain two protein classes. Proteins in the first class, called granule lattice (Grl), coassemble to form a crystalline lattice within the granule lumen. Lattice expansion acts as a propulsive mechanism during DCG release, and Grl proteins are essential for efficient exocytosis. The second protein class, defined by a C-terminal beta/gamma-crystallin domain, is poorly understood. Here, we have analyzed the function and sorting of Grt1p (granule tip), which was previously identified as an abundant protein in this family. Cells lacking all copies of GRT1, together with the closely related GRT2, accumulate wild-type levels of docked DCGs. Unlike cells disrupted in any of the major GRL genes, Delta GRT1 Delta GRT2 cells show no defect in secretion, indicating that neither exocytic fusion nor core expansion depends on GRT1. These results suggest that Grl protein sorting to DCGs is independent of Grt proteins. Consistent with this, the granule core lattice in Delta GRT1 Delta GRT2 cells appears identical to that in wild-type cells by electron microscopy, and the only biochemical component visibly absent is Grt1p itself. Moreover, gel filtration showed that Grl and Grt proteins in cell homogenates exist in nonoverlapping complexes, and affinity-isolated Grt1p complexes do not contain Grl proteins. These data demonstrate that two major classes of proteins in Tetrahymena DCGs are likely to be independently transported during DCG biosynthesis and play distinct roles in granule function. The role of Grt1p may primarily be postexocytic; consistent with this idea, DCG contents from Delta GRT1 Delta GRT2 cells appear less adhesive than those from the wild type.

Roles of sorting and chemical weathering in the geochemistry and magnetic susceptibility of Xiashu loess；East China

IEECAS SKLLQG

Effects of the initial size, stocking density and sorting on the growth of juvenile Pacific abalone, Haliotis discus hannai Ino

During winter months, a novel overwintering mode of transferring juvenile abalones to open seawaters in southern China rather than keeping them in closed land-based nursery systems in northern China is a popular practice. The initial size, stocking density and sorting are among the first considerations when establishing an abalone culture system. This study aimed to investigate the effects of these factors on the growth of juvenile Pacific abalone, Haliotis discus hannai Ino, during overwintering. Juvenile abalones were reared in multi-tier basket form for overwintering in open seawaters in southern China for 106 days. The daily growth rates (DGRs) in the shell length of all experimental groups ranged from 67.08 to 135.75 mu m day(-1), while the specific growth rates (SGRs) were 0.2447-0.3259% day(-1). Variance analysis indicated that both DGRs and SGRs in shell length were significantly affected by the initial body size and stocking density. Furthermore, the effects of stocking density on DGRs and SGRs varied with the initial size. However, sorting abalones according to their initial sizes may not be necessary in practice as sorting did not alter growth significantly at all densities in this study. Factors potentially affecting abalone growth such as genetic control and intraspecific competition were discussed.

Experimental Study on Flow and Sediment Movement in Cavity Circulations

This paper reports a flume experiment of flow and sediment movement in a cavity. The flow velocity, sediment concentration and the mechanism of hydraulic sorting in the circulation flow are discussed. The quantity and patterns of sediment deposition in the circulation area are studied as well.

DC dielectrophoretic focusing of particles in a serpentine microchannel

Focusing particles into a tight stream is usually a necessary step prior to separating and sorting them. We present herein a proof-of-concept experiment of a novel particle focusing technique in DC electrokinetic flow through a planar serpentine microchannel. This focusing stems from the cross-stream dielectrophoretic motion induced within the channel turns. The observed particle focusing behavior is consistent with the predicted particle trajectories from a numerical modeling.

木根麦冬rRNA基因进化的研究

木根麦冬（Ophiopogon xylorrhizus Wang et Dai）属于铃兰科（Convallariaceae）或广义百合科（Liliaceae s.l.）沿阶草族（Ophiopogoneae）沿阶草属（Ophiopogon Ker-Gawl.），属于典型的濒危植物。前人已从细胞学、种群生态学、生殖生物学和遗传结构与多样性等方面对木根麦冬进行了研究，但在分子进化和分子细胞遗传学水平上的研究近为空白。本文运用染色体的荧光原位杂交(FISH)、PCR扩增和克隆、DNA测序、系统发育重建等方法，对18S rDNA作了染色体原位定位，研究了木根麦冬的Ss rRNA基因结构特点，并重建了该基因的系统发育树，探讨了5S rRNA多基因家族的分子进化模式和木根麦冬的濒危机制。主要结果如下： 1．对木根麦冬三个居群七个个体、及其最近姐妹种林生麦冬（Ophiopogon svlvicola Wang et Tang）一个个体的5S rRNA基因进行了PCR扩增和TA克隆，在两个种中共得到1085个具有插入片段的阳性克隆。 2．对木根麦冬三个居群六个个体的294个SS rRNA基因克隆，及林生麦冬一个个体的45个克隆，总计339个克隆进行了DNA序列测定，这是目前已完成的最大的单个物种的5S rRNA数据。结果表明：两个种的序列高度多样化，在339个拷贝中仅仅有13对(3.8%)是相同的，序列长度变化在307bp-548bp之间，长度变异主要发生在间隔区，单个碱基的插入和缺失(indel)频率很高，5bp以上片段的插入，缺失有11个，插入的序列通常是其两侧序列的重复和倒位。术根麦冬序列的分化指数（sequence differentiation index，SDI）是0.078，林生麦冬是0.032，两个物种间是0.149，木根麦冬的序列之间的分化明显大于林生麦冬。 3．以PAUP程序对339个5S rRNA基因拷贝的DNA序列（包括编码区和间隔区）作了系统发育分析，结果如下：在得到一个唯一的最俭约树中，所有木根麦冬的拷贝被聚成一支，而林生麦冬的则被聚到另一支，统计支持率(bootstrap)达到lOO%，表明这两个物种所有的的5S rRNA基因拷贝分别来自各自的一个祖先拷贝（建立者拷贝），而其共同祖先的其它拷贝则在物种形成中或之后丢失：在多基因家族中如此长期而单一的拷贝偏选( sorting)过程尚未有前人报道;由此基因系统发育树可以看出，在这两个物种形成之后，“建立者拷贝”经历了多次扩增过程而形成了一个直系的（orthologous）多基因家族。 4．在木根麦冬分支中，很少有亚分支是全部由一个居群或一个个体的拷贝组成的，不同居群、不同个体的拷贝混合在同一个亚分支中;对基因系统发育树、序列多样性和序列分化指数分析表明，5S rRNA基因家族内一致化（homogeruzation）过程很弱，不同拷贝是独立进化的，这在串联．重复的多拷贝基因家族中是不寻常的;由上述分析我们推测，在术根麦冬的进化历史上，居群间的基因交流远远比今天频繁，可能是某些外在因素在近期发生变化，导致自交和自交衰退，并进而导致濒危。 5．利用荧光原位杂交技术，成功地将18S rRNA基因定位在木根麦冬减数分裂期的染色体上，两对强信号和一对弱信号分别位于三对二价体染色体上。

A COMPARATIVE-STUDY OF KARYOTYPES OF MUNTJACS BY CHROMOSOME PAINTING

We have used a combination of chromosome sorting, degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR), chromosome painting and digital image capturing and processing techniques for comparative chromosome analysis of members of the genus Muntiacus. Chromosome-specific ''paints'' from a female Indian muntjac were hybridised to the metaphase chromosomes of the Gongshan, Black, and Chinese muntjac by both single and three colour chromosome painting. Karyotypes and idiograms for the Indian, Gongshan, Black and Chinese muntjac were constructed, based on enhanced 4', 6-diamidino-2-phenylindole (DAPI) banding patterns. The hybridisation signal for each paint was assigned to specific bands or chromosomes for all of the above muntjac species. The interspecific chromosomal homology was demonstrated by the use of both enhanced DAPI banding and comparative chromosome painting. These results provide direct molecular cytogenetic evidence for the tandem fusion theory of the chromosome evolution of muntjac species.

Localization of Sry gene on Y chromosome of Muntjac munticus vaginalis

The chromosomes 1, Y-1, Y-2 of Muntjac munticus vaginalis were isolated by fluorescence activated chromosome sorting and amplified by degenerate oligonucleotide primed-polymerase chain reaction ( DOP-PCR). A primer pair within human Sry HMG box was design

The first non-mammalian CXCR3 in a teleost fish: Gene and expression in blood cells and central nervous system in the grass carp (Ctenopharyngodon idella)

A novel fish chemokine receptor gene, chemokine (C-X-C motif) receptor 3 (CXCR3)-like was isolated from the grass carp Ctenopharyngodon idella , with its full-length genomic sequence. The cDNA of grass carp CXCR3-like (gcCXCR3-like) consists of 1261 bp with a 49bp 5'-UTR and a 189 bp 3'-UTR. An open reading frame of 1023 bp encodes a 341-amino acid peptide, with seven transmembrane helices. The deduced amino acid sequence showed the same sequence identities (37.8%) with its counterparts in goat and human. The gcCXCR3-like gene consists of two exons, with one intervening intron, spaced over approximately 2 kb of genomic sequence. Phylogenetic analyses clearly demonstrated that the gcCXCR3-like resembles the CXCR3s of other vertebrates. Real-time PCR analysis showed that gcCXCR3-like was expressed in all tested organs except heart and the expression level of gcCXCR3-like was highest in brain. Flow cytometric analyses showed the positive rate of labelled leukocytes from the healthy grass carp was 17.3%, and the labelled leukocytes were divided into three types by cell sorting. Immunohistochemical localization revealed that gcCXCR3-like expressed in whole brain regions including cerebel, diencephalon, medulla oblongata, optic lobe, and rhinencephalon, and that the labelled leukocytes are actually populations of monocyte and/or phagocyte, lymphocyte and the granulocyte. It is considered that fish CXCR expression and their function may need to be investigated in both nervous and immune systems. (c) 2006 Elsevier Ltd. All rights reserved.

cDNA cloning and characterization of a novel SNX gene differentially expressed in previtellogenic oocytes of gibel carp

To understand the molecular events governing fish oogenesis, a multiple technique was used to identify the genes differentially expressed at different phases during fish oogenesis. This technique is a combination of suppression subtractive hybridization, SMART cDNA synthesis and RACE-PCR. Here we report the cDNA cloning and expression characterization of a novel SNX gene based on its differential transcription between previtellogenic and fully mature oocytes in naturally gynogenetic gibel carp. First, a cDNA fragment selectively expressed in previtellogenic oocytes was identified and used to screen a SMART cDNA library prepared from the same mRNA sample by RACE-PCR for cloning fully length cDNA. The full length cDNA was 1392-bp long and coded for a novel SNX protein with 225 amino acids. The 5' UTR had 72 bp and 3' UTR had 642 bp. Unlike most of maternal genes that are transcribed after vitellogenesis and stored in oocytes, this gene is expressed at a higher level in the previtellogenic oocytes and at a much lower level in fully matured oocytes. However, RT-PCR analysis of tissues showed it was ubiquitous transcription. The novel gene is named fish sorting nexin (fSNX), because it contains a conserved PX domain. The fact which major expression of the gene occurs in the previtellogenic oocytes suggests that it might have an important function in the oogenesis. (C) 2003 Elsevier Inc. All rights reserved.

A Simplified Soft-output QRD-M MIMO Detector

In this paper, a low-complexity soft-output QRD-M detection algorithm is proposed for high-throughput Multiple-input multiple-output (MIMO) systems. By employing novel expansion on demand and distributed sorting scheme, the proposed algorithm can reduce 70% and 85% foundational operations for 16-QAM and 64-QAM respectively compared to the conventional QRD-M algorithm. Furthermore, the proposed algorithm can yield soft information to improve the bit error rate (BER) performance. Simulation results show that the proposed algorithm can achieve a near-NIL detection performance with less foundational operations

The effects of sediment transport on grain-size distributions

Changes in statistics (mean, sorting, and skewness) describing grain-size distributions have long been used to speculate on the direction of sediment transport. We present a simple model whereby the distributions of sediment in transport are related to their source by a sediment transfer function which defines the relative probability that a grain within each particular class interval will be eroded and transported. A variety of empirically derived transfer functions exhibit negatively skewed distributions (on a phi scale). Thus, when a sediment is being eroded, the probability of any grain going into transport increases with diminishing grain size throughout more than half of its size range. This causes the sediment in transport to be finer and more negatively skewed than its source, whereas the remaining sediment (a lag) must become relatively coarser and more positively skewed. Flume experiments show that the distributions of transfer functions change from having a highly negative skewness to being nearly symmetrical (although still negatively skewed) as the energy of the transporting process increases. We call the two extremes low-energy and high-energy transfer functions , respectively. In an expanded sediment-transport model, successive deposits in the direction of transport are related by a combination of two transfer functions. If energy is decreasing and the transfer functions have low-energy distributions, successive deposits will become finer and more negatively skewed. If, however, energy is decreasing, but the initial transfer function has a high-energy distribution, successive deposits will become coarser and more positively skewed. The variance of the distributions of lags, sediment in transport, and successive deposits in the down-current direction must eventually decrease (i.e., the sediments will become better sorted). We demonstrate that it is possible for variance first to increase, but suggest that, in reality, an increasing variance in the direction of transport will seldom be observed, particularly when grain-size distributions are described in phi units. This model describing changes in sediment distributions was tested in a variety of environments where the transport direction was known. The results indicate that the model has real-world validity and can provide a method to predict the directions of sediment transport