Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation

Polyadenylation is an essential step for the maturation of almost all cellular mRNAs in eukaryotes. In human cells, most poly(A) sites are flanked by the upstream AAUAAA hexamer or a close variant, and downstream U/GU-rich elements. In yeast and plants, additional cis elements have been found to be located upstream of the poly(A) site, including UGUA, UAUA, and U-rich elements. In this study, we have developed a computer program named PROBE (Polyadenylation-Related Oligonucleotide Bidimensional Enrichment) to identify cis elements that may play regulatory roles in mRNA polyadenylation. By comparing human genomic sequences surrounding frequently used poly(A) sites with those surrounding less frequently used ones, we found that cis elements occurring in yeast and plants also exist in human poly(A) regions, including the upstream U-rich elements, and UAUA and UGUA elements. In addition, several novel elements were found to be associated with human poly(A) sites, including several G-rich elements. Thus, we suggest that many cis elements are evolutionarily conserved among eukaryotes, and human poly(A) sites have an additional set of cis elements that may be involved in the regulation of mRNA polyadenylation.     

Limitations of rapid parallel processing in the detection of long and short oriented line targets.

The purpose of this study was to determine whether the detectability of a uniquely oriented line element in a field of uniformly oriented line elements depends on element length. Displays containing various numbers of elements were presented briefly and followed by a mask. The length and orientation of the elements were varied. With longer (1.0-deg) elements, detection performance varied little with the number of elements present. With shorter (0.25-deg) elements, performance worsened as the element number increased, especially when the uniformly oriented elements were oblique. It seems that rapid spatially parallel processes facilitate detection of targets in many-element displays of long elements but not of short elements.     

Survey of transposable elements from rice genomic sequences

Oryza sativa L. (domesticated rice) is a monocotyledonous plant, and its 430 Mb genome has been targeted for complete sequencing. We performed a high-resolution computer-based survey for transposable elements on 910 Kb of rice genomic DNA sequences. Both class I and II transposable elements were present, contributing 19.9% of the sequences surveyed. Class II elements greatly outnumbered class I elements (166 versus 22), although class I elements made up a greater percentage (12.2% versus 6.6%) of nucleotides surveyed. Several Mutator-like elements (MULEs) were identified, including rice elements that harbor truncated host cellular genes. MITEs (miniature inverted-repeat transposable elements) account for 71.6% of the mined transposable elements and are clearly the predominant type of transposable element in the sequences examined. Moreover, a putative Stowaway transposase has been identified based on shared sequence similarity with the mined MITEs and previously identified plant mariner-like elements (MLEs). Members of a group of novel rice elements resembling the structurally unusual members of the Basho family in Arabidopsis suggest a wide distribution of these transposons among plants. Our survey provides a preview of transposable element diversity and abundance in rice, and allows for comparison with genomes of other plant species.     

奉节脐橙不同器官元素含量分布特征

对奉节脐橙果、叶、干、根中的必需大量元素 (N、K、Ca、Mg、P、S)、微量元素 (Fe、Mn、Cu、Zn、B、Mo)、有益元素 (Si、Co、F、Se、Ni、Sr)、有毒有害元素 (Hg、As、Cr、Cd、Pb、Sb、Bi)的分布特征进行分析 ,结果表明 :果、叶、干、根对各元素的吸收与富集特征具有明显的规律性 ,如叶、干、根中大量元素含量次序均为 Ca>N>K>Mg,叶、干、根中微量元素含量均有 Fe>Mn>Zn>Cu>Mo的规律 ,根、干、叶中有益微量元素含量次序均为 Si>Sr>F>Ni>Co>Se,叶、干、根中有毒有害元素含量次序均有 Pb>As>Sb >Hg的规律 ;在脐橙各器官中 ,叶是大量元素与有毒有害元素最富集的器官 ,根则是有益元素最富集的器官 ,有毒有害元素的 Cr、微量元素的 Mn、Fe、Mo也以根最为富集 ,干则是上述元素最不富集的器官 ,所有元素中 ,仅 Zn在干中最富集 ;大量元素 (除 N外 )、微量元素、有益元素在脐橙各器官的分配含量与地壳土壤背景值的分异含量趋势基本一致 ,土壤背景是这三类元素的主要控制因素。但有毒有害元素的分配形式则明显受人类活动的影响     

The potential of inductively coupled plasma mass spectrometry (ICP-MS) for the simultaneous determination of trace elements in whole blood, plasma and serum.

The advantages accruing to biochemical and clinical investigations from a method that allows the simultaneous quantification (RSD < or = 10%) of many elements in blood, plasma, and serum at concentrations equal to one-hundredth of the lower limits of the normal ranges are undeniable. The suitability of inductively coupled argon plasma low-resolution quadrupole mass spectrometry (ICP-MS), a simultaneous method with low detection limits, is evaluated for the quantification of inorganic constituents in whole blood, plasma, and serum with consideration of the dilution associated with the mineralization of the samples, of isobaric and polyatomic interferences and of normal ranges. Of the 3 bulk elements, the 3 major electrolytes, the 15 essential elements, the 8 toxic elements, the 4 therapeutic elements, and the 14 elements of potential interest (total of 47 elements) only 7 elements (Ca, Cu, K, Mg, Rb, Sr, Zn) can be simultaneously quantified under these rigorous conditions in serum and only 8 elements (additional element Pb) in whole blood. Quantification of elements in the Seronorm Standards "Whole Blood" and "Serum" showed, that this list of simultaneously determinable elements in these matrices is reasonable. Although this list is disappointingly short, the number of elements determinable simultaneously by ICP-MS is still larger than that by ICP-AES or GFAAS. Improved detectors, more efficient nebulizers, avoidance of interferences, better instrument design, and high-resolution mass spectrometers promise to increase the number of elements that can be determined simultaneously.     

辽宁碱蓬胆碱单加氧酶(CMO)基因启动子分离及功能元件分析

根据已知的辽宁碱蓬CMO cDNA 5′端序列设计两个基因特异的反向引物(CR1,CR2),通过衔接头PCR获得了CMO基因起始密码子上游498 bp的序列。根据所获得的序列设计两个基因特异的反向引物(CR3,CR4),用CR2、CR3、CR4分别与4个简并引物配对,通过TAIL-PCR扩增,获得了约2 kb的序列。经Sequencer软件拼接上述两段序列,获得了CMO基因起始密码子上游2,332 bp的序列。用TSSP-TCM软件分析此序列,预测出转录起始点(C)位于起始密码子上游128 bp处,由此我们获得了2,204 bp的SlCMO启动子序列。用PLACE软件分析此序列,发现该序列具有启动子的基本元件TATA-box、CAAT-box,包含多个胁迫诱导元件,如盐诱导元件GAAAAA,冷胁迫诱导元件CANNTG,ABA 响应因子NAACAA,水胁迫元件CGGTTG和伤害诱导元件GTTAGGTTC等,是一个强的胁迫诱导启动子。辽宁碱蓬胆碱单加氧酶基因盐诱导启动子的获得,为盐诱导启动子功能元件分析提供了可能,为进一步研究启动子结构与功能的相互关系、CMO基因的表达调控机制奠定了基础。     

云南罗平多依河景区苔藓植物区系研究

为了解云南罗平多依河景区的苔藓植物多样性和区系特征,对该区苔藓植物进行了调查,并对其区系地理成分进行了统计分析。结果表明,该区有苔藓植物34科59属116种(含变种和亚种),其优势科、属均反映了该苔藓区系以温带成分为主,并有部分热带亚热带成分。苔藓区系的地理成分复杂,以北温带分布型(27.03%)、热带亚洲分布型(25.23%)、东亚分布型(19.82%)和中国特有分布型(10.81%)占优势;以热带成分、北方温带成分和东亚成分为主导,分别占34.23%、35.14%和30.63%;反映了该苔藓植物区系温热并存且具有较高特有性的特征。与邻近13个地区的苔藓区系进行对比分析,多依河苔藓植物区系的物种丰富度较高(排第8位),与贵阳香纸沟的亲缘关系最近,这与两地相近的地理位置、海拔高度,以及相同的喀斯特河谷环境是分不开的。     

Enrichment for histone H3 lysine 9 methylation at Alu repeats in human cells

The aim of this study was to identify in human cells common targets of histone H3 lysine 9 (H3-Lys9) methylation, a modification that is generally associated with gene silencing. After chromatin immunoprecipitation using an H3-Lys9 methylated antibody, we cloned the recovered DNA and sequenced 47 independent clones. Of these, 38 clones (81%) contained repetitive elements, either short interspersed transposable element (SINE or Alu elements), long terminal repeat (LTR), long interspersed transposable element (LINE), or satellite region (ALR/Alpha) DNA, and three additional clones were near Alu elements. Further characterization of these repetitive elements revealed that 32 clones (68%) were Alu repeats, corresponding to both old Alu (23 clones) and young Alu (9 clones) subfamilies. Association of H3-Lys9 methylation was confirmed by chromatin immunoprecipitation-PCR using conserved Alu primers. In addition, we randomly selected 5 Alu repeats from the recovered clones and confirmed association with H3-Lys9 by PCR using primer sets flanking the Alu elements. Treatment with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine rapidly decreased the level of H3-Lys9 methylation in the Alu elements, suggesting that H3-Lys9 methylation may be related to the suppression of Alu elements through DNA methylation. Thus H3-Lys9 methylation is enriched at human repetitive elements, particularly Alu elements, and may play a role in the suppression of recombination by these elements.     

Topi, an IS630/Tc1/mariner-type transposable element in the African malaria mosquito, Anopheles gambiae

IS630/Tc1/mariner elements are diverse and widespread within insects. The African malaria mosquito, Anopheles gambiae, contains over 30 families of IS630/Tc1/mariner elements although few have been studied in any detail. To examine the history of Topi elements in An. gambiae populations, Topi elements (n=73) were sampled from five distinct populations of An. gambiae from eastern and western Africa and evaluated with respect to copy number, nucleotide diversity and insertion site-occupancy frequency. Topi 1 and 2 elements were abundant (10-34 per diploid genome) and highly diverse (pi=0.051). Elements from mosquitoes collected in Nigeria were Topi 2 elements and those from mosquitoes collected in Mozambique were Topi 1 elements. Of the 49 Topi transposase open reading frames sequenced none were found to be identical. Intact elements with complete transposase open reading frames were common, although based on insertion site-occupancy frequency data it appeared that genetic drift was the major force acting on these IS630/Tc1/mariner-type elements. Topi 3 elements were not recovered from any of the populations sampled in this study and appear to be rare elements in An. gambiae, possibly due to a recent introduction.     

西双版纳热带沟谷雨林中果蝇类及其食物无机化学元素特征的初步研究

本文对西双版纳热速 沟谷雨林中果蝇类（Drosophila属的11个种）及其食物（3种嗜食植物的果实和林下半腐枯落物）的19种无机化学元素含量进行了测定,果蝇体内测得其中15种无机化学元素,食物中测得其中14种化学元素,对无机化学元素的含量进行了分级,并对果蝇及其食物无机化学元素的组成和含量特征进行了分析和比较。     

Structure, divergence, and distribution of the CRR centromeric retrotransposon family in rice

The centromeric retrotransposon (CR) family in the grass species is one of few Ty3-gypsy groups of retroelements that preferentially transpose into highly specialized chromosomal domains. It has been demonstrated in both rice and maize that CRR (CR of rice) and CRM (CR of maize) elements are intermingled with centromeric satellite DNA and are highly concentrated within cytologically defined centromeres. We collected all of the CRR elements from rice chromosomes 1, 4, 8, and 10 that have been sequenced to high quality. Phylogenetic analysis revealed that the CRR elements are structurally diverged into four subfamilies, including two autonomous subfamilies (CRR1 and CRR2) and two nonautonomous subfamilies (noaCRR1 and noaCRR2). The CRR1/CRR2 elements contain all characteristic protein domains required for retrotransposition. In contrast, the noaCRR elements have different structures, containing only a gag or gag-pro domain or no open reading frames. The CRR and noaCRR elements share substantial sequence similarity in regions required for DNA replication and for recognition by integrase during retrotransposition. These data, coupled with the presence of young noaCRR elements in the rice genome and similar chromosomal distribution patterns between noaCRR1 and CRR1/CRR2 elements, suggest that the noaCRR elements were likely mobilized through the retrotransposition machinery from the autonomous CRR elements. Mechanisms of the targeting specificity of the CRR elements, as well as their role in centromere function, are discussed.     

Trace elements in agroecosystems and impacts on the environment.

Trace elements mean elements present at low concentrations (mg kg-1 or less) in agroecosystems. Some trace elements, including copper (Cu), zinc (Zn), manganese (Mn), iron (Fe), molybdenum (Mo), and boron (B) are essential to plant growth and are called micronutrients. Except for B, these elements are also heavy metals, and are toxic to plants at high concentrations. Some trace elements, such as cobalt (Co) and selenium (Se), are not essential to plant growth but are required by animals and human beings. Other trace elements such as cadmium (Cd), lead (Pb), chromium (Cr), nickel (Ni), mercury (Hg), and arsenic (As) have toxic effects on living organisms and are often considered as contaminants. Trace elements in an agroecosystem are either inherited from soil parent materials or inputs through human activities. Soil contamination with heavy metals and toxic elements due to parent materials or point sources often occurs in a limited area and is easy to identify. Repeated use of metal-enriched chemicals, fertilizers, and organic amendments such as sewage sludge as well as wastewater may cause contamination at a large scale. A good example is the increased concentration of Cu and Zn in soils under long-term production of citrus and other fruit crops. Many chemical processes are involved in the transformation of trace elements in soils, but precipitation-dissolution, adsorption-desorption, and complexation are the most important processes controlling bioavailability and mobility of trace elements in soils. Both deficiency and toxicity of trace elements occur in agroecosystems. Application of trace elements in fertilizers is effective in correcting micronutrient deficiencies for crop production, whereas remediation of soils contaminated with metals is still costly and difficult although phytoremediation appears promising as a cost-effective approach. Soil microorganisms are the first living organisms subjected to the impacts of metal contamination. Being responsive and sensitive, changes in microbial biomass, activity, and community structure as a result of increased metal concentration in soil may be used as indicators of soil contamination or soil environmental quality. Future research needs to focus on the balance of trace elements in an agroecosystem, elaboration of soil chemical and biochemical parameters that can be used to diagnose soil contamination with or deficiency in trace elements, and quantification of trace metal transport from an agroecosystem to the environment.     

Molecular cloning and phylogenetic analysis of the human endogenous retrovirus HERV-K long terminal repeat elements in various cancer cells

Long terminal repeats (LTRs) of the human endogenous retroviruses K family (HERV-K) have been found to affect expression of genes located nearby. It has been suggested that the HERV-K LTR elements contributed to the structural change in the genome and genetic variation connected to various diseases. We examined the HERV-K LTR elements in human cancer cells. Using genomic DNA from various cancer cells, we performed PCR amplification and identified forty-nine HERV-K LTR elements. Those LTR elements showed a high degree of sequence similarity with human-specific HERV-K LTR elements. A phylogenetic tree, obtained by the neighbor-joining method, revealed that twelve HERV-K LTR elements were closely related to human-specific HERV-K LTR elements. These elements proliferated recently and were detectable in many human cancer cell lines. These results suggest that HERV-K LTR could be implicated in a pathogenic role, although this phenomenon may not directly lead to human cancers. Further studies on the biological function and expression of HERV-K LTR elements in cancer cells are indicated.     

Evolutionary dynamics of the SGM transposon family in the Drosophila obscura species group

SGM (Drosophila subobscura, Drosophila guanche, and Drosophila madeirensis) transposons are a family of transposable elements (TEs) in Drosophila with some functional and structural similarities to miniature inverted-repeat transposable elements (MITEs). These elements were recently active in D. subobscura and D. madeirensis (1-2 MYA), but in D. guanche (3-4 MYA), they gave rise to a species-specifically amplified satellite DNA making up approximately 10% of its genome. SGM elements were already active in the common ancestor of all three species, giving rise to the A-type specific promoter section of the P:-related neogene cluster. SGM sequences are similar to elements found in other obscura group species, such as the ISY elements in D. miranda and the ISamb elements in Drosophila ambigua. SGM elements are composed of different sequence modules, and some of them, i.e., LS and LS-core, are found throughout the Drosophila and Sophophora radiation with similarity to more distantly related TEs. The LS-core module is highly enriched in the noncoding sections of the Drosophila melanogaster genome, suggesting potential regulatory host gene functions. The SGM elements can be considered as a model system elucidating the evolutionary dynamics of mobile elements in their arms race with host-directed silencing mechanisms and their evolutionary impact on the structure and composition of their respective host genomes.     

Novel fluorescence-based screen to identify small synthetic internal ribosome entry site elements

We report here a novel fluorescent protein-based screen to identify small, synthetic internal ribosome entry site (IRES) elements in vivo. A library of bicistronic plasmids encoding the enhanced blue and green fluorescent proteins (EBFP and EGFP) separated by randomized 50-nucleotide-long sequences was amplified in bacteria and delivered into mammalian cells via protoplast fusion. Cells that received functional IRES elements were isolated using the EBFP and EGFP reporters and fluorescence-activated cell sorting, and several small IRES elements were identified. Two of these elements were subsequently shown to possess IRES activity comparable to that of a variant of the encephalomyocarditis virus IRES element in a context-independent manner both in vitro and in vivo, and these elements functioned in multiple cell types. Although no sequence or structural homology was apparent between the synthetic IRES elements and known viral and cellular IRES elements, the two synthetic IRES elements specifically blocked poliovirus (PV) IRES-mediated translation in vitro. Competitive protein-binding experiments suggested that these IRES elements compete with PV IRES-mediated translation by utilizing some of the same factors as the PV IRES to direct translation. The utility of this fluorescent protein-based screen in identifying IRES elements with improved activity as well as in probing the mechanism of IRES-mediated translation is discussed.     

Subfamilies of CR1 non-LTR retrotransposons have different 5'UTR sequences but are otherwise conserved

CR1 elements and CR1-related (CR1-like) elements are a novel family of non-LTR retrotransposons that are found in all vertebrates (reptilia, amphibia, fish, and mammals), whereas more distantly related elements are found in several invertebrate species. CR1 elements have several features that distinguish them from other non-LTR retrotransposons. Most notably, their 3' termini lack a polyadenylic acid (poly A) tail and instead contain 2-4 copies of a unique 8 bp repeat. CR1 elements are present at approximately 100,000 copies in the chicken genome. The vast majority of these elements are severely 5' truncated and mutated; however, six subfamilies (CR1-A through CR1-F) are resolved by sequence comparisons. One of these subfamilies (i.e. CR1-B) previously was analyzed in detail. In the present study, we identified several full-length elements from the CR1-F subfamily. Although regions within the open reading frames and 3' untranslated regions of CR1-F and CR1-B elements are well conserved, their respective 5' untranslated regions are unrelated. Thus, our results suggest that new CR1 subfamilies form when elements with intact open reading frames acquire new 5' UTRs, which could, in principle, function as promoters.