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.     

Identification of two mariner-like elements in the genome of the mosquito Ochlerotatus atropalpus

Two distinct mariner-like elements, Atmar-1 and Atmar-2, were isolated from the genome of the mosquito Ochlerotatus atropalpus. Full-sized Atmar-1 elements, obtained by screening a genomic library, have a 1293-bp consensus sequence with 27-bp inverted terminal repeats and a 1047-bp open reading frame (ORF) encoding the transposase. The Atmar-2 elements were amplified by polymerase chain reaction from genomic DNA and contain the central part of the transposase ORF. Individual clones of both mariner elements contain deletions, frameshifts, and stop codons. The Atmar-1 elements are present in 370-1200 copies, while the Atmar-2 elements are present in approximately 100-300 copies per haploid genome. One of the Atmar-1 elements, Atmar-1.33, could be mobilized, suggesting the presence of functional Atmar-1 elements elsewhere in the genome. Phylogenetic analysis demonstrated that Atmar-1 elements belong to the irritans subfamily and Atmar-2 elements to the cecropia subfamily of mariner elements.     

Mobile elements in archaeal genomes

The recent availability of several archaeal genome sequences has provided a basis for detailed analyses of the frequency, location and phylogeny of archaeal mobile elements. All the known elements fall into two main types, autonomous insertion sequence (IS) elements and the non-autonomous miniature inverted repeat element (MITE)-like elements. Both classes are considered to be mobilized via transposases that are encoded by the IS elements, although mobility has only been demonstrated experimentally for a few elements. The number, and diversity, of the elements differs greatly between the genomes. At one extreme Sulfolobus solfataricus P2 and Halobacterium NRC-1 are very rich in elements while Methanobacterium thermoautotrophicum contains none. The former also show examples of complex clusters of interwoven elements. An analysis of the genomic distribution in S. solfataricus suggests that the putative oriC and terC regions act as barriers for the mobility of both IS and MITE-like elements. Moreover, the very high level of truncated IS elements in the genomes of S. solfataricus, Sulfolobus tokodaii and Thermoplasma volcanium suggests that there may be a cellular mechanism for selectively inactivating IS elements at a point when they become too numerous and disadvantageous for the cell. Phylogenetically, archaeal IS elements are confined to 11 of the 17 known families of bacterial and eukaryal IS elements where some generate distinct subgroups. Finally, DNA viruses, plasmids and DNA fragments can also be inserted into, and excised from, archaeal genomes by means of an integrase-mediated mechanism that has special archaeal characteristics.     

畜禽钙磷和微量元素营养研究进展

矿物元素在畜禽生长发育、新陈代谢、神经活动、免疫功能、内分泌等几乎所有的生命活动过程中都发挥着重要的生理作用,分为钙、磷、钠、镁等常量元素和铁、锰、钴、铜等微量元素。某种矿物元素摄入不足或在体内过量蓄积、矿物元素间比例失调,都将引起严重后果。随着畜禽养殖业的集约化规模化发展,饲用矿物元素用量迅速增加,但存在不合理使用的情况,造成了资源浪费和环境污染。因此,在满足畜禽营养需要量的前提下,合理地使用矿物元素剂型及剂量,实现降低矿物元素经畜禽粪污向环境中的排放量,不仅利于集约化畜禽养殖业的发展,同时也能有效降低畜禽粪污中的重金属含量,为种植业提供优良的有机肥来源,维护生态系统的平衡,促进种植业和养殖业的可持续健康发展。基于此,以畜禽体内含量最高的常量元素钙磷和微量元素为切入点,介绍了饲用矿物元素的应用现状、畜禽矿物元素基础需要量及合适的添加范围,着重综述了新型饲用微量元素的开发与应用进展,并探讨了矿物元素动态饲喂模式的可行性及有效性,以期为合理利用矿物元素资源及进一步解决全球生态农业研究的畜禽矿物元素导致的环境污染提供参考。     

Study on the Convergent Passages of Water Conducting Elements in Secondary Xylem of Fagaceae

Structural variations in the convergent passages of water conducting elements were described in secondary xylem of 70 species of Fagaceae. Two types of water conducting systems were recognized on the ground of water-flow directions. The convergent passages of the longitudinal system mainly exhibited in the forms as perforations between the ends of Vessel elements, lateral wall pitting between the lateral walls of vessel elements, pitting be-tween vessel elements and imperforate tracheary elements, and pitting between imperforate tracheary elements. The convergent passages in the transverse system consisted of pitting between vessel elements and ray cells, pitting between imperforated tracheary elements and ray cells and simple pitting between ray cells. In addition, the roles of vasicentric tracheids and broad rays played in terms of conducting effectiveness and efficiency as proposed by Zimmermann were discussed.     

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.     

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.     

Supernumerary chromosomal elements in lymphocytes cultured from phenotypically normal human adult males

In a group of phenotypically normal men there were approximately 0.24% of metaphase lymphocytes with extra chromosomal elements along with the regular 46 chromosomes. They ranged in size from small acrocentric-acentric elements to elements longer than any chromosome arm. These elements have been referred to as supernumerary chromosomal elements. No significant effects due to donor's age, smoking history, season, storage of blood samples prior to culture, or culture medium, were found either in the frequency of supernumerary elements per cell or in the frequency of cells with supernumerary elements. Furthermore, the same subject did not consistently exhibit supernumerary elements. Furthermore, the same subject did not consistently exhibit supernumerary elements when sampled during four successive quarters of the year. Some of these elements in pairs were identified by G-banding technique as translocation chromosomes bearing long arms of chromosome number 2 and presumptive short arms of chromosome 8, acentric long arms of chromosome 4, and iso-acentric chromosomes for the long arms of chromosome 5. Presumably, more than one type of cytogenetic event occurred in their formation. Circumstantial evidence has been presented to show that the means of elimination of these supernumerary elements is a process of chromosomal disintegration.     

Stowaway MITEs in Hordeum (Poaceae): evolutionary history, ancestral elements and classification

Given the lack of direct observational data relating to transposition of Stowaway miniature inverted repeat transposable elements, phylogenetic methods may provide a means of generating data that adds to our knowledge of these elements. In a phylogenetic framework the evolutionary history of homologous elements may be traced, and the nucleotide sequence of elements at or close to the time of insertion can be reconstructed. Based on a phylogeny of the diploid species of the genus Hordeum we explore evolutionary aspects of four non-homologous groups of Stowaway elements inserted into three nuclear genes: nucellin, xylose isomerase, and barley leucine zipper 1. The data illustrate how elements starting from a high degree of sequence similarity between terminal inverted repeat regions gradually degrade, and confirm previous notions about preferential insertion at particular TA target sites. It is shown how creation of consensus sequences as estimates of ancestral elements may be positively misleading. The Stowaway family of transposable elements is often further divided into subfamilies based on sequence similarity between elements. Sequence similarity data from the elements discovered in the xylose isomerase gene, and other elements found through BLAST searches in GenBank, reveal inconsistency in the rules used for classification. In order to reflect natural groups, a classification of transposable elements must be based on phylogenetic evidence rather than raw similarity.  © The Willi Hennig Society 2009.     

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.     

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.     

贵州两栖动物区系及地理区划的初步研究

本文报道贵州省两栖动物63种,其中省新纪录2种,即阔褶蛙和锯腿树蛙。将贵州划分为黔西高原中山、黔北中山峡谷、黔中山原丘陵、黔东南低山丘陵盆地和黔南低山河谷五个动物地理省。认为黔南低山河谷省属于向华南区过渡的华中地带。讨论了各动物地理省的地貌、气候、两栖动物区系特征及地理替代种类。分析了各动物地理省两栖动物区系的相似性及数量关系。     

壳斗科次生木质部水分输导分子间连接通道结构的研究

壳斗科次生木质部水分运输聚合体及其连接通道结构,根据水分运输方向可分纵向和横向两大系统。水分纵向运输通道有导管分子间的穿孔,导管分子侧壁间的管间纹孔,导管分子与无穿孔管状分子间的侧壁纹孔,无穿孔管状分子与无穿孔管状分子间的侧壁纹孔。     

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.     

Evolution of the LINE-like I element in the Drosophila melanogaster species subgroup

LINE-like retrotransposons, the so-called I elements, control the system of I-R (inducer-reactive) hybrid dysgenesis in Drosophila melanogaster. I elements are present in many Drosophila species. It has been suggested that active, complete I elements, located at different sites on the chromosomes, invaded natural populations of D. melanogaster recently (1920–1970). But old strains lacking active I elements have only defective I elements located in the chromocenter. We have cloned I elements from D. melanogaster and the melanogaster subgroup. In D. melanogaster, the nucleotide sequences of chromocentral I elements differed from those on chromosome arms by as much as 7%. All the I elements of D. mauritiana and D. sechellia are more closely related to the chromosomal I elements of D. melanogaster than to the chromocentral I elements in any species. No sequence difference was observed in the surveyed region between two chromosomal I elements isolated from D. melanogaster and one from D. simulans. These findings strongly support the idea that the defective chromocentral I elements of D. melanogaster originated before the species diverged and the chromosomal I elements were eliminated. The chromosomal I elements reinvaded natural populations of D. melanogaster recently, and were possibly introduced from D. simulans by horizontal transmission.     

Evolution of the LINE-like I element in the Drosophila melanogaster species subgroup

LINE-like retrotransposons, the so-called I elements, control the system of I-R (inducer-reactive) hybrid dysgenesis in Drosophila melanogaster. I elements are present in many Drosophila species. It has been suggested that active, complete I elements, located at different sites on the chromosomes, invaded natural populations of D. melanogaster recently (1920–1970). But old strains lacking active I elements have only defective I elements located in the chromocenter. We have cloned I elements from D. melanogaster and the melanogaster subgroup. In D. melanogaster, the nucleotide sequences of chromocentral I elements differed from those on chromosome arms by as much as 7%. All the I elements of D. mauritiana and D. sechellia are more closely related to the chromosomal I elements of D. melanogaster than to the chromocentral I elements in any species. No sequence difference was observed in the surveyed region between two chromosomal I elements isolated from D. melanogaster and one from D. simulans. These findings strongly support the idea that the defective chromocentral I elements of D. melanogaster originated before the species diverged and the chromosomal I elements were eliminated. The chromosomal I elements reinvaded natural populations of D. melanogaster recently, and were possibly introduced from D. simulans by horizontal transmission.     

Genomic organization and chromosomal distribution of rat ID elements.

Identifier (ID) elements are members of a family of short interspersed nuclear elements (SINEs) in rodents. We investigated the genomic organization and chromosomal distribution of the ID elements in the rat, mouse and Chinese hamster. Southern blot hybridization analysis revealed that the ID elements are widespread in the rat genome, but concentrated in the mouse and Chinese hamster genomes, and that the copy of ID elements in the rat is about 5 times and 50 times that in the mouse and Chinese hamster, respectively. FISH analysis showed that the ID elements are predominantly distributed in the R-band regions of rat chromosomes. In mouse and Chinese hamster chromosomes, no specific distribution pattern of the ID elements was found. Furthermore, we found a distinct group of derivative ID elements in the rat, which contain partially repeated ID core domains, by PCR amplification using an ID core sequence. Such derivatives were not found in either the mouse or Chinese hamster. These findings suggest that explosive amplification of the ID elements in the rat has been accompanied by the occurrence of derivative ID elements and a predominant localization to the R-band regions. Similar associations found in the Alu family, one of the human SINEs, allow us to speculate that the rat ID elements and the human Alu family have analogous functions in chromosomal organization.