Bioimaging of multiple elements by high‐resolution LA‐ICP‐MS reveals altered distribution of mineral elements in the nodes of rice mutants

Inter‐vascular transfer in rice (Oryza sativa) nodes is required for delivering mineral elements to developing tissues, which is mediated by various transporters in the nodes. However, the effect of these transporters on distribution of mineral elements in the nodes at a cellular level is still unknown. Here, we established a protocol for bioimaging of multiple elements at a cellular level in rice node by laser ablation‐inductively coupled plasma‐mass spectrometry (LA‐ICP‐MS), and compared the mineral distribution profile between wild‐type (WT) rice and mutants. Both relative comparison of mineral distribution normalized by endogenous ¹³C and quantitative analysis using spiked standards combined with soft ablation gave valid results. Overall, macro‐nutrients such as K and Mg were accumulated more in the phloem region, while micro‐nutrients such as Fe and Zn were highly accumulated at the inter‐vascular tissues of the node. In mutants of nodal Zn transporter OsHMA2, Zn localization pattern in the node tissues did not differ from that of WT; however, Zn accumulation in the inter‐vascular tissues was lower in uppermost node I but higher in the third upper node III compared with the WT. In contrast, Si deposition in the mutants of three nodal Si transporters Lsi2, Lsi3 and Lsi6 showed different patterns, which are consistent with the localization of these transporters. This improved LA‐ICP‐MS analysis combined with functional characterization of transporters will provide further insight into mineral element distribution mechanisms in rice and other plant species.     

Age-related attenuation in the elements in monkey sino-atrial node

Changes in trace elements of the sino-atrial (SA) node with aging was investigated using 24 hearts of the Japanese and rhesus monkeys of ages ranging from 27 d to 30 yr. With aging, sympathetic activity decreases and SA nodal function deterionates. The SA nodal tissue was removed from the anatomical position and was confirmed by means of histological observation. The elements, such as Ca, P, S, Mg, Na, Fe, and Zn, were analyzed using inductively coupled plasma-atomic emission spectrometry (ICP-AES). Advancing age never increased the contents of the trace elements, but decreased them. The correlation coefficients for the age-dependent attenuations were −0.561 (n=24, p<0.01) in Ca and −0.482 (n=24, p<0.05) in P. The correlations for the attenuations induced by other trace elements were not significant. Furthermore, close relationships of the elements between Ca and P, S, Zn, or Na contents, between P and Zn or Na contents, and between Zn and Na contents were observed. These results indicate that the elements in the monkey SA node are attenuated with an increase in age, presumably suggesting the age-related suppression of cardiac functions as a result of the histological alterations of the SA nodal cells.     

PACT: an efficient and powerful algorithm for generating area cladograms

Aim To introduce and describe the functioning of a new algorithm, phylogenetic analysis for comparing trees (PACT), for generating area cladograms that provide accurate representation of information contained in taxon–area cladograms. Methods PACT operates in the following steps. Convert all phylogenies to taxon–area cladograms. Convert all taxon–area cladograms to Venn diagrams. Choose any taxon–area cladogram from the set of taxon–area cladograms to be analysed and determine its elements. This will be the template area cladogram. Select a second taxon–area cladogram. Determine its elements. Document which elements in the second tree occur in the template tree (denoted by ‘Y’) and which do not (denoted by ‘N’). Each ‘Y’ indicates a match with previous pattern and these are combined. Each ‘N’ is a new element and is attached to the template area cladogram at the node where it is linked with a Y. This requires two rules: (1) ‘Y + Y = Y’ (combine common elements) as long as they are connected at the same node; and (2) ‘Y + N = YN’ (add novel elements to the template area cladogram at the node where they first appear). Once the novel elements in the second taxon–area cladogram have been added to the template area cladogram, see if any of them can be further combined. This requires three additional rules: (1) ‘Y(Y? = Y(Y?’ (do not combine Y's if they are attached at different nodes on the template area cladogram); (2) ‘Y + YN = YN’ (Y is part of group YN); and (3) ‘YN + YN = YNN’ (Y is the same for each, but each N is different). Repeat for all available taxon–area cladograms. Results Three exemplars demonstrate that PACT provides the most accurate area cladograms for vicariance‐driven biotic diversification, dispersal‐driven biotic diversification and taxon pulse‐driven biotic diversification. PACT can also be used as an a priori method of biogeographical analysis. Main conclusions PACT embodies all the strong points and none of the weaknesses of previously proposed methods of historical biogeography. It is most useful as an a posteriori method, but it is also superior to all previous a priori methods because it does not specify costs, or weights or probabilities, or likelihoods of particular biogeographical processes a priori and is thus sensitive to clade‐specific historical contingencies.     

Carpal development and morphology in archontan mammals

Carpal morphology and development in bats, colugos, tree shrews, murids, and sciurids were studied in order to homologize carpal elements. Prenatal coalescence of discrete cartilaginous templates with a loss of a center of ossification appears to be the most common method of reducing carpal elements in these mammals. Only bats and colugos showed postnatal ossification between discrete elements as a method of reducing carpal elements. Carpal morphology of tree shrews is more diverse than previously reported. Ptilocercus shows a highly derived carpal morphology that may be related to its relatively greater arboreality. Dendrogale exhibits what is most likely the ancestral tupaiid carpal morphology. Carpal morphologies of Tupaia, Urogale, and Anathana are identical to each other. Carpal morphology differs between megachiropterans and microchiropterans. These differences may be related to different aerodynamic constraints between the suborders. The carpal morphology of microchiropterans is diverse and may reflect different adaptive regimes between microchiropteran families. Carpal morphology of the colugos shows both megachiropteran and microchiropteran characters. The function of these characters in colugos and bats (stabilization of the carpus in dorsiflexion) is proposed to be similar, although the locomotor roles may be quite different between these taxa. J. Morphol. 235:135–155, 1998. © 1998 Wiley-Liss, Inc.     

中国主要农产品虚拟要素贸易网络结构特征分析

据虚拟水概念定义虚拟要素,并将其划分为虚拟资源要素和虚拟生态要素两类,选取虚拟资源要素中的耕地要素和虚拟生态要素中的化肥/农药要素为研究对象,定量分析2002—2016年以粮食贸易为载体的虚拟耕地、虚拟化肥/农药要素的贸易量,构建虚拟要素贸易网络,通过复杂网络的研究方法,结果表明:2002—2016年我国主要农产品虚拟耕地、化肥/农药要素的贸易总量呈下降趋势,降幅分别约25.51%、8.01%;虚拟耕地要素网络节点入度较大的为长江中下游、华南、西南地区,出度较大的为黄淮海和东北地区,虚拟化肥/农药要素网络与之相反;地区间节点强度的差异性大,虚拟耕地要素差值最大可达1459.56万hm~2,虚拟化肥/农药要素达61.38万t;二者网络节点度和强度的累积分布均符合幂律分布规律,其尾部的"重尾"现象揭示了节点度和强度的高可变性以及网络结构的脆弱性;虚拟耕地要素的输入区网络同配,输出区网络异配,揭示了地区间耕地要素的流动既呈集聚又有分散的态势,虚拟化肥/农药要素网络节点相关性皆为减函数,网络异配,揭示了虚拟化肥/农药要素在八大区域间联通的状况。网络结构特征分析为研究网络抗毁性特征和网络的优化调控机制奠定基础,为中国粮食贸易格局和粮价制定以及各个地区的农业种植结构调整提供理论依据。     

Elemental Composition in Two Water Beetles (<Emphasis Type="Italic">Dytiscus thianschanicus</Emphasis>, <Emphasis Type="Italic">Dytiscus persicus</Emphasis>) (Dytiscidae: Coleoptera) as Revealed by WDXRF Spectroscopy

In this study, concentrations of 34 different inorganic elements between Dytiscus thianschanicus and Dytiscus persicus collected from the environs of five Turkish cities were measured by wavelength dispersive X-ray fluorescence spectrometry. The two species were found to differ in both elemental composition and amount. The concentrations of Na, As, Br and Ba were found to differ significantly between D. thianschanicus and D. persicus. In addition, Mn and I concentrations for D. thianschanicus and Si, Zn for D. persicus between males and females were statistically significant. It is thought that metabolic differences between males and females of these insects may be behind the observed differences in these species. Differences in elemental composition were also seen between beetles from different localities, and the content of non-essential elements in an insect’s body may be a useful measure of the level of these elements in their habitats.     

Generation of rules for expert systems by statistical methods of fermentation data analysis

Five new methods for determining the relations between kinetic data of fermentations are described and applied to an industrial antibotic fermentation process. The input data for these method are the elements of the distance matrix d_ij, which quantify the sum of the deviation squares between the time dependent kinetics x (t) of the fermentation runs i and j. For each measurable or calculable kinetic state variable, one n x n distance matrix must be calculated where n is the number of fermentation runs. All methods compare these distance matrices by statistical or graph-theoretical approaches. The algorithms obtained are universally applicable if enough kinetic data are available, especially from more than 10 comparable fermentation runs. The algorithms were developed for the use in knowledge acquisition modules of expert systems.     

Fenestration in the myelin sheath of nerve fibers of the shrimp: A novel node of excitation for saltatory conduction

Giant nerve fibers of the shrimp family Penaeidae conduct impulses at the velocity highest among all animal species (∼210 m/s; highest in mammals = 120 m/s). We examined these giant and other small nerve fibers morphologically using a differential interference contrast microscope as well as an electron microscope, and found a very specialized form of excitable membrane that functions as a node for saltatory conduction of the impulse. This node appeared under the light microscope as a characteristic pattern of concentrically aligned rings in a very small spot of the myelin sheath. The diameter of the innermost ring of the node was about 5 μm, and the distance between these nodes was as long as 12 mm. Via an electron microscope, these nodes were characterized by a complete lack of the myelin sheath, forming a fenestration that has a tight junction with an axonal membrane. Voltage clamp measurements by a sucrose gap technique demonstrated that the axonal membrane at these fenestration nodes is exclusively excitable and that the large submyelinic space is a unique conductive pathway for loop currents for saltatory conduction through such fenestration nodes. © 1996 John Wiley & Sons, Inc.     

Molecular analysis of the genomic organization of the Hymenoptera Diadromus pulchellus and Eupelmus vuilleti

The genomic organization of two parasitic wasps was analyzed by DNA reassociation. Cot curves revealed a pattern with three types of components. A highly repetitive DNA, accounting for 15 to 25% of the genome, was identified as satellite DNA. The moderately repetitive DNA corresponds to 26 to 42% of the genome in both species, and shows large variations in complexity, repetitive frequency and a number of sub-components between males and females. These variations are seen as resulting from DNA amplification during somatic and sexual differentiation. Dot blot analyses show that such DNA amplifications concern several types of structural and regulatory genes. The presence of repeated mobile elements was studied by the Roninson method to compare the repeated sequence patterns of Diadromus pulchellus and Eupelmus vuilleti with those of Drosophila melanogaster. The occurrence and organization of mobile elements in these Hymenoptera differ from those of the neighboring order of Diptera. The repetitive and unique components define very large genomes (1 to 3 × 10⁹ base pairs). The genomic organization in Parasitica appears to be an extreme drosophilan type. We propose that the germinal genome of these parasitic wasps is primarily composed of satellite DNA blocks and very long stretches of unique sequences, separated by a few repeated and/or variously deleted, interspersed elements of each mobile element family.     

Visual discrimination of cues differing as for their number of elements, their shape or their orientation, by the ant Myrmica sabuleti

Using operant conditioning as a method, we study if Myrmica sabuleti workers can discriminate figures made of different numbers of the same element, different filled shapes or hollow forms and elements differently oriented. The ants effectively discriminate figures containing different numbers of the same element but without counting the elements: their distinguishing is based on the global aspect (dimensions, area) of the figures. They distinguish filled shapes as well as hollow forms when these look different if seen with convexity. For instance, they differentiate well between concave filled shapes or concave hollow forms. They see distinctly an element and the same one rotated if this element, seen with convexity, looks different after its rotation. They perceive until a 30° rotation of a vertical segment and until a 15° rotation of a horizontal segment. In conclusion, M. sabuleti workers are sensitive to the number of elements, dimension, shape, form and orientation of visual cues with the restriction that they probably see them with convexity.     

Gross chromosome rearrangements mediated by transposable elements in Drosophila melanogaster

A combination of cytogenetic and molecular analyses has shown that several different transposable elements are involved in the restructuring of Drosophila chromosomes. Two kinds of elements, P and hobo, are especially prone to induce chromosome rearrangements. The mechanistic details of this process are unclear, but, at least some of the time, it seems to involve ectopic recombination between elements inserted at different chromosomal sites; the available data suggest that these ectopic recombination events are much more likely to occure between elements in the same chromosome than between elements in different chromosomes. Other Drosophila transposons also appear to mediate chromosome restructuring by ectopic recombination; these include the retrotransposons BEL, roo, Docand I and the foldback element FB. In addition, two retrotransposons, HeT-A and TART, have been found to be associated specifically with the ends of Drosophila chromosomes. Very limited data indicate that transposon-mediated chromosome restructuring is occurring in natural populations of Drosophila. This suggests that transposable elements may help to shape the structure of the Drosophila genome and implies that they may have a similar role in other organisms.     

Genetic relationships of tetraploid<Emphasis Type="Italic"> Elymus</Emphasis> species and their genomic donor species inferred from polymerase chain reaction-restriction length polymorphism analysis of chloroplast gene regions

The genetic relationships of 38 individuals from 13 Elymus tetraploid species, two Pseudoroegneria species and one Hordeum species were examined using polymerase chain reaction-restriction length polymorphism analysis of chloroplast gene regions. The 13 Elymus species contain SH and SY genomes with either a single spikelet or multiple spikelets per rachis node. The Pseudoroegneria and Hordeum species contain an S genome with single spikelet per rachis node and an H genome with multiple spikelets per rachis node, respectively. Four chloroplast gene regions, trnD-trnT intron, trnK [tRNA-Lys (UUU) exon1]–trnK [tRNA-Lys (UUU) exon2], trnC-trnD, and rbcL were amplified with specific primers and subsequently digested with up to 16 different restriction enzymes. Interspecific variation was detected in the four regions. A dendrogram based on similarity matrices using the unweighted pair group method with arithmetic average algorithm separated the 38 individuals into two distinct groups: the Elymus and Pseudoroegneria species as one group and Horduem as a second group. This result corresponded well with previous findings, and strongly suggested that a Pseudoroegneria species is the maternal donor to tetraploid Elymus species. Unlike previous studies using nuclear genes, the chloroplast DNA used in this study could not clearly separate the SY-genome species from SH-genome species. No clear separation between the species with a single spikelet per rachis node and the species with multiple spikelets per rachis node was found. Intra-specific variation was detected for the species studied. These observations provide molecular evidence for the highly diverse nature of the Elymus gene pool based on morphological characteristics.Communicated by H.F. Linskens     

IS1237, a Repetitive Chromosomal Element from Clavibacter xyli subsp. cynodontis, Is Related to Insertion Sequences from Gram-Negative and Gram-Positive Bacteria

We describe here a repetitive chromosomal element, which appears to be an insertion sequence, isolated from Clavibacter xyli subsp. cynodontis, a gram-positive plant-associated bacterium. The element, IS1237, is 905 bp in size, is bounded by 19-bp perfect inverted repeats and 3-bp direct repeats, and appears at least 16 times in the genome. It contains three open reading frames which show similarity to open reading frames from various other insertion sequences. We have found that there are two groups of related mobile elements: one in which two open reading frames are read separately and the other in which these two open reading frames are fuse together to give one predicted protein product. Using one of these open reading frames to search amino acid sequence databases, we found two instances in which similar reading frames flank genes carried on plasmids. We believe therefore that these plasmid-borne genes may be parts of previously unidentified mobile elements. For IS1237, a frameshift in two of the open reading frames and a stop codon in the third may indicate that this particular copy of the element is no longer active in transposition. The similarity of IS1237 to other elements from both gram-negative and gram-positive bacteria provides further evidence that mobile elements have been transferred between these two bacterial groups.     

Taxon ordering in phylogenetic trees: a workbench test

Background  

Phylogenetic trees are an important tool for representing evolutionary relationships among organisms. In a phylogram or chronogram, the ordering of taxa is not considered meaningful, since complete topological information is given by the branching order and length of the branches, which are represented in the root-to-node direction. We apply a novel method based on a (λ + μ)-Evolutionary Algorithm to give meaning to the order of taxa in a phylogeny. This method applies random swaps between two taxa connected to the same node, without changing the topology of the tree. The evaluation of a new tree is based on different distance matrices, representing non-phylogenetic information such as other types of genetic distance, geographic distance, or combinations of these. To test our method we use published trees of Vesicular stomatitis virus, West Nile virus and Rice yellow mottle virus.     

Composite cis-acting epigenetic switches in eukaryotes: lessons from Drosophila Fab-7 for the Igf2-H19 imprinted domain

One of the central problems of eukaryotic gene regulation is to understand the mechanism(s) by which the activity of enhancer elements is circumscribed such that they only act upon their cognate promoter sequences. Studies on the bithorax gene complex (BX-C) in Drosophila have highlighted the potential problem of enhancer promiscuity and detailed molecular and genetic analyses are now providing insight into how this gene complex resolves the problem through the activity of boundary/silencer elements that can block the communication between enhancers and promoters. Analysis of the mouse Igf2–H19 imprinted locus also suggests a role for boundary/silencer elements, but in this case these elements are invoked to account for the preferential expression of Igf2 and H19 from the paternally and maternally inherited chromosomes respectively despite the presence of functional downstream enhancers. We discuss recent work that has illuminated both of these systems and consider what parallels exist between them.     

The transposable element impala, a fungal member of the Tc1-mariner superfamily

A new transposable element has been isolated from an unstable niaD mutant of the fungus Fusarium oxysporum. This element, called impala, is 1280 nucleotides long and has inverted repeats of 27 bp. Impala inserts into a TA site and leaves behind a footprint when it excises. The inserted element, impala-160, is cis-active, but is probably trans-defective owing to several stop codons and frameshifts. Similarities exist between the inverted repeats of impala and those of transposons belonging to the widely dispersed mariner and Tc1 families. Moreover, translation of the open reading frame revealed three regions showing high similarities with Tc1 from Caenorhabditis elegans and with the mariner element of Drosophila mauritiana. The overall comparison shows that impala occupies an intermediate position between the mariner and Tcl-like elements, suggesting that all these elements belong to the same superfamily. The degree of relatedness observed between these elements, described in different kingdoms, raises the question of their origin and evolution.     

A general method to isolate genes tagged by a high copy number transposable element

The Petunia hybrida line W138 contains more than 200 copies of the transposable element dTph1. In W138 progeny these elements give rise to new unstable mutations at high frequency. With the aim of isolating these mutated genes a method was developed to isolate dTph1 flanking sequences unique for mutant plants. This method is based on differential screening of cloned inverse polymerase chain reaction (IPCR) products originating from the mutated plant. It directly yields a probe for the mutated gene which can be used to screen pre-existing cDNA and genomic libraries. This method may be generally applicable to isolate genes tagged by other high copy number transposable elements, like Mutator (Mu) or Dissociation (Ds) in Zea mays.