Diversity and evolution of Pong-like elements in Bambusoideae subfamily

The PIF/IS5 is a recently discovered superfamily of DNA transposons which include Pong-like elements and PIF-like elements and has been successively detected in the genomes of many flowering plants, fungi and diverse animals. Here we present the first comprehensive characterization and analysis of Pong-like elements in Bambusoideae subfamily. Eighty-two Pong-like elements were cloned and sequenced from 44 representative species of Bambusoideae. Phylogenetic analysis of 82 distinct Pong-like elements sequences showed that Pong-like elements were widespread, diverse and abundant in Bambusoideae. A molecular phylogeny of Bambusoideae was established by using the internal transcribed spacer sequence of nuclear ribosomal DNA (ITS) information. The comparison between ITS and Pong-like elements based trees reveals obviously incongruent. The results suggest that 1) there are multiple Pong-like element families in Bambusoideae; 2) a single Pong-like element family could be present in multiple bamboo species; 3) Pong-like elements from the same family from different bamboo species could be more similar than elements from different families in the same bamboo species or closely related species.     

A branching-process model for the evolution of transposable elements incorporating selection

We have formulated a very general mathematical model to analyze the evolution of transposable genetic elements in prokaryotic populations. Transposable genetic elements are DNA sequences able to replicate and insert copies of themselves at new locations in the genome. This work characterizes the equilibrium distribution of copy number under the influence of copy number-dependent selection, transposition and deletion. Our principal results concern the equilibrium distribution of copy number in response to various selective regimes. For particular transposition patterns (e.g. unregulated transposition or copy number-dependent transposition), equilibrium distributions are calculated numerically for a variety of specific selection patterns. Selection is quantified through specification of the expected number of offspring for individuals of each type, which is generally a non-increasing function of copy number, in accord with the usual evolutionary speculations.     

Ferrocenyl-substituted allenylidene complexes of chromium, molybdenum and tungsten: Synthesis, structure and reactivity

Bis(ferrocenyl)-substituted allenylidene complexes, [(CO)₅MCCCFc₂] (1a-c, Fc = (C₅H₄)Fe(C₅H₅), M = Cr (a), Mo (b), W (c)) were obtained by sequential reaction of Fc₂CO with Me₃Si-CCH, KF/MeOH, n-BuLi, and [(CO)₅M(THF)]. For the synthesis of related mono(ferrocenyl)allenylidene chromium complexes, [(CO)₅CrCCC(Fc)R] (R = Ph, NMe₂), three different routes were developed: (a) reaction of the deprotonated propargylic alcohol HCCC(Fc)(Ph)OH with [(CO)₅Cr(THF)] followed by desoxygenation with Cl₂CO, (b) Lewis acid induced alcohol elimination from alkenyl(alkoxy)carbene complexes, [(CO)₅CrC(OR)CHC(NMe₂)Fc], and (c) replacement of OMe in [(CO)₅CrCCC(OMe)NMe₂] by Fc. Complex 1a was also formed when the mono(ferrocenyl)allenylidene complex [(CO)₅CrCCC(Fc)NMe₂] was treated first with Li[Fc] and the resulting adduct then with SiO₂. The replacement route (c) was also applied to the synthesis of an allenylidene complex (7a) with a CC spacer in between the ferrocenyl unit and C_γ of the allenylidene ligand, [(CO)₅CrCCC(NMe₂)-CCFc]. The related complex containing a CHCH spacer (9a) was prepared by condensation of [(CO)₅CrCCC(Me)NMe₂] with formylferrocene in the presence of NEt₃. The bis(ferrocenyl)-substituted allenylidene complexes 1a-c added HNMe₂ across the C_α-C_β bond to give alkenyl(dimethylamino)carbene complexes and reacted with diethylaminopropyne by regioselective insertion of the CC bond into the C_β-C_γ bond to afford alkenyl(diethylamino)allenylidene complexes, [(CO)₅MCCC(NEt₂)CMeCFc₂]. The structures of 5a, 7a, and 9a were established by X-ray diffraction studies.     

Minor elements in south-east Italy soils

Summary A number of soil samples from south-east Italy were analyzed for As, Bi, Cd, Cu, Hg, Li, Mn, Ni, Pb, Se, Sn, and Zn contents with the aim of estimating pollution degree in cultivated lands of region. The existence of linear relations among variables was detected assuming multiple regression models and analyzing then linear correlation coefficients.     

N,N-expeditious dialkylation of cyclen (1,4,7,10-tetraazacyclododecane). An astonishing reactivity of cyclen tricarbonyl molybdenum and chromium complexes

After reaction with alkyl iodides and subsequent oxidative removal of the M(CO)₃ triprotection, molybdenum and chromium fac-LM(CO)₃ complexes of cyclen (L) unexpectedly lead to N¹,N⁷-dialkylated cyclen derivatives.     

Hominoid cytogenetics and evolution

Much of the literature on the chromosomes of the Hominoidea exists in virtual isolation from both evolutionary theory and physical anthropology. Several unjustified speculations about hominoid affinities in the literature of cytogenetics may be attributed to the effects of this isolation. In this paper, the literature of comparative hominoid cytogenetics is reviewed, and that on chromosomal band patterns and repetitive DNA distributions relative to current evolutionary theory is discussed. These data are critically analyzed and shown to be more consistent with an orthodox hominoid phylogeny than with heterodox phylogenies. Rates and modes of karyotypic evolution are also discussed in an attempt to begin to assimilate the study of hominoid chromosomes within the framework of physical anthropology.     

Ontogenetic mechanisms and the evolution of Cactaceae

Abstract

The ancestors of cacti were leafy trees that had hard, woody trunks. The development of the cactus body is controlled by ontogenetic mechanisms that have evolved, and now they produce a body that is leafless, succulent and has a photosynthetic cortex. Specific changes include: bark formation is postponed and the epidermis and stomata function for many years; the outer cortex is a palisade cortex with intercellular spaces; there are cortical bundles that resemble leaf veins but which have secondary xylem and phloem. Wood development has changed dramatically such that water storage is maximized (increased ray parenchyma) and danger of water stress is minimized (increased paratracheal parenchyma, loss of fibers). Several genera have polymorphic wood: the plants produce one type of wood for several years, then later they produce a different type. It is possible that the extensive evolutionary changes have resulted from mutations in the controller regions of genes, not in the structural regions.     

Synthesis and characterization of deuterium-labelled (fulvene)M(CO)3 complexes (M = Cr, Mo)

The preparation and characterization of a series of deuterium-labelled (fulvene)M(CO)₃ (M = Cr, Mo) complexes is reported. (η⁵-6-Dimethylaminofulvene-d₂)Cr(CO)₃ and (η⁵-6-dimethylaminofulvene-d₂)Mo(CO)₃ were obtained in high yields by reacting the deuterated fulvene ligands with (MeCN)₃M(CO)₃ (M = Cr, Mo). In addition, syntheses of 6,6-diphenylfulvene-d₁₀ and 6,6-diphenyl-1,2-benzofulvene-d₁₀ as well as the corresponding tricarbonylchromium complexes are described.     

Correlated evolution of the cis-acting regulatory elements and developmental expression of the Drosophila Gld gene in seven species from the subgroup melanogaster

The tissue-specific expression patterns of glucose dehydrogenase (GLD) exhibit a high degree of inter specific variation in the adult reproductive tract among the species in the genus Drosophila. We chose to focus on the evolution of GLD expression and the evolution of the Gld promoter in seven closely related species in the mela-nogaster subgroup as a means of elucidating the relationship of changes in cis-acting regulatory elements in the Gld promoter region with changes in tissue-specific expression. Although little variation in tissue-specific patterns of GLD was found in nonreproductive tissues during development, a surprisingly high level of variation was observed in the expression of GLD in both developing and ma-ture reproductive organs. In some cases this variation is correlated with changes in sequence elements in the Gld promoter which were previously shown to direct tissue-specific expression in the reproductive tract. In particular D. teissieri adult males do not express GLD in their ejaculatory ducts, atypical of the melanogaster subgroup species. The Gld promoter region of D. teissieri specifically lacks all three of the TTAGA regulatory elements present in D. melanogaster. The TTAGA elements were previously shown to direct reporter gene expression to the ejaculatory duct. Together these data suggest the absence or presence of the TTAGA elements may be responsible for variation in the absence or presence of GLD in the ejaculatory duct among species. © 1994 Wiley-Liss, Inc.     

Theoretical studies on tetrahedral oxoanions MO4 (n=2, 3, 4; M=Cr, Mo, W)

The structure and bonding in MO₄ ⁿ⁻ (n=2, 3, 4; M=Cr, Mo, W) tetrahedral oxoanions have been investigated using density-functional methods. Good computational-experimental agreement for the geometrical parameters of the known species has been obtained which allowed the prediction of the cited parameters for those species that have not yet been isolated. The molecular-orbital analysis indicates that the chemical bonds mainly have d functions of the metal and p functions of oxygen. The electron affinities for the process MO₄ ⁿ⁻ + 1e → MO₄ ^(n + 1)− have also been calculated and their importance in relation with the preparation of the oxoanions MO₄ ⁿ⁻ (M=Mo, W; n=3, 4) not reported in the bibliography is discussed. Comparative studies of the electronic structures of oxoanions allow to explain their reactivities against nucleophilic and electrophilic attacks. The vibrational frequencies have been calculated and compared with the experimental values and the different relationships between the symmetric-stretching and antisymmetric-bending frequencies allow to confirm the assignations of the calculated spectra.     

The evolution and diversification of Dicers in plants

Most multicellular organisms regulate developmental transitions by microRNAs, which are generated by an enzyme, Dicer. Insects and fungi have two Dicer-like genes, and many animals have only one, yet the plant, Arabidopsis, has four. Examining the poplar and rice genomes revealed that they contain five and six Dicer-like genes, respectively. Analysis of these genes suggests that plants require a basic set of four Dicer types which were present before the divergence of mono- and dicotyledonous plants ( approximately 200 million years ago), but after the divergence of plants from green algae. A fifth type of Dicer seems to have evolved in monocots.     

Microbial transformation of elements: the case of arsenic and selenium

Microbial activity is responsible for the transformation of at least one third of the elements in the periodic table. These transformations are the result of assimilatory, dissimilatory, or detoxification processes and form the cornerstones of many biogeochemical cycles. Arsenic and selenium are two elements whose roles in microbial ecology have only recently been recognized. Known as "essential toxins", they are required in trace amounts for growth and metabolism but are toxic at elevated concentrations. Arsenic is used as an osmolite in some marine organisms while selenium is required as selenocysteine (i.e. the twenty-first amino acid) or as a ligand to metal in some enzymes (e.g. FeNiSe hydrogenase). Arsenic resistance involves a small-molecular-weight arsenate reductase (ArsC). The use of arsenic and selenium oxyanions for energy is widespread in prokaryotes with representative organisms from the Crenarchaeota, thermophilic bacteria, low and high G+C gram-positive bacteria, and Proteobacteria. Recent studies have shown that both elements are actively cycled and play a significant role in carbon mineralization in certain environments. The occurrence of multiple mechanisms involving different enzymes for arsenic and selenium transformation indicates several different evolutionary pathways (e.g. convergence and lateral gene transfer) and underscores the environmental significance and selective impact in microbial evolution of these two elements. Electronic Publication     

Chromosome evolution in the genus Ophioglossum L.

Cytological observations on eleven species of Ophioglossum revealed low gametic ( n ) chromosome numbers of 30, 34 and 60 in populations of O.eliminatum , contrasting with an earlier report of n = 90 in the same species. The rest of the species is based on n =120.Cytologically studied species of Ophioglossum exhibit a range of chromosome numbers from n = 30 in O.eliminatum to n =720 in O.reticulatum. The weighted highest common factor (HGF) from all the reported chromosome numbers in twelve species was found to be 30. This number is proposed as the palaeobasic chromosome number for the genuS. Reported chromosome numbers which are not multiples of 30 were subjected to sequential analysis, yielding three distinct ultimate base numbers, 4, 5 and 6, which can produce n = 30 in seven different ways. The neobasic number, n= 120, appears to have arisen through various combinations and permutations of these, theoretically 2401 routes; only a relatively few of these routes exist today, suggesting that extreme selection has been exerted against the majority, and further suggesting that Ophioglossum represents an evolutionary dead end through repeated cycles of polyploidy and is possibly at the verge of extinction. The stoichiometric model of evolution, which derives the various chromosome numbers possessed by the twelve species from the basic and ultimate basic chromosome numbers, is used to explain chromosomal evolution in the genus.     

Human evolution

The origin, history, and singularity of our species has fascinated storytellers, philosophers and scientists throughout, and doubtless before, recorded history. Anthropology, the modern-era discipline that deals with these issues, is a notoriously contentious field, perhaps because the topic at hand – the nature of our own species – is one that is difficult or impossible to approach in an unbiased way. Recently, molecular genetics has increasingly contributed to this field. Here, I briefly discuss three areas where I believe molecular studies are likely to be of decisive importance in the future. These concern the questions of where and when our species originated, what the genetic background for characters that differ between us and apes is, and how the phenotypic traits that vary among human groups have evolved.     

Morphology and the evolution of cycadeoidales

OneCycadeoidea stem one cycadeoidalean gynoecium and a bisporangiate cone attached to a slender cycadeoidalean trunkCycadeoidella japonica Ogura from the Cretaceous of Japan shows well-preserved internal structure that provides evidence for a better understanding of the morphological architecture of the cycadeoidalean plant. Structural details of the cone were confirmed. The ovule has an intergument enclosing a free nucellus and a thin outer envelope. Both reproductive and vegetative structures support the medullosan affinity of Cycadeoidales. The cone is interpreted as a compressed fertile shoot. Axillary cones characterizing some Cretaceous genera such asCycadeoidea andMonanthesia consist of a lateral shoot subtended by a frond that is the first leaf of the cone shoot itself. The origin of axillary buds in the Cycadeoidales is discussed. Heterochrony may have mediated the morphological changes that resulted in the establishment of the Cycadeoidales.     

Human evolution

The origin, history, and singularity of our species has fascinated storytellers, philosophers and scientists throughout, and doubtless before, recorded history. Anthropology, the modern-era discipline that deals with these issues, is a notoriously contentious field, perhaps because the topic at hand – the nature of our own species – is one that is difficult or impossible to approach in an unbiased way. Recently, molecular genetics has increasingly contributed to this field. Here, I briefly discuss three areas where I believe molecular studies are likely to be of decisive importance in the future. These concern the questions of where and when our species originated, what the genetic background for characters that differ between us and apes is, and how the phenotypic traits that vary among human groups have evolved.