A survey of transposable element classification systems--a call for a fundamental update to meet the challenge of their diversity and complexity.

The increase of publicly available sequencing data has allowed for rapid progress in our understanding of genome composition. As new information becomes available we should constantly be updating and reanalyzing existing and newly acquired data. In this report we focus on transposable elements (TEs) which make up a significant portion of nearly all sequenced genomes. Our ability to accurately identify and classify these sequences is critical to understanding their impact on host genomes. At the same time, as we demonstrate in this report, problems with existing classification schemes have led to significant misunderstandings of the evolution of both TE sequences and their host genomes. In a pioneering publication Finnegan (1989) proposed classifying all TE sequences into two classes based on transposition mechanisms and structural features: the retrotransposons (class I) and the DNA transposons (class II). We have retraced how ideas regarding TE classification and annotation in both prokaryotic and eukaryotic scientific communities have changed over time. This has led us to observe that: (1) a number of TEs have convergent structural features and/or transposition mechanisms that have led to misleading conclusions regarding their classification, (2) the evolution of TEs is similar to that of viruses by having several unrelated origins, (3) there might be at least 8 classes and 12 orders of TEs including 10 novel orders. In an effort to address these classification issues we propose: (1) the outline of a universal TE classification, (2) a set of methods and classification rules that could be used by all scientific communities involved in the study of TEs, and (3) a 5-year schedule for the establishment of an International Committee for Taxonomy of Transposable Elements (ICTTE).

Type II aromatic polyketide biosynthetic tailoring enzymes: diversity and adaptation in Streptomyces secondary metabolism.

Members of the bacterial genus Streptomyces are well known for their ability to produce an exceptionally wide selection of diverse secondary metabolites. These include natural bioactive chemical compounds which have potential applications in medicine, agriculture and other fields of commerce. The outstanding biosynthetic capacity derives from the characteristic genetic flexibility of Streptomyces secondary metabolism pathways: i) Clustering of the biosynthetic genes in chromosome regions redundant for vital primary functions, and ii) the presence of numerous genetic elements within these regions which facilitate DNA rearrangement and transfer between non-progeny species. Decades of intensive genetic research on the organization and function of the biosynthetic routes has led to a variety of molecular biology applications, which can be used to expand the diversity of compounds synthesized. These include techniques which, for example, allow modification and artificial construction of novel pathways, and enable gene-level detection of silent secondary metabolite clusters. Over the years the research has expanded to cover molecular-level analysis of the enzymes responsible for the individual catalytic reactions. In vitro studies of the enzymes provide a detailed insight into their catalytic functions, mechanisms, substrate specificities, interactions and stereochemical determinants. These are factors that are essential for the thorough understanding and rational design of novel biosynthetic routes. The current study is a part of a more extensive research project (Antibiotic Biosynthetic Enzymes; www.sci.utu.fi/projects/biokemia/abe), which focuses on the post-PKS tailoring enzymes involved in various type II aromatic polyketide biosynthetic pathways in Streptomyces bacteria. The initiative here was to investigate specific catalytic steps in anthracycline and angucycline biosynthesis through in vitro biochemical enzyme characterization and structural enzymology. The objectives were to elucidate detailed mechanisms and enzyme-level interactions which cannot be resolved by in vivo genetic studies alone. The first part of the experimental work concerns the homologous polyketide cyclases SnoaL and AknH. These catalyze the closure of the last carbon ring of the tetracyclic carbon frame common to all anthracycline-type compounds. The second part of the study primarily deals with tailoring enzymes PgaE (and its homolog CabE) and PgaM, which are responsible for a cascade of sequential modification reactions in angucycline biosynthesis. The results complemented earlier in vivo findings and confirmed the enzyme functions in vitro. Importantly, we were able to identify the amino acid -level determinants that influence AknH and SnoaL stereoselectivity and to determine the complex biosynthetic steps of the angucycline oxygenation cascade of PgaE and PgaM. In addition, the findings revealed interesting cases of enzyme-level adaptation, as some of the catalytic mechanisms did not coincide with those described for characterised homologs or enzymes of known function. Specifically, SnoaL and AknH were shown to employ a novel acid-base mechanism for aldol condenzation, whereas the hydroxylation reaction catalysed by PgaM involved unexpected oxygen chemistry. Owing to a gene-level fusion of two ancestral reading frames, PgaM was also shown to adopt an unusual quaternary sturucture, a non-covalent fusion complex of two alternative forms of the protein. Furthermore, the work highlighted some common themes encountered in polyketide biosynthetic pathways such as enzyme substrate specificity and intermediate reactivity. These are discussed in the final chapters of the work.

Invasive species and habitat degradation in Iberian streams: an analysis of their role in freshwater fish diversity loss

Mediterranean endemic freshwater fish are among the most threatened biota in the world. Distinguishing the role of different extinction drivers and their potential interactions is crucial for achieving conservation goals. While some authors argue that invasive species are a main driver of native species declines, others see their proliferation as a co-occurring process to biodiversity loss driven by habitat degradation. It is difficult to discern between the two potential causes given that few invaded ecosystems are free from habitat degradation, and that both factors may interact in different ways. Here we analyze the relative importance of habitat degradation and invasive species in the decline of native fish assemblages in the Guadiana River basin (southwestern Iberian Peninsula) using an information theoretic approach to evaluate interaction pathways between invasive species and habitat degradation (structural equation modeling, SEM). We also tested the possible changes in the functional relationships between invasive and native species, measured as the per capita effect of invasive species, using ANCOVA. We found that the abundance of invasive species was the best single predictor of natives’ decline and had the highest Akaike weight among the set of predictor variables examined. Habitat degradation neither played an active role nor influenced the per capita effect of invasive species on natives. Our analyses indicated that downstream reaches and areas close to reservoirs had the most invaded fish assemblages, independently of their habitat degradation status. The proliferation of invasive species poses a strong threat to the persistence of native assemblages in highly fluctuating environments. Therefore, conservation efforts to reduce native freshwater fish diversity loss in Mediterranean rivers should focus on mitigating the effect of invasive species and preventing future invasions

PHYTOSOCIOLOGY AND STRUCTURAL CHARACTERIZATION OF WOODY REGENERATION FROM A REFORESTATION WITH NATIVE SPECIES IN SOUTHEASTERN BRAZIL

ABSTRACT In Brazil, specifically in São Paulo State, there are guidelines based on the high diversity of tropical forests that instructs the restoration projects in the state (current SMA 32/2014). The main goal of this study was verify the importance and effectiveness of the high diversity of arboreal species originated from a reforestation, and its influence in a woody regenerating composition. We developed a phytosociologic study in a woody regenerating stratum of a nine year old reforestation at a Private Reserve of Natural Heritage (RPPN), in Mogi-Guaçu, São Paulo State. All specimens with height > 30 cm and Diameter at Breast Height (DBH) < 5 cm were evaluated. The woody regenerating diversity was smaller than the overstory diversity and the species composition was similar to the overstory. The Simpson index (1-D) was 0.85, Shannon index (H') was 2.46 and the Pielou index (J') was 0.60. The zoochoric dispersion syndrome was major among the species. Our results suggest that the use of high diversity of native seedlings in a reforestation leads to high diversity of species in woody regeneration stratum, after one decade of planting.

Floristic diversity of two crystalline rocky outcrops in the Brazilian northeast semi-arid region

Floristic composition and structure of vegetation were studied in two rocky outcrop areas in the semi-arid region of northeastern Brazil. From April 2007 to September 2008, 18 monthly field trips were carried out. Vascular plants were randomly collected throughout the outcrop areas. For structural analysis, 30 plots of 1 × 1 m were set in the vegetation islands. The checklist presented combines 211 species (69 families and 168 genera), although only 56 species were collected in the plots. Fabaceae (18 spp.; 8.5%), Asteraceae (17 spp.; 8%), Orchidaceae (13 spp.; 6.1%), Euphorbiaceae (13 spp.; 6.1%), Bromeliaceae (10 spp.; 4.7%), and Poaceae (eight spp.; 3.8%) are the richest families. Overall, 1,792 shrub and herbaceous specimens were counted in the plots. The Shannon-Wiener (H) diversity index values were 2.572 and 2.547 nats individual-1. The species that presented the highest absolute abundance values (number of plants) had low frequencies in the plots and vice-versa. The biological spectrum had a high proportion of phanerophytes and therophytes, followed by cryptophytes, chamaephytes, and hemicryptophytes. The studied flora shares floristic components similar to other rocky outcrop areas of the semi-arid region in northeastern Brazil, including in relation to dominant groups in the vegetation structure.

Chelating behavior of acylhydrazones towards transition metals:Spectral and structural aspects

The current work deals with the synthesis and characterization of metal complexes derived from some substituted acylhydrazones. The hydrazones under investigation were characterized by IR, UV, NMR spectral studies and the molecular structure of one of the hydrazones was solved by single crystal XRD studies. In the present work dioxovanadium(V), manganese(II), cobalt(II/III), nickel(II), copper(II), zinc(II) and cadmium(II) complexes were synthesized and characterized by various spectroscopic techniques, molar conductance measurements, magnetic susceptibility measurements and cyclic voltammetry. Single crystals of some of the complexes were isolated and characterized by single crystal X-ray diffraction.The thesis is divided into eight chapters. Chapter 1 gives an introduction on hydrazones, diversity in their chelating behavior and their application in various fields. This chapter also describes different analytical techniques employed for the characterization of hydrazones and their metal complexes. Chapter 2 includes the synthesis and characterization of two substituted acylhydrazones. This chapter also discusses how the coordination behavior of hydrazones under investigation is interesting. Chapters 3-8 discuss the synthesis and characterization of some transition metal complexes derived from the acylhydrazones under study.The hydrazones synthesized were found to exist in the amido form. Various characterization techniques were carried out to explore the structure of the synthesized complexes. The results indicate that both the hydrazones coordinate through the pyridyl and azomethine nitrogens and amide oxygen either in enolate or neutral form. Out of synthesized complexes V(V), Zn/Cd(II) and one of the cobalt complex was found to diamagnetic. We could isolate single crystals of some of the complexes and most of the complexes crystallized were found to have a distorted octahedral geometry. Thus X-ray crystallographic study which was used as major tool in the structure determination revealed that the hydrazones undergo a rotation about the azomethine bond on complexation. We hope the work presented in the thesis would be helpful for those who are working in the field of metal complexes and can further they can be utilized for various applications.

Transition Metal Complexes of Schiff Bases with Azide and Thiocyanate as Coligands:Spectral and Structural Investigations

Metallo-organic chemistry,incorporating the frontiers of both inorganic and organic chemical aspects,is a topic of utility concern.The first exploration of coordinated metal complexes dates back to the ninettenth century,during the days of Alfred Werner.Thereafter,inorganic chemistry witnessed a great outflow of coordination compounds,with unique structural characteristics and diverse applicatons.The diversity in structures exhibited by the coordination complexes of multidentate ligands have led to their usage as sensors,models for enzyme mimetic centers,medicines etc.The liganda chosen are of prime importance in determining the properties of coordination compounds.Schiff bases are compounds obtained by the condensation of an aidehyde or ketone with an amine.The chemical properties of Schiff bases and their complexes are widely explored in recent years owing to their pharmacological activity,their catalytic activities and so on.On the other hand pseudohalides like azide and thiocyanate are versatile candidates for the construction of dimeric or polymeric complexes having excellent properties and diverse applications.So a combination of the Schiff bases and the pseudohalogens for the synthesis of metal complexes can bring about interesting results.An attempt into this area is the besis of this Ph.D theis.

Low genetic diversity and functional constraint in loci encoding Plasmodium vivax P12 and P38 proteins in the Colombian population

Background Plasmodium vivax is one of the five species causing malaria in human beings, affecting around 391 million people annually. The development of an anti-malarial vaccine has been proposed as an alternative for controlling this disease. However, its development has been hampered by allele-specific responses produced by the high genetic diversity shown by some parasite antigens. Evaluating these antigens’ genetic diversity is thus essential when designing a completely effective vaccine. Methods The gene sequences of Plasmodium vivax p12 (pv12) and p38 (pv38), obtained from field isolates in Colombia, were used for evaluating haplotype polymorphism and distribution by population genetics analysis. The evolutionary forces generating the variation pattern so observed were also determined. Results Both pv12 and pv38 were shown to have low genetic diversity. The neutral model for pv12 could not be discarded, whilst polymorphism in pv38 was maintained by balanced selection restricted to the gene’s 5′ region. Both encoded proteins seemed to have functional/structural constraints due to the presence of s48/45 domains, which were seen to be highly conserved.

The relationship between L3 transfer and structural similarity across L3 development: raising across an experience in Brazilian Portuguese

The present study examines three competing models of morphosyntactic transfer in third language (L3) acquisition, examining the particular domain of the feature configuration of embedded T in L3 Brazilian Portuguese (BP) at the initial stages and then through development. The methodology alternates Spanish and English as the L1 and L2 to tease apart the source of transfer to L3 BP. Results from a scalar grammaticality acceptability task show unequivocal transfer of Spanish irrespective of Spanish’s status as an L1 or L2. The data thus support the Typological Primacy Model (Rothman 2010, 2011, 2013a, 2013b), which proposes that multilingual transfer is selected by factors related to comparative structural similarity. Given that Spanish transfer at the L3 initial stages creates the need for feature reconfiguration to converge on the target BP grammar, the second part of this chapter examines the developmental consequences of what the TPM models in cases of non-facilitative initial transfer, that is, the developmental path of feature reconfiguration of embedded T in L3 BP by English/Spanish bilinguals. Given what these data reveal, we address the role of regressive transfer as a correlate of L3 proficiency gains.

The diversity of arbuscular mycorrhizas of selected Australian Fabaceae

Members of the Australian native perennial Fabaceae have been little explored with regard to their root biology and the role played by arbuscular mycorrhizal (AM) fungi in their establishment, nutrition and long-term health. The ultimate goal of our research is to determine the dependency of native perennial legumes on their co-evolved AM fungi and conversely, the impact of AM fungal species in agricultural fields on the productivity of sown native perennial legume pastures. In this paper we investigate the colonisation morphology in roots and the AMF, identified by spores extracted from rhizosphere soil, from three replicate plots of each of the native legumes, Cullen australasicum, C. tenax and Lotus australis and the exotic legumes L. pedunculatus and Medicago sativa. The plants were grown in an agricultural field. The level and density of colonisation by AM fungi, and the frequency of intraradical and extraradical hyphae, arbuscules, intraradical spores and hyphal coils all differed between host plants and did not consistently differ between native and exotic species. However, there were strong similarities between species in the same genus. The three dominant species of AM fungi in rhizosphere soil also differed with host plant, but one fungus (Glomus mosseae) was always the most dominant. Sub-dominant AM species were the same between species in the same genus. No consistent differences in dominant spores were observed between the exotic and native Fabaceae species. Our results suggest that plant host influences the mycorrhizal community in the rhizosphere soil and that structural and functional differences in the symbiosis may occur at the plant genus level, not the species level or due to provenance.

Structural relationships in the solid state of the anti-chagas agent (E)-phenylethenylbenzofuroxan

The crystal structure and the vibrational spectrum of a potential drug for Chagas`s disease treatment, the (E)-isomer of phenylethenylbenzofuroxan 1 (5(6)(E)-[(2-phenylethenyl)]benzo[1,2-c]1,2,5-oxadiazole N-oxide), are reported. In order to provide insights into structural relationships, quantum mechanical calculations were employed starting from crystal structure. These results have given theoretical support to state interesting structural features, such as the effect of some intermolecular contacts on the molecule conformation and the electronic delocalization decreasing through atoms of the benzofuroxan moiety. Furthermore, the MOGUL comparative analysis in the Cambridge Structural Database provided additional evidences on these structural behaviors of compound 1. Intermolecular contacts interfere on the intramolecular geometry, as, for instance, on the phenyl group orientation, which is twisted by 12.32(6)A degrees from the ethenylbenzofuroxan plane. The experimental Raman spectrum of compound 1 presents unexpected frequency shift and also anomalous Raman activities. At last, the molecule skeleton deformation and the characteristic vibrational modes were correlated by matching the experimental Raman spectrum to the calculated one.

Sequence and Structural Analysis of the 5 ` Noncoding Region of Hepatitis C Virus in Patients With Chronic Infection

Hepatitis C virus (HCV), exhibits considerable genetic diversity, but presents a relatively well conserved 5 ` noncoding region (5 ` NCR) among all genotypes. In this study, the structural features and translational efficiency of the HCV 5 ` NCR sequences were analyzed using the programs RNAfold, RNAshapes and RNApdist and with a bicistronic dual luciferase expression system, respectively. RNA structure prediction software indicated that base substitutions will alter potentially the 5 ` NCR structure. The heterogeneous sequence observed on 5 ` NCR led to important changes in their translation efficiency in different cell culture lines. Interactions of the viral RNA with cellular transacting factors may vary according to the cell type and viral genome polymorphisms that may result in the translational efficiency observed. J. Med. Virol. 81: 1212-1219, 2009. (C) 2009 Wiley-Liss, Inc.

Cortical diversity in three species groups of Parmotrema sensu lato (Parmeliaceae, lichenized Ascomycota)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Genetic variability of porcine parvovirus isolates revealed by analysis of partial sequences of the structural coding gene VP2

The 3'-terminal 853 nt (and the putative 283 aa) sequence of the VP2-encoding gene from 29 field strains of porcine parvovirus (PPV) were determined and compared both to each other and with other published sequences. Sequences were examined using maximum-parsimony and statistical analyses for nucleotide diversity and sequence variability. Among the nucleotide sequences of the PPV field strains, 26 polymorphic sites were encountered; 22 polymorphic sites were detected in the putative amino acid sequence. Mapping polymorphic sites of protein data onto the three-dimensional (3D) structure of PPV VP2 revealed that almost all substitutions were located on the external surface of the viral capsid. Mapping amino acid substitutions to the alignment between PPV VP2 sequences and the 3D structure of canine parvovirus (CPV) capsid, many PPV substitutions were observed to map to regions of recognized antigenicity and/or to contain phenotypically important residues for CPV and other parvoviruses. In spite of the high sequence similarity, genetic analysis has shown the existence of at least two virus lineages among the samples. In conclusion, these results highlight the need for close surveillance on PPV genetic drift, with an assessment of its potential ability to modify the antigenic make-up of the virus.

Grass-dominated stream sites exhibit low fish species diversity and dominance by guppies: an assessment of two tropical pasture river basins

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)