Molecular cloning and characterization of a thioester-containing protein from Zhikong scallop Chlamys farreri

Thioester-containing proteins are a family of proteins characterized by the unique intrachain beta-cysteinyl-gamma-glutamyl thioester, which play important roles in innate immune responses. The cDNA of Zhikong scallop Chlamys farreri thioester-containing protein (designated as CfTEP) was cloned by expressed sequence tag (EST) and rapid amplification of cDNA ends (RACE) approaches. The full-length cDNA of CfTEP was of 4616 bp, consisting of a 5 '-terminal untranslated region (UTR) of 30 bp and a 3 ' UTR of 140 bp with a polyadenylation signal sequence AATAAA and a poly(A) tail. The CfTEP cDNA encoded a polypeptide of 1481 amino acids with the theoretical isoelectric point of 5.98 and the predicted molecular weight of 161.4 kDa. The deduced amino acid sequence of CfTEP contained the canonical thioester motif GCGEQ, nine potential N-glycosylation sites and a C-terminal distinctive cysteine signature. It also contained a presumed catalytic histidine and proteolytic cleavage sites that were similar to C3 molecules. The high similarity of CfTEP with the thioester-containing proteins in other organisms, such as the TEPs from insects, the complement component C3, C4, C5 and the protease inhibitor alpha(2)-macroglobulin indicated that CfTEP should be a member of TEP family. The phylogenetic analysis revealed that CfTEP was closely related to TEPs from mollusc, nematodes and insects, and they formed a separate branch apart from the branches of complements factors and alpha(2)-macroglobulins. The spatial expression of CfTEP transcripts in healthy and bacterial challenged scallops was examined by semi-quantitative RT-PCR. The CfTEP transcripts were mainly detected in the tissues of hepatopancreas and gonad, and remarkably up-regulated by Microbial challenge, which suggested that CfTEP was a constitutive and inducible acute-phase protein involved in immune defense. These results provided new insights into the role of CfTEP in scallop immune responses, as well as the evolutionary origin of this important, widespread and functionally diversified family of proteins. (c) 2007 Published by Elsevier Ltd.

Spatial variations of effective elastic thickness over the Ninetyeast Ridge and implications for its structure and tectonic evolution

We present new data on the strength of oceanic lithosphere along the Ninetyeast Ridge (NER) from two independent methods: spectral analysis (Bouguer coherence) using the fan wavelet transform technique, and spatial analysis (flexure inversion) with the convolution method. The two methods provide effective elastic thickness (T-e) patterns that broadly complement each other, and correlate well with known surface structures and regional-scale features. Furthermore, our study presents a new high resolution database on the Moho configuration, which obeys flexural isostasy, and exhibit regional correlations with the T-e variations. A continuous ridge structure with a much lower T-e value than that of normal oceanic lithosphere provides strong support for the hotspot theory. The derived T-e values vary over the northern (higher T-e similar to 10-20 km), central (anomalously low T-e similar to 0-5 km), and southern (low T-e similar to 5 km) segments of the NER. The lack of correlation of the T-e value with the progressive aging of the lithosphere implies differences in thermo-mechanical setting of the crust and underlying mantle in different parts of the NER, again indicating diversity in their evolution. The anomalously low T-e and deeper Moho (similar to 22 km) estimates of the central NER (between 0.5 degrees N and 17 degrees S) are attributed to the interaction of a hotspot with the Wharton spreading ridge that caused significant thermal rejuvenation and hence weakening of the lithosphere. The higher mechanical strength values in the northern NER (north of 0.5 degrees N) may support the idea of off-ridge emplacement and a relatively large plate motion at the time of volcanism. The low T-e and deeper Moho (similar to 22 km) estimates in the southern part (south of 17 degrees S) suggest that the lithosphere was weak and therefore younger at the time of volcanism, and this supports the idea that the southern NER was emplaced on the edge of the Indian plate. (C) 2013 Elsevier B.V. All rights reserved.

The influence of the accessory genome on bacterial pathogen evolution

Bacterial pathogens exhibit significant variation in their genomic content of virulence factors. This reflects the abundance of strategies pathogens evolved to infect host organisms by suppressing host immunity. Molecular arms-races have been a strong driving force for the evolution of pathogenicity, with pathogens often encoding overlapping or redundant functions, such as type III protein secretion effectors and hosts encoding ever more sophisticated immune systems. The pathogens’ frequent exposure to other microbes, either in their host or in the environment, provides opportunities for the acquisition or interchange of mobile genetic elements. These DNA elements accessorise the core genome and can play major roles in shaping genome structure and altering the complement of virulence factors. Here, we review the different mobile genetic elements focusing on the more recent discoveries and highlighting their role in shaping bacterial pathogen evolution.

The pgip family in soybean and three other legume species: evidence for a birth-and-death model of evolution

Background Polygalacturonase-inhibiting proteins (PGIPs) are leucine-rich repeat (LRR) plant cell wall glycoproteins involved in plant immunity. They are typically encoded by gene families with a small number of gene copies whose evolutionary origin has been poorly investigated. Here we report the complete characterization of the full complement of the pgip family in soybean (Glycine max [L.] Merr.) and the characterization of the genomic region surrounding the pgip family in four legume species. Results BAC clone and genome sequence analyses showed that the soybean genome contains two pgip loci. Each locus is composed of three clustered genes that are induced following infection with the fungal pathogen Sclerotinia sclerotiorum (Lib.) de Bary, and remnant sequences of pgip genes. The analyzed homeologous soybean genomic regions (about 126 Kb) that include the pgip loci are strongly conserved and this conservation extends also to the genomes of the legume species Phaseolus vulgaris L., Medicago truncatula Gaertn. and Cicer arietinum L., each containing a single pgip locus. Maximum likelihood-based gene trees suggest that the genes within the pgip clusters have independently undergone tandem duplication in each species. Conclusions The paleopolyploid soybean genome contains two pgip loci comprised in large and highly conserved duplicated regions, which are also conserved in bean, M. truncatula and C. arietinum. The genomic features of these legume pgip families suggest that the forces driving the evolution of pgip genes follow the birth-and-death model, similar to that proposed for the evolution of resistance (R) genes of NBS-LRR-type.

Adaptive evolution toward larger size in mammals

The notion that large body size confers some intrinsic advantage to biological species has been debated for centuries. Using a phylogenetic statistical approach that allows the rate of body size evolution to vary across a phylogeny, we find a long-term directional bias toward increasing size in the mammals. This pattern holds separately in 10 of 11 orders for which sufficient data are available and arises from a tendency for accelerated rates of evolution to produce increases, but not decreases, in size. On a branch-by-branch basis, increases in body size have been more than twice as likely as decreases, yielding what amounts to millions and millions of years of rapid and repeated increases in size away from the small ancestral mammal. These results are the first evidence, to our knowledge, from extant species that are compatible with Cope’s rule: the pattern of body size increase through time observed in the mammalian fossil record. We show that this pattern is unlikely to be explained by several nonadaptive mechanisms for increasing size and most likely represents repeated responses to new selective circumstances. By demonstrating that it is possible to uncover ancient evolutionary trends from a combination of a phylogeny and appropriate statistical models, we illustrate how data from extant species can complement paleontological accounts of evolutionary history, opening up new avenues of investigation for both.

Levy grant training scheme evolution : focus on Fiji and Singapore

This thesis examines the evolution of national training policy in Fiji since 1973 with a particular emphasis on the national levy-grant scheme that was introduced in Fiji in that same year. Developments in the Fiji National Training Council (FNTC) levy-grants scheme since its inception, including substantive amendments to the legislation in late 2002, form part of the scholarship. The thesis will provide an analytical narration of the training policy objectives and their transformation over a time span of almost three decades in the context of a small island nation. To inform this study, it was considered essential to compare the Fiji experience of levy grants schemes with other levy grants scheme. The author decided to use as the focal comparative benchmark the case of the Skills Development Fund (SDF) in Singapore. The SDF has been increasingly portrayed, by the World Bank, the International Labour Organisation and other influential agencies, as the best practice case when it comes to managing a training levy grants scheme. The thesis adopted a qualitative approach that utilized elements of case study, historical research, and key person interviews. The challenges of doing 'insider* research were explored because of its pertinence to the study. Because the study also involved the comparison of the policy experiences of two distinct countries, it was imperative to consider the issues and challenges of undertaking comparative research with particular reference to training matters- Given that training is often enmeshed with other human resources management issues, cognisance was taken of some of the broader debates in this regard. Following consideration of the methodological issues, the research paper explores the objectives of national training strategies and, in particular, issues relating to national competitiveness and skills development. The purpose is to situate the issue of training and skills development within the broader discourse of national development. Alternative approaches to the strategic role of training are considered both at the national and organisational level and some of the classic and current debates surrounding human capital investment are visited. The thesis then proceeds to examine the forms of, and rationale for government interventions in the area of training. One of the challenges both in practice and theoretically is to arrive at a consensual definition of training because of the constantly evolving context and boundaries in which training policies are fashioned. This provides the setting to examine the role that governments can and do play in skills development and how levy-grant schemes, in particular, contribute to the process. Three forms of levy grants schemes are identified and examined: levy-generating; levy-exemption; and levy-grant and reimbursement schemes. The levy-grant and reimbursement variant is the basic thrust of this thesis. In this regard, the UK experience with the levy-grant system from 1964 to 1981 is also reviewed. Some of the issues in relation to training levies are scrutinized including the levy as a sheltered source of training finance, levy rates, duration of levy, impact of levy on the quality and quantity of training, benefits to small businesses, links between training and strategic business objectives, repackaging of training to qualify for grants, and the process by which training levy policies are devised. In looking at the policy formulation, it was necessary to unpack the processes involved and explore the role of the state further. In relation to policy development and implementation, the consultation processes, role of bureaucrats, the policy context, and approaches to policy transfer are examined. In looking at the role of the state in policy development, the alternative roles of government are explored and the concepts of the 'developmental state' and the 'corporatist state* evaluated. The notion of the developmental state has particular relevance to this study given the emphasis placed by the Singaporean government on human resource development policies. This sets the scene for a detailed examination of the role of levy-grant training schemes in Fiji and Singapore. The Skills Development Fund in Singapore was developed as an integral component of national economic policy when the Singaporean government decided to break out of the 'low-skills' trap and move the economy towards a higher value adding structure. The levy-grant system was designed to complement the strategy by focusing on upgrading the skills of employees on lower incomes, the assumption being that employees on lower remuneration were more likely to need skills upgrading. The study notes that the early objectives of the SDF were displaced when it was revealed that the bulk of SDF expenditure was directed at higher level supervisory and management training. As a result, the SDF had to refocus its activities on small and medium enterprises and the workers who were likely to miss out on formal training opportunities. The Singaporean context also shows trade unions playing a significant role in worker education and literacy programmes financed under the SDF. To understand this requires some understanding of the historical linkages between the present Singaporean government and trade union leadership. Another aspect of the development of the SDF has been the constant shifting of the institutional responsibility for the scheme. As late as September 2003, the SDF was again moved, this time to the newly created Singapore Workforce Development Agency, with the focus turning to lifelong learning and assisting Singaporeans who are unemployed or made redundant as a result of the economic restructuring. The Fiji experience with the FNTC scheme is different. It evolved in the context of perceived skills shortages but there was a degree of ambiguity over its objectives. There were no specific linkages with economic policy. Relationships with other public training institutions and more recently, private training providers, have been fraught with difficulties. The study examines the origins of the policy, the early difficulties including perceived employer grievances, and the numerous external assessments of the Fiji levy-grant scheme noting that some of them were highly critical. The thesis also examines an attempted reform of the scheme in 1992-93 that proved unsuccessful and the more recent legislative reforms to the scheme in 2002 that have expanded the role of the scheme to encompass, inter alia, national occupational standards and accreditation activities. The thesis concludes by comparing the two schemes noting that the SDF is well entrenched as a policy instrument in Singapore whilst the FNTC is facing a struggle to assert its legitimacy in Fiji.

Evolution of distinct EGF domains with specific functions

EGF domains are extracellular protein modules cross-linked by three intradomain disulfides. Past studies suggest the existence of two types of EGF domain with three-disulfides, human EGF-like (hEGF) domains and complement C1r-like (cEGF) domains, but to date no functional information has been related to the two different types, and they are not differentiated in sequence or structure databases. We have developed new sequence patterns based on the different C-termini to search specifically for the two types of EGF domains in sequence databases. The exhibited sensitivity and specificity of the new pattern-based method represents a significant advancement over the currently available sequence detection techniques. We re-annotated EGF sequences in the latest release of Swiss-Prot looking for functional relationships that might correlate with EGF type. We show that important post-translational modifications of three-disulfide EGFs, including unusual forms of glycosylation and post-translational proteolytic processing, are dependent on EGF subtype. For example, EGF domains that are shed from the cell surface and mediate intercellular signaling are all hEGFs, as are all human EGF receptor family ligands. Additional experimental data suggest that functional specialization has accompanied subtype divergence. Based on our structural analysis of EGF domains with three-disulfide bonds and comparison to laminin and integrin-like EGF domains with an additional interdomain disulfide, we propose that these hEGF and cEGF domains may have arisen from a four-disulfide ancestor by selective loss of different cysteine residues.

Chromosomal mapping of repetitive DNAs in the beetle Dichotomius geminatus provides the first evidence for an association of 5S rRNA and histone H3 genes in insects, and repetitive DNA similarity between the B chromosome and A complement

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

Chromosomal mapping of rDNAs and H3 histone sequences in the grasshopper rhammatocerus brasiliensis (acrididae, gomphocerinae): extensive chromosomal dispersion and co-localization of 5S rDNA/H3 histone clusters in the A complement and B chromosome

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Chromosome evolution in the erythrinid fish, Erythrinus erythrinus (Teleostei : Characiformes)

The genus Erythrinus belongs to the family Erythrinidae, a neotropical fish group. This genus contains only two described species, Erythrinus erythrinus being the most widely distributed in South America. Six samples of this species from five distinct Brazilian localities and one from Argentina were studied cytogenetically. Four groups were identified on the basis of their chromosomal features. Group A comprises three samples, all with 2n = 54 chromosomes, a very similar karyotypic structure, and the absence of chromosome differentiation between males and females. One sample bears up to four supernumerary microchromosomes, which look like 'double minute chromosomes' in appearance. Groups B - D comprise the three remaining samples, all sharing an X1X1X2X2/X1X2Y sex chromosome system. Group B shows 2n = 54/53 chromosomes in females and males, respectively, and also shows up to three supernumerary microchromosomes. Groups C and D show 2n = 52/51 chromosomes in females and males, respectively, but differ in the number of metacentric, subtelocentric, and acrocentric chromosomes. In these three groups ( B - D), the Y is a metacentric chromosome clearly identified as the largest in the complement. The present results offer clear evidence that local samples of E. erythrinus retain exclusive and fixed chromosomal features, indicating that this species may represent a species complex.

Chromosome evolution in fishes: a new challenging proposal from Neotropical species

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

Disease evolution and outcomes in familial AML with germline CEBPA mutations

In-depth molecular investigation of familial leukemia has been limited by the rarity of recognized cases. This study examines the genetic events initiating leukemia and details the clinical progression of disease across multiple families harboring germ-line CEBPA mutations. Clinical data were collected from 10 CEBPA-mutated families, representing 24 members with acute myeloid leukemia (AML). Whole-exome (WES) and deep sequencing were performed to genetically profile tumors and define patterns of clonal evolution. Germline CEBPA mutations clustered within the N-terminal and were highly penetrant, with AML presenting at a median age of 24.5 years (range, 1.75-46 years). In all diagnostic tumors tested (n = 18), double CEBPA mutations (CEBPAdm) were detected, with acquired (somatic) mutations preferentially targeting the C-terminal. Somatic CEBPA mutations were unstable throughout the disease course, with different mutations identified at recurrence. Deep sequencing of diagnostic and relapse paired samples confirmed that relapse-associated CEBPA mutations were absent at diagnosis, suggesting recurrence was triggered by novel, independent clones. Integrated WES and deep sequencing subsequently revealed an entirely new complement of mutations at relapse, verifying the presentation of a de novo leukemic episode. The cumulative incidence of relapse in familial AML was 56% at 10 years (n = 11), and 3 patients experienced ≥3 disease episodes over a period of 17 to 20 years. Durable responses to secondary therapies were observed, with prolonged median survival after relapse (8 years) and long-term overall survival (10-year overall survival, 67%). Our data reveal that familial CEBPA-mutated AML exhibits a unique model of disease progression, associated with favorable long-term outcomes.

A phylogenomic approach to microbial evolution

To study the origin and evolution of biochemical pathways in microorganisms, we have developed methods and software for automatic, large-scale reconstructions of phylogenetic relationships. We define the complete set of phylogenetic trees derived from the proteome of an organism as the phylome and introduce the term phylogenetic connection as a concept that describes the relative relationships between taxa in a tree. A query system has been incorporated into the system so as to allow searches for defined categories of trees within the phylome. As a complement, we have developed the pyphy system for visualising the results of complex queries on phylogenetic connections, genomic locations and functional assignments in a graphical format. Our phylogenomics approach, which links phylogenetic information to the flow of biochemical pathways within and among microbial species, has been used to examine more than 8000 phylogenetic trees from seven microbial genomes. The results have revealed a rich web of phylogenetic connections. However, the separation of Bacteria and Archaea into two separate domains remains robust.

Evolution of vertebrate steroid receptors from an ancestral estrogen receptor by ligand exploitation and serial genome expansions

The evolution of novelty in tightly integrated biological systems, such as hormones and their receptors, seems to challenge the theory of natural selection: it has not been clear how a new function for any one part (such as a ligand) can be selected for unless the other members of the system (e.g., a receptor) are already present. Here I show—based on identification and phylogenetic analysis of steroid receptors in basal vertebrates and reconstruction of the sequences and functional attributes of ancestral proteins—that the first steroid receptor was an estrogen receptor, followed by a progesterone receptor. Genome mapping and phylogenetic analyses indicate that the full complement of mammalian steroid receptors evolved from these ancient receptors by two large-scale genome expansions, one before the advent of jawed vertebrates and one after. Specific regulation of physiological processes by androgens and corticoids are relatively recent innovations that emerged after these duplications. These findings support a model of ligand exploitation in which the terminal ligand in a biosynthetic pathway is the first for which a receptor evolves; selection for this hormone also selects for the synthesis of intermediates despite the absence of receptors, and duplicated receptors then evolve affinity for these substances. In this way, novel hormone-receptor pairs are created, and an integrated system of increasing complexity elaborated. This model suggests that ligands for some “orphan” receptors may be found among intermediates in the synthesis of ligands for phylogenetically related receptors.

Measuring genome evolution

The determination of complete genome sequences provides us with an opportunity to describe and analyze evolution at the comprehensive level of genomes. Here we compare nine genomes with respect to their protein coding genes at two levels: (i) we compare genomes as “bags of genes” and measure the fraction of orthologs shared between genomes and (ii) we quantify correlations between genes with respect to their relative positions in genomes. Distances between the genomes are related to their divergence times, measured as the number of amino acid substitutions per site in a set of 34 orthologous genes that are shared among all the genomes compared. We establish a hierarchy of rates at which genomes have changed during evolution. Protein sequence identity is the most conserved, followed by the complement of genes within the genome. Next is the degree of conservation of the order of genes, whereas gene regulation appears to evolve at the highest rate. Finally, we show that some genomes are more highly organized than others: they show a higher degree of the clustering of genes that have orthologs in other genomes.