Conserved and variable repeat structures in the Balbiani ring gene family in Chironomus tentans

Summary The four Balbiani ring (BR) genes, BR1, BR2.1, BR2.2, and BR6 in the midge Chironomus tentans constitute a gene family encoding secretory proteins with molecular weights of approximately 10⁶ daltons. The major part of each gene is known to consist of tandemly organized composite repeat units resulting in a hierarchic repeat arrangement.Here, we present the sequence organization of the 5 part of the BR2.2 and BR6 genes and describe the entire transcribed part of the two genes. As the BR1 and BR2.1 genes were also fully characterized recently, this allows the comparison of all genes in the BR gene family.All four genes share the same exon-intron structure and have evolved by gene duplications starting from a common ancestor, having the same overall organization as the BR genes of today.The genes encode proteins that have an approximately 10,000-amino acid residue extended central domain, flanked by a highly charged, 200-residue amino-terminal domain and a globular 110-residue carboxy-terminal domain. Exons 1–3 and the beginning of exon 4 encode the amino-terminal domain, which throughout contains many regions built from short repeats. These repeats are often degenerate as to repeat unit and sequence and are present in different numbers between the genes. In several instances these repeat structures, however, are conserved at the protein level where they form positively or negatively charged regions.Each BR gene has a 26–38-kb-long exon 4, which consists of an array of 125–150 repeat units and encodes the central domain. The number of repeat units appears to be largely preserved by selection and all repeat units in the array are very efficiently homogenized. Occasionally variant repeats have been introduced, presumably from another BR gene by gene conversion, and spread within the array.Introns 1–3 at the 5 end of the genes have diverged extensively in sequence and length between the genes. In contrast, intron 4 at the 3 end is virtually identical between three of the four genes, suggesting that gene conversion homogenizes the 3 ends of the genes, but not the 5 ends. Offprint requests to: L. Wieslander     

Mass spectrometric approaches to study enveloped viruses: New possibilities for structural biology and prophylactic medicine

This review considers principles of the use of mass spectrometry for the study of biological macromolecules. Some examples of protein identification, virion proteomics, testing vaccine preparations, and strain surveillance are represented. Possibilities of structural characterization of viral proteins and their posttranslational modifications are shown. The authors’ studies by MALDI-MS on S-acylation of glycoproteins from various families of enveloped viruses and on oligomerization of the influenza virus hemagglutinin transmembrane domains are summarized.     

RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets

Background

Fuelled by the advent and subsequent development of next generation sequencing technologies, metagenomics became a powerful tool for the analysis of microbial communities both scientifically and diagnostically. The biggest challenge is the extraction of relevant information from the huge sequence datasets generated for metagenomics studies. Although a plethora of tools are available, data analysis is still a bottleneck.

Results

To overcome the bottleneck of data analysis, we developed an automated computational workflow called RIEMS – Reliable Information Extraction from Metagenomic Sequence datasets. RIEMS assigns every individual read sequence within a dataset taxonomically by cascading different sequence analyses with decreasing stringency of the assignments using various software applications. After completion of the analyses, the results are summarised in a clearly structured result protocol organised taxonomically. The high accuracy and performance of RIEMS analyses were proven in comparison with other tools for metagenomics data analysis using simulated sequencing read datasets.

Conclusions

RIEMS has the potential to fill the gap that still exists with regard to data analysis for metagenomics studies. The usefulness and power of RIEMS for the analysis of genuine sequencing datasets was demonstrated with an early version of RIEMS in 2011 when it was used to detect the orthobunyavirus sequences leading to the discovery of Schmallenberg virus.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0503-6) contains supplementary material, which is available to authorized users.     

Contemporary evolution meets conservation biology II: impediments to integration and application

Conservation biology needs to be concerned not just with exogenous threats to populations, but also with the changing nature of populations themselves. In a previous review paper, we highlighted evolution in contemporary time (years to decades) as a largely overlooked aspect of population responses to environmental perturbations. We argued that these responses might affect the fate of natural, managed and exotic populations. In the present review, we discuss issues that may limit the integration of contemporary evolution into conservation biology—with the intent that recognition of these limitations may foster research, discussion and resolution. In particular, we consider (1) alternative perceptions of “evolutionary” and “ecological” time, (2) the role of contemporary evolution as an ecological process, (3) fitness as a bridge between evolution and conservation, and (4) challenges faced by conservation strategies based on gene flow estimation or manipulation. We close by highlighting some situations in which current conservation approaches and contemporary evolution may require reconciliation.     

Conserved and nonconserved structures in the secretory proteins encoded in the Balbiani ring genes ofChironomus tentans

Summary The large, repetitive Balbiani ring (BR) genes, BR 1, 2, and 6, inChironomus tentans originated from a short ancestral sequence and have all evolved according to analogous amplification schemes. We analyzed the structures of the BR-encoded secretory proteins and defined the parts that have been conserved during the evolutionary process. The BR products show striking similarities, with the BR 1 and BR 2 products being more similar to each other than to the BR 6 product. In the constant (C) region of the repeat units, 7 of the 30 amino acid residues are strictly conserved; 4 of these are the cysteine residues. The subrepeat (SR) regions of all the BR products are dominated by repeated tripeptide elements rich in proline and charged amino acid residues. Most of the amino acid replacements in both regions are conservative. Secondary structure predictions suggested that the C regions of the BR 1 and BR2 products have several elements of secondary structure: an -helix, a -strand, and one or two reverse turns, as in globular structures. The prediction for the C region of the BR 6 product is similar but lacks a -strand. The predictions for the intervening SR regions appear less conclusive, but are clearly different from those for the C regions, and suggest regular structures not differing in their conformational elements. The SR regions evolved from an ancestor sequence similar to the C region; thus, the BR products seem to represent an example of evolution from one structure to two differently folded products. It is proposed that the alignment and polymerization of the long BR proteins could be promoted by the repetitive structure of the molecules, due to the possibility of forming disulfide bridges between half-cystine residues and electrostatic interactions between the charged residues of the SR regions. The divergence among the BR products is discussed in relation to possible functional differences among the members of the BR gene family.     

An approach to quality management in structural biology: biophysical selection of proteins for successful crystallization

Aggregation, incorrect folding and low stability are common obstacles for protein structure determination, and are often discovered at a very late state of protein production. In many cases, however, the reasons for failure to obtain diffracting crystals remain entirely unknown. We report on the contribution of systematic biophysical characterization to the success in structural determination of human proteins of unknown fold. Routine analysis using dynamic light scattering (DLS), differential scanning calorimetry (DSC) and Fourier-transform infrared spectroscopy (FTIR) was employed to evaluate fold and stability of 263 purified protein samples (98 different human proteins). We found that FTIR-monitored temperature scanning may be used to detect incorrect folding and discovered a positive correlation between unfolding enthalpy measured with DSC and the size of small, globular proteins that may be used to estimate the quality of protein preparations. Furthermore, our work establishes that the risk of aggregation during concentration of proteins may be reduced through DLS monitoring. In summary, our study demonstrates that biophysical characterization provides an ideal tool to facilitate quality management for structural biology and many other areas of biological research.     

Energy landscapes and dynamics of ion translocation through membrane transporters: a meeting ground for physics,chemistry, and biology

Journal of Biological Physics - The dynamics of ion translocation through membrane transporters is visualized from a comprehensive point of view by a Gibbs energy landscape approach. The ΔG...     

Metagenomics in animal gastrointestinal ecosystem: a microbiological and biotechnological perspective

Metagenomics- the application of the genomics technologies to nonculturable microbial communities, is coming of age. These approaches can be used for the screening and selection of nonculturable rumen microbiota for assessing their role in gastrointestinal (GI) nutrition, plant material fermentation and the health of the host. The technologies designed to access this wealth of genetic information through environmental nucleic acid extraction have provided a means of overcoming the limitations of culture-dependent microbial genetic exploitation. The molecular procedures and techniques will result in reliable insights into the GI microbial structure and activity of the livestock gut microbes in relation to functional interactions, temporal and spatial relationships among different microbial consortia and dietary ingredients. Future developments and applications of these methods promise to provide the first opportunity to link distribution and identity of rumen microbes in their natural habitats with their genetic potential and in situ activities.     

All-Food-Seq (AFS): a quantifiable screen for species in biological samples by deep DNA sequencing

Background

DNA-based methods like PCR efficiently identify and quantify the taxon composition of complex biological materials, but are limited to detecting species targeted by the choice of the primer assay. We show here how untargeted deep sequencing of foodstuff total genomic DNA, followed by bioinformatic analysis of sequence reads, facilitates highly accurate identification of species from all kingdoms of life, at the same time enabling quantitative measurement of the main ingredients and detection of unanticipated food components.

Results

Sequence data simulation and real-case Illumina sequencing of DNA from reference sausages composed of mammalian (pig, cow, horse, sheep) and avian (chicken, turkey) species are able to quantify material correctly at the 1% discrimination level via a read counting approach. An additional metagenomic step facilitates identification of traces from animal, plant and microbial DNA including unexpected species, which is prospectively important for the detection of allergens and pathogens.

Conclusions

Our data suggest that deep sequencing of total genomic DNA from samples of heterogeneous taxon composition promises to be a valuable screening tool for reference species identification and quantification in biosurveillance applications like food testing, potentially alleviating some of the problems in taxon representation and quantification associated with targeted PCR-based approaches.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-639) contains supplementary material, which is available to authorized users.     

Bacterial motility: links to the environment and a driving force for microbial physics

Bacterial motility was recognized 300 years ago. Throughout this history, research into motility has led to advances in microbiology and physics. Thirty years ago, this union helped to make run and tumble chemotaxis the paradigm for bacterial movement. This review highlights how this paradigm has expanded and changed, and emphasizes the following points. The absolute magnitude of swimming speed is ecologically important because it helps determine vulnerability to Brownian motion, sensitivity to gradients, the type of receptors used and the cost of moving, with some bacteria moving at 1 mm s(-1). High costs for high speeds are offset by the benefit of resource translocation across submillimetre redox and other environmental gradients. Much of environmental chemotaxis appears adapted to respond to gradients of micrometres, rather than migrations of centimetres. In such gradients, control of ion pumps is particularly important. Motility, at least in the ocean, is highly intermittent and the speed is variable within a run. Subtleties in flagellar physics provide a variety of reorientation mechanisms. Finally, while careful physical analysis has contributed to our current understanding of bacterial movement, tactic bacteria are increasingly widely used as experimental and theoretical model systems in physics.     

A Consumer's Right to Choose a Midwife: Shifting Meanings for Reproductive Rights under Neoliberalism

The right to choose has long served as the ideological rallying cry for reproductive rights activists. Yet critical attention to the social, political, and economic conditions under which individuals make such choices has been central to anthropological research on reproduction. In the context of neoliberal public policy shifts that favor trust in the market to remedy all social and economic inequality, I explore how women's reproductive rights are becoming characterized by one's ability to consume uneven reproductive choices. Based on my ethnographic fieldwork with midwifery supporters in Virginia, I examine how organizers have begun to utilize consumer rights rhetoric in their struggle for legal access to midwives. One often-unintended result has been intensified divisions within this movement, particularly as low-income homebirthers feel unable to claim the identity of consumer. I use Virginia as a case study to raise broader questions about women's shifting strategies toward securing reproductive rights under neoliberalism.     

Identification of a cis-regulatory region of a gene in Arabidopsis thaliana whose induction by dehydration is mediated by abscisic acid and requires protein synthesis

The effect of the ATP-dependent exonuclease AddAB complex on the structural stability of plasmid pGP1 inBacillus subtilis was studied. Using deletion mutagenesis and gene amplification techniques,B. subtilis strains were constructed either lacking or overproducing the AddAB complex, a key enzyme in homologous recombination. The deletion mutant possessed no residual ATP-dependent nuclease activity; in contrast, the nuclease activity was up to 30 times higher in lysates of strains carrying multiple copies of theaddAB genes in the chromosome. Southern blot analyses of these strains indicated that a linear relationship exists between the number of chromosomal gene copies and the level of AddAB activity. The structural stability of pGP1 was analyzed in the AddAB-deficient and over-producing backgrounds. Frequencies of deletion formation in the plasmid, as monitored by the expression of the pGP1-encodedpenP-lacZ fusion on media containing X-gal, were shown to be increased at least 25-fold in theaddAB knock-out mutant, whereas the stability of pGP1 was improved up to 15-fold in strains verproducing the AddAB enzyme. A possible explanation for these findings is that interactions between AddAB and plasmid molecules prevent the formation of secondary structures that constitute potential deletion target sites, and thereby enhance the structural stability of plasmids.     

Microarray analysis of ageing-related signatures and their expression in tumors based on a computational biology approach

Ageing and cancer have been associated with genetic and genomic changes.The identification of common signatures between ageing and cancer can reveal shared molecular mechanisms underlying them.In this study,we collected ageing-related gene signatures from ten published studies involved in six different human tissues and an online resource.We found that most of these gene signatures were tissuespecific and a few were related to multiple tissues.We performed a genome-wide examination of the expression of these signatures in various human tumor types,and found that a large proportion of these signatures were universally differentially expressed among normal vs.tumor phenotypes.Functional analyses of the highly-overlapping genes between ageing and cancer using DAVID tools have identified important functional categories and pathways linking ageing with cancer.The convergent and divergent mechanisms between ageing and cancer are discussed.This study provides insights into the biology of ageing and cancer,suggesting the possibility of potential interventions aimed at postponing ageing and preventing cancer.     

Overt and covert competition in a promiscuous mammal: the importance of weaponry and testes size to male reproductive success

Male contests for access to receptive females are thought to have selected for the larger male body size and conspicuous weaponry frequently observed in mammalian species. However, when females copulate with multiple males within an oestrus, male reproductive success is a function of both pre- and postcopulatory strategies. The relative importance of these overt and covert forms of sexual competition has rarely been assessed in wild populations. The Soay sheep mating system is characterized by male contests for mating opportunities and high female promiscuity. We find that greater horn length, body size and good condition each independently influence a male's ability to monopolize receptive females. For males with large horns at least, this behavioural success translates into greater siring success. Consistent with sperm-competition theory, we also find that larger testes are independently associated with both higher copulation rates and increased siring success. This advantage of larger testes emerges, and strengthens, as the number of oestrous females increases, as dominant males can no longer control access to them all. Our results thus provide direct quantitative evidence that male reproductive success in wild populations of mammals is dependent upon the relative magnitude of both overt contest competition and covert sperm competition.     

Facies models for middle to late devonian Shallow-Marine carbonates,with comparisons to modern reefs: a guide for facies analysis

Summary Shallow marine tropical Devonian carbonates commonly were deposited in two major geologic settings, i.e., shallow shelf with shelf margin reef, and gently sloping ramp that grades into peritidal to supratidal, in places evaporitic facies. The facies types within these two settings can be grouped into a few distinct zones on the basis of water, energy, texture, amount of micrite, porosity, fossil assemblages, and indicaton fossils. These zones have been integrated into a composite facies model for shallow marine, tropical Devonian carbonates. The facies zones are easily recognizable in hand specimen and core, and can be used for fast and accurate facies analysis. Some facies recognizable in hand specimen or core do not easily fit into the integrated model and represent facies of short-lived depositional events, such as hurricanes or slump deposits, or spatially restricted areas, such as channel fills. Such facies have to be interpreted on a case-by-case basis by comparison to the surrounding facies and depositional framework through time. Comparisons with Cenozoic reefs reveal a number of similarities. In particular, large metazoans in both Devonian and Cenozoic reefs display a range of growth forms that is not species-specific. Furthermore, several metazoans display comparable growth forms in equivalent facies zones. For example, dendroid stromatoporoids, such asStachyodes, and branching coral, such asPorites porites, occur in equivalent facies zones.     

Hepatitis B in a high prevalence New Zealand population: a mathematical model applied to infection control policy

Background

Chronic hepatitis B (CHB) is a vaccine preventable disease of global public health importance. The prevalence of CHB in New Zealand's Tongan population is over 10%, a level consistent with endemic infection, which contrasts to the low overall New Zealand prevalence (<0.5%). Despite the introduction of infant vaccination in 1988, coverage among Tongan children is estimated to be only 53%.

Aims

To estimate the population benefit of additional public health control measures besides ‘business as usual’ infant vaccination for hepatitis B in high prevalence populations.

Methods

A mathematical model of hepatitis B virus (HBV) transmission was used to predict future CHB prevalence in the New Zealand Tongan population under different infection control strategies.

Results

Prevalence of CHB is predicted to plateau at 2% in the New Zealand Tongan population if coverage remains at current levels, which are therefore insufficient to achieve long-term elimination of HBV. The critical proportion of immunisation coverage for elimination of the virus is estimated to be 73%. The effect of screening for HBV carriage and early disease management was unable to be quantified, but is likely to reduce the population burden of HBV infection and thus contribute to accelerating elimination.

Conclusions and recommendations

Mathematical models are a useful tool to forecast the future burden of CHB under a range of control strategy scenarios in high prevalence populations. Serosurveillance and targeted vaccination has similarly arrested HBV transmission in time-series prevalence studies from Taiwan and Alaska. Such a policy may demonstrate similar efficacy in New Zealand ethnic groups with endemic HBV infection.     

Small angle neutron and X-ray scattering in structural biology: recent examples from the literature

Small angle scattering can provide unique structural information on the shape, domain organisation, and interactions of biomacromolecules in solution. Small angle neutron scattering (SANS) combined with deuterium labelling makes it possible to define the positions of specific components within a complex while small angle X-ray scattering (SAXS) provides more precise data on the overall shape. Here I review four recent publications, three of which were presented at the Neutrons in Biology meeting at the STFC Rutherford Appleton Laboratory in July 2007, that utilise SANS, SAXS, and complementary techniques to define the solution structure of large multidomain proteins and macromolecular complexes. These four papers emphasise the critical importance of sample quality and characterisation as well as the important role played by complementary techniques in building structural models based on small angle scattering data. They show the ability of SANS and SAXS in determining solution structures provides an important complementary structural technique for large, flexible, and glycosylated proteins where high resolution structural techniques, such as crystallography and NMR, cannot be applied.