How accurately is ncRNA aligned within whole-genome multiple alignments?

Background  

Multiple alignment of homologous DNA sequences is of great interest to biologists since it provides a window into evolutionary processes. At present, the accuracy of whole-genome multiple alignments, particularly in noncoding regions, has not been thoroughly evaluated.     

Mating behaviour in Schistosomes: are paired worms always faithful?

Previously assumed to be monogamous, the mating system of schistosomes has been the subject of some debate since recent findings have shown that change of mate can occur among these parasites. Here, Louis-Albert Tchuem Tchuenté, Vaughan R. Southgate, Claude Combes and Joseph Jourdane review progress made in the understanding of the mating behaviour of schistosomes, and highlight the importance of mating systems in the dynamics of natural transmission of schistosomiasis.     

Macrophage fusion: are somatic and cancer cells possible partners?

The fusion of cells is a fundamental biological event that plays a central role in a variety of developmental and homeostatic processes. Macrophages are present in all tissues and can initiate interaction and fusion. The putative macrophage-fusion machinery is still poorly understood, but some of its components have been identified. Macrophages recognize each other as < self > in order to fuse but some essential questions remain: do macrophages fuse with somatic cells to repair tissues and organs? Do macrophages fuse with tumor cells to trigger metastasis? Agnès Vignery discusses these novel and challenging ideas in this review.     

Infection prevalence and vector-borne transmission: are vectors always to blame?

The potential for vector-independent transmission of pathogens to occur in what is generally considered to be a vector-borne system is a subject that has received little direct attention. The circumstances under which such a process might take place could conceivably be described as 'occasional' under natural conditions and 'accidental' under unnatural conditions. A more immediate concern is the ability to detect the presence of vector-independent transmission in action and, where possible, to quantify its contribution to overall infection prevalence. As intrinsically difficult as this process might be, careful observation and the use of laboratory and field-scale experiments have indicated that alternative, vector-independent routes of transmission do exist and might contribute significantly to overall prevalence in some host-vector-pathogen systems.     

Macrophage fusion: are somatic and cancer cells possible partners?

Macrophages are present in all tissues and can fuse with themselves to differentiate into multinucleate osteoclasts or giant cells that play a central role in osteoporosis and chronic inflammatory diseases, respectively. Yet, the mechanism by which they fuse remains uncharacterized. The macrophage fusion receptor (MFR) and its ligand CD47 might mediate homotypic fusion of macrophages and allow for their recognition as 'self' before fusion. Although a novel process and controversial idea, macrophages might exploit a similar mechanism for fusion with somatic cells or tumor cells, with resultant organ repair or metastasis, respectively. Hence, macrophages might be the 'double-edged swords' of tissues.     

Plant secondary compounds as complementary resources: are they always complementary?

Generalist herbivores typically grow better on mixed- than on single-component diets. This response has been attributed to food complementarities that either enhance the utilization of nutrients or dilute the negative impacts of plant secondary compounds (PSC). For instance, when animals choose between foods that contain diverse PSC, they eat more than animals offered a food that contains just one PSC. In addition to their negative impacts on herbivore fitness, recent evidence suggests that at appropriate doses PSC may provide beneficial effects to herbivores (i.e., by reducing parasitic infections). Thus, complementarities among diverse PSC may not only influence an herbivore’s ability to consume food but also reduce the incidence of disease. We assessed the complementary effects of two PSC by offering sheep (Ovis aries) a choice of foods containing condensed tannins and saponins while challenged with a parasitic (Haemonchus contortus) infection. Animals offered a choice ate more than animals just offered tannins or saponins in single rations. However, sheep offered choices displayed greater fecal egg counts (an indirect measurement of parasitic burdens) than sheep offered single rations. Thus, saponin- and tannin-containing foods were complementary resources regarding nutrient intake but antagonistic regarding effects on parasitic loads. The nature of the relationship among PSC may depend on the dimension (i.e., nutrient intake, disease) where the interaction occurs. A unifying currency such as growth or reproductive output may help understand the trade-offs between costs (disease) and benefits (nutrient and medicine intake) for herbivores grazing multiple PSC.     

Amyloids of multiple species: are they helpful in survival?

Amyloids are primarily known for their roles in neurodegenerative disorders, as well as in systemic diseases like diabetes. Evolutionary forces tend to maintain a healthy set of heritable characteristics, while eliminating toxic or unfavourable elements; but amyloids seem to represent an exception to this fundamental concept. In addition to their presence in mammals, amyloids also persist in the proteome of many lower organisms that may be linked with possible roles in survival, which are still unexplored. Herein, we address some unanswered questions regarding amyloids: are these well‐structured proteinaceous aggregates a by‐product of inefficient folding events, or have they been retained in our protein repertoire for as yet unknown functional roles; and how do protein misfolding and associated disorders originate, despite the presence of protein quality‐control systems inside the cells? This review aims to extend our current understanding about the multifaceted useful properties of amyloids and their functional interactions with other molecular pathways in various species; this may provide new insights to identify novel therapeutic strategies for ageing and neurodegenerative diseases.     

How many hydrogen-bonded α-turns are possible?

The formation of α-turns is a possibility to reverse the direction of peptide sequences via five amino acids. In this paper, a systematic conformational analysis was performed to find the possible isolated α-turns with a hydrogen bond between the first and fifth amino acid employing the methods of ab initio MO theory in vacuum (HF/6-31G*, B3LYP/6-311?+?G*) and in solution (CPCM/HF/6-31G*). Only few α-turn structures with glycine and alanine backbones fulfill the geometry criteria for the i←(i?+?4) hydrogen bond satisfactorily. The most stable representatives agree with structures found in the Protein Data Bank. There is a general tendency to form additional hydrogen bonds for smaller pseudocycles corresponding to β- and γ-turns with better hydrogen bond geometries. Sometimes, this competition weakens or even destroys the i←(i?+?4) hydrogen bond leading to very stable double β-turn structures. This is also the reason why an “ideal” α-turn with three central amino acids having the perfect backbone angle values of an α-helix could not be localized. There are numerous hints for stable α-turns with a distance between the \( {{\hbox{C}}_\alpha } \)-atoms of the first and fifth amino acid smaller than 6-7 Å, but without an i←(i?+?4) hydrogen bond.     

How independent are TSE agents from their hosts?

Central to understanding the nature TSE agents (or prions) is how their genetic information is distinguished from the host. Are TSEs truly infectious diseases with host-independent genomes, or are they aberrations of a host component derived from the host genome? Recent experiments tested whether glycosylation of host PrP affects TSE strain characteristics. Wild-type mice were infected with 3 TSE strains passaged through transgenic mice with PrP devoid of glycans at 1 or both N-glycosylation sites. Strain-specific characteristics of 1 TSE strain changed but did not change for 2 others. Changes resulted from the selection of mutant TSE strains in a novel replicative environment. In general the properties of established TSEs support the genetic independence of TSE agents from the host, and specifically the primary structure of PrP does not directly encode TSE agent properties. However sporadic TSEs, challenge this independency. The prion hypothesis explains emerging TSEs relatively successfully but poorly accounts for the diversity and mutability of established TSE strains, or how many different infectious conformations are sustained thermodynamically. Research on early changes in RNA expression and events at the ribosome may inform the debate on TSE agent properties and their interaction with host cell machinery.     

Revealing the genetic basis of multiple sclerosis: are we there yet?

For more than 30 years the only genetic factor associated with susceptibility to multiple sclerosis (MS) was the human leukocyte antigen (HLA) region. Recent advancements in genotyping platforms and the development of more effective statistical methods resulted in the identification of 16 more genes by genome-wide association studies (GWAS) in the last three years alone. While the effect of each of these genes is modest compared to that of HLA, this list is expected to grow significantly in the near future, thus defining a complex landscape in which susceptibility may be determined by a combination of allelic variants in different pathways according to ethnic background, disease sub-type, and specific environmental triggers. A considerable overlap of susceptibility genes among multiple autoimmune diseases is becoming evident and integration of these genetic variants with our current knowledge of affected biological pathways will greatly improve our understanding of mechanisms of general autoimmunity and of tissue specificity.     

Carbon dioxide fixation in 'Archaeoglobus lithotrophicus': are there multiple autotrophic pathways?

Several representatives of the euryarchaeal class Archaeoglobi are able to grow facultative autotrophically using the reductive acetyl-CoA pathway, with 'Archaeoglobus lithotrophicus' being an obligate autotroph. However, genome sequencing revealed that some species harbor genes for key enzymes of other autotrophic pathways, i.e. 4-hydroxybutyryl-CoA dehydratase of the dicarboxylate/hydroxybutyrate cycle and the hydroxypropionate/hydroxybutyrate cycle and ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) of the Calvin-Benson cycle. This raised the question of whether only one or multiple autotrophic pathways are operating in these species. We searched for the presence of enzyme activities specific for the dicarboxylate/hydroxybutyrate or the hydroxypropionate/hydroxybutyrate cycles in 'A. lithotrophicus', but such enzymes could not be detected. Low Rubisco activity was detected that could not account for the carbon dioxide (CO(2)) fixation rate; in addition, phosphoribulokinase activity was not found. The generation of ribulose 1,5-bisphosphate from 5-phospho-D-ribose 1-pyrophosphate was observed, but not from AMP; these sources for ribulose 1,5-bisphosphate have been proposed before. Our data indicate that the reductive acetyl-CoA pathway is the only functioning CO(2) fixation pathway in 'A. lithotrophicus'.     

How independent are the appearances of n-mers in different genomes?

MOTIVATION: Analysis of statistical properties of DNA sequences is important for evolutional biology as well as for DNA probe and PCR technologies. These technologies, in turn, can be used for organism identification, which implies applications in the diagnosis of infectious diseases, environmental studies, etc. RESULTS: We present results of the correlation analysis of distributions of the presence/absence of short nucleotide subsequences of different length ('n-mers', n = 5-20) in more than 1500 microbial and virus genomes, together with five genomes of multicellular organisms (including human). We calculate whether a given n-mer is present or absent (frequency of presence) in a given genome, which is not the usually calculated number of appearances of n-mers in one or more genomes (frequency of appearance). For organisms that are not close relatives of each other, the presence/absence of different 7-20mers in their genomes are not correlated. For close biological relatives, some correlation of the presence of n-mers in this range appears, but is not as strong as expected. Suppressed correlations among the n-mers present in different genomes leads to the possibility of using random sets of n-mers (with appropriately chosen n) to discriminate genomes of different organisms and possibly individual genomes of the same species including human with a low probability of error.     

A possible non-sexual origin of mate preference: are male guppies mimicking fruit?

In most animals, the origins of mating preferences are not clear. The "sensory-bias" hypothesis proposes that biases in female sensory or neural systems are important in triggering sexual selection and in determining which male traits will become elaborated into sexual ornaments. Subsequently, other mechanisms can evolve for discriminating between high- and low-quality mates. Female guppies (Poecilia reticulata) generally show a preference for males with larger, more chromatic orange spots. It has been proposed that this preference originated because it enabled females to obtain high-quality mates. We present evidence for an alternative hypothesis, that the origin of the preference is a pleiotropic effect of a sensory bias for the colour orange, which might have arisen in the context of food detection. In field and laboratory experiments, adult guppies of both sexes were more responsive to orange-coloured objects than to objects of other colours, even outside a mating context. Across populations, variation in attraction to orange objects explained 94% of the inter-population variation in female mate preference for orange coloration on males. This is one of the first studies to show both an association between a potential trigger of a mate-choice preference and a sexually selected trait, and also that an innate attraction to a coloured inanimate object explains almost all of the observed variation in female mate choice. These results support the "sensory-bias" hypothesis for the evolution of mating preferences.     

Method selection for species distribution modelling: are temporally or spatially independent evaluations necessary?

To assess the realism of habitat projections in the context of climate change, we conduct independent evaluations of twelve species distribution models, including three novel ecosystem‐based modelling techniques. Habitat hindcasts for 24 western North American tree species were validated against 931 palaeoecological records from 6000, 11000, 14000, 16000 and 21000 yr before present. In addition, we evaluate regional extrapolations based on geographic splits of >55000 sample plots. Receiver operating characteristic analyses indicated excellent predictive accuracy for cross‐validations (median AUC of 0.90) and fair accuracy for independent regional and palaeoecological validations (0.78 and 0.75). Surprisingly, we found little evidence for over‐parameterisation in any method. Also, given high correlations found between model accuracies in non‐independent and independent evaluations, we conclude that non‐independent evaluations are effective model selection tools. Ecosystem‐based modelling approaches performed below average with respect to model sensitivity but excelled in specificity statistics and robustness against extrapolations far beyond training data, suggesting that they are well suited to reconstruct historical biogeographies and glacial refugia.     

Fractal characteristics of May-Grünwald-Giemsa stained chromatin are independent prognostic factors for survival in multiple myeloma

Background

The use of computerized image analysis for the study of nuclear texture features has provided important prognostic information for several neoplasias. Recently fractal characteristics of the chromatin structure in routinely stained smears have shown to be independent prognostic factors in acute leukemia. In the present study we investigated the influence of the fractal dimension (FD) of chromatin on survival of patients with multiple myeloma.

Methodology

We analyzed 67 newly diagnosed patients from our Institution treated in the Brazilian Multiple Myeloma Study Group. Diagnostic work-up consisted of peripheral blood counts, bone marrow cytology, bone radiograms, serum biochemistry and cytogenetics. The International Staging System (ISS) was used. In every patient, at least 40 digital nuclear images from diagnostic May-Grünwald-Giemsa stained bone marrow smears were acquired and transformed into pseudo-3D images. FD was determined by the Minkowski-Bouligand method extended to three dimensions. Goodness-of-fit of FD was estimated by the R² values in the log-log plots. The influence of diagnostic features on overall survival was analyzed in Cox regressions. Patients that underwent autologous bone marrow transplantation were censored at the day of transplantation.

Principal Findings

Median age was 56 years. According to ISS, 14% of the patients were stage I, 39% were stage II and 47% were stage III. Additional features of a bad prognosis were observed in 46% of the cases. When stratifying for ISS, both FD and its goodness-of-fit were significant prognostic factors in univariate analyses. Patients with higher FD values or lower goodness-of-fit showed a worse outcome. In the multivariate Cox-regression, FD, R², and ISS stage entered the final model, which showed to be stable in a bootstrap resampling study.

Conclusions

Fractal characteristics of the chromatin texture in routine cytological preparations revealed relevant prognostic information in patients with multiple myeloma.     

Combining multiple data sets in a likelihood analysis: which models are the best?

Until recently, phylogenetic analyses have been routinely based on homologous sequences of a single gene. Given the vast number of gene sequences now available, phylogenetic studies are now based on the analysis of multiple genes. Thus, it has become necessary to devise statistical methods to combine multiple molecular data sets. Here, we compare several models for combining different genes for the purpose of evaluating the likelihood of tree topologies. Three methods of branch length estimation were studied: assuming all genes have the same branch lengths (concatenate model), assuming that branch lengths are proportional among genes (proportional model), or assuming that each gene has a separate set of branch lengths (separate model). We also compared three models of among-site rate variation: the homogenous model, a model that assumes one gamma parameter for all genes, and a model that assumes one gamma parameter for each gene. On the basis of two nuclear and one mitochondrial amino acid data sets, our results suggest that, depending on the data set chosen, either the separate model or the proportional model represents the most appropriate method for branch length analysis. For all the data sets examined, one gamma parameter for each gene represents the best model for among-site rate variation. Using these models we analyzed alternative mammalian tree topologies, and we describe the effect of the assumed model on the maximum likelihood tree. We show that the choice of the model has an impact on the best phylogeny obtained.     

Prediction of charge-induced molecular alignment: residual dipolar couplings at pH 3 and alignment in surfactant liquid crystalline phases

Recently we reported that the alignment tensor of a biological macromolecule, which was dissolved in a dilute suspension of highly negatively charged filamentous phage at close to neutral pH, can be predicted from the molecule’s 3D charge distribution and shape (Zweckstetter et al. 2004). Here it is demonstrated that this approach is also applicable to alignment of proteins in liquid crystalline phases formed by filamentous phage at low pH. Residual dipolar couplings (RDCs) predicted by our simple electrostatic model for the B1 domain of protein G in fd phage at pH 3 fit very well with the experimental values. The sign of charge–shape predicted one-bond ¹H–¹⁵N dipolar couplings for the B1 domain of protein G (GB1) was inverted at pH 3 compared to neutral pH, in agreement with experimental observations. Our predictions indicate that this is a feature specific for GB1. In addition, it is shown that RDCs induced in the protein ubiquitin by the presence of a positively charged surfactant system comprising cetylpyridinium bromide/hexanol/sodium bromide can be predicted accurately by a simple electrostatic alignment model. This shows that steric and electrostatic interactions dominate weak alignment of biomolecules for a wide range of pH values both in filamentous phage and in surfactant liquid crystalline phases.