The universe: a cryogenic habitat for microbial life

Panspermia, an ancient idea, posits that microbial life is ubiquitous in the Universe. After several decades of almost irrational rejection, panspermia is at last coming to be regarded as a serious contender for the beginnings of life on our planet. Astronomical data is shown to be consistent with the widespread distribution of complex organic molecules and dust particles that may have a biological provenance. A minuscule (10(-21)) survival rate of freeze-dried bacteria in space is all that is needed to ensure the continual re-cycling of cosmic microbial life in the galaxy. Evidence that terrestrial life may have come from elsewhere in the solar system has accumulated over the past decade. Mars is seen by some as a possible source of terrestrial life, but some hundreds of billions of comets that enveloped the entire solar system, are a far more likely primordial reservoir of life. Comets would then have seeded Earth, Mars, and indeed all other habitable planetary bodies in the inner regions of the solar system. The implications of this point of view, which was developed in conjunction with the late Sir Fred Hoyle since the 1970s, are now becoming amenable to direct empirical test by studies of pristine organic material in the stratosphere. The ancient theory of panspermia may be on the verge of vindication, in which case the entire universe would be a grand crucible of cryomicrobiology.     

All the observed universe has contributed to life.

This paper presents evidence that virtually all electrons and nuclei of the atoms that are or have been part of living matter on Earth came from almost all stars in our and nearby galaxies and even from all other galaxies in the Universe that have produced observed high-energy gamma rays. However, a standard 70 kg human is always making about 7 3He, 600 40Ca, and 3000 14N nuclei every second by radioactive decay of 3H, 40K, and 14C, respectively.     

Marital coitus across the life course

It remains unclear whether the frequency of marital coitus does in fact decline universally across the life course, what shape that decay normally takes, and what best accounts for it: increasing marriage duration, women's age or age of their partners. Using cross-sectional Demographic and Health Survey (DHS) data of 91,744 non-abstaining women in their first marriage, a generalized linear model is used to determine if there is a consistent pattern in the life course pattern of degradation in the frequency of marital coitus. Datasets were drawn from nineteen countries in Asia, Africa and the Americas. Use of very large samples allows proper disentangling of the effects of women's age, husband's age and marital duration, and use of samples from multiple countries allows consideration of the influence of varied prevailing fertility regimes and fertility-related practices on life course trajectories. It is found that declining coital frequency over time seems a shared demographic feature of human populations, but whether marriage duration, wife's age or husband's age is most responsible for that decline varies by country. In many cases, coital frequency actually increases with women's age into their thirties, once husband's age and marriage duration are taken into account, but in most cases coital frequency declines with husband's age and marital duration.     

Composition and similarity of bovine rumen microbiota across individual animals

The bovine rumen houses a complex microbiota which is responsible for cattle's remarkable ability to convert indigestible plant mass into food products. Despite this ecosystem's enormous significance for humans, the composition and similarity of bacterial communities across different animals and the possible presence of some bacterial taxa in all animals' rumens have yet to be determined. We characterized the rumen bacterial populations of 16 individual lactating cows using tag amplicon pyrosequencing. Our data showed 51% similarity in bacterial taxa across samples when abundance and occurrence were analyzed using the Bray-Curtis metric. By adding taxon phylogeny to the analysis using a weighted UniFrac metric, the similarity increased to 82%. We also counted 32 genera that are shared by all samples, exhibiting high variability in abundance across samples. Taken together, our results suggest a core microbiome in the bovine rumen. Furthermore, although the bacterial taxa may vary considerably between cow rumens, they appear to be phylogenetically related. This suggests that the functional requirement imposed by the rumen ecological niche selects taxa that potentially share similar genetic features.     

The expanding polymerase universe

Over the past year, the number of known prokaryotic and eukaryotic DNA polymerases has exploded. Many of these newly discovered enzymes copy aberrant bases in the DNA template over which 'respectable' polymerases fear to tread. The next step is to unravel their functions, which are thought to range from error-prone copying of DNA lesions, somatic hypermutation and avoidance of skin cancer, to restarting stalled replication forks and repairing double-stranded DNA breaks.     

The universe of exons revisited

We study the distribution of exons in eukaryotic genes to determine whether one can detect the reuse of exon sequences and to use the frequency of such reuse to estimate how many ancestral exon sequences there might have been. We use two databases of exons. One contained 56,276 internal exons from putatively unrelated genes (less than 20% sequence identity) and the second contained 8917 internal exons from regions of these genes that are homologous and colinear with prokaryotic genes; these are ancient conserved regions (ACRs). At the 95% significance level we find 3500 exon-sequence matches in the large database and 500 matches in the ACR database. These matches correspond to groups of similar sequences. The size–rank relationship for these groups follows a power law, the size falling off as the inverse square root of the rank. This form of the power law distribution leads us to make an estimate for the size of a possible universe of ancestral exons. Using the data corresponding to the ACR regions, that universe is estimated to be about 15,000–30,000 in size.     

Phylogenetic similarity and structure of Agaricomycotina communities across a forested landscape

The Agaricomycotina are a phylogenetically diverse group of fungi that includes both saprotrophic and mycorrhizal species, and that form species – rich communities in forest ecosystems. Most species are infrequently observed, and this hampers assessment of the role that environmental heterogeneity plays in determining local community composition and in driving β‐diversity. We used a combination of phenetic (TRFLP) and phylogenetic approaches [Unifrac and Net Relatedness Index (NRI)] to examine the compositional and phylogenetic similarity of Agaricomycotina communities in forest floor and surface soil of three widely distributed temperate upland forest ecosystems (one, xeric oak – dominated and two, mesic sugar maple dominated). Generally, forest floor and soil communities had similar phylogenetic diversity, but there was little overlap of species or evolutionary lineages between these two horizons. Forest floor communities were dominated by saprotrophic species, and were compositionally and phylogenetically similar in all three ecosystems. Mycorrhizal species represented 30% to 90% of soil community diversity, and these communities differed compositionally and phylogenetically between ecosystems. Estimates of NRI revealed significant phylogenetic clustering in both the forest floor and soil communities of only the xeric oak‐dominated forest ecosystem, and may indicate that this ecosystem acts as a habitat filter. Our results suggest that environmental heterogeneity strongly influences the phylogenetic β‐diversity of soil inhabiting Agaricomycotina communities, but has only a small influence on forest floor β‐diversity. Moreover, our results suggest that the strength of community assembly processes, such as habitat filtering, may differ between temperate forest ecosystems.     

The limited universe of exons

The catalogue of mosaic proteins showing evidence of exon-shuffling continues to expand. The repeated use of exon modules suggests that current protein diversity could have been generated from a finite set of such exon modules, and that the size and character of this underlying exon universe can still be glimpsed in extant proteins.     

Integrating function across marine life cycles

Complex life cycles involve a set of discrete stages that candiffer dramatically in form and function. Transitions betweendifferent stages vary in nature and magnitude; likewise, thedegree of autonomy among stages enabled by these transitionscan vary as well. Because the selective value of traits is likelyto shift over ontogeny, the degree of autonomy among stagesis important for understanding how processes at one life-historystage alter the conditions for performance and selection atothers. We pose 3 questions that help to define a research focuson processes that integrate function across life cycles. First,to what extent do particular transitions between life-historystages allow those stages to function as autonomous units? Weidentify the roles that stages play in the life history, typesof transitions between stages, and 3 forces (structural, genetic/epigenetic,and experiential) that can contribute to integration among stages.Second, what are the potential implications of integration acrosslife cycles for assumptions and predictions of life-historytheory? We provide 3 examples where theory has traditionallyfocused on processes acting within stages in isolation fromothers. Third, what are the long-term consequences of carryoverof experience from one life cycle stage to the next? We distinguish3 scenarios: persistence (effects of prior experience persistthrough subsequent stages), amplification (effects persist andare magnified at subsequent stages), and compensation (effectsare compensated for and diminish at subsequent stages). We usethese scenarios to differentiate between effects of a carryoverof state and carryover into subsequent processes. The symposiumintroduced by our discussion is meant to highlight how discretestages can be functionally coupled, such that life cycle evolutionbecomes a more highly integrated response to selection thancan be deduced from the study of individual stages.     

A review of similarity between seed bank and standing vegetation across ecosystems

The relationship between above and belowground species composition has been researched in forests, grasslands, and wetlands to understand what mechanisms control community composition. I thoroughly reviewed 108 articles published between 1945 and 2006 that summarized and provided specific values on similarities between above and belowground communities to identify common trends among ecosystems. Using Sørenson's index of similarity, I found that standing vegetation and its associated seed bank was the least similar in forest ecosystems, most similar in grasslands, and of intermediate similarity in wetlands. I also discovered that species richness was not related to seed bank – vegetation similarity in any of the three ecosystems. Disturbances were a common mechanism driving community composition in all ecosystems, where similarity decreased with time since disturbance in forest and wetland ecosystems and increased with time since disturbance in grasslands. Knowing the relationships between seed bank and standing vegetation may help conservationists to manage against exotic species, plan for community responses to disturbances, restore diversity, and better understand the resilience of an ecosystem.     

Proteasomes and protein conjugation across domains of life

Like other energy-dependent proteases, proteasomes, which are found across the three domains of life, are self-compartmentalized and important in the early steps of proteolysis. Proteasomes degrade improperly synthesized, damaged or misfolded proteins and hydrolyse regulatory proteins that must be specifically removed or cleaved for cell signalling. In eukaryotes, proteins are typically targeted for proteasome-mediated destruction through polyubiquitylation, although ubiquitin-independent pathways also exist. Interestingly, actinobacteria and archaea also covalently attach small proteins (prokaryotic ubiquitin-like protein (Pup) and small archaeal modifier proteins (Samps), respectively) to certain proteins, and this may serve to target the modified proteins for degradation by proteasomes.     

Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation

MOTIVATION: Many bioinformatics data resources not only hold data in the form of sequences, but also as annotation. In the majority of cases, annotation is written as scientific natural language: this is suitable for humans, but not particularly useful for machine processing. Ontologies offer a mechanism by which knowledge can be represented in a form capable of such processing. In this paper we investigate the use of ontological annotation to measure the similarities in knowledge content or 'semantic similarity' between entries in a data resource. These allow a bioinformatician to perform a similarity measure over annotation in an analogous manner to those performed over sequences. A measure of semantic similarity for the knowledge component of bioinformatics resources should afford a biologist a new tool in their repertoire of analyses. RESULTS: We present the results from experiments that investigate the validity of using semantic similarity by comparison with sequence similarity. We show a simple extension that enables a semantic search of the knowledge held within sequence databases. AVAILABILITY: Software available from http://www.russet.org.uk.     

Seed size and plant strategy across the whole life cycle

We compiled information from the international literature to quantify the relationships between seed mass and survival through each of the hazards plants face between seed production and maturity. We found that small-seeded species were more abundant in the seed rain than large-seeded species. However, this numerical advantage was lost by seedling emergence. The disadvantage of small-seeded species probably results from size-selective post-dispersal seed predation, or the longer time small-seeded species spend in the soil before germination. Seedlings from large-seeded species have higher survival through a given amount of time as seedlings. However, this advantage seems to be countered by the greater time taken for large-seeded species to reach reproductive maturity: our data suggested no relationship, or perhaps a weak negative relationship, between seed size and survival from seedling emergence through to adulthood. A previous compilation showed that the inverse relationship between seed mass and the number of seeds produced per unit canopy area per year is countered by positive relationships between seed mass, plant size and plant longevity. Taken together, these data show that our old understanding of a species' seed mass as the result of a trade–off between producing a few large offspring, each with high survival probability, versus producing many small offspring each with a lower chance of successfully establishing was incomplete. It seems more likely that seed size evolves as part of a spectrum of life history traits, including plant size, plant longevity, juvenile survival rate and time to reproduction.