microRNAs and the evolution of complex multicellularity: identification of a large,diverse complement of microRNAs in the brown alga Ectocarpus

There is currently convincing evidence that microRNAs have evolved independently in at least six different eukaryotic lineages: animals, land plants, chlorophyte green algae, demosponges, slime molds and brown algae. MicroRNAs from different lineages are not homologous but some structural features are strongly conserved across the eukaryotic tree allowing the application of stringent criteria to identify novel microRNA loci. A large set of 63 microRNA families was identified in the brown alga Ectocarpus based on mapping of RNA-seq data and nine microRNAs were confirmed by northern blotting. The Ectocarpus microRNAs are highly diverse at the sequence level with few multi-gene families, and do not tend to occur in clusters but exhibit some highly conserved structural features such as the presence of a uracil at the first residue. No homologues of Ectocarpus microRNAs were found in other stramenopile genomes indicating that they emerged late in stramenopile evolution and are perhaps specific to the brown algae. The large number of microRNA loci in Ectocarpus is consistent with the developmental complexity of many brown algal species and supports a proposed link between the emergence and expansion of microRNA regulatory systems and the evolution of complex multicellularity.     

Biotic and abiotic parameters associated with an epizootic of Coelomomyces punctatus in a larval population of the mosquito Anopheles quadrimaculatus.

Biotic and abiotic parameters associated with an epizootic of the fungus Coelomomyces punctatus in larval populations of the mosquito Anopheles quadrimaculatus were investigated for three mosquito breeding seasons (1986-1988) in two adjacent farm ponds in North Carolina. In the first pond, the prevalence of infected larvae averaged 42% (range 0-85%) for collections made weekly from May 1 to November 20, 1986, but larvae did not occur in this pond in 1987. Infection rates in the adjacent pond, sampled during the mosquito breeding seasons of 1987 and 1988, declined from 10.9% (range 0-27.5%) in 1987 to 2.5% (range 0-14.2%) in 1988. Correlation analyses between the number of female copepods and fungal infection rates in sentinel mosquitoes were significant (P < 0.01) for Acanthocyclops robustus but insignificant for eight other species. Infections obtained in sentinel larvae placed in the ponds for 3 hr intervals indicated that C. punctatus infected larvae around sundown. Infection rates for field-collected larvae increased with the stage of larval development. However, experiments with sentinel larvae showed that early instars were more susceptible to infection than later instars, suggesting that the higher infection rates in late instars resulted from individual larvae being infected by two or more zygotes during larval development. Standard multiple regression analyses, used to determine the relationship between seasonal infection rates and water chemistry, weather variables, and the abundance of early and late instar larvae, showed that the abundance of late instars was the only independent variable common to linear models. The models only accounted for 20 and 9% of the variation in larval infection rates for 1987 and 1988, respectively. These results indicate that of the parameters examined, the seasonal abundance of the copepod, A. robustus, was the most important factor (or variable) correlated with the prevalence of mosquito infection.     

Sampling Techniques for the Enumeration of Microorganisms in the Diverticulum of the Anterior Thoracic Air Sac of Chickens

The swab, excise, flush, and agar microbial sampling techniques were applied randomly to the air sac cavities of 130 healthy broiler chickens of 56 to 70 days of age when slaughtered. Samples were obtained from both nonscalded and scalded chickens. The scalded chickens were immersed in the scald water (49 ± 0.5 C) for 120 sec immediately after severing the blood vessels from the outside at the base of the lower mandible. From these data, a selection was made of a sampling technique for the air sac cavity which would yield reproducible counts with the least amount of variation.

The flush and swab technique did not differ significantly and had less variation than did the excise and agar techniques. Even though no significant differences existed between the flush and swab techniques, the flush technique might be preferred because of the closed system present during the time in which the sample is obtained. The method of expressing microbial concentration in the air sac cavity might best be as “per air sac.”

     

Spatial and temporal population genetic structure of four northeastern Pacific littorinid gastropods: the effect of mode of larval development on variation at one mitochondrial and two nuclear DNA markers

We investigated the effect of development mode on the spatial and temporal population genetic structure of four littorinid gastropod species. Snails were collected from the same three sites on the west coast of Vancouver Island, Canada in 1997 and again in 2007. DNA sequences were obtained for one mitochondrial gene, cytochrome b ( Cyt b ), and for up to two nuclear genes, heat shock cognate 70 ( HSC70 ) and aminopeptidase N intron ( APN54 ). We found that the mean level of genetic diversity and long-term effective population sizes ( N _e) were significantly greater for two species, Littorina scutulata and L. plena , that had a planktotrophic larval stage than for two species, Littorina sitkana and L. subrotundata , that laid benthic egg masses which hatched directly into crawl-away juveniles. Predictably, two poorly dispersing species, L. sitkana and L. subrotundata , showed significant spatial genetic structure at an 11- to 65-km geographical scale that was not observed in the two planktotrophic species. Conversely, the two planktotrophic species had more temporal genetic structure over a 10-year interval than did the two direct-developing species and showed highly significant temporal structure for spatially pooled samples. The greater temporal genetic variation of the two planktotrophic species may have been caused by their high fecundity, high larval dispersal, and low but spatially correlated early survivorship. The sweepstakes-like reproductive success of the planktotrophic species could allow a few related females to populate hundreds of kilometres of coastline and may explain their substantially larger temporal genetic variance but lower spatial genetic variance relative to the direct-developing species.     

The evolutionary emergence of stochastic phenotype switching in bacteria

Stochastic phenotype switching - or bet hedging - is a pervasive feature of living systems and common in bacteria that experience fluctuating (unpredictable) environmental conditions. Under such conditions, the capacity to generate variable offspring spreads the risk of being maladapted in the present environment, against offspring likely to have some chance of survival in the future. While a rich subject for theoretical studies, little is known about the selective causes responsible for the evolutionary emergence of stochastic phenotype switching. Here we review recent work - both theoretical and experimental - that sheds light on ecological factors that favour switching types over non-switching types. Of particular relevance is an experiment that provided evidence for an adaptive origin of stochastic phenotype switching by subjecting bacterial populations to a selective regime that mimicked essential features of the host immune response. Central to the emergence of switching types was frequent imposition of 'exclusion rules' and 'population bottlenecks' - two complementary faces of frequency dependent selection. While features of the immune response, exclusion rules and bottlenecks are likely to operate in many natural environments. Together these factors define a set of selective conditions relevant to the evolution of stochastic switching, including antigenic variation and bacterial persistence.     

Partial protein domains: evolutionary insights and bioinformatics challenges

Protein domains are generally thought to correspond to units of evolution. New research raises questions about how such domains are defined with bioinformatics tools and sheds light on how evolution has enabled partial domains to be viable.With the rapid expansion in the number of determined protein sequences - over 92 million in UniProt in March 2015 - an ever-increasing number of biologists are using bioinformatics tools for annotation of these sequences. One widely used strategy is to identify occurrences of Pfam families within the sequence of interest [1]. A Pfam family is a multiple sequence alignment of the occurrences of a particular domain both in different species and in different regions of the same protein. The concept underpinning Pfam is that proteins typically comprise one or more domains (regions), each of which is an evolutionary unit that generally has a well-defined biological function. A significant sequence similarity between a query protein and a Pfam family provides the basis for annotations. Two recent articles [2,3] in Genome Biology evaluate the implications of having the query sequence only matching part of a Pfam family, which is an intriguing finding, given that a Pfam family is considered to be an evolutionary unit.     

A large-subunit mitochondrial ribosomal DNA sequence translocated to the nuclear genome of two stone crabs (Menippe)

Two DNA sequences that appear to be homologous to large-subunit mitochondrial ribosomal RNA genes have been identified in the stone crabs Menippe mercenaria and M. adina. Amplification from whole genomic DNA by polymerase chain reaction (PCR) with oligonucleotide primers based on conserved portions of large-subunit mitochondrial rRNA genes consistently amplified two products of similar length (565 and 567 bp). These products differed at 3% of their nucleotide bases, and could be distinguished by a HindIII site. Only one of these sequences (designated the A sequence) was detected by PCR in purified mitochondrial DNA. The other (designated the B sequence) hybridized to total genomic DNA at a level consistent with a nuclear genome location. It is unlikely that the type B product would have been recognized as a nuclear copy by examination of its sequence alone. This is the first report of a mitochondrial gene sequence translocated into the nuclear genome of a crustacean.