Functional genomics of a symbiotic community : shared traits in the olive fruit fly gut microbiota

The olive fruit fly Bactrocera oleae is a major pest of olives worldwide and houses a specialized gut microbiota dominated by the obligate symbiont “Candidatus Erwinia dacicola”. Ca. E. dacicola is thought to supplement dietary nitrogen to the host, with only indirect evidence for this hypothesis so far. Here, we sought to investigate the contribution of the symbiosis to insect fitness and explore the ecology of the insect gut. For this purpose, we examined the composition of bacterial communities associated with Cretan olive fruit fly populations, and inspected several genomes and one transcriptome assembly. We identified, and reconstructed the genome of, a novel component of the gut microbiota, Tatumella sp. TA1, which is stably associated with Mediterranean olive fruit fly populations. We also reconstructed a number of pathways related to nitrogen assimilation and interactions with the host. The results show that, despite variation in taxa composition of the gut microbial community, core functions related to the symbiosis are maintained. Functional redundancy between different microbial taxa was observed for genes involved in urea hydrolysis. The latter is encoded in the obligate symbiont genome by a conserved urease operon, likely acquired by horizontal gene transfer, based on phylogenetic evidence. A potential underlying mechanism is the action of mobile elements, especially abundant in the Ca. E. dacicola genome. This finding, along with the identification, in the studied genomes, of extracellular surface structure components that may mediate interactions within the gut community, suggest that ongoing and past genetic exchanges between microbes may have shaped the symbiosis

Visual Processing Speed in Capuchin Monkeys (Cebus apella) and Rhesus Macaques (Macaca mulatta)

Visual acuity is a defining feature of the primates. Humans can process visual stimuli at extremely rapid presentation durations, as short as 14 ms. Evidence suggests that other primates, including chimpanzees and rhesus macaques, can process visual information at similarly rapid rates. What is lacking is information on the abilities of New World monkeys, which is necessary to determine whether rapid processing is present across the primates or is specific to Old World primates. We tested capuchin (Cebus apella) and rhesus (Macaca mulatta) monkeys on a computerized matching-to-sample paradigm to determine the shortest presentation duration at which stimuli could be correctly identified. In Study 1, using clip art images, both species achieved presentation durations as short as 25 ms while maintaining high accuracy rates. In Study 2, we used logographic Asian language characters to see if stimuli that were more similar in appearance would reveal species differences. Neither species was as accurate, or achieved as short of presentation durations, as with clip-art images. In particular, capuchins were initially less accurate than rhesus in Study 2, but with experience, achieved similar accuracy rates and presentation durations. These data indicate that rapid visual processing abilities are widespread in the primate lineage, and that the form of the stimuli presented can have an effect on processing across species

A Holocene Record of Changing Arctic Ocean Ice Drift Analogous to the Effects of the Arctic Oscillation

The Arctic Oscillation (AO) controls the configuration of the Transpolar Drift (TPD). If thicker ice from the Beaufort Gyre were exported, the volume of fresh water/sea ice in the Nordic seas would significantly increase, decreasing the formation of North Atlantic deep water. This would cool large parts of the Northern Hemisphere and affect global climate. Therefore, in order to understand how the global climate system functions, it is imperative to know how the TPD changed over the last millennium or more. The provenance of grains in a sediment core located near the confluence of the TPD and the Beaufort Gyre provides a direct proxy for changes in seaice drift owing to these circulation systems. The core has more than 200 cm of Holocene sediment, with intervals dominated by grains from the Russian shelves alternating with intervals of abundant grains from North American sources. Grains matched to Russian shelves indicate that the TPD was shifted toward North America, similar to what occurs during a more positive phase of the AO. This condition alternated with intervals where few grains matched to Russian sources, presumably because the TPD was restricted to the Russian half of the Arctic, far from the core site. During the last 1300 years, increased influx of Russian grains occurred approximately every 50-150 years. This fluctuation might represent the long-term oscillation of the AO, which modulates the same TPD shift today

INNOVATION AND NATIONAL BROADBAND POLICIES: FACTS, FICTION AND UNANSWERED QUESTIONS IN THE NET NEUTRALITY DEBATE

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Large-scale and significant expression from pseudogenes in Sodalis glossinidius – a facultative bacterial endosymbiont

The majority of bacterial genomes have high coding efficiencies, but there are some genomes of intracellular bacteria that have low gene density. The genome of the endosymbiont Sodalis glossinidius contains almost 50 % pseudogenes containing mutations that putatively silence them at the genomic level. We have applied multiple ‘omic’ strategies, combining Illumina and Pacific Biosciences Single-Molecule Real-Time DNA sequencing and annotation, stranded RNA sequencing and proteome analysis to better understand the transcriptional and translational landscape of Sodalis pseudogenes, and potential mechanisms for their control. Between 53 and 74 % of the Sodalis transcriptome remains active in cell-free culture. The mean sense transcription from coding domain sequences (CDSs) is four times greater than that from pseudogenes. Comparative genomic analysis of six Illumina-sequenced Sodalis isolates from different host Glossina species shows pseudogenes make up ~40 % of the 2729 genes in the core genome, suggesting that they are stable and/or that Sodalis is a recent introduction across the genus Glossina as a facultative symbiont. These data shed further light on the importance of transcriptional and translational control in deciphering host–microbe interactions. The combination of genomics, transcriptomics and proteomics gives a multidimensional perspective for studying prokaryotic genomes with a view to elucidating evolutionary adaptation to novel environmental niches