Codon usage bias in Archaea

Synonymous codon usage bias has been extensively studied in Bacteria and Eukaryotes and yet there has been little investigation in the third domain of life, the Archaea. In this thesis I therefore examine the coding sequences of nearly 70 species of Archaea to explore patterns of codon bias. Heterogeneity in codon usage among genes was initially explored for a single species, Methanococcus maripaludis, where patterns were explained by a single major trend associated with expression level and attributed to natural selection. Unlike the bacterium Escherichia coli, selection was largely restricted to two-fold degenerate sites. Analyses of patterns of codon usage bias within genomes were extended to the other species of Archaea, where variation was more commonly explained by heterogeneity in G+C content and asymmetric base composition. By comparison with bacterial genomes, far fewer trends were found to be associated with expression level, implying a reduced prevalence of translational selection among Archaea. The strength of selected codon usage bias (S) was estimated for 67 species of Archaea, and revealed that natural selection has had less impact in shaping patterns of codon usage across Archaea than across many species of Bacteria. Variation in S was explained by the combined effects of growth rate and optimal growth temperature, with species growing at high temperatures exhibiting weaker than expected selection given growth rate. Such a relationship is expected if temperature kinetically modulates growth rate via its impact upon translation elongation, since rapid elongation rates at high temperatures reduce the selective benefit of optimal codon usage for the efficiency of translation. Consistent with this, growth temperature is negatively correlated with minimal generation time, and numbers of rRNA operons and tRNA genes are reduced at high growth temperatures. The large fraction of thermophilic Archaea relative to Bacteria account for the lower values of S observed. Two major trends were found to describe variation in codon usage among archaeal genomes; the first was attributed to GC3s and the second was associated with arginine codon usage and was linked both with growth temperature and the genome-wide excess of G over C content. The latter is unlikely to reflect thermophilic adaptation since the codon primarily underlying the trend appears to be selectively disfavoured. No correlations were observed with genome wide GC3s and optimal growth temperature and neither was GC3s associated with aerobiosis. The identities of optimal codons were explored and found to be invariant across U and C-ending two-fold degenerate amino acid groups. The identity of optimal codons and anticodons across four and six-fold degenerate amino acid groups was found to vary with mutational bias. As was first observed in M. maripaludis, selected codon usage bias was consistently greater across two-fold relative to four-fold degenerate amino acid groups across Archaea. This broad pattern could reflect ancestral patterns of optimal codon divergence, prevalent among four-fold but not two-fold degenerate amino acid groups. Consistent with this, the strength of selected codon usage bias was found to be reduced following the divergence of optimal codons, and implies that optimal codon divergence typically proceeds following the relaxation of selection. Finally, a method was developed to partition the strength of selection (S) into separate components reflecting selection for translational efficiency (Seff) and selection for translational accuracy (Sacc) by comparing the codon usage across conserved and nonconserved amino acid residues. While estimates of Sacc are somewhat sensitive to the designation of conserved sites, a general pattern emerged whereby accuracy-selected codon usage bias was consistently strongest across a subset of the most highly conserved sites. Several estimates of Sacc were consistently higher than the 95% range of null values regardless of the dataset, providing evidence for accuracy-selected codon usage bias in these species

Local cortical dynamics of burst suppression in the anaesthetized brain

Burst suppression is an electroencephalogram pattern that consists of a quasi-periodic alternation between isoelectric ‘suppressions’ lasting seconds or minutes, and high-voltage ‘bursts’. It is characteristic of a profoundly inactivated brain, occurring in conditions including hypothermia, deep general anaesthesia, infant encephalopathy and coma. It is also used in neurology as an electrophysiological endpoint in pharmacologically induced coma for brain protection after traumatic injury and during status epilepticus. Classically, burst suppression has been regarded as a ‘global’ state with synchronous activity throughout cortex. This assumption has influenced the clinical use of burst suppression as a way to broadly reduce neural activity. However, the extent of spatial homogeneity has not been fully explored due to the challenges in recording from multiple cortical sites simultaneously. The neurophysiological dynamics of large-scale cortical circuits during burst suppression are therefore not well understood. To address this question, we recorded intracranial electrocorticograms from patients who entered burst suppression while receiving propofol general anaesthesia. The electrodes were broadly distributed across cortex, enabling us to examine both the dynamics of burst suppression within local cortical regions and larger-scale network interactions. We found that in contrast to previous characterizations, bursts could be substantially asynchronous across the cortex. Furthermore, the state of burst suppression itself could occur in a limited cortical region while other areas exhibited ongoing continuous activity. In addition, we found a complex temporal structure within bursts, which recapitulated the spectral dynamics of the state preceding burst suppression, and evolved throughout the course of a single burst. Our observations imply that local cortical dynamics are not homogeneous, even during significant brain inactivation. Instead, cortical and, implicitly, subcortical circuits express seemingly different sensitivities to high doses of anaesthetics that suggest a hierarchy governing how the brain enters burst suppression, and emphasize the role of local dynamics in what has previously been regarded as a global state. These findings suggest a conceptual shift in how neurologists could assess the brain function of patients undergoing burst suppression. First, analysing spatial variation in burst suppression could provide insight into the circuit dysfunction underlying a given pathology, and could improve monitoring of medically-induced coma. Second, analysing the temporal dynamics within a burst could help assess the underlying brain state. This approach could be explored as a prognostic tool for recovery from coma, and for guiding treatment of status epilepticus. Overall, these results suggest new research directions and methods that could improve patient monitoring in clinical practice.Burroughs Wellcome Fund (Career Award at the Scientific Interface)National Institutes of Health (U.S.) (Director's Pioneer Award DP10D003646)National Institutes of Health (U.S.) (Transformative 1R01GM104948

Impact of translational selection on codon usage bias in the archaeon Methanococcus maripaludis

Patterns of codon usage have been extensively studied among Bacteria and Eukaryotes, but there has been little investigation of species from the third domain of life, the Archaea. Here, we examine the nature of codon usage bias in a methanogenic archaeon, Methanococcus maripaludis. Genome-wide patterns of codon usage are dominated by a strong A + T bias, presumably largely reflecting mutation patterns. Nevertheless, there is variation among genes in the use of a subset of putatively translationally optimal codons, which is strongly correlated with gene expression level. In comparison with Bacteria such as Escherichia coli, the strength of selected codon usage bias in highly expressed genes in M. maripaludis seems surprisingly high given its moderate growth rate. However, the pattern of selected codon usage differs between M. maripaludis and E. coli: in the archaeon, strongly selected codon usage bias is largely restricted to twofold degenerate amino acids (AAs). Weaker bias among the codons for fourfold degenerate AAs is consistent with the small number of tRNA genes in the M. maripaludis genome

Gathering in the City: An Annotated Bibliography and Review of the Literature About Human-Plant Interactions in Urban Ecosystems

The past decade has seen resurgence in interest in gathering wild plants and fungi in cities. In addition to gathering by individuals, dozens of groups have emerged in U.S., Canadian, and European cities to facilitate access to nontimber forest products (NTFPs), particularly fruits and nuts, in public and private spaces. Recent efforts within cities to encourage public orchards and food forests, and to incorporate more fruit and nut trees into street tree planting programs indicate a growing recognition among planners that gathering is an important urban activity. Yet the academic literature has little to say about urban gathering practices or the people who engage in them. This annotated bibliography and literature review is a step toward filling the gap in knowledge about the socioecological roles of NTFPs in urban ecosystems in the United States. Our objectives are to demonstrate that gathering—the collecting of food and raw materials—is a type of human-plant interaction that warrants greater attention in urban green space management, and to provide an overview of the literature on human-plant interactions—including gathering—in urban environments. Our review found that very few studies of urban gathering have been done. Consequently, we included gathering field guides, Web sites, and articles from the popular media in our search. These sources, together with the small number of scientific studies of urban gathering, indicated that people derive numerous benefits from gathering plants and fungi in U.S. cities. Gathering provides useful products, encourages physical activity, offers opportunities to connect with and learn about nature, helps strengthen social ties and cultural identities, and, in some contexts, can serve as a strategic tool for ecological restoration. These benefits parallel those identified in environmental psychology and cultural ecology studies of the effects of gardening and being in nature. The literature on human-plant interactions also emphasizes that humans need to be treated as endogenous factors in dynamic, socially and spatially heterogeneous urban ecosystems. Spatially explicit analyses of human-plant interactions show that the distribution of wealth and power within societies affects the composition, species distribution, and structure of urban ecologies. Our review also indicates that tensions exist between NTFP gatherers and land managers, as well as between gatherers and other citizens over gathering, particularly in public spaces. This tension likely is related to perceptions about the impact these practices have on cherished species and spaces. We conclude that gathering is an important urban activity and deserves a greater role in urban management given its social and potential ecological benefits. Research on urban gathering will require sensitivity to existing power imbalances and the use of theoretical frameworks and methodologies that assume humans are integral and not always negative components of ecosystems

Detection of Rift Valley Fever Virus RNA in Formalin-Fixed Mosquitoes by In Situ Hybridization (RNAscope®).

Rift Valley fever virus (RVFV) causes a zoonotic mosquito-borne haemorrhagic disease that emerges to produce rapid large-scale outbreaks in livestock within sub-Saharan Africa. A range of mosquito species in Africa have been shown to transmit RVFV, and recent studies have assessed whether temperate mosquito species are also capable of transmission. In order to support vector competence studies, the ability to visualize virus localization in mosquito cells and tissue would enhance the understanding of the infection process within the mosquito body. Here, the application of in situ hybridization utilizing RNAscope® to detect RVFV infection within the mosquito species, Culex pipiens, derived from the United Kingdom was demonstrated. Extensive RVFV replication was detected in many tissues of the mosquito with the notable exception of the interior of ovarian follicles

The lethal effect of soap on Schistosoma mansoni cercariae in water

Abstract Background Schistosomiasis is a parasitic disease which is spread through skin contact with water containing Schistosoma cercariae. Drug treatment has been the main control method, but it does not prevent reinfection. The use of soap can be a complementary measure to reduce transmission. Therefore, this study investigates the quantitative effect of different soaps on the mortality of Schistosoma mansoni cercariae. Methodology Four soaps including two powder soaps (Kleesoft and Omo) and two bar soaps (B29 and Rungu) which are used in a schistosomiasis-endemic Tanzanian village were studied. S. mansoni cercariae were exposed to powder soaps of 0 (control), 10, 50, 75, 100 and 1000 mg/L and to bar soaps of 0 (control), 100, 500 and 1000 mg/L. The highest concentration of 1000 mg/L was selected based on the laboratory-estimated average soap concentration during handwashing. Cercariae were observed under a microscope after 0, 5, 15, 30, 45 and 60 minutes of exposure to determine their survival. Conclusions All four soaps can kill S. mansoni cercariae and this lethal effect was related to soap concentration and exposure time. At the highest concentration of 1000 mg/L, all cercariae were dead at 5 minutes post-exposure with two powder soaps and Rungu, while 100% cercarial death was achieved between 5 minutes to 15 minutes for B29. Almost all cercariae survived after being exposed to 10 mg/L powder soaps and 100 mg/L bar soaps for 60 minutes. Powder soaps were more lethal than bar soaps. Considering the widely varying concentrations of soap during real-world hygiene activities and the necessity for a very high soap concentration to eliminate all cercariae in a short 5-minute exposure, providing the efficacy of soap in preventing schistosomiasis becomes challenging. Future studies should investigate whether soap can influence alternative mechanisms such as making cercariae unable to penetrate the skin, thereby providing protection

Chlorination of Schistosoma mansoni cercariae.

BACKGROUND: Schistosomiasis is a water-based disease acquired through contact with cercaria-infested water. Communities living in endemic regions often rely on parasite-contaminated freshwater bodies for their daily water contact activities, resulting in recurring schistosomiasis infection. In such instances, water treatment can provide safe water on a household or community scale. However, to-date there are no water treatment guidelines that provide information on how to treat water containing schistosome cercariae. Here, we rigorously test the effectiveness of chlorine against Schistosoma mansoni cercariae. METHOD: S. mansoni cercariae were chlorinated using sodium hypochlorite under lab and field condition. The water pH was controlled at 6.5, 7.0 or 7.5, the water temperature at 20°C or 27°C, and the chlorine dose at 1, 2 or 3 mg/l. Experiments were conducted up to contact times of 45 minutes. 100 cercariae were used per experiment, thereby achieving up to 2-log10 inactivations of cercariae. Experiments were replicated under field conditions at Lake Victoria, Tanzania. CONCLUSION: A CT (residual chlorine concentration x chlorine contact time) value of 26±4 mg·min/l is required to achieve a 2-log10 inactivation of S. mansoni cercariae under the most conservative condition tested (pH 7.5, 20°C). Field and lab-cultivated cercariae show similar chlorine sensitivities. A CT value of 30 mg·min/l is therefore recommended to disinfect cercaria-infested water, though safety factors may be required, depending on water quality and operating conditions. This CT value can be achieved with a chlorine residual of 1 mg/l after a contact time of 30 minutes, for example. This recommendation can be used to provide safe water for household and recreational water activities in communities that lack safe alternative water sources

Sectoral Impacts of Invasive Species in the United States and Approaches to Management

Invasive species have a major effect on many sectors of the U.S. economy and on the well-being of its citizens. Their presence impacts animal and human health, military readiness, urban vegetation and infrastructure, water, energy and transportations systems, and indigenous peoples in the United States (Table 9.1). They alter bio-physical systems and cultural practices and require significant public and private expenditure for control. This chapter provides examples of the impacts to human systems and explains mechanisms of invasive species’ establishment and spread within sectors of the U.S. economy. The chapter is not intended to be comprehensive but rather to provide insight into the range and severity of impacts. Examples provide context for ongoing Federal programs and initiatives and support State and private efforts to prevent the introduction and spread of invasive species and eradicate and control established invasive species

Parameters for effective sand filtration of <i>Schistosoma mansoni</i> cercariae from water

Abstract Schistosomiasis is a water-based neglected tropical disease that is prevalent in over 78 countries. It affects communities that are reliant on freshwater bodies contaminated with Schistosome cercariae for their daily water activities. Whilst treatment with the drug praziquantel is relatively effective, it does not prevent reinfection. One option for reducing schistosomiasis infection is providing at-risk communities with treated water, thereby reducing contact with cercaria-infested water for activities such as bathing or doing laundry. This study aims to establish design guidance for sand filtration to remove schistosome cercariae from water. Four sand filters were tested, varying from 300 to 2000 μm in sand grain size. Each filter was tested with a sand depth of 20 cm, which was increased until no cercariae were detected in the effluent. The required filter depth to remove 100% of cercariae ranged between 40 and 70 cm depending on sand grain size. Cercaria removal was more effective in filters with smaller sand grain size and larger filter depth. These results are valid for intermittent flow, for up to six cycle flushes. While more rigorous testing is needed, these initial results suggest that sand filters can be an effective way to treat cercaria-contaminated water in low-income settings.</jats:p

The Science Case for an Extended Spitzer Mission

Although the final observations of the Spitzer Warm Mission are currently scheduled for March 2019, it can continue operations through the end of the decade with no loss of photometric precision. As we will show, there is a strong science case for extending the current Warm Mission to December 2020. Spitzer has already made major impacts in the fields of exoplanets (including microlensing events), characterizing near Earth objects, enhancing our knowledge of nearby stars and brown dwarfs, understanding the properties and structure of our Milky Way galaxy, and deep wide-field extragalactic surveys to study galaxy birth and evolution. By extending Spitzer through 2020, it can continue to make ground-breaking discoveries in those fields, and provide crucial support to the NASA flagship missions JWST and WFIRST, as well as the upcoming TESS mission, and it will complement ground-based observations by LSST and the new large telescopes of the next decade. This scientific program addresses NASA's Science Mission Directive's objectives in astrophysics, which include discovering how the universe works, exploring how it began and evolved, and searching for life on planets around other stars.Comment: 75 pages. See page 3 for Table of Contents and page 4 for Executive Summar