Detection of unusual mutation within the VP1 region of different re-isolates of poliovirus Sabin vaccine

In the present study, a genomic analysis of full VP1 sequence region of 15 clinical re-isolates (14 healthy vaccinees and one bone marrow tumor patient) was conducted, aiming to the identification of mutations and to the assessment of their impact on virus fitness, providing also insights relevant with the natural evolution of Sabin strains. Clinical re-isolates were analyzed by RT-PCR, sequencing and computational analysis. Some re-isolates were characterized by an unusual mutational pattern in which non-synonymous mutations outnumbered the synonymous ones. Furthermore, the majority of amino-acid substitutions were located in the capsid exterior, specifically in N-Ags, near N-Ags and in the north rim of the canyon. Also mutations, which are well-known determinants of attenuation, were identified. The results of this study propose that some re-isolates are characterized by an evolutionary pattern in which non-synonymous mutations with a direct phenotypic impact on viral fitness are fixed in viral genomes, in spite of synonymous ones with no phenotypic impact on viral fitness. Results of the present retrospective characterization of Sabin clinical re-isolates, based on the full VP1 sequence, suggest that vaccine-derived viruses may make their way through narrow breaches and may evolve into transmissible pathogens even in adequately immunized populations. For this reason increased poliovirus laboratory surveillance should be permanent and full VP1 sequence analysis should be conducted even in isolates originating from healthy vaccinees.

Report of the 2010 assessment of the scientific assessment panel: future ozone and its impact on surface UV

SCIENTIFIC SUMMARY Globally averaged total column ozone has declined over recent decades due to the release of ozone-depleting substances (ODSs) into the atmosphere. Now, as a result of the Montreal Protocol, ozone is expected to recover from the effects of ODSs as ODS abundances decline in the coming decades. However, a number of factors in addition to ODSs have led to and will continue to lead to changes in ozone. Discriminating between the causes of past and projected ozone changes is necessary, not only to identify the progress in ozone recovery from ODSs, but also to evaluate the effectiveness of climate and ozone protection policy options. Factors Affecting Future Ozone and Surface Ultraviolet Radiation • At least for the next few decades, the decline of ODSs is expected to be the major factor affecting the anticipated increase in global total column ozone. However, several factors other than ODS will affect the future evolution of ozone in the stratosphere. These include changes in (i) stratospheric circulation and temperature due to changes in long-lived greenhouse gas (GHG) abundances, (ii) stratospheric aerosol loading, and (iii) source gases of highly reactive stratospheric hydrogen and nitrogen compounds. Factors that amplify the effects of ODSs on ozone (e.g., stratospheric aerosols) will likely decline in importance as ODSs are gradually eliminated from the atmosphere. • Increases in GHG emissions can both positively and negatively affect ozone. Carbon dioxide (CO2)-induced stratospheric cooling elevates middle and upper stratospheric ozone and decreases the time taken for ozone to return to 1980 levels, while projected GHG-induced increases in tropical upwelling decrease ozone in the tropical lower stratosphere and increase ozone in the extratropics. Increases in nitrous oxide (N2O) and methane (CH4) concentrations also directly impact ozone chemistry but the effects are different in different regions. • The Brewer-Dobson circulation (BDC) is projected to strengthen over the 21st century and thereby affect ozone amounts. Climate models consistently predict an acceleration of the BDC or, more specifically, of the upwelling mass flux in the tropical lower stratosphere of around 2% per decade as a consequence of GHG abundance increases. A stronger BDC would decrease the abundance of tropical lower stratospheric ozone, increase poleward transport of ozone, and could reduce the atmospheric lifetimes of long-lived ODSs and other trace gases. While simulations showing faster ascent in the tropical lower stratosphere to date are a robust feature of chemistry-climate models (CCMs), this has not been confirmed by observations and the responsible mechanisms remain unclear. • Substantial ozone losses could occur if stratospheric aerosol loading were to increase in the next few decades, while halogen levels are high. Stratospheric aerosol increases may be caused by sulfur contained in volcanic plumes entering the stratosphere or from human activities. The latter might include attempts to geoengineer the climate system by enhancing the stratospheric aerosol layer. The ozone losses mostly result from enhanced heterogeneous chemistry on stratospheric aerosols. Enhanced aerosol heating within the stratosphere also leads to changes in temperature and circulation that affect ozone. • Surface ultraviolet (UV) levels will not be affected solely by ozone changes but also by the effects of climate change and by air quality change in the troposphere. These tropospheric effects include changes in clouds, tropospheric aerosols, surface reflectivity, and tropospheric sulfur dioxide (SO2) and nitrogen dioxide (NO2). The uncertainties in projections of these factors are large. Projected increases in tropospheric ozone are more certain and may lead to reductions in surface erythemal (“sunburning”) irradiance of up to 10% by 2100. Changes in clouds may lead to decreases or increases in surface erythemal irradiance of up to 15% depending on latitude. Expected Future Changes in Ozone Full ozone recovery from the effects of ODSs and return of ozone to historical levels are not synonymous. In this chapter a key target date is chosen to be 1980, in part to retain the connection to previous Ozone Assessments. Noting, however, that decreases in ozone may have occurred in some regions of the atmosphere prior to 1980, 1960 return dates are also reported. The projections reported on in this chapter are taken from a recent compilation of CCM simulations. The ozone projections, which also form the basis for the UV projections, are limited in their representativeness of possible futures since they mostly come from CCM simulations based on a single GHG emissions scenario (scenario A1B of Emissions Scenarios. A Special Report of Working Group III of the Intergovernmental Panel on Climate Change, Cambridge University Press, 2000) and a single ODS emissions scenario (adjusted A1 of the previous (2006) Ozone Assessment). Throughout this century, the vertical, latitudinal, and seasonal structure of the ozone distribution will be different from what it was in 1980. For this reason, ozone changes in different regions of the atmosphere are considered separately. • The projections of changes in ozone and surface clear-sky UV are broadly consistent with those reported on in the 2006 Assessment. • The capability of making projections and attribution of future ozone changes has been improved since the 2006 Assessment. Use of CCM simulations from an increased number of models extending through the entire period of ozone depletion and recovery from ODSs (1960–2100) as well as sensitivity simulations have allowed more robust projections of long-term changes in the stratosphere and of the relative contributions of ODSs and GHGs to those changes. • Global annually averaged total column ozone is projected to return to 1980 levels before the middle of the century and earlier than when stratospheric halogen loading returns to 1980 levels. CCM projections suggest that this early return is primarily a result of GHG-induced cooling of the upper stratosphere because the effects of circulation changes on tropical and extratropical ozone largely cancel. Global (90°S–90°N) annually averaged total column ozone will likely return to 1980 levels between 2025 and 2040, well before the return of stratospheric halogens to 1980 levels between 2045 and 2060. • Simulated changes in tropical total column ozone from 1960 to 2100 are generally small. The evolution of tropical total column ozone in models depends on the balance between upper stratospheric increases and lower stratospheric decreases. The upper stratospheric increases result from declining ODSs and a slowing of ozone destruction resulting from GHG-induced cooling. Ozone decreases in the lower stratosphere mainly result from an increase in tropical upwelling. From 1960 until around 2000, a general decline is simulated, followed by a gradual increase to values typical of 1980 by midcentury. Thereafter, although total column ozone amounts decline slightly again toward the end of the century, by 2080 they are no longer expected to be affected by ODSs. Confidence in tropical ozone projections is compromised by the fact that simulated decreases in column ozone to date are not supported by observations, suggesting that significant uncertainties remain. • Midlatitude total column ozone is simulated to evolve differently in the two hemispheres. Over northern midlatitudes, annually averaged total column ozone is projected to return to 1980 values between 2015 and 2030, while for southern midlatitudes the return to 1980 values is projected to occur between 2030 and 2040. The more rapid return to 1980 values in northern midlatitudes is linked to a more pronounced strengthening of the poleward transport of ozone due to the effects of increased GHG levels, and effects of Antarctic ozone depletion on southern midlatitudes. By 2100, midlatitude total column ozone is projected to be above 1980 values in both hemispheres. • October-mean Antarctic total column ozone is projected to return to 1980 levels after midcentury, later than in any other region, and yet earlier than when stratospheric halogen loading is projected to return to 1980 levels. The slightly earlier return of ozone to 1980 levels (2045–2060) results primarily from upper stratospheric cooling and resultant increases in ozone. The return of polar halogen loading to 1980 levels (2050–2070) in CCMs is earlier than in empirical models that exclude the effects of GHG-induced changes in circulation. Our confidence in the drivers of changes in Antarctic ozone is higher than for other regions because (i) ODSs exert a strong influence on Antarctic ozone, (ii) the effects of changes in GHG abundances are comparatively small, and (iii) projections of ODS emissions are more certain than those for GHGs. Small Antarctic ozone holes (areas of ozone <220 Dobson units, DU) could persist to the end of the 21st century. • March-mean Arctic total column ozone is projected to return to 1980 levels two to three decades before polar halogen loading returns to 1980 levels, and to exceed 1980 levels thereafter. While CCM simulations project a return to 1980 levels between 2020 and 2035, most models tend not to capture observed low temperatures and thus underestimate present-day Arctic ozone loss such that it is possible that this return date is biased early. Since the strengthening of the Brewer-Dobson circulation through the 21st century leads to increases in springtime Arctic column ozone, by 2100 Arctic ozone is projected to lie well above 1960 levels. Uncertainties in Projections • Conclusions dependent on future GHG levels are less certain than those dependent on future ODS levels since ODS emissions are controlled by the Montreal Protocol. For the six GHG scenarios considered by a few CCMs, the simulated differences in stratospheric column ozone over the second half of the 21st century are largest in the northern midlatitudes and the Arctic, with maximum differences of 20–40 DU between the six scenarios in 2100. • There remain sources of uncertainty in the CCM simulations. These include the use of prescribed ODS mixing ratios instead of emission fluxes as lower boundary conditions, the range of sea surface temperatures and sea ice concentrations, missing tropospheric chemistry, model parameterizations, and model climate sensitivity. • Geoengineering schemes for mitigating climate change by continuous injections of sulfur-containing compounds into the stratosphere, if implemented, would substantially affect stratospheric ozone, particularly in polar regions. Ozone losses observed following large volcanic eruptions support this prediction. However, sporadic volcanic eruptions provide limited analogs to the effects of continuous sulfur emissions. Preliminary model simulations reveal large uncertainties in assessing the effects of continuous sulfur injections. Expected Future Changes in Surface UV. While a number of factors, in addition to ozone, affect surface UV irradiance, the focus in this chapter is on the effects of changes in stratospheric ozone on surface UV. For this reason, clear-sky surface UV irradiance is calculated from ozone projections from CCMs. • Projected increases in midlatitude ozone abundances during the 21st century, in the absence of changes in other factors, in particular clouds, tropospheric aerosols, and air pollutants, will result in decreases in surface UV irradiance. Clear-sky erythemal irradiance is projected to return to 1980 levels on average in 2025 for the northern midlatitudes, and in 2035 for the southern midlatitudes, and to fall well below 1980 values by the second half of the century. However, actual changes in surface UV will be affected by a number of factors other than ozone. • In the absence of changes in other factors, changes in tropical surface UV will be small because changes in tropical total column ozone are projected to be small. By the middle of the 21st century, the model projections suggest surface UV to be slightly higher than in the 1960s, very close to values in 1980, and slightly lower than in 2000. The projected decrease in tropical total column ozone through the latter half of the century will likely result in clear-sky surface UV remaining above 1960 levels. Average UV irradiance is already high in the tropics due to naturally occurring low total ozone columns and high solar elevations. • The magnitude of UV changes in the polar regions is larger than elsewhere because ozone changes in polar regions are larger. For the next decades, surface clear-sky UV irradiance, particularly in the Antarctic, will continue to be higher than in 1980. Future increases in ozone and decreases in clear-sky UV will occur at slower rates than those associated with the ozone decreases and UV increases that occurred before 2000. In Antarctica, surface clear-sky UV is projected to return to 1980 levels between 2040 and 2060, while in the Arctic this is projected to occur between 2020 and 2030. By 2100, October surface clear-sky erythemal irradiance in Antarctica is likely to be between 5% below to 25% above 1960 levels, with considerable uncertainty. This is consistent with multi-model-mean October Antarctic total column ozone not returning to 1960 levels by 2100. In contrast, by 2100, surface clear-sky UV in the Arctic is projected to be 0–10% below 1960 levels.

Can company-fund manager meetings convey informational benefits? Exploring the rationalisation of equity investment decision making by UK fund managers

Conventional economic theory, applied to information released by listed companies, equates ‘useful’ with ‘price-sensitive’. Stock exchange rules accordingly prohibit the selec- tive, private communication of price-sensitive information. Yet, even in the absence of such communication, UK equity fund managers routinely meet privately with the senior execu- tives of the companies in which they invest. Moreover, they consider these brief, formal and formulaic meetings to be their most important sources of investment information. In this paper we ask how that can be. Drawing on interview and observation data with fund managers and CFOs, we find evidence for three, non-mutually exclusive explanations: that the characterisation of information in conventional economic theory is too restricted, that fund managers fail to act with the rationality that conventional economic theory assumes, and/or that the primary value of the meetings for fund managers is not related to their investment decision making but to the claims of superior knowledge made to clients in marketing their active fund management expertise. Our findings suggest a disconnect between economic theory and economic policy based on that theory, as well as a corre- sponding limitation in research studies that test information-usefulness by assuming it to be synonymous with price-sensitivity. We draw implications for further research into the role of tacit knowledge in equity investment decision-making, and also into the effects of the principal–agent relationship between fund managers and their clients.

Characterization of the complex locus of bean encoding polygalacturonase-inhibiting proteins reveals subfunctionalization for defense against fungi and insects.

Polygalacturonase-inhibiting proteins (PGIPs) are extracellular plant inhibitors of fungal endopolygalacturonases (PGs) that belong to the superfamily of Leu-rich repeat proteins. We have characterized the full complement of pgip genes in the bean (Phaseolus vulgaris) genotype BAT93. This comprises four clustered members that span a 50-kb region and, based on their similarity, form two pairs (Pvpgip1/Pvpgip2 and Pvpgip3/Pvpgip4). Characterization of the encoded products revealed both partial redundancy and subfunctionalization against fungal-derived PGs. Notably, the pair PvPGIP3/PvPGIP4 also inhibited PGs of two mirid bugs (Lygus rugulipennis and Adelphocoris lineolatus). Characterization of Pvpgip genes of Pinto bean showed variations limited to single synonymous substitutions or small deletions. A three-amino acid deletion encompassing a residue previously identified as crucial for recognition of PG of Fusarium moniliforme was responsible for the inability of BAT93 PvPGIP2 to inhibit this enzyme. Consistent with the large variations observed in the promoter sequences, reverse transcription-PCR expression analysis revealed that the different family members differentially respond to elicitors, wounding, and salicylic acid. We conclude that both biochemical and regulatory redundancy and subfunctionalization of pgip genes are important for the adaptation of plants to pathogenic fungi and phytophagous insects.

Within-host evolution of Staphylococcus aureus during asymptomatic carriage

Background Staphylococcus aureus is a major cause of healthcare associated mortality, but like many important bacterial pathogens, it is a common constituent of the normal human body flora. Around a third of healthy adults are carriers. Recent evidence suggests that evolution of S. aureus during nasal carriage may be associated with progression to invasive disease. However, a more detailed understanding of within-host evolution under natural conditions is required to appreciate the evolutionary and mechanistic reasons why commensal bacteria such as S. aureus cause disease. Therefore we examined in detail the evolutionary dynamics of normal, asymptomatic carriage. Sequencing a total of 131 genomes across 13 singly colonized hosts using the Illumina platform, we investigated diversity, selection, population dynamics and transmission during the short-term evolution of S. aureus. Principal Findings We characterized the processes by which the raw material for evolution is generated: micro-mutation (point mutation and small insertions/deletions), macro-mutation (large insertions/deletions) and the loss or acquisition of mobile elements (plasmids and bacteriophages). Through an analysis of synonymous, non-synonymous and intergenic mutations we discovered a fitness landscape dominated by purifying selection, with rare examples of adaptive change in genes encoding surface-anchored proteins and an enterotoxin. We found evidence for dramatic, hundred-fold fluctuations in the size of the within-host population over time, which we related to the cycle of colonization and clearance. Using a newly-developed population genetics approach to detect recent transmission among hosts, we revealed evidence for recent transmission between some of our subjects, including a husband and wife both carrying populations of methicillin-resistant S. aureus (MRSA). Significance This investigation begins to paint a picture of the within-host evolution of an important bacterial pathogen during its prevailing natural state, asymptomatic carriage. These results also have wider significance as a benchmark for future systematic studies of evolution during invasive S. aureus disease.

Comparative genomics of Salmonella enterica serovars Derby and Mbandaka, two prevalent serovars associated with different livestock species in the UK

Background Despite the frequent isolation of Salmonella enterica sub. enterica serovars Derby and Mbandaka from livestock in the UK and USA little is known about the biological processes maintaining their prevalence. Statistics for Salmonella isolations from livestock production in the UK show that S. Derby is most commonly associated with pigs and turkeys and S. Mbandaka with cattle and chickens. Here we compare the first sequenced genomes of S. Derby and S. Mbandaka as a basis for further analysis of the potential host adaptations that contribute to their distinct host species distributions. Results Comparative functional genomics using the RAST annotation system showed that predominantly mechanisms that relate to metabolite utilisation, in vivo and ex vivo persistence and pathogenesis distinguish S. Derby from S. Mbandaka. Alignment of the genome nucleotide sequences of S. Derby D1 and D2 and S. Mbandaka M1 and M2 with Salmonella pathogenicity islands (SPI) identified unique complements of genes associated with host adaptation. We also describe a new genomic island with a putative role in pathogenesis, SPI-23. SPI-23 is present in several S. enterica serovars, including S. Agona, S. Dublin and S. Gallinarum, it is absent in its entirety from S. Mbandaka. Conclusions We discovered a new 37 Kb genomic island, SPI-23, in the chromosome sequence of S. Derby, encoding 42 ORFS, ten of which are putative TTSS effector proteins. We infer from full-genome synonymous SNP analysis that these two serovars diverged, between 182kya and 625kya coinciding with the divergence of domestic pigs. The differences between the genomes of these serovars suggest they have been exposed to different stresses including, phage, transposons and prolonged externalisation. The two serovars possess distinct complements of metabolic genes; many of which cluster into pathways for catabolism of carbon sources.

Alterations in predicted regulatory and coding regions of the sterol 14α-demethylase gene (CYP51) confer decreased azole sensitivity in the oilseed rape pathogen Pyrenopeziza brassicae

The incidence and severity of light leaf spot epidemics caused by the ascomycete fungus Pyrenopeziza brassicae on UK oilseed rape crops is increasing. The disease is currently controlled by a combination of host resistance, cultural practices and fungicide applications. We report decreases in sensitivities of modern UK P. brassicae isolates to the azole (imidazole and triazole) class of fungicides. By cloning and sequencing the P. brassicae CYP51 (PbCYP51) gene, encoding the azole target sterol 14α-demethylase, we identified two non-synonymous mutations encoding substitutions G460S and S508T associated with reduced azole sensitivity. We confirmed the impact of the encoded PbCYP51 changes on azole sensitivity and protein activity by heterologous expression in a Saccharomyces cerevisiae mutant YUG37::erg11 carrying a controllable promoter of native CYP51 expression. In addition, we identified insertions in the predicted regulatory regions of PbCYP51 in isolates with reduced azole sensitivity. The presence of these insertions was associated with enhanced transcription of PbCYP51 in response to sub-inhibitory concentrations of the azole fungicide tebuconazole. Genetic analysis of in vitro crosses of sensitive and resistant isolates confirmed the impact of PbCYP51 alterations in coding and regulatory sequences on a reduced sensitivity phenotype, as well as identifying a second major gene at another locus contributing to resistance in some isolates. The least sensitive field isolates carry combinations of upstream insertions and non-synonymous mutations, suggesting PbCYP51 evolution is on-going and the progressive decline in azole sensitivity of UK P. brassicae populations will continue. The implications for the future control of light leaf spot are discussed.

Rare variants in LRRK1 and Parkinson's disease

Approximately 20 % of individuals with Parkinson's disease (PD) report a positive family history. Yet, a large portion of causal and disease-modifying variants is still unknown. We used exome sequencing in two affected individuals from a family with late-onset PD to identify 15 potentially causal variants. Segregation analysis and frequency assessment in 862 PD cases and 1,014 ethnically matched controls highlighted variants in EEF1D and LRRK1 as the best candidates. Mutation screening of the coding regions of these genes in 862 cases and 1,014 controls revealed several novel non-synonymous variants in both genes in cases and controls. An in silico multi-model bioinformatics analysis was used to prioritize identified variants in LRRK1 for functional follow- up. However, protein expression, subcellular localization, and cell viability were not affected by the identified variants. Although it has yet to be proven conclusively that variants in LRRK1 are indeed causative of PD, our data strengthen a possible role for LRRK1 in addition to LRRK2 in the genetic underpinnings of PD but, at the same time, highlight the difficulties encountered in the study of rare variants identified by next-generation sequencing in diseases with autosomal dominant or complex patterns of inheritance.

A prolegomenon to the construct of the native speaker: heritage speaker bilinguals are natives too!

This Forum challenges the generally accepted position in the linguistic sciences—conscious or not—that monolingualism and nativeness are essentially synonymous in an exclusive way. We discuss two consequences of our position that naturalistic bilinguals and multilinguals exposed to a language in early childhood are also native speakers: (i) that bi-/multilinguals have multiple native languages;and (ii) nativeness can be applicable to a state of linguistic knowledge that is characterized by significant differences to the monolingual baseline.

A Linguistic Analysis of Spanglish: Relating Language to Identity.

According to the 2000 census, 35.3 million Hispanics live in the United States. This number comprises 12.5% of the overall population rendering the Latino community the largest minority in the United States. The Mexican community is not only the largest Hispanic group but also the fastest growing: from 1990 to 2000, the Mexican population grew 52.9% increasing from 13.5 million to 20.6 million (U.S. Department of Commerce News, 2001). The influx of Mexican immigrants coupled with the expansion of their community within the United States has created an unparalleled situation of language contact. Language is synonymous with identity (cf. Granger, 2004, and works cited within). To the extent that this is true, Spanish is synonymous with being Mexican and by extension, Chicano. With the advent of amnesty programs such as Immigration Reform and Control Act (IRCA), which naturalized millions of Mexican migrants, what was once a temporal migratory population has become increasingly permanent (Durand et al., 1999). In an effort to conserve Mexican traditions and identity, the struggle to preserve the mother tongue while at the same time acculturate to mainstream Americana has resulted in a variant of Spanglish that has received little attention. This paper will examine the variant of Spanglish seen in the greater Los Angeles area and liken it to the bi-national identity under which these Mexican Americans thrive.