Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation.

Cryptococcus neoformans is a pathogenic basidiomycetous yeast responsible for more than 600,000 deaths each year. It occurs as two serotypes (A and D) representing two varieties (i.e. grubii and neoformans, respectively). Here, we sequenced the genome and performed an RNA-Seq-based analysis of the C. neoformans var. grubii transcriptome structure. We determined the chromosomal locations, analyzed the sequence/structural features of the centromeres, and identified origins of replication. The genome was annotated based on automated and manual curation. More than 40,000 introns populating more than 99% of the expressed genes were identified. Although most of these introns are located in the coding DNA sequences (CDS), over 2,000 introns in the untranslated regions (UTRs) were also identified. Poly(A)-containing reads were employed to locate the polyadenylation sites of more than 80% of the genes. Examination of the sequences around these sites revealed a new poly(A)-site-associated motif (AUGHAH). In addition, 1,197 miscRNAs were identified. These miscRNAs can be spliced and/or polyadenylated, but do not appear to have obvious coding capacities. Finally, this genome sequence enabled a comparative analysis of strain H99 variants obtained after laboratory passage. The spectrum of mutations identified provides insights into the genetics underlying the micro-evolution of a laboratory strain, and identifies mutations involved in stress responses, mating efficiency, and virulence.

Phase II Archaeological Excavations at 99 Main Street, 18AP21 (Sign of the Whale), Annapolis, Maryland

Historical Annapolis Foundation (HAF) conducted terrestrial archaeological investigations at site 18AP21 in the city of Annapolis, Maryland. Excavations were carried out at this National Register site ostensibly as a Phase II project to evaluate the site and assess the need for further work. The site is at 99 Main Street in the center of downtown Annapolis, near the Annapolis waterfront. The project was carried out as part of the advanced work for the Annapolis History Center project, to be built in the adjoining buildings of 99 Main and 196 Green Streets. The buildings are the property of the Historic Annapolis Foundation and located in Maryland Research Unit 7. The excavations were undertaken by HAF, and funded by HAFF. The work was conducted for HAF and MHT, who holds an archaeological easement on the property. This preliminary phase of work included stratigraphic excavation of two testpit units. These two units revealed that the site of the existing 99 Main Street building was the location of three previous constructions. The current building at 99 Main Street, built in 1791, was preceded by an earlier brick dwelling, evidenced by a stout pier of bricks, which was attached to a wooden-sided structure that stood on a foundation of brick and stone. Ceramics indicate that these buildings date to the early-middle of the 18th century. A third structure of post-in-ground construction, evidenced by recovery of burned posts and wood fragments, likely existed prior to these, but evidence was scant. These excavations reveal that the site of 18AP21 holds potential for understanding Annapolis's early cultural developments, especially in the area of initial settlement and the origins of waterfront commerce. The assemblage of artifacts recovered includes a broad sample of common 18th century pottery such as creamware and Chinese export porcelain, and also includes some early colonial types such as tin-glazed earthenware and various red-bodied slipwares. The excavations do not provide conclusive evidence of the construction sequence. Consultation with MHT representatives indicates that further work at the site will likely be needed before modifications to the floor of the building can progress.

Comparison of dynamic balance in adolescent male soccer players from rwanda and the United States.

PURPOSE/BACKGROUND: Dynamic balance is an important component of motor skill development. Poor dynamic balance has previously been associated with sport related injury. However, the vast majority of dynamic balance studies as they relate to sport injury have occurred in developed North American or European countries. Thus, the purpose of this study was to compare dynamic balance in adolescent male soccer players from Rwanda to a matched group from the United States. METHODS: Twenty-six adolescent male soccer players from Rwanda and 26 age- and gender-matched control subjects from the United States were screened using the Lower Quarter Y Balance Test during their pre-participation physical. Reach asymmetry (cm) between limbs was examined for all reach directions. In addition, reach distance in each direction (normalized to limb length, %LL) and the composite reach score (also normalized to %LL) were examined. Dependent samples t-tests were performed with significant differences identified at p<0.05. RESULTS: Twenty-six male soccer players from Rwanda (R) were matched to twenty-six male soccer players from the United States (US). The Rwandan soccer players performed better in the anterior (R: 83.9 ± 3.2 %LL; US: 76.5 ± 6.6 %LL, p<0.01), posterolateral (R: 114.4 ± 8.3 %LL ; US: 106.5 ± 8.2 %LL, p<0.01) and composite (R: 105.6 ± 1.3 %LL; US: 97.8 ± 6.2 %LL, p<0.01) reach scores. No significant differences between groups were observed for reach asymmetry. CONCLUSIONS: Adolescent soccer players from Rwanda exhibit superior performance on a standardized dynamic balance test as comparison to similar athletes from the United States. The examination of movement abilities of athletes from countries of various origins may allow for a greater understanding of the range of true normative values for dynamic balance. LEVELS OF EVIDENCE: 3b.

Genomics research: world survey of public funding.

BACKGROUND: Over the past two decades, genomics has evolved as a scientific research discipline. Genomics research was fueled initially by government and nonprofit funding sources, later augmented by private research and development (R&D) funding. Citizens and taxpayers of many countries have funded much of the research, and have expectations about access to the resulting information and knowledge. While access to knowledge gained from all publicly funded research is desired, access is especially important for fields that have broad social impact and stimulate public dialogue. Genomics is one such field, where public concerns are raised for reasons such as health care and insurance implications, as well as personal and ancestral identification. Thus, genomics has grown rapidly as a field, and attracts considerable interest. RESULTS: One way to study the growth of a field of research is to examine its funding. This study focuses on public funding of genomics research, identifying and collecting data from major government and nonprofit organizations around the world, and updating previous estimates of world genomics research funding, including information about geographical origins. We initially identified 89 publicly funded organizations; we requested information about each organization's funding of genomics research. Of these organizations, 48 responded and 34 reported genomics research expenditures (of those that responded but did not supply information, some did not fund such research, others could not quantify it). The figures reported here include all the largest funders and we estimate that we have accounted for most of the genomics research funding from government and nonprofit sources. CONCLUSION: Aggregate spending on genomics research from 34 funding sources averaged around $2.9 billion in 2003-2006. The United States spent more than any other country on genomics research, corresponding to 35% of the overall worldwide public funding (compared to 49% US share of public health research funding for all purposes). When adjusted to genomics funding intensity, however, the United States dropped below Ireland, the United Kingdom, and Canada, as measured both by genomics research expenditure per capita and per Gross Domestic Product.

Contracting Freedom: Governance and East Indian Indenture in the British Atlantic, 1838-1917

This is a dissertation about identity and governance, and how they are mutually constituted. Between 1838 and 1917, the British brought approximately half a million East Indian laborers to the Atlantic to work on sugar plantations. The dissertation argues that contrary to previous historiographical assumptions, indentured East Indians were an amorphous mass of people drawn from various regions of British India. They were brought together not by their innate "Indian-ness" upon their arrival in the Caribbean, but by the common experience of indenture recruitment, transportation and plantation life. Ideas of innate "Indian-ness" were products of an imperial discourse that emerged from and shaped official approaches to governing East Indians in the Atlantic. Government officials and planters promoted visions of East Indians as "primitive" subjects who engaged in child marriage and wife murder. Officials mobilized ideas about gender to sustain racialized stereotypes of East Indian subjects. East Indian women were thought to be promiscuous, and East Indian men were violent and depraved (especially in response to East Indian women's promiscuity). By pointing to these stereotypes about East Indians, government officials and planters could highlight the promise of indenture as a civilizing mechanism. This dissertation links the study of governance and subject formation to complicate ideas of colonial rule as static. It uncovers how colonial processes evolved to handle the challenges posed by migrant populations.

The primary architects of indenture, Caribbean governments, the British Colonial Office, and planters hoped that East Indian indentured laborers would form a stable and easily-governed labor force. They anticipated that the presence of these laborers would undermine the demands of Afro-Creole workers for higher wages and shorter working hours. Indenture, however, was controversial among British liberals who saw it as potentially hindering the creation of a free labor market, and abolitionists who also feared that indenture was a new form of slavery. Using court records, newspapers, legislative documents, bureaucratic correspondence, memoirs, novels, and travel accounts from archives and libraries in Britain, Guyana, and Trinidad and Tobago, this dissertation explores how indenture was envisioned and constantly re-envisioned in response to its critics. It chronicles how the struggles between the planter class and the colonial state for authority over indentured laborers affected the way that indenture functioned in the British Atlantic. In addition to focusing on indenture's official origins, this dissertation examines the actions of East Indian indentured subjects as they are recorded in the imperial archive to explore how these people experienced indenture.

Indenture contracts were central to the justification of indenture and to the creation of a pliable labor force in the Atlantic. According to English common law, only free parties could enter into contracts. Indenture contracts limited the period of indenture and affirmed that laborers would be remunerated for their labor. While the architects of indenture pointed to contracts as evidence that indenture was not slavery, contracts in reality prevented laborers from participating in the free labor market and kept the wages of indentured laborers low. Further, in late nineteenth-century Britain, contracts were civil matters. In the British Atlantic, indentured laborers who violated the terms of their contracts faced criminal trials and their associated punishments such as imprisonment and hard labor. Officials used indenture contracts to exploit the labor and limit the mobility of indentured laborers in a manner that was reminiscent of slavery but that instead established indentured laborers as subjects with limited rights. The dissertation chronicles how indenture contracts spawned a complex inter-imperial bureaucracy in British India, Britain, and the Caribbean that was responsible for the transportation and governance of East Indian indentured laborers overseas.

DEGENERATE MUSIC?! MUSICAL CENSORSHIP IN THE THIRD REICH

In 1938, in Düsseldorf, the Nazis put on an exhibit entitled "Entartete Musik” (degenerate music), which included composers on the basis of their “racial origins” (i.e. Jews), or because of the “modernist style” of their music. Performance, publication, broadcast, or sale of music by composers deemed “degenerate” was forbidden by law throughout the Third Reich. Among these composers were some of the most prominent composers of the first half of the twentieth-century. They included Stravinsky, Schoenberg, Webern, Berg, Mahler, Ernst Krenek, George Gershwin, Kurt Weill, Erwin Schulhoff, and others. The music of nineteenth-century composers of Jewish origin, such as Mendelssohn and Meyerbeer, was also officially proscribed. In each of the three recitals for this project, significant works were performed by composers who were included in this exhibition, namely, Mendelssohn, Webern, Berg, Weill, and Hans Gal. In addition, as an example of self-censorship, a work of Karl Amadeus Hartmann was included. Hartmann chose “internal exile” by refusing to allow performance of his works in Germany during the Nazi regime. One notable exception to the above categories was a work by Beethoven that was presented as a bellwether of the relationship between music and politics. The range of styles and genres in these three recitals indicates the degree to which Nazi musical censorship cut a wide swath across Europe’s musical life with devastating consequences for its music and culture.

A noisy linear map underlies oscillations in cell size and gene expression in bacteria.

During bacterial growth, a cell approximately doubles in size before division, after which it splits into two daughter cells. This process is subjected to the inherent perturbations of cellular noise and thus requires regulation for cell-size homeostasis. The mechanisms underlying the control and dynamics of cell size remain poorly understood owing to the difficulty in sizing individual bacteria over long periods of time in a high-throughput manner. Here we measure and analyse long-term, single-cell growth and division across different Escherichia coli strains and growth conditions. We show that a subset of cells in a population exhibit transient oscillations in cell size with periods that stretch across several (more than ten) generations. Our analysis reveals that a simple law governing cell-size control-a noisy linear map-explains the origins of these cell-size oscillations across all strains. This noisy linear map implements a negative feedback on cell-size control: a cell with a larger initial size tends to divide earlier, whereas one with a smaller initial size tends to divide later. Combining simulations of cell growth and division with experimental data, we demonstrate that this noisy linear map generates transient oscillations, not just in cell size, but also in constitutive gene expression. Our work provides new insights into the dynamics of bacterial cell-size regulation with implications for the physiological processes involved.

Cumulative early life adversity predicts longevity in wild baboons.

In humans and other animals, harsh circumstances in early life predict morbidity and mortality in adulthood. Multiple adverse conditions are thought to be especially toxic, but this hypothesis has rarely been tested in a prospective, longitudinal framework, especially in long-lived mammals. Here we use prospective data on 196 wild female baboons to show that cumulative early adversity predicts natural adult lifespan. Females who experience ≥3 sources of early adversity die a median of 10 years earlier than females who experience ≤1 adverse circumstances (median lifespan is 18.5 years). Females who experience the most adversity are also socially isolated in adulthood, suggesting that social processes partially explain the link between early adversity and adult survival. Our results provide powerful evidence for the developmental origins of health and disease and indicate that close ties between early adversity and survival arise even in the absence of health habit and health care-related explanations.

Amplitude noise on supercontinuum generated in microstructure fiber: Measurements and simulations

Supercontinua generated in microstructure fiber can exhibit significant excess amplitude noise. We present experimental and numerical studies of the origins of this excess noise and its dependence on the input laser pulse parameters.

Embedding dynamic behaviour into a self-configuring software system

This paper describes a methodology for embedding dynamic behaviour into software components. The implications and system architecture requirements to support this adaptivity are discussed. This work is part of a European Commission funded and industry supported project to produce a reconfigurable middleware for use in automotive systems. Such systems must be trustable against illegal internal behaviour and activity with external origins, additional devices for example. Policy-based computing is used here as an example of embedded logic. A key contribution of this work is the way in which static and dynamic aspects of the system are interfaced, such that the behaviour can be changed very flexibly (even during run-time), without modification, recompilation or redeployment of the embedded application code. An implementation of these concepts is presented, focussing on achieving trust in the use of dynamic behaviour.

Writing about war: Jung, Much Ado About Nothing, and the Troy novels of Lindsay Clarke

Arguably, in a time of war literature, and indeed all writing, is saturated with deep psychic responses to conflict. So that not only in literary genres such as epic and tragedy, but also in the novel and comedy, can writing about war be discerned. C.G. Jung, Shakespeare and Lindsay Clarke are fundamentally writers of war who share allied literary strategies. Moreover, they diagnose similar origins to the malaise of a culture tending to war in the neglect of aspects of the feminine that patriarchy prefers to ignore. In repressing or evading the dark feminine, cultures as dissimilar as ancient Greece, the 21st century, Shakespeare's England and Jung's Europe prevent the healing energies of the conjunctio of masculine and feminine from stabilising an increasingly fragile consciousness. In the Troy novels of Clarke, Answer to Job by Jung and Much Ado About Nothing by Shakespeare, some attempt at spiritual nourishment is made through the writing. [From the Publisher]

Postcolonial futures: postcolonial literature and the Obama moment

Since the late 1970s the western academy has encouraged the development of postcolonial literary theory and the formulation of a postcolonial literary canon existing outside the prescriptive narratives of the ‘mother’ country and empire. Having lost faith in the binary oppositions underpinning such narratives, we turned to alternative fictions that contested the construction of the ‘other’, the world divided between the ‘West and the Rest’. The publication of Edward Said’s Orientalism in 1978 marked the beginning of the discipline now known as postcolonial studies with its new ways of understanding ‘the west’s’ relationship with ‘the east’ and, by extension, all the former colonies of empire. Despite these radical origins, however, postcolonialism’s more recent emphasis on the psychological and its affirmation of the hybrid text and self has, for many, served to obscure real economic social realities that have very little to do with the magical or wondrous textual expression of a postcolonial identity. This paper considers problems associated with defining the postcolonial and proposes that, in a literary context, we broaden its meaning to include texts traditionally outside the category of postcolonial literature. To extend the meaning of postcolonial is timely as we are now witnessing its relocation from ‘margin’ to ‘centre’ with the election of Barack Obama. This moment may be seen as a disruption of conventional understandings of what constitutes postcolonial literature, essentially as oppositional discourse that could only define itself as peripheral to, or ‘post’, metropolitan and economic concerns. [From the Author]

Is there a connection between high transport of water through the Rockall Trough and ecological changes in the North Sea?

Changes in the ecosystem of the North Sea may occur as pronounced inter-annual and step-wise shifts as well as gradual trends. Marked inter-annual shifts have occurred at least twice in the last two decades, the late 1980s and the late 1990s, that appear to reflect an increased inflow of oceanic water and species. Numerical modelling has demonstrated a link between altered rates of inflow of oceanic water into the northern North Sea and a regime shift after 1988. In 1989 and 1997 oceanic species not normally found in the North Sea were observed there, suggesting pulses of oceanic water had entered the basin and triggered the subsequent ecosystem change. The oceanic water has origins mainly west of Britain in the Rockall Trough, where the long-term mean volume transport is around 3.7Sv northwards (1Sv=10 super(6)m super(3)s super(1)), but in early 1989 and early 1998 was observed to be more than twice the mean value, reaching over 7Sv. These periods of high transport coinciding with the inferred pulses of oceanic water into the North Sea suggest a connection through the continental shelf edge current. Copyright 2001 International Council for the Exploration of the Sea

Particle Dynamics Particulate Carbon And The Oxygen Minimum In An Estuary

Profiles of suspended particulate load and its organic and inorganic carbon contents as well as salinity, dissolved oxygen, ammonia and divalent manganese have been recorded throughout the mixing region of the Tamar Estuary,Southwest England, in late summer when there was pronounced net oxygen consumption. The results indicate that trapping of particulate organic detritus (of both riverine and marine origins) within the high turbidity zone contributes to the localisation and buffering of the seasonal oxygen demand exerted within the low salinity region of the estuary.

Ocean acidification shows negligible impacts on high-latitude bacterial community structure in coastal pelagic mesocosms

The impact of ocean acidification and carbonation on microbial community structure was assessed during a large-scale in situ costal pelagic mesocosm study, included as part of the EPOCA 2010 Arctic campaign. The mesocosm experiment included ambient conditions (fjord) and nine mesocosms with pCO(2) levels ranging from similar to 145 to similar to 1420 mu atm. Samples for the present study were collected at ten time points (t-1, t1, t5, t7, t12, t14, t18, t22, t26 to t28) in seven treatments (ambient fjord (similar to 145), 2x similar to 185, similar to 270, similar to 685, similar to 820, similar to 1050 mu atm) and were analysed for "small" and "large" size fraction microbial community composition using 16S rRNA (ribosomal ribonucleic acid) amplicon sequencing. This high-throughput sequencing analysis produced similar to 20 000 000 16S rRNA V4 reads, which comprised 7000OTUs. The main variables structuring these communities were sample origins (fjord or mesocosms) and the community size fraction (small or large size fraction). The community was significantly different between the unenclosed fjord water and enclosed mesocosms (both control and elevated CO2 treatments) after nutrients were added to the mesocosms, suggesting that the addition of nutrients is the primary driver of the change in mesocosm community structure. The relative importance of each structuring variable depended greatly on the time at which the community was sampled in relation to the phytoplankton bloom. The sampling strategy of separating the small and large size fraction was the second most important factor for community structure. When the small and large size fraction bacteria were analysed separately at different time points, the only taxon pCO(2) was found to significantly affect were the Gammaproteobacteria after nutrient addition. Finally, pCO(2) treatment was found to be significantly correlated (non-linear) with 15 rare taxa, most of which increased in abundance with higher CO2.