Polyploidy Did Not Predate the Evolution of Nodulation in All Legumes

BACKGROUND: Several lines of evidence indicate that polyploidy occurred by around 54 million years ago, early in the history of legume evolution, but it has not been known whether this event was confined to the papilionoid subfamily (Papilionoideae; e.g. beans, medics, lupins) or occurred earlier. Determining the timing of the polyploidy event is important for understanding whether polyploidy might have contributed to rapid diversification and radiation of the legumes near the origin of the family; and whether polyploidy might have provided genetic material that enabled the evolution of a novel organ, the nitrogen-fixing nodule. Although symbioses with nitrogen-fixing partners have evolved in several lineages in the rosid I clade, nodules are widespread only in legume taxa, being nearly universal in the papilionoids and in the mimosoid subfamily (e.g., mimosas, acacias)--which diverged from the papilionoid legumes around 58 million years ago, soon after the origin of the legumes. METHODOLOGY/PRINCIPAL FINDINGS: Using transcriptome sequence data from Chamaecrista fasciculata, a nodulating member of the mimosoid clade, we tested whether this species underwent polyploidy within the timeframe of legume diversification. Analysis of gene family branching orders and synonymous-site divergence data from C. fasciculata, Glycine max (soybean), Medicago truncatula, and Vitis vinifera (grape; an outgroup to the rosid taxa) establish that the polyploidy event known from soybean and Medicago occurred after the separation of the mimosoid and papilionoid clades, and at or shortly before the Papilionoideae radiation. CONCLUSIONS: The ancestral legume genome was not fundamentally polyploid. Moreover, because there has not been an independent instance of polyploidy in the Chamaecrista lineage there is no necessary connection between polyploidy and nodulation in legumes. Chamaecrista may serve as a useful model in the legumes that lacks a paleopolyploid history, at least relative to the widely studied papilionoid models

Radio-Frequency Interference (RFI) Mitigation for the Soil, Moisture Active/Passive (SMAP) Radiometer

The presence of anthropogenic RFI is expected to adversely impact soil moisture measurement by NASA s Soil Moisture Active Passive mission. The digital signal processing approach and preliminary design for detecting and mitigating this RFI is presented in this paper. This approach is largely based upon the work of Johnson and Ruf

A Magnetic Bead-Integrated Chip for the Large Scale Manufacture of Normalized esiRNAs

The chemically-synthesized siRNA duplex has become a powerful and widely used tool for RNAi loss-of-function studies, but suffers from a high off-target effect problem. Recently, endoribonulease-prepared siRNA (esiRNA) has been shown to be an attractive alternative due to its lower off-target effect and cost effectiveness. However, the current manufacturing method for esiRNA is complicated, mainly in regards to purification and normalization on a large-scale level. In this study, we present a magnetic bead-integrated chip that can immobilize amplification or transcription products on beads and accomplish transcription, digestion, normalization and purification in a robust and convenient manner. This chip is equipped to manufacture ready-to-use esiRNAs on a large-scale level. Silencing specificity and efficiency of these esiRNAs were validated at the transcriptional, translational and functional levels. Manufacture of several normalized esiRNAs in a single well, including those silencing PARP1 and BRCA1, was successfully achieved, and the esiRNAs were subsequently utilized to effectively investigate their synergistic effect on cell viability. A small esiRNA library targeting 68 tyrosine kinase genes was constructed for a loss-of-function study, and four genes were identified in regulating the migration capability of Hela cells. We believe that this approach provides a more robust and cost-effective choice for manufacturing esiRNAs than current approaches, and therefore these heterogeneous RNA strands may have utility in most intensive and extensive applications

Reinterpreting Ethnic Patterns among White and African American Men Who Inject Heroin: A Social Science of Medicine Approach

BACKGROUND: Street-based heroin injectors represent an especially vulnerable population group subject to negative health outcomes and social stigma. Effective clinical treatment and public health intervention for this population requires an understanding of their cultural environment and experiences. Social science theory and methods offer tools to understand the reasons for economic and ethnic disparities that cause individual suffering and stress at the institutional level. METHODS AND FINDINGS: We used a cross-methodological approach that incorporated quantitative, clinical, and ethnographic data collected by two contemporaneous long-term San Francisco studies, one epidemiological and one ethnographic, to explore the impact of ethnicity on street-based heroin-injecting men 45 years of age or older who were self-identified as either African American or white. We triangulated our ethnographic findings by statistically examining 14 relevant epidemiological variables stratified by median age and ethnicity. We observed significant differences in social practices between self-identified African Americans and whites in our ethnographic social network sample with respect to patterns of (1) drug consumption; (2) income generation; (3) social and institutional relationships; and (4) personal health and hygiene. African Americans and whites tended to experience different structural relationships to their shared condition of addiction and poverty. Specifically, this generation of San Francisco injectors grew up as the children of poor rural to urban immigrants in an era (the late 1960s through 1970s) when industrial jobs disappeared and heroin became fashionable. This was also when violent segregated inner city youth gangs proliferated and the federal government initiated its “War on Drugs.” African Americans had earlier and more negative contact with law enforcement but maintained long-term ties with their extended families. Most of the whites were expelled from their families when they began engaging in drug-related crime. These historical-structural conditions generated distinct presentations of self. Whites styled themselves as outcasts, defeated by addiction. They professed to be injecting heroin to stave off “dopesickness” rather than to seek pleasure. African Americans, in contrast, cast their physical addiction as an oppositional pursuit of autonomy and pleasure. They considered themselves to be professional outlaws and rejected any appearance of abjection. Many, but not all, of these ethnographic findings were corroborated by our epidemiological data, highlighting the variability of behaviors within ethnic categories. CONCLUSIONS: Bringing quantitative and qualitative methodologies and perspectives into a collaborative dialog among cross-disciplinary researchers highlights the fact that clinical practice must go beyond simple racial or cultural categories. A clinical social science approach provides insights into how sociocultural processes are mediated by historically rooted and institutionally enforced power relations. Recognizing the logical underpinnings of ethnically specific behavioral patterns of street-based injectors is the foundation for cultural competence and for successful clinical relationships. It reduces the risk of suboptimal medical care for an exceptionally vulnerable and challenging patient population. Social science approaches can also help explain larger-scale patterns of health disparities; inform new approaches to structural and institutional-level public health initiatives; and enable clinicians to take more leadership in changing public policies that have negative health consequences

Collaborative research in contexts of inequality: the role of social reflexivity

This article reports on the role and value of social reflexivity in collaborative research in contexts of extreme inequality. Social reflexivity mediates the enablements and constraints generated by the internal and external contextual conditions impinging on the research collaboration. It fosters the ability of participants in a collaborative project to align their interests and collectively extend their agency towards a common purpose. It influences the productivity and quality of learning outcomes of the research collaboration. The article is written by fourteen members of a larger research team, which comprised 18 individuals working within the academic development environment in eight South African universities. The overarching research project investigated the participation of academics in professional development activities, and how contextual, i.e. structural and cultural, and agential conditions, influence this participation. For this sub-study on the experience of the collaboration by fourteen of the researchers, we wrote reflective pieces on our own experience of participating in the project towards the end of the third year of its duration. We discuss the structural and cultural conditions external to and internal to the project, and how the social reflexivity of the participants mediated these conditions. We conclude with the observation that policy injunctions and support from funding agencies for collaborative research, as well as support from participants' home institutions are necessary for the flourishing of collaborative research, but that the commitment by individual participants to participate, learn and share, is also necessary.DHE

Florbetapir F 18 amyloid PET and 36-month cognitive decline:a prospective multicenter study

This study was designed to evaluate whether subjects with amyloid beta (Aβ) pathology, detected using florbetapir positron emission tomorgraphy (PET), demonstrated greater cognitive decline than subjects without Aβ pathology. Sixty-nine cognitively normal (CN) controls, 52 with recently diagnosed mild cognitive impairment (MCI) and 31 with probable Alzheimer's disease (AD) dementia were included in the study. PET images obtained in these subjects were visually rated as positive (Aβ+) or negative (Aβ−), blind to diagnosis. Fourteen percent (10/69) of CN, 37% (19/52) of MCI and 68% (21/31) of AD were Aβ+. The primary outcome was change in ADAS-Cog score in MCI subjects after 36 months; however, additional outcomes included change on measures of cognition, function and diagnostic status. Aβ+ MCI subjects demonstrated greater worsening compared with Aβ− subjects on the ADAS-Cog over 36 months (5.66±1.47 vs −0.71±1.09, P=0.0014) as well as on the mini-mental state exam (MMSE), digit symbol substitution (DSS) test, and a verbal fluency test (P<0.05). Similar to MCI subjects, Aβ+ CN subjects showed greater decline on the ADAS-Cog, digit-symbol-substitution test and verbal fluency (P<0.05), whereas Aβ+ AD patients showed greater declines in verbal fluency and the MMSE (P<0.05). Aβ+ subjects in all diagnostic groups also showed greater decline on the CDR-SB (P<0.04), a global clinical assessment. Aβ+ subjects did not show significantly greater declines on the ADCS-ADL or Wechsler Memory Scale. Overall, these findings suggest that in CN, MCI and AD subjects, florbetapir PET Aβ+ subjects show greater cognitive and global deterioration over a 3-year follow-up than Aβ− subjects do

Rain-induced turbulence and air-sea gas transfer

Author Posting. © American Geophysical Union, 2009. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 114 (2009): C07009, doi:10.1029/2008JC005008.Results from a rain and gas exchange experiment (Bio2 RainX III) at the Biosphere 2 Center demonstrate that turbulence controls the enhancement of the air-sea gas transfer rate (or velocity) k during rainfall, even though profiles of the turbulent dissipation rate ɛ are strongly influenced by near-surface stratification. The gas transfer rate scales with ɛ inline equation for a range of rain rates with broad drop size distributions. The hydrodynamic measurements elucidate the mechanisms responsible for the rain-enhanced k results using SF6 tracer evasion and active controlled flux technique. High-resolution k and turbulence results highlight the causal relationship between rainfall, turbulence, stratification, and air-sea gas exchange. Profiles of ɛ beneath the air-sea interface during rainfall, measured for the first time during a gas exchange experiment, yielded discrete values as high as 10−2 W kg−1. Stratification modifies and traps the turbulence near the surface, affecting the enhancement of the transfer velocity and also diminishing the vertical mixing of mass transported to the air-water interface. Although the kinetic energy flux is an integral measure of the turbulent input to the system during rain events, ɛ is the most robust response to all the modifications and transformations to the turbulent state that follows. The Craig-Banner turbulence model, modified for rain instead of breaking wave turbulence, successfully predicts the near-surface dissipation profile at the onset of the rain event before stratification plays a dominant role. This result is important for predictive modeling of k as it allows inferring the surface value of ɛ fundamental to gas transfer.This work was funded by a generous grant from the David and Lucile Packard Foundation and the Lamont-Doherty Earth Observatory Climate Center. Additional funding was provided by the National Science Foundation (OCE-05-26677) and the Office of Naval Research Young Investigator Program (N00014-04-1-0621)