Genomic innovations linked to infection strategies across emerging pathogenic chytrid fungi

We acknowledge the Broad Institute Sequencing Platform and Imperial College London for generating the DNA and RNA sequence described here. Financial support was provided by a UK Natural Environmental Research Council (NERC NE/K012509/1) grant to MCF, a Wellcome Trust Fellowship to RF, a Morris Animal Foundation grant to FP, and by the National Human Genome Research Institute grant number U54HG003067 to the Broad Institute. E.V. is supported by the Research Foundation Flanders (FWO grant 12E6616N).Peer reviewedPublisher PD

More things in Heaven and Earth: spirit possession, mental disorder, and intentionality

Spirit possession is a common phenomenon around the world in which a non-corporeal agent is involved with a human host. This manifests in a range of maladies or in displacement of the host's agency and identity. Prompted by engagement with the phenomenon in North Africa, this paper draws connections between spirit possession, and the concepts of personhood and intentionality. It employs these concepts to articulate spirit possession, while also developing the intentional stance as formulated by Daniel Dennett. It argues for an understanding of spirit possession as the spirit stance: an intentional strategy that aims at predicting and explaining behaviour by ascribing to an agent (the spirit) beliefs and desires, but is only deployed once the mental states and activity of the subject (the person) fail specific normative distinctions. Applied to behaviours which are generally taken to signal mental disorder, the spirit stance preserves a peculiar form of intentionality where behaviour would otherwise be explained as a consequence of a malfunctioning physical mechanism. Centuries before the modern disciplines of psychoanalysis and phenomenological-psychopathology endeavoured to restore meaning to 'madness', the social institution of spirit possession had been preserving the intentionality of socially deviant behaviour

Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011

The degree to which molecular epidemiology reveals information about the sources and transmission patterns of an outbreak depends on the resolution of the technology used and the samples studied. Isolates of Escherichia coli O104:H4 from the outbreak centered in Germany in May–July 2011, and the much smaller outbreak in southwest France in June 2011, were indistinguishable by standard tests. We report a molecular epidemiological analysis using multiplatform whole-genome sequencing and analysis of multiple isolates from the German and French outbreaks. Isolates from the German outbreak showed remarkably little diversity, with only two single nucleotide polymorphisms (SNPs) found in isolates from four individuals. Surprisingly, we found much greater diversity (19 SNPs) in isolates from seven individuals infected in the French outbreak. The German isolates form a clade within the more diverse French outbreak strains. Moreover, five isolates derived from a single infected individual from the French outbreak had extremely limited diversity. The striking difference in diversity between the German and French outbreak samples is consistent with several hypotheses, including a bottleneck that purged diversity in the German isolates, variation in mutation rates in the two E. coli outbreak populations, or uneven distribution of diversity in the seed populations that led to each outbreak

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Draft Genome Sequence of \u3ci\u3eCercospora arachidicola\u3c/i\u3e, Causal Agent of Early Leaf Spot in Peanuts

Early leaf spot caused by Cercospora arachidicola S. Hori (teleomorph Mycosphaerella arachidis Deighton) is one of two important leaf spot diseases in peanut (Arachis hypogaea L.) responsible for significant economic loss to the industry (1, 2). Infections by C. arachidicola appear as small necrotic lesions on the leaves, petioles, or stems, which may be followed by premature defoliation, and, if left unmanaged on susceptible cultivars, can severely decrease yield (1). An effective, yet expensive, disease management strategy consists of multiple fungicide applications throughout the growing season (3). Other strategies such as strip-tillage instead of conventional tillage (4) or weather forecast models that predict disease outbreaks (5) can help minimize the number of fungicide treatments. However, the development of leaf-spot-resistant cultivars that require no fungicide application would be the most desirable means of control (6)

Sarcopenia Independently and Accurately Predicts Survival in Patients Undergoing Spine Surgery for Metastatic Tumors: A Multicenter Retrospective Cohort Study

BACKGROUND CONTEXT: Predicting survival and surgical morbidity in patients with spinal metastases would help guide clinical decision making and stratify treatments between surgical intervention and palliative care. PURPOSE: To evaluate whether the frailty/sarcopenia paradigm, as measured by psoas size, is strong predictor of survival in patients undergoing surgery for spinal metastasis. To directly compare psoas size with current standards of predicting survival for surgery for spinal metastasis, including Tokuhashi score, Tomita score, and Karnofsky Performance Status (KPS). STUDY DESIGN/SETTING: Multi-center retrospective cohort. PATIENT SAMPLE: Patients from four academic tertiary care centers who had undergone surgery for spinal metastasis. OUTCOME MEASURES: Overall mortality. METHODS: Morphometric measurements were taken of the psoas muscle at the L4 vertebral level \u3c200 days from surgery. Mortality hazard ratios were calculated using multivariate analysis, with variables included from past medical history, type and extent of tumor spread, type and intensity of surgery, and postoperative chemotherapy or radiation. RESULTS: A total of 271 patients from four institutes were identified. Psoas size was predictive of overall mortality; patients in the smallest psoas tertile had shorter overall survival compared to the middle (OR 0.52, p\u3c0.001) and largest tertile (OR 0.45, p\u3c0.001). Psoas size predicted overall mortality more strongly than Tokuhashi score (OR 0.91, p=0.010), Tomita score (OR 1.07, p=0.04), and KPS (OR 0.99, p=0.58). Psoas size was also predictive of 90-day survival; patients in the smallest psoas tertile had shorter 90-day survival compared to the middle (OR 0.24, p=0.003) and largest tertile (OR 0.16, p=0.001). Psoas size predicted 90-day mortality more strongly than Tokuhashi score (OR 0.73, p=0.002), Tomita score (OR 1.00, p=0.92), and KPS (OR 0.98, p=0.39). CONCLUSIONS: In patients undergoing surgery for spine metastases, psoas size as a surrogate for frailty/sarcopenia predicts 90-day and overall mortality, independent of demographical, functional, oncological and surgical characteristics. The sarcopenia/frailty paradigm is a stronger predictor of survival at these time points than the Tokuhashi score, Tomita score and KPS. Psoas size can be used in clinical decision-making to select which patients with metastatic spine tumors are appropriate surgical candidates. FDA DEVICE/DRUG STATUS: This abstract does not discuss or include any applicable devices or drugs

Sarcopenia Independently and Accurately Predicts Survival in Patients Undergoing Spine Surgery for Metastatic Tumors: A Multicenter Retrospective Cohort Study

BACKGROUND CONTEXT: Predicting survival and surgical morbidity in patients with spinal metastases would help guide clinical decision making and stratify treatments between surgical intervention and palliative care. PURPOSE: To evaluate whether the frailty/sarcopenia paradigm, as measured by psoas size, is strong predictor of survival in patients undergoing surgery for spinal metastasis. To directly compare psoas size with current standards of predicting survival for surgery for spinal metastasis, including Tokuhashi score, Tomita score, and Karnofsky Performance Status (KPS). STUDY DESIGN/SETTING: Multi-center retrospective cohort. PATIENT SAMPLE: Patients from four academic tertiary care centers who had undergone surgery for spinal metastasis. OUTCOME MEASURES: Overall mortality. METHODS: Morphometric measurements were taken of the psoas muscle at the L4 vertebral level \u3c200 days from surgery. Mortality hazard ratios were calculated using multivariate analysis, with variables included from past medical history, type and extent of tumor spread, type and intensity of surgery, and postoperative chemotherapy or radiation. RESULTS: A total of 271 patients from four institutes were identified. Psoas size was predictive of overall mortality; patients in the smallest psoas tertile had shorter overall survival compared to the middle (OR 0.52, p\u3c0.001) and largest tertile (OR 0.45, p\u3c0.001). Psoas size predicted overall mortality more strongly than Tokuhashi score (OR 0.91, p=0.010), Tomita score (OR 1.07, p=0.04), and KPS (OR 0.99, p=0.58). Psoas size was also predictive of 90-day survival; patients in the smallest psoas tertile had shorter 90-day survival compared to the middle (OR 0.24, p=0.003) and largest tertile (OR 0.16, p=0.001). Psoas size predicted 90-day mortality more strongly than Tokuhashi score (OR 0.73, p=0.002), Tomita score (OR 1.00, p=0.92), and KPS (OR 0.98, p=0.39). CONCLUSIONS: In patients undergoing surgery for spine metastases, psoas size as a surrogate for frailty/sarcopenia predicts 90-day and overall mortality, independent of demographical, functional, oncological and surgical characteristics. The sarcopenia/frailty paradigm is a stronger predictor of survival at these time points than the Tokuhashi score, Tomita score and KPS. Psoas size can be used in clinical decision-making to select which patients with metastatic spine tumors are appropriate surgical candidates. FDA DEVICE/DRUG STATUS: This abstract does not discuss or include any applicable devices or drugs