Species abundance patterns in an ecosystem simulation studied through Fisher's logseries

We have developed an individual-based evolving predator-prey ecosystem simulation that integrates, for the first time, a complex individual behaviour model, an evolutionary mechanism and a speciation process, at an acceptable computational cost. In this article, we analyse the species abundance patterns observed in the communities generated by our simulation, based on Fisher's logseries. We propose a rigorous methodology for testing abundance data against the logseries. We show that our simulation produces coherent results, in terms of relative species abundance, when compared to classical ecological patterns. Some preliminary results are also provided about how our simulation is supporting ecological field results

A repeat protein links Rubisco to form the eukaryotic carbon-concentrating organelle.

Biological carbon fixation is a key step in the global carbon cycle that regulates the atmosphere's composition while producing the food we eat and the fuels we burn. Approximately one-third of global carbon fixation occurs in an overlooked algal organelle called the pyrenoid. The pyrenoid contains the CO2-fixing enzyme Rubisco and enhances carbon fixation by supplying Rubisco with a high concentration of CO2 Since the discovery of the pyrenoid more that 130 y ago, the molecular structure and biogenesis of this ecologically fundamental organelle have remained enigmatic. Here we use the model green alga Chlamydomonas reinhardtii to discover that a low-complexity repeat protein, Essential Pyrenoid Component 1 (EPYC1), links Rubisco to form the pyrenoid. We find that EPYC1 is of comparable abundance to Rubisco and colocalizes with Rubisco throughout the pyrenoid. We show that EPYC1 is essential for normal pyrenoid size, number, morphology, Rubisco content, and efficient carbon fixation at low CO2 We explain the central role of EPYC1 in pyrenoid biogenesis by the finding that EPYC1 binds Rubisco to form the pyrenoid matrix. We propose two models in which EPYC1's four repeats could produce the observed lattice arrangement of Rubisco in the Chlamydomonas pyrenoid. Our results suggest a surprisingly simple molecular mechanism for how Rubisco can be packaged to form the pyrenoid matrix, potentially explaining how Rubisco packaging into a pyrenoid could have evolved across a broad range of photosynthetic eukaryotes through convergent evolution. In addition, our findings represent a key step toward engineering a pyrenoid into crops to enhance their carbon fixation efficiency

Network isolation and local diversity in neutral metacommunities

Biologists seek an understanding of the biological and environmental factors determining local community diversity. Recent advances in metacommunity ecology, and neutral theory in particular, highlight the importance of dispersal processes interacting with the spatial structure of a landscape for generating spatial patterns and maintaining biodiversity. The relative spatial isolation of a community is traditionally thought to have a large influence on local diversity. However, isolation remains an elusive concept to quantify, particularly in metacommunities with complex spatial structure. We represent the metacommunity as a network of local communities, and use network centrality measures to quantify the isolation of a local community. Using spatially explicit neutral theory, we examine how node position predicts variation in alpha diversity across a metacommunity. We find that diversity increases with node centrality in the network, but only when centrality is measured on a given scale in the network that widens with increasing dispersal rates and narrows with increasing evolutionary rates. More generally, complex biodiversity patterns form only when the underlying geography has structure on this critical scale. This provides a framework for understanding the influence of spatial geographic structure on global biodiversity patterns.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/79225/1/j.1600-0706.2010.18272.x.pd

Absence of toxicity with hypofractionated 3-dimensional radiation therapy for inoperable, early stage non-small cell lung cancer

PURPOSE: Hypofractionated radiotherapy may overcome repopulation in rapidly proliferating tumors such as lung cancer. It is more convenient for the patients and reduces health care costs. This study reports our results on patients with medically inoperable, early stage, non-small cell lung cancer (NSCLC) treated with hypofractionation. MATERIALS AND METHODS: Stage T1-2N0 NSCLC patients were treated with hypofractionation alone, 52.5 Gy/15 fractions, in 3 weeks, with 3-dimensional conformal planning. T1-2N1 patients with the hilar lymphnode close to the primary tumor were also eligible for this treatment. We did not use any approach to reduce respiratory motion, but it was monitored in all patients. Elective nodal radiotherapy was not performed. Routine follow up included assessment for acute and late toxicity and radiological tumor response. Median follow up time was 29 months for the surviving patients. RESULTS: Thirty-two patients with a median age of 76 years, T1 = 15 and T2 = 17, were treated. Median planning target volume (PTV) volume was 150cc and median V16 of both lungs was 13%. The most important finding of this study is that toxicity was minimal. Two patients had grade ≤ 2 acute pneumonitis and 3 had mild (grade 1) acute esophagitis. There was no late toxicity. Actuarial 1 and 2-year overall survival rates are 78% and 56%, cancer specific survival rates (CSS) are 90% and 74%, and local relapse free survival rates are 93% and 76% respectively. CONCLUSION: 3-D planning, involved field hypofractionation at a dose of 52.5 Gy in 15 daily fractions is safe, well tolerated and easy radiation treatment for medically inoperable lung cancer patients. It shortens by half the traditional treatment. Results compare favorably with previously published studies. Further studies are needed to compare similar technique with other treatments such as surgery and stereotactic radiotherapy

Redefining Water Security through Social Reproduction: Lessons Learned from Rajasthan's ‘Ocean of Sand’

One of the most urgent challenges facing the world today is ensuring local water security under rapid climate variability and change. This is of particular importance in a country like India, where over half of the people are involved in farming, and agricultural losses due to climate change are estimated to be as high as 30 per cent by 2080. This ethnography in the arid village of Bhiwadi, West Rajasthan empirically links the reintroduction of local water harvesting technologies with the building of sustainable social reproduction in subsistent communities. By emphasising both the role of gender and the informal economy – and institutions – this ethnography provides a more thorough picture of the individuals and collective actors involved in localised and resilient technologies within global economic and climatic processes

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COPI-coated vesicles mediate trafficking within the Golgi apparatus and from the Golgi to the endoplasmic reticulum. The structures of membrane protein coats, including COPI, have been extensively studied with in vitro reconstitution systems using purified components. Previously we have determined a complete structural model of the in vitro reconstituted COPI coat (Dodonova et al., 2017). Here, we applied cryo-focused ion beam milling, cryo-electron tomography and subtomogram averaging to determine the native structure of the COPI coat within vitrified Chlamydomonas reinhardtii cells. The native algal structure resembles the in vitro mammalian structure, but additionally reveals cargo bound beneath beta'-COP. We find that all coat components disassemble simultaneously and relatively rapidly after budding. Structural analysis in situ, maintaining Golgi topology, shows that vesicles change their size, membrane thickness, and cargo content as they progress from cis to trans, but the structure of the coat machinery remains constant

RNA promotes phase separation of glycolysis enzymes into yeast G bodies in hypoxia.

In hypoxic stress conditions, glycolysis enzymes assemble into singular cytoplasmic granules called glycolytic (G) bodies. G body formation in yeast correlates with increased glucose consumption and cell survival. However, the physical properties and organizing principles that define G body formation are unclear. We demonstrate that glycolysis enzymes are non-canonical RNA binding proteins, sharing many common mRNA substrates that are also integral constituents of G bodies. Targeting nonspecific endoribonucleases to G bodies reveals that RNA nucleates G body formation and maintains its structural integrity. Consistent with a phase separation mechanism of biogenesis, recruitment of glycolysis enzymes to G bodies relies on multivalent homotypic and heterotypic interactions. Furthermore, G bodies fuse in vivo and are largely insensitive to 1,6-hexanediol, consistent with a hydrogel-like composition. Taken together, our results elucidate the biophysical nature of G bodies and demonstrate that RNA nucleates phase separation of the glycolysis machinery in response to hypoxic stress