CLM-AG: An Agriculture Module for the Community Land Model version 3.5

It is estimated that 40% of all crops grown in the world today are grown using irrigation. As a consequence, shifting precipitation patterns due to climate change are viewed as a major threat to food security. This report presents the Community Land Model-Agriculture module (CLM-AG), which models crop growth and water stress. The CLM-AG model is a global generic crop model built in the framework of the Community Land Model version 3.5. This report describes the structure and main routines of the model. Two different evaluations of the model are then considered. First, at a global level, CLM-AG is run under a historic climatology and compared to the Global Agro-Ecological Zones, an existing model of irrigation need. Second, the irrigation need computed for the United States is compared to survey data from the United States Department of Agriculture. For both evaluations, CLM-AG results are comparable to either the model results or the surveyed data.Development of the IGSM applied in this research was supported by the U.S. Department of Energy, Office of Science (DE-FG02-94ER61937); the U.S. Environmental Protection Agency, EPRI, and other U.S. government agencies and a consortium of 40 industrial and foundation sponsors. For a complete list see http://globalchange.mit.edu/sponsors/current.htm

Analysis of U.S. Water Resources under Climate Change

The MIT Integrated Global System Model (IGSM) framework, extended to include a Water Resource System (WRS) component, is applied to an integrated assessment of effects of alternative climate policy scenarios on U.S. water systems. Climate results are downscaled to yield estimates of surface runoff at 99 river basins of the continental U.S., with an exploration of climate patterns that are relatively wet and dry over the region. These estimates are combined with estimated groundwater supplies. An 11-region economic model (USREP) sets conditions driving water requirements estimated for five use sectors, with detailed sub-models employed for analysis of irrigation and electric power. The water system of the interconnected basins is operated to minimize water stress. Results suggest that, with or without climate change, U.S. average annual water stress is expected to increase over the period 2041 to 2050, primarily because of an increase in water requirements, with the largest water stresses projected in the South West. Policy to lower atmospheric greenhouse gas concentrations has a beneficial effect, reducing water stress intensity and variability in the concerned basins.The Joint Program on the Science and Policy of Global Change is funded by the U.S. Department of Energy, Office of Science under grants DE-FG02-94ER61937, DE-FG02- 93ER61677, DEFG02-08ER64597, and DE-FG02-06ER64320; the U.S. Environmental Protection Agency under grants XA-83344601-0, XA-83240101, XA-83042801-0, PI-83412601- 0, RD-83096001, and RD-83427901-0; the U.S. National Science Foundation under grants SES- 0825915, EFRI-0835414, ATM-0120468, BCS-0410344, ATM-0329759, and DMS-0426845; the U.S. National Aeronautics and Space Administration under grants NNX07AI49G, NNX08AY59A, NNX06AC30A, NNX09AK26G, NNX08AL73G, NNX09AI26G, NNG04GJ80G, NNG04GP30G, and NNA06CN09A; the U.S. National Oceanic and Atmospheric Administration under grants DG1330-05-CN-1308, NA070AR4310050, and NA16GP2290; the U.S. Federal Aviation Administration under grant 06-C-NE-MIT; the Electric Power Research Institute under grant EPP32616/C15124; and a consortium of 40 industrial and foundation sponsors (for the complete list see http://globalchange.mit.edu/sponsors/current.html

Modeling Water Resource Systems under Climate Change: IGSM-WRS

Through the integration of a Water Resource System (WRS) component, the MIT Integrated Global System Model (IGSM) framework has been enhanced to study the effects of climate change on managed water-resource systems. Development of the WRS involves the downscaling of temperature and precipitation from the zonal representation of the IGSM to regional (latitude-longitude) scale, and the translation of the resulting surface hydrology to runoff at the scale of river basins, referred to as Assessment Sub-Regions (ASRs). The model of water supply is combined with analysis of water use in agricultural and non-agricultural sectors and with a model of water system management that allocates water among uses and over time and routes water among ASRs. Results of the IGSM-WRS framework include measures of water adequacy and ways it is influenced by climate change. Here we document the design of WRS and its linkage to other components of the IGSM, and present tests of consistency of model simulations with the historical record.The Joint Program on the Science and Policy of Global Change is funded by the U.S. Department of Energy, Office of Science under grants DE-FG02-94ER61937, DE-FG02-93ER61677, DEFG02- 08ER64597, and DE-FG02-06ER64320; the U.S. Environmental Protection Agency under grants XA-83344601-0, XA-83240101, XA-83042801-0, PI-83412601-0, RD-83096001, and RD- 83427901-0; the U.S. National Science Foundation under grants SES-0825915, EFRI-0835414, ATM-0120468, BCS-0410344, ATM-0329759, and DMS-0426845; the U.S. National Aeronautics and Space Administration under grants NNX07AI49G, NNX08AY59A, NNX06AC30A, NNX09AK26G, NNX08AL73G, NNX09AI26G, NNG04GJ80G, NNG04GP30G, and NNA06CN09A; the U.S. National Oceanic and Atmospheric Administration under grants DG1330-05-CN-1308, NA070AR4310050, and NA16GP2290; the U.S. Federal Aviation Administration under grant 06-C-NE-MIT; the Electric Power Research Institute under grant EPP32616/ C15124; and a consortium of 40 industrial and foundation sponsors (for the complete list see http://globalchange.mit.edu/sponsors/current.html)

The Future of Global Water Stress: An Integrated Assessment

We assess the ability of global water systems, resolved at 282 large river basins or Assessment Sub Regions (ASRs), to the meet water requirements over the coming decades under integrated projections of socioeconomic growth and climate change. We employ a Water Resource System (WRS) component embedded within the MIT Integrated Global System Model (IGSM) framework in a suite of simulations that consider a range of climate policies and regional hydroclimatic changes through the middle of this century. We find that for many developing nations water-demand increases due to population growth and economic activity have a much stronger effect on water stress than climate change. By 2050, economic growth and population change alone can lead to an additional 1.8 billion people living in regions with at least moderate water stress. Of this additional 1.8 billion people, 80% are found in developing countries. Uncertain regional climate change can play a secondary role to either exacerbate or dampen the increase in water stress due to socioeconomic growth. The strongest climate impacts on relative changes in water stress are seen over many areas in Africa, but strong impacts also occur over Europe, Southeast Asia and North America. The combined effects of socioeconomic growth and uncertain climate change lead to a 1.0 to 1.3 billion increase of the world's 2050 projected population living in regions with overly exploited water conditions— where total potential water requirements will consistently exceed surface-water supply. Under the context of the WRS model framework, this would imply that adaptive measures would be taken to meet these surface-water shortfalls and would include: water-use efficiency, reduced and/or redirected consumption, recurrent periods of water emergencies or curtailments, groundwater depletion, additional inter-basin transfers, and overdraw from flow intended to maintain environmental requirements.We assess the ability of global water systems, resolved at 282 large river basins or Assessment Sub Regions (ASRs), to the meet water requirements over the coming decades under integrated projections of socioeconomic growth and climate change. We employ a Water Resource System (WRS) component embedded within the MIT Integrated Global System Model (IGSM) framework in a suite of simulations that consider a range of climate policies and regional hydroclimatic changes through the middle of this century. We find that for many developing nations water-demand increases due to population growth and economic activity have a much stronger effect on water stress than climate change. By 2050, economic growth and population change alone can lead to an additional 1.8 billion people living in regions with at least moderate water stress. Of this additional 1.8 billion people, 80% are found in developing countries. Uncertain regional climate change can play a secondary role to either exacerbate or dampen the increase in water stress due to socioeconomic growth. The strongest climate impacts on relative changes in water stress are seen over many areas in Africa, but strong impacts also occur over Europe, Southeast Asia and North America. The combined effects of socioeconomic growth and uncertain climate change lead to a 1.0 to 1.3 billion increase of the world's 2050 projected population living in regions with overly exploited water conditions— where total potential water requirements will consistently exceed surface-water supply. Under the context of the WRS model framework, this would imply that adaptive measures would be taken to meet these surface-water shortfalls and would include: water-use efficiency, reduced and/or redirected consumption, recurrent periods of water emergencies or curtailments, groundwater depletion, additional inter-basin transfers, and overdraw from flow intended to maintain environmental requirements

Mycobacterium tuberculosis ClpP Proteases Are Co-transcribed but Exhibit Different Substrate Specificities

PMCID: PMC3613350This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Mutational Patterns in RNA Secondary Structure Evolution Examined in Three RNA Families

The goal of this work was to study mutational patterns in the evolution of RNA secondary structure. We analyzed bacterial tmRNA, RNaseP and eukaryotic telomerase RNA secondary structures, mapping structural variability onto phylogenetic trees constructed primarily from rRNA sequences. We found that secondary structures evolve both by whole stem insertion/deletion, and by mutations that create or disrupt stem base pairing. We analyzed the evolution of stem lengths and constructed substitution matrices describing the changes responsible for the variation in the RNA stem length. In addition, we used principal component analysis of the stem length data to determine the most variable stems in different families of RNA. This data provides new insights into the evolution of RNA secondary structures and patterns of variation in the lengths of double helical regions of RNA molecules. Our findings will facilitate design of improved mutational models for RNA structure evolution

Process intensification education contributes to sustainable development goals: Part 2

Achieving the United Nations sustainable development goals requires industry and society to develop tools and processes that work at all scales, enabling goods delivery, services, and technology to large conglomerates and remote regions. Process Intensification (PI) is a technological advance that promises to deliver means to reach these goals, but higher education has yet to totally embrace the program. Here, we present practical examples on how to better teach the principles of PI in the context of the Bloom's taxonomy and summarise the current industrial use and the future demands for PI, as a continuation of the topics discussed in Part 1. In the appendices, we provide details on the existing PI courses around the world, as well as teaching activities that are showcased during these courses to aid students’ lifelong learning. The increasing number of successful commercial cases of PI highlight the importance of PI education for both students in academia and industrial staff.We acknowledge the sponsors of the Lorentz’ workshop on“Educating in PI”: The MESA+Institute of the University of Twente,Sonics and Materials (USA) and the PIN-NL Dutch Process Intensi-fication Network. DFR acknowledges support by The Netherlands Centre for Mul-tiscale Catalytic Energy Conversion (MCEC), an NWO Gravitationprogramme funded by the Ministry of Education, Culture and Sci-ence of the government of The Netherlands. NA acknowledges the Deutsche Forschungsgemeinschaft (DFG)- TRR 63¨Integrierte Chemische Prozesse in flüssigen Mehrphasen-systemen¨(Teilprojekt A10) - 56091768. The participation by Robert Weber in the workshop and thisreport was supported by Laboratory Directed Research and Devel-opment funding at Pacific Northwest National Laboratory (PNNL).PNNL is a multiprogram national laboratory operated for theUS Department of Energy by Battelle under contract DE-AC05-76RL0183

The Diversification of the LIM Superclass at the Base of the Metazoa Increased Subcellular Complexity and Promoted Multicellular Specialization

Background: Throughout evolution, the LIM domain has been deployed in many different domain configurations, which has led to the formation of a large and distinct group of proteins. LIM proteins are involved in relaying stimuli received at the cell surface to the nucleus in order to regulate cell structure, motility, and division. Despite their fundamental roles in cellular processes and human disease, little is known about the evolution of the LIM superclass. Results: We have identified and characterized all known LIM domain-containing proteins in six metazoans and three nonmetazoans. In addition, we performed a phylogenetic analysis on all LIM domains and, in the process, have identified a number of novel non-LIM domains and motifs in each of these proteins. Based on these results, we have formalized a classification system for LIM proteins, provided reasonable timing for class and family origin events; and identified lineagespecific loss events. Our analysis is the first detailed description of the full set of LIM proteins from the non-bilaterian species examined in this study. Conclusion: Six of the 14 LIM classes originated in the stem lineage of the Metazoa. The expansion of the LIM superclass at the base of the Metazoa undoubtedly contributed to the increase in subcellular complexity required for the transition from a unicellular to multicellular lifestyle and, as such, was a critically important event in the history of animal multicellularity

Immunohistochemistry on a Panel of Emery-Dreifuss Muscular Dystrophy Samples Reveals Nuclear Envelope Proteins as Inconsistent Markers for Pathology

Reports of aberrant distribution for some nuclear envelope proteins in cells expressing a few Emery–Dreifuss muscular dystrophy mutations raised the possibility that such protein redistribution could underlie pathology and/or be diagnostic. However, this disorder is linked to 8 different genes encoding nuclear envelope proteins, raising the question of whether a particular protein is most relevant. Therefore, myoblast/fibroblast cultures from biopsy and tissue sections from a panel of nine Emery–Dreifuss muscular dystrophy patients (4 male, 5 female) including those carrying emerin and FHL1 (X-linked) and several lamin A (autosomal dominant) mutations were stained for the proteins linked to the disorder. As tissue-specific nuclear envelope proteins have been postulated to mediate the tissue-specific pathologies of different nuclear envelopathies, patient samples were also stained for several muscle-specific nuclear membrane proteins. Although linked proteins nesprin 1 and SUN2 and muscle-specific proteins NET5/Samp1 and Tmem214 yielded aberrant distributions in individual patient cells, none exhibited defects through the larger patient panel. Muscle-specific Tmem38A normally appeared in both the nuclear envelope and sarcoplasmic reticulum, but most patient samples exhibited a moderate redistribution favouring the sarcoplasmic reticulum. The absence of striking uniform defects in nuclear envelope protein distribution indicates that such staining will be unavailing for general diagnostics, though it remains possible that specific mutations exhibiting protein distribution defects might reflect a particular clinical variant. These findings further argue that multiple pathways can lead to the generally similar pathologies of this disorder while at the same time the different cellular phenotypes observed possibly may help explain the considerable clinical variation of EDMD