Factors controlling the last interglacial climate as simulated by LOVECLIM1.3

The last interglacial (LIG), also identified to the Eemian in Europe, began at approximately 130 kyr BP and ended at about 115 kyr BP (before present). More and more proxy-based reconstructions of the LIG climate are becoming more available even though they remain sparse. The major climate forcings during the LIG are rather well known and therefore models can be tested against paleoclimatic data sets and then used to better understand the climate of the LIG. However, models are displaying a large range of responses, being sometimes contradictory between them or with the reconstructed data. Here we would like to investigate causes of these differences. We focus on a single climate model, LOVECLIM, and we perform transient simulations over the LIG, starting at 135 kyr BP and run until 115 kyr BP. With these simulations, we test the role of the surface boundary conditions (the time-evolution of the Northern Hemisphere (NH) ice sheets) on the simulated LIG climate and the importance of the parameter sets (internal to the model, such as the albedos of the ocean and sea ice), which affect the sensitivity of the model. The magnitude of the simulated climate variations through the LIG remains too low compared to reconstructions for climate variables such as surface air temperature. Moreover, in the North Atlantic, the large increase in summer sea surface temperature towards the peak of the interglacial occurs too early (at ∼128 kyr BP) compared to the reconstructions. This feature as well as the climate simulated during the optimum of the LIG, between 131 and 121 kyr BP, does not depend on changes in surface boundary conditions and parameter sets. The additional freshwater flux (FWF) from the melting NH ice sheets is responsible for a temporary abrupt weakening of the North Atlantic meridional overturning circulation, which causes a strong global cooling in annual mean. However, the changes in the configuration (extent and albedo) of the NH ice sheets during the LIG only slightly impact the simulated climate. Together, configuration of and FWF from the NH ice sheets greatly increase the magnitude of the temperature variations over continents as well as over the ocean at the beginning of the simulation and reduce the difference between the simulated climate and the reconstructions. Lastly, we show that the contribution from the parameter sets to the climate response is actually very modest

Conversion of Glycerol to 3-Hydroxypropanoic Acid by Genetically Engineered Bacillus subtilis

3-Hydroxypropanoic acid (3-HP) is an important biomass-derivable platform chemical that can be converted into a number of industrially relevant compounds. There have been several attempts to produce 3-HP from renewable sources in cell factories, focusing mainly on Escherichia coli, Klebsiella pneumoniae, and Saccharomyces cerevisiae. Despite the significant progress made in this field, commercially exploitable large-scale production of 3-HP in microbial strains has still not been achieved. In this study, we investigated the potential of Bacillus subtilis as a microbial platform for bioconversion of glycerol into 3-HP. Our recombinant B. subtilis strains overexpress the two-step heterologous pathway containing glycerol dehydratase and aldehyde dehydrogenase from K. pneumoniae. Genetic engineering, driven by in silico optimization, and optimization of cultivation conditions resulted in a 3-HP titer of 10 g/L, in a standard batch cultivation. Our findings provide the first report of successful introduction of the biosynthetic pathway for conversion of glycerol into 3-HP in B. subtilis. With this relatively high titer in batch, and the robustness of B. subtilis in high density fermentation conditions, we expect that our production strains may constitute a solid basis for commercial production of 3-HP

Reconciling gene expression data with regulatory network models – a stimulon-based approach for integrated metabolic and regulatory modeling of Bacillus subtilis

The reconstruction of genome-scale metabolic models from genome annotations has become a routine practice in Systems Biology research. The potential of metabolic models for predictive biology is widely accepted by the scientific community, but these same models still lack the capability to account for the effect of gene regulation on metabolic activity. Our focus organism, Bacillus subtilis is most commonly found in soil, being subject to a wide variety of external environmental conditions. This reinforces the importance of the regulatory mechanisms that allow the bacteria to survive and adapt to such conditions. Existing integrated metabolic regulatory models are currently available for only a small number of well-known organisms (e.g E. coli and B. subtilis). The E. coli integrated model was proposed by Covert et al in 2004 and has slowly improved over the years. Goelzer et al. introduced the B. subtilis integrated model in 2008, covering only the central metabolic pathways. Different strategies were used in the two modeling efforts. The E. coli model is defined by a set of Boolean rules (turning genes ON and OFF) accounting mostly for transcription factors, gene interactions, involved metabolites, and some external conditions such as heat shock. The B. subtilis model introduces a set of more complex rules and also incorporates sigma factor activity into the modeling abstraction. Here we propose a genome-scale model for the regulatory network of B. subtilis, using a new stimulon-based approach. A stimulon is defined as the set of genes (that can be a part of the same operon(s) and regulon(s)) that respond in the same set of stimuli. The proposed stimulon-based approach allows for the inclusion of more types of regulation in the model. This methodology also abstracts away much of the complexity of regulatory mechanisms by directly connecting the activity of genes to the presence or absence of associated stimuli, a necessity in the many cases where details of regulatory mechanisms are poorly understood. Our model integrates regulatory network data from the Goelzer et al model, in addition to other available literature data. We then reconciled our model against a large set of high-quality gene expression data (tiled microarrays for 104 different conditions). The stimulons in our model were split or extended to improve consistency with our expression data, and the stimuli in our model were adjusted to improve consistency with the conditions of our expression experiments. The reconciliation with gene expression data revealed a significant number of exact or nearly exact matches between the manually curated regulons/stimulons and pure correlation-based regulons. Our reconciliation analysis of the 2011 SubtiWiki regulon release suggested many gene candidates for regulon extension that were subsequently included in the 2013 SubtiWiki update. Our enhanced model also includes an improved coverage of a wide range of different stress conditions. We then integrated our regulatory model with the latest metabolic reconstruction for B. subtilis, the iBsu1103V2 model (Tanaka et al. 2012). We applied this integrated metabolic regulatory model to the simulation of all growth phenotype data currently available for B. subtilis, demonstrating how the addition of regulatory constraints improved consistency of model predictions with experimentally observed phenotype data. This analysis of growth phenotype data unveiled phenotypes that could only be characterized with the addition of regulatory network constraints. All tools applied in the reconstruction, simulation, and curation of our new regulatory model are now publicly available as a part of the KBase framework. These tools permit the direct simulation of gene expression data using the regulon model alone, as well as the simulation of phenotypes and growth conditions using an integrated metabolic and regulatory model. We will highlight these new tools in the context of our reconstruction and analysis of the B. subtilis regulatory model

Ice Sheet Model Intercomparison Project (ISMIP6) contribution to CMIP6

Reducing the uncertainty in the past, present, and future contribution of ice sheets to sea-level change requires a coordinated effort between the climate and glaciology communities. The Ice Sheet Model Intercomparison Project for CMIP6 (ISMIP6) is the primary activity within the Coupled Model Intercomparison Project – phase 6 (CMIP6) focusing on the Greenland and Antarctic ice sheets. In this paper, we describe the framework for ISMIP6 and its relationship with other activities within CMIP6. The ISMIP6 experimental design relies on CMIP6 climate models and includes, for the first time within CMIP, coupled ice-sheet–climate models as well as standalone ice-sheet models. To facilitate analysis of the multi-model ensemble and to generate a set of standard climate inputs for standalone ice-sheet models, ISMIP6 defines a protocol for all variables related to ice sheets. ISMIP6 will provide a basis for investigating the feedbacks, impacts, and sea-level changes associated with dynamic ice sheets and for quantifying the uncertainty in ice-sheet-sourced global sea-level change

Núcleo extensionista Rondon IFPR: ação de extensão universitária em Ibirirama, ES

Anais do 35º Seminário de Extensão Universitária da Região Sul - Área temática: Tecnologia e ProduçãoO artigo tem o propósito de apontar o encaminhamento das ações extensionistas dos alunos do Campus Palmas do Instituto Federal do Paraná (IFPR) a partir da intermediação do Núcleo Extensionista Rondon IFPR (NER IFPR), criado com o intuito de concorrer aos editais do Projeto Rondon do Ministério da Defesa (MD), participar de ações de extensão de outras instituições, capacitar os estudantes para atuarem nos municípios selecionados para receber o Projeto e também para desenvolver atividades demandadas pela população de Palmas, PR, com relação as oito áreas da extensão com ênfase na Tecnologia e Produção e/ou Trabalho. A partir de então, o NER IFPR teve projetos aprovados nos três últimos editais do MD e atuou em três Operações nos municípios de Novo Acordo, TO, Ibitirama, ES, e Campo Novo de Rondônia, RO, municípios que apresentam importantes índices de vulnerabilidade social, além de ter sido convidado para atuar nas Operações do Núcleo Extensionista Rondon da Universidade do Estado de Santa Catarina (NER UDESC). Em tais Operações, houve a participação de 35 estudantes do Campus Palmas, os quais tiveram a oportunidade de viverem experiências e conhecimentos que não podem ser contemplados somente a partir da sala de aula, ao tempo em que ofereceram repostas simples e práticas às diferentes necessidades das localidades visitadas a partir dos seus próprios arranjos sociais, efetivando, dessa forma, a responsabilidade social das instituições universitárias a partir da extensão universitária, o bem estar das comunidades e a sua integração sociocultura

Coronal electron temperature in the protracted solar minimum, the cycle 24 mini maximum, and over centuries

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106800/1/jgra50869.pd

Simulating the Antarctic ice sheet in the late-Pliocene warm period: PLISMIP-ANT, an ice-sheet model intercomparison project

In the context of future climate change, understanding the nature and behaviour of ice sheets during warm intervals in Earth history is of fundamental importance. The late Pliocene warm period (also known as the PRISM interval: 3.264 to 3.025 million years before present) can serve as a potential analogue for projected future climates. Although Pliocene ice locations and extents are still poorly constrained, a significant contribution to sea-level rise should be expected from both the Greenland ice sheet and the West and East Antarctic ice sheets based on palaeo sea-level reconstructions. Here, we present results from simulations of the Antarctic ice sheet by means of an international Pliocene Ice Sheet Modeling Intercomparison Project (PLISMIP-ANT). For the experiments, ice-sheet models including the shallow ice and shelf approximations have been used to simulate the complete Antarctic domain (including grounded and floating ice). We compare the performance of six existing numerical ice-sheet models in simulating modern control and Pliocene ice sheets by a suite of five sensitivity experiments. We include an overview of the different ice-sheet models used and how specific model configurations influence the resulting Pliocene Antarctic ice sheet. The six ice-sheet models simulate a comparable present-day ice sheet, considering the models are set up with their own parameter settings. For the Pliocene, the results demonstrate the difficulty of all six models used here to simulate a significant retreat or re-advance of the East Antarctic ice grounding line, which is thought to have happened during the Pliocene for the Wilkes and Aurora basins. The specific sea-level contribution of the Antarctic ice sheet at this point cannot be conclusively determined, whereas improved grounding line physics could be essential for a correct representation of the migration of the grounding-line of the Antarctic ice sheet during the Pliocene

Reconciling gene expression data with regulatory network models

The reconstruction of genome-scale metabolic models from genome annotations has become a routine practice in Systems Biology research. The potential of metabolic models for predictive biology is widely accepted by the scientific community, but these same models still lack the capability to account for the effect of gene regulation on metabolic activity. Our focus organism, Bacillus subtilis is most commonly found in soil, being subject to a wide variety of external environmental conditions. This reinforces the importance of the regulatory mechanisms that allow the bacteria to survive and adapt to such conditions. We introduce a manually curated regulatory network for Bacillus subtilis, tapping into the notable resources for B. subtilis regulation. We propose the concept of Atomic Regulon, as a set of genes that share the same ON and OFF gene expression profile across multiple samples of experimental data. Atomic regulon inference uses prior knowledge from curated SEED subsystems, in addition to expression data to infer regulatory interactions. We show how atomic regulons for B. subtilis are able to capture many sets of genes corresponding to regulated operons in our manually curated network. Additionally, we demonstrate how atomic regulons can be used to help expand/ validate the knowledge of the regulatory networks and gain insights into novel biology