Protein Folding Database (PFD 2.0): an online environment for the International Foldeomics Consortium

The Protein Folding Database (PFD) is a publicly accessible repository of thermodynamic and kinetic protein folding data. Here we describe the first major revision of this work, featuring extensive restructuring that conforms to standards set out by the recently formed International Foldeomics Consortium. The database now adopts standards for data acquisition, analysis and reporting proposed by the consortium, which will facilitate the comparison of folding rates, energies and structure across diverse sets of proteins. Data can now be easily deposited using a rich set of deposition tools. Enhanced search tools allow sophisticated searching and graphical data analysis affords simple data analysis online. PFD can be accessed freely at

Geosciences / Identifying Spatio-Temporal Landslide Hotspots on North Island, New Zealand, by Analyzing Historical and Recent Aerial Photography

Accurate mapping of landslides and the reliable identification of areas most affected by landslides are essential for advancing the understanding of landslide erosion processes. Remote sensing data provides a valuable source of information on the spatial distribution and location of landslides. In this paper we present an approach for identifying landslide-prone “hotspots” and their spatio-temporal variability by analyzing historical and recent aerial photography from five different dates, ranging from 1944 to 2011, for a study site near the town of Pahiatua, southeastern North Island, New Zealand. Landslide hotspots are identified from the distribution of semi-automatically detected landslides using object-based image analysis (OBIA), and compared to hotspots derived from manually mapped landslides. When comparing the overlapping areas of the semi-automatically and manually mapped landslides the accuracy values of the OBIA results range between 46% and 61% for the producers accuracy and between 44% and 77% for the users accuracy. When evaluating whether a manually digitized landslide polygon is only intersected to some extent by any semi-automatically mapped landslide, we observe that for the natural-color images the landslide detection rate is 83% for 2011 and 93% for 2005; for the panchromatic images the values are slightly lower (67% for 1997, 74% for 1979, and 72% for 1944). A comparison of the derived landslide hotspot maps shows that the distribution of the manually identified landslides and those mapped with OBIA is very similar for all periods; though the results also reveal that mapping landslide tails generally requires visual interpretation. Information on the spatio-temporal evolution of landslide hotspots can be useful for the development of location-specific, beneficial intervention measures and for assessing landscape dynamics.FFG-ASAP-847970(VLID)165265

High sensitivity of future global warming to land carbon cycle processes

Unknowns in future global warming are usually assumed to arise from uncertainties either in the amount of anthropogenic greenhouse gas emissions or in the sensitivity of the climate to changes in greenhouse gas concentrations. Characterizing the additional uncertainty in relating CO2 emissions to atmospheric concentrations has relied on either a small number of complex models with diversity in process representations, or simple models. To date, these models indicate that the relevant carbon cycle uncertainties are smaller than the uncertainties in physical climate feedbacks and emissions. Here, for a single emissions scenario, we use a full coupled climate–carbon cycle model and a systematic method to explore uncertainties in the land carbon cycle feedback. We find a plausible range of climate–carbon cycle feedbacks significantly larger than previously estimated. Indeed the range of CO2 concentrations arising from our single emissions scenario is greater than that previously estimated across the full range of IPCC SRES emissions scenarios with carbon cycle uncertainties ignored. The sensitivity of photosynthetic metabolism to temperature emerges as the most important uncertainty. This highlights an aspect of current land carbon modelling where there are open questions about the potential role of plant acclimation to increasing temperatures. There is an urgent need for better understanding of plant photosynthetic responses to high temperature, as these responses are shown here to be key contributors to the magnitude of future change

Real-Time Hardware-in-the-Loop Simulation of Ares I Launch Vehicle

The Ares Real-Time Environment for Modeling, Integration, and Simulation (ARTEMIS) has been developed for use by the Ares I launch vehicle System Integration Laboratory at the Marshall Space Flight Center. The primary purpose of the Ares System Integration Laboratory is to test the vehicle avionics hardware and software in a hardware - in-the-loop environment to certify that the integrated system is prepared for flight. ARTEMIS has been designed to be the real-time simulation backbone to stimulate all required Ares components for verification testing. ARTE_VIIS provides high -fidelity dynamics, actuator, and sensor models to simulate an accurate flight trajectory in order to ensure realistic test conditions. ARTEMIS has been designed to take advantage of the advances in underlying computational power now available to support hardware-in-the-loop testing to achieve real-time simulation with unprecedented model fidelity. A modular realtime design relying on a fully distributed computing architecture has been implemented

Mass spectrometry-based proteomic analysis of the matrix microenvironment in pluripotent stem cell culture

The cellular microenvironment comprises soluble factors, support cells, and components of the extracellular matrix (ECM) that combine to regulate cellular behavior. Pluripotent stem cells utilize interactions between support cells and soluble factors in the microenvironment to assist in the maintenance of self-renewal and the process of differentiation. However, the ECM also plays a significant role in shaping the behavior of human pluripotent stem cells, including embryonic stem cells (hESCs) and induced pluripotent stem cells. Moreover, it has recently been observed that deposited factors in a hESC-conditioned matrix have the potential to contribute to the reprogramming of metastatic melanoma cells. Therefore, the ECM component of the pluripotent stem cell microenvironment necessitates further analysis. In this study we first compared the self-renewal and differentiation properties of hESCs grown on Matrigel™pre-conditioned by hESCs to those on unconditioned Matrigel™. We determined that culture on conditioned Matrigel™ prevents differentiation when supportive growth factors are removed from the culture medium. To investigate and identify factors potentially responsible for this beneficial effect, we performed a defined SILAC MS-based proteomics screen of hESC-conditioned Matrigel™. From this proteomics screen, we identified over 80 extracellular proteins in matrix conditioned by hESCs and induced pluripotent stem cells. These included matrix-associated factors that participate in key stem cell pluripotency regulatory pathways, such as Nodal/Activin and canonical Wnt signaling. This work represents the first investigation of stem-cell-derived matrices from human pluripotent stem cells using a defined SILAC MS-based proteomics approach. © 2012 by The American Society for Biochemistry and Molecular Biology, Inc

Human induced pluripotent stem cell-derived cardiac myocytes and sympathetic neurons in disease modelling

Human induced pluripotent stem cells (hiPSC) offer an unprecedented opportunity to generate model systems that facilitate a mechanistic understanding of human disease. Current differentiation protocols are capable of generating cardiac myocytes (hiPSC-CM) and sympathetic neurons (hiPSC-SN). However, the ability of hiPSC-derived neurocardiac co-culture systems to replicate the human phenotype in disease modelling is still in its infancy. Here, we adapted current methods for efficient and replicable induction of hiPSC-CM and hiPSC-SN. Expression of cell-type-specific proteins were confirmed by flow cytometry and immunofluorescence staining. The utility of healthy hiPSC-CM was tested with pressor agents to develop a model of cardiac hypertrophy. Treatment with angiotensin II (AngII) resulted in: (i) cell and nuclear enlargement, (ii) enhanced fetal gene expression, and (iii) FRET-activated cAMP responses to adrenergic stimulation. AngII or KCl increased intracellular calcium transients in hiPSC-SN. Immunostaining in neurocardiac co-cultures demonstrated anatomical innervation to myocytes, where myocyte cytosolic cAMP responses were enhanced by forskolin compared with monocultures. In conclusion, human iPSC-derived cardiac myocytes and sympathetic neurons replicated many features of the anatomy and (patho)physiology of these cells, where co-culture preparations behaved in a manner that mimicked key physiological responses seen in other mammalian systems. This article is part of the theme issue 'The heartbeat: its molecular basis and physiological mechanisms'

Microenvironmental regulation of telomerase isoforms in human embryonic stem cells

Recent evidence points to extra-telomeric, noncanonical roles for telomerase in regulating stem cell function. In this study, human embryonic stem cells (hESCs) were cultured in 20% or 2% O2 microenvironments for up to 5 days and evaluated for telomerase reverse transcriptase (TERT) expression and telomerase activity. Results showed increased cell survival and maintenance of the undifferentiated state with elevated levels of nuclear TERT in 2% O 2-cultured hESCs despite no significant difference in telomerase activity compared with their high-O2-cultured counterparts. Pharmacological inhibition of telomerase activity using a synthetic tea catechin resulted in spontaneous hESC differentiation, while telomerase inhibition with a phosphorothioate oligonucleotide telomere mimic did not. Reverse transcription polymerase chain reaction (RT-PCR) analysis revealed variations in transcript levels of full-length and alternate splice variants of TERT in hESCs cultured under varying O2 atmospheres. Steric-blocking of Δα and Δβ hTERT splicing using morpholino oligonucleotides altered the hTERT splicing pattern and rapidly induced spontaneous hESC differentiation that appeared biased toward endomesodermal and neuroectodermal cell fates, respectively. Together, these results suggest that post-transcriptional regulation of TERT under varying O2 microenvironments may help regulate hESC survival, self-renewal, and differentiation capabilities through expression of extra-telomeric telomerase isoforms. © 2014, Mary Ann Liebert, Inc