Evaluation of model systems for the study of protein association / incorporation of Beta-Methylamino-L-Alanine (BMAA)

β-methylamino-L-alanine (BMAA) is thought to be a contributing factor of Amyotrophic Lateral Sclerosis-Parkinsonism Dementia Complex (ALS/PDC). It has been shown that the levels of toxin ingestion by humans are too low to cause disease. However, it has recently been theorized that this toxin is bioaccumulated within cells. Via a process of slow release from this reservoir, the BMAA is able to bring about neurotoxicity. Mechanisms of uptake and bioaccumulation of BMAA have been proposed in several publications; however the mechanism of protein incorporation of BMAA has not yet been identified. Identifying suitable model systems would be a prerequisite in order for future studies on BMAA protein incorporation. Three specific models were therefore chosen for investigation; mammalian cell lines including C2C12 and HT29, a prokaryotic (E. coli) expression system and yeast cells. The cytotoxity of BMAA was established for the mammalian cell lines and further investigation of BMAA incorporation into cellular proteins was performed on all three above mentioned models. Samples were run on HPLC-MS in order to determine uptake of BMAA into cells or lack thereof. Results indicate negligible cytotoxicity as measured by MTT and CellTitre Blue assays, limited uptake and protein incorporation of BMAA within the prokaryotic model and insignificant uptake of BMAA by yeast cells. Although the uptake of BMAA in the prokaryotic model was not extensive, there was indeed uptake. BMAA was not only taken up into the cells but was also observed in inclusion body protein samples after hydrolysis. After further investigation and use, this model could very well provide researchers with information pertaining to the mechanism of association of BMAA with proteins. Although the other models provided negative results, this research was valuable in the sense that one can narrow down the number of possible model systems available. Also, in seeking models for studying protein association/incorporation, the use of the final target cell is not relevant or necessary as the purpose of the research was to identify a model system in which the mechanism of protein association/incorporation can, in future, be studied

Completion of a SCUBA survey of Lynds dark clouds and implications for low-mass star formation

We have carried out a survey of optically-selected dark clouds using the bolometer array SCUBA on the James Clerk Maxwell Telescope, at 850 microns wavelength. The survey covers a total of 0.5 square degrees and is unbiased with reference to cloud size, star formation activity, or the presence of infrared emission. Several new protostars and starless cores have been discovered; the protostars are confirmed through the detection of their accompanying outflows in CO(2-1) emission. The survey is believed to be complete for Class 0 and Class I protostars, and yields two important results regarding the lifetimes of these phases. First, the ratio of Class 0 to Class protostars in the sample is roughly unity, very different from the 1:10 ratio that has previously been observed for the rho Ophiuchi star-forming region. Assuming star formation to be a homogeneous process in the dark clouds, this implies that the Class 0 lifetime is similar to the Class I phase, which from infrared surveys has been established to be approximately 200,000 yr. It also suggests there is no rapid initial accretion phase in Class 0 objects. A burst of triggered star formation some 100,000 yr ago can explain the earlier results for rho Ophiuchus. Second, the number of starless cores is approximately twice that of the total number of protostars, indicating a starless core lifetime of approximately 800,000 yr. These starless cores are therefore very short-lived, surviving only two or three free-fall times. This result suggests that, on size scales of 10,000 AU at least, the dynamical evolution of starless cores is probably not controlled by magnetic processes.Comment: 67 pages including 32 figures (highly compressed). Accepted for publication in the Astronomical Journal. Available with full resolution (legible) figures at http://www.mrao.cam.ac.uk/%7ejsr/papers/lynds2.ps.g

Complex Structure in Class 0 Protostellar Envelopes III: Velocity Gradients in Non-Axisymmetric Envelopes, Infall or Rotation?

We present an interferometric kinematic study of morphologically complex protostellar envelopes based on observations of the dense gas tracers N2H+ and NH3. The strong asymmetric nature of most envelopes in our sample leads us to question the common interpretation of velocity gradients as rotation, given the possibility of projection effects in the observed velocities. Several "idealized" sources with well-ordered velocity fields and envelope structures are now analyzed in more detail. We compare the interferometric data to position-velocity diagrams of kinematic models for spherical rotating collapse and filamentary rotating collapse. For this purpose, we developed a filamentary parametrization of the rotating collapse model to explore the effects of geometric projection on the observed velocity structures. We find that most envelopes in our sample have PV structures that can be reproduced by an infalling filamentary envelope projected at different angles within the plane of the sky. The infalling filament produces velocity shifts across the envelope that can mimic rotation, especially when viewed at single-dish resolutions and the axisymmetric rotating collapse model does not uniquely describe any dataset. Furthermore, if the velocities are assumed to reflect rotation, then the inferred centrifugal radii are quite large in most cases, indicating significant fragmentation potential or more likely another component to the line-center velocity. We conclude that ordered velocity gradients cannot be interpreted as rotation alone when envelopes are non-axisymmetric and that projected infall velocities likely dominate the velocity field on scales larger than 1000 AU.Comment: 37 pages, 15 Figures, 2 Tables, Accepted to Ap

S3: Syntax- and semantic-guided repair synthesis via programming by examples

National Science Foundatio

Predicting streamflow with LSTM networks using global datasets

Streamflow predictions remain a challenge for poorly gauged and ungauged catchments. Recent research has shown that deep learning methods based on Long Short-Term Memory (LSTM) cells outperform process-based hydrological models for rainfall-runoff modeling, opening new possibilities for prediction in ungauged basins (PUB). These studies usually feature local datasets for model development, while predictions in ungauged basins at a global scale require training on global datasets. In this study, we develop LSTM models for over 500 catchments from the CAMELS-US data base using global ERA5 meteorological forcing and global catchment characteristics retrieved with the HydroMT tool. Comparison against an LSTM trained with local datasets shows that, while the latter generally yields superior performances due to the higher spatial resolution meteorological forcing (overall median daily NSE 0.54 vs. 0.71), training with ERA5 results in higher NSE in most catchments of Western and North-Western US (median daily NSE of 0.83 vs. 0.78). No significant changes in performance occur when substituting local with global data sources for deriving the catchment characteristics. These results encourage further research to develop LSTM models for worldwide predictions of streamflow in ungauged basins using available global datasets. Promising directions include training the models with streamflow data from different regions of the world and with higher quality meteorological forcing

Complex Structure in Class 0 Protostellar Envelopes II: Kinematic Structure from Single-Dish and Interferometric Molecular Line Mapping

We present a study of dense molecular gas kinematics in seventeen nearby protostellar systems using single-dish and interferometric molecular line observations. The non-axisymmetric envelopes around a sample of Class 0/I protostars were mapped in the N2H+ (J=1-0) tracer with the IRAM 30m, CARMA and PdBI as well as NH3 (1,1) with the VLA. The molecular line emission is used to construct line-center velocity and linewidth maps for all sources to examine the kinematic structure in the envelopes on spatial scales from 0.1 pc to ~1000 AU. The direction of the large-scale velocity gradients from single-dish mapping is within 45 degrees of normal to the outflow axis in more than half the sample. Furthermore, the velocity gradients are often quite substantial, the average being ~2.3 km\s\pc. The interferometric data often reveal small-scale velocity structure, departing from the more gradual large-scale velocity gradients. In some cases, this likely indicates accelerating infall and/or rotational spin-up in the inner envelope; the median velocity gradient from the interferometric data is ~10.7 km/s/pc. In two systems, we detect high-velocity HCO+ (J=1-0) emission inside the highest-velocity \nthp\ emission. This enables us to study the infall and rotation close to the disk and estimate the central object masses. The velocity fields observed on large and small-scales are more complex than would be expected from rotation alone, suggesting that complex envelope structure enables other dynamical processes (i.e. infall) to affect the velocity field.Comment: 85 Pages, 31 Figures, 11 Tables, Accepted to ApJ

Sustainable futures over the next decade are rooted in soil science

Funding information: Dutch Knowledge Base Program; European Commission, Grant/Award Number: NEW 810; Horizon 2020 Framework Programme, Grant/Award Numbers: 774378, 869625; Korea Environmental Industry and Technology Institute, Grant/Award Number: 2019002820004; Natural Environment Research Council, Grant/Award Number: NE/R016429/1; Svenska Forskningsrådet Formas, Grant/Award Number: 2017-00608; UK Research and Innovation, Grant/Award Number: NE/P019455/1Peer reviewedPublisher PD

The potential of C4 grasses for cellulosic biofuel production

With the advent of biorefinery technologies enabling plant biomass to be processed into biofuel, many researchers set out to study and improve candidate biomass crops. Many of these candidates are C4 grasses, characterized by a high productivity and resource use efficiency. In this review the potential of five C4 grasses as lignocellulosic feedstock for biofuel production is discussed. These include three important field crops-maize, sugarcane and sorghum-and two undomesticated perennial energy grasses-miscanthus and switchgrass. Although all these grasses are high yielding, they produce different products. While miscanthus and switchgrass are exploited exclusively for lignocellulosic biomass, maize, sorghum, and sugarcane are dual-purpose crops. It is unlikely that all the prerequisites for the sustainable and economic production of biomass for a global cellulosic biofuel industry will be fulfilled by a single crop. High and stable yields of lignocellulose are required in diverse environments worldwide, to sustain a year-round production of biofuel. A high resource use efficiency is indispensable to allow cultivation with minimal inputs of nutrients and water and the exploitation of marginal soils for biomass production. Finally, the lignocellulose composition of the feedstock should be optimized to allow its efficient conversion into biofuel and other by-products. Breeding for these objectives should encompass diverse crops, to meet the demands of local biorefineries and provide adaptability to different environments. Collectively, these C4 grasses are likely to play a central role in the supply of lignocellulose for the cellulosic ethanol industry. Moreover, as these species are evolutionary closely related, advances in each of these crops will expedite improvements in the other crops. This review aims to provide an overview of their potential, prospects and research needs as lignocellulose feedstocks for the commercial production of biofuel