Summary
Oscillospira is an under‐studied anaerobic bacterial genus from Clostridial cluster IV that has resisted cultivation for over a century since the first time it was observed. In recent years ...its 16S rRNA gene was identified in several human gut microbiota studies where it was often associated with interesting traits, especially leanness. However, very little is known about its metabolism or physiology. Here we used nearly complete genomes derived from shot‐gun metagenomic data from the human gut to analyze Oscillospira and related bacteria. We used sequence similarity, gene neighbourhood information and manual metabolic pathway curation to decipher key metabolic features of this intriguing bacterial genus. We infer that Oscillospira species are butyrate producers, and at least some of them have the ability to utilize glucuronate, a common animal‐derived sugar that is both produced by the human host and consumed by that host in diets rich in animal products. These findings could help explain diet‐related inter‐individual variation in faecal Oscillospira levels as well as the observation that the presence of this genus is reduced in diseases that involve inflammation.
This paper describes a new approach to online forecasting of power production from PV systems. The method is suited to online forecasting in many applications and in this paper it is used to predict ...hourly values of solar power for horizons of up to 36
h. The data used is 15-min observations of solar power from 21 PV systems located on rooftops in a small village in Denmark. The suggested method is a two-stage method where first a statistical normalization of the solar power is obtained using a clear sky model. The clear sky model is found using statistical smoothing techniques. Then forecasts of the normalized solar power are calculated using adaptive linear time series models. Both autoregressive (AR) and AR with exogenous input (ARX) models are evaluated, where the latter takes numerical weather predictions (NWPs) as input. The results indicate that for forecasts up to 2
h ahead the most important input is the available observations of solar power, while for longer horizons NWPs are the most important input. A root mean square error improvement of around 35% is achieved by the
ARX model compared to a proposed reference model.
Planetary boundaries for terrestrial inputs of reactive nitrogen (Nr) are transgressed and reducing the input of new Nr and its environmental impacts are major global challenges. Grain legumes fix ...dinitrogen (N
2
) in symbiosis with soil bacteria and use soil N sources, but often less efficient than cereals. Intercropping grain legumes with cereals may be a means of increasing use efficiency of soil N. Here, we estimate the global sole cropped grain legume acquisition of N from soil to approximately 14.2 Tg N year
−1
, which corresponds to one-third of the global synthetic fertilizer N use (109 Tg N year
−1
) for all crops, assuming that grain legumes recover on average 40% of the fertilizer N. Published data from grain legume-cereal intercrop experiments, employing stable
15
N isotope methods, have shown that due to competitive interactions and complementary N acquisition in intercrops, the cereals recover a more than proportional share of the soil N sources. As a consequence, the intercropped legume derives more of its N from the atmosphere, compared with when it is grown as legume sole crop. We estimated that the increased N use efficiency in intercropping can reduce the requirements for fossil-based fertilizer N by about 26% on a global scale. In addition, our estimates indicate that if all current grain legume sole crops would instead be intercropped with cereals, a potential net land saving would be achieved, when also replacing part of the current cereal sole crop area with intercropping. Intercropping has additional potential advantages such as increased yield stability and yield per unit area, reduced pest problems and reduced requirements for agrochemicals, while stimulating biodiversity. It is concluded that crop diversification by intercropping has the potential to reduce global requirements for synthetic fertilizer N and consequently support the development of more sustainable cropping systems.
Strategies for recovery of ammonia-inhibited thermophilic biogas process, were evaluated in batch and lab-scale reactors. Active methane producing biomass (digested cattle manure) was inhibited with ...NH
4Cl and subsequently, 3–5 days later, diluted with 50% of water, or with 50% digested manure, or with 50% fresh manure or kept undiluted. Dilution with fresh cattle manure resulted in the highest methane production rate during the recovery period while dilution with digested cattle manure gave a more balanced recovery according to the fluctuations in volatile fatty acids. Furthermore, the process recovery of a 7600
m
3 biogas plant suffering from ammonia inhibition was observed. The ammonia concentration was only gradually lowered via the daily feeding with cattle manure, as is the normal procedure at Danish full-scale biogas plants. Recovery took 31 days with a 40% methane loss and illustrates the need for development of efficient process recovery strategies.
At all but the slowest growth rates, Escherichia coli cell cycles overlap, and its nucleoid is segregated to daughter cells as a forked DNA circle with replication ongoing-a state fundamentally ...different from eukaryotes. We have solved the chromosome organization, structural dynamics, and segregation of this constantly replicating chromosome. It is locally condensed to form a branched donut, compressed so that the least replicated DNA spans the cell center and the newest DNA extends toward the cell poles. Three narrow zones at the cell center and quarters contain both the replication forks and nascent DNA and serve to segregate the duplicated chromosomal information as it flows outward. The overall pattern is smoothly self-replicating, except when the duplicated terminus region is released from the septum and recoils to the center of a sister nucleoid. In circular cross-section of the cell, the left and right arms of the chromosome form separate, parallel structures that lie in each cell half along the radial cell axis. In contrast, replication forks and origin and terminus regions are found mostly at the center of the cross section, balanced by the parallel chromosome arms. The structure is consistent with the model in which the nucleoid is a constrained ring polymer that develops by spontaneous thermodynamics. The ring polymer pattern extrapolates to higher growth rates and also provides a structural basis for the form of the chromosome during very slow growth.
Abstract
The prediction of protein subcellular localization is of great relevance for proteomics research. Here, we propose an update to the popular tool DeepLoc with multi-localization prediction ...and improvements in both performance and interpretability. For training and validation, we curate eukaryotic and human multi-location protein datasets with stringent homology partitioning and enriched with sorting signal information compiled from the literature. We achieve state-of-the-art performance in DeepLoc 2.0 by using a pre-trained protein language model. It has the further advantage that it uses sequence input rather than relying on slower protein profiles. We provide two means of better interpretability: an attention output along the sequence and highly accurate prediction of nine different types of protein sorting signals. We find that the attention output correlates well with the position of sorting signals. The webserver is available at services.healthtech.dtu.dk/service.php?DeepLoc-2.0.
Graphical Abstract
Graphical Abstract
DeepLoc 2.0 uses a transformer-based protein language model to predict multi-label subcellular localization and provides interpretability via the attention and sorting signal prediction.
The prediction of eukaryotic protein subcellular localization is a well-studied topic in bioinformatics due to its relevance in proteomics research. Many machine learning methods have been ...successfully applied in this task, but in most of them, predictions rely on annotation of homologues from knowledge databases. For novel proteins where no annotated homologues exist, and for predicting the effects of sequence variants, it is desirable to have methods for predicting protein properties from sequence information only.
Here, we present a prediction algorithm using deep neural networks to predict protein subcellular localization relying only on sequence information. At its core, the prediction model uses a recurrent neural network that processes the entire protein sequence and an attention mechanism identifying protein regions important for the subcellular localization. The model was trained and tested on a protein dataset extracted from one of the latest UniProt releases, in which experimentally annotated proteins follow more stringent criteria than previously. We demonstrate that our model achieves a good accuracy (78% for 10 categories; 92% for membrane-bound or soluble), outperforming current state-of-the-art algorithms, including those relying on homology information.
The method is available as a web server at http://www.cbs.dtu.dk/services/DeepLoc. Example code is available at https://github.com/JJAlmagro/subcellular_localization. The dataset is available at http://www.cbs.dtu.dk/services/DeepLoc/data.php.
jjalma@dtu.dk.
The ability to predict local structural features of a protein from the primary sequence is of paramount importance for unraveling its function in absence of experimental structural information. Two ...main factors affect the utility of potential prediction tools: their accuracy must enable extraction of reliable structural information on the proteins of interest, and their runtime must be low to keep pace with sequencing data being generated at a constantly increasing speed. Here, we present NetSurfP‐2.0, a novel tool that can predict the most important local structural features with unprecedented accuracy and runtime. NetSurfP‐2.0 is sequence‐based and uses an architecture composed of convolutional and long short‐term memory neural networks trained on solved protein structures. Using a single integrated model, NetSurfP‐2.0 predicts solvent accessibility, secondary structure, structural disorder, and backbone dihedral angles for each residue of the input sequences. We assessed the accuracy of NetSurfP‐2.0 on several independent test datasets and found it to consistently produce state‐of‐the‐art predictions for each of its output features. We observe a correlation of 80% between predictions and experimental data for solvent accessibility, and a precision of 85% on secondary structure 3‐class predictions. In addition to improved accuracy, the processing time has been optimized to allow predicting more than 1000 proteins in less than 2 hours, and complete proteomes in less than 1 day.
The biomass production potential at temperate latitudes (56°N), and the quality of the biomass for energy production (anaerobic digestion to methane and direct combustion) were investigated for the ...green macroalgae, Ulva lactuca. The algae were cultivated in a land based facility demonstrating a production potential of 45T (TS) ha−1y−1. Biogas production from fresh and macerated U. lactuca yielded up to 271ml CH4 g−1 VS, which is in the range of the methane production from cattle manure and land based energy crops, such as grass-clover. Drying of the biomass resulted in a 5–9-fold increase in weight specific methane production compared to wet biomass. Ash and alkali contents are the main challenges in the use of U. lactuca for direct combustion. Application of a bio-refinery concept could increase the economical value of the U. lactuca biomass as well as improve its suitability for production of bioenergy.
The majority of all genes have so far been identified and annotated systematically through in silico gene finding. Here we report the finding of 3662 strand-specific transcriptionally active regions ...(TARs) in the genome of Bacillus subtilis by the use of tiling arrays. We have measured the genome-wide expression during mid-exponential growth on rich (LB) and minimal (M9) medium. The identified TARs account for 77.3% of the genes as they are currently annotated and additionally we find 84 putative non-coding RNAs (ncRNAs) and 127 antisense transcripts. One ncRNA, ncr22, is predicted to act as a translational control on cstA and an antisense transcript was observed opposite the housekeeping sigma factor sigA. Through this work we have discovered a long conserved 3' untranslated region (UTR) in a group of membrane-associated genes that is predicted to fold into a large and highly stable secondary structure. One of the genes having this tail is efeN, which encodes a target of the twin-arginine translocase (Tat) protein translocation system.
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