ResidueFinder: extracting individual residue mentions from protein literature

Background The revolution in molecular biology has shown how protein function and structure are based on specific sequences of amino acids. Thus, an important feature in many papers is the mention of the significance of individual amino acids in the context of the entire sequence of the protein. MutationFinder is a widely used program for finding mentions of specific mutations in texts. We report on augmenting the positive attributes of MutationFinder with a more inclusive regular expression list to create ResidueFinder, which finds mentions of native amino acids as well as mutations. We also consider parameter options for both ResidueFinder and MutationFinder to explore trade-offs between precision, recall, and computational efficiency. We test our methods and software in full text as well as abstracts. Results We find there is much more variety of formats for mentioning residues in the entire text of papers than in abstracts alone. Failure to take these multiple formats into account results in many false negatives in the program. Since MutationFinder, like several other programs, was primarily tested on abstracts, we found it necessary to build an expanded regular expression list to achieve acceptable recall in full text searches. We also discovered a number of artifacts arising from PDF to text conversion, which we wrote elements in the regular expression library to address. Taking into account those factors resulted in high recall on randomly selected primary research articles. We also developed a streamlined regular expression (called “cut”) which enables a several hundredfold speedup in both MutationFinder and ResidueFinder with only a modest compromise of recall. All regular expressions were tested using expanded F-measure statistics, i.e., we compute Fβ for various values of where the larger the value of β the more recall is weighted, the smaller the value of β the more precision is weighted. Conclusions ResidueFinder is a simple, effective, and efficient program for finding individual residue mentions in primary literature starting with text files, implemented in Python, and available in SourceForge.net. The most computationally efficient versions of ResidueFinder could enable creation and maintenance of a database of residue mentions encompassing all articles in PubMed.

Mixing crop residues induces a synergistic effect on microbial biomass and an additive effect on soil organic matter priming

Applying crop residues is a widely used strategy to increase soil organic matter (SOM) in arable soils because of its recorded effects on increasing microbial biomass and consequently necromass. However, fresh residue inputs could also prime the decomposition of native SOM, resulting in accelerated SOM depletion and greenhouse gas (GHG) emission. Increasing the botanical diversity of the crops grown in arable systems has been promoted to increase the delivery of multiple ecological functions, including increasing soil microbial biomass and SOM. Whether mixtures of fresh residues from different crops grown in polyculture contribute to soil carbon (C) pools to a greater extent than would be expected from applying individual residues (i.e., the mixture produces a non-additive synergistic effect) has not been systematically tested and is currently unknown. In this study, we used 13C isotope labelled cover crop residues (i.e., buckwheat, clover, radish, and sunflower) to track the fate of plant residue-derived C and C derived from the priming of SOM in treatments comprising a quaternary mixture of the residues and the average effect of the four individual residues one day after residue incorporation in a laboratory microcosm experiment. Our results indicate that, despite all treatments receiving the same amount of plant residue-derived C (1 mg C g-1 soil), the total microbial biomass in the treatment receiving the residue mixture was significantly greater, by 26% (3.69 μg C g-1), than the average microbial biomass observed in treatments receiving the four individual components of the mixture one day after applying crop residues. The greater microbial biomass C in the quaternary mixture, compared to average of the individual residue treatments, that can be attributed directly to the plant residue applied was also significantly greater, by 132% (3.61 μg C g-1). However, there was no evidence that the mixture resulted in any more priming of native SOM than average priming observed in the individual residue treatments. The soil microbial community structure, assessed using phospholipid fatty acid (PLFA) analysis, was significantly (P < 0.001) different in the soil receiving the residue mixture, compared to the average structures of the communities in soil receiving four individual residues. Differences in the biomass of fungi, general bacteria, and Gram-positive bacteria were responsible for the observed synergistic effect of crop residue mixtures on total microbial biomass and residue-derived microbial biomass, especially biomarkers 16:0, 18:2ω6 and 18:3ω3. Our study demonstrates that applying a mixture of crop residues increases soil microbial biomass to a greater extent than would be expected from applying individual residues and that this occurs either due to faster decomposition of the crop residues or greater carbon use efficiency (CUE), rather than priming the decomposition of native SOM. Therefore, growing crop polycultures (e.g., cover crop mixtures) and incorporating mixtures of the resulting crop residues into the soil could be an effective method to increase microbial biomass and ultimately C stocks in arable soils.

The mixture of cover crop residues induced a synergistic effect on microbial communities and an additive effect on soil organic matter priming

&lt;p&gt;Applying cover crop residues to increase soil organic matter (SOM) is a widely used strategy to sustainably intensify agricultural systems.&amp;#160; However, fresh residue inputs create &amp;#8220;hot spots&amp;#8221; of microbial activity during decomposition which could also &amp;#8220;prime&amp;#8221; the decomposition of native SOM, resulting in accelerated SOM depletion and greenhouse gas emissions. Microbes exert control over SOM decomposition and stabilisation as a consequence of their carbon use efficiency (CUE), the balance between microbial catabolism and anabolism. The CUE during residue decomposition and the extent to which native SOM decomposition is primed by residue addition may depend on residue biochemical quality.&amp;#160; Given that cover crops may be grown in monoculture, or in species mixes with the aim of providing multiple benefits to agricultural ecosystem services, it is important to understand whether applying cover crop residues as a mixture results in a different CUE and soil carbon stock, than would be expected by observations made on the application of individual residues. We used &lt;sup&gt;13&lt;/sup&gt;C labelled cover crop residues (buckwheat, clover, radish, and sunflower) to track the fate of cover crop residue-derived carbon and SOM derived carbon in treatments comprising a quaternary mixture of the residues and the average effect of the four individual residues (non-mixture) one day after residue incorporation in a laboratory microcosm experiment. The soil microbial community composition was measured by phospholipid-derived fatty acids (PLFA) fingerprint. Our results indicate that, despite all treatments receiving the same amount of plant-added carbon (1 mg C g&lt;sup&gt;-1&lt;/sup&gt; soil), the total microbial biomass (&lt;sup&gt;12&lt;/sup&gt;C + &lt;sup&gt;13&lt;/sup&gt;C) in the treatment receiving the residue mixture was significantly greater, by 3.69 &amp;#181;g C g&lt;sup&gt;-1&lt;/sup&gt;, than the average microbial biomass observed in the four treatments receiving individual components of the mixture. The microbial biomass in the quaternary mixture, compared to the average of the individual residue treatments, that can be attributed directly to the plant matter applied, was also significantly greater by 3.61 &amp;#181;g C g&lt;sup&gt;-1&lt;/sup&gt;. However, there was no evidence that the mixture resulted in any more priming of native SOM than average priming observed in the individual residue treatments. The soil microbial community structure measured by analysis of similarities (ANOSM) was significantly different in the soil receiving the residue mixture, compared to the average structure of the four communities in soils receiving individual residues. Differences in the biomass of fungi and Gram-positive bacteria were responsible for the observed synergistic effect of cover crop residue mixtures on total microbial biomass and plant-derived microbial biomass; especially biomarkers 16:0, 18:1&amp;#969;9, 18:2&amp;#969;6 and 18:3&amp;#969;3. Our study demonstrates that applying a mixture of cover crop residues initially increases soil microbial biomass to a greater extent than would be expected from applying individual components of the mixture and that this increase may occur either due to faster decomposition of the cover crop residues or greater CUE, but not due to greater priming of native SOM decomposition. Therefore, applying cover crop residue mixtures could be an effective method to increase soil microbial biomass, and ultimately soil carbon stocks in arable soils.&lt;/p&gt;

Bioinspired approach toward molecular electrets: synthetic proteome for materials

Molecular-level control of charge transfer (CT) is essential for both, organic electronics and solar-energy conversion, as well as for a wide range of biological processes. This article provides an overview of the utility of local electric fields originating from molecular dipoles for directing CT processes. Systems with ordered dipoles, i.e. molecular electrets, are the centerpiece of the discussion. The conceptual evolution from biomimicry to biomimesis, and then to biological inspiration, paves the roads leading from testing the understanding of how natural living systems function to implementing these lessons into optimal paradigms for specific applications. This progression of the evolving structure-function relationships allows for the development of bioinspired electrets composed of non-native aromatic amino acids. A set of such non-native residues that are electron-rich can be viewed as a synthetic proteome for hole-transfer electrets. Detailed considerations of the electronic structure of an individual residue prove of key importance for designating the points for optimal injection of holes (i.e. extraction of electrons) in electret oligomers. This multifaceted bioinspired approach for the design of CT molecular systems provides unexplored paradigms for electronic and energy science and engineering.

High-resolution phenotypic landscape of the RNA Polymerase II trigger loop

The active site of multicellular RNA polymerases have a “trigger loop” (TL) that multitasks in substrate selection, catalysis, and translocation. To dissect the Saccharomyces cerevisiae RNA polymerase II TL at individual-residue resolution, we quantitatively phenotyped nearly all TL single variants en masse. Three major mutant classes, revealed by phenotypes linked to transcription defects or various stresses, have distinct distributions among TL residues. We find that mutations disrupting an intra-TL hydrophobic pocket, proposed to provide a mechanism for substrate-triggered TL folding through destabilization of a catalytically inactive TL state, confer phenotypes consistent with pocket disruption and increased catalysis. Furthermore, allele-specific genetic interactions among TL and TL-proximal domain residues support the contribution of the funnel and bridge helices (BH) to TL dynamics. Our structural genetics approach incorporates structural and phenotypic data for high-resolution dissection of transcription mechanisms and their evolution, and is readily applicable to other essential yeast proteins.