PEPPI: Whole-proteome protein-protein interaction prediction through structure and sequence similarity, functional association, and machine learning

Proteome-wide identification of protein-protein interactions is a formidable task which has yet to be sufficiently addressed by experimental methodologies. Many computational methods have been developed to predict proteome-wide interaction networks, but few leverage both the sensitivity of structural information and the wide availability of sequence data. We present PEPPI, a pipeline which integrates structural similarity, sequence similarity, functional association data, and machine learning-based classification through a naïve Bayesian classifier model to accurately predict protein-protein interactions at a proteomic scale. Through benchmarking against a set of 798 ground truth interactions and an equal number of noninteractions, we have found that PEPPI attains 4.5% higher AUROC than the best of other state-of-the-art methods. As a proteomic-scale application, PEPPI was applied to model the interactions which occur between SARS-CoV-2 and human host cells during coronavirus infection, where 403 high-confidence interactions were identified with predictions covering 73% of a gold standard dataset from PSICQUIC and demonstrating significant complementarity with the most recent high-throughput experiments. PEPPI is available both as a webserver and in a standalone version and should be a powerful and generally applicable tool for computational screening of protein-protein interactions.

The chamber kui is the genre of the kazakh academical music

Since the formation of the chamber and instrumental music in Kazakhstan, the traditional instrumental genrekui – has become the vector of creative search, the basis for the synthesis of national and western musical thinking. The purpose of this article is to reveal the features of the traditional genre within the framework of academic music and to present a new genre – chamber kui.The expression of kui in the works is functionally represented in a variety of ways. The embodiment of the semantics of kui in its figurative meaning is given in the title of the work. When using the folk instrumental genre in professional writing, the authors give a functional association to it presented in the work in the form of a fragment (melody or accompaniment). The next point in the gradation of kui features in the chamber and instrumental works of composers of Kazakhstan is the dominance of its features: motor skills, variant-variational development of form, texture, throughout the work or part of it.The formation of a new genre – chamber kui was the result of creative searches for the synthesis of Kazakh folk instrumental creativity-kui, the connection of the laws of its formation and shaping with the achievements of European creative experience. In form, these pieces are kui (alternation of three register zones characteristic of the traditional genre), in harmony, quart-quint consonances are used, recreating the overtone density of the dombra timbre in the sound of the European instrument.

Identifying Features of Pakistani Learners Writing Through MDA and Coh-Metrix

Learner language has been a source of interest for researchers of all times as it possesses common features of language in use. For investigating this, Multi-dimensional analysis (MDA) by Biber is one such approach that empirically studies practiced language and establishes grounds for those varieties too which are striving for their place in linguistic cline (Crossely, et al., 2014). The present research is an effort to explore common patterns of learner language, which are explored throughCoh-Metrix (an online data tagging tool used to assess cohesion, coherence,readability level, etc.) to study those features and their respective functions while partially using MDA methodology. Following Biber's methodology,Factor analysis was conducted, and four dimensions were identified, which provided clues for the functional association of these dimensions. The results show that Pakistani learners' argumentative writing possesses narrative features and is dominatingly overlapping at the level of vocabulary,syntactic constructions, and passage development, and even in argumentation. These findings help us to establish the fact that Pakistani English has its own identity. These results are helpful for linguists as well as teachers as the knowledge of common linguistic and syntactic structures can be assessed easily while keeping in mind the grade level of the students.

NetGenes: A Database of Essential Genes Predicted Using Features From Interaction Networks

Essential gene prediction models built so far are heavily reliant on sequence-based features, and the scope of network-based features has been narrow. Previous work from our group demonstrated the importance of using network-based features for predicting essential genes with high accuracy. Here, we apply our approach for the prediction of essential genes to organisms from the STRING database and host the results in a standalone website. Our database, NetGenes, contains essential gene predictions for 2,700+ bacteria predicted using features derived from STRING protein–protein functional association networks. Housing a total of over 2.1 million genes, NetGenes offers various features like essentiality scores, annotations, and feature vectors for each gene. NetGenes database is available from https://rbc-dsai-iitm.github.io/NetGenes/.

The morphological variability of Maltese ‘cart ruts’ and its implications

Hundreds of ‘cart ruts’ – pairs of incised parallel grooves in the bedrock – are found across the Maltese archipelago in the central Mediterranean. The age, functional association, formation processes, and taphonomic alteration of these ruts, which occur here with a globally unrivalled frequency, has been much debated. Generally seen as being created by erosion from vehicles such as wheeled carts, or alternatively being cut into the rock to facilitate movement of such vehicles, specific models range from the use of carts to move soil in the Neolithic to them reflecting classical era stone quarrying, and many other possibilities. One interesting aspect concerns the morphological variability of the cart ruts, such as the notion that they have a standard gauge (width between ruts), and that this gauge is very similar to that of modern railway tracks. Evaluating the morphological variability of the cart ruts contributes to an understanding of the phenomenon, as, for instance, we might expect that if they date to different periods, with different functions, and/or were extensively modified by geomorphological processes this will be reflected in the character of their morphological variability. The analysis suggests that cart ruts are fairly standardised in terms of basic measurements such as widths and depth, perhaps suggesting that they are of a consistent age and function. This study identified a need for definitional clarity as the commonly cited gauge measurements are not taken in the same way as gauge is defined for railway tracks. There are hints of rut shape changes reflecting extensive use and or processes such as limestone dissolution, which give insights into their formation histories.

Correction to: Detecting differentially methylated regions using a fast wavelet-based approach to functional association analysis

A Correction to this paper has been published: https://doi.org/10.1186/s12859-021-03979-y

enviLink: A database linking contaminant biotransformation rules to enzyme classes in support of functional association mining

Motivation: The ability to assess and engineer biotransformation of chemical contaminants present in the environment requires knowledge on which enzymes can catalyze specific contaminant biotransformation reactions. For the majority of over 100000 chemicals in commerce such knowledge is not available. Enumeration of enzyme classes potentially catalyzing observed or de novo predicted contaminant biotransformation reactions can support research that aims at experimentally uncovering enzymes involved in contaminant biotransformation in complex natural microbial communities. Database: enviLink is a new data module integrated into the enviPath database and contains 316 theoretically derived linkages between generalized biotransformation rules used for contaminant biotransformation prediction in enviPath and 3rd level EC classes. Rule-EC linkages have been derived using two reaction databases, i.e., Eawag-BBD in enviPath, focused on contaminant biotransformation reactions, and KEGG. 32.6% of identified rule-EC linkages overlap between the two databases, whereas 40.2% and 27.2%, respectively, are originating from Eawag-BBD and KEGG only. Implementation and availability: enviLink is encoded in RDF triples as part of the enviPath RDF database. enviPath is hosted on a public webserver (envipath.org) and all data is freely available for non-commercial use. enviLink can be searched online for individual transformation rules of interest (https://tinyurl.com/y63ath3k) and is also fully downloadable from the supporting materials (i.e., Jupyter notebook enviLink and tsv files provided through GitHub at https://github.com/emanuel-schmid/enviLink).

Interaction of 7SK with the Smn complex modulates snRNP production

Gene expression requires tight coordination of the molecular machineries that mediate transcription and splicing. While the interplay between transcription kinetics and spliceosome fidelity has been investigated before, less is known about mechanisms regulating the assembly of the spliceosomal machinery in response to transcription changes. Here, we report an association of the Smn complex, which mediates spliceosomal snRNP biogenesis, with the 7SK complex involved in transcriptional regulation. We found that Smn interacts with the 7SK core components Larp7 and Mepce and specifically associates with 7SK subcomplexes containing hnRNP R. The association between Smn and 7SK complexes is enhanced upon transcriptional inhibition leading to reduced production of snRNPs. Taken together, our findings reveal a functional association of Smn and 7SK complexes that is governed by global changes in transcription. Thus, in addition to its canonical nuclear role in transcriptional regulation, 7SK has cytosolic functions in fine-tuning spliceosome production according to transcriptional demand.