Translation Function Research Articles

Canonical partition function and distance dependent correlation functions of a quasi-one-dimensional system of hard disks

The canonical NLT partition function of a quasi-one dimensional (q1D) one-file system of equal hard disks Pergamenshchik [19] provides an analytical description of the thermodynamics and ordering in this system (a pore) as a function of linear density Nd/L where d is the disk diameter. We derive the analytical formulae for the distance dependence of the translational pair distribution function and the distribution function of distances between next neighbor disks, and then demonstrate their use by calculating the translational order in the pore. In all cases, the order is found to be of a short range and to exponentially decay with the disks' separation. The correlation length presented for different pore widths and densities shows a non-monotonic dependence with a maximum at Nd/L=1 and tends to the 1D value for a vanishing pore width. The results indicate a special role of this density when the pore length L is equal exactly to N disk diameters. Comparison between the theoretical results for an infinite system and the results of a molecular dynamics simulation for a finite system with periodic boundary conditions is presented and discussed.

EMDL-ac4C: identifying N4-acetylcytidine based on ensemble two-branch residual connection DenseNet and attention.

Introduction: N4-acetylcytidine (ac4C) is a critical acetylation modification that has an essential function in protein translation and is associated with a number of human diseases. Methods: The process of identifying ac4C sites by biological experiments is too cumbersome and costly. And the performance of several existing computational models needs to be improved. Therefore, we propose a new deep learning tool EMDL-ac4C to predict ac4C sites, which uses a simple one-hot encoding for a unbalanced dataset using a downsampled ensemble deep learning network to extract important features to identify ac4C sites. The base learner of this ensemble model consists of a modified DenseNet and Squeeze-and-Excitation Networks. In addition, we innovatively add a convolutional residual structure in parallel with the dense block to achieve the effect of two-layer feature extraction. Results: The average accuracy (Acc), mathews correlation coefficient (MCC), and area under the curve Area under curve of EMDL-ac4C on ten independent testing sets are 80.84%, 61.77%, and 87.94%, respectively. Discussion: Multiple experimental comparisons indicate that EMDL-ac4C outperforms existing predictors and it greatly improved the predictive performance of the ac4C sites. At the same time, EMDL-ac4C could provide a valuable reference for the next part of the study. The source code and experimental data are available at: https://github.com/13133989982/EMDLac4C.

Functions of Circular RNA in Human Diseases and Illnesses.

Circular RNAs (circRNAs) represent single-stranded RNA species that contain covalently closed 3' and 5' ends that provide them more stability than linear RNA, which has free ends. Emerging evidence indicates that circRNAs perform essential functions in many DNA viruses, including coronaviruses, Epstein-Barr viruses, cytomegalovirus, and Kaposi sarcoma viruses. Recent studies have confirmed that circRNAs are present in viruses, including DNA and RNA viruses, and play various important functions such as evading host immune response, disease pathogenesis, protein translation, miRNA sponges, regulating cell proliferation, and virus replication. Studies have confirmed that circRNAs can be biological signatures or pathological markers for autoimmune diseases, neurological diseases, and cancers. However, our understanding of circRNAs in DNA and RNA viruses is still limited, and functional evaluation of viral and host circRNAs is essential to completely understand their biological functions. In the present review, we describe the metabolism and cellular roles of circRNA, including its roles in various diseases and viral and cellular circRNA functions. Circular RNAs are found to interact with RNA, proteins, and DNA, and thus can modulate cellular processes, including translation, transcription, splicing, and other functions. Circular RNAs interfere with various signaling pathways and take part in vital functions in various biological, physiological, cellular, and pathophysiological processes. We also summarize recent evidence demonstrating cellular and viral circRNA's roles in DNA and RNA viruses in this growing field of research.

Encoding de Finetti's coherence within Łukasiewicz logic and MV-algebras

The present paper investigates proof-theoretical and algebraic properties for the probability logic FP(Ł,Ł), meant for reasoning on the uncertainty of Łukasiewicz events. Methodologically speaking, we will consider a translation function between formulas of FP(Ł,Ł) to the propositional language of Łukasiewicz logic that allows us to apply the latter and the well-developed theory of MV-algebras directly to probabilistic reasoning. More precisely, leveraging on such translation map, we will show proof-theoretical properties for FP(Ł,Ł) and introduce a class of algebras with respect to which FP(Ł,Ł) will be proved to be locally sound and complete. Finally, we will apply these previous results to investigate what we called “probabilistic unification problem”. In this respect, we will prove that Ghilardi's algebraic view on unification can be extended to our case and, on par with the Łukasiewicz propositional case, we show that probabilistic unification is of nullary type.

The communicative potential of Russian-speaking and English-speaking voice systems

The article describes the analysis of the "spontaneous" dialogue of two Russian and foreign voice systems. The study is relevant because the possibilities of communication of the introduction spontaneously dialogue between Russian-speaking and foreign voice systems have not been studied by now. The objects of research have become two Russian-speaking systems – Alice by Yandex, voice assistant application by Sberbank; two English voice systems – Siri by Apple Ink and Google Assistant, including their Russian version. The choice is due to their popularity among native speakers of the Russian language, which was determined by the requests of these voice assistants on the Internet. The sampling period was from January 1, 2021 to December 20, 2022. Russian-speaking and English-speaking voice systems were selected by a continuous sampling method. The article draws conclusions, including about the communicative capabilities of Russian-speaking voice systems and foreign analogues with a built-in translation function into Russian. The scientific novelty is the analysis of "spontaneous" dialogic speech and the analysis of its compliance with the norms of the modern Russian language. At the end of the article there are results of the analysis of foreign phrases and expressions with a small number of variants are summarized to generate a response to the user based on materials from the corpus of the Russian language. Also, it is not uncommon to identify features of machine translation in foreign voice analogues, unlike Russian-speaking voice assistants.

The central inflammatory regulator IκBζ: induction, regulation and physiological functions.

IκBζ (encoded by NFKBIZ) is the most recently identified IkappaB family protein. As an atypical member of the IkappaB protein family, NFKBIZ has been the focus of recent studies because of its role in inflammation. Specifically, it is a key gene in the regulation of a variety of inflammatory factors in the NF-KB pathway, thereby affecting the progression of related diseases. In recent years, investigations into NFKBIZ have led to greater understanding of this gene. In this review, we summarize the induction of NFKBIZ and then elucidate its transcription, translation, molecular mechanism and physiological function. Finally, the roles played by NFKBIZ in psoriasis, cancer, kidney injury, autoimmune diseases and other diseases are described. NFKBIZ functions are universal and bidirectional, and therefore, this gene may exert a great influence on the regulation of inflammation and inflammation-related diseases.

Crystallography of homophase twisted bilayers: coincidence, union lattices and space groups.

This paper presents the basic tools used to describe the global symmetry of so-called bilayer structures obtained when two differently oriented crystalline monoatomic layers of the same structure are superimposed and displaced with respect to each other. The 2D nature of the layers leads to the use of complex numbers that allows for simple explicit analytical expressions of the symmetry properties involved in standard bicrystallography [Gratias & Portier (1982). J. Phys. Colloq. 43, C6-15-C6-24; Pond & Vlachavas (1983). Proc. R. Soc. Lond. Ser. A, 386, 95-143]. The focus here is on the twist rotations such that the superimposition of the two layers generates a coincidence lattice. The set of such coincidence rotations plotted as a function of the lengths of their coincidence lattice unit-cell nodes exhibits remarkable arithmetic properties. The second part of the paper is devoted to determination of the space groups of the bilayers as a function of the rigid-body translation associated with the coincidence rotation. These general results are exemplified with a detailed study of graphene bilayers, showing that the possible symmetries of graphene bilayers with a coincidence lattice, whatever the rotation and the rigid-body translation, are distributed in only six distinct types of space groups. The appendix discusses some generalized cases of heterophase bilayers with coincidence lattices due to specific lattice constant ratios, and mechanical deformation by elongation and shear of a layer on top of an undeformed one.

ARL6IP1 mediates small-molecule-induced alleviation of Alzheimer pathology through FXR1-dependent BACE1 translation initiation

Exploring the potential lead compounds for Alzheimer's disease (AD) remains one of the challenging tasks. Here, we report that the plant extract conophylline (CNP) impeded amyloidogenesis by preferentially inhibiting BACE1 translation via the 5' untranslated region (5'UTR) and rescued cognitive decline in an animal model of APP/PS1 mice. ADP-ribosylation factor-like protein 6-interacting protein 1 (ARL6IP1) was then found to mediate the effect of CNP on BACE1 translation, amyloidogenesis, glial activation, and cognitive function. Through analysis of the 5'UTR-targetd RNA-binding proteins by RNA pulldown combined with LC-MS/MS, we found that FMR1 autosomal homolog 1 (FXR1) interacted with ARL6IP1 and mediated CNP-induced reduction of BACE1 by regulating the 5'UTR activity. Without altering the protein levels of ARL6IP1 and FXR1, CNP treatment promoted ARL6IP1 interaction with FXR1 and inhibited FXR1 binding to the 5'UTR both invitro and invivo. Collectively, CNP exhibited a therapeutic potential for AD via ARL6IP1. Through pharmacological manipulation, we uncovered a dynamic interaction between FXR1 and the 5'UTR in translational control of BACE1, adding to the understanding of the pathophysiology of AD.

Distance-Independent Background Light Estimation Method

A distance-independent background light estimation method is proposed for underwater overhead images. The method addresses the challenge of the absence of the farthest point in underwater overhead images by adopting a global perspective to select the optimal solution and estimate the background light by minimizing the loss function. Moreover, to enhance the information retention in the images, a translation function is employed to adjust the transmission map values within the range of [0.1, 0.95]. Additionally, the method capitalizes on the redundancy of image information and the similarity of adjacent frames, resulting in higher computational efficiency. The comparative experimental results show that the proposed method has better restoration performance on underwater images in various scenarios, especially in handling color bias and preserving information.

Comparative Genomic Analyses of Lactococcus garvieae Isolated from Bovine Mastitis in China.

Lactococcus garvieae is an emerging zoonotic pathogen, but there are few reports regarding bovine mastitis. The prevalence of L. garvieae represents an increasing disease threat and global public health risk. Thirty-nine L. garvieae isolates were obtained from 2,899 bovine clinical mastitis milk samples in 6 provinces of China from 2017 to 2021. Five clonal complexes were determined from 32 multilocus sequence types (MLSTs) of L. garvieae: sequence type 46 (ST46) was the predominant sequence type, and 13 novel MLSTs were identified. All isolates were resistant to chloramphenicol and clindamycin, but susceptible to penicillin, ampicillin, amoxicillin-clavulanic acid, imipenem, ceftiofur, enrofloxacin, and marbofloxacin. Based on genomic analyses, L. garvieae had 6,310 genes, including 1,015 core, 3,641 accessory, and 1,654 unique genes. All isolates had virulence genes coding for collagenase, fibronectin-binding protein, glyceraldehyde-3-phosphate dehydrogenase, superoxide dismutase, and NADH oxidase. Most isolates had lsaD and mdtA antimicrobial resistance (AMR) genes. Based on COG (Clusters of Orthologous Genes database) results, the functions of defense, transcription and replication, and recombination and repair were enhanced in unique genes, whereas functions of translation, ribosomal structure, and biogenesis were enhanced in core genes. The KEGG functional categories enriched in unique genes included human disease and membrane transport, whereas COG functional categories enriched in core genes included energy metabolism, nucleotide metabolism, and translation. No gene was significantly associated with host specificity. In addition, analysis of core genome single nucleotide polymorphisms (SNPs) implied potential host adaptation of some isolates in several sequence types. In conclusion, this study characterized L. garvieae isolated from mastitis and detected potential adaptations of L. garvieae to various hosts. IMPORTANCE This study provides important genomic insights into a bovine mastitis pathogen, Lactococcus garvieae. Comprehensive genomic analyses of L. garvieae from dairy farms have not been reported. This study is a detailed and comprehensive report of novel features of isolates of L. garvieae, an important but poorly characterized bacterium, recovered in the past 5 years in 6 Chinese provinces. We documented diverse genetic features, including predominant sequence type ST46 and 13 novel MLSTs. Lactococcus garvieae had 6,310 genes, including 1,015 core, 3,641 accessory, and 1,654 unique genes. All isolates had virulence genes coding for collagenase, fibronectin-binding protein, glyceraldehyde-3-phosphate dehydrogenase, superoxide dismutase, and NADH oxidase and resistance to chloramphenicol and clindamycin. Most isolates had lsaD and mdtA antimicrobial resistance genes. However, no gene was significantly associated with host specificity. This is the first report that characterized L. garvieae isolates from bovine mastitis and revealed potential host adaptations of L. garvieae to various hosts.

Translation as meaning negotiator

ABSTRACT The article engages with the meaning-making function of translation. Three case studies demonstrate how translation performs its work of counteracting semiotic-semantic entropy. The first two cases show that translation can combat this entropy by rendering the less familiar with the more familiar by oscillating between its terminological and impressionistic types. These two cases observe translation between music as a semiotic domain and biochemistry, on the one hand, and language, on the other. The third case study looks at how translation negotiates meaning between language and painting. In all these cases, translation performs its negentropic work, but it does so via more or less complex negotiations of meaning.

Practical prescribed-time tracking control for uncertain strict-feedback systems with guaranteed performance under unknown control directions

In this paper, we consider the practical prescribed-time performance guaranteed tracking control problem for a class of uncertain strict-feedback systems subject to unknown control direction. Due to the existence of unknown nonlinearities and uncertainties, it is challenging to design a controller that can ensure the stability of closed-loop system within a predetermined finite time while maintaining the specified transient performance. The underlying problem becomes further complex as the control directions are unknown. To deal with the above problems, a special translation function as well as Nussbaum type function are introduced in the prescribed performance control (PPC) framework. Finally, a PPC as well as preset finite time tracking control scheme is designed, and its effectiveness is confirmed by both theoretical analysis and numerical simulation.

M6A readers ECT2/ECT3/ECT4 enhance mRNA stability through direct recruitment of the poly(A) binding proteins in Arabidopsis

BackgroundRNA N6-methyladenosine (m6A) modification is critical for plant growth and crop yield. m6A reader proteins can recognize m6A modifications to facilitate the functions of m6A in gene regulation. ECT2, ECT3, and ECT4 are m6A readers that are known to redundantly regulate trichome branching and leaf growth, but their molecular functions remain unclear.ResultsHere, we show that ECT2, ECT3, and ECT4 directly interact with each other in the cytoplasm and perform genetically redundant functions in abscisic acid (ABA) response regulation during seed germination and post-germination growth. We reveal that ECT2/ECT3/ECT4 promote the stabilization of their targeted m6A-modified mRNAs, but have no function in alternative polyadenylation and translation. We find that ECT2 directly interacts with the poly(A) binding proteins, PAB2 and PAB4, and maintains the stabilization of m6A-modified mRNAs. Disruption of ECT2/ECT3/ECT4 destabilizes mRNAs of ABA signaling-related genes, thereby promoting the accumulation of ABI5 and leading to ABA hypersensitivity.ConclusionOur study reveals a unified functional model of m6A mediated by m6A readers in plants. In this model, ECT2/ECT3/ECT4 promote stabilization of their target mRNAs in the cytoplasm.

Effects of heat and hyposalinity on the gene expression in Acropora pruinosa larvae

IntroductionClimate change has resulted in elevated sea surface temperature as well as increased frequency of extreme weather events, e.g. cyclones and rainstorms, which could lead to reduced seawater salinity. While temperature effects on corals have been widely examined, the combined effects of both temperature and salinity on corals, especially their early stages, remain poorly known. This study aimed to examine how the larvae of Acropora pruinosa in a marginal coral habitat, Hong Kong, respond to high temperature (+5°C ambient, HT), low salinity (26 psu, LS), and the combined effects of both stressors (HTLS).MethodsWe recorded larval survival and settlement success under different experimental treatments, and used RNA-Seq technique to compare the gene expression patterns of these larvae to understand the underlying molecular mechanism of stress responses.ResultsOur results showed that the survivorship of coral larvae was not affected in all experimental treatments, with all larvae surviving through the 72-hour period of the experiment. Yet, larval settlement was compromised under all stress treatments. The settlement rates were 39.3%, 12%, and 0% for the elevated temperature, reduced salinity, and the combined treatment, respectively, which were all significantly lower than that under the control treatment (78%). We demonstrated that low salinity (LS) triggered responsive gene sets with functions in ATP production, protein translation, and receptor for neuroactive ligands. In addition, high temperature (HT) treatment also triggered MAPK and NF-kB signaling and apoptosis in these coral larvae. The combined stressor treatment (HTLS) acted synergistically, resulting in the up-regulation of intracellular transducers that could trigger the intrinsic apoptosis pathway. This may explain the total failure in larval settlement under HTLS that could further increase larval vulnerability in the natural environment.DiscussionOur results provide new insights into the molecular responses of coral larvae and represent an essential first step in expanding ourunderstanding of the mechanisms of tolerance that may be exhibited by coral larvae exposed to multiple stressors.

Stop or Not: Genome-Wide Profiling of Reassigned Stop Codons in Ciliates.

Bifunctional stop codons that have both translation and termination functions in the same species are important for understanding the evolution and function of genetic codes in living organisms. Considering the high frequency of bifunctional codons but limited number of available genomes in ciliates, we de novo sequenced seven representative ciliate genomes to explore the evolutionary history of stop codons. We further propose a stop codon reassignment quantification method (stopCR) that can identify bifunctional codons and measure their frequencies in various eukaryotic organisms. Using our newly developed method, we found two previously undescribed genetic codes, illustrating the prevalence of bifunctional stop codons in ciliates. Overall, evolutionary genomic analyses suggest that gain or loss of reassigned stop codons in ciliates is shaped by their living environment, the eukaryotic release factor 1, and suppressor tRNAs. This study provides novel clues about the functional diversity and evolutionary history of stop codons in eukaryotic organisms.

Likelihood-based docking of models into cryo-EM maps.

Optimized docking of models into cryo-EM maps requires exploiting an understanding of the signal expected in the data to minimize the calculation time while maintaining sufficient signal. The likelihood-based rotation function used in crystallography can be employed to establish plausible orientations in a docking search. A phased likelihood translation function yields scores for the placement and rigid-body refinement of oriented models. Optimized strategies for choices of the resolution of data from the cryo-EM maps to use in the calculations and the size of search volumes are based on expected log-likelihood-gain scores computed in advance of the search calculation. Tests demonstrate that the new procedure is fast, robust and effective at placing models into even challenging cryo-EM maps.

Alterations of ribosomal RNA pseudouridylation in human breast cancer.

RNA modifications are key regulatory factors for several biological and pathological processes. They are abundantly represented on ribosomal RNA (rRNA), where they contribute to regulate ribosomal function in mRNA translation. Altered RNA modification pathways have been linked to tumorigenesis as well as to other human diseases. In this study we quantitatively evaluated the site-specific pseudouridylation pattern in rRNA in breast cancer samples exploiting the RBS-Seq technique involving RNA bisulfite treatment coupled with a new NGS approach. We found a wide variability among patients at different sites. The most dysregulated positions in tumors turned out to be hypermodified with respect to a reference RNA. As for 2'O-methylation level of rRNA modification, we detected variable and stable pseudouridine sites, with the most stable sites being the most evolutionary conserved. We also observed that pseudouridylation levels at specific sites are related to some clinical and bio-pathological tumor features and they are able to distinguish different patient clusters. This study is the first example of the contribution that newly available high-throughput approaches for site specific pseudouridine detection can provide to the understanding of the intrinsic ribosomal changes occurring in human tumors.

Comparative metagenomic analysis reveals rhizosphere microbial community composition and functions help protect grapevines against salt stress.

Soil salinization is a serious abiotic stress for grapevines. The rhizosphere microbiota of plants can help counter the negative effects caused by salt stress, but the distinction between rhizosphere microbes of salt-tolerant and salt-sensitive varieties remains unclear. This study employed metagenomic sequencing to explore the rhizosphere microbial community of grapevine rootstocks 101-14 (salt tolerant) and 5BB (salt sensitive) with or without salt stress. Compared to the control (treated with ddH2O), salt stress induced greater changes in the rhizosphere microbiota of 101-14 than in that of 5BB. The relative abundances of more plant growth-promoting bacteria, including Planctomycetes, Bacteroidetes, Verrucomicrobia, Cyanobacteria, Gemmatimonadetes, Chloroflexi, and Firmicutes, were increased in 101-14 under salt stress, whereas only the relative abundances of four phyla (Actinobacteria, Gemmatimonadetes, Chloroflexi, and Cyanobacteria) were increased in 5BB under salt stress while those of three phyla (Acidobacteria, Verrucomicrobia, and Firmicutes) were depleted. The differentially enriched functions (KEGG level 2) in 101-14 were mainly associated with pathways related to cell motility; folding, sorting, and degradation functions; glycan biosynthesis and metabolism; xenobiotics biodegradation and metabolism; and metabolism of cofactors and vitamins, whereas only the translation function was differentially enriched in 5BB. Under salt stress, the rhizosphere microbiota functions of 101-14 and 5BB differed greatly, especially pathways related to metabolism. Further analysis revealed that pathways associated with sulfur and glutathione metabolism as well as bacterial chemotaxis were uniquely enriched in 101-14 under salt stress and therefore might play vital roles in the mitigation of salt stress on grapevines. In addition, the abundance of various sulfur cycle-related genes, including genes involved in assimilatory sulfate reduction (cysNC, cysQ, sat, and sir), sulfur reduction (fsr), SOX systems (soxB), sulfur oxidation (sqr), organic sulfur transformation (tpa, mdh, gdh, and betC), increased significantly in 101-14 after treatment with NaCl; these genes might mitigate the harmful effects of salt on grapevine. In short, the study findings indicate that both the composition and functions of the rhizosphere microbial community contribute to the enhanced tolerance of some grapevines to salt stress.

English-Chinese Corpus Collection and Artificial Intelligence Translation Based on Dynamic Clustering Model

This paper studies the English-Chinese corpus collection system and artificial intelligence translation function based on the dynamic clustering model. This paper attempts to introduce the semantic analysis of English-Chinese parallel corpora into the semantic recognition system. By labeling different levels of the corpus, including grammatical labeling, shallow semantic labeling and deep semantic labeling, the corresponding English-Chinese translation teaching system is designed, and the teaching system is improved by using the comparatively systematic teaching effects in actual teaching. On the basis of self-built Chinese-English parallel corpus, this paper extracts the Chinese high-frequency verb "to improve" to discover and summarize its English translation rules in different texts.

Phosphoproteomics Profiling Defines a Target Landscape of the Basophilic Protein Kinases AKT, S6K, and RSK in Skeletal Myotubes.

Phosphorylation-dependent signal transduction plays an important role in regulating the functions and fate of skeletal muscle cells. Central players in the phospho-signaling network are the protein kinases AKT, S6K, and RSK as part of the PI3K-AKT-mTOR-S6K and RAF-MEK-ERK-RSK pathways. However, despite their functional importance, knowledge about their specific targets is incomplete because these kinases share the same basophilic substrate motif RxRxxp[ST]. To address this, we performed a multifaceted quantitative phosphoproteomics study of skeletal myotubes following kinase inhibition. Our data corroborate a cross talk between AKT and RAF, a negative feedback loop of RSK on ERK, and a putative connection between RSK and PI3K signaling. Altogether, we report a kinase target landscape containing 49 so far unknown target sites. AKT, S6K, and RSK phosphorylate numerous proteins involved in muscle development, integrity, and functions, and signaling converges on factors that are central for the skeletal muscle cytoskeleton. Whereas AKT controls insulin signaling and impinges on GTPase signaling, nuclear signaling is characteristic for RSK. Our data further support a role of RSK in glucose metabolism. Shared targets have functions in RNA maturation, stability, and translation, which suggests that these basophilic kinases establish an intricate signaling network to orchestrate and regulate processes involved in translation.