Complex Folding Research Articles

Experiments and simulation on ZIKV NS2B-NS3 protease reveal its complex folding

Zika virus has been identified in various body fluids such as semen, urine, saliva, cerebrospinal fluid, and vaginal secretion of an infected individual. The pH of these fluids varies from mildly acidic to mildly alkaline. So it is imperative to understand the impact of these conditions on viral protein functioning. We investigated the NS2B-NS3 protease stability and its activity in different denaturing environments. Finding indicates that NS2B-NS3 protease maintains stability at pH 4.8–8.7. Thus it suggests that the complex remains functionally active to hydrolyze the polyprotein within a diverse environmental condition such as variable pH. Despite a stable structure at a broad pH range, a change in environmental conditions dramatically influence its protease activity. Moreover, it is susceptible to structural transformation leading to increased β-strand or helix content in the presence of alcohol. This study may help further to understand the folding-function relationship of the general flaviviral protease complex.

Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates

The series of RNA folding events that occur during transcription can critically influence cellular RNA function. Here, we present reconstructing RNA dynamics from data (R2D2), a method to uncover details of cotranscriptional RNA folding. We model the folding of the Escherichia coli signal recognition particle (SRP) RNA and show that it requires specific local structural fluctuations within a key hairpin to engender efficient cotranscriptional conformational rearrangement into the functional structure. All-atom molecular dynamics simulations suggest that this rearrangement proceeds through an internal toehold-mediated strand-displacementmechanism, which can be disrupted with a point mutation that limits local structural fluctuations and rescued with compensating mutations that restore these fluctuations. Moreover, a cotranscriptional folding intermediate could be cleaved invitro by recombinant E.coli RNase P, suggesting potential cotranscriptional processing. These results from experiment-guided multi-scale modeling demonstrate that even an RNA with a simple functional structure can undergo complex folding and processing during synthesis.

Mapping Distinct Sequences of Structure Formation Differentiating Multiple Folding Pathways of a Small Protein

To determine experimentally how the multiple folding pathways of a protein differ, in the order in which the structural parts are assembled, has been a long-standing challenge. To resolve whether structure formation during folding can progress in multiple ways, the complex folding landscape of monellin has been characterized, structurally and temporally, using the multisite time-resolved FRET methodology. After an initial heterogeneous polypeptide chain collapse, structure formation proceeds on parallel pathways. Kinetic analysis of the population evolution data across various protein segments provides a clear structural distinction between the parallel pathways. The analysis leads to a phenomenological model that describes how and when discrete segments acquire structure independently of each other in different subensembles of protein molecules. When averaged over all molecules, structure formation is seen to progress as α-helix formation, followed by core consolidation, then β-sheet formation, and last end-to-end distance compaction. Parts of the protein that are closer in the primary sequence acquire structure before parts separated by longer sequence.

Origami Folding by Multifingered Hands with Motion Primitives.

Origami, a traditional Japanese art, is an example of superior handwork produced by human hands. Achieving such extreme dexterity is one of the goals of robotic technology. In the work described in this paper, we developed a new general-purpose robot system with sufficient capabilities for performing Origami. We decomposed the complex folding motions into simple primitives and generated the overall motion as a combination of these primitives. Also, to measure the paper deformation in real-time, we built an estimator using a physical simulator and a depth camera. As a result, our experimental system achieved consecutive valley folds and a squash fold.

Effective Folding Line Processing with a Press Method in Origami Forming Using a Low-cost and Simple V-shaped Punch Tool System

Bent products have recently been applied widely in various structures. The method of sharp bending has the advantage of producing bent products with a fine appearance. Meanwhile, it has been recently shown that origami forming can be applied as a free manufacturing method that creates a fine appearance using complex folding lines. Sharp bending and origami forming both require folding lines. Folding lines are produced to make a V-groove before bending. Cutting V-grooves for folding lines requires machining center plants and long working times, which are not suitable for mass production. This paper presents newly developed and convenient V-shaped punch tools for folding line processing in sharp bending and origami forming. As a result, origami forming is expected to be adopted as a press method using V-shaped punch tools. Additionally, this paper reports on the findings of deformation behavior and mechanism obtained in experiments on folding line processing. The investigation for three-dimensional plate deformation around the V-shaped punch terminal shows extended folding line by terminal effect. Phenomena and the required load of V-shape punch indentation are considered in determining the mechanism of V-shape punch indentation from the results of finite element analyses and experiments on groove formation using V-shaped punch tool system.

Slow Transition Path Times Reveal a Complex Folding Barrier in a Designed Protein.

De-novo designed proteins have received wide interest as potential platforms for nano-engineering and biomedicine. While much work is being done in the design of thermodynamically stable proteins, the folding process of artificially designed proteins is not well-studied. Here we used single-molecule force spectroscopy by optical tweezers to study the folding of ROSS, a de-novo designed 2x2 Rossmann fold. We measured a barrier crossing time in the millisecond range, much slower than what has been reported for other systems. While long transition times can be explained by barrier roughness or slow diffusion, we show that isotropic roughness cannot explain the measured transition path time distribution. Instead, this study shows that the slow barrier crossing of ROSS is caused by the population of three short-lived high-energy intermediates. In addition, we identify incomplete and off-pathway folding events with different barrier crossing dynamics. Our results hint at the presence of a complex transition barrier that may be a common feature of many artificially designed proteins.

The 3D Pattern of the Rainbow Trout (Oncorhynchus mykiss) Enterocytes and Intestinal Stem Cells.

We previously showed that, according to the frequency and distribution of specific cell types, the rainbow trout (RT) intestinal mucosa can be divided in two regions that form a complex nonlinear three-dimensional (3D) pattern and have a different renewal rate. This work had two aims. First, we investigated whether the unusual distribution of cell populations reflects a similar distribution of functional activities. To this end, we determined the protein expression pattern of three well-defined enterocytes functional markers: peptide transporter 1 (PepT1), sodium–glucose/galactose transporter 1 (SGLT-1), and fatty-acid-binding protein 2 (Fabp2). Second, we characterized the structure of RT intestinal stem-cell (ISC) niche and determined whether the different proliferative is accompanied by a different organization and/or extension of the stem-cell population. We studied the expression and localization of well-characterized mammal ISC markers: LGR5, HOPX, SOX9, NOTCH1, DLL1, and WNT3A. Our results indicate that morphological similarity is associated with similar function only between the first portion of the mid-intestine and the apical part of the complex folds in the second portion. Mammal ISC markers are all expressed in RT, but their localization is completely different, suggesting also substantial functional differences. Lastly, higher renewal rates are supported by a more abundant ISC population.

The role of three-dimensional chromatin structure changes in tumor progression

The human genome is not a linear structure, but a three-dimensional structure through complex folding and assembly. Chromosome structure capture technology can detect the three-dimensional construction of chromatin. Hi-C sequencing data of various tumors indicate that the chromatin topology associated domains changed during tumor progression and is related to copy number variation. In addition, transformation of the genomic compartment is related to gene expression. However, current researches on three-dimensional structures of tumoral chromatin are still in the stage of exploration, and some conclusions are too superficial to be applied to the clinic immediately, which requires further study.

Structural modularity of the XIST ribonucleoprotein complex

Long noncoding RNAs are thought to regulate gene expression by organizing protein complexes through unclear mechanisms. XIST controls the inactivation of an entire X chromosome in female placental mammals. Here we develop and integrate several orthogonal structure-interaction methods to demonstrate that XIST RNA-protein complex folds into an evolutionarily conserved modular architecture. Chimeric RNAs and clustered protein binding in fRIP and eCLIP experiments align with long-range RNA secondary structure, revealing discrete XIST domains that interact with distinct sets of effector proteins. CRISPR-Cas9-mediated permutation of the Xist A-repeat location shows that A-repeat serves as a nucleation center for multiple Xist-associated proteins and m6A modification. Thus modular architecture plays an essential role, in addition to sequence motifs, in determining the specificity of RBP binding and m6A modification. Together, this work builds a comprehensive structure-function model for the XIST RNA-protein complex, and suggests a general strategy for mechanistic studies of large ribonucleoprotein assemblies.

Archean Rocks of the Diorite Window Block in the Southern Framing of the Monchegorsk (2.5 Ga) Layered Mafic-Ultramafic Complex (Kola Peninsula, Russia)

The intermediate rocks classified as diorite-gneisses occur within the southern part of the Monchegorsk (2.5 Ga) layered mafic-ultramafic complex (Kola Peninsula, Russia). These diorite-gneisses belong to a block historically known as the diorite window (DW) block. The same rocks occur in a framing of the Monchegorsk complex. The DW block is predominantly composed of diorite-gneisses and, to a lesser degree, of amphibolites. Multi-ordinal banding, complex folding, boudinage and metamorphic transformations, garnet porphyroblasts, and tourmaline veinlets are typical of the diorite-gneisses. In accordance with the U-Pb isotope data, the age of the diorite-gneisses in the DW block is 2736.0 ± 4.6 Ma. The Sm-Nd mineral (garnet, biotite, and tourmaline) isochron for the DW rocks has yielded an age of 1806 ± 23 Ma (related to the processes of the Svecofennian orogeny). The DW diorite-gneisses are compared with the metadiorites of the Gabbro-10 massif. The latter is a part of the Monchegorsk complex, with U-Pb crystallization age of 2498 ± 6 Ma. On the basis of geological and isotope-geochemical data, it is shown that the DW rocks belong to the Archean basement while the Gabbro-10 metadiorites probably represent one of the late-magmatic phases of the Monchegorsk complex.

Insights into the Kinetic Partitioning Folding Dynamics of the Human Telomeric G-Quadruplex from Molecular Simulations and Machine Learning.

The human telomeric DNA G-quadruplex follows a kinetic partitioning folding mechanism. The underlying folding landscape potentially has many minima separated by high free-energy barriers. However, using current theoretical models to characterize this complex folding landscape has remained a challenging problem. In this study, by developing a hybrid atomistic structure-based model that merges structural information on the hybrid-1, hybrid-2, and chair-type G-quadruplex topologies, we investigated a kinetic partitioning folding process of human telomeric DNA involving three native folds. The model was validated as it reproduced the experimental observation that the hybrid-1 conformation is the major fold and the hybrid-2 conformation is kinetically more accessible. A three-step mechanism was revealed for the formation of the hybrid-1 conformation, while a two-step mechanism was demonstrated for the formation of hybrid-2 and chair-type conformations. Likewise, a class of state in which structures adopted inappropriate combinations of syn/anti guanine nucleotides was found to greatly slow down the folding process. In addition, by employing the XGBoost machine learning algorithm, three interatom distances and six dihedral angles were identified as essential internal coordinates to represent the low-dimensional folding landscape. The strategy of coupling the multibasin model and the machine learning algorithm may be useful to investigate the conformational dynamics of other multistate biomolecules.

Flexoelectric fluid membrane vesicles in spherical confinement

The morphology of spherically confined flexoelectric fluid membrane vesicles in an external uniform electric field is studied numerically. Due to the deformations induced by the confinement, the membrane becomes polarized resulting in an interaction with the external field. The equilibrium shapes of the vesicle without electric field can be classified in a geometrical phase diagram as a function of scaled area and reduced volume (Kahraman O. et al., EPL, 97 (2012) 68008; Kahraman O. et al., New. J. Phys., 14 (2012) 095021). When the area of the membrane is only slightly larger than the area of the confining sphere, a single axisymmetric invagination appears. A non-vanishing electric field induces an additional elongation of the confined vesicle which is either perpendicular or parallel depending on the sign of the electric field parameter. Higher values of the surface area or the electric field parameter can reduce the symmetry of the system leading to more complex folding. We present the resulting shapes and show that transition lines are shifted in the presence of an electric field. The obtained folding patterns could be of interest for biophysical and technological applications alike.

Screening the underlying molecular mechanisms involved in the development of heart failure

Heart failure (HF) causes a great socioeconomic and medical burden in our societies. We aimed to screen the molecular mechanisms related to the development of HF that may lead to new therapeutic targets. We incorporated four expression datasets (GSE5406, GSE1869, GSE29819, and GSE42955) of dilated cardiomyopathy (DCM) from GEO repository to identify differentially expressed genes (DEGs) between 33 controls and 111 patients. WGCNA package, MetaQC, MetaDE, and Metapath packages of Meta-omics, affy, and limma R packages have been used in the bioinformatics analysis for the assessment of quality control, differentially expressed genes and enrichment of detected genes. Search Tool for the Retrieval Interacting Genes (STRING) was used as well for the analysis of protein-protein interaction (PPI) network. Using the false discovery rate (FDR) cut-off of 0.0001, 508 genes (229 up-regulated and 279 down-regulated), were differentially expressed by the Fisher's method. The most enrichment Gene Ontology (GO) terms contain genes involved in oxidative phosphorylation (OXPHOS), proteasome complex, and protein folding related pathways. Finally, to increase the significance of our study, the identified DEGs by meta-analysis cross-checked by the results of the DEGs analysis of patients with right ventricular dysfunction (GSE29819, that contains 6 controls and 7 patients samples). Overall, our bioinformatic-based study provided a preliminary molecular profile which is worth to be further investigated as possible new therapeutic targets.

SO019A PREDICTIVE MODEL OF MORTALITY IN ACUTE RENAL FAILURE IN THE CRITICAL PATIENT: USEFULNESS OF ARTIFICIAL INTELLIGENCE

Abstract Background and Aims Patients with Acute Renal Failure (ARF) have a high risk of mortality, especially those who enter the Intensive Care Unit (ICU). In this population, predictive models of mortality on prognostic scales, such as SAPS-II (Simplified Acute Physiology Score II), linearly relate risk factors without taking into account the complex relationship's variables can have. There are models where Machine Learning (ML) techniques have been used, but there is still room for improvement. The implementation of deep artificial neural networks (DANN) can be challenging. The literature models, using SAPS-II report an accuracy, f1 and ROC area (receiver operating curve) in ranges of 0.538-0.621, 0.333-0.377 and 0.781-0.809 respectively. The best results with ML are improved in neural networks of a hidden layer or random forest, being the best performance in the latter: accuracy 0.715-0.741, F1 0.449-0.470 and ROC between 0.862-0.870. The aim is to evaluate and improve the predictive capacity of ML techniques for the prediction of mortality in patients with ARF admitted to the ICU, through the use of the open database MIMIC-III (Medical Information Martfor Intensive Care III). Method Design: Retrospective analysis of historical cooperation of 20,928 patients with ARF from Beth Israel Deaconess (Boston), from 2001 to 2012. Method: ML algorithm based on DANN. Creation of a model to predict in-hospital mortality after discharge from the ICU with the variables of the first 24 hours after admission to the ICU. To evaluate the robustness of the model has been performed cross-validation by separating the samples into different combinations of training and test data (k-folds). The unavailable variables haematological with means extracted from the training set of the respective fold. The DANN trained with the complex relationship's variables folds, two hidden layers of 75 and 40 neurons respectively. Inclusion criteria: > 16 years, AKI according to KDIGO criteria and predictive variables based on SAPS-II. Variables: Age, sex, type of admission, number of admissions in ICU, heart rate, blood pressure, temperature, PaO2, FiO2, sodium, potassium, bilirubin, bicarbonate, urea, leukocytes, diuresis and diagnosis of ICD-9 (metastatic cancer, haematological malignancies). Results Accuracy: 76.7% 0 ± 1.7%, f1: 86.6% ± 1.9%, RO area: 0.859 ± 0.006, sensitivity: 75.7% ± 2.8%, specificity: 80.5% ± 2.9%. Conclusion The use of Machine Learning techniques based on deep artificial neural networks can improve the predictive ability of mortality in acute renal failure of the critically ill patient of traditional clinical risk scales and even current Machine Learning models.

Evaluation of active tectonics using geomorphic indices in a mountainous basin of Iran

ABSTRACTThis study aims to evaluate the tectonic activities of the Vark basin, located in the great basin of Dez River in northwestern Iran, using geomorphologic indices combined with the geographical information system technique. Some geomorphic indices were used to achieve this aim. In this regard, the indices of stream length (SL), drainage asymmetry (Af), hypsometric integral (Hi), valley floor ratio (Vf), basin shape (Bs), and mountain sinuosity (Smf) were estimated to reach an average index of relative tectonics (Iat), indicating the intensity classes of tectonic activity. The mean SL,Hi,Vf, andBsvalues were estimated as 2273, 0.55, 0.45, and 1.75, respectively, regarding the active class of tectonic activity. Therefore, considering theAfandSmfindices with values of 27 and 1.14, the basin was categorised as having semi-active conditions. The overallIat, with a value of 1.33, represented the very high class (1.0 <Iat< 1.5) of tectonic activity. Hence, by calculating the index of relative active tectonics, the study area is observed as the intensive class concerning tectonic movements. Overall, the mean values of theIatfor all sub-basins were calculated as 1.50, 1.17, and 1.83, revealing the very high and high classes of active tectonics in the basin. The results obtained on tectonic activity were further confirmed during field observations by examining the structurally complex joints, folds, slips, faults, and fractures of the area, which reflect the dynamic nature of the regional tectonics.

Geochemical Evolution and Groundwater Flow System in Batujajar Groundwater Basin Area, West Java, Indonesia

DOI:10.17014/ijog.7.1.87-104Batujajar and its surrounding areas, situated in the west of the Bandung Basin, are geologically composed of various Tertiary rock formations with complex fold and fault systems. Springs and drilled wells in sandstone aquifers, tuffaceous sand, and tuffaceous breccias mark the development of their aquifer systems. This study aimed to determine the characteristics of the hydrogeochemistry by analyzing major ions and stable isotopes (18O and 2H) of thirty-four hydrogeological objects. The groundwater flow pattern in this area is controlled by northwest-southeast lineament, as indicated by the emergence of springs along the transition zone between areas with high and low lineament density. In order of dominance, the groundwater facies are as follows:Ca-Mg-HCO3>Ca-HCO3>Ca-Na-Mg-HCO3>Na-Ca-HCO3. Hydrochemical evolutions were detected from the change of cations from Ca2+ to Mg2+ and then Na+, and this is believed to be the product of cation exchange and dissolution of silicate minerals. However, evolutions toward anion changes were not apparent yet, meaning that HCO3- ions still prevail, or in other words the groundwater flow system is local. Nevertheless, the geological and hydrogeochemical analyses, along with the relative compositions of stable isotopes, revealed that the groundwater had three systems, namely shallow, intermediate, and deep groundwater flows; all of which were segmented in three subgroundwater basins (Sub-GWB). Aquifer systems with shallow to intermediate groundwater flow were found in Sub-GWB-A, Sub-GWB-B, and Sub-GWB-C, while the other ones with deep groundwater flow system were identified in Sub-GWB-B and Sub-GWB-C.Fracture system has an important role as a connector between recharge system in hilly areas and discharge system in plain areas.

Numerical simulation and dimension reduction analysis of electromagnetic logging while drilling of horizontal wells in complex structures

Electromagnetic logging while drilling (LWD) is one of the key technologies of the geosteering and formation evaluation for high-angle and horizontal wells. In this paper, we solve the dipole source-generated magnetic/electric fields in 2D formations efficiently by the 2.5D finite difference method. Particularly, by leveraging the field’s rapid attenuation in spectral domain, we propose truncated Gauss–Hermite quadrature, which is several tens of times faster than traditional inverse fast Fourier transform. By applying the algorithm to the LWD modeling under complex formations, e.g., folds, fault and sandstone pinch-outs, we analyze the feasibility of the dimension reduction from 2D to 1D. For the formations with smooth lateral changes, like folds, the simplified 1D model’s results agree well with the true responses, which indicate that the 1D simplification with sliding window is feasible. However, for the formation structures with drastic rock properties changes and sharp boundaries, for instance, faults and sandstone pinch-outs, the simplified 1D model will lead to large errors and, therefore, 2.5D algorithms should be applied to ensure the accuracy.

A Detailed Study of Rainbow Trout (Onchorhynchus mykiss) Intestine Revealed That Digestive and Absorptive Functions Are Not Linearly Distributed along Its Length.

Simple SummaryAquaculture is the fastest growing food-producing sector due to the increase of fish intended for human consumption. However, aquaculture growth generates concerns, since carnivorous fish are extensively fed using fish-meal and fish-oil. This constitutes a severe limit to the aquaculture industry, questioning its sustainability. Consequently, alternative feeds are continuously searched through extensive in vivo feeding trials. Undoubtedly, to evaluate their impact on the gastrointestinal tract health, detailed knowledge of the intestine morphology and physiology is required. To date, extensive studies have been performed in several livestock species; however, available information on fish is limited nowadays, most importantly because their alimentary canal is able to easily adapt to external stimuli, and their intestinal morphology is affected by external factors. Therefore, it is essential to establish accurate reference values, especially along the productive cycle of animals raised in standardized conditions. Here, we performed a detailed characterization of the epithelial cells lining the intestinal mucosa in rainbow trout along the first year of development. We studied the absorptive and secretory activity as well as its ability to self-renewal. Our results indicate that, in this species, both digestive and absorptive functions are not linearly distributed along the intestinal length.To increase the sustainability of trout farming, the industry requires alternatives to fish-based meals that do not compromise animal health and growth performances. To develop new feeds, detailed knowledge of intestinal morphology and physiology is required. We performed histological, histochemical, immunohistochemical and morphometric analysis at typical time points of in vivo feeding trials (50, 150 and 500 g). Only minor changes occurred during growth whereas differences characterized two compartments, not linearly distributed along the intestine. The first included the pyloric caeca, the basal part of the complex folds and the villi of the distal intestine. This was characterized by a significantly smaller number of goblet cells with smaller mucus vacuoles, higher proliferation and higher apoptotic rate but a smaller extension of fully differentiated epithelial cells and by the presence of numerous pinocytotic vacuolization. The second compartment was formed by the proximal intestine and the apical part of the posterior intestine complex folds. Here we observed more abundant goblet cells with bigger vacuoles, low proliferation rate, few round apoptotic cells, a more extended area of fully differentiated cells and no pinocytotic vacuoles. Our results suggest that rainbow trout intestine is physiologically arranged to mingle digestive and absorptive functions along its length.

The Huncal Member of the Vaca Muerta Formation, Neuquén Basin of Argentina: Insight into biostratigraphy, structure, U-Pb detrital zircon ages and provenance

In the western sector of the Neuquén Basin, the organic-rich shales of the Vaca Muerta Formation are intercalated with turbidite sandstone intervals and slump structures integrated in the Huncal Member. The age of the Huncal sandstones based on the integration of the ammonite faunas, calcareous nannofossils and U-Pb analysis is late Berriasian in their type locality. The origin of this deposit is probably related with two lobes of turbiditic sandstones linked with a progradational regressive phase. Sandstones are lithic arkoses and feldspathic litharenites derived from recycled orogenic and dissected arc sources. The U-Pb ages confirm a mixed sedimentary provenance from the south and southeastern margins of the basin, specifically from Paleozoic and Triassic–Jurassic rocks of the North Patagonian Massif and the Huincul High. The complex fold and fault system described in the sandstone levels was interpreted as the result of slump processes with a main transport direction to the SW and W. Sandstone deposits with slump structures assignable to the Huncal Member are present throughout the entire basin from the Tithonian to the Valanginian in the Vaca Muerta Formation. Therefore, the Huncal Member is a diachronic lithostratigraphic unit and its deposition probably depended on different factors such as relative sea level changes, the position in the ramp system or in the platform and slope configuration and internal morphostructural features of the Neuquén Basin.

Long Non-coding RNA in Plants in the Era of Reference Sequences.

The discovery of non-coding RNAs (ncRNAs), and the subsequent elucidation of their functional roles, was largely delayed due to the misidentification of non-protein-coding parts of DNA as “junk DNA,” which forced ncRNAs into the shadows of their protein-coding counterparts. However, over the past decade, insight into the important regulatory roles of ncRNAs has led to rapid progress in their identification and characterization. Of the different types of ncRNAs, long non-coding RNAs (lncRNAs), has attracted considerable attention due to their mRNA-like structures and gene regulatory functions in plant stress responses. While RNA sequencing has been commonly used for mining lncRNAs, a lack of widespread conservation at the sequence level in addition to relatively low and highly tissue-specific expression patterns challenges high-throughput in silico identification approaches. The complex folding characteristics of lncRNA molecules also complicate target predictions, as the knowledge about the interaction interfaces between lncRNAs and potential targets is insufficient. Progress in characterizing lncRNAs and their targets from different species may hold the key to efficient identification of this class of ncRNAs from transcriptomic and potentially genomic resources. In wheat and barley, two of the most important crops, the knowledge about lncRNAs is very limited. However, recently published high-quality genomes of these crops are considered as promising resources for the identification of not only lncRNAs, but any class of molecules. Considering the increasing demand for food, these resources should be used efficiently to discover molecular mechanisms lying behind development and a/biotic stress responses. As our understanding of lncRNAs expands, interactions among ncRNA classes, as well as interactions with the coding sequences, will likely define novel functional networks that may be modulated for crop improvement.