RNA molecules display distinctive organization at nuclear speckles.

RNA molecules often play critical roles in assisting the formation of membraneless organelles in eukaryotic cells. Yet, little is known about the organization of RNAs within membraneless organelles. Here, using super-resolution imaging and nuclear speckles as a model system, we demonstrate that different sequence domains of RNA transcripts exhibit differential spatial distributions within speckles.

Deciphering RNA splicing logic with interpretable machine learning.

Machine learning methods, particularly neural networks trained on large datasets, are transforming how scientists approach scientific discovery and experimental design. However, current state-of-the-art neural networks are limited by their uninterpretability: Despite their excellent accuracy, they cannot describe how they arrived at their predictions. Here, using an "interpretable-by-design" approach, we present a neural network model that provides insights into RNA splicing, a fundamental process in the transfer of genomic information into functional biochemical products.

Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events.

Background: The Ccr4-Not complex is mostly known as the major eukaryotic deadenylase. However, several studies have uncovered roles of the complex, in particular of the Not subunits, unrelated to deadenylation and relevant for translation. In particular, the existence of Not condensates that regulate translation elongation dynamics has been reported.

Splicing at the phase-separated nuclear speckle interface: a model.

Phase-separated membraneless bodies play important roles in nucleic acid biology. While current models for the roles of phase separation largely focus on the compartmentalization of constituent proteins, we reason that other properties of phase separation may play functional roles. Specifically, we propose that interfaces of phase-separated membraneless bodies could have functional roles in spatially organizing biochemical reactions.

Regnase-1 RNase is required for mRNA and miRNA profile remodelling during larva-to-adult metamorphosis.

Metamorphosis is an intricate developmental process in which large-scale remodelling of mRNA and microRNA (miRNA) profiles leads to orchestrated tissue remodelling and organogenesis. Whether, which, and how, ribonucleases (RNases) are involved in the RNA profile remodelling during metamorphosis remain unknown. Human Regnase-1 (also known as MCPIP1 and Zc3h12a) RNase remodels RNA profile by cleaving specific RNAs and is a crucial modulator of immune-inflammatory and cellular defence.

Fabrication, mechanical property and in vitro evaluation of poly (L-lactic acid-co-ε-caprolactone) core-shell nanofiber scaffold for tissue engineering.

Coaxial electrospinning, in which Poly (L-lactic acid-co-ε-caprolactone) (PLC) with different Lactic acid (LA) to caprolactone (CL) ratio (75:25 and 50:50) were employed to electrospin core-shell nanofibers which could mimic the native extracellular matrix for tissue engineering applications. Core-shell nanofibrous scaffolds of PLC (50:50)/BSA (426 ± 157 nm) and PLC (75:25)/BSA (427 ± 197 nm) were fabricated and model drug bovine serum albumin (BSA) was entrapped in the core layer. The morphology, core-shell structure and sustained release behaviors were evaluated by Scanning electron microscopy (SEM), transmission electron microscopy (TEM), inverted fluorescence microscopy, water contact angle test and in vitro release test, respectively.

RNA methyltransferase BCDIN3D is crucial for female fertility and miRNA and mRNA profiles in Drosophila ovaries.

RNA methyltransferases post-transcriptionally add methyl groups to RNAs, which can regulate their fates and functions. Human BCDIN3D (Bicoid interacting 3 domain containing RNA methyltransferase) has been reported to specifically methylate the 5'-monophosphates of pre-miR-145 and cytoplasmic tRNAHis. Methylation of the 5'-monophosphate of pre-miR-145 blocks its cleavage by the miRNA generating enzyme Dicer, preventing generation of miR-145.

DEAD-box RNA helicase Belle posttranscriptionally promotes gene expression in an ATPase activity-dependent manner.

Belle (human ortholog DDX3) is a conserved DEAD-box RNA helicase implicated in regulating gene expression. However, the molecular mechanisms by which Belle/DDX3 regulates gene expression are poorly understood. Here we performed systematic mutational analysis to determine the contributions of conserved motifs within Belle to its in vivo function.

Author Correction: LOTUS domain protein MARF1 binds CCR4-NOT deadenylase complex to post-transcriptionally regulate gene expression in oocytes.

The originally published version of this Article contained an error in Figure 1a, in which the length of the protein fragment produced by the MARF1 null allele was incorrectly labelled as '34aa' rather than the corrected '103aa'.Also, the second sentence of the third paragraph of the Results originally read 'The MARF1null allele has a 241-nt-long deletion introduced at proximal to the N-terminal end of the protein, which produced a premature stop codon, resulting in production of the N-terminal 34 aa fragment of MARF1 (Fig. 1a).

LOTUS domain protein MARF1 binds CCR4-NOT deadenylase complex to post-transcriptionally regulate gene expression in oocytes.

Post-transcriptional regulation of gene expression plays an essential role during oocyte maturation. Here we report that Drosophila MARF1 (Meiosis Regulator And mRNA Stability Factor 1), which consists of one RNA-recognition motif and six tandem LOTUS domains with unknown molecular function, is essential for oocyte maturation. When tethered to a reporter mRNA, MARF1 post-transcriptionally silences reporter expression by shortening reporter mRNA poly-A tail length and thereby reducing reporter protein level.

An RNA-binding protein Blanks plays important roles in defining small RNA and mRNA profiles in testes.

Blanks is a testes-specific RNA-binding protein required for post-meiotic spermiogenesis. However, Blanks's role in regulating RNA populations in the testes remains unknown. We performed small RNA and mRNA high-throughput sequencing in mutant testes and controls.

Kinetic Analysis of Small Silencing RNA Production by Human and Drosophila Dicer Enzymes In Vitro.

Dicer enzymes produce small silencing RNAs such as microRNAs (miRNAs) and small interfering RNAs (siRNAs), which then are loaded into Argonaute proteins and act as sequence-specific guides. A powerful tool to understand the molecular mechanism of small silencing RNA production by Dicers is an in vitro RNA processing assay using recombinant Dicer proteins. Such biochemical analyses have elucidated the substrate specificities and kinetics of Dicers, the mechanism by which the length of small RNAs produced by Dicers is determined, and the effects of Dicer-partner proteins and endogenous small molecules such as ATP and inorganic phosphate on small RNA production by Dicers, among others.

Natural myocardial ECM patch drives cardiac progenitor based restoration even after scarring.

Objective: To evaluate the regenerative capacity of non-supplemented and bioactive patches made of decellularized porcine cardiac extracellular matrix (pcECM) and characterize the biological key factors involved in possible cardiac function (CF) restoration following acute and 8weeks chronic MI.

Background: pcECM is a key natural biomaterial that can affect cardiac regeneration following myocardial infarction (MI), through mechanisms, which are still not clearly understood.

Methods: Wistar rats underwent MI and received pcECM patch (pcECM-P) treatment in either acute or chronic inflammatory phases.

Common miR-590 Variant rs6971711 Present Only in African Americans Reduces miR-590 Biogenesis.

MicroRNAs (miRNAs) are recognized as important regulators of cardiac development, hypertrophy and fibrosis. Recent studies have demonstrated that genetic variations which cause alterations in miRNA:target interactions can lead to disease. We hypothesized that genetic variations in miRNAs that regulate cardiac hypertrophy/fibrosis might be involved in generation of the cardiac phenotype in patients diagnosed with hypertrophic cardiomyopathy (HCM).

Simultaneous Delivery of Highly Diverse Bioactive Compounds from Blend Electrospun Fibers for Skin Wound Healing.

Blend emulsion electrospinning is widely perceived to destroy the bioactivity of proteins, and a blend emulsion of water-soluble and nonsoluble molecules is believed to be thermodynamically unstable to electrospin smoothly. Here we demonstrate a method to retain the bioactivity of disparate fragile biomolecules when electrospun. Using bovine serum albumin as a carrier protein; water-soluble vitamin C, fat soluble vitamin D3, steroid hormone hydrocortisone, peptide hormone insulin, thyroid hormone triiodothyronine (T3), and peptide epidermal growth factor (EGF) were simultaneously blend-spun into PLGA-collagen nanofibers.

Carbon nanotubes reinforced composites for biomedical applications.

This review paper reported carbon nanotubes reinforced composites for biomedical applications. Several studies have found enhancement in the mechanical properties of CNTs-based reinforced composites by the addition of CNTs. CNTs reinforced composites have been intensively investigated for many aspects of life, especially being made for biomedical applications.

Biomimetic nanocomposites to control osteogenic differentiation of human mesenchymal stem cells.

The design of biomimetic nanomaterials that can directly influence the behavior of cells and facilitate the regeneration of tissues and organs has become an active area of research. Here, the production of materials based on nano-hydroxyapatite composites in scaffolds with nanofibrous and nanoporous topographies, designed to mimic the native bone matrix for applications in bone tissue engineering, is reported. Human mesenchymal stem cells grown on these nanocomposites are stimulated to rapidly produce bone minerals in situ, even in the absence of osteogenic supplements in the cell-culture medium.

Injectable hydrogel incorporating with nanoyarn for bone regeneration.

Traditional bone grafting requires an open surgical approach to the graft application sites with the attendant complications of a large surgical scar, increased pain and a longer post-operative recovery. To overcome these limitations, there is a great need for the development of better bone graft substitutes. In this study, we developed a novel injectable system which was a biomimetic bone substitute consisted of Poly (L-lactide-co-ε-caprolactone) (P(LLA-CL)) nanoyarns suspended in type I collagen hydrogel (Col).

Efficacy of cold light bleaching using different bleaching times and their effects on human enamel.

This study investigated the efficacy of cold light bleaching using different bleaching times and the effects thereof on tooth enamel. Before and after bleaching, stained tooth specimens were subjected to visual and instrumental colorimetric assessments using Vita Shade Guide and spectrophotometric shade matching. Enamel surface alterations were examined using scanning electron microscopy (SEM) to analyze surface morphology, surface microhardness (SMH) measurement to determine changes in mechanical properties, and X-ray diffraction (XRD) to characterize post-bleaching enamel composition.

Surface modification of PLLA nano-scaffolds with laminin multilayer by LbL assembly for enhancing neurite outgrowth.

In this study, PLLA nanofibers are fabricated by electrospinning and their surfaces are modified by laminin/chitosan (LN/CS) polyelectrolyte multilayer. Surface C/N ratio determined by XPS analysis quantitatively indicates of discrete coating layers on the nanofibers. The amount of LN deposited sustainably increases with LbL assembly processing, approximately 60 ng mm(-2) LN per cycle of LN/CS deposition.

Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state.

In the metazoan germline, piwi proteins and associated piwi-interacting RNAs (piRNAs) provide a defense system against the expression of transposable elements. In the cytoplasm, piRNA sequences guide piwi complexes to destroy complementary transposon transcripts by endonucleolytic cleavage. However, some piwi family members are nuclear, raising the possibility of alternative pathways for piRNA-mediated regulation of gene expression.

Cell viability and angiogenic potential of a bioartificial adipose substitute.

An implantable scaffold pre-seeded with cells needs to remain viable and encourage rapid angiogenesis in order to replace injured tissues, especially for tissue defect repairs. We created a bioartificial adipose graft composed of an electrospun 3D nanofibrous scaffold and fat tissue excised from New Zealand white rabbits. Cell viability and angiogenesis potential of the bioartificial substitute were examined during four weeks of culture in Dulbecco's Modified Eagle Medium by immunohistochemical staining with LIVE/DEAD® cell kit and PECAM-1 antibody, respectively.

Enhanced osteogenic differentiation with 3D electrospun nanofibrous scaffolds.

Aim: Developing 3D scaffolds mimicking the nanoscale structure of the native extracellular matrix is important in tissue regeneration. In this study, we aimed to demonstrate the novelty of 3D nanofibrous scaffolds and compare their efficiency with 2D nanofibrous scaffolds.

Materials & Methods: The 2D poly(L-lactic acid)/collagen nanofibrous scaffolds were 2D meshes fabricated by the conventional electrospinning technique, whereas the 3D poly(L-lactic acid)/collagen nanofibrous scaffolds were fabricated by a modified electrospinning technique using a dynamic liquid support system.

Biomimetic surface modification of titanium surfaces for early cell capture by advanced electrospinning.

The time required for osseointegration with a metal implant having a smooth surface ranges from three to six months. We hypothesized that biomimetic coating surfaces with poly(lactic-co-glycolic acid) (PLGA)/collagen fibers and nano-hydroxyapatite (n-HA) on the implant would enhance the adhesion of mesenchymal stem cells. Therefore, this surface modification of dental and bone implants might enhance the process of osseointegration.