Miracle-dz/UniFAR-FTUs huggingface dataset:
mir-21 is associated with inactive low molecular weight Argonaute complexes in thyroid cancer cell lines

Thyroid cancer is the most prevalent endocrine malignancy. We and others have shown that several microRNAs, which are post-transcriptional gene regulators, are aberrantly expressed in anaplastic thyroid cancer (ATC) and papillary thyroid cancer (PTC) tissues, as well as cell lines derived from these cancers. In the cell, miRNAs are bound to Argonaute (AGO) proteins as what could be termed low molecular weight RNA-Induced Silencing Complexes (LMW-RISCs) that can assemble with additional proteins, mRNA, and translation machinery into high molecular weight RISCs (HMW-RISCs) that exert regulatory function. In this study, we sought to analyze the association of miRNAs with RISC complexes in ATC and PTC. For ATC and PTC lines, miRNA species were enriched in both HMW-RISC and LMW-RISC cellular fractions, compared with intermediate molecular weight fractions and very low molecular weight (AGO-poor) fractions. Furthermore, 60% of all miRNAs were slightly more abundant in LMW-RISC versus HMW-RISC fractions by ~2-4 fold. Surprisingly, miR-21-5p, one of the most abundant miRNAs in both ATC and PTC lines and one of the most widely studied oncogenic miRNAs in many solid tumors, was consistently one the least abundant miRNAs in HMW-RISC and the most enriched miRNA in LMW-RISC fractions. These findings may suggest that miR-21 has a role or roles distinct from canonical post-transcriptional regulation in cancer. Furthermore, the methodology described here is a useful way to assess the distribution of miR-21 between HMW and LMW-RISCs and may help to reveal the true roles of this miRNA in thyroid cancer development, progression, and treatment.
MeSSII interplays the amylose and amylopectin biosynthesis by protein interactions in cassava storage root

Starch is a glucose polymer synthesized by green plants for energy storage, and is crucial for plant growth and reproduction. The biosynthesis of starch polysaccharides is mediated by members of the large starch synthase (SS) protein superfamily. Here, we showed that in cassava storage roots, soluble starch synthase II (MeSSII) plays an important role in starch biosynthesis via forming protein complexes with other starch biosynthetic enzymes by directly interacting with MeSSI, MeSBEII and MeISAII. The MeSSII-RNAi cassava lines showed increased amylose content and reduced intermediate chain of amylopectin (B1 type) biosynthesis in their storage roots, leading to altered starch physico-chemical properties. Further gel permeation chromatography analysis of starch biosynthetic enzymes between the wild type and MeSSII-RNAi lines confirmed the key rule of MeSSII in the organization of heteromeric starch synthetic protein complexes, including the MeSSII-MeSSI-MeGBSSI and MeSBEII-MeSSI-MeSSII-MeISAII-MeISAI complexes. The lack of MeSSII in cassava also reduced the binding capacity of the MeSSI, MeSBEII, MeISAI, and MeISAII to starch granules. Our results show a close coordination between granule-bound starch synthase and amylopectin biosynthetic enzymes, which implies that the processes of amylose synthesis and amylopectin synthesis are directly interrelated. These findings shed light on the key components of the starch biosynthesis machinery in root crops. One Sentence Summary Here, by focusing on cassava SSII, we elucidated its function and the molecular mechanism by which it chaperones the starch synthase complex to regulate starch biosynthesis in cassava storage roots.
Determining structures of biomacromolecular complexes from ambiguous NMR restraints and cryoEM data

Integrated structural biology aims at combining different techniques to tackle challenging systems. Where individual techniques are not delivering structures of suitable quality, harnessing the strengths of various methods can often overcome this problem. X-ray crystallography and NMR have been the two most widely applied structural biology disciplines. In recent years cryoelectron microscopy (cryoEM) has become ever more powerful and is now capable of providing structures at resolutions comparable to those common in X-ray crystallography. Unfortunately, both NMR and cryoEM have inherent limitations on the system under study. However, the two techniques can be considered somewhat complementary as NMR has an upper and cryoEM a lower molecular weight (MW) limit. Here, we present a joint NMR and cryoEM methodology for the determination of biomacromolecular structures at the boundary region between the MW limits of the two techniques. The method relies on measuring chemical shift perturbations, which is the most readily accessible NMR parameter for characterizing the interaction of biomacromolecular complexes. Low-resolution cryoEM information yields global information on the shape of the complex and is used for complementing the local NMR data. We have successfully applied this method to the model system histidine-containing phosphoprotein (HPr) in complex with the glucose-specific acceptor protein IIAGlc from Escherichia coli.
Exploiting prior knowledge about biological macromolecules in cryo-EM structure determination

Three-dimensional reconstruction of the electron scattering potential of biological macromolecules from electron cryo-microscopy (cryo-EM) projection images is an ill-posed problem. The most popular cryo-EM software solutions to date rely on a regularisation approach that is based on the prior assumption that the scattering potential varies smoothly over three-dimensional space. Although this approach has been hugely successful in recent years, the amount of prior knowledge it exploits compares unfavourably to the knowledge about biological structures that has been accumulated over decades of research in Structural Biology. Here, we present a regularisation framework for cryo-EM structure determination that exploits prior knowledge about biological structures through a convolutional neural network that is trained on known macromolecular structures. We insert this neural network into the iterative cryo-EM structure determination process through an approach that is inspired by Regularisation by Denoising. We show that the new regularisation approach yields better reconstructions than the current state-of-the-art for simulated data and discuss options to extend this work for application to experimental cryo-EM data.
Third-generation dual-source computed tomography of the abdomen: comparison of radiation dose and image quality of 80kVp and 80/150kVp with tin filter

Objective To compare the radiation dose, objective and subjective image quality, and diagnostic performances of 80 kVp and 80/150 kVp with tin filter (80/Sn150 kVp) computed tomography (CT) in oncology patients. Methods One hundred forty-five consecutive oncology patients who underwent third-generation dual-source dual-energy CT of the abdomen for evaluation of malignant visceral, peritoneal, extraperitoneal, and bone tumor were retrospectively recruited. Two radiologists independently reviewed each observation in 80 kVp CT and 80/Sn150 kVp CT. Modified line-density profile of the tumor and contrast-to-noise ratio (CNR) were measured. Diagnostic confidence, lesion conspicuity, and subjective image quality were calculated and compared between image sets. Results Modified line-density profile analysis revealed higher attenuation differences between the tumor and the normal tissue in 80 kVp CT than in 80/Sn150 kVp CT (127 vs. 107, P = 0.05). The 80 kVp CT showed increased CNR in the liver (8.0 vs. 7.6) and the aorta (18.9 vs. 16.3) than the 80/Sn150 kVp CT. The 80 kVp CT yielded higher enhancement of organs (4.9 ± 0.2 vs. 4.7 ± 0.4, P < 0.001) and lesion conspicuity (4.9 ± 0.3 vs. 4.8 ± 0.5, P = 0.035) than the 80/Sn150 kVp CT; overall image quality and confidence index were comparable. The effective dose reduced by 45.2% with 80 kVp CT (2.3 mSv ± 0.9) compared to 80/Sn150 kVp CT (4.1 mSv ± 1.5). Conclusions The 80 kVp CT performed similar or better than 80/Sn150 kVp CT for abdominal tumor evaluation with 45.2% radiation dose reduction in oncology patients.
A regulatory program for initiation of Wnt signaling during posterior regeneration

Whole-body regeneration requires the re-establishment of body axes for appropriate patterning of new and old tissue. Wnt signaling has been utilized to correctly regenerate tissues along the primary axis in many animals. However, the causal molecular mechanisms that first launch Wnt signaling during regeneration are poorly characterized. We used the acoel worm Hofstenia miamia to identify processes that initiate Wnt signaling. Transcriptome profiling, in situ hybridization, and functional studies revealed a Wnt ligand, wnt-3, as an early wound-induced gene specifically activated in posterior-facing wound sites and was required for establishing posterior identity during regeneration. wnt-3 was upregulated upon amputation in stem cells, and its inhibition affected stem cell proliferation. Ectopic expression of anterior markers in wnt-3 RNAi head fragments was stem cell dependent. Chromatin accessibility data revealed that wnt-3 activation during regeneration required input from the general wound response. Additionally, the expression of a different Wnt ligand, wnt-1, prior to amputation was required for activation of wound-induced wnt-3 expression. Our study establishes a gene regulatory network for initiating Wnt signaling in posterior tissues in a bilaterian.
Disarrangement of Endoplasmic reticulum-mitochondria communication impairs Ca2+ homeostasis in FRDA

Friedreich ataxia (FRDA) is a neurodegenerative disorder characterized by neuromuscular and neurological manifestations. It is caused by mutations in gene FXN, which results in loss of the mitochondrial protein frataxin. Endoplasmic Reticulum-mitochondria associated membranes (MAMs) are inter-organelle structures involved in the regulation of essential cellular processes, including lipid metabolism and calcium signaling. In the present study, we have analyzed in both, unicellular and multicellular models of FRDA, an analysis of calcium management and of integrity of MAMs. We observed that function of MAMs is compromised in our cellular model of FRDA, which was improved upon treatment with antioxidants. In agreement, promoting mitochondrial calcium uptake was sufficient to restore several defects caused by frataxin deficiency in Drosophila Melanogaster. Remarkably, our findings describe for the first time frataxin as a member of the protein network of MAMs, where interacts with two of the main proteins implicated in endoplasmic reticulum-mitochondria communication. These results suggest a new role of frataxin, indicate that FRDA goes beyond mitochondrial defects and highlight MAMs as novel therapeutic candidates to improve patient’s conditions.
Mps1 expression is critical for chromosome orientation and segregation in yeast with high ploidy

In aneuploid cancer cells, the chromosome segregation apparatus is sensitive to increased chromosome number. The conserved protein kinase, Mps1, is a critical actor of this machinery, orienting the chromosomes properly on the spindle. Abnormally high levels of this kinase have been found in tumors with elevated chromosome number. However, it remains unclear, mechanistically, if and how cells with higher ploidy become dependent upon increased Mps1 levels. To answer these questions, we explored Mps1 dependence in yeast cells with increased sets of chromosomes. We discovered that having more chromosomes affects the ability of cells to orient chromosomes properly. The cells with increased numbers of chromosomes are particularly sensitive to the reduction of Mps1 activity. In mps1 loss of function mutants, cells display an extended prometaphase with a longer spindle and a delay in orienting properly the chromosomes. Altogether, our results suggest that increased numbers of chromosomes render cells more dependent on Mps1 for orienting chromosomes on the spindle. The phenomenon described here may be relevant in understanding why hyperdiploid cancer cells become excessively reliant on high Mps1 expression for successful chromosome segregation. Author summary Most cells in solid tumors usually carry far more chromosomes than normal cells. Losing or gaining chromosomes during cell division can lead to aneuploidy (an abnormal number of chromosomes), cancer, and other diseases. Mps1 is a master regulator of cell division that is critical to keep the correct number chromosomes in each daughter cell. This master regulator has been shown to target and affect the function of various actors involved in cell division. Abnormally high levels of this master regulator are found in tumors with elevated chromosome numbers. The high levels of this regulator appear to be protecting these tumor cells. To answer if and how cells with higher ploidy become so dependent of Mps1, we generated yeast cells with increased set of chromosomes. Here, we report that cells with elevated chromosome number are particularly sensitive to the reduction of Mps1 level. In cells with higher ploidy and reduced level of Mps1, the progression during cell division is delayed. In the mutant cells, their ability to properly orient and segregate their chromosomes on the spindle is greatly reduced.
Function of a novel nasal protrusion for oral-shelling within an adaptive radiation of pupfishes

Dietary specialization on hard prey items, such as mollusks and crustaceans, is commonly observed in a diverse array of fish species. Many fish consume these types of prey by crushing the shell to consume the soft tissue within, but a few fishes extricate the soft tissue without breaking the shell using a method known as oral shelling. Oral shelling involves pulling a mollusk from its shell and may be a way to subvert an otherwise insurmountable shell defense. However, the biomechanical requirements and potential adaptations for oral shelling are unknown. Here, we test the hypothesis that a novel nasal protrusion is an adaptation for oral shelling in a durophagous pupfish (Cyprinodon brontotheroides). We first demonstrate oral shelling in this species and then predicted that a larger nasal protrusion would allow pupfish to consume larger snails. Durophagous pupfish are found within an endemic radiation of pupfish on San Salvador Island, Bahamas. We took advantage of closely related sympatric species and outgroups to test: 1) whether durophagous pupfish shell and consume more snails than other species, 2) if F1 and F2 durophagous hybrids consume similar amounts of snails as purebred durophagous pupfish, and 3) to determine if nasal protrusion size in parental and hybrid populations increases the maximum diameter snail consumed. We found that durophagous pupfish and their hybrids consumed the most snails, but did not find a strong association between nasal protrusion size and maximum snail size consumed within the parental or F2 hybrid population, suggesting that the size of their novel nasal protrusion does not provide a major benefit in oral shelling. Instead, we suggest that nasal protrusion may increase feeding efficiency, act as a sensory organ, or is a sexually selected trait, and that a strong feeding preference may be most important for oral shelling. Significance Statement Specialization on hard-shell prey items (i.e. durophagy) is a common dietary niche among fishes. Oral shelling is a rare technique used by some durophagous fish to consume prey items like snails; however, adaptations for oral shelling are still unknown. Here, we document the first evidence of oral shelling in a cyprinodontiform fish, the durophagous pupfish (Cyprinodon brontotheroides), and experimentally test whether its novel nasal protrusion is an adaptation for oral shelling using hybrid feeding trials.
Microbiota Succession and Chemical Composition Involved in the Radish Fermentation Process in Different Containers

Traditional Chinese fermented vegetables are a type of brine-salted fermented vegetable product. During the spontaneous fermentation, various compounds are produced, degraded, and converted, influencing the quality of the fermented pickle. To ascertain the effect of different containers on the fermentation process of the pickles, this study investigated the bacterial diversity and the chemical composition characteristics of the pickle (radish) fermented in commonly used containers including glass jars (GL), porcelain jars (PO), and plastic jars (PL). The correlation between chemical compounds and microbial community was further analyzed. The changes in pH values suggested that PL may facilitate the quickest fermentation of the pickles, while the process in PO progressed at the lowest rate. The PL brine samples contained higher levels of lactic acid and threonine, while more abundant volatile chemical compounds were evident in PO. The container materials had no significant influence on the microbial structure, wherein Lactobacillus was the absolute dominant genus in all containers. But container material did have an effect on the abundance of specific genus, such as Lactococcus and Pediococcus. The correlation between these major genera was also analyzed and gene function prediction indicated that the top three pathways were: carbohydrate metabolism, amino acid metabolism, and energy metabolism. Lactobacillus negatively correlated with methionine, tyrosine, lysine, and arginine, but positively correlated with ammonia, and lactic acid and acetic acid both just correlated with Pediococcus. This study provides new insights into the microbiota succession and chemical compounds involved in the vegetable fermentation.
NCOR1 Orchestrates Transcriptional Landscapes and Effector Functions of CD4+ T Cells

The differentiation of naïve CD4+ T cells into T helper (Th) subsets is key for a functional immune response and has to be tightly controlled by transcriptional and epigenetic processes. However, the function of cofactors that connect gene-specific transcription factors with repressive chromatin-modifying enzymes in Th cells is yet unknown. Here we demonstrate an essential role for nuclear receptor corepressor 1 (NCOR1) in regulating naïve CD4+ T cell and Th1/Th17 effector transcriptomes. Moreover, NCOR1 binds to a conserved cis-regulatory element within the Ifng locus and controls the extent of IFNγ expression in Th1 cells. Further, NCOR1 controls the survival of activated CD4+ T cells and Th1 cells in vitro, while Th17 cell survival was not affected in the absence of NCOR1. In vivo, effector functions were compromised since adoptive transfer of NCOR1-deficient CD4+ T cells resulted in attenuated colitis due to lower frequencies of IFNγ+ and IFNγ+IL-17A+ Th cells and overall reduced CD4+ T cell numbers. Collectively, our data demonstrate that the coregulator NCOR1 shapes transcriptional landscapes in CD4+ T cells and controls Th1/Th17 effector functions.
Driving Performance in Patients With Idiopathic Cervical Dystonia; A Driving Simulator Pilot Study

Objective: To explore driving performance and driving safety in patients with cervical dystonia (CD) on a simulated lane tracking, intersections and highway ride and to compare it to healthy controls. Design: This study was performed as an explorative between groups comparison. Participants: Ten CD patients with idiopathic CD, 30 years or older, stable on botulinum toxin treatment for over a year, holding a valid driver's license and being an active driver were compared with 10 healthy controls, matched for age and gender. Main outcome measures: Driving performance and safety, measured by various outcomes from the simulator, such as the standard deviation of the lateral position on the road, rule violations, percentage of line crossings, gap distance, and number of collisions. Fatigue and driving effort were measured with the Borg CR-10 scale and self-perceived fitness to drive was assessed with Fitness to Drive Screening. Results: Except for a higher percentage of line crossings on the right side of the road by controls (median percentage 2.30, range 0.00–37.00 vs. 0.00, range 0.00–9.20, p = 0.043), no differences were found in driving performance and driving safety during the simulator rides. Fatigue levels were significantly higher in CD patients just before (p = 0.005) and after (p = 0.033) the lane tracking ride (patients median fatigue levels before 1.5 (range 0.00–6.00) and after 1.5 (range 0.00–7.00) vs. controls median fatigue levels before and after 0.00 (no range). No significant differences were found on self-perceived fitness to drive. Conclusion: In patients with CD there were no indications that driving performance or driving safety were significant different from healthy controls in a simulator. Patients reported higher levels of fatigue both before and after driving compared to controls in accordance with the non-motor symptoms known in CD.
Chemical Biology of Autophagy-Related Proteins With Posttranslational Modifications: From Chemical Synthesis to Biological Applications

Macroautophagy (hereafter referred to as autophagy) is an evolutionarily conserved lysosomal degradation pathway in all eukaryotic cells, which is critical for maintaining cell homeostasis. A series of autophagy-related (ATG) proteins are involved in the regulation of autophagy. The activities of ATG proteins are mainly modulated by posttranslational modifications (PTMs), such as phosphorylation, lipidation, acetylation, ubiquitination, and sumoylation. To tackle molecular mechanisms of autophagy, more and more researches are focusing on the roles of PTMs in regulation of the activity of ATG proteins and autophagy process. The protein ligation techniques have emerged as powerful tools for the chemical engineering of proteins with PTMs, and provided effective methods to elucidate the molecular mechanism and physiological significance of PTMs. Recently, several ATG proteins with PTM were prepared by protein ligation techniques such as native chemical ligation (NCL), expressed protein ligation (EPL), peptide hydrazide-based NCL, and Sortase A-mediated ligation (SML). More importantly, the synthesized ATG proteins are successfully used to probe the mechanism of autophagy. In this review, we summarize protein ligation techniques for the preparation of ATG proteins with PTMs. In addition, we highlight the biological applications of synthetic ATG proteins to probe the autophagy mechanism.
Biochemical Functions of Glutathione S-Transferase Family of Salix babylonica

Glutathione S-transferases (GSTs) are ubiquitous enzymes that are encoded by a large gene family, and they contribute to the detoxification of endogenous or xenobiotic compounds and oxidative stress metabolism in plants. Although the GSTs gene family has been reported in many land plants, our knowledge of the evolution and function of the willow GSTs is still limited. In this study, 22 full-length GST genes were cloned from Salix babylonica and divided into three classes based on the conserved domain analysis, phylogenetic tree and gene structure: tau, phi and DHAR. The tissue-specific expression patterns were substantially different among the tau and phi GSTs. The Salix GST proteins showed functional divergences in the substrate specificities, substrate activities and kinetic characteristics. The site-directed mutagenesis studies revealed that a single amino acid mutation (Ile/Val53→Thr53) resulted in the lowest activity of SbGSTU7 among the Salix GSTs. These results suggest that non-synonymous substitution of an amino acid at the putative glutathione-binding site may play an important role in the divergence of enzymatic functions of Salix GST family.