Adjacency-hopping de Bruijn Sequences for Non-repetitive Coding

A special type of cyclic sequences named adjacency-hopping de Bruijn sequences is introduced in this paper. It is theoretically proved the existence of such sequences, and the number of such sequences is derived. These sequences guarantee that all neighboring codes are different while retaining the uniqueness of subsequences, which is a significant characteristic of original de Bruijn sequences in coding and matching. At last, the adjacency-hopping de Bruijn sequences are applied to structured light coding, and a color fringe pattern coded by such a sequence is presented. In summary, the proposed sequences demonstrate significant advantages in structured light coding by virtue of the uniqueness of subsequences and the adjacency-hopping characteristic, and show potential for extension to other fields with similar requirements of non-repetitive coding and efficient matching

Crystal Structure of the Caenorhabditis elegans Apoptosome Reveals an Octameric Assembly of CED-4

SummaryThe CED-4 homo-oligomer or apoptosome is required for initiation of programmed cell death in Caenorhabditis elegans by facilitating autocatalytic activation of the CED-3 caspase zymogen. How the CED-4 apoptosome assembles and activates CED-3 remains enigmatic. Here we report the crystal structure of the complete CED-4 apoptosome and show that it consists of eight CED-4 molecules, organized as a tetramer of an asymmetric dimer via a previously unreported interface among AAA+ ATPases. These eight CED-4 molecules form a funnel-shaped structure. The mature CED-3 protease is monomeric in solution and forms an active holoenzyme with the CED-4 apoptosome, within which the protease activity of CED-3 is markedly stimulated. Unexpectedly, the octameric CED-4 apoptosome appears to bind only two, not eight, molecules of mature CED-3. The structure of the CED-4 apoptosome reveals shared principles for the NB-ARC family of AAA+ ATPases and suggests a mechanism for the activation of CED-3

Structure-property-performance relationships of lactic acid-based deep eutectic solvents with different hydrogen bond acceptors for corn stover pretreatment

Herein, ten types of lactic acid-based deep eutectic solvents (DESs) with differently structured hydrogen bond acceptors (HBAs) were used for corn stover pretreatment. Among the tested DESs, those composed of HBAs with short alkyl chain were more effective to remove lignin and xylan, resulting in higher enzymatic digestion of the pretreated solids than their counterparts with long alky chain. Also, functional groups of HBAs demonstrated significant effects on biomass deconstruction. In order to interpret the different pretreatment performance of the tested DESs, Kamlet-Taft solvent polarity parameters of the tested DESs were correlated to their lignocellulose pretreatment performance. It was found that hydrogen bond acidity (Kamlet-Taft alpha parameter) had strong positive relationships with pretreatment efficacy of the studied DESs. These findings not only clarified the structure-property-performance relationships of the DESs, but also provided novel insights into design and selection of DESs for lignocellulose pretreatment

An Overview of Adverse Outcome Pathway Links between PM_2.5 Exposure and Cardiac Developmental Toxicity

Fine particulate matter (PM2.5) is a significant risk factor for birth defects. As the first and most important organ to develop during embryogenesis, the heart’s potential susceptibility to PM2.5 has attracted growing concern. Despite several studies supporting the cardiac developmental toxicity of PM2.5, the diverse study types, models, and end points have prevented the integration of mechanisms. In this Review, we present an adverse outcome pathway framework to elucidate the association between PM2.5-induced molecular initiating events and adverse cardiac developmental outcomes. Activation of the aryl hydrocarbon receptor (AhR) and excessive generation of reactive oxygen species (ROS) were considered as molecular initiating events. The excessive production of ROS induced oxidative stress, endoplasmic reticulum stress, DNA damage, and inflammation, resulting in apoptosis. The activation of the AhR inhibited the Wnt/β-catenin pathway and then suppressed cardiomyocyte differentiation. Impaired cardiomyocyte differentiation and persistent apoptosis resulted in abnormalities in the cardiac structure and function. All of the aforementioned events have been identified as key events (KEs). The culmination of these KEs ultimately led to the adverse outcome, an increased morbidity of congenital heart defects (CHDs). This work contributes to understanding the causes of CHDs and promotes the safety evaluation of PM2.5.</sub

The crystal structure of human ferroptosis suppressive protein 1 in complex with flavin adenine dinucleotide and nicotinamide adenine nucleotide

Abstract Ferroptosis is a recently discovered form of regulated cell death characterized by its distinct dependence on iron and the peroxidation of lipids within cellular membranes. Ferroptosis plays a crucial role in physiological and pathological situations and has attracted the attention of numerous scientists. Ferroptosis suppressive protein 1 (FSP1) is one of the main regulators that negatively regulates ferroptosis through the GPX4‐independent FSP1–CoQ10–NAD(P)H axis and is a potential therapeutic target for ferroptosis‐related diseases. However, the crystal structure of FSP1 has not been resolved, which hinders the development of therapeutic strategies targeting FSP1. To unravel this puzzle, we purified the human FSP1 (hFSP1) protein using the baculovirus eukaryotic cell expression system and solved its crystal structure at a resolution of 1.75 Å. Furthermore, we evaluated the oxidoreductase activity of hFSP1 with NADH as the substrate and identified E156 as the key amino acid in maintaining hFSP1 activity. Interestingly, our results indicated that hFSP1 exists and functions in a monomeric state. Mutagenesis analysis revealed the critical role of the C‐terminal domain in the binding of substrate. These findings significantly enhance our understanding of the functional mechanism of FSP1 and provide a precise model for further drug development

KDM5B promotes SMAD4 loss-driven drug resistance through activating DLG1/YAP to induce lipid accumulation in pancreatic ductal adenocarcinoma

Abstract Inactivated suppressor of mothers against decapentaplegic homolog (SMAD) 4 significantly affects cancer development in pancreatic ductal adenocarcinoma (PDAC). However, the contribution of smad4 loss to drug resistance in PDAC is largely undetermined. In the present study, we reported that the loss of SMAD4 endows PDAC cells the ability to drug resistance through upregulating histone lysine demethylase, Lysine-Specific Demethylase 5B (KDM5B, also known as JARID1B or PLU1). Upregulated KDM5B was found in PDAC, associated with poor prognosis and recurrence of PDAC patients. Upregulated KDM5B promotes PDAC tumor malignancy, i.e. cancer cells stemness and drug resistance in vitro and in vivo, while KDM5B knockout exerts opposite effects. Mechanistically, loss of Smad4-mediated upregulation of KDM5B promotes drug resistance through inhibiting the discs-large homolog 1 (DLG1), thereby facilitating nuclear translocation of YAP to induce de novo lipogenesis. Moreover, m6A demethylase FTO is involved in the upregulation of KDM5B by maintaining KDM5B mRNA stability. Collectively, the present study suggested FTO-mediated KDM5B stabilization in the context of loss of Smad4 activate DLG1/YAP1 pathway to promote tumorigenesis by reprogramming lipid accumulation in PDAC. Our study confirmed that the KDM5B-DLG1-YAP1 pathway axis plays a crucial role in the genesis and progression of PDAC, and KDM5B was expected to become a target for the treatment of PDAC. The schematic diagram of KDM5B-DLG1-YAP pathway axis in regulating drug resistance of PDAC to gemcitabine (GEM). In the context of SMAD4 loss PDAC cells, FTO-mediated stabilization and upregulation of KDM5B promotes drug resistance through directly targeting DLG1 to promote YAP1 translocation to nucleus to induce de novo lipogenesis (DNL)

The relationship between gut microbiota and short chain fatty acids in the renal calcium oxalate stones disease

The relationship of gut microbiota and calcium oxalate stone has been limited investigated, especially with no study of gut microbiota and short chain fatty acids (SCFAs) in nephrolithiasis. We provided Sprague Dawley rats of renal calcium oxalate stones with antibiotics and examined the renal crystals deposition. We also performed a case‐control study by analyzing 16S rRNA microbial profiling, shotgun metagenomics and SCFAs in 153 fecal samples from non‐kidney stone (NS) controls, patients with occasional renal calcium oxalate stones (OS) and patients with recurrent stones (RS). Antibiotics reduced bacterial load in feces and could promote the formation of renal calcium crystals in model rats. In addition, both OS and RS patients exhibited higher fecal microbial diversity than NS controls. Several SCFAs‐producing gut bacteria, as well as metabolic pathways associated with SCFAs production, were considerably lower in the gut microbiota among the kidney stone patients compared with the NS controls. Representation of genes involved in oxalate degradation showed no significance difference among groups. However, fecal acetic acid concentration was the highest in RS patients with high level of urinary oxalate, which was positively correlated with genes involvement in oxalate synthesis. Administration of SCFAs reduced renal crystals. These results shed new light on bacteria and SCFAs, which may promote the development of treatment strategy in nephrolithiasis.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/156429/3/fsb220780.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156429/2/fsb220780-sup-0002-TableS1-S6.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156429/1/fsb220780_am.pd

Myeloid-specific targeting of Notch ameliorates murine renal fibrosis via reduced infiltration and activation of bone marrow-derived macrophage

Abstract Macrophages play critical roles in renal fibrosis. However, macrophages exhibit ontogenic and functional heterogeneities, and which population of macrophages contributes to renal fibrosis and the underlying mechanisms remain unclear. In this study, we genetically targeted Notch signaling by disrupting the transcription factor recombination signal binding protein-Jκ (RBP-J), to reveal its role in regulation of macrophages during the unilateral ureteral obstruction (UUO)-induced murine renal fibrosis. Myeloid-specific disruption of RBP-J attenuated renal fibrosis with reduced extracellular matrix deposition and myofibroblast activation, as well as attenuated epithelial-mesenchymal transition, likely owing to the reduced expression of TGF-β. Meanwhile, RBP-J deletion significantly hampered macrophage infiltration and activation in fibrotic kidney, although their proliferation appeared unaltered. By using macrophage clearance experiment, we found that kidney resident macrophages made negligible contribution, but bone marrow (BM)-derived macrophages played a major role in renal fibrogenesis. Further mechanistic analyses showed that Notch blockade reduced monocyte emigration from BM by down-regulating CCR2 expression. Finally, we found that myeloid-specific Notch activation aggravated renal fibrosis, which was mediated by CCR2+ macrophages infiltration. In summary, our data have unveiled that myeloid-specific targeting of Notch could ameliorate renal fibrosis by regulating BM-derived macrophages recruitment and activation, providing a novel strategy for intervention of this disease

Structure of the human gonadotropin-releasing hormone receptor GnRH1R reveals an unusual ligand binding mode

The human gonadotropin-releasing hormone receptor GnRH1R is a GPCR with an important role in the human reproductive system and of interest as a drug target. Here, the authors present the 2.8 Å crystal structure of human GnRH1R with the high affinity antagonist drug Elagolix and the observed unusual ligand binding mode was further analysed with functional assays and molecular docking studies